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In JoVE (1)
- Human Neuroendocrine Tumor Cell Lines as a Three-Dimensional Model for the Study of Human Neuroendocrine Tumor Therapy
Other Publications (52)
- Clinical and Experimental Pharmacology & Physiology
- Pharmacology & Therapeutics
- The Journal of Biological Chemistry
- Journal of Medicinal Chemistry
- Advances in Protein Chemistry
- Annual Review of Pharmacology and Toxicology
- Journal of Computational Chemistry
- The Journal of Biological Chemistry
- Differentiation; Research in Biological Diversity
- Biochemical and Biophysical Research Communications
- The Journal of Chemical Physics
- Protein Science : a Publication of the Protein Society
- Journal of Computational Chemistry
- Current Cancer Drug Targets
- The Journal of Obstetrics and Gynaecology Research
- The Australian & New Zealand Journal of Obstetrics & Gynaecology
- The Journal of Physical Chemistry. A
- The Journal of Physical Chemistry. A
- Food and Chemical Toxicology : an International Journal Published for the British Industrial Biological Research Association
- The Journal of Chemical Physics
- Journal of Magnetic Resonance (San Diego, Calif. : 1997)
- Biochimica Et Biophysica Acta
- Environmental Science & Technology
- Molecular Nutrition & Food Research
- Biophysical Journal
- Journal of Environmental Monitoring : JEM
- Biochimica Et Biophysica Acta
- The Journal of Biological Chemistry
- Environmental Science & Technology
- The Journal of Chemical Physics
- Biochimica Et Biophysica Acta
- Journal of Computational Chemistry
- The Journal of Physical Chemistry. A
- Journal of Medicinal Chemistry
- The Journal of Physical Chemistry. B
- Journal of Magnetic Resonance (San Diego, Calif. : 1997)
- Chemical Biology & Drug Design
- Epigenetics : Official Journal of the DNA Methylation Society
- Clinical and Vaccine Immunology : CVI
- Journal of Environmental Management
- The Journal of Parasitology
- Methods in Molecular Biology (Clifton, N.J.)
- Immunological Investigations
- Molecular Biology of the Cell
Articles by Chung Wong in JoVE
Human Neuroendocrine Tumor Cell Lines as a Three-Dimensional Model for the Study of Human Neuroendocrine Tumor Therapy
Chung Wong1, Evan Vosburgh1,2, Arnold J. Levine2,3, Lei Cong2, Eugenia Y. Xu1,2
1Raymond and Beverly Sackler Foundation, 2The Cancer Institute of New Jersey, University of Medicine and Dentistry of New Jersey, 3School of Natural Sciences, Institute for Advanced Study, Princeton, New Jersey
We present a simple agarose overlay platform to grow 3D multicellular spheroids using neuroendocrine cancer cell lines. This method provides a very convenient way to examine the effect of therapeutic drugs on the neuroendocrine tumor cells. It could also help us establish human neuroendocrine tumor spheroids for cancer therapy.
Other articles by Chung Wong on PubMed
Clinical and Experimental Pharmacology & Physiology. Sep, 2002 | Pubmed ID: 12165038
1. Sulphotransferases are a superfamily of enzymes involved in both detoxification and bioactivation of endogenous and exogenous compounds. The arylsulphotransferase SULT1A1 has been implicated in a decreased activity and thermostability when the wild-type arginine at position 213 of the coding sequence is substituted by a histidine. SULT1A1 is the isoform primarily associated with the conversion of dietary N-OH arylamines to DNA binding adducts and is therefore of interest to determine whether this polymorphism is linked to colorectal cancer. 2. Genotyping, using polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis, was performed using DNA samples of healthy control subjects (n = 402) and patients with histologically proven colorectal cancer (n = 383). Both control and test populations possessed similar frequencies for the mutant allele (32.1 and 31%, respectively; P = 0.935). Results were not altered when age and gender were considered as potential confounders in a logistic regression analysis. 3. Examination of the sulphonating ability of the two allozymes with respect to the substrates p-nitrophenol and paracetamol showed that the affinity and rate of sulphonation was unaffected by substitution of arginine to histidine at position 213 of the amino acid sequence. 4. From this study, we conclude that the SULT1A1 R213H polymorphism is not linked with colorectal cancer in this elderly Australian population.
Designing Specific Protein Kinase Inhibitors: Insights from Computer Simulations and Comparative Sequence/structure Analysis
Pharmacology & Therapeutics. Feb-Mar, 2002 | Pubmed ID: 12191609
Protein kinases are important targets for designing therapeutic drugs. We describe here a computational approach to extend the usefulness of a single protein-inhibitor structure in aiding the design of protein kinase inhibitors. This approach is based on using sensitivity analysis to identify the most significant functional groups of a lead compound in accounting for binding affinity and on using comparative sequence/structure analysis to examine whether these functional groups would present specificity. A sensitivity analysis study is similar to genetic or chemical modification experiments in which specific features of a lead compound are modified to examine whether they affect properties such as binding affinity. In this study, the binding affinity was estimated by using an implicit-solvent model in which the electrostatic contributions were obtained by solving the Poisson equation, and the hydrophobic effects were accounted for by using surface-area-dependent terms. The comparative sequence/structure analysis involves the study of the amino acid distributions of a large number of protein kinases (384 in this study) near the ligand-binding sites. This analysis provides useful guiding principles for designing specific inhibitors targeted towards a particular kinase. Here, we illustrate the utility of these computational approaches by applying them to identify the determinants of the recognition between the protein kinase A and two of its inhibitors. One inhibitor, balanol, binds to the ATP-binding pocket. The other, protein kinase inhibitor, binds to the substrate-binding site. These analyses have helped to construct pharmacophore models for mining new drug leads from small-molecule libraries and for suggesting how a lead compound or a peptide inhibitor may be modified to generate selective inhibitors.
E2F Modulates Keratinocyte Squamous Differentiation: Implications for E2F Inhibition in Squamous Cell Carcinoma
The Journal of Biological Chemistry. Aug, 2003 | Pubmed ID: 12754218
E2F regulation is essential for normal cell cycle progression. Therefore, it is not surprising that squamous cell carcinoma cell lines (SCC) overexpress E2F1 and exhibit deregulated E2F activity when compared with normal keratinocytes. Indeed, deliberate E2F1 deregulation has been shown to induce hyperplasia and skin tumor formation. In this study, we report on a dual role for E2F as a mediator of keratinocyte proliferation and modulator of squamous differentiation. Overexpression of E2F isoforms in confluent primary keratinocyte cultures resulted in suppression of differentiation-associated markers. Moreover, we found that the DNA binding domain and the trans-activation domain of E2F1 are important in mediating suppression of differentiation. Use of a dominant/negative form of E2F1 (E2F d/n) found that E2F inhibition alone is sufficient to suppress the activity of proliferation-associated markers but is not capable of inducing differentiation markers. However, if the E2F d/n is expressed in differentiated keratinocytes, differentiation marker activity is further induced, suggesting that E2F may act as a modulator of squamous differentiation. We therefore examined the effects of E2F d/n in a differentiation-insensitive SCC cell line. We found that treatment with the differentiating agent, 12-O-tetradecanoyl-phorbol-13-acetate (TPA), or expression of E2F d/n alone had no effect on differentiation markers. However, a combination of E2F d/n + TPA induced the expression of differentiation markers. Combined, these data indicate that E2F may play a key role in keratinocyte differentiation. These data also illustrate the unique potential of anti-E2F therapies in arresting proliferation and inducing differentiation of SCCs.
Journal of Medicinal Chemistry. Jul, 2003 | Pubmed ID: 12852762
The cyclin-dependent protein kinases are important targets in drug discovery because of their role in cell cycle regulation. In this computational study, we have applied a continuum solvent model to study the interactions between cyclin-dependent kinase 2 (CDK2) and analogues of the clinically tested anticancer agent flavopiridol. The continuum solvent model uses Coulomb's law to account for direct electrostatic interactions, solves the Poisson equation to obtain the electrostatic contributions to solvation energy, and calculates scaled solvent-accessible surface area to account for hydrophobic interactions. The computed free energy of binding gauges the strength of protein-ligand interactions. Our model was first validated through a study on the binding of a number of flavopiridol derivatives to CDK2, and its ability to identify potent inhibitors was observed. The model was then used to aid in the design of novel CDK2 inhibitors with the aid of a computational sensitivity analysis. Some of these hypothetical structures could be significantly more potent than the lead compound flavopiridol. We applied two approaches to gain insights into designing selective inhibitors. One relied on the comparative analysis of the binding pocket for several hundred protein kinases to identify the parts of a lead compound whose modifications might lead to selective compounds. The other was based on building and using homology models for energy calculations. The homology models appear to be able to classify ligand potency into groups but cannot yet give reliable quantitative results.
Biopolymers. Oct, 2003 | Pubmed ID: 14517913
Helix-capping motifs are believed to play an important role in stabilizing alpha-helices and defining helix start and stop signals. We performed microsecond scale Brownian dynamics simulations to study ten XAAD sequences, with X = (A,E,I,L,N,Q,S,T,V,Y), to examine their propensity to form helix capping motifs and correlate these results with those obtained from analyzing a structural database of proteins. For the widely studied capping box motif S**D, where the asterisk can be any amino acid residue, the simulations suggested that one of the two hydrogen bonds proposed earlier as a stabilizing factor might not be as important. On the other hand, side-chain interactions between the capping residue and the third residue downstream on the polypeptide chain might also play a role in stabilizing this motif. These results are consistent with explicit-solvent molecular dynamics simulations of two capping box motifs found in the proteins BPTI and alpha-dendrotoxin. Principal component analysis of the SAAD trajectory showed that the first three principal components, after those corresponding to translational-rotational motion were removed, accounted for more than half of the conformational fluctuations. The first component separated the conformational space into two parts with the all-helical conformation and the capping box motif lying largely in one part. The second component, on the other hand, could be used to describe conformational transitions between the all-helical form and the capping box motif.
Brownian Dynamics Simulations of Ion Atmospheres Around Polyalanine and B-DNA: Effects of Biomolecular Dielectric
Biopolymers. Oct, 2003 | Pubmed ID: 14579311
We have extended an earlier Brownian dynamics simulation algorithm for simulating the structural dynamics of ions around biomolecules to accommodate dielectric inhomogeneity. The electrostatic environment of a biomolecule immersed in water was obtained by numerically solving the Poisson equation with the biomolecule treated as a low dielectric region and the solvent treated as a high dielectric region. Instead of using the mean-field type approximations of ion interactions as in the Poisson-Boltzmann model, the ions were treated explicitly by allowing them to evolve dynamically under the electrostatic field of the biomolecule. This model thus accounts for ion-ion correlations and the finite-size effects of the ions. For a 13-residue alpha-helical polyalanine and a 12-base-pair bp B-form DNA, we found that the choice of the dielectric constant of the biomolecule has much larger effects on the mean ionic structure around the biomolecule than on the fluctuational and dynamical properties of the ions surrounding the biomolecule.
Annual Review of Pharmacology and Toxicology. 2003 | Pubmed ID: 12142469
Although computational techniques are increasingly being used in computer-aided drug design, the effects due to protein flexibility are still ignored in many applications. This review revisits rigorous statistical mechanical methods for predicting binding affinity, discusses some recent developments for improving their speed and reliability, and examines faster approximate models for facilitating virtual screening and lead optimization.
Journal of Computational Chemistry. Aug, 2004 | Pubmed ID: 15185335
Examining the potential for electrostatic complementarity between a ligand and a receptor is a useful technique for rational drug design, and can demonstrate how a system prioritizes interactions when allowed to optimize its charge distribution. In this computational study, we implemented the previously developed, continuum solvent-based charge optimization theory with a simple, quadratic programming algorithm and the UHBD Poisson-Boltzmann solver. This method allows one to compute the best set of point charges for a ligand or ligand region based on the ligand and receptor shape, and the receptor partial charges, by optimizing the binding free energy obtained from a continuum-solvent model. We applied charge optimization to a fragment of the heat-stable protein kinase inhibitor (PKI) of protein kinase A (PKA), to three flavopiridol inhibitors of CDK2, and to cyclin A which interacts with CDK2 to regulate the cell cycle. We found that a combination of global (involving every charge) and local (involving only charges in a local region) optimization can give useful hints for designing better inhibitors. Although some parts of an inhibitor may already contribute significantly to binding, we found that they could still be the most important targets for modifications to obtain stronger binders. In studying the binding of flavopiridol inhibitors to CDK2, comparable binding affinity could be obtained regardless of whether the net charges of the inhibitors were constrained to -2, -1, 0, 1, or 2 during the optimization. This provides flexibility in inhibitor design when a certain net charge of the inhibitor is desired in addition to strong binding affinity. For the study of the PKA-PKI and CDK2-cyclin A interfaces, we identified residues whose charge distributions are already close to optimal and those whose charge distributions could be refined to further improve binding.
The DIX Domain Protein Coiled-coil-DIX1 Inhibits C-Jun N-terminal Kinase Activation by Axin and Dishevelled Through Distinct Mechanisms
The Journal of Biological Chemistry. Sep, 2004 | Pubmed ID: 15262978
Axin, Ccd1 (coiled-coil-DIX1), and dishevelled (Dvl or Dsh) are three known DIX domain proteins that play important roles in Wnt signaling. In addition, Dvl and Axin can activate the mitogen-activated protein kinase JNK via distinct mechanisms, through interaction with MEKK1/4 and Rac GTPase, respectively. Axin utilizes two distinct domains for interaction with MEKK1 and MEKK4. JNK activation by Axin is regulated by several factors in the Wnt pathway, whereas little is known about cross-regulation of Dvl-mediated JNK activation. In the present study, we have investigated whether Ccd1 could play a regulatory role in Axin- and Dvl-mediated JNK activation. Here we show that Ccd1 drastically inhibited JNK activation both by Axin and by Dvl. Although DIX domains are sufficient for dimer formation between Dvl and Ccd1, Ccd1 also required its coiled-coil domain for inhibition of JNK activation by Dvl. Interestingly, Rac remained associated with Dvl heterodimerized with Ccd1. How Ccd1 blocks Rac/Dvl signaling to JNK is unclear. In contrast, Axin, when complexed with Ccd1, did not bind to MEKK1. Furthermore, Ccd1 physically interacted with MEKK4 in their physiological concentrations and prevented MEKK4 from binding to Axin. Reduction of Ccd1 protein by small interfering RNA could elevate JNK signaling as assayed with an AP1-dependent transcriptional reporter. We have therefore demonstrated that Ccd1 inhibits Axin-mediated JNK activation by simultaneously adopting two distinct mechanisms, one through conformational changes that disallow MEKK1 binding and the other via direct sequestration of MEKK4.
AP-2 Transcription Factor Family Member Expression, Activity, and Regulation in Human Epidermal Keratinocytes in Vitro
Differentiation; Research in Biological Diversity. Jun, 2004 | Pubmed ID: 15270775
The AP-2 transcription factor family is presumed to play an important role in the regulation of the keratinocyte squamous differentiation program; however, limited functional data are available to support this. In the present study, the activity and regulation of AP-2 were examined in differentiating human epidermal keratinocytes. We report that (1) AP-2 transcriptional activity decreases in differentiated keratinocytes but remains unchanged in differentiation-insensitive squamous cell carcinoma cell lines, (2) diminished AP-2 transcriptional activity is associated with a loss of specific DNA-bound AP-2 complexes, and (3) there is an increase in the ability of cytoplasmic extracts, derived from differentiated keratinocytes, to phosphorylate AP-2 alpha and AP-2 beta when cells differentiate. In contrast, extracts from differentiation-insensitive squamous cell carcinoma cells are unable to phosphorylate AP-2 proteins. Finally, the phosphorylation of recombinant AP-2 alpha by cytosolic extracts from differentiated keratinocytes is associated with decreased AP-2 DNA-binding activity. Combined, these data indicate that AP-2 trans-activation and DNA-binding activity decrease as keratinocytes differentiate, and that this decreased activity is associated with an enhanced ability to phosphorylate AP-2 alpha and beta.
Biochemical and Biophysical Research Communications. Nov, 2004 | Pubmed ID: 15474455
The inhibition of E2F has been demonstrated to be important in the initiation of squamous differentiation by two independent manners: promotion of growth arrest and the relief of the differentiation-suppressive properties of E2Fs. E2F6 is reported to behave as a transcriptional repressor of the E2F family. In this study, we examined the ability of E2F6 to act as the molecular switch required for E2F inhibition in order for keratinocytes to enter a terminal differentiation programme. Results demonstrated that whilst E2F6 was able to suppress E2F activity in proliferating keratinocytes, it did not modulate squamous differentiation in a differentiated keratinocyte. Furthermore, inhibition of E2F, by overexpressing E2F6, was not sufficient to sensitise either proliferating keratinocytes or the squamous cell carcinoma cell line, KJD-1/SV40, to differentiation-inducing agents. Significantly, although E2F6 could suppress E2F activity in proliferating cells, it could not inhibit proliferation of KJD-1/SV40 cells. These results demonstrate that E2F6 does not contain the domains required for modulation of squamous differentiation and imply isoform-specific functions for individual E2F family members.
The Journal of Chemical Physics. Oct, 2004 | Pubmed ID: 15485251
The algorithm by Northrup, Allison, and McCammon [J. Chem. Phys. 80, 1517 (1984)] has been used for two decades for calculating the diffusion-influenced rate-constants of enzymatic reactions. Although many interesting results have been obtained, the algorithm is based on the assumption that substrate-substrate interactions can be neglected. This approximation may not be valid when the concentration of the ligand is high. In this work, we constructed a simulation model that can take substrate-substrate interactions into account. We first validated the model by carrying out simulations in ways that could be compared to analytical theories. We then carried out simulations to examine the possible effects of substrate-substrate interactions on diffusion-controlled reaction rates. For a substrate concentration of 0.1 mM, we found that the diffusion-controlled reaction rates were not sensitive to whether substrate-substrate interactions were included. On the other hand, we observed significant influence of substrate-substrate interactions on calculated reaction rates at a substrate concentration of 0.1M. Therefore, a simulation model that takes substrate-substrate interactions into account is essential for reliably predicting diffusion-controlled reaction rates at high substrate concentrations, and one such simulation model is presented here.
Release of ADP from the Catalytic Subunit of Protein Kinase A: a Molecular Dynamics Simulation Study
Protein Science : a Publication of the Protein Society. Jan, 2005 | Pubmed ID: 15608120
Substrate phosphorylation by cAMP-dependent-protein kinase A (protein kinase A, PKA) has been studied extensively. Phosphoryl transfer was found to be fast, whereas ADP release was found to be the slow, rate-limiting step. There is also evidence that ADP release may be preceded by a partially rate-limiting conformational change. However, the atomic details of the conformational change and the mode of ADP release are difficult to obtain experimentally. In this work, we studied ADP release from PKA by carrying out molecular dynamics simulations with different pulling forces applied to the ligand. The detailed ADP release pathway and the associated conformational changes were analyzed. The ADP release process was found to involve a swinging motion with the phosphate of ADP anchored to the Gly-rich loop, so that the more buried adenine base and ribose ring came out before the phosphate. In contrast to the common belief that a hinge-bending motion was responsible for the opening of the ligand-binding cleft, our simulations showed that the small lobe exhibited a large amplitude "rocking" motion when the ligand came out. The largest conformational change of the protein was observed at about the first quarter time point along the release pathway. Two prominent intermediate states were observed in the release process.
E2F Suppression and Sp1 Overexpression Are Sufficient to Induce the Differentiation-specific Marker, Transglutaminase Type 1, in a Squamous Cell Carcinoma Cell Line
Oncogene. May, 2005 | Pubmed ID: 15735752
Recently, E2F function has expanded to include the regulation of differentiation in human epidermal keratinocytes (HEKs). We extend these findings to report that in HEKs, Sp1 is a differentiation-specific activator and a downstream target of E2F-mediated suppression of the differentiation-specific marker, transglutaminase type 1 (TG-1). Deletion of elements between -0.084 to -0.034 kb of the TG-1 promoter disabled E2F1-induced suppression of promoter activity. Electrophoretic mobility shift assays (EMSAs) demonstrated that Sp1 and Sp3 bound this region. Protein expression analysis suggested that squamous differentiation was accompanied by increased Sp1/Sp3 ratio. Cotransfection of proliferating HEKs or the squamous cell carcinoma (SCC) cell line, KJD-1/SV40, with an E2F inhibitor (E2Fd/n) and Sp1 expression plasmid was sufficient to activate the TG-1 promoter. The suppression of Sp1 activity by E2F in differentiated cells appeared to be indirect since we found no evidence of an Sp1/E2F coassociation on the TG-1 promoter fragment. Moreover, E2F inhibition in the presence of a differentiation stimulus induced Sp1 protein. These data demonstrate that (i) Sp1 can act as a differentiation stimulus, (ii) E2F-mediated suppression of differentiation-specific markers is indirect via Sp1 inhibition and (iii) a combination of E2F inhibition and Sp1 activation could form the basis of a differentiation therapy for SCCs.
Relative Contributions of Desolvation, Inter- and Intramolecular Interactions to Binding Affinity in Protein Kinase Systems
Journal of Computational Chemistry. May, 2005 | Pubmed ID: 15754303
In several previous studies, we performed sensitivity analysis to gauge the relative importance of different atomic partial charges in determining protein-ligand binding. In this work, we gain further insights by decomposing these results into three contributions: desolvation, intramolecular interactions, and intermolecular interactions, again based on a Poisson continuum electrostatics model. Three protein kinase-inhibitor systems have been analyzed: CDK2-deschloroflavopiridol, PKA-PKI, and LCK-PP2. Although our results point out the importance of specific intermolecular interactions to the binding affinity, they also reveal the remarkable contributions from the solvent-mediated intramolecular interactions in some cases. Thus, it is necessary to look beyond analyzing protein-ligand interactions to understand protein-ligand recognition or to gain insights into designing ligands and proteins. In analyzing the contributions of the three components to the overall binding free energy, the PKA-PKI system with a much larger ligand was found to behave differently from the other two systems with smaller ligands. In the former case, the intermolecular interactions are very favorable, and together with the favorable solvent-mediated intramolecular interactions, they overcome the large desolvation penalties to give a favorable electrostatics contribution to the overall binding affinity. On the other hand, the other two systems with smaller ligands only present modest intermolecular interactions and they are not or are only barely sufficient to overcome the desolvation penalty even with the aid of the favorable intramolecular contributions. As a result, the binding affinity of these two systems do not or only barely benefit from electrostatics contributions.
Current Cancer Drug Targets. Mar, 2005 | Pubmed ID: 15810874
In this review we provide a brief background on the cell cycle and then focus on two novel and emerging areas of cell cycle research that may prove to have significant relevance to the development of novel anticancer agents. In particular, we review the emerging evidence to suggest that histone deacetylase inhibitors may possess cancer cell-specific cytotoxicity due to their ability to target a novel G2/M checkpoint. We also review the recent literature supporting the proposition that inhibition of E2F activity in epithelial cancer cells may prove to be a useful differentiation therapy that operates via cell cycle-dependent and cell cycle-independent mechanisms.
The Journal of Obstetrics and Gynaecology Research. Aug, 2005 | Pubmed ID: 16018773
To evaluate and compare laparoscopic-assisted surgical staging with conventional laparotomy for the treatment of endometrial carcinoma.
Direct Estimation of Entropy Loss Due to Reduced Translational and Rotational Motions Upon Molecular Binding
Biopolymers. Dec, 2005 | Pubmed ID: 16078192
The entropic cost due to the loss of translational and rotational (T-R) degree of freedom upon binding has been well recognized for several decades. Tightly bound ligands have higher entropic costs than loosely bound ligands. Quantifying the ligand's residual T-R motions after binding, however, is not an easy task. We describe an approach that uses a reduced Hessian matrix to estimate the contributions due to translational and rotational degrees of freedom to entropy change upon molecular binding. The calculations use a harmonic model for the bound state but only include the T-R degrees of freedom. This approximation significantly speeds up entropy calculations because only 6 x 6 matrices need to be treated, which makes it easier to be used in computer-aided drug design for studying many ligands. The methodological connection with other methods is discussed as well. We tested this approximation by applying it to study the binding of ATP, peptide inhibitor (PKI), and several bound water molecules to protein kinase A (PKA). These ligands span a wide range in size. The model gave reasonable estimates of the residual T-R entropy of bound ligands or water molecules. The residual T-R entropy demonstrated a wide range of values, e.g., 4 to 16 cal/K.mol for the bound water molecules of PKA.
The Australian & New Zealand Journal of Obstetrics & Gynaecology. Oct, 2005 | Pubmed ID: 16171472
Catheterisation of the bladder was routinely performed before gynaecological laparoscopy, but such an established practice is not evidence based and may lead to an increase in postoperative urinary symptoms and urinary tract infection.
Proteins. Dec, 2005 | Pubmed ID: 16245317
Even if the structure of a receptor has been determined experimentally, it may not be a conformation to which a ligand would bind when induced fit effects are significant. Molecular docking using such a receptor structure may thus fail to recognize a ligand to which the receptor can bind with reasonable affinity. Here, we examine one way to alleviate this problem by using an ensemble of receptor conformations generated from a molecular dynamics simulation for molecular docking. Two molecular dynamics simulations were conducted to generate snapshots for protein kinase A: one with the ligand bound, the other without. The ligand, balanol, was then docked to conformations of the receptors presented by these trajectories. The Lamarckian genetic algorithm in Autodock [Goodsell et al. J Mol Recognit 1996;9(1):1-5; Morris et al. J Comput Chem 1998;19(14):1639-1662] was used in the docking. Three ligand models were used: rigid, flexible, and flexible with torsional potentials. When the snapshots were taken from the molecular dynamics simulation of the protein-ligand complex, the correct docking structure could be recovered easily by the docking algorithm in all cases. This was an easier case for challenging the docking algorithm because, by using the structure of the protein in a protein-ligand complex, one essentially assumed that the protein already had a pocket to which the ligand can fit well. However, when the snapshots were taken from the ligand-free protein simulation, which is more useful for a practical application when the structure of the protein-ligand complex is not known, several clusters of structures were found. Of the 10 docking runs for each snapshot, at least one structure was close to the correctly docked structure when the flexible-ligand models were used. We found that a useful way to identify the correctly docked structure was to locate the structure that appeared most frequently as the lowest energy structure in the docking experiments to different snapshots.
Calculation of Solvation Free Energy from Quantum Mechanical Charge Density and Continuum Dielectric Theory
The Journal of Physical Chemistry. A. Apr, 2006 | Pubmed ID: 16599457
We have combined ultrasoft pseudopotential density functional theory utilizing plane wave basis with a Poisson-Boltzmann/solvent-accessible surface area (PB/SA) model to calculate the solvation free energy of small neutral organic compounds in water. The solute charge density obtained from density functional theory was directly used in solving the Poisson-Boltzmann equation to obtain the reaction field. The polarized electronic wave function of the solute in the solvent was solved by including the reaction field in the density functional Hamiltonian. The quantum mechanical and Poisson-Boltzmann equations were solved self-consistently until the charge density and reaction field converged. Using the solute charge density directly instead of a point-charge representation permitted asymmetric distortion and spreading out of the electron cloud. Because the electron density could leave the van der Waals surface to penetrate into the high-dielectric solvent, the reaction field generated by this density was generally smaller than that obtained by using the point-charge representation. In applying this model to calculate the solvation free energy of 31 small neutral organic molecules spanning a range of 25 kcal/mol, we obtained a root-mean-square error of only 1.3 kcal/mol if we allowed one adjustable parameter to shift the calculated solvation free energy.
Molecular Dynamics Simulation of Laser Desorption of a Fragment of Protein Kinase A from Two MALDI Matrices
The Journal of Physical Chemistry. A. Apr, 2006 | Pubmed ID: 16623462
We have carried out molecular dynamics simulations to study the desorption of a dephosphorylated fragment of protein kinase A from two matrices, sinapic acid (SA) and 2,5-dihydroxybenzoic acid (DHB), after laser excitation. We have examined the results as a function of the laser fluence and of the burial depth of the guest peptide in the matrices. In most cases, we found that the energy transferred from the matrix to the guest peptide was not sufficiently large to fragment the peptide. Exceptions occurred when the peptide was more buried. This finding suggested that protein analytes might be less likely to break into smaller fragments if they were placed closer to the surface of the matrix. We have also examined how likely the guest peptide could form small clusters with the matrix molecules and found that the results depended on the degree of burial of the peptide, on the laser fluence, and on which matrix was used. Generally, stable clusters were more likely to be formed for guest peptides that were more buried, at a lower laser fluence, and in the SA rather than the DHB matrix. In addition, we found that the DHB matrix was broken down more easily by the laser than the SA matrix.
Sevoflurane-induced Oxidative Stress and Cellular Injury in Human Peripheral Polymorphonuclear Neutrophils
Food and Chemical Toxicology : an International Journal Published for the British Industrial Biological Research Association. Aug, 2006 | Pubmed ID: 16678324
Sevoflurane is an inhalation anesthetic used for general anesthesia. Several studies have demonstrated that reactive oxygen species (ROS) exist in cardioprotection when preconditioned with sevoflurane. Moreover, sevoflurane can also directly trigger the formation of peroxynitrite. Up to now, information pertinent to the effect of sevoflurane on cellular injuries in human polymorphonuclear neutrophils (PMN) is scant. In this study, we demonstrated that sevoflurane significantly increases intracellular H2O2 and/or peroxide, superoxide, and nitric oxide (NO) in PMN within 1h treatment. Intensification of intracellular glutathione (GSH) depletion in PMN has been demonstrated with the presence of sevoflurane. Inhibition of sevoflurane-mediated intracellular H2O2 and/or peroxide in PMN by catalase, mannitol, dexamethasone, N-acetylcysteine (NAC) and trolox, but not superoxide dismutase (SOD) pretreatment, was observed. Among them, catalase has the best effect scavenging intracellular H2O2 and/or peroxide, suggesting that H2O2 is the major ROS during sevoflurane treatment. Two apoptotic critical factors-lowering of the mitochondrial transmembrane potential (DeltaPsim) and activation of caspase 3/7-were significantly increased after 1h of sevoflurane treatment. Apoptosis of PMN were determined by comet assay and flow cytometric analysis of annexin V-FITV protein binding to the cell surface. Exposure of PMN to sevoflurane markedly increased apoptosis in a dose-dependent manner. In summary, these results are important for demonstrating the oxidative stress and cellular injury on sevoflurane-treated human PMN.
Rank-ordering Protein-ligand Binding Affinity by a Quantum Mechanics/molecular Mechanics/Poisson-Boltzmann-surface Area Model
The Journal of Chemical Physics. Jan, 2007 | Pubmed ID: 17228977
Theoretical Studies of the Effect of the Dipolar Field in Multiple Spin-echo Sequences with Refocusing Pulses of Finite Duration
Journal of Magnetic Resonance (San Diego, Calif. : 1997). Apr, 2007 | Pubmed ID: 17257870
It has been observed recently that the finite duration of refocusing rf pulses in a multiecho acquisition of the signal formed under the influence of the dipolar field leads to significant signal attenuation [S. Kennedy, Z. Chen, C.K. Wong, E.W.-C. Kwok, J. Zhong, Investigation of multiple-echo spin-echo signal acquisition under distant dipole-dipole interactions, Proc. Int. Soc. Magn. Reson. Med. 13 (2005) 2288]. Hereto, we quantify the phenomenon by evaluating analytically the influences of both the distant dipolar field (DDF) and transverse relaxation T2 on the magnetization in a multiecho pulse sequence based on correlation spectroscopy revamped by asymmetric z-gradient echo detection (CRAZED). Analytic expressions for the magnetization were obtained, which demonstrate explicitly the origin of rephased signal in the presence of the finite pi pulses in the multiecho train. The expressions also explain the effects of the DDF and T2 during the refocusing pulses on the signal strength, and show the substantial signal dependence on the phase of the rf pulses. We show that when the DDF effect during the pulse is canceled, the signal rises primarily during the free evolution time in the acquisition period. This elucidates the signal attenuation when the rf pulses cover a significant proportion of time in the sequence. In addition, we performed an optimization on the number of refocusing pulses that maximizes the total acquired signal using parameters for water, brain white matter, and muscle. We found that maximal signal-to-noise ratio is obtained when the pulse duration approximately equals the free evolution time in the samples with a wide range of T2.
Biochimica Et Biophysica Acta. Jun, 2007 | Pubmed ID: 17379327
Both Caspase-3 and Caspase-9 play critical roles in the execution of mitochondria-mediated apoptosis. Caspase-9 binds to Apaf-1 in the presence of cytochrome c and dATP/ATP, and is activated by self-cleavage. Caspase-3 is activated by cleavage of caspase-8 and caspase-9. Over hundred direct caspase-3 substrates are identified whereas only few direct caspase-9 substrates are known. Here, we demonstrate that Ring1B, a component of polycomb protein complex that plays important roles in modulating chromatin structures, is a direct substrate of active caspase-3 and caspase-9 both in vitro and in vivo. The specific cleavage sites for caspase-3 and caspase-9 were mapped to Asp(175) and Asp(208), respectively. Importantly, cleavage of Ring1B by active caspases-3 and caspase-9 triggers the redistribution of Ring1B, from exclusive nuclear localization to even distribution throughout the entire cell. The transcriptional repression activity of Ring1B was also disrupted by caspase cleavage. Our data suggest that caspases-3 and caspase-9 play novel roles in transcription by regulating polycomb protein function through direct cleaving of Ring1B.
Environmental Science & Technology. Jun, 2007 | Pubmed ID: 17612154
Synthetic musk compounds are used as additives in many consumer products, including perfumes, deodorants, and detergents. Earlier studies have reported the occurrence of synthetic musks in environmental and wildlife samples collected in the United States. In this study, human breast milk samples collected from Massachusetts, were analyzed for the determination of concentrations of synthetic musks such as musk xylene (1-tert-butyl-3,5-dimethyl-2,4,6-trinitrobenzene), musk ketone (4-tert-butyl-2,6-dimethyl-3,5-dinitroacetophenone), HHCB (1,3,4,6,7,8-hexahydro-4,6,6,7,8,8-hexamethylcyclopenta[gamma]-2-benzopyran), AHTN (7-acetyl-1,1,3,4,4,6-hexamethyl-1,2,3,4-tetrahydronaphthalene), and HHCB-lactone, the oxidation product of HHCB. In addition, we estimated the daily intake of synthetic musks by infants based on the ingestion rate of breast milk. Synthetic musks were found in most of the samples analyzed, and the concentrations ranged from < 2 to 150 ng musk xylene/g, < 2 to 238 ng musk ketone/ g, < 5 to 917 ng HHCB/g, < 5 to 144 ng AHTN/g, and < 10 to 88.0 ng HHCB-lactone/g, on a lipid weight basis. The concentrations of HHCB were higher than the concentrations of other synthetic musks in breast milk samples. The mean concentration of HHCB (220 ng/g, lipid weight) was 5 times greater than the concentrations reported 10 years ago for breast milk samples collected in Germany and Denmark. Maternal age was not correlated with the concentrations of musk xylene, musk ketone, HHCB, or AHTN. There was a trend of decreasing concentrations of musk xylene, musk ketone, HHCB, and AHTN, with the number of children previously breast-fed, although the correlation was not significant. Based on average daily ingestion rate of breast milk, an infant is estimated to ingest 297 +/- 229 ng musk xylene, 780 +/- 805 ng musk ketone, 1830 +/- 1170 ng HHCB, 565 +/- 614 ng AHTN, and 649 +/- 598 ng HHCB-lactone per day. The ingestion rate of synthetic musks by infants in the United States is lower than that estimated for persistent organic pollutants (POPs) such as polychlorinated biphenyls (PCBs). Based on the residue patterns and accumulation features, it can be concluded that the exposure characteristics for synthetic musks are different from those of POPs, and that the major source of exposure to synthetic musks is probably via dermal absorption or inhalation.
The Efficacy of Protective Effects of Tannic Acid, Gallic Acid, Ellagic Acid, and Propyl Gallate Against Hydrogen Peroxide-induced Oxidative Stress and DNA Damages in IMR-90 Cells
Molecular Nutrition & Food Research. Aug, 2007 | Pubmed ID: 17628875
There is increasing evidence that reactive oxygen species (ROS) are intimately involved in the oxidative damage of tissues for a wide variety of pulmonary diseases. Thus, it is desirable to search for chemopreventive agents that can counteract ROS-mediated injury to the pulmonary tissues. Using a human lung fibroblast IMR-90 cells as the experimental model, we first demonstrated that nearly 90% of intracellular ROS could be removed when H(2)O(2)-treated cells (200 microM) simultaneously incubated with 10 microg/mL of tannic acid (TA), gallic acid (GA), ellagic acid (EA), and propyl gallate (PA). Using C(11)-BODIPY(581/591 )as a lipid peroxidation probe, we also attested that all these compounds examined (10 microg/mL) could alleviate H(2)O(2)-evoked lipid peroxidation phenomena. Next, we examined the protective effects of these compounds on the depletion of intracellular glutathione (iGSH) in H(2)O(2)-treated cells using CMF-DA probe. Interestingly, PA was demonstrated to be the only compound that could effectively protect the integrity of iGSH from being depleted by this system. Finally, the protective effects of these compounds against oxidative DNA damage were evaluated using 8-oxoguanine formation as a marker. Our data indicated that all four compounds suppressed the formation of 8-oxoguanine effectively. Taken together, our data suggested that TA, GA, EA, and PA can protect cells from oxidative stress.
Biophysical Journal. Dec, 2007 | Pubmed ID: 17766352
Using the docking of p-nitrocatechol sulfate to Yersinia protein tyrosine phosphatase YopH as an example, we showed that an approach based on mining minima followed by cluster and similarity analysis could generate useful insights into docking pathways. Our simulation treated both the ligand and the protein as flexible molecules so that the coupling between their motion could be properly accounted for. Our simulation identified three docking poses; the one with the lowest energy agreed well with experimental structure. The model also predicted the side-chain conformations of the amino acids lying in the binding pocket correctly with the exception of three residues that appeared to be stabilized by two structural water molecules in the crystal structure. The implicit solvent model employed in the simulation could not capture such effects well. We also found four major pathways leading to these docking poses after the ligand entered the mouth of the binding pocket. In addition, the sulfate group of p-nitrocatechol sulfate was found to be important both in binding the ligand to the pocket and in guiding the ligand to dock into the pocket. The coupling of the motion between the protein and the ligand also played an important role in facilitating ligand loading and unloading.
Polybrominated Diphenyl Ethers and Organochlorine Pesticides in Human Breast Milk from Massachusetts, USA
Journal of Environmental Monitoring : JEM. Nov, 2007 | Pubmed ID: 17968447
Concentrations of polybrominated diphenyl ethers (PBDEs), and organochlorine pesticides (OCPs; DDTs, HCHs, CHLs, and HCB) were measured in human breast milk samples collected across Massachusetts, USA, in 2004. Seventeen PBDE congeners were found in the samples, ranging in concentration from 0.06 to 1910 ng g(-1) lipid wt. BDE-47 (2,2',4,4'-tetraBDE), BDE-99 (2,2',4,4',5-pentaBDE), and BDE-100 (2,2',4,4',6-pentaBDE) were the major congeners detected in breast milk samples. Overall mean (+/-SD) concentrations of DDTs, HCHs, CHLs, and HCB were 64.5 +/- 75, 18.9 +/- 19, 32.4 +/- 36, and 2.3 +/- 2.2 ng g(-1) lipid wt, respectively. Concentrations of PBDEs were strongly correlated with concentrations of OCPs in the samples. Based on the concentrations of organohalogens and the intake rates of breast milk by infants in the United States, daily ingestion rates of contaminants were calculated. The median ingestion rates for PBDEs, HCHs, DDTs, CHLs, and HCB were 4.0, 212, 141, 44, and 5.79 ng kg(-1) body wt day(-1), respectively. The estimated daily intake of organohalogens by infants was compared with threshold reference values suggested by the United States Environmental Protection Agency (USEPA) and the Agency for Toxic Substances and Disease Registry (ATSDR), for calculation of hazard quotients (HQs). HQs for individual organohalogens and the sum of HQ for all organohalogens were calculated as HQ indices (HQI). The results suggest that one or more of the contaminants analyzed in this study exceeded the threshold reference values in at least 26% of the breast milk samples.
Biochimica Et Biophysica Acta. Jan, 2008 | Pubmed ID: 17996742
Quite a few reviews on molecular docking have already appeared. This mini-review focuses on methods that incorporate protein flexibility in docking rather than those that treat protein targets as rigid molecules. This is still a challenging problem but there are encouraging recent advances. These methods will be reviewed particularly in light of their applications to protein kinases and phosphatases. In addition to obtaining correct docking pose, recent developments on exploring docking pathways are also highlighted.
The Journal of Biological Chemistry. Apr, 2008 | Pubmed ID: 18281287
MicroRNA (miRNA) are important regulators of many biological processes, but the targets for most miRNA are still poorly defined. In this study, we profiled the expression of miRNA during myogenesis, from proliferating myoblasts through to terminally differentiated myotubes. Microarray results identified six significantly differentially expressed miRNA that were more than 2-fold different in myotubes. From this list, miRNA-26a (miR-26a), an up-regulated miRNA, was further examined. Overexpression of miR-26a in murine myogenic C2C12 cells induced creatine kinase activity, an enzyme that markedly increases during myogenesis. Further, myoD and myogenin mRNA expression levels were also up-regulated. These results suggest that increased expression of miR-26a promotes myogenesis. Through a bioinformatics approach, we identified the histone methyltransferase, Enhancer of Zeste homolog 2 (Ezh2), as a potential target of miR-26a. Overexpression of miR-26a suppressed the activity of a luciferase reporter construct fused with the 3'-untranslated region of Ezh2. In addition, miR-26a overexpression decreased Ezh2 mRNA expression. These results reveal a model of regulation during myogenesis whereby the up-regulation of miR-26a acts to post-transcriptionally repress Ezh2, a known suppressor of skeletal muscle cell differentiation.
Environmental Science & Technology. Apr, 2008 | Pubmed ID: 18497172
Perfluorinated compounds (PFCs), notably perfluorooctanesulfonate (PFOS) and perfluorooctanoic acid (PFOA), have been reported in human blood. Furthermore, the occurrence of PFCs in the blood of newborn babies, coupled with the need to study the potential association of PFC exposure with birth outcomes in neonates, suggests the need for determining the sources and magnitude of exposure in infants. In this study, nine PFCs were measured in 45 human breast milk samples collected in 2004 from Massachusetts, U.S.A. PFOS and PFOA were the predominant PFCs found at mean concentrations of 131 and 43.8 pg/mL, respectively. Comparison of the ratio of PFOS to PFOA in human milk with the ratios published for human serum from the U.S. female population suggested preferential partitioning of PFOA to milk. Concentrations of PFOA were significantly higher in the milk of mothers nursing for the first time (n = 34) than in the milk of mothers who have previously nursed (n = 8). Based on the estimated body weight and milk intake, the average and highest daily intakes of total PFCs by infants were 23.5 and 87.1 ng/kg bw, respectively. We found that the daily ingestion rates of PFOS and PFOA did not exceed the tolerable daily intake recommended by the U.K. Food Standards Agency. This is the first study to measure the occurrence of PFCs in human milk from the U.S.A.
The Journal of Chemical Physics. Jul, 2008 | Pubmed ID: 18624485
We have developed a method to improve the description of solute cavity defined by the interlocking-sphere model for continuum-solvent electrostatics calculations. Many models choose atomic radii from a finite set of atom types or uses an even smaller set developed by Bondi [J. Phys. Chem. 68, 441 (1964)]. The new model presented here allowed each atom to adapt its radius according to its chemical environment. This was achieved by first approximating the electron density of a molecule by a superposition of atom-centered spherical Gaussian functions. The parameters of the Gaussian functions were then determined by optimizing a function that minimized the difference between the properties from the model and those from ab initio quantum calculations. These properties included the electrostatics potential on molecular surface and the electron density within the core of each atom. The size of each atom was then determined by finding the radius at which the electron density associated with the atom fell to a prechosen value. This value was different for different chemical elements and was chosen such that the averaged radius for each chemical element in a training set of molecules matched its Bondi radius. Thus, our model utilized only a few adjustable parameters-the above density cutoff values for different chemical elements-but had the flexibility of allowing every atom to adapt its radius according to its chemical environment. This variable-radii model gave better solvation energy for 31 small neutral molecules than the Bondi radii did, especially for a quantum mechanics/Poisson-Boltzmann approach we developed earlier. The improvement was most significant for molecules with large dipole moment. Future directions for further improvement are also discussed.
Biochimica Et Biophysica Acta. Dec, 2008 | Pubmed ID: 18708124
Severe acute respiratory syndrome (SARS) coronavirus (CoV) spread from China to more than 30 countries, causing severe outbreaks of atypical pneumonia and over 800 deaths worldwide. CoV primarily infects the upper respiratory and gastrointestinal tract; however, SARS-CoV has a unique pathogenesis because it infects both the upper and lower respiratory tracts and leads to human respiratory diseases. SARS-CoV genome has shown containing 14 open reading frames (ORFs) and 8 of them encode novel proteins. Previous reports show that overexpression of ORF-3a, ORF-3b and ORF-7a induce apoptosis. In this report, we demonstrate that overexpression of ORF-6 also induces apoptosis and that Caspase-3 inhibitor and JNK inhibitor block ORF-6 induced apoptosis. Importantly, the protein level of ER chaperon protein, GRP94, was up-regulated when ORF-6 was overexpressed. All these data suggest that ORF-6 induces apoptosis via Caspase-3 mediated, ER stress and JNK-dependent pathways.
Proteins. Apr, 2008 | Pubmed ID: 17957770
By docking flexible balanol to a rigid model of protein kinase A (PKA), we found that a new simulated annealing protocol termed disrupted velocity simulated annealing (DIVE-SA) outperformed the replica-exchange method and the traditional simulated annealing method in identifying the correct docking pose. In this protocol, the atomic velocities were reassigned periodically to encourage the system to sample a large conformational space. We also found that scaling potential energy surface to reduce structural transition barriers could further facilitate docking. The DIVE-SA method was then evaluated on its ability to perform flexible ligand-flexible protein docking of three ligands (balanol, a balanol analog, and ATP) to PKA. To reduce computational time and to avoid possible unphysical structural changes resulting from the use of nonoptimal force fields, a soft restrain was applied to keep the root-mean-square-deviation (RMSD) between instantaneous protein structures and a chosen reference structure small. Because the restrain was applied to the overall RMSD rather than to individual atoms, a protein could still experience relatively large conformational changes during docking. To examine the impact of applying such a restrain on docking, we constructed two semi-flexible protein models by choosing two different crystal structures as reference. Both the balanol analog and ATP were able to dock to either one of these semi-flexible protein models. On the other hand, balanol could only dock well to one of them. Further analysis indicated that the restrain on the glycine-rich loop was too strong, preventing it to adjust its structure to accommodate balanol in the binding pocket of PKA. Removing the restrain on the glycine-rich loop resulted in much better docking poses. This finding demonstrates the important role that the flexibility of the glycine-rich loop play in accepting different ligands and should profitably not be restrained in molecular docking so that more diverse ligands can be studied.
Journal of Computational Chemistry. Mar, 2009 | Pubmed ID: 18711718
Protein kinases have high structural plasticity: their structure can change significantly, depending on what ligands are bound to them. Rigid-protein docking methods are not capable of describing such effects. Here, we present a new flexible-ligand flexible-protein docking model in which the protein can adopt conformations between two extremes observed experimentally. The model utilized a molecular dynamics-based simulated annealing cycling protocol and a distance-dependent dielectric model to perform docking. By testing this model on docking four diverse ligands to protein kinase A, we found that the ligands were able to dock successfully to the protein with the proper conformations of the protein induced. By imposing relatively soft conformational restraints to the protein during docking, this model reduced computational costs yet permitted essential conformational changes that were essential for these inhibitors to dock properly to the protein. For example, without adequate movement of the glycine-rich loop, it was difficult for the ligands to move from the surface of the protein to the binding site. In addition, these simulations called for better ways to compare simulation results with experiment other than using the popular root-mean-square deviation between the structure of a ligand in a docking pose and that in experiment because the structure of the protein also changed. In this work, we also calculated the correlation coefficient between protein-ligand/protein-protein distances in the docking structure and those in the crystal structure to check how well a ligand docked into the binding site of the protein and whether the proper conformation of the protein was induced.
The Journal of Physical Chemistry. A. Apr, 2009 | Pubmed ID: 19334696
Although various groups have studied the phosphorylation mechanism of the insulin receptor tyrosine kinase (IRK), an unanimous picture has not yet emerged. In this work, we performed a computational study to gain further insights. We first built a structural model of the reactant complex with the guide of several crystal structures and previous computational studies of the cyclic AMP-dependent protein kinase. We then optimized the structure by performing geometry optimization using a quantum mechanical model containing nearly 300 atoms. A reaction path was then traced between the reactant and the product by using a multiple coordinate-driven method. The calculations mapped out a sequence of structural changes depicting the conversion of the reactant to the product. Analysis of the structural changes revealed the formation of a dissociative transition state and the involvement of a proton transfer from the hydroxyl group of the tyrosyl residue of the peptide substrate to a conserved aspartate in the active site of the enzyme. The proton transfer began well before the transition state was reached and finished only shortly before the product was completely formed. In addition, the formation of a hydrogen bonding network among Arg1136, Asp1132, the gamma-phosphate of ATP, and the tyrosine residue of the substrate appeared to hold the latter two in a near-attack position for reaction. The model estimated a reaction barrier of 14 kcal/mol, semiquantitatively in accord with experiment.
Journal of Medicinal Chemistry. Sep, 2009 | Pubmed ID: 19702309
We modeled the kinetics of drug binding to protein kinases in the EGF signaling pathway relevant to non-small-cell lung cancer and found that binding kinetics could influence therapeutic potential, that fast binding kinetics was advantageous for most targets with a couple of exceptions, that targeting some protein kinases could enhance rather than attenuate the pathway, and that IC(50) could be sensitive to the kinetic parameters of drug binding.
Docking Flexible Peptide to Flexible Protein by Molecular Dynamics Using Two Implicit-solvent Models: an Evaluation in Protein Kinase and Phosphatase Systems
The Journal of Physical Chemistry. B. Oct, 2009 | Pubmed ID: 19845408
Reliable prediction of protein-ligand docking pose requires proper account of induced fit effects. Treating both the ligand and the protein as flexible molecules is still challenging because many degrees of freedom are involved. Peptides are one type of ligand that are particularly difficult to study because of their extreme flexibility. In this study, we tested a molecular dynamics-based simulated-annealing cycling protocol in docking peptides to four protein kinases and two phosphatases using two implicit-solvent models: a distance-dependent dielectric model (epsilon(r) = 4r) and a version of the Generalized Born model termed GBMV. We found that the simpler epsilon(r) = 4r model identified docking pose better than the more expensive GBMV model. In addition, rescoring structures obtained from one implicit-solvent model with the other identified good docking poses for all six systems studied. Including protein energy in scoring also improved results.
Theoretical Analysis of the Sensitivity of Dipolar Field Signal to Local Field Variations by Perturbative Expansion of the Magnetization
Journal of Magnetic Resonance (San Diego, Calif. : 1997). Mar, 2010 | Pubmed ID: 20022774
A perturbation method based on the integral form of the Bloch equation is used to calculate the distant dipolar field (DDF) signal formed by the correlation spectroscopy revamped by asymmetric z-gradient echo detection (CRAZED) sequence in the presence of a susceptibility-induced field. The properties of the DDF signal are analyzed through the series expansion of the magnetization, and the first order DDF result is applied to study the use of the DDF effect to probe sub-voxel field distributions. Numerical calculations are carried out with the sub-voxel field distributions modeled by rectangular tubes of uniform frequency shifts (the block model) and cylinders of a finite susceptibility difference (the blood vessel model) using the parameters for brain at 9.4T. The DDF signal is found to exhibit features arising from the sub-voxel structures.
Chemical Biology & Drug Design. Aug, 2010 | Pubmed ID: 20560978
Yersinia pestis causes diseases ranging from gastrointestinal syndromes to bubonic plague and could be misused as a biological weapon. As its protein tyrosine phosphatase YopH has already been demonstrated as a potential drug target, we have developed two series of forty salicylic acid derivatives and found sixteen to have micromolar inhibitory activity. We designed these ligands to have two chemical moieties connected by a flexible hydrocarbon linker to target two pockets in the active site of the protein to achieve binding affinity and selectivity. One moiety possessed the salicylic acid core intending to target the phosphotyrosine-binding pocket. The other moiety contained different chemical fragments meant to target a nearby secondary pocket. The two series of compounds differed by having hydrocarbon linkers with different lengths. Before experimental co-crystal structures are available, we have performed molecular docking to predict how these compounds might bind to the protein and to generate structural models for performing binding affinity calculation to aid future optimization of these series of compounds.
Quantitative Analysis of Promoter Methylation in Exfoliated Epithelial Cells Isolated from Breast Milk of Healthy Women
Epigenetics : Official Journal of the DNA Methylation Society. Oct, 2010 | Pubmed ID: 20716965
Promoter methylation analysis of genes frequently silenced in breast cancer is a promising indicator of breast cancer risk, as these methylation events are thought to occur long before presentation of disease. The numerous exfoliated epithelial cells present in breast milk may provide the breast epithelial DNA needed for detailed methylation analysis and assessment of breast cancer risk. Fresh breast milk samples and health, lifestyle, and reproductive history questionnaires were collected from 111 women. Pyrosequencing analysis was conducted on DNA isolated from the exfoliated epithelial cells immunomagnetically separated from the total cell population in the breast milk of 102 women. A total of 65 CpG sites were examined in six tumor suppressor genes: PYCARD (also known as ASC or TMS1), CDH1, GSTP1, RBP1 (also known as CRBP1), SFRP1, and RASSF1. A sufficient quantity of DNA was obtained for meaningful analysis of promoter methylation; women donated an average of 86 ml of milk with a mean yield of 32,700 epithelial cells per ml. Methylation scores were in general low as expected of benign tissue, but analysis of outlier methylation scores revealed a significant relationship between breast cancer risk, as indicated by previous biopsy, and methylation score for several CpG sites in CDH1, GSTP1, SFRP1, and RBP1. Methylation of RASSF1 was positively correlated with women's age irrespective of her reproductive history. Promoter methylation patterns in DNA from breast milk epithelial cells can likely be used to assess breast cancer risk. Additional studies of women at high breast cancer risk are warranted.
Clinical and Vaccine Immunology : CVI. Jan, 2011 | Pubmed ID: 21084463
In order to develop a completely safe immunogen to replace the traditional inactivated vaccine, a tandem-repeat multiple-epitope recombinant vaccine against foot-and-mouth disease (FMD) virus (FMDV) type O was developed. It contained three copies each of residues 141 to 160 and 200 to 213 of VP1 of the O/China/99 strain of FMDV coupled with a swine immunoglobulin G heavy-chain constant region (scIgG). The data showed that the multiple-epitope recombinant vaccine elicited high titers of anti-FMDV specific antibodies in swine at 30 days postvaccination (dpv) and conferred complete protection against a challenge with 10³ 50% swine infective doses of the O/China/99 strain. The anti-FMDV specific antibody titers were not significantly different between the multiple-epitope recombinant vaccine and the traditional vaccine (t test, P > 0.05). The number of 50% pig protective doses was 6.47, which is higher than the number recommended by the World Organization for Animal Health. The multiple-epitope recombinant vaccine resulted in a duration of immunity of at least 6 months. We speculate that the multiple-epitope recombinant vaccine is a promising vaccine that may replace the traditional inactivated vaccine for the prevention and control of FMD in swine in the future.
Journal of Environmental Management. Jul, 2011 | Pubmed ID: 21450395
Titania nanotubes are gaining prominence in photocatalysis, owing to their excellent physical and chemical properties such as high surface area, excellent photocatalytic activity, and widespread availability. They are easily produced by a simple and effective hydrothermal method under mild temperature and pressure conditions. This paper reviews and analyzes the mechanism of titania nanotube formation by hydrothermal treatment. It further examines the parameters that affect the formation of titania nanotubes, such as starting material, sonication pretreatment, hydrothermal temperature, washing process, and calcination process. Finally, the effects of the presence of dopants on the formation of titania nanotubes are analyzed.
Influence of Kinetics of Drug Binding on EGFR Signaling: a Comparative Study of Three EGFR Signaling Pathway Models
Proteins. Aug, 2011 | Pubmed ID: 21638335
We used three models of the epidermal growth factor receptor (EGFR) signaling pathway mimicking three different cell lines to study the effects of kinetics of drug binding on influencing molecular signaling in the pathways. With no incubation of drugs before the external cue epidermal growth factor (EGF) was applied, we found that fast kinetics of binding to protein kinases was advantageous in suppressing the production of the Extracellular signal-regulated kinase (ERK) that triggers cell proliferation, with some exceptions. Incubation of a drug with a protein kinase target for an hour before a pathway was initiated with an external cue made kinetics less significant, so did high concentration of drugs. In addition, we found that applying a drug to a protein kinase mostly affected downstream signaling although upstream events were also affected in a few cases. In examining whether applying two drugs to two protein kinase targets in the pathways could produce synergistic effects, we found positive, negative, or no effects, depending on the protein kinases targeted and the pathway model considered.
The Journal of Parasitology. Apr, 2012 | Pubmed ID: 22017401
Despite the great effort that has been given to control the disease, schistosomiasis remains the most important human helminth infection in terms of morbidity and mortality. Natural infection of schistosomes induces very little protective immunity against reinfection. Moreover, effective schistosome vaccines for practical use have not been developed. These parasites appear to have evolved highly effective modulatory mechanisms on their host's immune system that promote the parasites' survival and also hinder the development of effective strategies for treatment of the disease. Understanding of the mechanisms of schistosome-mediated immune modulation would be most helpful in schistosomiasis prevention and control. Previously, we have identified from Schistosoma japonicum an anti-inflammatory protein, Sj16, which suppresses thioglycollate-induced peritoneal inflammation in BALB/c mice, as well as thioglycollate-mediated peritoneal macrophage maturation, while modulating cytokine and chemokine production from peritoneal cells. In the present study, we have further investigated the modulatory effect of Sj16 on the host's adaptive immunity to heterologous antigens with the use of recombinant Sj16 (rSj16) expressed and purified from Escherichia coli . Results from this study indicate that rSj16 significantly suppresses antibody production, in addition to Th1 and Th2 responses to heterologous antigens in the BALB/c mouse model. Our study also reveals that rSj16 suppresses lipopolysaccharide-induced major histocompatibility complex II expression and IL-12 production, while increasing IL-10 production in resident peritoneal macrophages. These results may partially explain why parasite-related antigens cannot mount a protective immunity during early stages of schistosome infection.
Methods in Molecular Biology (Clifton, N.J.). 2012 | Pubmed ID: 22183543
Previously, we examined the application of a molecular dynamics-based simulated annealing cycling protocol to docking peptides to proteins using two implicit-solvent models: a distance-dependent dielectric model (ε(r) = 4r) and a version of the Generalized Born model termed GBMV. We found that rescoring structures obtained from one implicit-solvent model with the other could improve the identification of the correct docking pose. Here, we guide interested readers on how to perform a similar study, using the docking between a hexapeptide and the protein phosphatase YopH inYersinia pestis as an example.
Human Dendritic Cells Engineered to Secrete Interleukin-18 Activate MAGE-A3-specific Cytotoxic T Lymphocytes in Vitro
Immunological Investigations. 2012 | Pubmed ID: 22490235
Adoptive cell transfer (ACT) involves the administration of tumor specific cytotoxic T lymphocytes (CTLs) into a patient to kill cancer cells. Although a promising cancer therapy, limitations on the generation of activated CTLs have restricted ATC's clinical application. Interleukin-18 (IL-18) is an interferon-γ (IFN-γ) inducing factor that plays an important functional role in regulating CTLs. Here, we attempt to use dendritic cells (DCs) modified with a recombinant adenovirus encoding IL-18 (rAd/IL-18) to improve the generation of activated tumor-specific CTLs. These engineered DCs secrete IL-18, increase the expression of co-stimulatory molecules, and enhance the cytotoxic efficacy of melanoma antigen 3 (MAGE-A3)-specific CTLs in vitro. We show that stimulation of CTLs with rAd/IL-18-loaded DCs increases the specific lysis of MAGE-A3-expressing human breast cancer MCF-7 cells, and at the same time increases the production of activated MAGE-A3-specific CTLs. Our results indicate that transducing DCs with rAd/IL-18 increases both the maturation of DCs and the activation level of MAGE-A3-specific CTLs, greatly enhancing the cytotoxic efficacy of CTLs towards tumor cells.
Cell Survival, DNA Damage, and Oncogenic Transformation After a Transient and Reversible Apoptotic Response
Molecular Biology of the Cell. Jun, 2012 | Pubmed ID: 22535522
Apoptosis serves as a protective mechanism by eliminating damaged cells through programmed cell death. After apoptotic cells pass critical checkpoints, including mitochondrial fragmentation, executioner caspase activation, and DNA damage, it is assumed that cell death inevitably follows. However, this assumption has not been tested directly. Here we report an unexpected reversal of late-stage apoptosis in primary liver and heart cells, macrophages, NIH 3T3 fibroblasts, cervical cancer HeLa cells, and brain cells. After exposure to an inducer of apoptosis, cells exhibited multiple morphological and biochemical hallmarks of late-stage apoptosis, including mitochondrial fragmentation, caspase-3 activation, and DNA damage. Surprisingly, the vast majority of dying cells arrested the apoptotic process and recovered when the inducer was washed away. Of importance, some cells acquired permanent genetic changes and underwent oncogenic transformation at a higher frequency than controls. Global gene expression analysis identified a molecular signature of the reversal process. We propose that reversal of apoptosis is an unanticipated mechanism to rescue cells from crisis and propose to name this mechanism "anastasis" (Greek for "rising to life"). Whereas carcinogenesis represents a harmful side effect, potential benefits of anastasis could include preservation of cells that are difficult to replace and stress-induced genetic diversity.
Simulation Reveals Two Major Docking Pathways Between the Hexapeptide GDYMNM and the Catalytic Domain of the Insulin Receptor Protein Kinase
Proteins. Aug, 2012 | Pubmed ID: 22619075
Extending a previous mining-minima approach to identifying the docking pathways between the hexapeptide GDYMNM and the catalytic domain of the insulin receptor tyrosine kinase (IRK), we found two major docking pathways connecting the binding pocket and the surface of the protein. One pathway was more likely to lead to phosphate transfer from ATP to the peptide as the distance between the γ-phosphate of ATP and the hydroxyl oxygen of the target tyrosine approached one that could facilitate reaction. The movement of the peptide along the pathways was found to couple with residues in the activation loop of the protein. Although these residues might not affect binding affinity, they might influence the kinetics of peptide entrance and release. Proteins 2012; © 2012 Wiley Periodicals, Inc.