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Find video protocols related to scientific articles indexed in Pubmed.
Electrostatic analysis of bacterial expansins.
Proteins
PUBLISHED: 09-17-2014
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Expansins are a family of proteins with plant cell wall remodeling-activity, which bind cell wall components through hydrophobic and electrostatic interactions. A shallow area on the surface of the protein serves as the polysaccharide binding site (PBS) and it is composed of conserved residues. However, electric charge differences on the opposite face of the PBS produce basic, neutral or acidic proteins. An analysis of forty-four bacterial expansins, homologues of BsEXLX1, revealed two main groups defined by: a) the presence or absence of disulfide bonds; and b) by the proteins isoelectric point (pI). We determined the location of the residues responsible for the pI on the structure of representative expansins. Our results suggest that the electric charge at the opposite site of the PBS may help in substrate differentiation among expansins from different species; in addition, electrostatic polarization between the front and the back of the molecule could affect expansin activity on cellulose. © Proteins 2014;. © 2014 Wiley Periodicals, Inc.
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A novel TctA citrate transporter from an activated sludge metagenome: structural and mechanistic predictions for the TTT family.
Proteins
PUBLISHED: 01-14-2014
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We isolated a putative citrate transporter of the tripartite tricarboxylate transporter (TTT) class from a metagenomic library of activated sludge from a sewage treatment plant. The transporter, dubbed TctA_ar, shares ?50% sequence identity with TctA of Comamonas testosteroni (TctA_ct) and other ?-Proteobacteria, and contains two 20-amino acid repeat signature sequences, considered a hallmark of this particular transporter class. The structures for both TctA_ar and TctA_ct were modeled with I-TASSER and two possible structures for this transporter family were proposed. Docking assays with citrate resulted in the corresponding sets of proposed critical residues for function. These models suggest functions for the 20-amino acid repeats in the context of the two different architectures. This constitutes the first attempt at structure modeling of the TTT family, to the best of our knowledge, and could aid functional understanding of this little-studied family.
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PcExl1 a novel acid expansin-like protein from the plant pathogen Pectobacterium carotovorum, binds cell walls differently to BsEXLX1.
PLoS ONE
PUBLISHED: 01-01-2014
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Microbial expansins act on plant cell walls similarly to plant expansins, albeit their loosening activity levels are tenfold lesser compared to plant expansins. We report the characterization of an expansin-like gene from the plant pathogen Pectobacterium carotovorum, named exl1. PcExl1 is an acidic protein that binds cellulose (Avicel), and weakens filter paper. The acidic nature of PcExl1 confers different binding properties when compared to Bacillus subtilis BsEXLX1, which is a basic protein. PcExl1 binding to wheat cell wall increased when acidic components were depleted, reaching a similar level to the binding to Avicel, indicating that cellulose is the target of PcExl1.
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Segmental motions of rat thymidylate synthase leading to half-the-sites behavior.
Biopolymers
PUBLISHED: 01-23-2010
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Thymidylate synthase (TS) is a homodimeric enzyme with two equivalent active sites composed of residues from both subunits. Despite the structural symmetry of the enzyme, certain experimental results are consistent with half-the-sites activity, suggesting negative cooperativity between the active sites. To gain insight into the mechanism behind this phenomenon, we explore segmental motions of rat TS in the absence of ligands, with normal mode analysis as a tool. Using solvent accessible surface area of the active site pocket as a monitor of the degree of opening of the active sites, we classified the first 25 nontrivial normal modes, obtained from the web server of the program ElNémo, according to the behavior of the active sites. We found seven modes that open and close both sites symmetrically and nine that do so in an anticorrelated fashion. We characterized the motions of these modes by visual inspection and through measurement of distances between selected atoms lining the active site pockets. The segments that regulate access to the active site correspond to the loop containing R44, helix K, and a long loop containing residues 103-125, in agreement with a large body of crystallographic studies. These elements can be activated together or in isolation. There are more asymmetric modes than symmetric ones in the set we analyzed, probably accounting for the half-the-sites behavior of the enzyme. Three of the asymmetric modes result in changes at the dimer interface and indicate the endpoints of possible communication pathways between the active sites.
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On the consequences of placing amino groups at the TBP-DNA interface. Does TATA really matter?
J. Mol. Recognit.
PUBLISHED: 07-08-2009
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The TATA-box binding protein (TBP) belongs to a family of structural proteins involved in transcription in eukaryotic cells. TBP binds in the minor groove of DNA and recognizes specifically the consensus sequence: 5 TATAWAWR 3 (W = A or T). Recent reports show that the TATA-box is only present in 10% of all human polymerase II promoters. Therefore, TBP must bind frequently to low affinity DNA sequences, possibly with help of other transcription factors. In order to understand the intramolecular and intermolecular interactions that lead to the consensus sequence preferred by TBP, we use high resolution crystallographic structures of cognate TBP-DNA complexes as templates onto which 16 dinucleotide repeating sequence DNA oligomers were built. The binding free energy of each complex was calculated using the Molecular Mechanics/Poisson-Boltzmann Solvent Accessible (MM-PBSA) approximation. Parsing of the free energy components allowed us to identify the most important contributions to sequence selectivity: DNA deformation and the interaction energy between TBP residues and DNA bases, as expected. Surprisingly, poor interaction energies lead to larger deformation costs, suggesting strategies to improve affinity and selectivity. Local analysis of the TBP-DNA interface allowed us to build interaction and deformation energy tables that were used, without the need to fit their relative weights, to predict successfully both the consensus sequence for TBP, and relative binding affinities for a collection of TATA box variants.
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What is Visualize?

JoVE Visualize is a tool created to match the last 5 years of PubMed publications to methods in JoVE's video library.

How does it work?

We use abstracts found on PubMed and match them to JoVE videos to create a list of 10 to 30 related methods videos.

Video X seems to be unrelated to Abstract Y...

In developing our video relationships, we compare around 5 million PubMed articles to our library of over 4,500 methods videos. In some cases the language used in the PubMed abstracts makes matching that content to a JoVE video difficult. In other cases, there happens not to be any content in our video library that is relevant to the topic of a given abstract. In these cases, our algorithms are trying their best to display videos with relevant content, which can sometimes result in matched videos with only a slight relation.