Tertiary Structure Modeling
Tertiary Structure Modeling - Related Videos
01:21
Tertiary Healthcare System
0 Views •
2023
Specialized care provided over an extended period is called tertiary care. Usually, a primary or secondary care physician will refer a patient to tertiary care. A patient's maximum physical and mental function is restored in tertiary care, which is caused due to the impact of a chronic illness or condition. Tertiary care aims to achieve the highest level of functioning possible while managing chronic illness. For example, a patient who falls and fractures their hip will need secondary care to...
01:12
Nomenclature of Secondary and Tertiary Amines
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2025
The secondary and tertiary amines are derivatives of ammonia, where two and three of its hydrogens are replaced by alkyl groups, respectively. Secondary and tertiary amines can be symmetrical with identical alkyl groups attached to the nitrogen atom or unsymmetrical when more than one type of alkyl group is present. The standard nomenclature of secondary and tertiary amines is similar to the names given to the primary amines. They are generally named alkylamines. As depicted in Figure 1, for...
10:50
Assessment of Immunologically Relevant Dynamic Tertiary Structural Features of the HIV-1 V3 Loop Crown R2 Sequence by ab initio Folding
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Cited by 10 •
2010
The crown region of different V3 loop sequences of the surface envelope glycoprotein (gp120) of HIV-1 can be structurally characterized in many cases by in silico folding of positions 10 to 22 of the loop using a state-of-the-art ab initio folding algorithm. Here we demonstrate the folding and evaluation of this region of the V3 loop from the R2 strain of HIV-1, a uniquely neutralization sensitive strain with puzzling functional properties.
13:37
Split-and-pool Synthesis and Characterization of Peptide Tertiary Amide Library
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Cited by 5 •
2014
Peptide tertiary amides (PTAs) are a superfamily of peptidomimetics that include but are not limited to peptides, peptoids and N-methylated peptides. Here we describe a synthetic method which combines both split-and-pool and sub-monomer strategies to synthesize a one-bead one-compound library of PTAs.
16:41
A Protocol for Computer-Based Protein Structure and Function Prediction
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Cited by 79 •
2011
Guidelines for computer based structural and functional characterization of protein using the I-TASSER pipeline is described. Starting from query protein sequence, 3D models are generated using multiple threading alignments and iterative structural assembly simulations. Functional inferences are thereafter drawn based on matches to proteins with known structure and functions.
FAQs
Side-chain interactions guide the estimated arrangement toward a stable three-dimensional conformation. Hydrophobic effects, hydrogen bonds, ionic forces, and disulfide bonds each contribute to the predicted structure, although their combined influence determines the final result. Examining these interactions helps researchers interpret why a model adopts a particular shape and how that shape may support protein function.
Homologous structures provide related structural information that can guide reconstruction from an amino acid sequence. Instead of relying only on calculated interactions, the model can use an experimentally characterized related structure as a reference for estimating the target protein’s shape. This approach is especially useful when researchers need structural insight but lack direct structural measurements for the protein under study.
Energy-based calculations and molecular simulations help evaluate possible protein conformations by considering how molecular interactions contribute to structural stability. They provide computational routes for estimating arrangements that may be favorable, complementing information derived from related structures. Their value lies in exploring or assessing conformations when sequence information alone does not directly reveal the biologically relevant shape.
Amino acid sequence information can serve as the starting point, while related structural data may provide additional guidance. The modeling process then estimates how interactions among side chains could produce a stable conformation, using homologous structures, energy-based calculations, or molecular simulations. The selected inputs and computational approach determine what structural evidence contributes to the reconstruction.
A predicted three-dimensional model allows researchers to examine how a mutation might alter the arrangement of residues or the interactions that support structural stability. By relating these possible structural changes to protein function, investigators can develop a mechanistic interpretation of experimental findings. The models therefore connect sequence variation with structural hypotheses rather than treating mutations as isolated sequence changes.
Models can help identify potential binding sites, making them useful for examining where drug-related interactions might occur. They also support protein engineering by providing structural guidance when researchers want to relate sequence changes to conformation and function. In both settings, the approach is particularly valuable when direct structural measurements are difficult, provided the resulting predictions are sufficiently reliable.