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Protein and Protein Structure

Protein and Protein Structure

Proteins are one of the most abundant organic molecules in living systems and have the most diverse range of functions of all macromolecules. Proteins may be structural, regulatory, contractile, or protective. They may serve in transport, storage, or membranes; or they may be toxins or enzymes. Their structures, like their functions, vary greatly. They are all, however, amino acid polymers arranged in a linear sequence.
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Updated: Mar 26, 2026

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Investigating Protein Sequence-structure-dynamics Relationships with Bio3D-web

Published on: July 16, 2017

Selection on protein structure, interaction, and sequence.

Peter B Chi^1,2, David A Liberles¹

¹Department of Biology and Center for Computational Genetics and Genomics, Temple University, Philadelphia, Pennsylvania, 19122.

Protein Science : a Publication of the Protein Society

|January 26, 2016

Summary

This summary is machine-generated.

Understanding evolutionary protein changes requires modeling selective forces like folding stability and ligand binding. This approach moves beyond statistics to explain context-dependent sequence evolution and predict unobserved sequences.

Keywords:

mutation-selection models neutral evolution protein evolution sequence-structure-function map

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Area of Science:

Molecular Evolution
Computational Biology
Biophysics

Background:

Predicting amino acid substitutions is crucial for molecular evolution.
Statistical methods alone cannot capture context-dependent sequence changes (epistasis).
Biological processes must be integrated to understand evolutionary constraints.

Purpose of the Study:

To provide an overview of selective forces acting on amino acid substitutions.
To discuss modeling approaches for these forces.
To enable extrapolation to unobserved protein sequences.

Main Methods:

Review of selection pressures including folding stability, binding affinity, protein dynamics, and aggregation.
Discussion of modeling strategies for these evolutionary factors.
Consideration of protein expression levels and mutation bias.

Main Results:

Selection acts on multiple protein properties, including stability, specificity, dynamics, and aggregation.
Interplay between these forces and protein expression/mutation bias influences evolution.
Modeling these factors allows for a deeper understanding of sequence divergence.

Conclusions:

A comprehensive understanding of selective forces is essential for accurate modeling of protein evolution.
Integrating biophysical and biochemical factors improves predictions beyond statistical methods.
This framework aids in understanding epistasis and predicting novel protein sequences.