Chapter 3 - Protein Structure Analysis

Abstract

The analysis on protein structures provides plenty of information about the factors governing the folding and stability of proteins, the nature of interactions between amino acid residues and with the surrounding medium, the preferred amino acid residues in protein environment, the location of residues in the interior/surface of a protein, amino acid clusters, etc. The analysis provides useful information predicting the secondary and tertiary structures of proteins. The assignment of secondary structures based on a hydrogen-bonding pattern is helpful for predicting the secondary structures from amino acid sequence and evaluating the performance of different methods. The secondary structure information is used for predicting three-dimensional structures of proteins, protein stability upon mutations, binding site residues in protein-protein, protein–DNA, protein–RNA complexes, etc. The concept of solvent accessibility is widely used to understand the location of amino acid residues in protein structures and their contribution to the stability of proteins. The stability of protein structures can be estimated from the computation of different free energy contributions, such as hydrophobic free energy, electrostatic free energy, hydrogen bonding free energy, and van der Waals free energy. The calculation of these free energy terms reveals the importance of these interactions to the folding and stability of protein structures. Protein structures are used to derive several properties of amino acid residues. These properties reflect the behavior of amino acid residues in protein environment, which can be used for prediction algorithms.