Abstract
The constant increase in the number of solved protein structures is of great help in understanding the basic principles behind protein folding and evolution. 3-D structural knowledge is valuable in designing and developing methods for comparison, modelling and prediction of protein structures. These approaches for structure analysis can be directly implicated in studying protein function and for drug design. The backbone of a protein structure favours certain local conformations which include α-helices, β-strands and turns. Libraries of limited number of local conformations (Structural Alphabets) were developed in the past to obtain a useful categorization of backbone conformation. Protein Block (PB) is one such Structural Alphabet that gave a reasonable structure approximation of 0.42 Å. In this study, we use PB description of local structures to analyse conformations that are preferred sites for structural variations and insertions, among group of related folds. This knowledge can be utilized in improving tools for structure comparison that work by analysing local structure similarities. Conformational differences between homologous proteins are known to occur often in the regions comprising turns and loops. Interestingly, these differences are found to have specific preferences depending upon the structural classes of proteins. Such class-specific preferences are mainly seen in the all-β class with changes involving short helical conformations and hairpin turns. A test carried out on a benchmark dataset also indicates that the use of knowledge on the class specific variations can improve the performance of a PB based structure comparison approach. The preference for the indel sites also seem to be confined to a few backbone conformations involving β-turns and helix C-caps. These are mainly associated with short loops joining the regular secondary structures that mediate a reversal in the chain direction. Rare β-turns of type I’ and II’ are also identified as preferred sites for insertions.
Highlights
The three dimensional structure of protein provides precise details on its functional properties like ligand binding or catalysis [1,2]
The extent of conservation of local backbone conformations were identified in terms of Protein Block (PB)
Local Structure Substitutions The changes in local backbone conformation were deduced by looking at PB replacements among homologous structures
Summary
The three dimensional structure of protein provides precise details on its functional properties like ligand binding or catalysis [1,2]. The functional properties can be studied by comparing related structures. The analysis of similarities (or variations) in protein structural features among related proteins, demands efficient means of comparing protein folds. Certain regions of a protein structure can be prone to variations, which arise due to structural flexibility or evolutionarily acquired changes. These variations can be either restricted to local regions in the backbone or involve large movements that alter the conformational state of the protein. Unlike the conformational alteration caused by large flexible movements, the local backbone changes are not likely to be affected by the nature of the global fold. The preferences associated with the variations in the backbone conformations can be extracted as a general feature
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