Sensitivity of protein rigidity analysis to small structural variations: a large-scale comparative analysis

TL;DR

This study evaluates how small structural differences in protein crystal structures affect rigidity analysis results, highlighting its utility as a comparative tool and revealing new insights into trypsin's rigidity.

Contribution

It provides a large-scale comparative analysis demonstrating the sensitivity of rigidity analysis to minor structural variations in proteins.

Findings

Rigidity analysis varies with small structural differences.

Best used as a comparative tool for structural variations.

Uncovered a new peculiarity in trypsin rigidity.

Abstract

Rigidity analysis using the "pebble game" can usefully be applied to protein crystal structures to obtain information on protein folding, assembly and the structure-function relationship. However, previous work using this technique has not made clear how sensitive rigidity analysis is to small structural variations. We present a comparative study in which rigidity analysis is applied to multiple structures, derived from different organisms and different conditions of crystallisation, for each of several different proteins. We find that rigidity analysis is best used as a comparative tool to highlight the effects of structural variation. Our use of multiple protein structures brings out a previously unnoticed peculiarity in the rigidity of trypsin.