Deciphering the shape and deformation of secondary structures through local conformation analysis.

ABSTRACT:

Background

Protein deformation has been extensively analysed through global methods based on RMSD, torsion angles and Principal Components Analysis calculations. Here we use a local approach, able to distinguish among the different backbone conformations within loops, α-helices and β-strands, to address the question of secondary structures' shape variation within proteins and deformation at interface upon complexation.

Results

Using a structural alphabet, we translated the 3 D structures of large sets of protein-protein complexes into sequences of structural letters. The shape of the secondary structures can be assessed by the structural letters that modeled them in the structural sequences. The distribution analysis of the structural letters in the three protein compartment

SUBMITTER: Baussand J 

PROVIDER: S-EPMC3224362 | biostudies-literature | 2011 Feb

REPOSITORIES: biostudies-literature