Rapid simulation of protein motion: merging flexibility, rigidity and normal mode analyses

Abstract

Protein function frequently involves conformational changes with large amplitude on timescales which are difficult and computationally expensive to access using molecular dynamics. In this paper, we report on the combination of three computationally inexpensive simulation methods-normal mode analysis using the elastic network model, rigidity analysis using the pebble game algorithm, and geometric simulation of protein motion-to explore conformational change along normal mode eigenvectors. Using a combination of ELNEMO and FIRST/FRODA software, large-amplitude motions in proteins with hundreds or thousands of residues can be rapidly explored within minutes using desktop computing resources. We apply the method to a representative set of six proteins covering a range of sizes and structural characteristics and show that the method identifies specific types of motion in each case and determines their amplitude limits.

34 pages, 22 Figures, Phys. Biol. 9 (2012)

References in corpus (2)

• Sensitivity of protein rigidity analysis to small structural variations: a large-scale comparative analysis
• Comparative analysis of rigidity across protein families

Cited by in corpus (6)

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• Characterizing the folding core of the cyclophilin A - cyclosporin A complex I: hydrogen exchange data and rigidity analysis
• Characterizing the folding core of the cyclophilin A - cyclosporin A complex II: improving folding core predictions by including mobility
• Normal-mode driven exploration of protein domain motions