CRANKITE: A fast polypeptide backbone conformation sampler

Abstract

Background: CRANKITE is a suite of programs for simulating backbone conformations of polypeptides and proteins. The core of the suite is an efficient Metropolis Monte Carlo sampler of backbone conformations in continuous three-dimensional space in atomic details.

Methods: In contrast to other programs relying on local Metropolis moves in the space of dihedral angles, our sampler utilizes local crankshaft rotations of rigid peptide bonds in Cartesian space.

Results: The sampler allows fast simulation and analysis of secondary structure formation and conformational changes for proteins of average length.

Figure 1

(A) Polypeptide model. The orientations of perfectly planar and rigid peptide bonds are given by the orthonormal triplets (x, y, z), with z pointing along the C_α-C_α direction. Other peptide bond atoms lie in the plane yz. The position of the side-chain atoms R is specified by the vectors n and c. (B) Local Metropolis moves. Two types of moves are used in this work: a crankshaft rotation around the line connecting 2 C_α atoms in the middle of the chain, and a random rotation at the termini around a random axis passing through the C_α atom. From Podtelezhnikov and Wild (2005) [8].

Figure 2

Dihedral angle evolution. In these simulations a 16-mer polypeptide underwent conversion for an α-helix to a β-sheet conformation. Changes in dihedral angles for residues 3, 4, 5, 6 are shown in black, red, blue, and green respectively. Snapshots were collected every 4096 steps.