Fast procedure for reconstruction of full-atom protein models from reduced representations - PubMed (original) (raw)

Fast procedure for reconstruction of full-atom protein models from reduced representations

Piotr Rotkiewicz et al. J Comput Chem. 2008.

Abstract

We introduce PULCHRA, a fast and robust method for the reconstruction of full-atom protein models starting from a reduced protein representation. The algorithm is particularly suitable as an intermediate step between coarse-grained model-based structure prediction and applications requiring an all-atom structure, such as molecular dynamics, protein-ligand docking, structure-based function prediction, or assessment of quality of the predicted structure. The accuracy of the method was tested on a set of high-resolution crystallographic structures as well as on a set of low-resolution protein decoys generated by a protein structure prediction algorithm TASSER. The method is implemented as a standalone program that is available for download from http://cssb.biology.gatech.edu/skolnick/files/PULCHRA.

(c) 2008 Wiley Periodicals, Inc.

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Figures

Figure 1

Figure 1

Frame of reference used for reconstruction of the backbone and side chain atoms. The vectors r1, r2, and r3 are used to construct a local system of coordinates, vx, vy, and vz, according to equations 4a–c. The local system of coordinates is used to rebuild the backbone plate between the ith and i+1thα-carbons and the side chain atoms of the ithα-carbon. The distances r3, r4, and r5 are used to choose a proper side chain and peptide plate conformation from a fragment library.

Figure 2

Figure 2

Hydrogen bond pattern optimization procedure. The peptide bond atoms are rotated around a virtual Cα-Cα bond, while the bond energy is calculated according to the DSSP formula (Eq.5). The optimal conformation within a (−10°, 10°) range of the γ angle is stored.

Figure 3

Figure 3

Optimization of side chain positions. The side chain is rotated by an angle γ around a Cα-CM vector until the total number of clashes with other heavy atoms is minimized. Additionally, the χ1 angle is calculated and tested against the allowed range to exclude nonphysical side chain conformations.

Figure 4

Figure 4

Example of a punched ring. The arginine side chain is threaded through a phenylalanine aromatic ring. The n vector is the ring plane normal, and r1 and r2 are vectors connecting the ring center, c, with the Cγ and Cδ atoms of an arginine side chain. The signs of scalar products of n and r vectors determine the positions of the atoms with respect to the ring plane. If two atoms are positioned on alternate sides of the ring, within a certain distance from a ring center, the ring is considered to be punched by the side chain.

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