Assembly of polypeptide and protein backbone conformations from low energy ensembles of short fragments: Development of strategies and construction of models for myoglobin, lysozyme, and thymosin β₄

Abstract

Recently we developed methods for the construction of knowledge-based mean fields from a data base of known protein structures. As shown previously, this approach can be used to calculate ensembles of probable conformations for short fragments of polypeptide chains. Here we develop procedures for the assembly of short fragments to complete three-dimensional models of polypeptide chains.The amino acid sequence of a given protein is decomposed into all possible overlapping fragments of a given length, and an ensemble of probable conformations is calculated for each fragment. The fragments are assembled to a complete model by choosing appropriate conformations from the individual ensembles and by averaging over equivalent angles. Finally a consistent model is obtained by rebuilding the conformation from the average angles. From the average angles the local variability of the structure can be calculated, which is a useful criterion for the reliability of the model.The procedure is applied to the calculation of the local backbone conformations of myoglobin and lysozyme whose structures have been solved by X-ray analysis and thymosin &, a polypeptide of 43 amino acid residues whose structure was recently investigated by NMR spectroscopy. We demonstrate that substantial fractions of the calculated local backbone conformations are similar to the experimentally determined structures.Keywords: knowledge-based prediction; molecular force field; protein folding; protein modeling; statistical mechanicsThe calculation of polypeptide and protein conformations from amino acid sequences belongs to the most interesting problems in molecular biology. A wealth of information on protein systems has accumulated from experimental and theoretical studies but in spite of enormous efforts the problem is still unsolved. Folding and unfolding of many protein chains are reversible processes that can be induced by changing the physical parameters of the environment. This has been demonstrated 30 years ago on ribonuclease (Anfinsen,

Conformation of thymosin β4 in water determined by NMR spectroscopy

“…This procedure calculated the thymosin structure to be very close to the NMR structure of thymosin in the alcoholic solution and not to that of thymosin p4 in pure water (Sippl et al, 1992). A similar result to that obtained in alcohol solution is found for thymosin p4 by Garnier-Osguthorpe-Robson secondary-structure prediction (Voelter, 1992).…”

“…It is also interesting to compare the conformation of thymosin p4 derived from the NMR experiment with that predicted by the method of knowledge-based mean fields derived from a data base of known protein structures (Sippl et al, 1992). This procedure calculated the thymosin structure to be very close to the NMR structure of thymosin in the alcoholic solution and not to that of thymosin p4 in pure water (Sippl et al, 1992).…”

A fast conformational search strategy for finding low energy structures of model proteins

“…There have been many important advances on the road to developing a computer protein folding algorithm (Levitt & Warshel, 1975;Kuntz et al, 1976;Wilson & Doniach, 1989;Skolnick & Kolinski, 1990;Covell, 1992Covell, , 1994Sippl et al, 1992;Vajda et al, 1993;Hinds & Levitt, 1994;Kolinski & Skolnick, 1994;Monge et al, 1994;Wallqvist et al, 1994;Boczko & Brooks, 1995;Srinivasan & Rose, 1995;Sun et al, 1995;Yue & Dill, 1996). In order to devise a computer method that can predict the native structure of a protein from its amino acid sequence alone, it is necessary to have an adequate energy function applied to an appropriate chain representation and searched with a fast conformational search method.…”

Ab initio construction of polypeptide fragments: Accuracy of loop decoy discrimination by an all‐atom statistical potential and the AMBER force field with the Generalized Born solvation model

“…6 -8 Finally, conformation generation coupled with an effective selection method is a popular approach to protein structure prediction, for both comparative modeling and ab initio methods. 9,10 To be useful in such a variety of contexts, conformational ensembles should: (1) explicitly represent all heavy mainchain atoms; (2) contain only conformations satisfying stereochemical rules such as reasonable bond lengths, angles, and torsions, 11 excluded volume, and exhibit / combinations within the allowable regions of the Ramachandran plot 12 ; (3) contain a representative sample of the conformational space accessible within the surrounding environment, including conformations near the native structure; (4) be efficiently and reliably generated.…”