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Protein Science (2004), 13:1636-1650. Published by Cold Spring Harbor Laboratory Press. Copyright © 2004 The Protein Society
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Some fundamental aspects of building protein structures from fragment libraries

J. Bradley Holmes and Jerry Tsai

Department of Biophysics and Biochemistry, Texas A&M University, College Station, Texas 77843, USA

(RECEIVED October 28, 2003; FINAL REVISION March 12, 2004; ACCEPTED March 19, 2004)



Abstract

We have investigated some of the basic principles that influence generation of protein structures using a fragment-based, random insertion method. We tested buildup methods and fragment library quality for accuracy in constructing a set of known structures. The parameters most influential in the construction procedure are bond and torsion angles with minor inaccuracies in bond angles alone causing >6 Å C{alpha}RMSD for a 150-residue protein. Idealization to a standard set of values corrects this problem, but changes the torsion angles and does not work for every structure. Alternatively, we found using Cartesian coordinates instead of torsion angles did not reduce performance and can potentially increase speed and accuracy. Under conditions simulating ab initio structure prediction, fragment library quality can be suboptimal and still produce near-native structures. Using various clustering criteria, we created a number of libraries and used them to predict a set of native structures based on nonnative fragments. Local C{alpha}RMSD fit of fragments, library size, and takeoff/landing angle criteria weakly influence the accuracy of the models. Based on a fragment’s minimal perturbation upon insertion into a known structure, a seminative fragment library was created that produced more accurate structures with fragments that were less similar to native fragments than the other sets. These results suggest that fragments need only contain native-like subsections, which when correctly overlapped, can recreate a native-like model. For fragment-based, random insertion methods used in protein structure prediction and design, our findings help to define the parameters this method needs to generate near-native structures.

Keywords: protein structure prediction; fragment library; torsion angle space; Cartesian space; takeoff/landing angles

Reprint requests to: Jerry Tsai, Department of Biophysics and Biochemistry, Texas A&M University, College Station, TX 77843, USA; e-mail: JerryTsai{at}tamu.edu; fax: (979) 845-9274.

Article and publication are at http://www.proteinscience.org/cgi/doi/10.1110/ps.03494504.


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