Article

A stochastic method for the reconstruction of protein structures from one-dimensional structural profiles.

Institut für Festkörperphysik, Technische Universität Darmstadt, Hochschulstrasse 6, 64289 Darmstadt, Germany.
Gene (impact factor: 2.34). 07/2008; 422(1-2):47-51. DOI:10.1016/j.gene.2008.06.004 pp.47-51
Source: PubMed

ABSTRACT We discuss a computational approach for reconstructing the native structures of proteins from the knowledge of a structural profile - the first eigenvector of the contact map of the native structure itself. The procedure consists in carrying out Monte Carlo simulations of a tube model of the protein structure with an energy bias towards the target structural profile. We present the reconstruction of two small proteins and address problems arising in the reconstruction of larger proteins. Our results indicate that an accurate physico-chemical energy function should be used in conjunction with the structural profile bias in order to achieve accurate reconstructions.

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    Article: Defining an essence of structure determining residue contacts in proteins.
    R Sathyapriya, Jose M Duarte, Henning Stehr, Ioannis Filippis, Michael Lappe
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    ABSTRACT: The network of native non-covalent residue contacts determines the three-dimensional structure of a protein. However, not all contacts are of equal structural significance, and little knowledge exists about a minimal, yet sufficient, subset required to define the global features of a protein. Characterisation of this "structural essence" has remained elusive so far: no algorithmic strategy has been devised to-date that could outperform a random selection in terms of 3D reconstruction accuracy (measured as the Ca RMSD). It is not only of theoretical interest (i.e., for design of advanced statistical potentials) to identify the number and nature of essential native contacts-such a subset of spatial constraints is very useful in a number of novel experimental methods (like EPR) which rely heavily on constraint-based protein modelling. To derive accurate three-dimensional models from distance constraints, we implemented a reconstruction pipeline using distance geometry. We selected a test-set of 12 protein structures from the four major SCOP fold classes and performed our reconstruction analysis. As a reference set, series of random subsets (ranging from 10% to 90% of native contacts) are generated for each protein, and the reconstruction accuracy is computed for each subset. We have developed a rational strategy, termed "cone-peeling" that combines sequence features and network descriptors to select minimal subsets that outperform the reference sets. We present, for the first time, a rational strategy to derive a structural essence of residue contacts and provide an estimate of the size of this minimal subset. Our algorithm computes sparse subsets capable of determining the tertiary structure at approximately 4.8 A Ca RMSD with as little as 8% of the native contacts (Ca-Ca and Cb-Cb). At the same time, a randomly chosen subset of native contacts needs about twice as many contacts to reach the same level of accuracy. This "structural essence" opens new avenues in the fields of structure prediction, empirical potentials and docking.
    PLoS Computational Biology 12/2009; 5(12):e1000584. · 5.22 Impact Factor
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Keywords

accurate physico-chemical energy function
 
accurate reconstructions
 
computational approach
 
contact map
 
energy bias
 
first eigenvector
 
larger proteins
 
Monte Carlo simulations
 
native structure
 
native structures
 
protein structure
 
proteins
 
small proteins
 
structural profile
 
structural profile bias
 
target structural profile