Reconstruction of protein structures from a vectorial representation

Abstract

We show that the contact map of the native structure of globular proteins can be reconstructed starting from the sole knowledge of the contact map's principal eigenvector, and present an exact algorithm for this purpose. Our algorithm yields a unique contact map for all 221 globular structures of PDBselect25 of length $N\le 120$. We also show that the reconstructed contact maps allow in turn for the accurate reconstruction of the three-dimensional structure. These results indicate that the reduced vectorial representation provided by the principal eigenvector of the contact map is equivalent to the protein structure itself. This representation is expected to provide a useful tool in bioinformatics algorithms for protein structure comparison and alignment, as well as a promising intermediate step towards protein structure prediction.

4 pages, 1 figure

References in corpus (2)

• Structural Determinant of Protein Designability
• Statistical properties of contact vectors

Cited by in corpus (9)

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• Nature of protein family signatures: Insights from singular value analysis of position-specific scoring matrices
• On the optimal contact potential of proteins
• Stochastic reconstruction of protein structures from effective connectivity profiles
• Evaluating functions of positive-definite matrices using colored noise thermostats
• Conservation of statistical results under the reduction of pair-contact interactions to solvation interactions
• Predicting Residue-wise Contact Orders of Native Protein Structure from Amino Acid Sequence
• Properties of contact matrices induced by pairwise interactions in proteins