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Open Access Research article

Hinge Atlas: relating protein sequence to sites of structural flexibility

Samuel C Flores12, Long J Lu2, Julie Yang2, Nicholas Carriero3 and Mark B Gerstein234*

Author Affiliations

1 Department of Physics, Yale University, Bass 432, 266 Whitney Ave., New Haven, CT, USA

2 Department of Molecular Biophysics and Biochemistry, Yale University, Bass 432, 266 Whitney Ave., New Haven, CT, USA

3 Department of Computer Science, Yale University, Bass 432, 266 Whitney Ave., New Haven, CT, USA

4 Computational Biology and Bioinformatics Program, Yale University, Bass 432, 266 Whitney Ave., New Haven, CT, USA

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BMC Bioinformatics 2007, 8:167  doi:10.1186/1471-2105-8-167

Published: 22 May 2007

Abstract

Background

Relating features of protein sequences to structural hinges is important for identifying domain boundaries, understanding structure-function relationships, and designing flexibility into proteins. Efforts in this field have been hampered by the lack of a proper dataset for studying characteristics of hinges.

Results

Using the Molecular Motions Database we have created a Hinge Atlas of manually annotated hinges and a statistical formalism for calculating the enrichment of various types of residues in these hinges.

Conclusion

We found various correlations between hinges and sequence features. Some of these are expected; for instance, we found that hinges tend to occur on the surface and in coils and turns and to be enriched with small and hydrophilic residues. Others are less obvious and intuitive. In particular, we found that hinges tend to coincide with active sites, but unlike the latter they are not at all conserved in evolution. We evaluate the potential for hinge prediction based on sequence.

Motions play an important role in catalysis and protein-ligand interactions. Hinge bending motions comprise the largest class of known motions. Therefore it is important to relate the hinge location to sequence features such as residue type, physicochemical class, secondary structure, solvent exposure, evolutionary conservation, and proximity to active sites. To do this, we first generated the Hinge Atlas, a set of protein motions with the hinge locations manually annotated, and then studied the coincidence of these features with the hinge location. We found that all of the features have bearing on the hinge location. Most interestingly, we found that hinges tend to occur at or near active sites and yet unlike the latter are not conserved. Less surprisingly, we found that hinge residues tend to be small, not hydrophobic or aliphatic, and occur in turns and random coils on the surface. A functional sequence based hinge predictor was made which uses some of the data generated in this study. The Hinge Atlas is made available to the community for further flexibility studies.