NDLI: StoneHinge: Hinge prediction by network analysis of individual protein structures

Content Provider	PubMed Central
Author	Keating, Kevin S. Flores, Samuel C. Gerstein, Mark B. Kuhn, Leslie A.
Copyright Year	2009
Abstract	Hinge motions are important for molecular recognition, and knowledge of their location can guide the sampling of protein conformations for docking. Predicting domains and intervening hinges is also important for identifying structurally self-determinate units and anticipating the influence of mutations on protein flexibility and stability. Here we present StoneHinge, a novel approach for predicting hinges between domains using input from two complementary analyses of noncovalent bond networks: StoneHingeP, which identifies domain-hinge-domain signatures in ProFlex constraint counting results, and StoneHingeD, which does the same for DomDecomp Gaussian network analyses. Predictions for the two methods are compared to hinges defined in the literature and by visual inspection of interpolated motions between conformations in a series of proteins. For StoneHingeP, all the predicted hinges agree with hinge sites reported in the literature or observed visually, although some predictions include extra residues. Furthermore, no hinges are predicted in six hinge-free proteins. On the other hand, StoneHingeD tends to overpredict the number of hinges, while accurately pinpointing hinge locations. By determining the consensus of their results, StoneHinge improves the specificity, predicting 11 of 13 hinges found both visually and in the literature for nine different open protein structures, and making no false-positive predictions. By comparison, a popular hinge detection method that requires knowledge of both the open and closed conformations finds 10 of the 13 known hinges, while predicting four additional, false hinges.
Related Links	http://dx.doi.org/10.1002/pro.38
Ending Page	371
Page Count	13
Starting Page	359
File Format	PDF
ISSN	09618368
e-ISSN	1469896X
Journal	Protein Science : A Publication of the Protein Society
Issue Number	2
Volume Number	18
Language	English
Publisher	Wiley Subscription Services, Inc., A Wiley Company
Publisher Date	2009-02-01
Access Restriction	Open
Rights Holder	Wiley Subscription Services, Inc., A Wiley Company
Subject Keyword	Biochemistry Molecular Biology Research in Higher Education
Content Type	Text
Resource Type	Article
Subject	Medicine Molecular Biology Biochemistry

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