Dynamic protein domains: identification, interdependence, and stability.

Biophysical Journal
Semen O YesylevskyyAlexander P Demchenko

Abstract

Existing methods of domain identification in proteins usually provide no information about the degree of domain independence and stability. However, this information is vital for many areas of protein research. The recently developed hierarchical clustering of correlation patterns (HCCP) technique provides machine-based domain identification in a computationally simple and physically consistent way. Here we present the modification of this technique, which not only allows determination of the most plausible number of dynamic domains but also makes it possible to estimate the degree of their independence (the extent of correlated motion) and stability (the range of environmental conditions, where domains remain intact). With this technique we provided domain assignments and calculated intra- and interdomain correlations and interdomain energies for >2500 test proteins. It is shown that mean intradomain correlation of motions can serve as a quantitative criterion of domain independence, and the HCCP stability gap is a measure of their stability. Our data show that the motions of domains with high stability are usually independent. In contrast, the domains with moderate stability usually exhibit a substantial degree of correlated ...Continue Reading

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Citations

Jul 5, 2013·PLoS Computational Biology·Lyudmyla DoroshMaria Stepanova
Feb 23, 2012·Scientific Reports·Ramachandra M Bhaskara, Narayanaswamy Srinivasan
Sep 4, 2008·Proteins·Semen O Yesylevskyy, Valery N Kharkyanen
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Aug 1, 2006·Biophysical Journal·Semen O YesylevskyyAlexander P Demchenko
Sep 20, 2017·International Journal of Molecular Sciences·Alexander V FoninKonstantin K Turoverov
Nov 16, 2007·Proteins·Semen O YesylevskyyAlexander P Demchenko
Apr 28, 2012·Journal of Computational Chemistry·Semen O Yesylevskyy
Feb 1, 2008·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Maria Stepanova
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Jan 31, 2009·Biochemistry·N BlinovM Stepanova
Dec 6, 2017·Journal of Chemical Theory and Computation·Lorenzo BoninsegnaCecilia Clementi
Nov 13, 2021·Biophysical Journal·Genevieve KunkelAnna Tarakanova

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