MOTIVATION: The function of a protein depends not only on its structure but also on its dynamics. This is at the basis of a large body of experimental and theoretical work on protein dynamics. Further insight into the dynamics-function relationship can be gained by studying the evolutionary divergence of protein motions. To investigate this, we need appropriate comparative dynamics methods. The most used dynamical similarity score is the correlation between the root mean square fluctuations (RMSF) of aligned residues. Despite its usefulness, RMSF is in general less evolutionarily conserved than the native structure. A fundamental issue is whether RMSF is not as conserved as structure because dynamics is less conserved or because RMSF is not the best property to use to study its conservation. RESULTS: We performed a systematic assessment of several scores that quantify the (dis)similarity between protein fluctuation patterns. We show that the best scores perform as well as or better than structural dissimilarity, as assessed by their consistency with the SCOP classification. We conclude that to uncover the full extent of the evolutionary conservation of protein fluctuation patterns, it is important to measure the directions of fluctuations and their correlations between sites. CONTACT: Nathalie.Reuter@mbi.uib.no SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics Online.
MOTIVATION: The function of a protein depends not only on its structure but also on its dynamics. This is at the basis of a large body of experimental and theoretical work on protein dynamics. Further insight into the dynamics-function relationship can be gained by studying the evolutionary divergence of protein motions. To investigate this, we need appropriate comparative dynamics methods. The most used dynamical similarity score is the correlation between the root mean square fluctuations (RMSF) of aligned residues. Despite its usefulness, RMSF is in general less evolutionarily conserved than the native structure. A fundamental issue is whether RMSF is not as conserved as structure because dynamics is less conserved or because RMSF is not the best property to use to study its conservation. RESULTS: We performed a systematic assessment of several scores that quantify the (dis)similarity between protein fluctuation patterns. We show that the best scores perform as well as or better than structural dissimilarity, as assessed by their consistency with the SCOP classification. We conclude that to uncover the full extent of the evolutionary conservation of protein fluctuation patterns, it is important to measure the directions of fluctuations and their correlations between sites. CONTACT: Nathalie.Reuter@mbi.uib.no SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics Online.
Authors: Nicholas Warren; Alexander Strom; Brianna Nicolet; Kristine Albin; Joshua Albrecht; Brenna Bausch; Megan Dobbe; Megan Dudek; Samuel Firgens; Chad Fritsche; Anthony Gunderson; Joseph Heimann; Cheng Her; Jordan Hurt; Dmitri Konorev; Matthew Lively; Stephanie Meacham; Valentina Rodriguez; Stephanie Tadayon; David Trcka; Yer Yang; Sudeep Bhattacharyya; Sanchita Hati Journal: Protein J Date: 2014-04 Impact factor: 2.371
Authors: Mariah E Dorner; Ryan D McMunn; Thomas G Bartholow; Brecken E Calhoon; Michelle R Conlon; Jessica M Dulli; Samuel C Fehling; Cody R Fisher; Shane W Hodgson; Shawn W Keenan; Alyssa N Kruger; Justin W Mabin; Daniel L Mazula; Christopher A Monte; Augustus Olthafer; Ashley E Sexton; Beatrice R Soderholm; Alexander M Strom; Sanchita Hati Journal: Protein Sci Date: 2015-07-16 Impact factor: 6.725
Authors: H Adrian Bunzel; J L Ross Anderson; Donald Hilvert; Vickery L Arcus; Marc W van der Kamp; Adrian J Mulholland Journal: Nat Chem Date: 2021-08-19 Impact factor: 24.427
Authors: Tina Perica; Yasushi Kondo; Sandhya P Tiwari; Stephen H McLaughlin; Katherine R Kemplen; Xiuwei Zhang; Annette Steward; Nathalie Reuter; Jane Clarke; Sarah A Teichmann Journal: Science Date: 2014-12-19 Impact factor: 47.728