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Paul C. Whitford
Researcher at Northeastern University
Publications - 95
Citations - 4107
Paul C. Whitford is an academic researcher from Northeastern University. The author has contributed to research in topics: Energy landscape & Transfer RNA. The author has an hindex of 31, co-authored 82 publications receiving 3524 citations. Previous affiliations of Paul C. Whitford include Los Alamos National Laboratory & Rice University.
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Journal ArticleDOI
Conformational transitions in adenylate kinase. Allosteric communication reduces misligation.
TL;DR: These findings provide a mechanistic explanation for the observed 1:1:1 correspondence between LID domain closure, NMP domainclosure, and substrate turnover.
Journal ArticleDOI
Excited states of ribosome translocation revealed through integrative molecular modeling.
Paul C. Whitford,Aqeel Ahmed,Yanan Yu,Scott P. Hennelly,Florence Tama,Christian M. T. Spahn,José N. Onuchic,Karissa Y. Sanbonmatsu +7 more
TL;DR: This work presents a methodology (MDfit) that utilizes molecular dynamics simulations to generate configurations of excited states that are consistent with available biophysical and biochemical measurements and presents a sequence of configurations suggested to be associated with transfer RNA movement through the ribosome.
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Magnesium Fluctuations Modulate RNA Dynamics in the SAM-I Riboswitch
Ryan L. Hayes,Jeffrey K. Noel,Udayan Mohanty,Paul C. Whitford,Scott P. Hennelly,José N. Onuchic,Karissa Y. Sanbonmatsu +6 more
TL;DR: This work investigates the interplay between RNA and Mg(2+) at atomic resolution through ten 2-μs explicit solvent molecular dynamics simulations of the SAM-I riboswitch with varying ion concentrations to observe a layer of outer-sphere coordinated Mg (2+) that is transiently bound but strongly coupled to the RNA.
Journal ArticleDOI
Connecting the Kinetics and Energy Landscape of tRNA Translocation on the Ribosome
Paul C. Whitford,Scott C. Blanchard,Jamie H. D. Cate,Jamie H. D. Cate,Karissa Y. Sanbonmatsu +4 more
TL;DR: This analysis, in conjunction with previously reported experimental rates of translocation, provides an upper-bound estimate of the free-energy barriers associated with translocation.
Journal ArticleDOI
Extracting function from a β-trefoil folding motif
TL;DR: These studies provide a systematic approach to mapping the functional genomics of a fold family via structural differences and hypothesize that functional regions are not central to the β-trefoil motif and cause slow folding.