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Microsecond timescale backbone conformational dynamics in ubiquitin studied with NMR R 1ρ relaxation experiments
Author(s) -
Massi Francesca,
Grey Michael J.,
Palmer Arthur G.
Publication year - 2005
Publication title -
protein science
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 3.353
H-Index - 175
eISSN - 1469-896X
pISSN - 0961-8368
DOI - 10.1110/ps.041139505
Subject(s) - microsecond , chemistry , ubiquitin , relaxation (psychology) , protein dynamics , side chain , chemical shift , reaction rate constant , molecular dynamics , resonance (particle physics) , crystallography , kinetics , computational chemistry , biochemistry , polymer , organic chemistry , physics , atomic physics , gene , psychology , social psychology , quantum mechanics , astronomy
NMR spin relaxation experiments are used to characterize the dynamics of the backbone of ubiquitin. Chemical exchange processes affecting residues Ile 23, Asn 25, Thr 55, and Val 70 are characterized using on‐ and off‐resonance rotating‐frame 15 N R 1ρ relaxation experiments to have a kinetic exchange rate constant of 25,000 sec −1 at 280 K. The exchange process affecting residues 23, 25, and 55 appears to result from disruption of N‐cap hydrogen bonds of the α‐helix and possibly from repacking of the side chain of Ile 23. Chemical exchange processes affecting other residues on the surface of ubiquitin are identified using 1 H‐ 15 N multiple quantum relaxation experiments. These residues are located near or at the regions known to interact with various enzymes of the ubiquitin‐dependent protein degradation pathway.