Microsecond Dynamics in Ubiquitin Probed by Solid-State 15N NMR Spectroscopy R1ρ Relaxation Experiments under Fast MAS (60-110 kHz)

被引:35
作者
Lakomek, Nils-Alexander [1 ]
Penzel, Susanne [1 ]
Lends, Alons [1 ]
Cadalbert, Riccardo [1 ]
Ernst, Matthias [1 ]
Meier, Beat H. [1 ]
机构
[1] Swiss Fed Inst Technol, Lab Phys Chem, Vladimir Prelog Weg 2, CH-8093 Zurich, Switzerland
基金
瑞士国家科学基金会;
关键词
biophysics; molecular dynamics; NMR spectroscopy; proteins; solid-state structures; RESIDUAL DIPOLAR COUPLINGS; PROTEIN BACKBONE DYNAMICS; LIQUID-CRYSTALLINE PHASE; MODEL-FREE ANALYSIS; SLOW MOTIONS; CONFORMATIONAL FLEXIBILITY; COLLECTIVE MOTION; CROSS-VALIDATION; ORDER PARAMETERS; SPIN RELAXATION;
D O I
10.1002/chem.201701738
中图分类号
O6 [化学];
学科分类号
0703 ;
摘要
N-15 R-1 rho relaxation experiments in solid-state NMR spectroscopy are sensitive to timescales and amplitudes of internal protein motions in the hundreds of nano-to microsecond time window, which is difficult to probe by solution-state NMR spectroscopy. By using N-15 R-1 rho relaxation experiments, a simplified approach to detect low microsecond protein dynamics is described and residue-specific correlation times are determined from the ratio of N-15 R-1 rho rate constants at different magic angle spinning frequencies. Micro-crystalline ubiquitin exhibits small-amplitude dynamics on a timescale of about 1 mu s across the entire protein, and larger amplitude motions, also on the 1 mu s timescale, for several sites, including the beta(1)-beta(2) turn and the N terminus of the a helix. According to the analysis, the microsecond protein backbone dynamics are of lower amplitude than that concluded in previous solid-state NMR spectroscopy studies, but persist across the entire protein with a rather uniform timescale of 1 mu s.
引用
收藏
页码:9425 / 9433
页数:9
相关论文
共 63 条
[51]   Quantitative Analysis of Protein Backbone Dynamics in Microcrystalline Ubiquitin by Solid-State NMR Spectroscopy [J].
Schanda, Paul ;
Meier, Beat H. ;
Ernst, Matthias .
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 2010, 132 (45) :15957-15967
[52]   Solid-state NMR spectroscopy of 10% 13C labeled ubiquitin:: spectral simplification and stereospecific assignment of isopropyl groups [J].
Schubert, Mario ;
Manolikas, Theofanis ;
Rogowski, Marco ;
Meier, Beat H. .
JOURNAL OF BIOMOLECULAR NMR, 2006, 35 (03) :167-173
[53]   Characterization of fibril dynamics on three timescales by solid-state NMR [J].
Smith, Albert A. ;
Testori, Emilie ;
Cadalbert, Riccardo ;
Meier, Beat H. ;
Ernst, Matthias .
JOURNAL OF BIOMOLECULAR NMR, 2016, 65 (3-4) :171-191
[54]   Allosteric switch regulates protein-protein binding through collective motion [J].
Smith, Colin A. ;
Ban, David ;
Pratihar, Supriya ;
Giller, Karin ;
Paulat, Maria ;
Becker, Stefan ;
Griesinger, Christian ;
Lee, Donghan ;
de Groot, Bert L. .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2016, 113 (12) :3269-3274
[55]   Rotational diffusion anisotropy of human ubiquitin from N-15 NMR relaxation [J].
Tjandra, N ;
Feller, SE ;
Pastor, RW ;
Bax, A .
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY, 1995, 117 (50) :12562-12566
[56]   NMR evidence for slow collective motions in cyanometmyoglobin [J].
Tolman, JR ;
Flanagan, JM ;
Kennedy, MA ;
Prestegard, JH .
NATURE STRUCTURAL BIOLOGY, 1997, 4 (04) :292-297
[57]   STRUCTURE OF UBIQUITIN REFINED AT 1.8 A RESOLUTION [J].
VIJAYKUMAR, S ;
BUGG, CE ;
COOK, WJ .
JOURNAL OF MOLECULAR BIOLOGY, 1987, 194 (03) :531-544
[58]   The CCPN data model for NMR spectroscopy: Development of a software pipeline [J].
Vranken, WF ;
Boucher, W ;
Stevens, TJ ;
Fogh, RH ;
Pajon, A ;
Llinas, P ;
Ulrich, EL ;
Markley, JL ;
Ionides, J ;
Laue, ED .
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS, 2005, 59 (04) :687-696
[59]   Simultaneous NMR study of protein structure and dynamics using conservative mutagenesis [J].
Yao, Lishan ;
Voegeli, Beat ;
Torchia, Dennis A. ;
Bax, Ad .
JOURNAL OF PHYSICAL CHEMISTRY B, 2008, 112 (19) :6045-6056
[60]  
Zhou D. H., 2007, ANGEW CHEM, V119, P8532, DOI [10.1002/ange.200702905, DOI 10.1002/ANGE.200702905]