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Nat Commun. 2017 Jul 27;8(1):145. doi: 10.1038/s41467-017-00165-8.

Slow conformational exchange and overall rocking motion in ubiquitin protein crystals.

Author information

1
Université Grenoble Alpes, 71 avenue des martyrs, F-38044, Grenoble, France.
2
CEA, Institut de Biologie Structurale, 71 avenue des martyrs, F-38044, Grenoble, France.
3
CNRS, Institut de Biologie Structurale, 71 avenue des martyrs, F-38044, Grenoble, France.
4
Laboratory of Biomolecular NMR, St. Petersburg State University, St. Petersburg, 199034,, Russia.
5
European Synchrotron Radiation Facility, 71 avenue des martyrs, F-38044, Grenoble, France.
6
Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47907-2084,, USA.
7
Laboratory of Biomolecular NMR, St. Petersburg State University, St. Petersburg, 199034,, Russia. nikolai@purdue.edu.
8
Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47907-2084,, USA. nikolai@purdue.edu.
9
Université Grenoble Alpes, 71 avenue des martyrs, F-38044, Grenoble, France. paul.schanda@ibs.fr.
10
CEA, Institut de Biologie Structurale, 71 avenue des martyrs, F-38044, Grenoble, France. paul.schanda@ibs.fr.
11
CNRS, Institut de Biologie Structurale, 71 avenue des martyrs, F-38044, Grenoble, France. paul.schanda@ibs.fr.

Abstract

Proteins perform their functions in solution but their structures are most frequently studied inside crystals. Here we probe how the crystal packing alters microsecond dynamics, using solid-state NMR measurements and multi-microsecond MD simulations of different crystal forms of ubiquitin. In particular, near-rotary-resonance relaxation dispersion (NERRD) experiments probe angular backbone motion, while Bloch-McConnell relaxation dispersion data report on fluctuations of the local electronic environment. These experiments and simulations reveal that the packing of the protein can significantly alter the thermodynamics and kinetics of local conformational exchange. Moreover, we report small-amplitude reorientational motion of protein molecules in the crystal lattice with an ~3-5° amplitude on a tens-of-microseconds time scale in one of the crystals, but not in others. An intriguing possibility arises that overall motion is to some extent coupled to local dynamics. Our study highlights the importance of considering the packing when analyzing dynamics of crystalline proteins.X-ray crystallography is the main method for protein structure determination. Here the authors combine solid-state NMR measurements and molecular dynamics simulations and show that crystal packing alters the thermodynamics and kinetics of local conformational exchange as well as overall rocking motion of protein molecules in the crystal lattice.

PMID:
28747759
PMCID:
PMC5529581
DOI:
10.1038/s41467-017-00165-8
[Indexed for MEDLINE]
Free PMC Article

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