Rapid visualization of hydrogen positions in protein neutron crystallographic structures

被引:24
作者
Munshi, Parthapratim [1 ,2 ]
Chung, Shang-Lin [1 ]
Blakeley, Matthew P. [3 ]
Weiss, Kevin L. [1 ]
Myles, Dean A. A. [1 ]
Meilleur, Flora [1 ,4 ]
机构
[1] Oak Ridge Natl Lab, Neutron Sci Directorate, Oak Ridge, TN 37831 USA
[2] Middle Tennessee State Univ, Dept Chem, Murfreesboro, TN 37132 USA
[3] Inst Laue Langevin, F-38042 Grenoble, France
[4] N Carolina State Univ, Dept Mol & Struct Biochem, Raleigh, NC 27695 USA
来源
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY | 2012年 / 68卷
基金
美国国家科学基金会;
关键词
D-XYLOSE ISOMERASE; RESOLUTION X-RAY; PYROCOCCUS-FURIOSUS; MACROMOLECULAR CRYSTALLOGRAPHY; CRYSTAL DIFFRACTOMETER; ANGSTROM RESOLUTION; LAUE DIFFRACTION; ALDOSE REDUCTASE; CONCANAVALIN-A; RUBREDOXIN;
D O I
10.1107/S0907444911048402
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
Neutron crystallography is a powerful technique for experimental visualization of the positions of light atoms, including hydrogen and its isotope deuterium. In recent years, structural biologists have shown increasing interest in the technique as it uniquely complements X-ray crystallographic data by revealing the positions of D atoms in macromolecules. With this regained interest, access to macromolecular neutron crystallography beamlines is becoming a limiting step. In this report, it is shown that a rapid data-collection strategy can be a valuable alternative to longer data-collection times in appropriate cases. Comparison of perdeuterated rubredoxin structures refined against neutron data sets collected over hours and up to 5 d shows that rapid neutron data collection in just 14 h is sufficient to provide the positions of 269 D atoms without ambiguity.
引用
收藏
页码:35 / 41
页数:7
相关论文
共 48 条
[1]   Structure of HIV-1 protease in complex with potent inhibitor KNI-272 determined by high-resolution X-ray and neutron crystallography [J].
Adachi, Motoyasu ;
Ohhara, Takashi ;
Kurihara, Kazuo ;
Tamada, Taro ;
Honjo, Eijiro ;
Okazaki, Nobuo ;
Arai, Shigeki ;
Shoyama, Yoshinari ;
Kimura, Kaname ;
Matsumura, Hiroyoshi ;
Sugiyama, Shigeru ;
Adachi, Hiroaki ;
Takano, Kazufumi ;
Mori, Yusuke ;
Hidaka, Koushi ;
Kimura, Tooru ;
Hayashi, Yoshio ;
Kiso, Yoshiaki ;
Kuroki, Ryota .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2009, 106 (12) :4641-4646
[2]   PHENIX:: building new software for automated crystallographic structure determination [J].
Adams, PD ;
Grosse-Kunstleve, RW ;
Hung, LW ;
Ioerger, TR ;
McCoy, AJ ;
Moriarty, NW ;
Read, RJ ;
Sacchettini, JC ;
Sauter, NK ;
Terwilliger, TC .
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 2002, 58 :1948-1954
[3]   Joint X-ray and neutron refinement with phenix.refine [J].
Afonine, Pavel V. ;
Mustyakimov, Marat ;
Grosse-Kunstleve, Ralf W. ;
Moriarty, Nigel W. ;
Langan, Paul ;
Adams, Paul D. .
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 2010, 66 :1153-1163
[4]   LSCALE -: the new normalization, scaling and absorption correction program in the Daresbury Laue software suite [J].
Arzt, S ;
Campbell, JW ;
Harding, MM ;
Hao, Q ;
Helliwell, JR .
JOURNAL OF APPLIED CRYSTALLOGRAPHY, 1999, 32 :554-562
[5]   Crystal structure of rubredoxin from Pyrococcus furiosus at 0.95 Å resolution, and the structures of N-terminal methionine and formylmethionine variants of Pf Rd.: Contributions of N-terminal interactions to thermostability [J].
Bau, R ;
Rees, DC ;
Kurtz, DM ;
Scott, RA ;
Huang, HS ;
Adams, MWW ;
Eidsness, MK .
JOURNAL OF BIOLOGICAL INORGANIC CHEMISTRY, 1998, 3 (05) :484-493
[6]   Comparison of hydrogen determination with X-ray and neutron crystallography in a human aldose reductase-inhibitor complex [J].
Blakeley, M. P. ;
Mitschler, A. ;
Hazemann, I. ;
Meilleur, F. ;
Myles, D. A. A. ;
Podjarny, A. .
EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS, 2006, 35 (07) :577-583
[7]   Neutron crystallography: opportunities, challenges, and limitations [J].
Blakeley, Matthew P. ;
Langan, Paul ;
Niimura, Nobuo ;
Podjarny, Alberto .
CURRENT OPINION IN STRUCTURAL BIOLOGY, 2008, 18 (05) :593-600
[8]   Quantum model of catalysis based on a mobile proton revealed by subatomic x-ray and neutron diffraction studies of h-aldose reductase [J].
Blakeley, Matthew P. ;
Ruiz, Federico ;
Cachau, Raul ;
Hazemann, Isabelle ;
Meilleur, Flora ;
Mitschler, Andre ;
Ginell, Stephan ;
Afonine, Pavel ;
Ventura, Oscar N. ;
Cousido-Siah, Alexandra ;
Haertlein, Michael ;
Joachimiak, Andrzej ;
Myles, Dean ;
Podjarny, Alberto .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2008, 105 (06) :1844-1848
[9]   Neutron macromolecular crystallography with LADI-III [J].
Blakeley, Matthew P. ;
Teixeira, Susana C. M. ;
Petit-Haertlein, Isabelle ;
Hazemann, Isabelle ;
Mitschler, Andre ;
Haertlein, Michael ;
Howard, Eduardo ;
Podjarny, Alberto D. .
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 2010, 66 :1198-1205
[10]   The 15-K neutron structure of saccharide-free concanavalin A [J].
Blakeley, MP ;
Kalb, AJ ;
Helliwell, JR ;
Myles, DAA .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2004, 101 (47) :16405-16410