Literature DB >> 16389451

Recent results on hydrogen and hydration in biology studied by neutron macromolecular crystallography.

N Niimura1, S Arai, K Kurihara, T Chatake, I Tanaka, R Bau.   

Abstract

Neutron diffraction provides an experimental method of directly locating hydrogen atoms in proteins, a technique complimentary to ultra-high-resolution [1, 2] X-ray diffraction. Three different types of neutron diffractometers for biological macromolecules have been constructed in Japan, France and the United States, and they have been used to determine the crystal structures of proteins up to resolution limits of 1.5-2.5 A. Results relating to hydrogen positions and hydration patterns in proteins have been obtained from these studies. Examples include the geometrical details of hydrogen bonds, H/D exchange in proteins and oligonucleotides, the role of hydrogen atoms in enzymatic activity and thermostability, and the dynamical behavior of hydration structures, all of which have been extracted from these structural results and reviewed. Other techniques, such as the growth of large single crystals, the preparation of fully deuterated proteins, the use of cryogenic techniques, and a data base of hydrogen and hydration in proteins, will be described.

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Year:  2006        PMID: 16389451     DOI: 10.1007/s00018-005-5418-3

Source DB:  PubMed          Journal:  Cell Mol Life Sci        ISSN: 1420-682X            Impact factor:   9.261


  15 in total

1.  High-resolution X-ray study of the effects of deuteration on crystal growth and the crystal structure of proteinase K.

Authors:  Toshiyuki Chatake; Takuya Ishikawa; Yasuhide Yanagisawa; Taro Yamada; Ichiro Tanaka; Satoru Fujiwara; Yukio Morimoro
Journal:  Acta Crystallogr Sect F Struct Biol Cryst Commun       Date:  2011-10-25

2.  Automated electron-density sampling reveals widespread conformational polymorphism in proteins.

Authors:  P Therese Lang; Ho-Leung Ng; James S Fraser; Jacob E Corn; Nathaniel Echols; Mark Sales; James M Holton; Tom Alber
Journal:  Protein Sci       Date:  2010-07       Impact factor: 6.725

3.  Joint X-ray and neutron refinement with phenix.refine.

Authors:  Pavel V Afonine; Marat Mustyakimov; Ralf W Grosse-Kunstleve; Nigel W Moriarty; Paul Langan; Paul D Adams
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2010-10-20

Review 4.  Protein crystallography for non-crystallographers, or how to get the best (but not more) from published macromolecular structures.

Authors:  Alexander Wlodawer; Wladek Minor; Zbigniew Dauter; Mariusz Jaskolski
Journal:  FEBS J       Date:  2007-11-23       Impact factor: 5.542

Review 5.  Neutrons for biologists: a beginner's guide, or why you should consider using neutrons.

Authors:  Jeremy H Lakey
Journal:  J R Soc Interface       Date:  2009-08-05       Impact factor: 4.118

6.  Seeing the chemistry in biology with neutron crystallography.

Authors:  Paul Langan; Julian C-H Chen
Journal:  Phys Chem Chem Phys       Date:  2013-07-15       Impact factor: 3.676

7.  A neutron crystallographic analysis of T6 porcine insulin at 2.1 A resolution.

Authors:  Wakari Iwai; Taro Yamada; Kazuo Kurihara; Yuki Ohnishi; Yoichiro Kobayashi; Ichiro Tanaka; Haruyuki Takahashi; Ryota Kuroki; Taro Tamada; Nobuo Niimura
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2009-09-16

8.  phenix.model_vs_data: a high-level tool for the calculation of crystallographic model and data statistics.

Authors:  Pavel V Afonine; Ralf W Grosse-Kunstleve; Vincent B Chen; Jeffrey J Headd; Nigel W Moriarty; Jane S Richardson; David C Richardson; Alexandre Urzhumtsev; Peter H Zwart; Paul D Adams
Journal:  J Appl Crystallogr       Date:  2010-05-22       Impact factor: 3.304

9.  Joint X-ray/neutron crystallographic study of HIV-1 protease with clinical inhibitor amprenavir: insights for drug design.

Authors:  Irene T Weber; Mary Jo Waltman; Marat Mustyakimov; Matthew P Blakeley; David A Keen; Arun K Ghosh; Paul Langan; Andrey Y Kovalevsky
Journal:  J Med Chem       Date:  2013-06-28       Impact factor: 7.446

10.  Rapid determination of hydrogen positions and protonation states of diisopropyl fluorophosphatase by joint neutron and X-ray diffraction refinement.

Authors:  Marc-Michael Blum; Marat Mustyakimov; Heinz Rüterjans; Kai Kehe; Benno P Schoenborn; Paul Langan; Julian C-H Chen
Journal:  Proc Natl Acad Sci U S A       Date:  2009-01-09       Impact factor: 11.205

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