Literature DB >> 23852376

Seeing the chemistry in biology with neutron crystallography.

Paul Langan1, Julian C-H Chen.   

Abstract

New developments in macromolecular neutron crystallography have led to an increasing number of structures published over the last decade. Hydrogen atoms, normally invisible in most X-ray crystal structures, become visible with neutrons. Using X-rays allows one to see structure, while neutrons allow one to reveal the chemistry inherent in these macromolecular structures. A number of surprising and sometimes controversial results have emerged; because it is difficult to see or predict hydrogen atoms in X-ray structures, when they are seen by neutrons they can be in unexpected locations with important chemical and biological consequences. Here we describe examples of chemistry seen with neutrons for the first time in biological macromolecules over the past few years.

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Year:  2013        PMID: 23852376      PMCID: PMC5360379          DOI: 10.1039/c3cp51760h

Source DB:  PubMed          Journal:  Phys Chem Chem Phys        ISSN: 1463-9076            Impact factor:   3.676


  48 in total

1.  Neutron structure and mechanistic studies of diisopropyl fluorophosphatase (DFPase).

Authors:  Julian C H Chen; Marat Mustyakimov; Benno P Schoenborn; Paul Langan; Marc Michael Blum
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2010-10-20

2.  Structure of the pure-spermine form of Z-DNA (magnesium free) at 1-A resolution.

Authors:  M Egli; L D Williams; Q Gao; A Rich
Journal:  Biochemistry       Date:  1991-12-03       Impact factor: 3.162

3.  Low-barrier hydrogen bonds and enzymic catalysis.

Authors:  W W Cleland; M M Kreevoy
Journal:  Science       Date:  1994-06-24       Impact factor: 47.728

4.  Binding of a designed substrate analogue to diisopropyl fluorophosphatase: implications for the phosphotriesterase mechanism.

Authors:  Marc-Michael Blum; Frank Löhr; Andre Richardt; Heinz Rüterjans; Julian C-H Chen
Journal:  J Am Chem Soc       Date:  2006-10-04       Impact factor: 15.419

5.  Ultrahigh resolution drug design I: details of interactions in human aldose reductase-inhibitor complex at 0.66 A.

Authors:  E I Howard; R Sanishvili; R E Cachau; A Mitschler; B Chevrier; P Barth; V Lamour; M Van Zandt; E Sibley; C Bon; D Moras; T R Schneider; A Joachimiak; A Podjarny
Journal:  Proteins       Date:  2004-06-01

6.  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

7.  Neutron diffraction identifies His 57 as the catalytic base in trypsin.

Authors:  A A Kossiakoff; S A Spencer
Journal:  Nature       Date:  1980-11-27       Impact factor: 49.962

8.  Low-barrier hydrogen bond in photoactive yellow protein.

Authors:  Shigeo Yamaguchi; Hironari Kamikubo; Kazuo Kurihara; Ryota Kuroki; Nobuo Niimura; Nobutaka Shimizu; Yoichi Yamazaki; Mikio Kataoka
Journal:  Proc Natl Acad Sci U S A       Date:  2009-01-02       Impact factor: 11.205

9.  Short hydrogen bonds in photoactive yellow protein.

Authors:  Spencer Anderson; Sean Crosson; Keith Moffat
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2004-05-21

10.  Water in crystalline fibers of dihydrate β-chitin results in unexpected absence of intramolecular hydrogen bonding.

Authors:  Daisuke Sawada; Yoshiharu Nishiyama; Paul Langan; V Trevor Forsyth; Satoshi Kimura; Masahisa Wada
Journal:  PLoS One       Date:  2012-06-19       Impact factor: 3.240

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  7 in total

1.  Production, crystallization and neutron diffraction of fully deuterated human myelin peripheral membrane protein P2.

Authors:  Saara Laulumaa; Matthew P Blakeley; Arne Raasakka; Martine Moulin; Michael Härtlein; Petri Kursula
Journal:  Acta Crystallogr F Struct Biol Commun       Date:  2015-10-23       Impact factor: 1.056

2.  Joint neutron crystallographic and NMR solution studies of Tyr residue ionization and hydrogen bonding: Implications for enzyme-mediated proton transfer.

Authors:  Ryszard Michalczyk; Clifford J Unkefer; John-Paul Bacik; Tobias E Schrader; Andreas Ostermann; Andrey Y Kovalevsky; Robert McKenna; Suzanne Zoë Fisher
Journal:  Proc Natl Acad Sci U S A       Date:  2015-04-20       Impact factor: 11.205

3.  Protein kinase A in the neutron beam: Insights for catalysis from directly observing protons.

Authors:  Oksana Gerlits; Kevin L Weiss; Matthew P Blakeley; Gianluigi Veglia; Susan S Taylor; Andrey Kovalevsky
Journal:  Methods Enzymol       Date:  2020-01-17       Impact factor: 1.600

4.  Crystallization, neutron data collection, initial structure refinement and analysis of a xyloglucan heptamer bound to an engineered carbohydrate-binding module from xylanase.

Authors:  Mats Ohlin; Laura von Schantz; Tobias E Schrader; Andreas Ostermann; Derek T Logan; S Zoë Fisher
Journal:  Acta Crystallogr F Struct Biol Commun       Date:  2015-07-29       Impact factor: 1.056

Review 5.  Biophysical, Biochemical, and Cell Based Approaches Used to Decipher the Role of Carbonic Anhydrases in Cancer and to Evaluate the Potency of Targeted Inhibitors.

Authors:  Mam Y Mboge; Anusha Kota; Robert McKenna; Susan C Frost
Journal:  Int J Med Chem       Date:  2018-07-16

Review 6.  Neutron Crystallography for the Study of Hydrogen Bonds in Macromolecules.

Authors:  Esko Oksanen; Julian C-H Chen; Suzanne Zoë Fisher
Journal:  Molecules       Date:  2017-04-07       Impact factor: 4.411

7.  Structural comparison of protiated, H/D-exchanged and deuterated human carbonic anhydrase IX.

Authors:  K Koruza; B Lafumat; M Nyblom; B P Mahon; W Knecht; R McKenna; S Z Fisher
Journal:  Acta Crystallogr D Struct Biol       Date:  2019-08-22       Impact factor: 7.652

  7 in total

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