Literature DB >> 18250329

Quantum model of catalysis based on a mobile proton revealed by subatomic x-ray and neutron diffraction studies of h-aldose reductase.

Matthew P Blakeley1, Federico Ruiz, Raul Cachau, Isabelle Hazemann, Flora Meilleur, Andre Mitschler, Stephan Ginell, Pavel Afonine, Oscar N Ventura, Alexandra Cousido-Siah, Michael Haertlein, Andrzej Joachimiak, Dean Myles, Alberto Podjarny.   

Abstract

We present results of combined studies of the enzyme human aldose reductase (h-AR, 36 kDa) using single-crystal x-ray data (0.66 A, 100K; 0.80 A, 15K; 1.75 A, 293K), neutron Laue data (2.2 A, 293K), and quantum mechanical modeling. These complementary techniques unveil the internal organization and mobility of the hydrogen bond network that defines the properties of the catalytic engine, explaining how this promiscuous enzyme overcomes the simultaneous requirements of efficiency and promiscuity offering a general mechanistic view for this class of enzymes.

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Year:  2008        PMID: 18250329      PMCID: PMC2538850          DOI: 10.1073/pnas.0711659105

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN: 0027-8424            Impact factor:   11.205


  15 in total

1.  SHELXL: high-resolution refinement.

Authors:  G M Sheldrick; T R Schneider
Journal:  Methods Enzymol       Date:  1997       Impact factor: 1.600

2.  Molecular modeling studies of the binding modes of aldose reductase inhibitors at the active site of human aldose reductase.

Authors:  Y S Lee; Z Chen; P F Kador
Journal:  Bioorg Med Chem       Date:  1998-10       Impact factor: 3.641

Review 3.  Aldose reductase in glucose toxicity: a potential target for the prevention of diabetic complications.

Authors:  C Yabe-Nishimura
Journal:  Pharmacol Rev       Date:  1998-03       Impact factor: 25.468

4.  A neutron image plate quasi-Laue diffractometer for protein crystallography.

Authors:  F Cipriani; J C Castagna; C Wilkinson; M S Lehmann; G Büldt
Journal:  Basic Life Sci       Date:  1996

5.  Modelling the catalytic reaction in human aldose reductase.

Authors:  P Várnai; W G Richards; P D Lyne
Journal:  Proteins       Date:  1999-11-01

6.  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

7.  Retention of NADPH-linked quinone reductase activity in an aldo-keto reductase following mutation of the catalytic tyrosine.

Authors:  B P Schlegel; K Ratnam; T M Penning
Journal:  Biochemistry       Date:  1998-08-04       Impact factor: 3.162

8.  Novel NADPH-binding domain revealed by the crystal structure of aldose reductase.

Authors:  J M Rondeau; F Tête-Favier; A Podjarny; J M Reymann; P Barth; J F Biellmann; D Moras
Journal:  Nature       Date:  1992-01-30       Impact factor: 49.962

Review 9.  Hydrogen and hydration in proteins.

Authors:  Nobuo Niimura; Toshiyuki Chatake; Kazuo Kurihara; Mitsuru Maeda
Journal:  Cell Biochem Biophys       Date:  2004       Impact factor: 2.194

10.  Probing the active site of human aldose reductase. Site-directed mutagenesis of Asp-43, Tyr-48, Lys-77, and His-110.

Authors:  I Tarle; D W Borhani; D K Wilson; F A Quiocho; J M Petrash
Journal:  J Biol Chem       Date:  1993-12-05       Impact factor: 5.157

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  38 in total

1.  B-factor Analysis and Conformational Rearrangement of Aldose Reductase.

Authors:  Ganesaratnam K Balendiran; J Rajendran Pandian; Evin Drake; Anubhav Vinayak; Malkhey Verma; Duilio Cascio
Journal:  Curr Proteomics       Date:  2014       Impact factor: 0.837

2.  Room-temperature ultrahigh-resolution time-of-flight neutron and X-ray diffraction studies of H/D-exchanged crambin.

Authors:  Julian C-H Chen; Zoë Fisher; Andrey Y Kovalevsky; Marat Mustyakimov; B Leif Hanson; Vladimir V Zhurov; Paul Langan
Journal:  Acta Crystallogr Sect F Struct Biol Cryst Commun       Date:  2012-01-21

3.  X-ray structure of perdeuterated diisopropyl fluorophosphatase (DFPase): perdeuteration of proteins for neutron diffraction.

Authors:  Marc Michael Blum; Stephen J Tomanicek; Harald John; B Leif Hanson; Heinz Rüterjans; Benno P Schoenborn; Paul Langan; Julian C H Chen
Journal:  Acta Crystallogr Sect F Struct Biol Cryst Commun       Date:  2010-03-26

4.  The mobile proton hypothesis in fragmentation of protonated peptides: a perspective.

Authors:  Robert Boyd; Arpád Somogyi
Journal:  J Am Soc Mass Spectrom       Date:  2010-04-29       Impact factor: 3.109

5.  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

6.  Hemoglobin redux: combining neutron and X-ray diffraction with mass spectrometry to analyse the quaternary state of oxidized hemoglobins.

Authors:  Timothy C Mueser; Wendell P Griffith; Andrey Y Kovalevsky; Jingshu Guo; Sean Seaver; Paul Langan; B Leif Hanson
Journal:  Acta Crystallogr D Biol Crystallogr       Date:  2010-10-20

7.  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

8.  A preliminary neutron crystallographic study of an A-DNA crystal.

Authors:  Ricardo M F Leal; Susana C M Teixeira; Matthew P Blakeley; Edward P Mitchell; V Trevor Forsyth
Journal:  Acta Crystallogr Sect F Struct Biol Cryst Commun       Date:  2009-02-12

9.  Implementation of the riding hydrogen model in CCTBX to support the next generation of X-ray and neutron joint refinement in Phenix.

Authors:  Dorothee Liebschner; Pavel V Afonine; Alexandre G Urzhumtsev; Paul D Adams
Journal:  Methods Enzymol       Date:  2020-02-13       Impact factor: 1.600

10.  What are the current limits on determination of protonation state using neutron macromolecular crystallography?

Authors:  Dorothee Liebschner; Pavel V Afonine; Nigel W Moriarty; Paul D Adams
Journal:  Methods Enzymol       Date:  2020-02-13       Impact factor: 1.600

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