Literature DB >> 25919807

Docking and migration of carbon monoxide in nitrogenase: the case for gated pockets from infrared spectroscopy and molecular dynamics.

Leland B Gee1, Igor Leontyev2, Alexei Stuchebrukhov1, Aubrey D Scott1, Vladimir Pelmenschikov3, Stephen P Cramer1,4.   

Abstract

Evidence of a CO docking site near the FeMo cofactor in nitrogenase has been obtained by Fourier transform infrared spectroscopy-monitored low-temperature photolysis. We investigated the possible migration paths for CO from this docking site using molecular dynamics calculations. The simulations support the notion of a gas channel with multiple internal pockets from the active site to the protein exterior. Travel between pockets is gated by the motion of protein residues. Implications for the mechanism of nitrogenase reactions with CO and N2 are discussed.

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Year:  2015        PMID： 25919807      PMCID： PMC4522414          DOI： 10.1021/acs.biochem.5b00216

Source DB:  PubMed          Journal:  Biochemistry        ISSN： 0006-2960            Impact factor:   3.162


  50 in total

1.  Mechanism of Molybdenum Nitrogenase.

Authors:  Barbara K. Burgess; David J. Lowe
Journal:  Chem Rev       Date:  1996-11-07       Impact factor: 60.622

2.  Theoretical investigation of infrared spectra and pocket dynamics of photodissociated carbonmonoxy myoglobin.

Authors:  David R Nutt; Markus Meuwly
Journal:  Biophys J       Date:  2003-12       Impact factor: 4.033

3.  Probing electric fields in protein cavities by using the vibrational stark effect of carbon monoxide.

Authors:  Hartwig Lehle; Jan M Kriegl; Karin Nienhaus; Pengchi Deng; Stephanus Fengler; G Ulrich Nienhaus
Journal:  Biophys J       Date:  2004-12-13       Impact factor: 4.033

4.  Ligand migration through hemeprotein cavities: insights from laser flash photolysis and molecular dynamics simulations.

Authors:  Stefania Abbruzzetti; Francesca Spyrakis; Axel Bidon-Chanal; F Javier Luque; Cristiano Viappiani
Journal:  Phys Chem Chem Phys       Date:  2013-06-03       Impact factor: 3.676

5.  Efficient mapping of ligand migration channel networks in dynamic proteins.

Authors:  Tu-Liang Lin; Guang Song
Journal:  Proteins       Date:  2011-06-02

6.  GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit.

Authors:  Sander Pronk; Szilárd Páll; Roland Schulz; Per Larsson; Pär Bjelkmar; Rossen Apostolov; Michael R Shirts; Jeremy C Smith; Peter M Kasson; David van der Spoel; Berk Hess; Erik Lindahl
Journal:  Bioinformatics       Date:  2013-02-13       Impact factor: 6.937

7.  Insights into substrate binding at FeMo-cofactor in nitrogenase from the structure of an alpha-70(Ile) MoFe protein variant.

Authors:  Ranjana Sarma; Brett M Barney; Stephen Keable; Dennis R Dean; Lance C Seefeldt; John W Peters
Journal:  J Inorg Biochem       Date:  2009-11-26       Impact factor: 4.336

8.  Infrared spectroscopy of photodissociated carboxymyoglobin at low temperatures.

Authors:  J O Alben; D Beece; S F Bowne; W Doster; L Eisenstein; H Frauenfelder; D Good; J D McDonald; M C Marden; P P Moh; L Reinisch; A H Reynolds; E Shyamsunder; K T Yue
Journal:  Proc Natl Acad Sci U S A       Date:  1982-06       Impact factor: 11.205

9.  CAVER: a new tool to explore routes from protein clefts, pockets and cavities.

Authors:  Martin Petrek; Michal Otyepka; Pavel Banás; Pavlína Kosinová; Jaroslav Koca; Jirí Damborský
Journal:  BMC Bioinformatics       Date:  2006-06-22       Impact factor: 3.169

10.  Structural characterization of CO-inhibited Mo-nitrogenase by combined application of nuclear resonance vibrational spectroscopy, extended X-ray absorption fine structure, and density functional theory: new insights into the effects of CO binding and the role of the interstitial atom.

Authors:  Aubrey D Scott; Vladimir Pelmenschikov; Yisong Guo; Lifen Yan; Hongxin Wang; Simon J George; Christie H Dapper; William E Newton; Yoshitaka Yoda; Yoshihito Tanaka; Stephen P Cramer
Journal:  J Am Chem Soc       Date:  2014-11-03       Impact factor: 15.419
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  3 in total

Review 1.  Reduction of Substrates by Nitrogenases.

Authors:  Lance C Seefeldt; Zhi-Yong Yang; Dmitriy A Lukoyanov; Derek F Harris; Dennis R Dean; Simone Raugei; Brian M Hoffman
Journal:  Chem Rev       Date:  2020-03-16       Impact factor: 60.622

2.  Low frequency dynamics of the nitrogenase MoFe protein via femtosecond pump probe spectroscopy - Observation of a candidate promoting vibration.

Authors:  Margherita Maiuri; Ines Delfino; Giulio Cerullo; Cristian Manzoni; Vladimir Pelmenschikov; Yisong Guo; Hongxin Wang; Leland B Gee; Christie H Dapper; William E Newton; Stephen P Cramer
Journal:  J Inorg Biochem       Date:  2015-07-14       Impact factor: 4.155

3.  Infrared spectroscopy of the nitrogenase MoFe protein under electrochemical control: potential-triggered CO binding.

Authors:  P Paengnakorn; P A Ash; S Shaw; K Danyal; T Chen; D R Dean; L C Seefeldt; K A Vincent
Journal:  Chem Sci       Date:  2016-10-27       Impact factor: 9.825
  3 in total

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