Literature DB >> 18310235

The kinetics of ligand migration in crystallized myoglobin as revealed by molecular dynamics simulations.

Massimiliano Anselmi1, Alfredo Di Nola, Andrea Amadei.   

Abstract

By using multiple molecular dynamics trajectories of photolyzed carbon monoxide (CO) within crystallized myoglobin, a quantitative description of CO diffusion and corresponding kinetics was obtained. Molecular dynamics results allowed us to construct a detailed kinetic model of the migration process, shedding light on the kinetic mechanism and relevant steps of CO migration and remarkably-well reproducing the available experimental data as provided by time-resolved Laue x-ray diffraction.

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Year:  2008        PMID： 18310235      PMCID： PMC2480659          DOI： 10.1529/biophysj.107.124529

Source DB:  PubMed          Journal:  Biophys J        ISSN： 0006-3495            Impact factor:   4.033


  23 in total

1.  A steric mechanism for inhibition of CO binding to heme proteins.

Authors:  G S Kachalova; A N Popov; H D Bartunik
Journal:  Science       Date:  1999-04-16       Impact factor: 47.728

2.  Complex landscape of protein structural dynamics unveiled by nanosecond Laue crystallography.

Authors:  Dominique Bourgeois; Beatrice Vallone; Friedrich Schotte; Alessandro Arcovito; Adriana E Miele; Giuliano Sciara; Michael Wulff; Philip Anfinrud; Maurizio Brunori
Journal:  Proc Natl Acad Sci U S A       Date:  2003-07-07       Impact factor: 11.205

3.  Extended molecular dynamics simulation of the carbon monoxide migration in sperm whale myoglobin.

Authors:  Cecilia Bossa; Massimiliano Anselmi; Danilo Roccatano; Andrea Amadei; Beatrice Vallone; Maurizio Brunori; Alfredo Di Nola
Journal:  Biophys J       Date:  2004-06       Impact factor: 4.033

4.  Unveiling functional protein motions with picosecond x-ray crystallography and molecular dynamics simulations.

Authors:  Gerhard Hummer; Friedrich Schotte; Philip A Anfinrud
Journal:  Proc Natl Acad Sci U S A       Date:  2004-10-15       Impact factor: 11.205

5.  Photolysis of the carbon monoxide complex of myoglobin: nanosecond time-resolved crystallography.

Authors:  V Srajer; T Teng; T Ursby; C Pradervand; Z Ren; S Adachi; W Schildkamp; D Bourgeois; M Wulff; K Moffat
Journal:  Science       Date:  1996-12-06       Impact factor: 47.728

6.  Initial trajectory of carbon monoxide after photodissociation from myoglobin at cryogenic temperatures.

Authors:  T Y Teng; V Srajer; K Moffat
Journal:  Biochemistry       Date:  1997-10-07       Impact factor: 3.162

7.  Cavities in proteins: structure of a metmyoglobin-xenon complex solved to 1.9 A.

Authors:  R F Tilton; I D Kuntz; G A Petsko
Journal:  Biochemistry       Date:  1984-06-19       Impact factor: 3.162

8.  A study of vibrational relaxation of B-state carbon monoxide in the heme pocket of photolyzed carboxymyoglobin.

Authors:  D E Sagnella; J E Straub
Journal:  Biophys J       Date:  1999-07       Impact factor: 4.033

9.  Dynamics of ligand binding to myoglobin.

Authors:  R H Austin; K W Beeson; L Eisenstein; H Frauenfelder; I C Gunsalus
Journal:  Biochemistry       Date:  1975-12-02       Impact factor: 3.162

10.  Photolysis-induced structural changes in single crystals of carbonmonoxy myoglobin at 40 K.

Authors:  T Y Teng; V Srajer; K Moffat
Journal:  Nat Struct Biol       Date:  1994-10
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  12 in total

1.  An atomistic view on human hemoglobin carbon monoxide migration processes.

Authors:  M Fátima Lucas; Víctor Guallar
Journal:  Biophys J       Date:  2012-02-21       Impact factor: 4.033

2.  Dynamic features of carboxy cytoglobin distal mutants investigated by molecular dynamics simulations.

Authors:  Cong Zhao; Weihong Du
Journal:  J Biol Inorg Chem       Date:  2016-02-03       Impact factor: 3.358

3.  Full kinetics of CO entry, internal diffusion, and exit in myoglobin from transition-path theory simulations.

Authors:  Tang-Qing Yu; Mauro Lapelosa; Eric Vanden-Eijnden; Cameron F Abrams
Journal:  J Am Chem Soc       Date:  2015-02-23       Impact factor: 15.419

4.  Effects of distal mutation on the dynamic properties of carboxycytoglobin: a molecular dynamics simulation study.

Authors:  Cong Zhao; Bingbing Zhang; Weihong Du
Journal:  J Biol Inorg Chem       Date:  2013-09-14       Impact factor: 3.358

Review 5.  Ligand diffusion in globins: simulations versus experiment.

Authors:  Ron Elber
Journal:  Curr Opin Struct Biol       Date:  2010-01-29       Impact factor: 6.809

6.  Dynamics comparison of two myoglobins with a distinct heme active site.

Authors:  Ying-Wu Lin; Yi-Mou Wu; Li-Fu Liao
Journal:  J Mol Model       Date:  2011-07-30       Impact factor: 1.810

7.  Identification of Mutational Hot Spots for Substrate Diffusion: Application to Myoglobin.

Authors:  David De Sancho; Adam Kubas; Po-Hung Wang; Jochen Blumberger; Robert B Best
Journal:  J Chem Theory Comput       Date:  2015-04-14       Impact factor: 6.006

8.  The structure of neuroglobin at high Xe and Kr pressure reveals partial conservation of globin internal cavities.

Authors:  Tommaso Moschetti; Uwe Mueller; Jörg Schulze; Maurizio Brunori; Beatrice Vallone
Journal:  Biophys J       Date:  2009-09-16       Impact factor: 4.033

9.  A computational study of water and CO migration sites and channels inside myoglobin.

Authors:  Mauro Lapelosa; Cameron F Abrams
Journal:  J Chem Theory Comput       Date:  2013-02-12       Impact factor: 6.006

10.  Molecular dynamics simulation of the neuroglobin crystal: comparison with the simulation in solution.

Authors:  Massimiliano Anselmi; Maurizio Brunori; Beatrice Vallone; Alfredo Di Nola
Journal:  Biophys J       Date:  2008-07-18       Impact factor: 4.033
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