Literature DB >> 12023251

Myoglobin-CO conformational substate dynamics: 2D vibrational echoes and MD simulations.

Kusai A Merchant1, David E Thompson, Qing-Hua Xu, Ryan B Williams, Roger F Loring, Michael D Fayer.   

Abstract

Two-dimensional (2D) infrared vibrational echoes were performed on horse heart carbonmonoxymyoglobin (MbCO) in water over a range of temperatures. The A(1) and A(3) conformational substates of MbCO are found to have different dephasing rates with different temperature dependences. A frequency-frequency correlation function derived from molecular dynamics simulations on MbCO at 298 K is used to calculate the vibrational echo decay. The calculated decay shows substantial agreement with the experimentally measured decays. The 2D vibrational echo probes protein dynamics and provides an observable that can be used to test structural assignments for the MbCO conformational substates.

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Year:  2002        PMID： 12023251      PMCID： PMC1302116          DOI： 10.1016/S0006-3495(02)75669-5

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


  14 in total

1.  Vibrational population relaxation of carbon monoxide in the heme pocket of photolyzed carbonmonoxy myoglobin: comparison of time-resolved mid-IR absorbance experiments and molecular dynamics simulations.

Authors:  D E Sagnella; J E Straub; T A Jackson; M Lim; P A Anfinrud
Journal:  Proc Natl Acad Sci U S A       Date:  1999-12-07       Impact factor: 11.205

2.  Two-dimensional time-frequency ultrafast infrared vibrational echo spectroscopy.

Authors:  K A Merchant; D E Thompson; M D Fayer
Journal:  Phys Rev Lett       Date:  2001-04-23       Impact factor: 9.161

3.  Influence of the heme pocket conformation on the structure and vibrations of the Fe-CO bond in myoglobin: a QM/MM density functional study.

Authors:  C Rovira; B Schulze; M Eichinger; J D Evanseck; M Parrinello
Journal:  Biophys J       Date:  2001-07       Impact factor: 4.033

4.  Ligand binding to heme proteins. VI. Interconversion of taxonomic substates in carbonmonoxymyoglobin.

Authors:  J B Johnson; D C Lamb; H Frauenfelder; J D Müller; B McMahon; G U Nienhaus; R D Young
Journal:  Biophys J       Date:  1996-09       Impact factor: 4.033

5.  Multiple conformational states of proteins: a molecular dynamics analysis of myoglobin.

Authors:  R Elber; M Karplus
Journal:  Science       Date:  1987-01-16       Impact factor: 47.728

6.  Dynamic protein structures: infrared evidence for four discrete rapidly interconverting conformers at the carbon monoxide binding site of bovine heart myoglobin.

Authors:  W S Caughey; H Shimada; M G Choc; M P Tucker
Journal:  Proc Natl Acad Sci U S A       Date:  1981-05       Impact factor: 11.205

7.  Connection between the taxonomic substates and protonation of histidines 64 and 97 in carbonmonoxy myoglobin.

Authors:  J D Müller; B H McMahon; E Y Chien; S G Sligar; G U Nienhaus
Journal:  Biophys J       Date:  1999-08       Impact factor: 4.033

8.  Conformational substates and motions in myoglobin. External influences on structure and dynamics.

Authors:  M K Hong; D Braunstein; B R Cowen; H Frauenfelder; I E Iben; J R Mourant; P Ormos; R Scholl; A Schulte; P J Steinbach
Journal:  Biophys J       Date:  1990-08       Impact factor: 4.033

9.  Crystal structures of myoglobin-ligand complexes at near-atomic resolution.

Authors:  J Vojtechovský; K Chu; J Berendzen; R M Sweet; I Schlichting
Journal:  Biophys J       Date:  1999-10       Impact factor: 4.033

10.  Neutron diffraction study of carbonmonoxymyoglobin.

Authors:  X D Cheng; B P Schoenborn
Journal:  J Mol Biol       Date:  1991-07-20       Impact factor: 5.469
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  22 in total

1.  Myoglobin-CO substate structures and dynamics: multidimensional vibrational echoes and molecular dynamics simulations.

Authors:  Kusai A Merchant; W G Noid; Ryo Akiyama; Ilya J Finkelstein; Alexei Goun; Brian L McClain; Roger F Loring; M D Fayer
Journal:  J Am Chem Soc       Date:  2003-11-12       Impact factor: 15.419

2.  Viscosity-dependent protein dynamics.

Authors:  Ilya J Finkelstein; Aaron M Massari; M D Fayer
Journal:  Biophys J       Date:  2007-05-15       Impact factor: 4.033

Review 3.  Applications of two-dimensional infrared spectroscopy.

Authors:  Amanda L Le Sueur; Rachel E Horness; Megan C Thielges
Journal:  Analyst       Date:  2015-07-07       Impact factor: 4.616

4.  Influence of histidine tag attachment on picosecond protein dynamics.

Authors:  Megan C Thielges; Jean K Chung; Jun Y Axup; Michael D Fayer
Journal:  Biochemistry       Date:  2011-06-06       Impact factor: 3.162

5.  Protein dynamics in cytochrome P450 molecular recognition and substrate specificity using 2D IR vibrational echo spectroscopy.

Authors:  Megan C Thielges; Jean K Chung; Michael D Fayer
Journal:  J Am Chem Soc       Date:  2011-02-24       Impact factor: 15.419

6.  Site-Specific 1D and 2D IR Spectroscopy to Characterize the Conformations and Dynamics of Protein Molecular Recognition.

Authors:  Sashary Ramos; Megan C Thielges
Journal:  J Phys Chem B       Date:  2019-03-21       Impact factor: 2.991

7.  Conformational switching between protein substates studied with 2D IR vibrational echo spectroscopy and molecular dynamics simulations.

Authors:  Sayan Bagchi; Dayton G Thorpe; Ian F Thorpe; Gregory A Voth; M D Fayer
Journal:  J Phys Chem B       Date:  2010-12-03       Impact factor: 2.991

8.  3-picolyl azide adenine dinucleotide as a probe of femtosecond to picosecond enzyme dynamics.

Authors:  Samrat Dutta; Yun-Liang Li; William Rock; Jon C D Houtman; Amnon Kohen; Christopher M Cheatum
Journal:  J Phys Chem B       Date:  2011-12-15       Impact factor: 2.991

9.  Two-dimensional IR spectroscopy of protein dynamics using two vibrational labels: a site-specific genetically encoded unnatural amino acid and an active site ligand.

Authors:  Megan C Thielges; Jun Y Axup; Daryl Wong; Hyun Soo Lee; Jean K Chung; Peter G Schultz; Michael D Fayer
Journal:  J Phys Chem B       Date:  2011-08-31       Impact factor: 2.991

10.  Neuroglobin dynamics observed with ultrafast 2D-IR vibrational echo spectroscopy.

Authors:  Haruto Ishikawa; Ilya J Finkelstein; Seongheun Kim; Kyungwon Kwak; Jean K Chung; Keisuke Wakasugi; Aaron M Massari; Michael D Fayer
Journal:  Proc Natl Acad Sci U S A       Date:  2007-10-04       Impact factor: 11.205
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