← Back to Search
Dynamics Of Geminate Rebinding Of NO With Cytochrome C In Aqueous Solution Using Femtosecond Vibrational Spectroscopy.
Jooyoung Kim, J. Park, T. Lee, Manho Lim
Published 2012 · Chemistry, Medicine
Save to my Library
Download PDFAnalyze on Scholarcy
Using femtosecond vibrational spectroscopy, we investigated the rebinding dynamics of NO to cytochrome c (Cytc) and a model heme, microperoxidase-8 (Mp), after photodeligation of CytcNO in D(2)O solution and MpNO in an 81% glycerol/water (v/v) mixture at room temperature. Whereas the stretching mode of the NO band in MpNO was described by a Gaussian centered at 1653 cm(-1) with a full width at half-maximum (fwhm) of 41 cm(-1), that in CytcNO revealed an asymmetric structured band that peaked at 1619 cm(-1) with an fwhm of about 27 cm(-1). The structured NO band in CytcNO was well described by the sum of three Gaussians, and its shape did not evolve with time but its amplitude decayed exponentially with a time constant of 7 ± 1 ps. The transient NO band in MpNO also decayed exponentially with a time constant of 8 ± 1 ps. Rebinding of NO to Cytc was slightly faster than that of NO to Mp and was almost complete by 30 ps, which was much faster than the rebinding of NO to myoglobin (Mb). When the deligated NO was constrained near the Fe atom either by a viscous solvent or by the protein matrix, it rebound to heme Fe much faster than CO, suggesting that NO has a higher propensity for binding to heme Fe and the high reactivity governed the rebinding kinetics. Moreover, the faster ligand rebinding in Cytc than in Mb suggests that Cytc does not have a primary docking site (PDS)-like structure found in Mb that suppresses rebinding by restraining ligand motion and the PDS can also hold the deligated NO in a manner that impedes NO rebinding; however, due to higher NO reactivity with heme Fe, the impediment is not as efficient as for CO.
This paper references
Picosecond primary structural transition of the heme is retarded after nitric oxide binding to heme proteins
S. Kruglik (2010)
The pH dependence of the stereochemistry around the heme group in NO–cytochrome c (horse heart)
Tetsushiko Yoshimura (1988)
Identification of conformational substates involved in nitric oxide binding to ferric and ferrous myoglobin through difference Fourier transform infrared spectroscopy (FTIR).
L. Miller (1997)
Proximal and distal influences on ligand binding kinetics in microperoxidase and heme model compounds.
W. Cao (2004)
Native and unfolded cytochrome c--comparison of dynamics using 2D-IR vibrational echo spectroscopy.
S. Kim (2008)
Geminate recombination of O2 and hemoglobin.
D. A. Chernoff (1980)
Dynamics of Geminate Recombination of NO with Myoglobin in Aqueous Solution Probed by Femtosecond Mid-IR Spectroscopy
S. Kim (2004)
Dynamics of CO Rebinding to Protoheme in Viscous Solutions
T. Lee (2009)
Main chain and side chain dynamics of a heme protein: 15N and 2H NMR relaxation studies of R. capsulatus ferrocytochrome c2.
P. Flynn (2001)
Protein conformational relaxation and ligand migration in myoglobin: a nanosecond to millisecond molecular movie from time-resolved Laue X-ray diffraction.
V. Šrajer (2001)
Nonexponential relaxation after ligand dissociation from myoglobin: a molecular dynamics simulation.
K. Kuczera (1993)
Perturbations of the distal heme pocket in human myoglobin mutants probed by infrared spectroscopy of bound CO: correlation with ligand binding kinetics.
S. Balasubramanian (1993)
Nonexponential protein relaxation: dynamics of conformational change in myoglobin.
M. Lim (1993)
Measurements of the photodissociation quantum yields of MbNO and MbO(2) and the vibrational relaxation of the six-coordinate heme species.
X. Ye (2002)
Rebinding and relaxation in the myoglobin pocket.
A. Ansari (1987)
Geminate recombination of carbon monoxide to myoglobin.
E. R. Henry (1983)
Noise suppression in femtosecond mid-infrared light sources.
P. Hamm (2000)
Protein folding dynamics of cytochrome c seen by transient grating and transient absorption spectroscopies.
Jungkweon Choi (2011)
Transient and time-resolved optical studies of photolyzed carbonmonoxy hemoglobin and myoglobin.
Findsen Ew (1990)
Ultrafast dynamics of ligands within heme proteins.
M. Vos (2008)
Direct observation of ligand rebinding pathways in hemoglobin using femtosecond mid-IR spectroscopy.
S. Kim (2012)
Photochemistry of nitric oxide adducts of water-soluble iron(III) porphyrin and ferrihemoproteins studied by nanosecond laser photolysis
M. Hoshino (1993)
FTIR and resonance Raman studies of nitric oxide binding to H93G cavity mutants of myoglobin.
M. R. Thomas (2001)
Heme protein dynamics revealed by geminate nitric oxide recombination in mutants of iron and cobalt myoglobin.
Y. Kholodenko (1999)
Fast events in protein folding.
W. Eaton (1996)
Structural dynamics of myoglobin: FTIR-TDS study of NO migration and binding.
K. Nienhaus (2008)
Temperature-dependent studies of NO recombination to heme and heme proteins.
D. Ionașcu (2005)
High-resolution refinement of yeast iso-1-cytochrome c and comparisons with other eukaryotic cytochromes c.
G. Louie (1990)
STRUCTURE OF THE AMIDE I BAND OF PEPTIDES MEASURED BY FEMTOSECOND NONLINEAR-INFRARED SPECTROSCOPY
P. Hamm (1998)
Absorption band III kinetics probe the picosecond heme iron motion triggered by nitric oxide binding to hemoglobin and myoglobin.
Byung-Kuk Yoo (2012)
Protein conformation-controlled rebinding barrier of NO and its binding trajectories in myoglobin and hemoglobin at room temperature.
S. Kim (2012)
Kinetics of hemoglobin and transition state theory.
A. Szabó (1978)
Structural dynamics of myoglobin probed by femtosecond infrared spectroscopy of the amide band
S. Kim (2003)
Dependence of NO Recombination Dynamics in Horse Myoglobin on Solution Glycerol Content
A. P. Shreve (1999)
Ligand binding and protein relaxation in heme proteins: a room temperature analysis of nitric oxide geminate recombination
J. Petrich (1991)
Geminate recombination of diatomic ligands CO, O2, and NO with myoglobin.
K. N. Walda (1994)
Distal pocket residues affect picosecond ligand recombination in myoglobin. An experimental and molecular dynamics study of position 29 mutants.
Q. Gibson (1992)
Dynamics of ligand binding to myoglobin.
R. Austin (1975)
Dynamics of nitric oxide rebinding and escape in horseradish peroxidase.
X. Ye (2006)
Ultrafast rotation and trapping of carbon monoxide dissociated from myoglobin
Manho Lim (1997)
Nitric oxide binding to ferrous native horse heart cytochrome c and to its carboxymethylated derivative: a spectroscopic and thermodynamic study.
P. Ascenzi (1994)
Dynamics of ultrafast rebinding of CO to carboxymethyl cytochrome c.
Jooyoung Kim (2009)
Model systems for interacting heme moieties. II. The ferriheme octapeptide of cytochrome c.
D. Urry (1967)
Water (H2O and D2O) molar absorptivity in the 1000-4000 cm-1 range and quantitative infrared spectroscopy of aqueous solutions.
Venyaminov SYu (1997)
Studies on the Reaction Mechanism for Reductive Nitrosylation of Ferrihemoproteins in Buffer Solutions
M. Hoshino (1996)
Picosecond Structural Dynamics of Myoglobin following Photolysis of Carbon Monoxide
Timothy P. Causgrove and (1996)
Crystal structure of photolysed carbonmonoxy-myoglobin
I. Schlichting (1994)
Picosecond and nanosecond geminate recombination of myoglobin with carbon monoxide, oxygen, nitric oxide and isocyanides
K. Jongeward (1988)
CO cage recombination in hemoglobin: Picosecond photolysis and nanosecond observation
S. Pin (1986)
Temperature-dependent heme kinetics with nonexponential binding and barrier relaxation in the absence of protein conformational substates
X. Ye (2007)
Protein conformation-induced modulation of ligand binding kinetics: a femtosecond mid-IR study of nitric oxide binding trajectories in myoglobin.
S. Kim (2005)
Watching a Protein as it Functions with 150-ps Time-Resolved X-ray Crystallography
F. Schotte (2003)
Chirped wavepacket dynamics of HgBr from the photolysis of HgBr2 in solution
M. Lim (1998)
Photophysics and reactivity of heme proteins: a femtosecond absorption study of hemoglobin, myoglobin, and protoheme.
J. Petrich (1988)
Why nitric oxide
T. Traylor (1992)
Mechanisms of Ligand Recognition in Myoglobin
B. Springer (1994)
Microperoxidase 8 catalysed nitrogen oxides formation from oxidation of N-hydroxyguanidines by hydrogen peroxide.
R. Ricoux (2003)
Protein response to photodissociation of CO from carbonmonoxymyoglobin probed by time-resolved infrared spectroscopy of the amide I band.
T. Causgrove (1993)
Photolysis-induced structural changes in single crystals of carbonmonoxy myoglobin at 40 K
T. Teng (1994)
Geminate carbon monoxide rebinding to a c-type haem.
G. Silkstone (2005)
Viscosity-dependent dynamics of CO rebinding to microperoxidase-8 in glycerol/water solution.
J. Park (2010)
Production of a ‘Cytochrome c’ with Myoglobin-like Properties by Alkylating the Cyanide Complex with Bromoacetate
Abel Schejter (1965)
Hemes and hemoproteins. 1: Preparation and analysis of the heme-containing octapeptide (microperoxidase-8) and identification of the monomeric form in aqueous solution.
J. Aron (1986)
Fast events in protein folding initiated by nanosecond laser photolysis.
C. Jones (1993)
Connection between the taxonomic substates and protonation of histidines 64 and 97 in carbonmonoxy myoglobin.
J. Müller (1999)
Resonance Raman spectroscopic studies of the nitric oxide adducts of cobaltous-reconstituted myoglobin and hemoglobin
S. Hu (1993)
Nitric oxide and myoglobins.
J. K. Møller (2002)
Ultrafast measurements of geminate recombination of NO with site-specific mutants of human myoglobin.
J. Petrich (1994)
Folding dynamics of ferrocytochrome C in a denaturant-free environment probed by transient grating spectroscopy.
Jungkweon Choi (2008)
Ligand Dynamics in an Electron Transfer Protein
G. Silkstone (2007)
This paper is referenced by
Structural Interpretation of Metastable States in Myoglobin-NO.
M. Soloviov (2016)
Implications of short time scale dynamics on long time processes
Krystel El Hage (2017)
Free energy simulations for protein ligand binding and stability
Krystel El Hage (2018)
Modulation of ligand–heme reactivity by binding pocket residues demonstrated in cytochrome c' over the femtosecond–second temporal range
Henry J. Russell (2013)
Reactive molecular dynamics: From small molecules to proteins
M. Meuwly (2019)
Picosecond dynamics of photoexcited DNO-bound myoglobin probed by femtosecond vibrational spectroscopy.
T. Lee (2015)
High-Dimensional Potential Energy Surfaces for Molecular Simulations
Oliver T. Unke (2019)
Solvent Composition Drives the Rebinding Kinetics of Nitric Oxide to Microperoxidase
Padmabati Mondal (2018)
Direct observation of the low-spin Fe(III)-NO(radical) intermediate state during rebinding of NO to photodeligated ferric cytochrome c.
J. Park (2013)
Vibrational Relaxation of Cyanate or Thiocyanate Bound to Ferric Heme Proteins Studied by Femtosecond Infrared Spectroscopy
Seongchul Park (2014)
Ultrafast photoinduced processes in metal - containing molecular complexes and in proteins
Roberto Monni (2015)
NO binding kinetics in myoglobin investigated by picosecond Fe K-edge absorption spectroscopy
M. Silatani (2015)
Time-resolved infrared spectroscopic studies of ligand dynamics in the active site from cytochrome c oxidase.
M. Vos (2015)
Atomistic simulations of the reactive processes in the heme-containing proteins
M. Soloviov (2015)
Strukturelle Interpretation metastabiler Zustände in Myoglobin-NO
M. Soloviov (2016)
Structural changes and picosecond to second dynamics of cytochrome c in interaction with nitric oxide in ferrous and ferric redox states.
S. Kruglik (2017)
Femtosecond X-ray emission study of the spin cross-over dynamics in haem proteins
D. Kinschel (2020)
Infrared and UV-visible time-resolved techniques for the study of tetrapyrrole-based proteins
H. Russell (2013)
Geminate rebinding dynamics of nitric oxide to ferric hemoglobin in D2O solution.
J. Park (2013)
Non-conventional force fields for applications in spectroscopy and chemical reaction dynamics.
D. Koner (2020)
Ultrafast X-ray Spectroscopy of Heme Proteins
D. Kinschel (2020)