Ligand recombination and a hierarchy of solvent slaved dynamics: the origin of kinetic phases in hemeproteins.

PubWeight™: 0.90‹?›

🔗 View Article (PMC 1975397)

Published in Gene on May 10, 2007

Authors

Uri Samuni1, David Dantsker, Camille J Roche, Joel M Friedman

Author Affiliations

1: Albert Einstein College of Medicine, Department of Physiology and Biophysics, Bronx, New York 10461, USA.

Articles cited by this

The energy landscapes and motions of proteins. Science (1991) 18.93

Dynamics of ligand binding to myoglobin. Biochemistry (1975) 17.10

The role of solvent viscosity in the dynamics of protein conformational changes. Science (1992) 4.52

Watching a protein as it functions with 150-ps time-resolved x-ray crystallography. Science (2003) 4.12

Slaving: solvent fluctuations dominate protein dynamics and functions. Proc Natl Acad Sci U S A (2002) 3.40

Cavities in proteins: structure of a metmyoglobin-xenon complex solved to 1.9 A. Biochemistry (1984) 3.05

Ligand binding to heme proteins: connection between dynamics and function. Biochemistry (1991) 2.85

The role of structure, energy landscape, dynamics, and allostery in the enzymatic function of myoglobin. Proc Natl Acad Sci U S A (2001) 2.75

Ligand binding and conformational motions in myoglobin. Nature (2000) 2.74

Protein conformational relaxation and ligand migration in myoglobin: a nanosecond to millisecond molecular movie from time-resolved Laue X-ray diffraction. Biochemistry (2001) 2.73

High-resolution crystal structures of distal histidine mutants of sperm whale myoglobin. J Mol Biol (1993) 2.37

Mapping the pathways for O2 entry into and exit from myoglobin. J Biol Chem (2000) 2.31

Complex landscape of protein structural dynamics unveiled by nanosecond Laue crystallography. Proc Natl Acad Sci U S A (2003) 1.92

Protein folding is slaved to solvent motions. Proc Natl Acad Sci U S A (2006) 1.88

Linkage of functional and structural heterogeneity in proteins: dynamic hole burning in carboxymyoglobin. Science (1987) 1.87

X-ray structure determination of a metastable state of carbonmonoxy myoglobin after photodissociation. Proc Natl Acad Sci U S A (1996) 1.86

Kinetic pathways and barriers for ligand binding to myoglobin. J Biol Chem (1996) 1.79

Picosecond time-resolved X-ray crystallography: probing protein function in real time. J Struct Biol (2004) 1.79

Geminate recombination of carbon monoxide to myoglobin. J Mol Biol (1983) 1.75

Ligand migration in sperm whale myoglobin. Biochemistry (1997) 1.74

The role of cavities in protein dynamics: crystal structure of a photolytic intermediate of a mutant myoglobin. Proc Natl Acad Sci U S A (2000) 1.63

Solvent composition and viscosity effects on the kinetics of CO binding to horse myoglobin. Biochemistry (1998) 1.62

Extended subnanosecond structural dynamics of myoglobin revealed by Laue crystallography. Proc Natl Acad Sci U S A (2006) 1.61

Spectroscopic evidence for conformational relaxation in myoglobin. Proc Natl Acad Sci U S A (1992) 1.53

Investigations of optical line shapes and kinetic hole burning in myoglobin. Biochemistry (1991) 1.51

Transient Raman study of CO-haemoprotein photolysis: origin of the quantum yield. Nature (1980) 1.43

Structural and functional effects of apolar mutations of the distal valine in myoglobin. J Mol Biol (1995) 1.37

A reduction of protein specific motions in co-ligated myoglobin embedded in a trehalose glass. Eur Biophys J (1998) 1.35

Structural dynamics of ligand diffusion in the protein matrix: A study on a new myoglobin mutant Y(B10) Q(E7) R(E10). Biophys J (1999) 1.29

Unveiling functional protein motions with picosecond x-ray crystallography and molecular dynamics simulations. Proc Natl Acad Sci U S A (2004) 1.28

Mosaic energy landscapes of liquids and the control of protein conformational dynamics by glass-forming solvents. J Phys Chem B (2005) 1.24

Binding of xenon to sperm whale myoglobin. Nature (1965) 1.23

Reactive line-shape narrowing in low-temperature inhomogeneous geminate recombination of CO to myoglobin. Biochemistry (1988) 1.22

Time-dependent atomic coordinates for the dissociation of carbon monoxide from myoglobin. Acta Crystallogr D Biol Crystallogr (2006) 1.20

Hydration, slaving and protein function. Biophys Chem (2002) 1.17

Water penetration and binding to ferric myoglobin. Biochemistry (2001) 1.16

Kinetic, structural, and spectroscopic identification of geminate states of myoglobin: a ligand binding site on the reaction pathway. Biochemistry (1987) 1.13

Structural dynamics of myoglobin: effect of internal cavities on ligand migration and binding. Biochemistry (2003) 1.12

T state hemoglobin binds oxygen noncooperatively with allosteric effects of protons, inositol hexaphosphate, and chloride. J Biol Chem (1997) 1.12

Investigation of laser-induced long-lived states of photolyzed MbCO. Biochemistry (1991) 1.11

New insights into allosteric mechanisms from trapping unstable protein conformations in silica gels. Proc Natl Acad Sci U S A (2004) 1.11

Dynamics of proteins encapsulated in silica sol-gel glasses studied with IR vibrational echo spectroscopy. J Am Chem Soc (2006) 1.10

High and low oxygen affinity conformations of T state hemoglobin. Protein Sci (2001) 1.10

Sol-gel trapping of functional intermediates of hemoglobin: geminate and bimolecular recombination studies. Biochemistry (2000) 1.09

Ligand dynamics in a protein internal cavity. Proc Natl Acad Sci U S A (2003) 1.09

Competition with xenon elicits ligand migration and escape pathways in myoglobin. Biophys J (2004) 1.09

Controlling ligand binding in myoglobin by mutagenesis. J Biol Chem (2001) 1.08

A hierarchy of functionally important relaxations within myoglobin based on solvent effects, mutations and kinetic model. Biochim Biophys Acta (2005) 1.08

The influence of aqueous versus glassy solvents on protein dynamics: vibrational echo experiments and molecular dynamics simulations. J Am Chem Soc (2005) 1.07

Complexity in proteins. Nat Struct Biol (1995) 1.06

Beta 93 modified hemoglobin: kinetic and conformational consequences. Biochemistry (2001) 1.06

The position 68(E11) side chain in myoglobin regulates ligand capture, bond formation with heme iron, and internal movement into the xenon cavities. J Biol Chem (2005) 1.05

Structural dynamics of myoglobin: spectroscopic and structural characterization of ligand docking sites in myoglobin mutant L29W. Biochemistry (2003) 1.03

Spectroscopically and kinetically distinct conformational populations of sol-gel-encapsulated carbonmonoxy myoglobin. A comparison with hemoglobin. J Biol Chem (2002) 1.02

Internal dynamics and protein-matrix coupling in trehalose-coated proteins. Biochim Biophys Acta (2005) 1.01

Structural and functional significance of inhomogeneous line broadening of band III in hemoglobin and Fe-Mn hybrid hemoglobins. Biochemistry (1990) 1.01

Molecular dynamics simulation of carboxy-myoglobin embedded in a trehalose-water matrix. Biophys J (2001) 1.00

Myoglobin cavities provide interior ligand pathway. Protein Sci (2004) 1.00

The realization of sub-nanosecond pump and probe experiments at the ESRF. European Synchrotron Radiation Facility. Faraday Discuss (2003) 1.00

Dynamics of carbon monoxide binding by heme proteins. Science (1973) 1.00

Kinetic hole burning, hole filling, and conformational relaxation in heme proteins: direct evidence for the functional significance of a hierarchy of dynamical processes. Biochemistry (1997) 0.98

Modulation of reactivity and conformation within the T-quaternary state of human hemoglobin: the combined use of mutagenesis and sol-gel encapsulation. Biochemistry (2006) 0.98

Orientational distribution of CO before and after photolysis of MbCO and HbCO: a determination using time-resolved polarized Mid-IR spectroscopy. J Am Chem Soc (2004) 0.96

Spectroscopic and functional characterization of T state hemoglobin conformations encapsulated in silica gels. Biochemistry (2004) 0.93

Temperature dependent quaternary state relaxation in sol-gel encapsulated hemoglobin. Biospectroscopy (1999) 0.92

Ligand binding to heme proteins. V. Light-induced relaxation in proximal mutants L89I and H97F of carbonmonoxymyoglobin. Biophys J (1995) 0.92

Dehydration and crystallization of trehalose and sucrose glasses containing carbonmonoxy-myoglobin. Biophys J (1999) 0.91

Molecular dynamics simulation of sucrose- and trehalose-coated carboxy-myoglobin. Proteins (2005) 0.90

Evidence for two geminate rebinding states following laser photolysis of R state hemoglobin encapsulated in wet silica gels. J Phys Chem B (2005) 0.89

Role of solvent on protein-matrix coupling in MbCO embedded in water-saccharide systems: a Fourier transform infrared spectroscopy study. Biophys J (2006) 0.87

Determination of microscopic rate constants for CO binding and migration in myoglobin encapsulated in silica gels. J Phys Chem B (2005) 0.87

Structural dynamics of myoglobin: an infrared kinetic study of ligand migration in mutants YQR and YQRF. Biophys Chem (2004) 0.86

Geminate rebinding in trehalose-glass embedded myoglobins reveals residue-specific control of intramolecular trajectories. J Mol Biol (2002) 0.86

Functional characterization of heme proteins encapsulated in wet nanoporous silica gels. J Nanosci Nanotechnol (2001) 0.86

Oxygen equilibrium properties of myoglobin locked in the liganded and unliganded conformations. J Am Chem Soc (2003) 0.84

The transition from inhomogeneous to homogeneous kinetics in CO binding to myoglobin. Biophys J (1994) 0.84

Geminate rebinding in R-state hemoglobin: kinetic and computational evidence for multiple hydrophobic pockets. J Am Chem Soc (2005) 0.83

Kinetic modulation in carbonmonoxy derivatives of truncated hemoglobins: the role of distal heme pocket residues and extended apolar tunnel. J Biol Chem (2003) 0.83

Viscosity-dependent relaxation significantly modulates the kinetics of CO recombination in the truncated hemoglobin TrHbN from Mycobacterium tuberculosis. J Biol Chem (2004) 0.82

Light-induced protein-matrix uncoupling and protein relaxation in dry samples of trehalose-coated MbCO at room temperature. Cell Biochem Biophys (2005) 0.81

Ultrafast time-resolved IR studies of protein-ligand interactions. Methods Mol Biol (2005) 0.76

Articles by these authors

Antimicrobial and healing efficacy of sustained release nitric oxide nanoparticles against Staphylococcus aureus skin infection. J Invest Dermatol (2009) 2.16

Sustained release nitric oxide from long-lived circulating nanoparticles. Free Radic Biol Med (2010) 1.71

Susceptibility of Gram-positive and -negative bacteria to novel nitric oxide-releasing nanoparticle technology. Virulence (2011) 1.63

Sustained release nitric oxide releasing nanoparticles: characterization of a novel delivery platform based on nitrite containing hydrogel/glass composites. Nitric Oxide (2008) 1.50

The use of nitric oxide releasing nanoparticles as a treatment against Acinetobacter baumannii in wound infections. Virulence (2010) 1.18

Nitric oxide releasing nanoparticles are therapeutic for Staphylococcus aureus abscesses in a murine model of infection. PLoS One (2009) 1.11

A hierarchy of functionally important relaxations within myoglobin based on solvent effects, mutations and kinetic model. Biochim Biophys Acta (2005) 1.08

Demonstration of antibiofilm and antifungal efficacy of chitosan against candidal biofilms, using an in vivo central venous catheter model. J Infect Dis (2010) 1.06

The position 68(E11) side chain in myoglobin regulates ligand capture, bond formation with heme iron, and internal movement into the xenon cavities. J Biol Chem (2005) 1.05

A pathway of structural changes produced by monastrol binding to Eg5. J Biol Chem (2006) 1.04

Oral ectomesenchymal chondromyxoid tumor: case report and literature review. Oral Surg Oral Med Oral Pathol Oral Radiol Endod (2009) 1.04

Nitric oxide-releasing nanoparticles accelerate wound healing by promoting fibroblast migration and collagen deposition. Am J Pathol (2012) 1.03

Reversal of hemoglobin-induced vasoconstriction with sustained release of nitric oxide. Am J Physiol Heart Circ Physiol (2010) 1.02

Spectroscopically and kinetically distinct conformational populations of sol-gel-encapsulated carbonmonoxy myoglobin. A comparison with hemoglobin. J Biol Chem (2002) 1.02

Conjugation of multiple copies of polyethylene glycol to hemoglobin facilitated through thiolation: influence on hemoglobin structure and function. Protein J (2005) 1.01

Nitrite reductase activity of sol-gel-encapsulated deoxyhemoglobin. Influence of quaternary and tertiary structure. J Biol Chem (2006) 1.01

Modulation of reactivity and conformation within the T-quaternary state of human hemoglobin: the combined use of mutagenesis and sol-gel encapsulation. Biochemistry (2006) 0.98

Structural bases for heme binding and diatomic ligand recognition in truncated hemoglobins. J Inorg Biochem (2005) 0.97

Reactions of Mycobacterium tuberculosis truncated hemoglobin O with ligands reveal a novel ligand-inclusive hydrogen bond network. Biochemistry (2003) 0.94

Reactivity of glass-embedded met hemoglobin derivatives toward external NO: implications for nitrite-mediated production of bioactive NO. J Am Chem Soc (2009) 0.94

Conformational dependence of hemoglobin reactivity under high viscosity conditions: the role of solvent slaved dynamics. J Am Chem Soc (2007) 0.94

Spectroscopic and functional characterization of T state hemoglobin conformations encapsulated in silica gels. Biochemistry (2004) 0.93

The use of chitosan to damage Cryptococcus neoformans biofilms. Biomaterials (2009) 0.93

Nitric oxide-releasing nanoparticles accelerate wound healing in NOD-SCID mice. Nanomedicine (2012) 0.92

Exogenous nitric oxide prevents cardiovascular collapse during hemorrhagic shock. Resuscitation (2011) 0.91

Sugar-derived glasses support thermal and photo-initiated electron transfer processes over macroscopic distances. J Biol Chem (2006) 0.89

Trehalose glass-facilitated thermal reduction of metmyoglobin and methemoglobin. J Am Chem Soc (2002) 0.89

HBOC vasoactivity: interplay between nitric oxide scavenging and capacity to generate bioactive nitric oxide species. Antioxid Redox Signal (2013) 0.89

NO reactions with sol-gel and solution phase samples of the ferric nitrite derivative of HbA. Nitric Oxide (2009) 0.89

Enhanced molecular volume of conservatively pegylated Hb: (SP-PEG5K)6-HbA is non-hypertensive. Artif Cells Blood Substit Immobil Biotechnol (2005) 0.89

Functional and spectroscopic characterization of half-liganded iron-zinc hybrid hemoglobin: evidence for conformational plasticity within the T state. Biochemistry (2003) 0.87

Geminate rebinding in trehalose-glass embedded myoglobins reveals residue-specific control of intramolecular trajectories. J Mol Biol (2002) 0.86

Glass matrix-facilitated thermal reduction: a tool for probing reactions of met hemoglobin with nitrite and nitric oxide. J Phys Chem B (2010) 0.85

UV resonance Raman study of beta93-modified hemoglobin A: chemical modifier-specific effects and added influences of attached poly(ethylene glycol) chains. Biochemistry (2002) 0.85

Binding and release of iron by gel-encapsulated human transferrin: evidence for a conformational search. Proc Natl Acad Sci U S A (2002) 0.84

Domain-specific effector interactions within the central cavity of human adult hemoglobin in solution and in porous sol-gel matrices: evidence for long-range communication pathways. Biochemistry (2004) 0.84

The hemoglobins of the sub-Antarctic fish Cottoperca gobio, a phyletically basal species--oxygen-binding equilibria, kinetics and molecular dynamics. FEBS J (2009) 0.84

Osmolyte-induced perturbations of hydrogen bonding between hydration layer waters: correlation with protein conformational changes. J Phys Chem B (2009) 0.84

The absence of proximal strain in the truncated hemoglobins from Mycobacterium tuberculosis. J Am Chem Soc (2004) 0.84

Structural and functional studies indicating altered redox properties of hemoglobin E: implications for production of bioactive nitric oxide. J Biol Chem (2011) 0.83

Semihemoglobins, high oxygen affinity dimeric forms of human hemoglobin respond efficiently to allosteric effectors without forming tetramers. J Biol Chem (2004) 0.83

Improved antimicrobial efficacy with nitric oxide releasing nanoparticle generated S-nitrosoglutathione. Nitric Oxide (2011) 0.83

Molecular level probing of preferential hydration and its modulation by osmolytes through the use of pyranine complexed to hemoglobin. J Biol Chem (2006) 0.83

Kinetic modulation in carbonmonoxy derivatives of truncated hemoglobins: the role of distal heme pocket residues and extended apolar tunnel. J Biol Chem (2003) 0.83

Enhanced nitrite reductase activity associated with the haptoglobin complexed hemoglobin dimer: functional and antioxidative implications. Nitric Oxide (2012) 0.83

Generating S-nitrosothiols from hemoglobin: mechanisms, conformational dependence, and physiological relevance. J Biol Chem (2013) 0.82

Nitric oxide nanoparticles: pre-clinical utility as a therapeutic for intramuscular abscesses. Virulence (2012) 0.82

Viscosity-dependent relaxation significantly modulates the kinetics of CO recombination in the truncated hemoglobin TrHbN from Mycobacterium tuberculosis. J Biol Chem (2004) 0.82

Probing the conformation of hemoglobin presbyterian in the R-state. J Protein Chem (2003) 0.81

A nanoparticle delivery vehicle for S-nitroso-N-acetyl cysteine: sustained vascular response. Nitric Oxide (2012) 0.81

Ligand binding to truncated hemoglobin N from Mycobacterium tuberculosis is strongly modulated by the interplay between the distal heme pocket residues and internal water. J Biol Chem (2008) 0.81

Nitric oxide releasing nanoparticle synthesis and characterization. Methods Mol Biol (2011) 0.81

Proximal ligand motions in H93G myoglobin. Eur J Biochem (2002) 0.80

Intersubunit interactions associated with Tyr42 alpha stabilize the quaternary-T tetramer but are not major quaternary constraints in deoxyhemoglobin. Biochemistry (2005) 0.80

Distal heme pocket conformers of carbonmonoxy derivatives of Ascaris hemoglobin: evidence of conformational trapping in porous sol-gel matrices. J Biol Chem (2003) 0.79

Multiple active site conformers in the carbon monoxide complexes of trematode hemoglobins. J Biol Chem (2006) 0.79

Nitrosoglutathione generating nitric oxide nanoparticles as an improved strategy for combating Pseudomonas aeruginosa-infected wounds. J Drugs Dermatol (2012) 0.77

Charge density-dependent modifications of hydration shell waters by Hofmeister ions. J Am Chem Soc (2009) 0.77

Combining the influence of two low O2 affinity-inducing chemical modifications of the central cavity of hemoglobin. Biochemistry (2007) 0.77

Conformational changes in hemoglobin S (betaE6V) imposed by mutation of the beta Glu7-beta Lys132 salt bridge and detected by UV resonance Raman spectroscopy. J Biol Chem (2002) 0.77

Proteins in motion: resonance Raman spectroscopy as a probe of functional intermediates. Methods Mol Biol (2005) 0.77

Rationale for early versus late intervention with arthroscopy for treatment of inflammatory/degenerative temporomandibular joint disorders. J Oral Maxillofac Surg (2010) 0.76

Localized increase of tissue oxygen tension by magnetic targeted drug delivery. Nanotechnology (2014) 0.76

Posttransfusion Increase of Hematocrit per se Does Not Improve Circulatory Oxygen Delivery due to Increased Blood Viscosity. Anesth Analg (2017) 0.76

Similar experience. N Y State Dent J (2010) 0.75

Dilate, dilute, constrict, or else in treating hemorrhage? Crit Care Med (2011) 0.75

Reverse micelles as a tool for probing solvent modulation of protein dynamics: Reverse micelle encapsulated hemoglobin. Chem Phys (2013) 0.75

A conversation with NYSDA President Joel M. Friedman, D.D.S. N Y State Dent J (2013) 0.75

Cavernous sinus thrombosis secondary to fracture of posterior maxillary sinus wall. Case report. N Y State Dent J (2009) 0.75