Atomic level computational identification of ligand migration pathways between solvent and binding site in myoglobin

scientific article

Atomic level computational identification of ligand migration pathways between solvent and binding site in myoglobin is …
instance of (P31):
scholarly articleQ13442814

External links are
P819ADS bibcode2008PNAS..105.9204R
P356DOI10.1073/PNAS.0710825105
P932PMC publication ID2453746
P698PubMed publication ID18599444
P5875ResearchGate publication ID5252836

P2093author name stringT M Murali
Alexey V Onufriev
Jory Z Ruscio
Maulik Shukla
Michael G Prisant
Deept Kumar
P2860cites workCrystal structures of myoglobin-ligand complexes at near-atomic resolutionQ27619924
Structure of a ligand-binding intermediate in wild-type carbonmonoxy myoglobinQ27621686
Ligand binding and conformational motions in myoglobinQ27621799
Complex landscape of protein structural dynamics unveiled by nanosecond Laue crystallographyQ27641645
Structural and functional effects of apolar mutations of the distal valine in myoglobinQ27730347
Crystal structure of photolysed carbonmonoxy-myoglobinQ27730727
Diffractive optics-based heterodyne-detected four-wave mixing signals of protein motion: from "protein quakes" to ligand escape for myoglobin.Q30328193
Myoglobin cavities provide interior ligand pathway.Q30336343
Cavities in proteins: structure of a metmyoglobin-xenon complex solved to 1.9 A.Q30412998
Discovery of new ligand binding pathways in myoglobin by random mutagenesisQ30417694
Imaging the migration pathways for O2, CO, NO, and Xe inside myoglobinQ30477827
Unveiling functional protein motions with picosecond x-ray crystallography and molecular dynamics simulationsQ30834929
Competition with xenon elicits ligand migration and escape pathways in myoglobin.Q31034382
Myoglobin: the hydrogen atom of biology and a paradigm of complexityQ31149692
Human myoglobin recognition of oxygen: dynamics of the energy landscapeQ33583265
Photolysis of the carbon monoxide complex of myoglobin: nanosecond time-resolved crystallography.Q34408873
Extended molecular dynamics simulation of the carbon monoxide migration in sperm whale myoglobinQ40285392
Kinetic pathways and barriers for ligand binding to myoglobinQ41027258
Cavities and packing defects in the structural dynamics of myoglobinQ41954505
Molecular dynamics simulation of sperm whale myoglobin: effects of mutations and trapped CO on the structure and dynamics of cavitiesQ42250847
Mapping the pathways for O2 entry into and exit from myoglobin.Q43507874
Discrimination between oxygen and carbon monoxide and inhibition of autooxidation by myoglobin. Site-directed mutagenesis of the distal histidineQ44319082
Watching a protein as it functions with 150-ps time-resolved x-ray crystallographyQ44484615
Ligand binding to a hemoprotein lacking the distal histidine. The myoglobin from aplysia limacina (Val(E7)).Q46960997
Dynamics of carbon monoxide binding by heme proteinsQ47983167
The escape process of carbon monoxide from myoglobin to solution at physiological temperature.Q48843848
Neutron diffraction study of carbonmonoxymyoglobinQ52445691
Internal cavities and buried waters in globular proteins.Q52638970
Structure of alkaline metmyoglobin-xenon complex.Q52745138
Reaction of myoglobin with phenylhydrazine: a molecular doorstop.Q53872053
The role of the distal histidine in myoglobin and haemoglobin.Q54738832
Structure of myoglobin-ethyl isocyanide histidine as a swinging door for ligand entryQ59599947
Dynamics of ligand binding to heme proteinsQ66990363
The role of Val68(E11) in ligand binding to sperm whale myoglobin. Site-directed mutagenesis of a synthetic geneQ68340357
Geminate recombination of carbon monoxide to myoglobinQ71743864
Binding of CO to myoglobin from a heme pocket docking site to form nearly linear Fe-C-OQ71967826
An x-ray study of azide methaemoglobinQ72922745
Ultrafast rotation and trapping of carbon monoxide dissociated from myoglobinQ73369166
P433issue27
P407language of work or nameEnglishQ1860
P1104number of pages6
P304page(s)9204-9209
P577publication date2008-07-01
P1433published inProceedings of the National Academy of Sciences of the United States of AmericaQ1146531
P1476titleAtomic level computational identification of ligand migration pathways between solvent and binding site in myoglobin
P478volume105

Reverse relations

cites work (P2860)
Q36682347A computational study of water and CO migration sites and channels inside myoglobin
Q51591347A microscopic model for gas diffusion dynamics in a [NiFe]-hydrogenase.
Q41845213Accelerating electrostatic surface potential calculation with multi-scale approximation on graphics processing units
Q41969002Alkyl isocyanides serve as transition state analogues for ligand entry and exit in myoglobin
Q42921248An N log N approximation based on the natural organization of biomolecules for speeding up the computation of long range interactions
Q41384613An atomistic view on human hemoglobin carbon monoxide migration processes.
Q44202923Binding pockets and pathways for dioxygen through the KijD3 N-oxygenase in complex with flavin mononucleotide cofactor and a 3-aminoglucose substrate: predictions from molecular dynamics simulations
Q28658133Biophysical highlights from 54 years of macromolecular crystallography
Q27666414Blocking the Gate to Ligand Entry in Human Hemoglobin
Q42279084Computational investigation of O2 diffusion through an intra-molecular tunnel in AlkB; influence of polarization on O2 transport.
Q35881942Cooperativity in Binding Processes: New Insights from Phenomenological Modeling
Q30525332Determination of ligand pathways in globins: apolar tunnels versus polar gates
Q37559672Dynamic void distribution in myoglobin and five mutants
Q84629348Dynamics comparison of two myoglobins with a distinct heme active site
Q36342813Exploration of gated ligand binding recognizes an allosteric site for blocking FABP4-protein interaction
Q30381624Finding molecular dioxygen tunnels in homoprotocatechuate 2,3-dioxygenase: implications for different reactivity of identical subunits.
Q50899059From dioxygen storing to dioxygen sensing with neuroglobins: an insight from molecular mechanics.
Q33901963Full kinetics of CO entry, internal diffusion, and exit in myoglobin from transition-path theory simulations
Q30575954Functional consequences of the open distal pocket of dehaloperoxidase-hemoglobin observed by time-resolved X-ray crystallography
Q30536931Hydrophobic effect drives oxygen uptake in myoglobin via histidine E7
Q60490600Identification of Mutational Hot Spots for Substrate Diffusion: Application to Myoglobin
Q30403204Influence of histidine tag attachment on picosecond protein dynamics.
Q30574665Internal water and microsecond dynamics in myoglobin
Q46068436Kinetics and thermodynamics of gas diffusion in a NiFe hydrogenase
Q90145807Lessons Learned from 50 Years of Hemoglobin Research: Unstirred and Cell-Free Layers, Electrostatics, Baseball Gloves, and Molten Globules
Q36599471Ligand and interfacial dynamics in a homodimeric hemoglobin
Q37684289Ligand diffusion in globins: simulations versus experiment
Q52884878Ligand discrimination of myoglobin in solution: an iron L-edge X-ray absorption study of the active centre.
Q35921991Mechanistic insight into the blocking of CO diffusion in [NiFe]-hydrogenase mutants through multiscale simulation.
Q89673230Menthol Binding to the Human α4β2 Nicotinic Acetylcholine Receptor Facilitated by Its Strong Partitioning in the Membrane
Q51590304Microscopic Characterization of Membrane Transporter Function by In Silico Modeling and Simulation.
Q36164522Migration of PIP2 lipids on voltage-gated potassium channel surface influences channel deactivation
Q47617911Migration of PIP2 on KCNQ2 Surface Revealed by Molecular Dynamics Simulations
Q38256073Modulating distal cavities in the α and β subunits of human HbA reveals the primary ligand migration pathway
Q43017615Molecular dynamics study of hell's gate globin I (HGbI) from a methanotrophic extremophile: oxygen migration through a large cavity
Q41908232Multiphoton absorption of myoglobin-nitric oxide complex: relaxation by D-NEMD of a stationary state
Q53387642On the Quest of Dioxygen by Monomeric Sarcosine Oxidase. A Molecular Dynamics Investigation.
Q45265253On the pathways for CO egress from carboxy human cytoglobin. A molecular-dynamics investigation
Q33893619Oxygen Pathways and Allostery in Monomeric Sarcosine Oxidase via Single-Sweep Free-Energy Reconstruction
Q36201131Oxygen diffusion pathways in a cofactor-independent dioxygenase.
Q39050030Partially Assembled Nucleosome Structures at Atomic Detail
Q40071793Protein collective motions coupled to ligand migration in myoglobin
Q35679040Quantifying the importance of protein conformation on ligand migration in myoglobin
Q41489269Quantitative delineation of how breathing motions open ligand migration channels in myoglobin and its mutants
Q35016350Relating diffusion along the substrate tunnel and oxygen sensitivity in hydrogenase.
Q41065604Restoring histone deacetylase activity by waste product release. A view from molecular mechanics simulations with mammalian HDAC8.
Q28656517Straight-chain alkyl isocyanides open the distal histidine gate in crystal structures of myoglobin
Q41633843The cellular membrane as a mediator for small molecule interaction with membrane proteins
Q37842302The quest for a functional substrate access tunnel in FeFe hydrogenase.
Q41904946Theoretical investigations of nitric oxide channeling in Mycobacterium tuberculosis truncated hemoglobin N.
Q35682384Two-dimensional IR spectroscopy of protein dynamics using two vibrational labels: a site-specific genetically encoded unnatural amino acid and an active site ligand
Q48178136Understanding How H-NOX (Heme Nitric Oxide/Oxygen) domain works needs first clarifying how diatomic gases are relocated inside this sensing protein. A molecular-mechanics approach
Q37124752pH-dependent mechanism of nitric oxide release in nitrophorins 2 and 4

Search more.