ArticleBiophysical journal2004
Extended molecular dynamics simulation of the carbon monoxide migration in sperm whale myoglobin.
Article in Biophysical journal, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
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39 citing papers in PubMed, 137 citations in OpenAlex.
- Are Protein Cavities and Pockets Commonly Used by Redox Active Signalling Molecules?Plants (Basel, Switzerland) · 2023Review
- Dynamic multiple-scattering treatment of X-ray absorption: Parameterization of a new molecular dynamics force field for myoglobin.Structural dynamics (Melville, N.Y.) · 2018Article
- Dynamic features of carboxy cytoglobin distal mutants investigated by molecular dynamics simulations.Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry · 2016Article
- Identification of Mutational Hot Spots for Substrate Diffusion: Application to Myoglobin.Journal of chemical theory and computation · 2015Article
- Full kinetics of CO entry, internal diffusion, and exit in myoglobin from transition-path theory simulations.Journal of the American Chemical Society · 2015Article
- Article
- Implementing electrostatic polarization cannot fill the gap between experimental and theoretical measurements for the ultrafast fluorescence decay of myoglobin.Journal of molecular modeling · 2014Article
- Dynamic void distribution in myoglobin and five mutants.Scientific reports · 2014Article
- Effects of distal mutation on the dynamic properties of carboxycytoglobin: a molecular dynamics simulation study.Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry · 2013Article
- Molecular dynamics study of hell's gate globin I (HGbI) from a methanotrophic extremophile: oxygen migration through a large cavity.Journal of molecular modeling · 2013Article
- Hydrophobic effect drives oxygen uptake in myoglobin via histidine E7.The Journal of biological chemistry · 2013Article
- Exploring the diffusion of molecular oxygen in the red fluorescent protein mCherry using explicit oxygen molecular dynamics simulations.The journal of physical chemistry. B · 2013Article
- A computational study of water and CO migration sites and channels inside myoglobin.Journal of chemical theory and computation · 2013Article
- Heme orientation modulates histidine dissociation and ligand binding kinetics in the hexacoordinated human neuroglobin.Journal of biological inorganic chemistry : JBIC : a publication of the Society of Biological Inorganic Chemistry · 2013Article
- An atomistic view on human hemoglobin carbon monoxide migration processes.Biophysical journal · 2012Article
- Quantifying the importance of protein conformation on ligand migration in myoglobin.Biophysical journal · 2012Article
- Fluorescent protein barrel fluctuations and oxygen diffusion pathways in mCherry.The Journal of chemical physics · 2011Article
- Role of the distal hydrogen-bonding network in regulating oxygen affinity in the truncated hemoglobin III from Campylobacter jejuni.Biochemistry · 2011Article
- Blocking the gate to ligand entry in human hemoglobin.The Journal of biological chemistry · 2011Article
- Protein collective motions coupled to ligand migration in myoglobin.Biophysical journal · 2010Article
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Authors and funding
7 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We report the results of an extended molecular dynamics simulation on the migration of photodissociated carbon monoxide in wild-type sperm whale myoglobin. Our results allow following one possible ligand migration dynamics from the distal pocket to the Xe1 cavity via a path involving the other xenon binding cavities and momentarily two additional packing defects along the pathway. Comparison with recent time resolved structural data obtained by Laue crystallography with subnanosecond to millisecond resolution shows a more than satisfactory agreement. In fact, according to time resolved crystallography, CO, after photolysis, can occupy the Xe1 and Xe4 cavities. However, no information on the trajectory of the ligand from the distal pocket to the Xe1 is available. Our results clearly show one possible path within the protein. In addition, although our data refer to a single trajectory, the local dynamics of the ligand in each cavity is sufficiently equilibrated to obtain local structural and thermodynamic information not accessible to crystallography. In particular, we show that the CO motion and the protein fluctuations are strictly correlated: free energy calculations of the migration between adjacent cavities show that the migration is not a simple diffusion but is kinetically or thermodynamically driven by the collective motions of the protein; conversely, the protein fluctuations are influenced by the ligand in such a way that the opening/closure of the passage between adjacent cavities is strictly correlated to the presence of CO in its proximity. The compatibility between time resolved crystallographic experiments and molecular dynamics simulations paves the way to a deeper understanding of the role of internal dynamics and packing defects in the control of ligand binding in heme proteins.
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