Skip to main content
OSTI.GOVU.S. Department of Energy Office of Scientific and Technical Information
U.S. Department of Energy
Office of Scientific and Technical Information
 

Dynamic void distribution in myoglobin and five mutants

Journal Article · · Scientific Reports
DOI:https://doi.org/10.1038/srep04011· OSTI ID:1624688
 [1];  [2];  [3]
  1. Univ. of Texas, Austin, TX (United States). Dept. of Chemical Engineering; DOE/OSTI
  2. Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
  3. Univ. of Texas, Austin, TX (United States). Dept. of Chemical Engineering
+ Show Author Affiliations
Globular proteins contain cavities/voids that play specific roles in controlling protein function. Elongated cavities provide migration channels for the transport of ions and small molecules to the active center of a protein or enzyme. Using Monte Carlo and Molecular Dynamics on fully atomistic protein/water models, a new computational methodology is introduced that takes into account the protein’s dynamic structure and maps all the cavities in and on the surface. To demonstrate its utility, the methodology is applied to study cavity structure in myoglobin and five of its mutants. Computed cavity and channel size distributions reveal significant differences relative to the wild type myoglobin. Computer visualization of the channels leading to the heme center indicates restricted ligand access for the mutants consistent with the existing interpretations. The new methodology provides a quantitative measure of cavity structure and distributions and can become a valuable tool for the structural characterization of proteins.
Research Organization:
Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)
Sponsoring Organization:
USDOE Office of Science (SC), Basic Energy Sciences (BES). Chemical Sciences, Geosciences & Biosciences Division
OSTI ID:
1624688
Journal Information:
Scientific Reports, Journal Name: Scientific Reports Journal Issue: 1 Vol. 4; ISSN 2045-2322
Publisher:
Nature Publishing GroupCopyright Statement
Country of Publication:
United States
Language:
English

References (48)

Accessibility to internal cavities and ligand binding sites monitored by protein crystallographic thermal factors journal May 1998
Analytical shape computation of macromolecules: I. molecular area and volume through alpha shape journal October 1998
Application of molecular dynamics and free energy perturbation methods to metalloporphyrin-ligand systems ii: Co and dioxygen binding to myoglobin journal November 1993
The interpretation of protein structures: Estimation of static accessibility journal February 1971
Structure of myoglobin-ethyl isocyanide histidine as a swinging door for ligand entry journal May 1989
Revisiting and parallelizing SHAKE journal October 2005
Oxidation of nitrogen oxides by bound dioxygen in hemoproteins journal January 1981
Reaction of myoglobin with phenylhydrazine: a molecular doorstop journal January 1984
Cavities in proteins: structure of a metmyoglobin xenon complex solved to 1.9 .ANG. journal June 1984
Ligand Migration in Sperm Whale Myoglobin † journal September 1997
MOIL-opt: Energy-Conserving Molecular Dynamics on a GPU/CPU System journal August 2011
Enhanced sampling in molecular dynamics: use of the time-dependent Hartree approximation for a simulation of carbon monoxide diffusion through myoglobin journal December 1990
The Escape Process of Carbon Monoxide from Myoglobin to Solution at Physiological Temperature journal September 2004
Mapping the Network of Pathways of CO Diffusion in Myoglobin journal December 2009
Molecular Dynamics Study on the Solvent Dependent Heme Cooling Following Ligand Photolysis in Carbonmonoxy Myoglobin journal March 2007
Toward Quantitative Simulations of Carbon Monoxide Escape Pathways in Myoglobin † journal May 2008
The role of the distal histidine in myoglobin and haemoglobin journal November 1988
Discovery of new ligand binding pathways in myoglobin by random mutagenesis journal April 1994
Diffusive dynamics on multidimensional rough free energy surfaces journal October 2007
Atomic level computational identification of ligand migration pathways between solvent and binding site in myoglobin journal July 2008
Mapping the Pathways for O 2 Entry Into and Exit from Myoglobin journal October 2000
Ligand pathways in myoglobin: A review of trp cavity mutations journal January 2007
Efficient molecular surface rendering by linear-time pseudo-Gaussian approximation to Lee–Richards surfaces ( PGALRS ) journal February 2010
‘It's hollow’: the function of pores within myoglobin journal August 2010
Extended Molecular Dynamics Simulation of the Carbon Monoxide Migration in Sperm Whale Myoglobin journal June 2004
Accessibility to internal cavities and ligand binding sites monitored by protein crystallographic thermal factors journal May 1998
Analytical shape computation of macromolecules: I. molecular area and volume through alpha shape journal October 1998
Computation of Lattice Sums: Generalization of the Ewald Method journal March 1965
The interpretation of protein structures: Estimation of static accessibility journal February 1971
Solvent accessible surface area and excluded volume in proteins journal September 1984
Discrimination between Oxygen and Carbon Monoxide and Inhibition of Autooxidation by Myoglobin journal February 1989
Oxidation of nitrogen oxides by bound dioxygen in hemoproteins journal January 1981
Cavity size distribution in the interior of globular proteins journal February 2007
A search for ligand diffusion pathway in myoglobin using a metadynamics simulation journal October 2008
Elucidation of Rate Variations for a Diels−Alder Reaction in Ionic Liquids from QM/MM Simulations journal November 2006
Elucidation of Hydrolysis Mechanisms for Fatty Acid Amide Hydrolase and Its Lys142Ala Variant via QM/MM Simulations journal December 2006
Liquid Structure via Cavity Size Distributions journal November 2000
Computational Exploration of Mobile Ion Distributions around RNA Duplex journal June 2010
A smooth, nonsingular, and faithful discretization scheme for polarizable continuum models: The switching/Gaussian approach journal December 2010
Comparison of simple potential functions for simulating liquid water journal July 1983
Ligand migration pathway and protein dynamics in myoglobin: A time-resolved crystallographic study on L29W MbCO journal August 2005
Mapping the Pathways for O 2 Entry Into and Exit from Myoglobin journal October 2000
Cavities and packing defects in the structural dynamics of myoglobin journal August 2001
Efficient molecular surface rendering by linear-time pseudo-Gaussian approximation to Lee–Richards surfaces ( PGALRS ) journal February 2010
Analytical molecular surface calculation journal October 1983
Average protein density is a molecular-weight-dependent function journal October 2004
Ligand diffusion in the catalase from Proteus mirabilis : A molecular dynamics study journal October 2001
Imaging the Migration Pathways for O2, CO, NO, and Xe Inside Myoglobin journal September 2006

Cited By (1)

Ultrathin Graphene-Protein Supercapacitors for Miniaturized Bioelectronics journal May 2017

Similar Records

Trans effects in nitric oxide binding to myoglobin cavity mutant H93G
Journal Article · Tue Apr 16 00:00:00 EDT 1996 · Biochemistry (Eaton) · OSTI ID:508406
Ligand binding and proton exchange dynamics in site-specific mutants of human myoglobin
Thesis/Dissertation · Tue Dec 31 23:00:00 EST 1991 · OSTI ID:7233884
Amphitrite ornata Dehaloperoxidase (DHP): Investigations of Structural Factors That Influence the Mechanism of Halophenol Dehalogenation Using ;Peroxidase-like; Myoglobin Mutants and ;Myoglobin-like; DHP Mutants
Journal Article · Mon May 14 00:00:00 EDT 2012 · Biochemistry-US · OSTI ID:1032656

Related Subjects

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY
Computational biophysics
Computational chemistry
Science & technology - other topics