A one-dimensional reaction coordinate for identification of transition states from explicit solvent P(fold)-like calculations.

A one-dimensional reaction coordinate for identification of transition states from explicit solvent P(fold)-like calculations. Research Abstract Details 

Research Abstract Table of Contents

Jump to the:

A one-dimensional reaction coordinate for identification of transition states from explicit solvent P(fold)-like calculations. Abstract Text:

David A C Beck,Valerie Daggett,David A C Beck,Valerie Daggett,

A properly identified transition state ensemble (TSE) in a molecular dynamics (MD) simulation can reveal a tremendous amount about how a protein folds and offer a point of comparison to experimentally derived Phi(F) values, which reflect the degree of structure in these transient states. In one such method of TSE identification, dubbed P(fold), MD simulations of individual protein structures taken from an unfolding trajectory are used to directly assess an input structure's probability of folding before unfolding, and P(fold) is, by definition, 0.5 for the TSE. Other, less computationally intensive methods, such as multidimensional scaling (MDS) of the pairwise root mean-squared deviation (RMSD) matrix of the conformations sampled in a thermal unfolding trajectory, have also been used to identify the TSE. Identification of the TSE is made from the original MD simulation without the need to run further simulations. Here we present a P(fold)-like study and describe methods for identification of the TSE through the derivation of a high fidelity, bounded, one-dimensional reaction coordinate for protein folding. These methods are applied to the engrailed homeodomain. The TSE identified by this approach is essentially identical to the TSE identified previously by MDS of the pairwise RMSD matrix. However, the cost of performing P(fold), or even our reduced P(fold)-like calculations, is at least 36,000 times greater than the MDS method.

A one-dimensional reaction coordinate for identification of transition states from explicit solvent P(fold)-like calculations. Publishing Authors By Initials

DA Beck,V Daggett,DA Beck,V Daggett,

For similar abstracts research abstracts see: abstracts research

PUBMED ID PMID:

MEDLINE DATE:

A one-dimensional reaction coordinate for identification of transition states from explicit solvent P(fold)-like calculations. Journal Published:

PUBLICATION TYPE: Research Support, N.I.H., Extr

Journal: Biophysical journal

VOLUME: 93

Page Numbers: 3382-91

Journal Abbreviation: Biophys. J.

ISSN: 0006-3495

DAY: 15

MONTH: Nov

YEAR: 2007

A one-dimensional reaction coordinate for identification of transition states from explicit solvent P(fold)-like calculations. Information

Number of References:

LANGUAGE: eng

NlmUniqueID: 370626

A one-dimensional reaction coordinate for identification of transition states from explicit solvent P(fold)-like calculations. Keywords Mesh Terms:

KEYWORDS:

MESH TERMS:

Chemical & Substance for Abstract: A one-dimensional reaction coordinate for identification of transition states from explicit solvent P(fold)-like calculations. Information

Substance Name:

Registry Number:

Grant and Affiliation Information for A one-dimensional reaction coordinate for identification of transition states from explicit solvent P(fold)-like calculations.

AFFILIATION: Department of Bioengineering, University of Washington, Seattle, Washington 98195-5061, USA.

Country: United States

AGENCY: United States NIGMS

GRANT: T32 GM 08268

ACRONYM: GM

MEDLINETA: Biophys J

REFSOURCE:

DATABASENAME:

ACCESSION NUMBER:

Number Hits: 0

A one-dimensional reaction coordinate for identification of transition states from explicit solvent Pfold-like calculations Related Publications

• A one-dimensional reaction coordinate for identification of transition states from explicit solvent P(fold)-like calculations.
• A rubric for grading or editing student papers.
• Combining experiment and simulation in protein folding: closing the gap for small model systems.
• Conformational Changes below the T(m): Molecular Dynamics Studies of the Thermal Pretransition of Ribonuclease A.
• Conformational entropy of alanine versus glycine in protein denatured states.
• Coronary, ventricular, and pulmonary abnormalities associated with rupture of the interventricular septum complicating myocardial infarction.
• Different disease-causing mutations in transthyretin trigger the same conformational conversion.
• Direct observation of microscopic reversibility in single-molecule protein folding.
• Dynameomics: a multi-dimensional analysis-optimized database for dynamic protein data.
• Dynameomics: design of a computational lab workflow and scientific data repository for protein simulations.
• Dynameomics: mass annotation of protein dynamics and unfolding in water by high-throughput atomistic molecular dynamics simulations.
• Exploring the energy landscape of protein folding using replica-exchange and conventional molecular dynamics simulations.
• Folding mechanisms of proteins with high sequence identity but different folds.
• Formation of Ice-like Water Structure on the Surface of an Antifreeze Protein.
• Four human thiopurine s-methyltransferase alleles severely affect protein structure and dynamics.
• Microscopic reversibility of protein folding in molecular dynamics simulations of the engrailed homeodomain.
• Molecular Basis for the Structural Instability of Human DJ-1 Induced by the L166P Mutation Associated with Parkinson's Disease.
• Molecular mechanism for low pH triggered misfolding of the human prion protein.
• Non-Hodgkin's lymphoma of thyroid.
• Protein folding-simulation.
• Side-Chain Dynamics Are Critical for Water Permeation through Aquaporin-1.
• Simulations of macromolecules in protective and denaturing osmolytes: properties of mixed solvent systems and their effects on water and protein structure and dynamics.
• Structural properties of prion protein protofibrils and fibrils: an experimental assessment of atomic models.
• Surgical management of postinfarction ventricular septal rupture.
• The Histamine N-Methyltransferase T105I Polymorphism Affects Active Site Structure and Dynamics.
• The intrinsic conformational propensities of the 20 naturally occurring amino acids and reflection of these propensities in proteins.
• Transposition of Three Amino Acids Transforms the Human Metabotropic Glutamate Receptor (mGluR)-3-Positive Allosteric Modulation Site to mGluR2, and Additional Characterization of the mGluR2-Positive Allosteric Modulation Site.
• Ultrasound for detecting peristalsis.