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Title: Biomolecular Simulation of Base Excision Repair and Protein Signaling

Abstract

The goal of the Biomolecular Simulation of Base Excision Repair and Protein Signaling project is to enhance our understanding of the mechanism of human polymerase-β, one of the key enzymes in base excision repair (BER) and the cell-signaling enzymes cyclic-AMP-dependent protein kinase. This work used molecular modeling and simulation studies to specifically focus on the • dynamics of DNA and damaged DNA • dynamics and energetics of base flipping in DNA • mechanism and fidelity of nucleotide insertion by BER enzyme human polymerase-β • mechanism and inhibitor design for cyclic-AMP-dependent protein kinase. Molecular dynamics simulations and electronic structure calculations have been performed using the computer resources at the Molecular Science Computing Facility at the Environmental Molecular Sciences Laboratory.

Authors:
; ; ; ; ; ;
Publication Date:
Research Org.:
Pacific Northwest National Laboratory (PNNL), Richland, WA (US), Environmental Molecular Sciences Laboratory (EMSL)
Sponsoring Org.:
USDOE
OSTI Identifier:
877558
Report Number(s):
PNNL-15687
2401; KP1704020; TRN: US200608%%481
DOE Contract Number:
AC05-76RL01830
Resource Type:
Technical Report
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; COMPUTERS; DESIGN; DNA; ELECTRONIC STRUCTURE; ENZYMES; EXCISION REPAIR; NUCLEOTIDES; PROTEINS; SIMULATION; Environmental Molecular Sciences Laboratory

Citation Formats

Straatsma, TP, McCammon, J A, Miller, John H, Smith, Paul E, Vorpagel, Erich R, Wong, Chung F, and Zacharias, Martin W. Biomolecular Simulation of Base Excision Repair and Protein Signaling. United States: N. p., 2006. Web. doi:10.2172/877558.
Straatsma, TP, McCammon, J A, Miller, John H, Smith, Paul E, Vorpagel, Erich R, Wong, Chung F, & Zacharias, Martin W. Biomolecular Simulation of Base Excision Repair and Protein Signaling. United States. doi:10.2172/877558.
Straatsma, TP, McCammon, J A, Miller, John H, Smith, Paul E, Vorpagel, Erich R, Wong, Chung F, and Zacharias, Martin W. Fri . "Biomolecular Simulation of Base Excision Repair and Protein Signaling". United States. doi:10.2172/877558. https://www.osti.gov/servlets/purl/877558.
@article{osti_877558,
title = {Biomolecular Simulation of Base Excision Repair and Protein Signaling},
author = {Straatsma, TP and McCammon, J A and Miller, John H and Smith, Paul E and Vorpagel, Erich R and Wong, Chung F and Zacharias, Martin W},
abstractNote = {The goal of the Biomolecular Simulation of Base Excision Repair and Protein Signaling project is to enhance our understanding of the mechanism of human polymerase-β, one of the key enzymes in base excision repair (BER) and the cell-signaling enzymes cyclic-AMP-dependent protein kinase. This work used molecular modeling and simulation studies to specifically focus on the • dynamics of DNA and damaged DNA • dynamics and energetics of base flipping in DNA • mechanism and fidelity of nucleotide insertion by BER enzyme human polymerase-β • mechanism and inhibitor design for cyclic-AMP-dependent protein kinase. Molecular dynamics simulations and electronic structure calculations have been performed using the computer resources at the Molecular Science Computing Facility at the Environmental Molecular Sciences Laboratory.},
doi = {10.2172/877558},
journal = {},
number = ,
volume = ,
place = {United States},
year = {Fri Mar 03 00:00:00 EST 2006},
month = {Fri Mar 03 00:00:00 EST 2006}
}

Technical Report:

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  • No abstract prepared.
  • Oncology Overviews are a service of the International Cancer Research Data Bank (ICRDB) Program of the National Cancer Institute, intended to facilitate and promote the exchange of information between cancer scientists by keeping them aware of literature related to their research being published by other laboratories throughout the world. Each Oncology Overview represents a survey of the literature associated with a selected area of cancer research. It contains abstracts of articles which have been selected and organized by researchers associated with the field. Contents: The effect of the cell cycle on excision repair in eukaryotes; Enhancement of excision repair inmore » prokaryotes by mutagens and carcinogens--The adaptive response; Enhancement of excision repair in eukaryotes by mutagen and carcinogen exposure; Alterations of excision repair during carcinogenesis; Effects of eukaryotic cell differentiation on excision repair; Age-related factors affecting excision repair; Reviews on gene expression and excision repair.« less
  • Oncology Overviews are a service of the International Cancer Research Data Bank (ICRDB) Program of the National Cancer Institute, intended to facilitate and promote the exchange of information between cancer scientists by keeping them aware of literature related to their research being published by other laboratories throughout the world. Each Oncology Overview represents a survey of the literature associated with a selected area of cancer research. It contains abstracts of articles which have been selected and organized by researchers associated with the field. Contents: Specific mechanisms of excision of chemically modified bases; Specific mechanisms of excision of radiation-induced damage; Formationmore » and excision of apurinic and apyridiminic sites; Repair processes in excision repair of DNA damage; Restoration of chromatin after excision repair; Other studies of excision repair; Intragenomic distribution of excision repair; Interrelationship of repair pathways; Reviews of enzymology and mechanisms of excision repair.« less
  • Abstract not provided.