Abstract

Resources are requested for a computational approach to problems in peptide and nucleic acid biochemistry involving the simulation of the effects of salt on structure and dynamics. Application and development of new simulation methods serves to check the approximate analytic methods and to study more complicated systems inappropriate for our current theories. We hope to extend these supercomputing projects supported by NIH and an NSF Grand Challenge Application project. Three ongoing scientific projects will be described: 1) Salt effects in Peptide Solutions, 2) Antiviral Triplex forming Oligonucleotides, 3) Techniques for Simulating Protein Solutions. The goal of the project is to produce a detailed and accurate picture of selected inter- and intramolecular distributions for the chosen biomolecules in aqueous solution which will be compared with new experimental structural studies such as those produced by Xray and neutron diffraction difference measurements and NMR/NOE experiments.

  Funding Agency

Agency
National Institute of Health (NIH)
Institute
National Center for Research Resources (NCRR)
Type
Biotechnology Resource Grants (P41)
Project #
5P41RR004293-09
Application #
6309519
Study Section
Project Start
1999-12-01
Project End
2000-11-30
Budget Start
1998-10-01
Budget End
1999-09-30
Support Year
9
Fiscal Year
2000
Total Cost
$24,318
Indirect Cost

  Institution

Name
Cornell University
Department
Type
DUNS #
872612445
City
Ithaca
State
NY
Country
United States
Zip Code
14850

  Publications

Chiang, Chi-Tung; Shores, Kevin S; Freindorf, Marek et al. (2008) Size-restricted proton transfer within toluene-methanol cluster ions. J Phys Chem A 112:11559-65
Kazmierkiewicz, Rajmund; Liwo, Adam; Scheraga, Harold A (2003) Addition of side chains to a known backbone with defined side-chain centroids. Biophys Chem 100:261-80
Kazmierkiewicz, Rajmund; Liwo, Adam; Scheraga, Harold A (2002) Energy-based reconstruction of a protein backbone from its alpha-carbon trace by a Monte-Carlo method. J Comput Chem 23:715-23
Liwo, Adam; Arlukowicz, Piotr; Czaplewski, Cezary et al. (2002) A method for optimizing potential-energy functions by a hierarchical design of the potential-energy landscape: application to the UNRES force field. Proc Natl Acad Sci U S A 99:1937-42
Scheraga, Harold A; Pillardy, Jaroslaw; Liwo, Adam et al. (2002) Evolution of physics-based methodology for exploring the conformational energy landscape of proteins. J Comput Chem 23:28-34
Scheraga, Harold A; Vila, Jorge A; Ripoll, Daniel R (2002) Helix-coil transitions re-visited. Biophys Chem 101-102:255-65
Pillardy, J; Arnautova, Y A; Czaplewski, C et al. (2001) Conformation-family Monte Carlo: a new method for crystal structure prediction. Proc Natl Acad Sci U S A 98:12351-6
Vila, J A; Ripoll, D R; Scheraga, H A (2001) Influence of lysine content and pH on the stability of alanine-based copolypeptides. Biopolymers 58:235-46
Pillardy, J; Czaplewski, C; Liwo, A et al. (2001) Recent improvements in prediction of protein structure by global optimization of a potential energy function. Proc Natl Acad Sci U S A 98:2329-33
Vila, J A; Ripoll, D R; Scheraga, H A (2000) Physical reasons for the unusual alpha-helix stabilization afforded by charged or neutral polar residues in alanine-rich peptides. Proc Natl Acad Sci U S A 97:13075-9

Showing the most recent 10 out of 20 publications