Abstract

Diffusion governs elements of such biological processes as enzymatic activity, signal transduction, gene expression, cytoskeletal remodeling,and intercellular communication. The broad objectives of this work are to provide new computer simulation tools that will enable the detailed analysis of the role of molecular diffusion in biological processes at the subcellular and cellular levels, and the application of these tools to selected problems where close contact with experimental work is possible.
Specific aims for the next project period include the following. (a) Methods will be developed to allow more detailed interaction models to be used in Brownian dynamics simulations of biomolecular diffusion. (b) Methods will be developed to allow more rapid calculation of electrostatic interactions of large molecules (>100,000 atoms) during Brownian dynamics simulations. (c) Methods will be developed to allow simulations of diffusional processes at cellular scales. (d) Applications will be made to protein-protein diffusional encounter, to protein-membrane diffusional encounter, and to diffusion and reaction of neurotransmitter in model synapses. Training of undergraduate, graduate and postdoctoral students will continue to be a key aspect of this project.

  Funding Agency

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM031749-23
Application #
6763247
Study Section
Molecular and Cellular Biophysics Study Section (BBCA)
Program Officer
Wehrle, Janna P
Project Start
1983-06-01
Project End
2007-06-30
Budget Start
2004-07-01
Budget End
2005-06-30
Support Year
23
Fiscal Year
2004
Total Cost
$305,835
Indirect Cost

  Institution

Name
University of California San Diego
Department
Pharmacology
Type
Schools of Medicine
DUNS #
804355790
City
La Jolla
State
CA
Country
United States
Zip Code
92093

  Publications

Guan, W; Cheng, X; Huang, J et al. (2018) RPYFMM: Parallel Adaptive Fast Multipole Method for Rotne-Prager-Yamakawa Tensor in Biomolecular Hydrodynamics Simulations. Comput Phys Commun 227:99-108
Jurrus, Elizabeth; Engel, Dave; Star, Keith et al. (2018) Improvements to the APBS biomolecular solvation software suite. Protein Sci 27:112-128
Huang, Yu-Ming M; Huber, Gary A; Wang, Nuo et al. (2018) Brownian dynamic study of an enzyme metabolon in the TCA cycle: Substrate kinetics and channeling. Protein Sci 27:463-471
Caliman, Alisha D; Miao, Yinglong; McCammon, James A (2018) Mapping the allosteric sites of the A2A adenosine receptor. Chem Biol Drug Des 91:5-16
Utesch, Tillmann; de Miguel Catalina, Alejandra; Schattenberg, Caspar et al. (2018) A Computational Modeling Approach Predicts Interaction of the Antifungal Protein AFP from Aspergillus giganteus with Fungal Membranes via Its ?-Core Motif. mSphere 3:
Zhang, Jingbo; Wang, Nuo; Miao, Yinglong et al. (2018) Identification of SLAC1 anion channel residues required for CO2/bicarbonate sensing and regulation of stomatal movements. Proc Natl Acad Sci U S A 115:11129-11137
Miao, Yinglong; McCammon, J Andrew (2018) Mechanism of the G-protein mimetic nanobody binding to a muscarinic G-protein-coupled receptor. Proc Natl Acad Sci U S A 115:3036-3041
Palermo, Giulia; Chen, Janice S; Ricci, Clarisse G et al. (2018) Key role of the REC lobe during CRISPR-Cas9 activation by 'sensing', 'regulating', and 'locking' the catalytic HNH domain. Q Rev Biophys 51:
Ricci, Clarisse G; Li, Bo; Cheng, Li-Tien et al. (2017) ""Martinizing"" the Variational Implicit Solvent Method (VISM): Solvation Free Energy for Coarse-Grained Proteins. J Phys Chem B 121:6538-6548
Dick, Benjamin L; Patel, Ashay; McCammon, J Andrew et al. (2017) Effect of donor atom identity on metal-binding pharmacophore coordination. J Biol Inorg Chem 22:605-613

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