Department of Biochemistry
4-403 BSB
Iowa City, IA 52242-1109 USA phone: 877-846-8569
or 319-335-7932
fax: (319) 335-9570
biochem@uiowa.edu
Department of Biochemistry
Associate Professor of Biochemistry, PhD
51 Newton Rd
Biochemistry/Univ. of Iowa
Iowa City, IA 52242
Research Interests
Work in my laboratory focuses on using molecular simulation techniques to address a variety of fundamental biophysical questions. Research areas in which we have recently published work include: (1) simulation of diffusion and association of proteins in highly concentrated solutions (such as those that are found inside living cells), (2) simulation of amino acid associations at the very high temperatures encountered by hyperthermophilic organisms, (3) computational prediction of drug-receptor interactions, with a view to identifying all cellular targets of current anti-cancer drugs, and (4) computational prediction of functionally important residues in proteins given only the protein?s structure. Other research areas that we have recently developed interests in include: (1) computational identification of cryptic binding sites in proteins that might be used to develop novel inhibitors, (2) molecular simulations of protein folding in physiological conditions (including the effects of chaperonins), (3) modeling the role of conformational flexibility in protein-protein association events, and (4) experimentally measuring the affinities of drug-receptor interactions to provide reliable data for testing our computational methods.
Students in my laboratory come from a wide range of backgrounds, and do not have to be experts in the use of computers: most of our work involves developing ideas in our heads, and computer simulations are typically only used to test these ideas. To complement our simulation work, we will in the near future also be increasingly conducting our own experiments: students joining my laboratory will therefore have the opportunity to undertake combined theoretical & experimental research projects.
Recent Publications
Thomas, A.S., Elcock, A.H. (2007) Molecular dynamics simulations of hydrophobic associations in aqueous salt solutions indicate between water hydrogen bonding and the Hofmeister effect. J. Am. Chem. Soc. Dec 5; 129(48):14887-98.
Rockey, W.J., Elcock, A.H. (2006) Structure selection for protein kinase docking and virtual screening: homology models or crystal structures? Curr Protein Pept Sci., Oct;7(5):437-57. Review.
McGuffee, S.R., Elcock, A.H. (2006) Atomically detailed simulations of concentrated protein solutions: the effects of salt, pH, point mutations, and protein concentration in simulations of 1000-molecule systems. J Am Chem Soc., Sep 20; 128(37):12098-110.
Elcock, A.H. (2006) Molecular simulations of cotranslational protein folding: fragment stabilities, folding cooperativity, and trapping in the ribosome. PLoS 2:824-841.
Thomas, A.S., and Elcock, A.H. (2006) Direct observation of salt effects on molecular interactions through explicit-solvent molecular dynamics simulations: Differential effects on electrostatic and hydrophobic interactions and comparisons to Poisson-Boltzmann theory. J. Am. Chem. Soc. 128:7796-7806.
Frembgen-Kesner T.F. and Elcock, A.H. (2006) Computational sampling of a cryptic drug binding site in a protein receptor: Explicit solvent molecular dynamics and inhibitor docking to p38 MAP kinase. J. Mol. Biol. 359:202-241.
Rocky, W.M., and Elcock, A.H. (2005) Rapid computational identification of the targets of protein kinase inhibitors. J. Med. Chem. 48:4138-4152.
Elcock, A.H. (2004) Molecular simulations of diffusion and association in multimacromolecular systems. Methods Enzym. 383: 166-198.
Thomas, A.S., & Elcock, A.H. (2004) Molecular simulations suggest protein salt bridges are uniquely suited to life at high temperature. J. Am Chem. Soc. 126: 2208-2214.
Yang, H. and Elcock, A.H. (2003) Association lifetimes of hydrophobic amino acid pairs measured directly from molecular dynamics simulations. J. Am. Chem. Soc 125: 13968-13969.
Elcock, A.H. (2003) Atomic-level observation of macromolecular crowding effects: Escape of a protein from the GroEL case. Proc. Natl. Acad. Sci. USA 100: 2340-2344.
Rockey, W.M. and Elcock, A.H. (2002) Progress toward virtual screening for drug side effects. Proteins 48(4): 664-671. Elcock, A.H. (2002) Atomistic simulations of competition between substrates binding to an enzyme. Biophys. J. 82: 2326-2332.
Elcock, A. H. (2002) Modeling supramolecular assemblages. Curr. Opin. Struct. Biol. 12: 154-160.
Affiliations
Biochemistry DepartmentComments or questions about our Web site? Contact the Webmaster.