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
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Department of Biochemistry
Adrian Elcock, PhD
Carver College of Medicine
University of Iowa
51 Newton Rd, 4-530 BSB
Iowa City, IA 52242
Lab web site
Phone: (319) 335-6643
Lab Phone: (319) 335-7894
Fax: (319) 335-9570
adrian-elcock@uiowa.edu
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
Elcock, A.H. (2010) Models of macromolecular crowding effects and the need for quantitative comparisons with experiment. Curr Opin Struct Biol. Apr;20(2):196-206. Download reprint pdf
McGuffee, S.R., Elcock, A.H. (2010) Diffusion, crowding & protein stability in a dynamic molecular model of the bacterial cytoplasm. PLoS Comput Biol. Mar 5;6(3):e1000694. Download reprint pdf
Zhu, S., Elcock, A.H. (2010) A Complete Thermodynamic Characterization of Electrostatic and Hydrophobic Associations in the Temperature Range 0 to 100 degrees C from Explicit-Solvent Molecular Dynamics Simulations. Journal of Chemical Theory and Computation 6 (4):1293-1306.
Brandt, F., Etchells, S.A., Ortiz, J.O., Elcock, A.H., Hartl, F.U., Baumeister, W. (2009) The native 3D organization of bacterial polysomes. Cell. Jan 23; 136(2):261-271. Download reprint pdf
Frembgen-Kesner, T., Elcock, A.H. (2009) Striking Effects of Hydrodynamic Interactions on the Simulated Diffusion and Folding of Proteins. Journal of Chemical Theory and Computation 5 (2):242-256.
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. Download reprint pdf
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. Download reprint pdf
Elcock, A.H. (2006) Molecular simulations of cotranslational protein folding: fragment stabilities, folding cooperativity, and trapping in the ribosome. PLoS 2:824-841. Download reprint pdf
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. Download reprint pdf
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. Download reprint pdf
Rocky, W.M., and Elcock, A.H. (2005) Rapid computational identification of the targets of protein kinase inhibitors. J. Med. Chem. 48:4138-4152. Download reprint pdf
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