Biochemistry

Adrian H. Elcock, PhD

Portrait

Professor of Biochemistry

Contact Information

Primary Office: 4-530 BSB
Iowa City, IA 52242
Phone: 319-335-6643

Email: adrian-elcock@uiowa.edu
Web: Elcock Laboratory

Education

BSc, Department of Chemistry, University of East Anglia
DrPH, Department of Chemistry, Oxford University

Fellowship, Department of Chemistry and Biochemistry, University of California, San Diego

Education/Training Program Affiliations

Department of Biochemistry PhD
Interdisciplinary Graduate Program in Translational Biomedicine
Medical Scientist Training Program

Research Summary

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 and experimental research projects.

Selected Publications

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Schrodt M, Andrews C, Elcock A.  Large-Scale Analysis of 48 DNA and 48 RNA Tetranucleotides Studied by 1 μs Explicit-Solvent Molecular Dynamics Simulations..  Journal of chemical theory and computation.  2015 December 8. 11(12):5906-17.
[PubMed]

Cressiot B, Braselmann E, Oukhaled A, Elcock A, Pelta J, Clark P.  Dynamics and Energy Contributions for Transport of Unfolded Pertactin through a Protein Nanopore..  ACS nano.  2015 September 22. 9(9):9050-61.
[PubMed]

Li  S, Elcock A.  Residue-Specific Force Field (RSFF2) Improves the Modeling of Conformational Behavior of Peptides and Proteins..  The journal of physical chemistry letters.  2015 June 4. 6(11):2127-33.
[PubMed]

Frembgen-Kesner T, Andrews C, Li  S, Ngo N, Shubert S, Jain A, Olayiwola O, Weishaar M, Elcock A.  Parametrization of Backbone Flexibility in a Coarse-Grained Force Field for Proteins (COFFDROP) Derived from All-Atom Explicit-Solvent Molecular Dynamics Simulations of All Possible Two-Residue Peptides..  Journal of chemical theory and computation.  2015 May 12. 11(5):2341-54.
[PubMed]

Brown R, Andrews C, Elcock A.  Stacking Free Energies of All DNA and RNA Nucleoside Pairs and Dinucleoside-Monophosphates Computed Using Recently Revised AMBER Parameters and Compared with Experiment..  Journal of chemical theory and computation.  2015 May 12. 11(5):2315-28.
[PubMed]

Li  S, Andrews C, Frembgen-Kesner T, Miller M, Siemonsma S, Collingsworth T, Rockafellow I, Ngo N, Campbell B, Brown R, Guo C, Schrodt M, Liu Y, Elcock A.  Molecular Dynamics Simulations of 441 Two-Residue Peptides in Aqueous Solution: Conformational Preferences and Neighboring Residue Effects with the Amber ff99SB-ildn-NMR Force Field..  Journal of chemical theory and computation.  2015 March 10. 11(3):1315-29.
[PubMed]

Andrews C, Elcock A.  COFFDROP: A Coarse-Grained Nonbonded Force Field for Proteins Derived from All-Atom Explicit-Solvent Molecular Dynamics Simulations of Amino Acids.  J Chem Theory Comput.  2014. 10(11):5178-5194.
[PubMed]

Azzaz A, Vitalini M, Thomas A, Price J, Blacketer M, Cryderman D, Zirbel L, Woodcock C, Elcock A, Wallrath L, Shogren-Knaak M.  Human heterochromatin protein 1α promotes nucleosome associations that drive chromatin condensation.  J Biol Chem.  2014. 289(10):6850-61.
[PubMed]

Theillet F, Binolfi A, Frembgen-Kesner T, Hingorani K, Sarkar M, Kyne C, Li C, Crowley P, Gierasch L, Pielak G, Elcock A, Gershenson A, Selenko P.  Physicochemical properties of cells and their effects on intrinsically disordered proteins (IDPs).  Chem Rev.  2014. 114(13):6661-714.
[PubMed]

Randak C, Dong Q, Ver Heul A, Elcock A, Welsh M.  ATP and AMP mutually influence their interaction with the ATP-binding cassette (ABC) adenylate kinase cystic fibrosis transmembrane conductance regulator (CFTR) at separate binding sites .  J Biol Chem.  2013 September. 288(38):27691-701.
[PubMed]

Date Last Modified: 04/12/2016 - 14:29:46