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Alan Grossfield

TitleAssociate Professor
InstitutionSchool of Medicine and Dentistry
DepartmentBiochemistry and Biophysics
AddressUniversity of Rochester Medical Center
School of Medicine and Dentistry
601 Elmwood Ave, Box 712
Rochester NY 14642
 
 Overview
My research interests revolve around the use of computer modeling to understand the structure and thermodynamics of biological molecules. In particular, I am most interested in understanding the biology and physics of lipid-protein interactions. These interactions underlie a fantastic array of biological processes, including cell-signaling by GPCRs and some immune reactions, specifically the action of antimicrobial peptides.

 
 Selected Publications
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  1. Romo TD, Grossfield A. Unknown unknowns: the challenge of systematic and statistical error in molecular dynamics simulations. Biophys J. 2014 Apr 15; 106(8):1553-4.
    View in: PubMed
  2. Leioatts N, Mertz B, Martínez-Mayorga K, Romo TD, Pitman MC, Feller SE, Grossfield A, Brown MF. Retinal ligand mobility explains internal hydration and reconciles active rhodopsin structures. Biochemistry. 2014 Jan 21; 53(2):376-85.
    View in: PubMed
  3. Horn JN, Kao TC, Grossfield A. Coarse-grained molecular dynamics provides insight into the interactions of lipids and cholesterol with rhodopsin. Adv Exp Med Biol. 2014; 796:75-94.
    View in: PubMed
  4. Kimura T, Vukoti K, Lynch DL, Hurst DP, Grossfield A, Pitman MC, Reggio PH, Yeliseev AA, Gawrisch K. Global fold of human cannabinoid type 2 receptor probed by solid-state (13) C-, (15) N-MAS NMR and molecular dynamics simulations. Proteins. 2014 Mar; 82(3):452-65.
    View in: PubMed
  5. Horn JN, Cravens A, Grossfield A. Interactions between Fengycin and Model Bilayers Quantified by Coarse-Grained Molecular Dynamics. Biophys J. 2013 Oct 1; 105(7):1612-23.
    View in: PubMed
  6. Seckler JM, Leioatts N, Miao H, Grossfield A. The interplay of structure and dynamics: Insights from a survey of HIV-1 reverse transcriptase crystal structures. Proteins. 2013 Oct; 81(10):1792-801.
    View in: PubMed
  7. Horn JN, Romo TD, Grossfield A. Simulating the mechanism of antimicrobial lipopeptides with all-atom molecular dynamics. Biochemistry. 2013 Aug 20; 52(33):5604-10.
    View in: PubMed
  8. Grossfield A. Special issue on lipid-protein interactions. Chem Phys Lipids. 2013 Apr; 169:1.
    View in: PubMed
  9. Olausson BE, Grossfield A, Pitman MC, Brown MF, Feller SE, Vogel A. Molecular dynamics simulations reveal specific interactions of post-translational palmitoyl modifications with rhodopsin in membranes. J Am Chem Soc. 2012 Mar 7; 134(9):4324-31.
    View in: PubMed
  10. Horn JN, Sengillo JD, Lin D, Romo TD, Grossfield A. Characterization of a potent antimicrobial lipopeptide via coarse-grained molecular dynamics. Biochim Biophys Acta. 2012 Feb; 1818(2):212-8.
    View in: PubMed
  11. Romo TD, Bradney LA, Greathouse DV, Grossfield A. Membrane binding of an acyl-lactoferricin B antimicrobial peptide from solid-state NMR experiments and molecular dynamics simulations. Biochim Biophys Acta. 2011 Aug; 1808(8):2019-30.
    View in: PubMed
  12. Grossfield A. Recent progress in the study of G protein-coupled receptors with molecular dynamics computer simulations. Biochim Biophys Acta. 2011 Jul; 1808(7):1868-78.
    View in: PubMed
  13. Romo TD, Grossfield A. Validating and improving elastic network models with molecular dynamics simulations. Proteins. 2011 Jan; 79(1):23-34.
    View in: PubMed
  14. Hurst DP, Grossfield A, Lynch DL, Feller S, Romo TD, Gawrisch K, Pitman MC, Reggio PH. A lipid pathway for ligand binding is necessary for a cannabinoid G protein-coupled receptor. J Biol Chem. 2010 Jun 4; 285(23):17954-64.
    View in: PubMed
  15. Romo TD, Grossfield A, Pitman MC. Concerted interconversion between ionic lock substates of the beta(2) adrenergic receptor revealed by microsecond timescale molecular dynamics. Biophys J. 2010 Jan 6; 98(1):76-84.
    View in: PubMed
  16. Khelashvili G, Grossfield A, Feller SE, Pitman MC, Weinstein H. Structural and dynamic effects of cholesterol at preferred sites of interaction with rhodopsin identified from microsecond length molecular dynamics simulations. Proteins. 2009 Aug 1; 76(2):403-17.
    View in: PubMed
  17. Romo TD, Grossfield A. LOOS: an extensible platform for the structural analysis of simulations. Conf Proc IEEE Eng Med Biol Soc. 2009; 2009:2332-5.
    View in: PubMed
  18. Grossfield A, Pitman MC, Feller SE, Soubias O, Gawrisch K. Internal hydration increases during activation of the G-protein-coupled receptor rhodopsin. J Mol Biol. 2008 Aug 29; 381(2):478-86.
    View in: PubMed
  19. O'Neil LL, Grossfield A, Wiest O. Base flipping of the thymine dimer in duplex DNA. J Phys Chem B. 2007 Oct 11; 111(40):11843-9.
    View in: PubMed
  20. Lau PW, Grossfield A, Feller SE, Pitman MC, Brown MF. Dynamic structure of retinylidene ligand of rhodopsin probed by molecular simulations. J Mol Biol. 2007 Sep 28; 372(4):906-17.
    View in: PubMed
  21. Grossfield A, Feller SE, Pitman MC. Convergence of molecular dynamics simulations of membrane proteins. Proteins. 2007 Apr 1; 67(1):31-40.
    View in: PubMed
  22. Martínez-Mayorga K, Pitman MC, Grossfield A, Feller SE, Brown MF. Retinal counterion switch mechanism in vision evaluated by molecular simulations. J Am Chem Soc. 2006 Dec 27; 128(51):16502-3.
    View in: PubMed
  23. Jiao D, King C, Grossfield A, Darden TA, Ren P. Simulation of Ca2+ and Mg2+ solvation using polarizable atomic multipole potential. J Phys Chem B. 2006 Sep 21; 110(37):18553-9.
    View in: PubMed
  24. Grossfield A, Feller SE, Pitman MC. Contribution of omega-3 fatty acids to the thermodynamics of membrane protein solvation. J Phys Chem B. 2006 May 11; 110(18):8907-9.
    View in: PubMed
  25. Grossfield A, Feller SE, Pitman MC. A role for direct interactions in the modulation of rhodopsin by omega-3 polyunsaturated lipids. Proc Natl Acad Sci U S A. 2006 Mar 28; 103(13):4888-93.
    View in: PubMed
  26. Pitman MC, Grossfield A, Suits F, Feller SE. Role of cholesterol and polyunsaturated chains in lipid-protein interactions: molecular dynamics simulation of rhodopsin in a realistic membrane environment. J Am Chem Soc. 2005 Apr 6; 127(13):4576-7.
    View in: PubMed
  27. Grossfield A. Dependence of ion hydration on the sign of the ion's charge. J Chem Phys. 2005 Jan 8; 122(2):024506.
    View in: PubMed
  28. Drozdov AN, Grossfield A, Pappu RV. Role of solvent in determining conformational preferences of alanine dipeptide in water. J Am Chem Soc. 2004 Mar 3; 126(8):2574-81.
    View in: PubMed
  29. Grossfield A, Ren P, Ponder JW. Ion solvation thermodynamics from simulation with a polarizable force field. J Am Chem Soc. 2003 Dec 17; 125(50):15671-82.
    View in: PubMed
  30. Grossfield A, Sachs J, Woolf TB. Dipole lattice membrane model for protein calculations. Proteins. 2000 Nov 1; 41(2):211-23.
    View in: PubMed
  31. Petrache HI, Grossfield A, MacKenzie KR, Engelman DM, Woolf TB. Modulation of glycophorin A transmembrane helix interactions by lipid bilayers: molecular dynamics calculations. J Mol Biol. 2000 Sep 22; 302(3):727-46.
    View in: PubMed
  32. Woolf TB, Grossfield A, Tychko M. Differences between apo and three holo forms of the intestinal fatty acid binding protein seen by molecular dynamics computer calculations. Biophys J. 2000 Feb; 78(2):608-25.
    View in: PubMed

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