- Cho KJ, Park JH, Piggot AM, Salim AA, Gorfe AA, Parton RG, Capon RJ, Lacey E, and Hancock JF. (2012) Staurosporines disrupt phosphatidylserine trafficking and mislocalize Ras proteins. J Biol Chem. 287, 43573-43584.
- Gorfe AA and Hocker JH. (2012) Membrane targeting: Methods. In: eLS. John Wiley & Sons, Ltd: Chichester. 1-6.
- Janosi L, Li Z, Hancock JF and Gorfe AA. (2012) Organization, dynamics and segregation of Ras nanoclusters in membrane domains. Proc Natl Acad Sci. 109, 8097-8102.
- Li Z and Gorfe AA. (2012) What drives the clustering of membrane-bound Ras? Small GTPases. 3, 244-247.
- Li Z, Janosi L and Gorfe AA. (2012) Formation and domain-partitioning of H-ras peptide nanoclusters: Effects of peptide concentration and lipid composition. J Am Chem Soc. 134, 17278-1728.
- Prakash P, Sayyed-Ahmad A and Gorfe AA. (2012) The role of conserved waters in conformational transitions of Q61H K-ras. PLoS Comput Biol. 8, e1002394.
- Prakash P, Sayyed-Ahmad A, Zhou Y, Volk DE, Gorenstein DG, Dial EJ, Lichtenberger LM, Gorfe AA. (2012) Aggregation behanvior of ibuprofen, cholic acid and didecylphosphatidylcholine micelles. Biochim Biophysica Acta 1818: 3040-3047.
- Roach AN, Wang Z, Wu P, Zhang F, Chan R, Yonekubo Y, Paolo GD, Gorfe AA, Du G. (2012) Phosphatidic acid regulation of PIPKI is critical for actin cytoskeletal reorganization. J Lipid Res. 53, 2598-2609. PMCID: PMC3494241.
- Grant BJ, Lukman S, Hocker H, Sayyah J, Heller Brown J, McCammon JA, Gorfe AA. (2011) Novel Allosteric Sites on Ras for Lead Generation. PLoS ONE, 6, e25711.
- Durrant JD, Cao R, Gorfe AA, Zhu W, Li J, Sankovsky A, Oldfield E, McCammon JA. (2011) Non-Bisphosphonate Inhibitors of Isoprenoid Biosynthesis Identified via Computer-Aided Drug Design. Chemical Biology and Drug Design, 78:323-32.
- Janosi L and Gorfe AA. (2010) Simulating POPC and POPC/POPG Bilayers: Conserved packing and altered surface reactivity. J Chem Theory Comput. 16, 3267-3273.
- Janosi L and Gorfe AA. (2010) Importance of the sphingosine base double bond geometry for the structural and thermodynamic properties of sphingomyelin bilayers. Biophys J. 99, 2957–2966. (FEATURED ARTICLE)
- Grant, BJ, McCammon JA and Gorfe AA (2010) Conformational selection in G-proteins: lessons from Ras and Rho. Biophys J. 99, L87-L89. (FEATURED ARTICLE).
- Janosi L and Gorfe AA (2010) Segregation of negatively charged phospholipids by the polycationic and farnesylated membrane anchor of Kras. Biophys J. 99, 3666-3674.
- Zhou, Lu B-Z and Gorfe AA (2010) Continuum Electromechanical Modeling of Protein Membrane Interactions. Phys Rev E. 82, 41923-41928.
- Lukman, S, Grant, B, Gorfe, AA, Grant, G and McCammon, JA. The distinct conformational dynamics of K-ras and H-ras A59G. PLoS Comput Biol 6, e1000922; 2010.
- Sayyed-Ahmad, A, Lichtenberger, LM and Gorfe, AA. Structure and Dynamics of Cholic Acid and Dodecylphosphocholine−Cholic Acid Aggregates. Langmuir 26, 13407-13414; 2010.
- Abankwa, D, Gorfe, AA, Inder, K and Hancock, JF. Ras membrane orientation and nanodomain localization generate isoform diversity. Proc Nat'l Ac Sc USA 2010, 107:1130-1135.
- Gorfe, AA. Mechanisms of allostery and membrane attachment in Ras GTPases: implications for anti-cancer drug discovery. Curr Med Chem 2010, 17:1-9.
- Grant, B, Gorfe, AA, and McCammon, JA. Large conformational changes in proteins: signaling and other functions. Curr Opin Struct Biol 2010, 20:142-147.
Alemayehu Gorfe, Ph.D.
UTHSC-Medical School, (713) 500-7538
Gorfe Research Group website
Ph.D.: University of Zurich, Switzerland, 2003
- University of Zurich, Switzerland, 2005
- Univeristy of California, San Diego, 2008
Our Group uses computer simulation approaches to study biomedically relevant biological systems, with emphasis on the following topics: spatiotemporal membrane-organization of cell signaling components, membrane permeation, membrane-organized signaling complexes, interfacial interactions, allostery in surface-bound protein complexes, and drug design. These studies are driven by the need to understand and exploit the principles of specificity in cell signaling and molecular transport, and the opportunity created by the advent of petaflop computational resources coupled with major progresses in coarse-grained modeling. These resources will enable us to simulate processes and systems in a wide range of time and length scales, so that normal and aberrant properties of protein-protein and protein-membrane complexes can be studied at the atomic, molecular and supramolecular levels of detail. The results from such studies will shed light on, for exmaple, the basis of allosteric communication in signaling complexes and molecular recognition. To this end, we develop and apply a variety of computational techniques, including classical and advanced molecular and Brownian dynamics simulations, structural bioinformatics, and binding free energy calculations.
A tutorial in my laboratory would provide experience with modern techniques in biomolecular simulations, including molecular dynamics and Brownian dynamics simulations; structure based drug design; structural boinformatics; continuum electrostatics and theoretical approaches for investigating the thermodynamic principles underlying the assembly and function of supramolecular complexes.