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Publications/Citations (GS)

• Janosi L, Li Z, Hancock JF and Gorfe AA
  Organization, Dynamics and Segregation of Ras Nanoclusters in Membrane Domains
  PNAS, 2012 (Early Edition, p1-6).
• Prakash P, Sayyed-Ahmad A and Gorfe AA
  The Role of Conserved Waters in Conformational Transitions of Q61H K-ras
  PLoS Computational Biology, 2012, 8(2), e1002394.
• Gorfe AA and Hocker JH
  Membrane Targeting: Methods
  In: eLS. John Wiley & Sons, Ltd: Chichester (2012).
• Grant BJ, Lukman S, Hocker H, Sayyah J, Heller Brown J, McCammon JA, Gorfe AA
  Novel Allosteric Sites on Ras for Lead Generation
  PLoS ONE, 2011, 6, e25711.
• Durrant JD, Cao R, Gorfe AA, Zhu W, Li J, Sankovsky A, Oldfield E, McCammon JA
  Non-Bisphosphonate Inhibitors of Isoprenoid Biosynthesis Identified via Computer-Aided Drug Design
  Chemical Biology and Drug Design, 2011, 78:323-32.
• Zhou Y, Lu B-Z and Gorfe AA
  Continuum Electromechanical Modeling of Protein-Membrane Interaction
  Physical Review E, 2010, 82: 041923-041928.
• Janosi L and Gorfe AA
  Segregation of negatively charged phospholipids by the polycationic and farnesylated membrane anchor of Kras
  Biophysical Journal, 2010, 99:3666-3674.
• Grant JN, McCammon JA and Gorfe AA
  Conformational Selection in G-proteins: Lessons from Ras and Rho (Featured Article).
  Biophysical Journal, 2010, 99:L87-L89.
• Janosi L and Gorfe AA
  Simulating POPC and POPC/POPG bilayers: Conserved packing and altered surface reactivity.
  Journal of Chemical Theory and Computation, 2010, 16:3267-3273.
• Janosi L and Gorfe AA
  Importance of the sphingosine base double bond geometry for the structural and thermodynamic properties of sphingomyelin bilayers (Featured Article).
  Biophysical Journal, 2010, 99 (9):2957–2966.
• Lukman S, Grant B, Gorfe AA, Grant G and McCammon JA
  The distinct conformational dynamics of K-ras and H-ras A59G.
  PLoS Computational Biology 2010, 6:e1000922.
• Sayyed-Ahmad A, Lichtenberger LM and Gorfe AA
  Structure and Dynamics of Cholic Acid and Dodecylphosphocholine−Cholic Acid Aggregates.
  Langmuir, 2010, 26:13407-13414.
• Abankwa D, Gorfe AA, Inder K and Hancock JF
  Membrane orientation and nanodomain organization generate Ras isoform diversity.
  Proceedings of the National Academy of Sciences USA, 2010, 107:1130-1135
• Gorfe AA
  Mechanisms of allostery and membrane attachment in Ras GTPases: Implications for anti-cancer drug discovery.
  Current Medicinal Chemistry, 2010, 17, 1-9
• Grant BJ, Gorfe AA, McCammon JA.
  Large conformational changes in proteins: Signaling and other functions.
  Current Opinion in Structuctral Biology, 2010, 20, 142-147.
• Burke JE, Babakhani A, Gorfe AA, Kokotos G, Li S, Woods VL Jr, McCammon JA and Dennis EA
  Location of Inhibitors Bound to Group IVA Phospholipase A(2) Determined by Molecular Dynamics and Deuterium Exchange Mass Spectrometry.
  Journal of the American Chemical Society, 2009, 131:8083-91.
• Edreira MM, Li S, Wong S, Gorfe AA, Ribeiro-Neto F, Woods VL Jr, and Altschuler DL
  Phosphorylation-induced conformational change in Rap1B: Allosteric effects on switch domain and effector loop.
  Journal of Biological Chemistry, 2009, 284:27480-6
• Gorfe AA, Lu B-Z, Yu Z, and McCammon JA
  Enzyme activity versus structural dynamics: The case of acetylcholinesterase tetramer (Featured Article). 
  Biophysical Journal, 2009, 97:897-905
• Khavrutskii I, Gorfe AA, Lu B-Z and McCammon JA
  Free energy for the permeation of Na+ and Cl- ions and their ion-pair through zwitterionic dimyristoyl phosphatidylcholine lipid bilayer by umbrella integration with harmonic fourier Beads.
  Journal of the American Chemical Society, 2009, 131:1706-16
• Grant B, Gorfe AA and McCammon JA
  Ras Conformational Switching: Simulating Nucleotide Dependent Conformational Transitions with Accelerated Molecular dynamics.  
  PLoS Computational Biology, 2009, 5:e1000325
• Gorfe AA and McCammon JA 
  Similar membrane affinity of mono- and di-S-acylated Ras membrane anchors: A new twist in the role of protein lipidation. 
  Journal of the American Chemical Society, 2008, 130, 12624-12625
• Abankwa D, Gorfe AA, Hancock JF
  Mechanisms of Ras membrane organization and signalling: Ras on a rocker. 
  Cell Cycle, 2008, 7, 2667-2673
• Gorfe AA, Baron R and McCammon JA
  Water-membrane partition thermodynamics of an amphiphilic lipopeptide: An enthalpy driven hydrophobic effect. 
  Biophysical Journal, 2008, 95, 3269-33277
• Babkhani A, Gorfe AA, Kim J and McCammon JA
  Thermodynamics of peptide insertion and aggregation in a lipid bilayer. 
  Journal of Physical Chemistry B, 2008, 112, 10528-10534
• Gorfe AA, Grant B and McCammon JA
  Mapping the nucleotide and isoform dependent structural and dynamical features of Ras proteins. 
  Structure, 2008, 16, 885-896
• Abankwa D, Hanzal-Bayer M, Ariotti N, Plowman SJ, Gorfe AA, Parton RG, McCammon JA, Hancock JF,
  A novel switch region regulates H-ras membrane orientation and signal output. 
  The EMBO Journal, 2008, 27, 727-735
• Gorfe AA, Chang CA, Ivanov I and McCammon JA
  Dynamics of the acetylcholinesterase tetramer. 
  Biophysical Journal, 2008, 94,1144-1154
• Gorfe AA, Babakhani A and McCammon JA
  H-ras protein in a bilayer: Interaction and structure perturbation. 
  Journal of the American Chemical Society, 2007, 129, 12280-12286
• Gorfe AA, Babakhani A and McCammon JA
  Free Energy profile of H-ras membrane anchor upon membrane insertion. 
  Angewadte Chemie International Edition, 2007, 46, 8234 - 8237
• Abankwa D, Gorfe AA, Hancock JF
  Ras nanoclusters: Molecular structure and assembly (Review). 
  Seminars in Cell and Developmental Biology, 2007, 18, 599-607
• Gorfe AA and Caflisch A.
  Ser170 controls the conformational multiplicity of the 166-175 loop in prion proteins: Implication for conversion and species barrier. 
  FASEB Journal,   2007, 21,3279-3287
• Babakhani A, Gorfe AA, Gullingsrud J, Kim J and McCammon JA.
  Peptide insertion, positioning, and stabilization in a membrane: Insight from an all-atom molecular cynamics simulation.
  Biopolymers, 2007, 85:490-497
• Gorfe AA, Hanzal-Bayer M, Abankwa D, Hancock JF and McCammon JA.
  Structure and dynamics of the full-length lipid-modified H-ras protein in complex with a DMPC bilayer.
  Journal of Medicinal Chemistry, 2007, 50:674-84
This paper has been recommended as: Must Read F1000 Factor 6.0
• Gorfe AA and Caflisch A.
  Functional plasticity in the substrate binding site of beta-secretase (BACE).
  Structure, 2005, 13:1487-1498
• Gorfe AA, Pellarin R and Caflisch A.
  Membrane localization and flexibility of a lipidated ras peptide studied by molecular dynamics simolations.
  Journal of the American Chemical Society, 2004, 126:15277-15286
• Gorfe AA, Caflisch A, Jelesarov I.
  The role of flexibility and hydration on the sequence-specific DNA recognition by the Tn916 integrase protein: a molecular dynamics analysis.
  Journal of Molecular Recognition, 2004, 17: 120-31
• Gorfe AA, Jelesarov I.
  Energetics of sequence-specific protein-DNA association: Computational analysis of integrase Tn916 binding to its target DNA.
  Biochemistry, 2003, 42:11568-76
• Milev S, Gorfe AA, Karshikoff A, Clubb RT, Bosshard HR, Jelesarov I.
  Energetics of sequence-specific protein-DNA association: Conformational stability of the DNA binding domain of integrase Tn916 and its cognate DNA duplex.
  Biochemistry, 2003, 42:3492-502
• Milev S, Gorfe AA, Karshikoff A, Clubb RT, Bosshard HR, Jelesarov I.
  Energetics of sequence-specific protein-DNA association: Binding of integrase Tn916 to its target DNA.
  Biochemistry, 2003, 42(12):3481-91
• Phelan P, Gorfe AA, Jelesarov I, Marti DN, Warwicker J, Bosshard HR.
  Salt bridges destabilize a leucine zipper designed for maximized ion pairing between helices.
  Biochemistry, 2002, 41:2998-3008
• Gorfe AA, Ferrara P, Caflisch A, Marti DN, Bosshard HR, Jelesarov I.
  Calculation of protein ionization equilibria with conformational sampling: pK(a) of a model leucine zipper, GCN4 and barnase.
  Proteins, 2002, 46:41-60
• Gorfe AA, Brandsdal BO, Leiros HK, Helland R, Smalas AO.
  Electrostatics of mesophilic and psychrophilic trypsin isoenzymes: Qualitative evaluation of electrostatic differences at the substrate binding site.
  Proteins, 2000, 40:207-17
• PhD thesis, University of Zurich (2003)
  Protein Ionization Equilibria and Protein-DNA Binding: Conformational Dynamics and Thermodynamics From a Computational Perspective.
• MSc thesis, University of Tromsoe (1999)
  Electrostatics of Mesophilic and Psycrophilic Trypsin Iso-enzymes: Qualitative and Quantitative Evaluations Based on Continuum Models.