Publications

  1. Alemayehu A. Gorfe, Sandrasegaram Gnanakaran, Editorial, Current Opinion in Structural Biology, Volume 89, 2024, 102938.
  2. Eltzschig H, Ruan W, Li T, Lee J, Bang IH, Deng W, Ma X, Yoo S-H, Kim B, Li J, Yuan X, Wang Y-Y, Liang Y, Deberge M, Zhang D, Zhou Z, Wang Y, Gorham J, Aranki S, Nair R, Li L, Narula J, Zhao Z, Gorfe AA, Muehlschlegel J, Tsai K-L. “The BMAL1/HIF2A heterodimer modulates circadian variations of myocardial injury”. Submitted. Pre-print.
  3. Hutchins CM and Gorfe AA “Intrinsically disordered membrane anchors of Rheb, RhoA and DiRas3 small GTPases: Molecular dynamics, membrane organization, and interactions”. J Phys Chem B. 2024, 128, 27, 6518–6528
  4. Hutchins CM and Gorfe AA “From disorder comes function: Regulation of small GTPase function by intrinsically disordered lipidated membrane anchor”. Curr Opi Str Biol. Volume 87, August 2024, 102869.
  5. Araya MK, Chen W, Ke Y, Zhou Y, Gorfe AA, Hancock JF, and Liu J. “Differential lipid binding specificities of RAP1A and RAP1B are encoded by the amino acid sequence of the membrane anchors”. Published online July 13, 2024.
  6. Pagba CV, Gupta AK, Dilsha K, Sadrpour P, Jakubec J, Prakash P, van der Hoeven D, Cho K-J, Gilbertson S and Gorfe AA “Biophysical and biochemical characterization of structurally diverse small molecule hits for KRAS inhibition”, ChemBioChem 2024, e202300827.
  7. Araya MK and Gorfe AA “Conformational ensemble dependent lipid recognition and segregation by prenylated intrinsically disordered regions in small GTPases”, Commun Biol, 6, Article number: 1111 (2023)
  8. Rehl KM, Selvakumar J, Hoang D, Arumugam K, Gorfe AA, Cho K-J “A novel ferrocene derivative blocks KRAS plasma membrane localization and function by oxidative modification at His95”, Life Science Alliance, Sep 4;6(11):e202302094, 2023. doi: 10.26508/lsa.202302094
  9. Liang X, Jung SU, Fong LW, Bildik G, Gray JP, Mao W, Zhang S, Millward SW, Gorfe AA, Zhou Y, Lu Z; Bast RC “Membrane anchoring of the DIRAS3 N-terminal extension permits tumor suppressor function”, iScience, 26, 108151, 2023.
  10. Pagba CV, Gupta AK and Gorfe AA “Small molecule inhibition of KRAS through conformational selection”, ACS Omega, Aug 18;8(34):31419-31426, 2023. doi: 10.1021/acsomega.3c04013.
  11. Gorfe AA “Biophysics of Cancer”, Biophysical Journal 121, E01–E02, October 4, 2022.
  12. Pagba CV, Gupta AK, Naji AK, van der Hoeven D, Churion K, Liang X, Jakubec J, Hook M, Zuo Y, de Kraatz MM, Frost JA and Gorfe AA “A KRAS inhibitor that simultaneously inhibits nucleotide exchange activity and effector engagement”, ACS Bio Med Chem Au, 2, 6, 617–62, 2022.
  13. Araya MK, Zhou Y and Gorfe AA “Remodeling of the plasma membrane by surface-bound protein monomers and oligomers: The critical role of intrinsically disordered regions”, J Mem Biol, 255, 651–663, 2022.
  14. Araya MK and Gorfe AA “Phosphatidylserine and phosphatidylethanolamine asymmetry have negligible effect on the global structure, dynamics and interactions of the KRAS lipid anchor”, J Phys Chem B, 126(24):4491-4500, 2022.
  15. Janosi L and Gorfe AA “Interaction between proteins and biological membranes” in ‘Protein Interactions: The Molecular Basis of Interactomics’, Helms and Kalinina Eds, Wiley; 2022, 1st Edition.
  16. Prakash P and Gorfe AA “Determinants of membrane orientation dynamics in lipid-modified small GTPases”, JACS Au 2022, 2, 128−135.
  17. Hancock JF and Gorfe AA “Building insights into KRAS signaling complexes”, Nat Struct Mol Biol, 28, 773-778, 2021.
  18. Wang X, Gorfe AA and Putkey JF “Antipsychotic Phenothiazine Drugs Bind to KRAS in vitro”, 2021, J Biomol NMR 75, 233–244, 2021.
  19. Zhou Y, Gorfe AA and Hancock JF “RAS nanoclusters selectively sort distinct lipid headgroups and acyl chains”, 2021, Front. Mol. Biosci., 17.
  20. Nair V, Yin G, Zhang J, Hancock JF, Campbell SL and Gorfe AA “Monoubiquitination of KRAS at Lysine104 and Lysine147 Modulates its Dynamics and Interaction with Partner Proteins”, 2021, J Phys Chem B, 125, 18, 4681–4691.
  21. Nair V and Gorfe AA “Molecular dynamics simulation of lipid-modified signaling proteins”, 2021, in Irina S. Moreira et al. (eds.), Computational Design of Membrane Proteins, Methods in Molecular Biology, vol. 2315.
  22. Zhou Y, Prakash P, Liang H, Gorfe AA and Hancock JF “The KRAS and other prenylated polybasic domain membrane anchors recognize phosphatidylserine based on acyl chain structure”, 2021, Proc Natl Acad Sci USA, 118(6):e2014605118.
  23. Sepuru MK, Nair V, Prakash P, Gorfe AA, and Rajarathnam K “Long-range coupled motions underlie ligand recognition by a chemokine receptor”, 2020, iScience, 23, 12, 101858.
  24. Abankwa D and Gorfe AA “Mechanisms of Ras membrane organization and signaling: Ras rocks again”, Biomolecules 2020, 10(11), 1522.
  25. Lin X and Gorfe AA “Transmembrane Potential of Physiologically Relevant Model Membranes: Effects of Membrane Asymmetry”, 2020, J. Chem. Phys. 153, 105103.
  26. Yin G, Zhang J, Nair V, Harrison J, Chaia A, Petela J, Gorfe AA and Campbell SL “KRAS ubiquitination at lysine 104 retains exchange factor regulation by dynamically modulating the conformation of the interface”, 2020, iScience, 23, 101448.
  27. Quah SY, Tan MS, Ho KL, Abdul Manan N, Sagineedu SR, Gorfe AA, Deb PK, Stanslas J “In silico and STD-NMR approaches to unravel the binding mode of an andrographolide derivative to K-Ras oncoprotein”, 2020, Future Med Chem, Sep 7. doi: 10.4155/fmc-2020-0104.
  28. Sayyed-Ahmad A and Gorfe AA “How to make an undruggable enzyme druggable: Lessons from Ras Proteins”, Chapter 6 – Adv Protein Chem Struct Biol, 2020, 122:181-202. doi: 10.1016/bs.apcsb.2020.05.003.
  29. Gillson J, Ramaswamy Y, Singh G, Gorfe AA, Pavlakis N, Samra J, Mittal A and Sahni S “Small molecule KRAS inhibitors – the future for targeted pancreatic cancer therapy?” 2020, Cancers, 12(5), 1341.
  30. Lu S, Li Z, Gorfe AA and Zhang L “Intracellular Ca2+ regulation of H+/Ca2+ antiporter YfkE mediated by a Ca2+ mini-sensor”, 2020, Proc Natl Acad Sci USA, 17(19):10313-10321.
  31. Gorfe AA and Sligar SG “Membrane-bound Ras as a conformational clock”, 2020, Biophysical Journal, 118, 1–3.
  32. Durham RJ, Paudyal N, MacLean D, Berka V, Carrillo E, Dolino DW, Bhatia NK, Gorfe AA and Jayaraman V “Conformational spread and dynamics in allostery of NMDA receptors”, 2020, Proc Natl Acad Sci USA, 117 (7) 3839-3847.
  33. Prakash P and Gorfe AA “Probing the conformational and energy landscapes of KRAS membrane orientation”, 2019, Journal of Physical Chemistry B, 17;123(41):8644-8652.
  34. Gorfe AA, Cho KJ “Approaches to inhibiting oncogenic K-Ras”, 2019, Small GTPases, Aug 22:1-10.
  35. Mohammad K, Gorfe AA and Sayyed-Ahmad A “Conformational and dynamical effects of Tyr32 phosphorylation in K-Ras: Molecular dynamics simulation and Markov State models analysis”, 2019, 12;123(36):7667-7675.
  36. Liang H, Mu H, Jean-Francois F, Lakshman B, Sarkar-Banerjee S, Zhuang Y, Zeng Y, Gao W, Nissley DV, Gorfe AA, Zhao W, Zhou Y “Membrane curvature sensing of the lipid-anchored K-Ras small GTPase”, 2019, Life Science Alliance, Jul 11;2(4). pii: e20190034.
  37. Gupta AK, Wang X, Pagba CV, Prakash P, Sarkar-Banerjee S, Putkey J, Gorfe AA “Multi-target, ensemble-based virtual screening yields novel allosteric KRAS inhibitors at high success rate”, 2019, Chem Biol Drug Des, 1-16.
  38. Prakash P, Hancock JF, Gorfe AA “Three distinct regions of cRaf kinase domain interact with membrane”, 2019, Sci Rep, 14;9(1):2057.
  39. Mccarthy M, Pagba CV, Prakash P, Naji AK, van der Hoeveni D, Liang H, Gupta AK, Zhou Y, Cho K-J, Hancock JF, Gorfe AA “Discovery of high affinity non-covalent allosteric KRAS inhibitors that disrupt effector binding”, 2019, ACS Omega, 4 (2), 2921–2930.
  40. Lin X, Gorfe AA “Understanding Membrane Domain-Partitioning Thermodynamics of Transmembrane Domains with Potential of Mean Force Calculations”, 2019, J Phys Chem B, 7;123(5):1009-1016.
  41. Prakash P, Litwin D, Liang H, Sarkar-Banerjee S, Dolino D, Zhou Y, Hancock JF, Jayaraman V, Gorfe AA, “Dynamics of Membrane-Bound G12V-KRAS From Simulations and Single-Molecule FRET in Native Nanodiscs”, 2019, Biophys J 116(2):179-183.
  42. Lin X, Nair V, Zhou Y, Gorfe AA “Membrane Potential and Dynamics in a Ternary Lipid Mixture: Insights from Molecular Dynamics Simulations”, 2018, Phys Chem Chem Phys 23, 15591-16296.
  43. Lin X, Gorfe AA, Levental I “Protein Partitioning into Ordered Membrane Domains: Insights from Simulations”, 2018, Biophys J 114(8):1936-1944.
  44. Zhou Y, Prakash P, Gorfe AA, and Hancock JF “Ras and the Plasma Membrane: A Complicated Relationship”, Cold Spring Harb Perspectives in Med. 8, a031831.
  45. Lorent JS, Blanca D-R, Lin X, Spring K, Gorfe AA, Levental KR and Levental I “Structural determinants and functional consequences of protein affinity for membrane rafts”, Nature Communications, 2017, 8: 1219
  46. Sarkar-Bannerjee S, Sayyed-Ahmad A, Prakash P, Cho K-J, Waxham MN, Hancock JF and Gorfe AA “Spatiotemporal analysis of K-Ras plasma membrane interactions reveals multiple high order homo-oligomeric complexes”, Journal of the American Chemical Society, 2017, 139 (38), 13466–13475.
  47. Sayyed-Ahmad A, Prakash P, Gorfe AA “Distinct dynamics and interaction patterns in H- and K-Ras oncogenic P-loop mutants”, Proteins: Structure Function and Bioinformatics, 2017, 85(9):1618-1632.
  48. Sayyed-Ahmad A, Gorfe AA “Mixed-probe simulation and probe-derived surface topography map analysis for ligand binding site identification”, Journal of Chemical Theory and Computation, 2017, 13(4):1851-1861.
  49. Prakash P, Sayyed-Ahmad A, Cho K-J, Dolino DM, Chen W, Li H, Grant BJ, Hancock JF, Gorfe AA “Computational and biochemical characterization of two partially overlapping interfaces and multiple weak-affinity K-Ras dimers”, Scientific Reports, 2017, 7:40109.
  50. Zhou Y, Prakash P, Liang H, Cho KJ, Gorfe AA and Hancock JF. “Lipid-Sorting Specificity Encoded in K-Ras Membrane Anchor Regulates Signal Output”, Cell, 2016, 168: 1–13.
  51. Cho KJ, Casteel DE, Prakash P, Tan L, van der Hoeven D, Salim AA, Kim C, Capon RJ, Lacey E, Cunha SR, Gorfe AA, Hancock JF. “AMPK and eNOS signaling regulates K-Ras plasma membrane interactions via cGMP-dependent Protein Kinase 2”, 2016, Mol Cell Biol, 36(24):3086-3099.
  52. Lin X, Lorent JH, Skinkle AD, Levental KR, Waxham MN, Gorfe AA, Levental I. “Domain Stability in Biomimetic Membranes Driven by Lipid Polyunsaturation”, Journal of Physical Chemistry B, 2016, 120(46):11930-11941.
  53. Lin X, Zhang S, Ding H, Levental I and Gorfe AA, “The Aliphatic Chain of Cholesterol Modulates Bilayer Interleaflet Coupling and Domain Registration”, FEBS Letters, 2016, 590: 3368–3374.
  54. Prakash P and Gorfe AA, “Membrane orientation dynamics of lipid-modified small GTPases”, Small GTPases, 2016, Aug 11:1-10.
  55. Sayyed-Ahmad A, Cho K-J, Hancock JF and Gorfe AA, “Computational Equilibrium Thermodynamic and Kinetic Analysis of K-Ras Dimerization through an Effector Binding Surface Suggest Limited Functional Role”, Journal of Physical Chemistry B, 2016, 120(33):8547-8556.
  56. Levental KR, Lorent JH, Lin X, Skinkle AD, Surma MA, Stockenbojer EA, Gorfe AA, Levental I “Polyunsaturated lipids regulate membrane domain stability by tuning membrane order”, Biophysical Journal, 2016, 110(8):1800-1810.
  57. Prakash P, Zhou Y, Liang H, Hancock JF and Gorfe AA, “Oncogenic K-Ras binds to an anionic membrane in two distinct orientations: A molecular dynamics analysis”, Biophysical Journal, 2016, 110 (5), 1125–1138.
  58. Lin X, Li Z and Gorfe AA, “Reversible Effects of Peptide Concentration and Lipid Composition on H-Ras Lipid Anchor Clustering”, Biophysical Journal, 2015, 109(12):2467-70.
  59. Prakash P, Sayyed-Ahmad A and Gorfe AA, “pMD-membrane: A method for ligand binding site identification in membrane-bound proteins”, PLoS Comput Biol, 2015, 11(10): e1004469.
  60. McCarthy M, Prakash P and Gorfe AA “Computational allosteric ligand binding site identification on Ras proteins”, Acta Biochim Biophys Sin, 2015, 1–8.
  61. Prakash P, Hancock JF and Gorfe AA, “Binding hotspots on K-Ras: Consensus ligand binding sites and other reactive regions from probe-based molecular dynamics analysis”, Proteins 2015, 83(5): 898-909.
  62. Li Z and Gorfe AA, “Receptor-mediated membrane adhesion of lipid-polymer hybrid (LPH) nanoparticles studied by dissipative particle dynamics simulations”, Nanoscale, 2015, 7, 814-824.
  63. Li Z and Gorfe AA, “Modulation of a Small Two-Domain Lipid Vesicle by Linactants”, Journal of Physical Chemistry B, 2014, 18(30): 9028-9036.
  64. Li H and Gorfe AA, “Membrane Remodeling by Surface-Bound Protein Aggregates: Insights from Coarse-Grained Molecular Dynamics Simulation”, The Journal of Physical Chemistry Letters, 2014, 5(8): 1457-1462.
  65. Prakash P and Gorfe AA, “Overview of simulation studies on the enzymatic activity and conformational dynamics of the GTPase Ras”, Molecular Simulation, 2014, 40(10-11): 839-847.
  66. Hocker HJ, Maharaj N and Gorfe AA, “LIBSA – Method for the determination of ligand-binding preference to allosteric sites on receptor ensembles”, Journal of Chemical Information and Modeling, 2014, 24;54(2):530-538.
  67. Ramaswamy SS, Maclean DM, Gorfe AA, Jayaraman V, “Proton mediated conformational changes in an Acid Sensing Ion Channel”, Journal of Biological Chemistry, 2013, 288(50): 35896-35905.
  68. Li Z and Gorfe AA, “Deformation of a Two-domain Lipid Bilayer due to Asymmetric Insertion of Lipid-modified Ras Peptides”, Soft Matter, 2013, 9: 11249-11256.
  69. Prakash P and Gorfe AA, “Phosphatidylcholine attenuates aggregation of non-steroidal anti-inflammatory drugs with bile acids”, Biochemistry, 2013, 52(42): 7461–7469.
  70. Brand CS, Hocker HJ, Gorfe AA, Cavasotto CN, and Dessauer CW, “Isoform Selectivity of Adenylyl Cyclase Inhibitors: Characterization of Known and Novel Compounds”, Journal of Pharmacology and Experimental Therapeutics, 2013, 347(2):265-275.
  71. Li H and Gorfe AA, “Aggregation of lipid-anchored full-length H-Ras in lipid bilayers: Simulations with the MARTINI force field”, PLoS ONE, 2013, 8(7):e71018.
  72. Prakash P and Gorfe AA, “Lessons from computer simulations of Ras proteins in solution and in membrane”, BBA-General Subjects, 2013, 1830(110): 5211-5218.
  73. Hocker JH, Kwang-Jin C, Chung-Ying KC, Rambahal N, Sagineedu SR, Shaari K, Stanslas J, Hancock JF, Gorfe AA, “Andrographolide derivatives inhibit guanine nucleotide exchange and abrogate oncogenic Ras function”, Proceedings of the National Academy of Sciences USA, 2013, 110(25):10201-10206.
  74. Cho KJ, Park JH, Piggot AM, Salim AA, Gorfe AA, Parton RG, Capon RJ, Lacey E and Hancock JF, “Staurosporines disrupt phosphatidylserine trafficking and mislocalize Ras proteins”, Journal of Biological Chemistry, 2012: 287(52):43573-84.
  75. Li Z, Janosi L and Gorfe AA, “Formation and Domain-partitioning of H-ras Peptide Nanoclusters: Effects of Peptide Concentration and Lipid Composition”, Journal of the American Chemical Society, 2012, 134(41):17278-85.
  76. Li Z and Gorfe AA, “What drives the clustering of membrane-bound Ras? (Commentary)”, Small GTPases, 2012, 30;3(4): 244-247.
  77. Roach AN, Wang Z, Wu P, Zhang F, Chan R, Yonekubo Y, Paolo GD, Gorfe AA, Du G, “Phosphatidic acid regulation of PIPKI is critical for actin cytoskeletal reorganization”, Journal of Lipid Research, 2012, 53(12): 2598-2609.
  78. Prakash P, Sayyed-Ahmad A, Zhou Y, Volk DE, Gorenstein DG, Dial EJ, Lichtenberger LM and Gorfe AA, “Aggregation Behavior of Ibuprofen, Cholic Acid and Dodecylphosphocholine Micelles”, BBA-Biomembrane, 2012, 1818(12): 340-347.
  79. Janosi L, Li Z, Hancock JF and Gorfe AA, “Organization, Dynamics and Segregation of Ras Nanoclusters in Membrane Domains”, Proceedings of the National Academy of Sciences USA, 2012, 109(21): 8097-102.
  80. 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.
  81. Gorfe AA and Hocker JH, “Membrane Targeting: Methods”,eLS. John Wiley & Sons, Ltd: Chichester (2012).
  82. 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.
  83. 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.
  84. Grant BJ, Gorfe AA, McCammon JA, “Large conformational changes in proteins: Signaling and other functions”, Current Opinion in Structural Biology,2010, 20, 142-147.
  85. Zhou Y, Lu B-Z and Gorfe AA, “Continuum Electromechanical Modeling of Protein-Membrane Interaction”, Physical Review E, 2010, 82: 041923-041928.
  86. 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.
  87. 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.
  88. Gorfe AA, “Mechanisms of allostery and membrane attachment in Ras GTPases: Implications for anti-cancer drug discovery”, Current Medicinal Chemistry, 2010, 17, 1-9.
  89. 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.
  90. 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.
  91. 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.
  92. Sayyed-Ahmad A, Lichtenberger LM and Gorfe AA, “Structure and Dynamics of Cholic Acid and Dodecylphosphocholine−Cholic Acid Aggregates”, Langmuir, 2010, 26:13407-13414.
  93. 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.
  94. 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.
  95. 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.
  96. 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.
  97. 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
  98. 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.
  99. 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.
  100. Abankwa D, Gorfe AA, Hancock JF, “Mechanisms of Ras membrane organization and signaling: Ras on a rocker”, Cell Cycle, 2008, 7, 2667-2673.
  101. 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.
  102. 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.
  103. 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.
  104. 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.
  105. Gorfe AA, Chang CA, Ivanov I and McCammon JA, “Dynamics of the acetylcholinesterase tetramer”, Biophysical Journal, 2008, 94,1144-1154.
  106. Abankwa D, Gorfe AA, Hancock JF, “Ras nanoclusters: Molecular structure and assembly (Review)”, Seminars in Cell and Developmental Biology, 2007, 18, 599-607.
  107. 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.
  108. 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.
  109. 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.
  110. 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.
  111. 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.
  112. Gorfe AA and Caflisch A, “Functional plasticity in the substrate binding site of beta-secretase (BACE)”, Structure, 2005, 13:1487-1498.
  113. Gorfe AA, Pellarin R and Caflisch A, “Membrane localization and flexibility of a lipidated ras peptide studied by molecular dynamics simulations”, Journal of the American Chemical Society, 2004, 126:15277-15286.
  114. 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.
  115. 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.
  116. 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.
  117. 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.
  118. 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.
  119. 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.
  120. 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.