2. Welcome to the Gorfe Research Group
  3. Publications

Publications

  1. Zhou Y, Zhang D, Gorfe AA and Yang H. Spatiotemporal function and regulation of phosphatidylserine. Under Review
  2. Bhardwaj VK and Gorfe AA. Ligand-induced decoupling of residue networks and the molecular basis of GPR174 Inhibition. Under Review.
  3. Pagba CV, Dilsha K, Rakshya O, Liang X, Jakubec J, Sianoya AC, Gilbertson S, and Gorfe AA. Synthesis and biochemical characterization of investigational pyrazolopyrimidine-based allosteric KRAS modulators.  ACS Med Chem Lett (2026). (external link)
  4. Addis AG, Jakubec J, Sanchez J, Pagba CV and Gorfe AA. Identification and Testing of Potential Noncovalent Small-Molecule KRAS Inhibitors Through Virtual Screening.  J Chem Info Model. (external link)
  5. Sianoya AC, Zou Y, Pagba CV, Jakubec J, Planque SA, Frost JA, Medina PAB, Gorfe AA. MRTX1133 is a potent non-covalent KRAS (G12C) inhibitor with tissue-specific activity. Mol Cancer Ther (2026).  https://doi.org/10.1158/1535-7163.MCT-25-1087. (external link)
  6. Sianoya AC, Bhardwaj VK and Gorfe AA “Ras-membrane interaction and oligomerization: there is more than meets the eye”, Biochem Soc Trans (2025). (external link)
  7. Wei Ruan, Tao Li, In Hyuk Bang, Jaewoong Lee, Wankun Deng, Xinxin Ma, Cong Luo, Fang Du, Seung-Hee Yoo, Boyun Kim, Jiwen Li, Xiaoyi Yuan, Katherine Figarella, Yu A An, Yin-Ying Wang, Yafen Liang, Matthew Deberge, Dongze Zhang, Zhen Zhou, Yanyu Wang, Josh Gorham, Jonathan G. Seidman, Christine E. Seidman, Sary F. Aranki, Ragini Nair, Lei Li, Jagat Narula, Zhongming Zhao, Alemayehu A. Gorfe, Jochen Daniel Muehlschlegel, Kuang-Lei Tsai, and Holger K. Eltzschig. “BMAL1/HIF2A heterodimer modulates circadian variations of myocardial injury”. Nature (2025). (external link)
  8. Alemayehu A. Gorfe, Sandrasegaram Gnanakaran, Editorial, Current Opinion in Structural Biology, Volume 89, 2024, 102938. (external link)
  9. 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 (external link)
  10. 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. (external link)
  11. 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. (external link)
  12. 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. (external link)
  13. 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) (external link)
  14. 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 (external link)
  15. 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. (external link)
  16. 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. (external link)
  17. Gorfe AA “Biophysics of Cancer”, Biophysical Journal 121, E01–E02, October 4, 2022. (external link)
  18. 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. (external link)
  19. 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. (external link)
  20. 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. (external link)
  21. 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. (external link)
  22. Prakash P and Gorfe AA “Determinants of membrane orientation dynamics in lipid-modified small GTPases”, JACS Au 2022, 2, 128−135. (external link)
  23. Hancock JF and Gorfe AA “Building insights into KRAS signaling complexes”, Nat Struct Mol Biol, 28, 773-778, 2021. (external link)
  24. Wang X, Gorfe AA and Putkey JF “Antipsychotic Phenothiazine Drugs Bind to KRAS in vitro”, 2021, J Biomol NMR 75, 233–244, 2021. (external link)
  25. Zhou Y, Gorfe AA and Hancock JF “RAS nanoclusters selectively sort distinct lipid headgroups and acyl chains”, 2021, Front. Mol. Biosci., 17. (external link)
  26. 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. (external link)
  27. 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. (external link)
  28. 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. (external link)
  29. 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. (external link)
  30. Abankwa D and Gorfe AA “Mechanisms of Ras membrane organization and signaling: Ras rocks again”, Biomolecules 2020, 10(11), 1522. (external link)
  31. Lin X and Gorfe AA “Transmembrane Potential of Physiologically Relevant Model Membranes: Effects of Membrane Asymmetry”, 2020, J. Chem. Phys. 153, 105103. (external link)
  32. 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. (external link)
  33. 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. (external link)
  34. 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. (external link)
  35. 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. (external link)
  36. 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. (external link)
  37. Gorfe AA and Sligar SG “Membrane-bound Ras as a conformational clock”, 2020, Biophysical Journal, 118, 1–3. (external link)
  38. 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. (external link)
  39. 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. (external link)
  40. Gorfe AA, Cho KJ “Approaches to inhibiting oncogenic K-Ras”, 2019, Small GTPases, Aug 22:1-10. (external link)
  41. 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. (external link)
  42. 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. (external link)
  43. 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. (external link)
  44. Prakash P, Hancock JF, Gorfe AA “Three distinct regions of cRaf kinase domain interact with membrane”, 2019, Sci Rep, 14;9(1):2057. (external link)
  45. 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. (external link)
  46. 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. (external link)
  47. 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. (external link)
  48. 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. (external link)
  49. Lin X, Gorfe AA, Levental I “Protein Partitioning into Ordered Membrane Domains: Insights from Simulations”, 2018, Biophys J 114(8):1936-1944. (external link)
  50. 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. (external link)
  51. 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 (external link)
  52. 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. (external link)
  53. 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 (external link).
  54. 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 (external link).
  55. 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. (external link)
  56. 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. (external link)
  57. 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. (external link)
  58. 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. (external link)
  59. 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. (external link)
  60. Prakash P and Gorfe AA, “Membrane orientation dynamics of lipid-modified small GTPases”, Small GTPases, 2016, Aug 11:1-10. (external link)
  61. 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. (external link)
  62. 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. (external link)
  63. 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. (external link)
  64. 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. (external link)
  65. 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. (external link)
  66. McCarthy M, Prakash P and Gorfe AA “Computational allosteric ligand binding site identification on Ras proteins”, Acta Biochim Biophys Sin, 2015, 1–8. (external link)
  67. 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. (external link)
  68. 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. (external link)
  69. 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. (external link)
  70. 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. (external link)
  71. 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. (external link)
  72. 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. (external link)
  73. 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. (external link)
  74. 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. (external link)
  75. Prakash P and Gorfe AA, “Phosphatidylcholine attenuates aggregation of non-steroidal anti-inflammatory drugs with bile acids”, Biochemistry, 2013, 52(42): 7461–7469. (external link)
  76. 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. (external link)
  77. 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. (external link)
  78. 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. (external link)
  79. 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. (external link)
  80. 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. (external link)
  81. 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. (external link)
  82. Li Z and Gorfe AA, “What drives the clustering of membrane-bound Ras? (Commentary)”, Small GTPases, 2012, 30;3(4): 244-247. (external link)
  83. 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. (external link)
  84. 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. (external link)
  85. 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. (external link)
  86. 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. (external link)
  87. Gorfe AA and Hocker JH, “Membrane Targeting: Methods”,eLS. John Wiley & Sons, Ltd: Chichester (2012). (external link)
  88. 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. (external link)
  89. 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. (external link)
  90. Grant BJ, Gorfe AA, McCammon JA, “Large conformational changes in proteins: Signaling and other functions”, Current Opinion in Structural Biology,2010, 20, 142-147. (external link)
  91. Zhou Y, Lu B-Z and Gorfe AA, “Continuum Electromechanical Modeling of Protein-Membrane Interaction”, Physical Review E, 2010, 82: 041923-041928. (external link)
  92. 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. (external link)
  93. 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. (external link)
  94. Gorfe AA, “Mechanisms of allostery and membrane attachment in Ras GTPases: Implications for anti-cancer drug discovery”, Current Medicinal Chemistry, 2010, 17, 1-9. (external link)
  95. 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. (external link)
  96. 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. (external link)
  97. 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. (external link)
  98. Sayyed-Ahmad A, Lichtenberger LM and Gorfe AA, “Structure and Dynamics of Cholic Acid and Dodecylphosphocholine−Cholic Acid Aggregates”, Langmuir, 2010, 26:13407-13414. (external link)
  99. 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. (external link)
  100. 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. (external link)
  101. 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. (external link)
  102. 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. (external link)
  103. 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 (external link)
  104. 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. (external link)
  105. 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. (external link)
  106. Abankwa D, Gorfe AA, Hancock JF, “Mechanisms of Ras membrane organization and signaling: Ras on a rocker”, Cell Cycle, 2008, 7, 2667-2673. (external link)
  107. 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. (external link)
  108. 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. (external link)
  109. 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. (external link)
  110. 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. (external link)
  111. Gorfe AA, Chang CA, Ivanov I and McCammon JA, “Dynamics of the acetylcholinesterase tetramer”, Biophysical Journal, 2008, 94,1144-1154. (external link)
  112. Abankwa D, Gorfe AA, Hancock JF, “Ras nanoclusters: Molecular structure and assembly (Review)”, Seminars in Cell and Developmental Biology, 2007, 18, 599-607. (external link)
  113. 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. (external link)
  114. Gorfe AA, Babakhani A and McCammon JA, “Free Energy profile of H-ras membrane anchor upon membrane insertion”, Angewandte Chemie International Edition, 2007, 46, 8234 – 8237. (external link)
  115. 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. (external link)
  116. 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. (external link)
  117. 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. (external link)
  118. Gorfe AA and Caflisch A, “Functional plasticity in the substrate binding site of beta-secretase (BACE)”, Structure, 2005, 13:1487-1498. (external link)
  119. 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. (external link)
  120. 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. (external link)
  121. 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. (external link)
  122. 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. (external link)
  123. 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. (external link)
  124. 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. (external link)
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