Publications



Gorfe_publications

Hualin Li 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. 


Prakash P and Gorfe AA
Overview of simulation studeis on the enzymatic activity and conformational dynamics of the GTPase Ras 
Molecular Simulation (published online: March 14, 2014)  

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. 


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. 


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. 


Prakash P and Gorfe AA
Phosphatidylcholine attenuates aggregation of non-steroidal anti-inflammatory drugs with bile acids 
Biochemistry, 2013, 52(42): 7461–7469. 


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. 


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. 


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 

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. 


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. 


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. 


Li Z and Gorfe AA
What drives the clustering of membrane-bound Ras? (Commentary) 
Small GTPases, 2012, 30;3(4): 244-247.

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.


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-Biomembranes, 2012, 1818(12): 340-347. 


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. 


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. 


Grant BJ, Gorfe AA, McCammon JA. 
Large conformational changes in proteins: Signaling and other functions.
Current Opinion in Structuctral Biology, 2010, 20, 142-147. 
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
 

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 

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, 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 

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, 50:674-84This 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 


Theses (2):

Gorfe AA (PhD thesis, University of Zurich, 2003)
Protein Ionization Equilibria and Protein-DNA Binding: Conformational Dynamics and Thermodynamics From a Computational Perspective. 

Gorfe AA (MSc thesis, University of Tromsoe, 1999)
Electrostatics of Mesophilic and Psycrophilic Trypsin Iso-enzymes: Qualitative and Quantitative Evaluations Based on Continuum Models.