A. Gorfe

发表

Multi‐target, ensemble‐based virtual screening yields novel allosteric KRAS inhibitors at high success rate

Amit K. Gupta, Xu Wang, C. Pagba, 2019, Chemical biology & drug design.

Discovery of High-Affinity Noncovalent Allosteric KRAS Inhibitors That Disrupt Effector Binding

Amit K. Gupta, C. Pagba, Priyanka Prakash, 2019, ACS omega.

Conformational selection in G-proteins: lessons from Ras and Rho.

J Andrew McCammon, Barry J Grant, J. Mccammon, 2010, Biophysical journal.

Large conformational changes in proteins: signaling and other functions.

J Andrew McCammon, Barry J Grant, J. Mccammon, 2010, Current opinion in structural biology.

Calculation of protein ionization equilibria with conformational sampling: pKa of a model leucine zipper, GCN4 and barnase

Amedeo Caflisch, Hans Rudolf Bosshard, A. Caflisch, 2002, Proteins.

Computational allosteric ligand binding site identification on Ras proteins.

Priyanka Prakash, Priyanka Prakash, A. Gorfe, 2015, Acta biochimica et biophysica Sinica.

Ras nanoclusters: molecular structure and assembly.

A. Gorfe, J. Hancock, D. Abankwa, 2007, Seminars in cell & developmental biology.

Phosphorylation-induced Conformational Changes in Rap1b

Sheng Li, Virgil L. Woods, Sergio E. Wong, 2009, The Journal of Biological Chemistry.

Novel Allosteric Sites on Ras for Lead Generation

Harrison J. Hocker, J. Mccammon, A. Gorfe, 2011, PloS one.

Discovery of allosteric non-covalent KRAS inhibitors that bind with sub-micromolar affinity and disrupt effector binding

Amit K. Gupta, C. Pagba, Priyanka Prakash, 2018, bioRxiv.

Mixed-Probe Simulation and Probe-Derived Surface Topography Map Analysis for Ligand Binding Site Identification.

A. Gorfe, A. Sayyed-Ahmad, 2017, Journal of chemical theory and computation.

Binding hotspots on K‐ras: Consensus ligand binding sites and other reactive regions from probe‐based molecular dynamics analysis

Priyanka Prakash, A. Gorfe, J. Hancock, 2015, Proteins.

Andrographolide derivatives inhibit guanine nucleotide exchange and abrogate oncogenic Ras function

Khozirah Shaari, Harrison J. Hocker, Nandini Rambahal, 2013, Proceedings of the National Academy of Sciences.

Lessons from computer simulations of Ras proteins in solution and in membrane.

Priyanka Prakash, Priyanka Prakash, A. Gorfe, 2013, Biochimica et biophysica acta.

Isoform Selectivity of Adenylyl Cyclase Inhibitors: Characterization of Known and Novel Compounds

Claudio N Cavasotto, Harrison J. Hocker, C. Dessauer, 2013, The Journal of Pharmacology and Experimental Therapeutics.

H-ras protein in a bilayer: interaction and structure perturbation.

J. Mccammon, A. Gorfe, A. Babakhani, 2007, Journal of the American Chemical Society.

Mapping the nucleotide and isoform-dependent structural and dynamical features of Ras proteins.

J Andrew McCammon, Barry J Grant, J. Mccammon, 2008, Structure.

A novel switch region regulates H‐ras membrane orientation and signal output

J Andrew McCammon, Daniel Abankwa, Robert G Parton, 2008, The EMBO journal.

KRAS Ubiquitination at Lysine 104 Retains Exchange Factor Regulation by Dynamically Modulating the Conformation of the Interface

A. Gorfe, J. Harrison, S. Campbell, 2020, iScience.

Membrane curvature sensing of the lipid-anchored K-Ras small GTPases

Suparna Sarkar-Banerjee, A. Gorfe, Hong Liang, 2018, bioRxiv.

Aggregation of Lipid-Anchored Full-Length H-Ras in Lipid Bilayers: Simulations with the MARTINI Force Field

Alemayehu A. Gorfe, A. Gorfe, Hualin Li, 2013, PloS one.

Domain Stability in Biomimetic Membranes Driven by Lipid Polyunsaturation.

M. Waxham, A. Gorfe, K. Levental, 2016, The journal of physical chemistry. B.

Membrane localization and flexibility of a lipidated ras peptide studied by molecular dynamics simulations.

A. Caflisch, R. Pellarin, A. Gorfe, 2004, Journal of the American Chemical Society.

What drives the clustering of membrane-bound Ras?

A. Gorfe, Zhenlong Li, 2012, Small GTPases.

Formation and domain partitioning of H-ras peptide nanoclusters: effects of peptide concentration and lipid composition.

A. Gorfe, L. Janosi, Zhenlong Li, 2012, Journal of the American Chemical Society.

Long-Range Coupled Motions Underlie Ligand Recognition by a Chemokine Receptor

Priyanka Prakash, A. Gorfe, K. Rajarathnam, 2020, iScience.

Dynamics of the Acetylcholinesterase Tetramer

J. Mccammon, Chia-En Chang, A. Gorfe, 2007, Biophysical journal.

Membrane Targeting: Methods

Harrison J. Hocker, A. Gorfe, 2012 .

Dynamics of Membrane-Bound G12V-KRAS from Simulations and Single-Molecule FRET in Native Nanodiscs.

Douglas B. Litwin, Priyanka Prakash, Suparna Sarkar-Banerjee, 2019, Biophysical journal.

Computational and biochemical characterization of two partially overlapping interfaces and multiple weak-affinity K-Ras dimers

Wei Chen, Hongyang Li, Priyanka Prakash, 2017, Scientific Reports.

Understanding Membrane Domain-Partitioning Thermodynamics of Transmembrane Domains with Potential of Mean Force Calculations.

A. Gorfe, Xubo Lin, 2019, The journal of physical chemistry. B.

Conformational spread and dynamics in allostery of NMDA receptors

A. Gorfe, David M. Maclean, V. Jayaraman, 2020, Proceedings of the National Academy of Sciences.

The aliphatic chain of cholesterol modulates bilayer interleaflet coupling and domain registration

A. Gorfe, Xubo Lin, I. Levental, 2016, FEBS letters.

Mechanisms of Ras Membrane Organization and Signaling: Ras Rocks Again

A. Gorfe, D. Abankwa, 2020, Biomolecules.

Protein Partitioning into Ordered Membrane Domains: Insights from Simulations.

A. Gorfe, Xubo Lin, I. Levental, 2018, Biophysical journal.

The KRAS and other prenylated polybasic domain membrane anchors recognize phosphatidylserine acyl chain structure

Priyanka Prakash, A. Gorfe, Hong Liang, 2021, Proceedings of the National Academy of Sciences.

KRAS Inhibitor that Simultaneously Inhibits Nucleotide Exchange Activity and Effector Engagement

J. Frost, Amit K. Gupta, C. Pagba, 2022, ACS Bio & Med Chem Au.

Remodeling of the Plasma Membrane by Surface-Bound Protein Monomers and Oligomers: The Critical Role of Intrinsically Disordered Regions

A. Gorfe, Yong Zhou, Mussie K. Araya, 2022, The Journal of Membrane Biology.

Lipid-Sorting Specificity Encoded in K-Ras Membrane Anchor Regulates Signal Output

Priyanka Prakash, Alemayehu A. Gorfe, Priyanka Prakash, 2017, Cell.

Phosphatidylserine and Phosphatidylethanolamine Asymmetry Have a Negligible Effect on the Global Structure, Dynamics, and Interactions of the KRAS Lipid Anchor.

A. Gorfe, Mussie K. Araya, 2022, The journal of physical chemistry. B.

Building insights into KRAS signaling complexes

A. Gorfe, J. Hancock, 2021, Nature Structural & Molecular Biology.

Membrane-Bound Ras as a Conformational Clock.

S. Sligar, A. Gorfe, 2020, Biophysical journal.

Salt bridges destabilize a leucine zipper designed for maximized ion pairing between helices.

J. Warwicker, A. Gorfe, H. Bosshard, 2002, Biochemistry.

Membrane curvature sensing of the lipid-anchored K-Ras small GTPase

Suparna Sarkar-Banerjee, A. Gorfe, Hong Liang, 2019, Life Science Alliance.

Intracellular Ca2+ regulation of H+/Ca2+ antiporter YfkE mediated by a Ca2+ mini-sensor

A. Gorfe, Shuo Lu, Zhenlong Li, 2020, Proceedings of the National Academy of Sciences.

Structure and dynamics of cholic acid and dodecylphosphocholine-cholic acid aggregates.

A. Gorfe, L. Lichtenberger, A. Sayyed-Ahmad, 2010, Langmuir : the ACS journal of surfaces and colloids.

Transmembrane potential of physiologically relevant model membranes: Effects of membrane asymmetry.

A. Gorfe, Xubo Lin, 2020, The Journal of chemical physics.

Simulating POPC and POPC/POPG Bilayers: Conserved Packing and Altered Surface Reactivity.

A. Gorfe, L. Janosi, 2010, Journal of chemical theory and computation.

LIBSA – A Method for the Determination of Ligand-Binding Preference to Allosteric Sites on Receptor Ensembles

Alemayehu A. Gorfe, Harrison J. Hocker, Nandini Rambahal, 2014, J. Chem. Inf. Model..

Location of inhibitors bound to group IVA phospholipase A2 determined by molecular dynamics and deuterium exchange mass spectrometry.

Virgil L. Woods, J. Mccammon, E. Dennis, 2009, Journal of the American Chemical Society.

Free Energy for the Permeation of Na+ and Cl− Ions and Their Ion-Pair through a Zwitterionic Dimyristoyl Phosphatidylcholine Lipid Bilayer by Umbrella Integration with Harmonic Fourier Beads

J. Mccammon, A. Gorfe, B. Lu, 2009, Journal of the American Chemical Society.

Three distinct regions of cRaf kinase domain interact with membrane

Priyanka Prakash, A. Gorfe, J. Hancock, 2019, Scientific Reports.

Functional Plasticity in the Substrate Binding Site of β-Secretase

A. Caflisch, A. Gorfe, 2005 .

Long-Range Coupled Motions Underlie Ligand Recognition by a Chemokine Receptor

Priyanka Prakash, A. Gorfe, K. Rajarathnam, 2020, bioRxiv.

The Role of Conserved Waters in Conformational Transitions of Q61H K-ras

Priyanka Prakash, Abdallah Sayyed-Ahmad, Alemayehu A. Gorfe, 2012, PLoS Comput. Biol..

Overview of simulation studies on the enzymatic activity and conformational dynamics of the GTPase Ras

Priyanka Prakash, A. Gorfe, 2014, Molecular simulation.

How to make an undruggable enzyme druggable: lessons from ras proteins.

A. Gorfe, A. Sayyed-Ahmad, 2020, Advances in protein chemistry and structural biology.

Membrane orientation dynamics of lipid-modified small GTPases

Priyanka Prakash, Priyanka Prakash, A. Gorfe, 2017, Small GTPases.

Mechanisms of allostery and membrane attachment in Ras GTPases: implications for anti-cancer drug discovery.

A. Gorfe, 2010, Current medicinal chemistry.

Conformational and Dynamical Effects of Tyr32 Phosphorylation in K-Ras: Molecular Dynamics Simulation and Markov State Models Analysis.

A. Gorfe, A. Sayyed-Ahmad, M. Khaled, 2019, The journal of physical chemistry. B.

Spatiotemporal Analysis of K-Ras Plasma Membrane Interactions Reveals Multiple High Order Homo-oligomeric Complexes.

M. Neal Waxham, Priyanka Prakash, Alemayehu A. Gorfe, 2017, Journal of the American Chemical Society.

Structural determinants and functional consequences of protein affinity for membrane rafts

A. Gorfe, K. Levental, Xubo Lin, 2017, Nature Communications.

Segregation of negatively charged phospholipids by the polycationic and farnesylated membrane anchor of Kras.

A. Gorfe, L. Janosi, 2010, Biophysical journal.

Small Molecule KRAS Inhibitors: The Future for Targeted Pancreatic Cancer Therapy?

N. Pavlakis, J. Samra, A. Gorfe, 2020, Cancers.

Biophysics of cancer.

A. Gorfe, 2022, Biophysical journal.

Structure and dynamics of the full-length lipid-modified H-Ras protein in a 1,2-dimyristoylglycero-3-phosphocholine bilayer.

J. Mccammon, A. Gorfe, J. Hancock, 2007, Journal of medicinal chemistry.

In silico and saturation transfer difference NMR approaches to unravel the binding mode of an andrographolide derivative to K-Ras oncoprotein.

A. Gorfe, J. Stanslas, S. Sagineedu, 2020, Future medicinal chemistry.

Monoubiquitination of KRAS at Lysine104 and Lysine147 Modulates Its Dynamics and Interaction with Partner Proteins.

A. Gorfe, J. Hancock, S. Campbell, 2021, The journal of physical chemistry. B.

Distinct dynamics and interaction patterns in H‐ and K‐Ras oncogenic P‐loop mutants

Priyanka Prakash, Abdallah Sayyed-Ahmad, Priyanka Prakash, 2017, Proteins.

Mechanisms of Ras membrane organization and signaling: Ras on a rocker

A. Gorfe, J. Hancock, D. Abankwa, 2008, Cell cycle.

RAS Nanoclusters Selectively Sort Distinct Lipid Headgroups and Acyl Chains

A. Gorfe, Yong Zhou, J. Hancock, 2021, Frontiers in Molecular Biosciences.

Approaches to inhibiting oncogenic K-Ras

A. Gorfe, Kwang-jin Cho, 2019, Small GTPases.

Ras and the Plasma Membrane: A Complicated Relationship.

Priyanka Prakash, A. Gorfe, Yong Zhou, 2018, Cold Spring Harbor perspectives in medicine.

AMPK and Endothelial Nitric Oxide Synthase Signaling Regulates K-Ras Plasma Membrane Interactions via Cyclic GMP-Dependent Protein Kinase 2

Priyanka Prakash, A. Gorfe, Dharini van der Hoeven, 2016, Molecular and Cellular Biology.

AMPK and eNOS signaling regulates K-Ras plasma membrane interactions via cGMP-dependent Protein Kinase 2

Priyanka Prakash, A. Gorfe, Kwang-jin Cho, 2016 .

Water-Membrane Partition Thermodynamics of an Amphiphilic Lipopeptide: An Enthalpy-Driven Hydrophobic Effect

J. Mccammon, R. Baron, A. Gorfe, 2008, Biophysical journal.

Non-Bisphosphonate Inhibitors of Isoprenoid Biosynthesis Identified via Computer-Aided Drug Design

Jacob D. Durrant, J. Mccammon, E. Oldfield, 2011, Chemical biology & drug design.

Ser170 controls the conformational multiplicity of the loop 166–175 in prion proteins: implication for conversion and species barrier

A. Caflisch, A. Gorfe, 2007, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

Enzymatic activity versus structural dynamics: the case of acetylcholinesterase tetramer.

Zeyun Yu, Benzhuo Lu, J. Andrew McCammon, 2009, Biophysical journal.

Organization, dynamics, and segregation of Ras nanoclusters in membrane domains

A. Gorfe, J. Hancock, John F Hancock, 2012, Proceedings of the National Academy of Sciences.

Ras membrane orientation and nanodomain localization generate isoform diversity

A. Gorfe, J. Hancock, K. Inder, 2010, Proceedings of the National Academy of Sciences.

Computational Equilibrium Thermodynamic and Kinetic Analysis of K-Ras Dimerization through an Effector Binding Surface Suggests Limited Functional Role.

A. Gorfe, Kwang-jin Cho, J. Hancock, 2016, The journal of physical chemistry. B.

Oncogenic K-Ras Binds to an Anionic Membrane in Two Distinct Orientations: A Molecular Dynamics Analysis.

Priyanka Prakash, Priyanka Prakash, A. Gorfe, 2016, Biophysical journal.

Reversible Effects of Peptide Concentration and Lipid Composition on H-Ras Lipid Anchor Clustering.

Xubo Lin, A. Gorfe, Xubo Lin, 2015, Biophysical journal.

The Distinct Conformational Dynamics of K-Ras and H-Ras A59G

Suryani Lukman, Guy H. Grant, James Andrew McCammon, 2010, PLoS Comput. Biol..

Polyunsaturated Lipids Regulate Membrane Domain Stability by Tuning Membrane Order.

M. A. Surma, A. Gorfe, K. Levental, 2016, Biophysical journal.

Probing the Conformational and Energy Landscapes of KRAS Membrane Orientation.

Priyanka Prakash, A. Gorfe, 2019, The journal of physical chemistry. B.

Ras Conformational Switching: Simulating Nucleotide-Dependent Conformational Transitions with Accelerated Molecular Dynamics

James Andrew McCammon, Barry J. Grant, Alemayehu A. Gorfe, 2009, PLoS Comput. Biol..

Determinants of Membrane Orientation Dynamics in Lipid-Modified Small GTPases

Priyanka Prakash, A. Gorfe, 2021, JACS Au.

Molecular Dynamics Simulation of Lipid-Modified Signaling Proteins.

A. Gorfe, Vinay V Nair, 2021, Methods in molecular biology.

pMD-Membrane: A Method for Ligand Binding Site Identification in Membrane-Bound Proteins

Priyanka Prakash, Abdallah Sayyed-Ahmad, Alemayehu A. Gorfe, 2015, PLoS Comput. Biol..

Deformation of a Two-domain Lipid Bilayer due to Asymmetric Insertion of Lipid-modified Ras Peptides.

A. Gorfe, Zhenlong Li, 2013, Soft matter.

Modulation of a Small Two-Domain Lipid Vesicle by Linactants

A. Gorfe, Zhenlong Li, 2014, The journal of physical chemistry. B.

Phosphatidic acid regulation of PIPKI is critical for actin cytoskeletal reorganization[S]

A. Gorfe, G. Du, R. Chan, 2012, Journal of Lipid Research.

Continuum electromechanical modeling of protein-membrane interactions.

Benzhuo Lu, A. Gorfe, Y. C. Zhou, 2010, Physical review. E, Statistical, nonlinear, and soft matter physics.

Antipsychotic phenothiazine drugs bind to KRAS in vitro

J. Putkey, Xu Wang, A. Gorfe, 2021, Journal of Biomolecular NMR.

Structural determinants and functional consequences of protein affinity for membrane rafts

A. Gorfe, K. Levental, Xubo Lin, 2017, Nature Communications.

Membrane potential and dynamics in a ternary lipid mixture: insights from molecular dynamics simulations.

A. Gorfe, Yong Zhou, Xubo Lin, 2018, Physical chemistry chemical physics : PCCP.

Aggregation behavior of ibuprofen, cholic acid and dodecylphosphocholine micelles.

D. Volk, D. Gorenstein, Priyanka Prakash, 2012, Biochimica et biophysica acta.

Membrane Remodeling by Surface-Bound Protein Aggregates: Insights from Coarse-Grained Molecular Dynamics Simulation

A. Gorfe, Hualin Li, 2014, The journal of physical chemistry letters.

Phosphatidylcholine attenuates aggregation of nonsteroidal anti-inflammatory drugs with bile acid.

Priyanka Prakash, A. Gorfe, 2013, Biochemistry.

Receptor-mediated membrane adhesion of lipid-polymer hybrid (LPH) nanoparticles studied by dissipative particle dynamics simulations.

A. Gorfe, Zhenlong Li, 2015, Nanoscale.

Proton-mediated Conformational Changes in an Acid-sensing Ion Channel*

S. Ramaswamy, A. Gorfe, David M. Maclean, 2013, The Journal of Biological Chemistry.

Functional plasticity in the substrate binding site of beta-secretase.

A. Caflisch, A. Gorfe, 2005, Structure.

Electrostatics of mesophilic and psychrophilic trypsin isoenzymes: Qualitative evaluation of electrostatic differences at the substrate binding site

B. Brandsdal, A. Gorfe, R. Helland, 2000, Proteins.

A new ferrocene derivative blocks KRAS localization and function by oxidative modification at His95

A. Gorfe, Kwang-jin Cho, K. Arumugam, 2023, bioRxiv.

Importance of the sphingosine base double-bond geometry for the structural and thermodynamic properties of sphingomyelin bilayers.

A. Gorfe, L. Janosi, 2010, Biophysical journal.

Aggregation Behavior of Indomethacin, Cholic Acid & POPC

A. Gorfe, L. Lichtenberger, P. Srivastava, 2012 .

Three distinct regions of cRaf kinase domain interact with membrane

Priyanka Prakash, A. Gorfe, J. Hancock, 2019, Scientific Reports.

A new ferrocene derivative blocks K-Ras localization and function by oxidative modification at His95

A. Gorfe, Kwang-jin Cho, Rhonda L Pitsch, 2023, Life science alliance.

The role of flexibility and hydration on the sequence‐specific DNA recognition by the Tn916 integrase protein: a molecular dynamics analysis

Amedeo Caflisch, A. Caflisch, A. Gorfe, 2004, Journal of molecular recognition : JMR.

Energetics of sequence-specific protein-DNA association: binding of integrase Tn916 to its target DNA.

Stoyan Milev, Hans Rudolf Bosshard, Andrey Karshikoff, 2003, Biochemistry.

Phosphatidylcholine attenuates aggregation of nonsteroidal anti-inflammatory drugs with bile acid.

Priyanka Prakash, A. Gorfe, 2013, Biochemistry.

Location of inhibitors bound to group IVA phospholipase A2 determined by molecular dynamics and deuterium exchange mass spectrometry.

Virgil L. Woods, E. Dennis, A. Gorfe, 2009, Journal of the American Chemical Society.

Conformational ensemble dependent lipid recognition and segregation by prenylated intrinsically disordered regions in small GTPases

A. Gorfe, Mussie K. Araya, 2023, bioRxiv.

Dynamics of Membrane-Bound G12V-KRAS from Simulations and Single-Molecule FRET in Native Nanodiscs.

Douglas B. Litwin, Priyanka Prakash, Suparna Sarkar-Banerjee, 2020, Biophysical journal.

Oncogenic K-Ras Binds to an Anionic Membrane in Two Distinct Orientations: A Molecular Dynamics Analysis.

Priyanka Prakash, A. Gorfe, Hong Liang, 2016, Biophysical journal.

Polyunsaturated Lipids Regulate Membrane Domain Stability by Tuning Membrane Order.

M. A. Surma, A. Gorfe, K. Levental, 2016, Biophysical journal.

A novel switch region regulates H‐ras membrane orientation and signal output

A. Gorfe, J. Hancock, S. Plowman, 2008, The EMBO journal.

Peptide insertion, positioning, and stabilization in a membrane: insight from an all-atom molecular dynamics simulation.

J. Gullingsrud, A. Gorfe, J. Andrew McCammon, 2007, Biopolymers.

Ser170 controls the conformational multiplicity of the loop 166–175 in prion proteins: implication for conversion and species barrier

A. Caflisch, A. Gorfe, 2007, FASEB journal : official publication of the Federation of American Societies for Experimental Biology.

Isoform Selectivity of Adenylyl Cyclase Inhibitors: Characterization of Known and Novel Compounds

Harrison J. Hocker, C. Dessauer, A. Gorfe, 2013, The Journal of Pharmacology and Experimental Therapeutics.

Thermodynamics of Peptide Insertion and Aggregation in a Lipid Bilayer

A. Gorfe, Judy E. Kim, J. McCammon, 2008, The journal of physical chemistry. B.

Computational Identification of Noncoding Driver Mutations Based on Impact on RNA Processing

A. Gorfe, S. Prijic, K. Zhu, 2020 .

LIBSA – A Method for the Determination of Ligand-Binding Preference to Allosteric Sites on Receptor Ensembles

Harrison J. Hocker, A. Gorfe, Nandini Rambahal, 2014, J. Chem. Inf. Model..