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Biophysics of cancer

Biophysical journal, 2022-10, Vol.121 (19), p.E1-E2

Gorfe, Alemayehu A

2022

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

Biophysical journal, 2016-03, Vol.110 (5), p.1125-1138

2016

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Protein Partitioning into Ordered Membrane Domains: Insights from Simulations

Biophysical journal, 2018-04, Vol.114 (8), p.1936-1944

2018

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

Cell, 2017-01, Vol.168 (1-2), p.239-251.e16

2017

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Probing the Conformational and Energy Landscapes of KRAS Membrane Orientation

The journal of physical chemistry. B, 2019-10, Vol.123 (41), p.8644-8652

2019

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Structural determinants and functional consequences of protein affinity for membrane rafts

Nature communications, 2017-10, Vol.8 (1), p.1219-10, Article 1219

2017

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Polyunsaturated Lipids Regulate Membrane Domain Stability by Tuning Membrane Order

Biophysical journal, 2016-04, Vol.110 (8), p.1800-1810

2016

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Aggregation of lipid-anchored full-length H-Ras in lipid bilayers: simulations with the MARTINI force field

PloS one, 2013-07, Vol.8 (7), p.e71018-e71018

2013

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

The journal of physical chemistry. B, 2019-09, Vol.123 (36), p.7667-7675

2019

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

The Journal of chemical physics, 2020-09, Vol.153 (10), p.105103-105103

2020

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

Proceedings of the National Academy of Sciences - PNAS, 2012-05, Vol.109 (21), p.8097-8102

2012

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Intrinsically Disordered Membrane Anchors of Rheb, RhoA, and DiRas3 Small GTPases: Molecular Dynamics, Membrane Organization, and Interactions

The journal of physical chemistry. B, 2024-07, Vol.128 (27), p.6518-6528

2024

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From disorder comes function: Regulation of small GTPase function by intrinsically disordered lipidated membrane anchor

Current opinion in structural biology, 2024-08, Vol.87, p.102869-102869, Article 102869

2024

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Novel allosteric sites on Ras for lead generation

PloS one, 2011-10, Vol.6 (10), p.e25711-e25711

2011

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

Proceedings of the National Academy of Sciences - PNAS, 2021-02, Vol.118 (6), p.1-10

2021

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Mechanisms of Ras Membrane Organization and Signaling: Ras Rocks Again

Biomolecules (Basel, Switzerland), 2020-11, Vol.10 (11), p.1522

2020

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Ras and the Plasma Membrane: A Complicated Relationship

Cold Spring Harbor perspectives in medicine, 2018-10, Vol.8 (10), p.a031831

2018

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

The journal of physical chemistry. B, 2019-02, Vol.123 (5), p.1009-1016

2019

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

Journal of chemical theory and computation, 2017-04, Vol.13 (4), p.1851-1861

2017

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

The journal of physical chemistry. B, 2022-06, Vol.126 (24), p.4491-4500

2022

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Large conformational changes in proteins: signaling and other functions

Current opinion in structural biology, 2010-04, Vol.20 (2), p.142-147

2010

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

Proteins, structure, function, and bioinformatics, 2017-09, Vol.85 (9), p.1618-1632

2017

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

Biophysical journal, 2015-12, Vol.109 (12), p.2467-2470

2015

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The role of conformational dynamics in intrinsically disordered lipid anchors of peripheral membrane proteins in specifying interactions with membrane lipids

Biophysical journal, 2023-02, Vol.122 (3), p.449a-449a

2023

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

PLoS computational biology, 2015-10, Vol.11 (10), p.e1004469-e1004469

2015

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Biophysics of cancer

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

Protein Partitioning into Ordered Membrane Domains: Insights from Simulations

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

Probing the Conformational and Energy Landscapes of KRAS Membrane Orientation

Structural determinants and functional consequences of protein affinity for membrane rafts

Polyunsaturated Lipids Regulate Membrane Domain Stability by Tuning Membrane Order

Aggregation of lipid-anchored full-length H-Ras in lipid bilayers: simulations with the MARTINI force field

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

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

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

Intrinsically Disordered Membrane Anchors of Rheb, RhoA, and DiRas3 Small GTPases: Molecular Dynamics, Membrane Organization, and Interactions

From disorder comes function: Regulation of small GTPase function by intrinsically disordered lipidated membrane anchor

Novel allosteric sites on Ras for lead generation

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

Mechanisms of Ras Membrane Organization and Signaling: Ras Rocks Again

Ras and the Plasma Membrane: A Complicated Relationship

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

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

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

Large conformational changes in proteins: signaling and other functions

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

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

The role of conformational dynamics in intrinsically disordered lipid anchors of peripheral membrane proteins in specifying interactions with membrane lipids

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

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