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1

Intracellular Ca2+ Regulation of H+/Ca2+ Antiporter YfkE Mediated by a Ca2+ Mini-Sensor

Zheng, Lei, Lu, Shuo, Gorfe, Alemayehu A., Li, Zhenlong

Journal:

Biophysical Journal

Year:

2020

File:

PDF, 46 KB

2020

2

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

Zhou, Yong, Prakash, Priyanka, Liang, Hong, Cho, Kwang-Jin, Gorfe, Alemayehu A., Hancock, John F.

Journal:

Year:

2017

Language:

english

File:

PDF, 7.28 MB

english, 2017

3

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

McCarthy, Michael J., Pagba, Cynthia V., Prakash, Priyanka, Naji, Ali K., van der Hoeven, Dharini, Liang, Hong, Gupta, Amit K., Zhou, Yong, Cho, Kwang-Jin, Hancock, John F., Gorfe, Alemayehu A.

Journal:

Year:

2019

Language:

english

File:

PDF, 4.00 MB

english, 2019

4

Membrane-bound Ras as a conformational clock

Gorfe, Alemayehu A., Sligar, Stephen G.

Journal:

Biophysical Journal

Year:

2020

Language:

english

File:

PDF, 698 KB

english, 2020

5

Lipid-Anchored Ras Proteins Sense/Modulate Plasma Membrane Curvature in an Isoform- Specific Manner

Liang, Hong, Gorfe, Alemayehu, Hancock, John F., Zhou, Yong

Journal:

Biophysical Journal

Year:

2018

Language:

english

File:

PDF, 56 KB

english, 2018

6

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

Alemayehu A. Gorfe, Bjørn O. Brandsdal, Hanna-Kirsti S. Leiros, Ronny Helland, Arne O. Smalås

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2000

Language:

english

File:

PDF, 1.32 MB

english, 2000

7

Importance of the Sphingosine Base Double-Bond Geometry for the Structural and Thermodynamic Properties of Sphingomyelin Bilayers

Janosi, Lorant, Gorfe, Alemayehu

Journal:

Biophysical Journal

Year:

2010

Language:

english

File:

PDF, 1.25 MB

english, 2010

8

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

Gorfe, Alemayehu A., Baron, Riccardo, McCammon, J. Andrew

Journal:

Biophysical Journal

Year:

2008

Language:

english

File:

PDF, 401 KB

english, 2008

9

In Search of Ras Inhibitors

Gorfe, Alemayehu A.

Journal:

Biophysical Journal

Year:

2014

Language:

english

File:

PDF, 42 KB

english, 2014

10

Equilibrium Thermodynamics and Kinetics of K-Ras Dimerization through an Effector Binding Surface

Sayyed-Ahmed, Abdallah, Gorfe, Alemayehu A.

Journal:

Journal of Physical Chemistry B

Year:

2016

Language:

english

File:

PDF, 1.63 MB

english, 2016

11

Mapping the Nucleotide and Isoform-Dependent Structural and Dynamical Features of Ras Proteins

Alemayehu A. Gorfe, Barry J. Grant, J. Andrew McCammon

Journal:

Year:

2008

Language:

english

File:

PDF, 2.11 MB

english, 2008

12

Energetics of Sequence-Specific Protein−DNA Association: Binding of Integrase Tn916 to Its Target DNA †

Milev, Stoyan, Gorfe, Alemayehu A., Karshikoff, Andrey, Clubb, Robert T., Bosshard, Hans Rudolf, Jelesarov, Ilian

Journal:

Year:

2003

Language:

english

File:

PDF, 181 KB

english, 2003

13

Formation and Domain Partitioning of H-ras Peptide Nanoclusters: Effects of Peptide Concentration and Lipid Composition

Li, Zhenlong, Janosi, Lorant, Gorfe, Alemayehu A

Journal:

Journal of the American Chemical Society

Year:

2012

Language:

english

File:

PDF, 2.89 MB

english, 2012

14

Sa1733 NSAID-Induced Lower Gut Injury: Importance of NSAID-Bile Acid Mixed Micelles and Bacteria

Lichtenberger, Lenard M., Phan, Tri M., Dial, Elizabeth, Gorfe, Alemayehu A., Srivastava, Priyanka P., Zhou, Yong, Bhattarai, Deepa, Uray, Karen S.

Journal:

Gastroenterology

Year:

2015

Language:

english

File:

PDF, 69 KB

english, 2015

15

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

Prakash, Priyanka, Sayyed-Ahmad, Abdallah, Gorfe, Alemayehu A., Briggs, James M.

Journal:

PLoS Computational Biology

Year:

2012

Language:

english

File:

PDF, 1.18 MB

english, 2012

16

Abrogating Ras Abnormal Function by Targeting Membrane Bound Ras Monomers and Oligomers

Prakash Srivastava, Priyanka, Gorfe, Alemayehu A.

Journal:

Biophysical Journal

Year:

2015

Language:

english

File:

PDF, 40 KB

english, 2015

17

The Aliphatic Chain of Cholesterol Modulates Bilayer Interleaflet Coupling and Domain Registration

Lin, Xubo, Zhang, Siya, Ding, Hui, Levental, Ilya, Gorfe, Alemayehu A.

Journal:

Year:

2016

Language:

english

File:

PDF, 559 KB

english, 2016

18

Protein Partitioning into Ordered Membrane Domains: Insights from Simulations

Lin, Xubo, Gorfe, Alemayehu A., Levental, Ilya

Journal:

Biophysical Journal

Year:

2018

Language:

english

File:

PDF, 5.13 MB

english, 2018

19

The Molecular Basis of Cluster Formation by Membrane-Bound Lipidated Ras

Gorfe, Alemayehu A., Li, Zhenlong, Janosi, Lorant

Journal:

Biophysical Journal

Year:

2012

Language:

english

File:

PDF, 59 KB

english, 2012

20

What drives the clustering of membrane-bound Ras?

Li, Zhenlong, Gorfe, Alemayehu A.

Journal:

Year:

2012

Language:

english

File:

PDF, 1019 KB

english, 2012

21

Structural determinants and functional consequences of protein affinity for membrane rafts

Lorent, Joseph H., Diaz-Rohrer, Blanca, Lin, Xubo, Spring, Kevin, Gorfe, Alemayehu A., Levental, Kandice R., Levental, Ilya

Journal:

Nature Communications

Year:

2017

Language:

english

File:

PDF, 1.70 MB

english, 2017

22

Segregation of Negatively Charged Phospholipids by the Polycationic and Farnesylated Membrane Anchor of Kras

Janosi, Lorant, Gorfe, Alemayehu A.

Journal:

Biophysical Journal

Year:

2010

Language:

english

File:

PDF, 1.05 MB

english, 2010

23

Structure and Dynamics of Cholic Acid and Dodecylphosphocholine−Cholic Acid Aggregates

Sayyed-Ahmad, Abdallah, Lichtenberger, Lenard M., Gorfe, Alemayehu A.

Journal:

Year:

2010

Language:

english

File:

PDF, 4.93 MB

english, 2010

24

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

Prakash, Priyanka, Zhou, Yong, Liang, Hong, Hancock, John F., Gorfe, Alemayehu A.

Journal:

Biophysical Journal

Year:

2016

Language:

english

File:

PDF, 3.85 MB

english, 2016

25

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

Sayyed-Ahmad, Abdallah, Gorfe, Alemayehu A.

Journal:

Journal of Chemical Theory and Computation

Year:

2017

Language:

english

File:

PDF, 6.07 MB

english, 2017

26

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

Abankwa, Daniel, Gorfe, Alemayehu A., Hancock, John F.

Journal:

Year:

2008

Language:

english

File:

PDF, 659 KB

english, 2008

27

Multi-Conformer Hierarchical Virtual Screening Workflow to Identify Potential K-Ras Inhibitors

Gupta, Amit K., Prakash, Priyanka, Putkey, John A., Gorfe, Alemayehu A.

Journal:

Biophysical Journal

Year:

2017

Language:

english

File:

PDF, 65 KB

english, 2017

28

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

Sayyed-Ahmad, Abdallah, Prakash, Priyanka, Gorfe, Alemayehu A.

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2017

Language:

english

File:

PDF, 2.58 MB

english, 2017

29

Intracellular Ca 2+ regulation of H + /Ca 2+ antiporter YfkE mediated by a Ca 2+ mini-sensor

Lu, Shuo, Li, Zhenlong, Gorfe, Alemayehu A., Zheng, Lei

Journal:

Proceedings of the National Academy of Sciences

Year:

2020

File:

PDF, 2.02 MB

2020

30

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

Abankwa, Daniel, Hanzal-Bayer, Michael, Ariotti, Nicolas, Plowman, Sarah J, Gorfe, Alemayehu A, Parton, Robert G, McCammon, J Andrew, Hancock, John F

Journal:

The EMBO Journal

Year:

2008

Language:

english

File:

PDF, 516 KB

english, 2008

31

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

Prakash, Priyanka, Sayyed-Ahmad, Abdallah, Gorfe, Alemayehu A., Shehu, Amarda

Journal:

PLoS Computational Biology

Year:

2015

Language:

english

File:

PDF, 6.04 MB

english, 2015

32

Structurally-Diverse Non-Covalent Allosteric KRAS Inhibitors Structurally Diverse Non-Covalent Allosteric KRAS Inhibitors

Pagba, Cynthia, Gupta, Amit K., McCarthy, Michael, Zhou, Yong, Gorfe, Alemayehu A.

Journal:

Biophysical Journal

Year:

2020

File:

PDF, 44 KB

2020

33

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

Janosi, Lorant, Gorfe, Alemayehu A.

Journal:

Journal of Chemical Theory and Computation

Year:

2010

Language:

english

File:

PDF, 3.71 MB

english, 2010

34

Segregation of Negatively Charged Phospholipids by the Polycationic and Farnesylated Membrane Anchor of Kras

Gorfe, Alemayehu A.

Journal:

Biophysical Journal

Year:

2011

Language:

english

File:

PDF, 34 KB

english, 2011

35

Su1749 Biophysical Evidence That NSAIDs Form Mixed Micelles With Bile Acids as a Possible Mechanism of NSAID-Induced Lower Gut Injury

Gorfe, Alemayehu A., Volk, David E., Gorenstein, David, Dial, Elizabeth, Lichtenberger, Lenard M.

Journal:

Gastroenterology

Year:

2012

Language:

english

File:

PDF, 64 KB

english, 2012

36

Continuum electromechanical modeling of protein-membrane interactions

Zhou, Y. C., Lu, Benzhuo, Gorfe, Alemayehu A.

Journal:

Physical Review E

Year:

2010

Language:

english

File:

PDF, 2.90 MB

english, 2010

37

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

Prakash, Priyanka, Sayyed-Ahmad, Abdallah, Cho, Kwang-Jin, Dolino, Drew M., Chen, Wei, Li, Hongyang, Grant, Barry J., Hancock, John F., Gorfe, Alemayehu A.

Journal:

Scientific Reports

Year:

2017

Language:

english

File:

PDF, 1.88 MB

english, 2017

38

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

Lin, Xubo, Gorfe, Alemayehu A.

Journal:

The Journal of Chemical Physics

Year:

2020

File:

PDF, 4.70 MB

2020

39

Free Energy Profile of H-ras Membrane Anchor upon Membrane Insertion

Alemayehu A. Gorfe, Arneh Babakhani, J. Andrew McCammon

Journal:

Angewandte Chemie

Year:

2007

Language:

english

File:

PDF, 737 KB

english, 2007

40

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

Alemayehu A. Gorfe, Philippe Ferrara, Amedeo Caflisch, Daniel N. Marti, Hans Rudolf Bosshard, Ilian Jelesarov

Journal:

Proteins: Structure, Function, and Bioinformatics

Year:

2002

Language:

english

File:

PDF, 541 KB

english, 2002

41

Structure and Dynamics of the Full-Length Lipid-Modified H-Ras Protein in a 1,2-Dimyristoylglycero-3-phosphocholine Bilayer

Gorfe, Alemayehu A., Hanzal-Bayer, Michael, Abankwa, Daniel, Hancock, John F., McCammon, J. Andrew

Journal:

Journal of Medicinal Chemistry

Year:

2007

Language:

english

File:

PDF, 1.42 MB

english, 2007

42

Similar Membrane Affinity of Mono- and Di-S-acylated Ras Membrane Anchors: A New Twist in the Role of Protein Lipidation

Gorfe, Alemayehu A., McCammon, J. Andrew

Journal:

Journal of the American Chemical Society

Year:

2008

Language:

english

File:

PDF, 486 KB

english, 2008

43

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

Li, Hualin, Gorfe, Alemayehu A

Journal:

The Journal of Physical Chemistry Letters

Year:

2014

Language:

english

File:

PDF, 5.39 MB

english, 2014

44

Lipid Bilayer Membrane Shape Remodeling by Lipid-Modified Ras Proteins

Li, Zhenlong, Janosi, Lorant, Abebe Gorfe, Alemayehu

Journal:

Biophysical Journal

Year:

2012

Language:

english

File:

PDF, 39 KB

english, 2012

45

eLS || Membrane Targeting: Methods

Gorfe, Alemayehu A

Year:

2001

Language:

english

File:

PDF, 165 KB

english, 2001

46

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

Prakash, Priyanka, Gorfe, Alemayehu A.

Journal:

Molecular Simulation

Year:

2014

Language:

english

File:

PDF, 226 KB

english, 2014

47

Free Energy Profile of H-ras Membrane Anchor upon Membrane Insertion

Alemayehu A. Gorfe, Arneh Babakhani, J. Andrew McCammon

Journal:

Angewandte Chemie International Edition

Year:

2007

Language:

english

File:

PDF, 737 KB

english, 2007

48

Enzymatic Activity versus Structural Dynamics: The Case of Acetylcholinesterase Tetramer

Gorfe, Alemayehu A., Lu, Benzhuo, Yu, Zeyun, McCammon, J. Andrew

Journal:

Biophysical Journal

Year:

2009

Language:

english

File:

PDF, 496 KB

english, 2009

49

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

Grant, Barry J., Gorfe, Alemayehu A., McCammon, J. Andrew, Briggs, James M.

Journal:

PLoS Computational Biology

Year:

2009

Language:

english

File:

PDF, 744 KB

english, 2009

50

H-ras Protein in a Bilayer: Interaction and Structure Perturbation

Gorfe, Alemayehu A., Babakhani, Arneh, McCammon, J. Andrew

Journal:

Journal of the American Chemical Society

Year:

2007

Language:

english

File:

PDF, 702 KB

english, 2007

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