Zhen-lu Li

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A “Tug of War” Maintains a Dynamic Protein–Membrane Complex: Molecular Dynamics Simulations of C-Raf RBD-CRD Bound to K-Ras4B at an Anionic Membrane

Matthias Buck, Priyanka Prakash, Zhen-Lu Li, 2018, ACS central science.

A “Tug of War” maintains a dynamic protein-membrane complex as shown in all-atom simulations of C-Raf RBD-CRD bound to K-Ras4B at an anionic membrane

M. Buck, Priyanka Prakash, Zhen-lu Li, 2017, bioRxiv.

A “Tug of War” maintains a dynamic protein-membrane complex: MD simulations of C-Raf RBD-CRD bound to K-Ras4B at an anionic membrane

M. Buck, Priyanka Prakash, Zhen-lu Li, 2017 .

Interaction of peptides with cell membranes: insights from molecular modeling

Yu-qiang Ma, Zhen-lu Li, Hong-ming Ding, 2016, Journal of physics. Condensed matter : an Institute of Physics journal.

Modified Potential Functions Result in Enhanced Predictions of a Protein Complex by All-Atom MD Simulations, Confirming a Step-wise Association Process for Native PPIs

M. Buck, Zhen-lu Li, 2019 .

Protein Association Pathways and Dynamics with Improved Potential Functions in all atom MD Simulations

M. Buck, Zhen-lu Li, 2018, bioRxiv.

K-Ras G-domain binding with signaling lipid phosphatidylinositol (4,5)-phosphate (PIP2): membrane association, protein orientation, and function

M. Buck, Zhen-lu Li, D. Manor, 2019, The Journal of Biological Chemistry.

The RNA-binding site of poliovirus 3C protein doubles as a phosphoinositide-binding domain

C. Cameron, D. Boehr, M. Buck, 2017, bioRxiv.

Plexin-Bs enhance their GAP activity with a novel activation switch loop generating a cooperative enzyme

M. Buck, Zhen-lu Li, L. Tamagnone, 2020, Cellular and Molecular Life Sciences.

Microsecond MD Simulations of the Plexin-B1 RBD: 2. N-H Probability Densities and Conformational Entropy in Ligand-Free, Rac1-Bound, and Dimer RBD.

M. Zerbetto, E. Meirovitch, M. Buck, 2022, The journal of physical chemistry. B.

Trimeric receptor-binding domain of SARS-CoV-2 acts as a potent inhibitor of ACE2 receptor-mediated viral entry

M. Buck, P. Ramakrishnan, T. Xiao, 2022, iScience.

Raf promotes dimerization of the Ras G-domain with increased allosteric connections

J. Groves, C. Mattos, M. Buck, 2020, Proceedings of the National Academy of Sciences.

Neuropilin-1 assists SARS-CoV-2 infection by stimulating the separation of Spike protein S1 and S2

M. Buck, Zhen-lu Li, 2021, Biophysical journal.

Neuropilin-1 Assists SARS-CoV-2 Infection by Stimulating the Separation of Spike Protein Domains S1 and S2

M. Buck, Zhen-lu Li, 2021, bioRxiv.

Computational analysis of interior mutations of SARS-CoV-2 Spike protein suggest a balance of protein stability and S2: S1 separation propensity

M. Buck, Zhen-lu Li, 2022, Computational and Structural Biotechnology Journal.

Microsecond MD Simulations of the Plexin-B1 RBD: N-H Probability Density as Descriptor of Structural Dynamics, Dimerization-Related Conformational Entropy, and Transient Dimer Asymmetry.

M. Zerbetto, E. Meirovitch, M. Buck, 2022, The journal of physical chemistry. B.

Beyond history and “on a roll”: The list of the most well‐studied human protein structures and overall trends in the protein data bank

M. Buck, Zhen-lu Li, 2020, Protein science : a publication of the Protein Society.

Plexin-Bs enhance their GAP activity with a novel activation switch loop generating a cooperative enzyme

M. Buck, Zhen-lu Li, L. Tamagnone, 2019, Cellular and Molecular Life Sciences.

K-Ras G-domain binding with signaling lipid phosphoinositides: PIP2 association, orientation, function

M. Buck, Zhen-lu Li, D. Manor, 2018, bioRxiv.

Raf promotes dimerization of the Ras G‐domain

J. Groves, C. Mattos, M. Buck, 2020, The FASEB Journal.

Computational Design of Myristoylated Cell Penetrating Peptides Targeting Oncogenic K-Ras.G12D at the Effector Binding Membrane Interface.

Matthias Buck, Zhen-Lu Li, M. Buck, 2019, Journal of chemical information and modeling.

Computational Design of Myristoylated Cell Penetrating Peptides Targeting Oncogenic K-Ras.G12D at the Effector Binding Membrane Interface

M. Buck, Zhen-lu Li, 2019, bioRxiv.

Probing the hierarchical dynamics of DNA-sperm nuclear transition protein complex through fuzzy interaction and mesoscale condensation

Zhen-lu Li, Shangqiang Xie, Congran Yue, 2023, bioRxiv.

Proteome-scale Analysis of Vertebrate Protein Thermoadaptation Modulated by Dynamic Allostery and Protein Solvation

M. Buck, Zhen-lu Li, 2020, bioRxiv.

Influence of different membrane environments on the behavior of cholesterol

Yu-qiang Ma, Zhen-lu Li, Hong-ming Ding, 2014 .

Computational studies of the principle of dynamic-change-driven protein interactions.

C. Mattos, M. Buck, Zhen-lu Li, 2022, Structure.

Computational Modeling Reveals that Signaling Lipids Modulate the Orientation of K-Ras4A at the Membrane Reflecting Protein Topology.

Matthias Buck, Zhen-Lu Li, M. Buck, 2017, Structure.

K-Ras at Anionic Membranes: Orientation, Orientation…Orientation. Recent Simulations and Experiments.

M. Buck, Zhen-lu Li, S. Cao, 2016, Biophysical journal.

Modified Potential Functions Result in Enhanced Predictions of a Protein Complex by All-Atom MD Simulations, Confirming a Step-wise Association Process for Native PPIs.

M. Buck, Zhen-lu Li, 2019, Journal of chemical theory and computation.

Pattern, Pathways and Dynamics of EphA2 SAM and SHIP2 SAM Heterodimer Association Revealed by All-Atom Molecular Dynamics Simulation

M. Buck, Zhen-lu Li, 2018 .

The RNA-Binding Site of Poliovirus 3C Protein Doubles as a Phosphoinositide-Binding Domain

C. Cameron, M. Buck, P. Cremer, 2017, bioRxiv.

Molecular dynamics simulations of membrane deformation induced by amphiphilic helices of Epsin, Sar1p, and Arf1

Zhen-lu Li, Z. Li 李, 2017, bioRxiv.

Molecular dynamics simulations of membrane deformation induced by the amphiphilic helices of Epsin, Sar1p and Arf1

Zhen-lu Li, 2017, bioRxiv.

A “Tug of War” Maintains a Dynamic Protein–Membrane Complex: Molecular Dynamics Simulations of C-Raf RBD-CRD Bound to K-Ras4B at an Anionic Membrane

M. Buck, Priyanka Prakash, Zhen-lu Li, 2018, ACS central science.

Translocation of polyarginines and conjugated nanoparticles across asymmetric membranes

Yu-qiang Ma, Zhen-lu Li, Hong-ming Ding, 2013 .

Computational insights into the conformational transition of STING: mechanistic, energetic considerations, and the influence of crucial mutations

Zhen-lu Li, Shangqiang Xie, Sai Shi, 2023, bioRxiv.

Keys to Amyloid City: Computation and NMR Reveal Potential TDP-43 ALS Intermediates.

M. Buck, Zhen-lu Li, W. Michael Babinchak, 2018, Biophysical journal.