Search Results - "Abrams, Cameron F."

Large-scale conformational sampling of proteins using temperature-accelerated molecular dynamics by Abrams, Cameron F, Vanden-Eijnden, Eric

“…We show how to apply the method of temperature-accelerated molecular dynamics (TAMD) in collective variables [Maragliano L, Vanden-Eijnden E (2006) Chem Phys…”
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“DFG-Flip” in the Insulin Receptor Kinase Is Facilitated by a Helical Intermediate State of the Activation Loop by Vashisth, Harish, Maragliano, Luca, Abrams, Cameron F.

“…We have characterized a large-scale inactive-to-active conformational change in the activation-loop of the insulin receptor kinase domain at the atomistic…”
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Full Kinetics of CO Entry, Internal Diffusion, and Exit in Myoglobin from Transition-Path Theory Simulations by Yu, Tang-Qing, Lapelosa, Mauro, Vanden-Eijnden, Eric, Abrams, Cameron F

“…We use Markovian milestoning molecular dynamics (MD) simulations on a tessellation of the collective variable space for CO localization in myoglobin to…”
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Lipid flip-flop vs. lateral diffusion in the relaxation of hemifusion diaphragms by Gardner, Jasmine M., Abrams, Cameron F.

“…Molecular dynamics simulations of a solvent-free coarse-grained lipid model are used to characterize the mechanisms by which lipid-bilayer hemifusion diaphragm…”
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On-the-fly free energy parameterization via temperature accelerated molecular dynamics by Abrams, Cameron F., Vanden-Eijnden, Eric

“…[Display omitted] ► Our method can determine parameters of a free energy in molecular simulations. ► Free-energy gradients from temperature-accelerated MD are…”
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A Computational Study of Water and CO Migration Sites and Channels Inside Myoglobin by Lapelosa, Mauro, Abrams, Cameron F

“…Pathways are computed for transport of H2O and CO in myoglobin (Mb), using the single sweep and zero-temperature string methods in a fully atomistic,…”
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Interaction of Human ACE2 to Membrane-Bound SARS-CoV-1 and SARS-CoV-2 S Glycoproteins by Anand, Sai Priya, Chen, Yaozong, Prévost, Jérémie, Gasser, Romain, Beaudoin-Bussières, Guillaume, Abrams, Cameron F, Pazgier, Marzena, Finzi, Andrés

“…Severe acute respiratory syndrome virus 2 (SARS-CoV-2) is responsible for the current global coronavirus disease 2019 (COVID-19) pandemic, infecting millions…”
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Oxygen Pathways and Allostery in Monomeric Sarcosine Oxidase via Single-Sweep Free-Energy Reconstruction by Bucci, Anthony, Abrams, Cameron F

“…Monomeric sarcosine oxidase (MSOX) is a flavoprotein D-amino acid oxidase with reported sarcosine and oxygen activation sites on the re and si faces of the…”
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Comparison of Crosslinking Algorithms in Molecular Dynamics Simulation of Thermosetting Polymers by Jang, Changwoon, Sirk, Timothy W., Andzelm, Jan W., Abrams, Cameron F.

“…The generation of fully cross‐linked structure is a central task in molecular dynamics simulations of thermosetting polymers. Several algorithms for generating…”
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The HIV-1 Env gp120 Inner Domain Shapes the Phe43 Cavity and the CD4 Binding Site by Prévost, Jérémie, Tolbert, William D, Medjahed, Halima, Sherburn, Rebekah T, Madani, Navid, Zoubchenok, Daria, Gendron-Lepage, Gabrielle, Gaffney, Althea E, Grenier, Melissa C, Kirk, Sharon, Vergara, Natasha, Han, Changze, Mann, Brendan T, Chénine, Agnès L, Ahmed, Adel, Chaiken, Irwin, Kirchhoff, Frank, Hahn, Beatrice H, Haim, Hillel, Abrams, Cameron F, Smith, 3rd, Amos B, Sodroski, Joseph, Pazgier, Marzena, Finzi, Andrés

“…The HIV-1 envelope glycoproteins (Env) undergo conformational changes upon interaction of the gp120 exterior glycoprotein with the CD4 receptor. The gp120…”
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Identification of gp120 Residue His105 as a Novel Target for HIV‑1 Neutralization by Small-Molecule CD4-Mimics by Fritschi, Christopher J, Liang, Shuaiyi, Mohammadi, Mohammadjavad, Anang, Saumya, Moraca, Francesca, Chen, Junhua, Madani, Navid, Sodroski, Joseph G, Abrams, Cameron F, Hendrickson, Wayne A, Smith, Amos B

“…The design and synthesis of butyl chain derivatives at the indane ring 3-position of our lead CD4-mimetic compound BNM-III-170 that inhibits human…”
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Energetics and Mechanism of the Normal-to-Amyloidogenic Isomerization of β2-Microglobulin: On-the-Fly String Method Calculations by Stober, Spencer T, Abrams, Cameron F

“…We use on-the-fly finite temperature string method in collective variables to study the transition from a normal to an amyloidogenic conformation of…”
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All-Atom Models of the Membrane-Spanning Domain of HIV-1 gp41 from Metadynamics by Gangupomu, Vamshi K., Abrams, Cameron F.

“…The 27-residue membrane-spanning domain (MSD) of the HIV-1 glycoprotein gp41 bears conserved sequence elements crucial to the biological function of the virus,…”
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A Model of Peptide Triazole Entry Inhibitor Binding to HIV‑1 gp120 and the Mechanism of Bridging Sheet Disruption by Emileh, Ali, Tuzer, Ferit, Yeh, Herman, Umashankara, Muddegowda, Moreira, Diogo R. M, LaLonde, Judith M, Bewley, Carole A, Abrams, Cameron F, Chaiken, Irwin M

“…Peptide triazole (PT) entry inhibitors prevent HIV-1 infection by blocking the binding of viral gp120 to both the HIV-1 receptor and the coreceptor on target…”
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Peptide Triazole Thiol Irreversibly Inactivates Metastable HIV-1 Env by Accessing Conformational Triggers Intrinsic to Virus–Cell Entry by Ang, Charles Gotuaco, Carter, Erik, Haftl, Ann, Zhang, Shiyu, Rashad, Adel A., Kutzler, Michele, Abrams, Cameron F., Chaiken, Irwin M.

“…KR13, a peptide triazole thiol previously established to inhibit HIV-1 infection and cause virus lysis, was evaluated by flow cytometry against JRFL…”
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Roles of the Coupling Agent and Surfactant in Droplet Structure in Sizing Emulsions: A Molecular Dynamics Simulations Study by Zarrini, Salman, Abrams, Cameron F

“…Sizing emulsions used as glass fiber surface treatments in composites manufacturing are aqueous suspensions of hydrophobic film formers, surface coupling…”
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Testing Convergence of Different Free-Energy Methods in a Simple Analytical System with Hidden Barriers by Paz, S., Abrams, Cameron

“…In this work, we study the influence of hidden barriers on the convergence behavior of three free-energy calculation methods: well-tempered metadynamics…”
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Optimizing String Method’s Reproducibility Using Generalized Solute Tempering Replica Exchange by Shrivastav, Gourav, Abrams, Cameron F

“…Obtaining accurate and reproducible free energies from molecular simulations is somewhat tricky due to incomplete knowledge of crucial slow degrees of freedom…”
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Entropic Overcompensation of the N501Y Mutation on SARS-CoV‑2 S Binding to ACE2 by Vergara, Natasha Gupta, Gatchel, Megan, Abrams, Cameron F.

“…Recent experimental work has shown that the N501Y mutation in the SARS-CoV-2 S glycoprotein’s receptor binding domain (RBD) increases binding affinity to the…”
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Epoxy Polymer Networks with Improved Thermal and Mechanical Properties via Controlled Dispersion of Reactive Toughening Agents by Sharifi, Majid, Jang, Changwoon, Abrams, Cameron F, Palmese, Giuseppe R

“…Highly cross-linked polymers are extensively used in the formulation of protective coatings, adhesives, and composite materials. The inherent densely…”
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