CHARMM-GUI Input Generator for NAMD, Gromacs, Amber, Openmm, and CHARMM/OpenMM Simulations using the CHARMM36 Additive Force Field
Jumin Lee,Xi Cheng,Jason M. Swails,Min Sun Yeom,Peter Eastman,Justin A. Lemkul,Shuai Wei,Joshua Buckner,Jong Cheol Jeong,Yifei Qi,Sunhwan Jo,Vijay S. Pande,David A. Case,Charles L. Brooks,Alexander D. MacKerell,Jeffery B. Klauda,Wonpil Im +16 more
TL;DR: The optimal simulation protocol for each program has been implemented in CHARMM-GUI and is expected to be applicable to the remainder of the additive C36 FF including the proteins, nucleic acids, carbohydrates, and small molecules.
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Abstract: Proper treatment of nonbonded interactions is essential for the accuracy of molecular dynamics (MD) simulations, especially in studies of lipid bilayers. The use of the CHARMM36 force field (C36 FF) in different MD simulation programs can result in disagreements with published simulations performed with CHARMM due to differences in the protocols used to treat the long-range and 1-4 nonbonded interactions. In this study, we systematically test the use of the C36 lipid FF in NAMD, GROMACS, AMBER, OpenMM, and CHARMM/OpenMM. A wide range of Lennard-Jones (LJ) cutoff schemes and integrator algorithms were tested to find the optimal simulation protocol to best match bilayer properties of six lipids with varying acyl chain saturation and head groups. MD simulations of a 1,2-dipalmitoyl-sn-phosphatidylcholine (DPPC) bilayer were used to obtain the optimal protocol for each program. MD simulations with all programs were found to reasonably match the DPPC bilayer properties (surface area per lipid, chain order para...
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CHARMM-GUI ligand reader and modeler for CHARMM force field generation of small molecules
TL;DR: The output from Ligand Reader & Modeler can be used in other CHARMM‐GUI modules to build a protein‐ligand simulation system for all supported simulation programs, such as CHARMM, NAMD, GROMACS, AMBER, GENESIS, LAMMPS, Desmond, OpenMM, and CHARMM/OpenMM.
Externalized histone H4 orchestrates chronic inflammation by inducing lytic cell death.
Carlos Silvestre-Roig,Quinte Braster,Kanin Wichapong,Ernest Y. Lee,Jean Marie Teulon,Nihel Berrebeh,Janine Winter,José M. Adrover,Giancarlo Santiago Santos,Alexander Froese,Patricia Lemnitzer,Almudena Ortega-Gomez,Raphael Chevre,Julian A. Marschner,Ariane Schumski,Carla Winter,Laura Perez-Olivares,Chang Pan,Nicole Paulin,Tom Schoufour,Helene Hartwig,Silvia González-Ramos,Frits Kamp,Remco T. A. Megens,Kerri A. Mowen,Matthias Gunzer,Lars Maegdefessel,Lars Maegdefessel,Tilman M. Hackeng,Esther Lutgens,Mat J.A.P. Daemen,Julia von Blume,Hans-Joachim Anders,Viacheslav O. Nikolaev,Jean-Luc Pellequer,Christian Weber,Christian Weber,Andrés Hidalgo,Andrés Hidalgo,Gerry A. F. Nicolaes,Gerard C. L. Wong,Oliver Soehnlein +41 more
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Structure of the Nanobody-Stabilized Active State of the Kappa Opioid Receptor
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TL;DR: A crystal structure of human KOP in complex with the potent epoxymorphinan opioid agonist MP1104 and an active-state-stabilizing nanobody is provided and key residues that propagate larger-scale structural rearrangements and transducer binding are illuminated that elucidate the structural determinants of KOP pharmacology, function, and biased signaling.
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Abstract: Cell membranes contain a large variety of lipid types and are crowded with proteins, endowing them with the plasticity needed to fulfill their key roles in cell functioning. The compositional complexity of cellular membranes gives rise to a heterogeneous lateral organization, which is still poorly understood. Computational models, in particular molecular dynamics simulations and related techniques, have provided important insight into the organizational principles of cell membranes over the past decades. Now, we are witnessing a transition from simulations of simpler membrane models to multicomponent systems, culminating in realistic models of an increasing variety of cell types and organelles. Here, we review the state of the art in the field of realistic membrane simulations and discuss the current limitations and challenges ahead.
336
Activation of the Unfolded Protein Response by Lipid Bilayer Stress
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