CHARMM-GUI Membrane Builder Toward Realistic Biological Membrane Simulations
Emilia L. Wu,Xi Cheng,Sunhwan Jo,Huan Rui,Kevin C. Song,Eder M. Dávila-Contreras,Yifei Qi,Jumin Lee,Viviana Monje-Galvan,Richard M. Venable,Jeffery B. Klauda,Wonpil Im +11 more
TLDR
The new features and major improvements in Membrane Builder that allow users to robustly build realistic biological membrane systems are described, including addition of new lipid types, including phosphoinositides, cardiolipin (CL), sphingolipids, bacterial lipids, and ergosterol.Abstract:
CHARMM-GUI Membrane Builder, http://www.charmm-gui.org/input/membrane, is a web-based user interface designed to interactively build all-atom protein/membrane or membrane-only systems for molecular dynamics simulations through an automated optimized process. In this work, we describe the new features and major improvements in Membrane Builder that allow users to robustly build realistic biological membrane systems, including (1) addition of new lipid types, such as phosphoinositides, cardiolipin (CL), sphingolipids, bacterial lipids, and ergosterol, yielding more than 180 lipid types, (2) enhanced building procedure for lipid packing around protein, (3) reliable algorithm to detect lipid tail penetration to ring structures and protein surface, (4) distance-based algorithm for faster initial ion displacement, (5) CHARMM inputs for P21 image transformation, and (6) NAMD equilibration and production inputs. The robustness of these new features is illustrated by building and simulating a membrane model of the polar and septal regions of E. coli membrane, which contains five lipid types: CL lipids with two types of acyl chains and phosphatidylethanolamine lipids with three types of acyl chains. It is our hope that CHARMM-GUI Membrane Builder becomes a useful tool for simulation studies to better understand the structure and dynamics of proteins and lipids in realistic biological membrane environments. © 2014 Wiley Periodicals, Inc.read more
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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.
Journal ArticleDOI
Computational Lipidomics with insane: A Versatile Tool for Generating Custom Membranes for Molecular Simulations
Tsjerk A. Wassenaar,Tsjerk A. Wassenaar,Helgi I. Ingólfsson,Rainer A. Böckmann,D. Peter Tieleman,Siewert J. Marrink +5 more
TL;DR: A comprehensive method for building membrane containing systems, characterized by simplicity and versatility, and a survey of properties for a large range of lipids as a start of a computational lipidomics project.
Journal ArticleDOI
Structural insights into µ-opioid receptor activation
Weijiao Huang,Aashish Manglik,AJ Venkatakrishnan,Toon Laeremans,Evan N. Feinberg,Adrian L. Sanborn,Hideaki E. Kato,Kathryn E. Livingston,Thor S. Thorsen,Ralf C. Kling,Sébastien Granier,Peter Gmeiner,Stephen M. Husbands,John R. Traynor,William I. Weis,Jan Steyaert,Ron O. Dror,Brian K. Kobilka +17 more
TL;DR: A 2.1 Å X-ray crystal structure of the murine μOR bound to the morphinan agonist BU72 and a G protein mimetic camelid antibody fragment is reported, revealing an extensive polar network between the ligand-binding pocket and the cytoplasmic domains appears to play a similar role in signal propagation for all three G-protein-coupled receptors.
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Beyond Shielding: The Roles of Glycans in the SARS-CoV-2 Spike Protein
Lorenzo Casalino,Zied Gaieb,Jory A. Goldsmith,Christy K. Hjorth,Abigail C. Dommer,Aoife M. Harbison,Carl A Fogarty,Emilia P. Barros,Bryn C. Taylor,Jason S. McLellan,Elisa Fadda,Rommie E. Amaro +11 more
TL;DR: An essential structural role of N-glycans at sites N165 and N234 in modulating the conformational dynamics of the spike’s receptor binding domain (RBD) is revealed, which reduces binding to ACE2 as a result of the RBD conformational shift toward the “down” state.
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Predictive compound accumulation rules yield a broad-spectrum antibiotic
Michelle F. Richter,Bryon S. Drown,Andrew P. Riley,Alfredo Garcia,Tomohiro Shirai,Riley L. Svec,Paul J. Hergenrother +6 more
TL;DR: These guidelines were then applied to convert deoxynybomycin, a natural product that is active only against Gram-positive organisms, into an antibiotic with activity against a diverse panel of multi-drug-resistant Gram-negative pathogens.
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