Journal ArticleDOI
PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data
Daniel R. Roe,Thomas E. Cheatham +1 more
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TLDR
PTRAJ and its successor CPPTRAJ are described, two complementary, portable, and freely available computer programs for the analysis and processing of time series of three-dimensional atomic positions and the data therein derived.Abstract:
We describe PTRAJ and its successor CPPTRAJ, two complementary, portable, and freely available computer programs for the analysis and processing of time series of three-dimensional atomic positions (i.e., coordinate trajectories) and the data therein derived. Common tools include the ability to manipulate the data to convert among trajectory formats, process groups of trajectories generated with ensemble methods (e.g., replica exchange molecular dynamics), image with periodic boundary conditions, create average structures, strip subsets of the system, and perform calculations such as RMS fitting, measuring distances, B-factors, radii of gyration, radial distribution functions, and time correlations, among other actions and analyses. Both the PTRAJ and CPPTRAJ programs and source code are freely available under the GNU General Public License version 3 and are currently distributed within the AmberTools 12 suite of support programs that make up part of the Amber package of computer programs (see http://ambe...read more
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Journal ArticleDOI
Intracellular cavity of sensor domain controls allosteric gating of TRPA1 channel.
Lucie Zimova,Viktor Sinica,Anna Kadkova,Lenka Vyklicka,Vlastimil Zima,Ivan Barvík,Viktorie Vlachova +6 more
TL;DR: Findings suggest that alterations to the cavity may underlie chronic pain or itch in patients, and identify conserved polar residues facing the putative lower crevice of the sensor domain that were crucial determinants of the electrophilic, voltage, and calcium sensitivity of the TRPA1 channel.
Journal ArticleDOI
Differential utilization of binding loop flexibility in T cell receptor ligand selection and cross-reactivity
TL;DR: Study of the flexibility of two structurally well characterized αβ TCRs, A6 and DMF5 found that the two receptors utilize loop motion very differently in ligand binding and cross-reactivity, suggesting changes in nanosecond-level TCR structural dynamics do not contribute to T cell signaling.
Journal ArticleDOI
14-3-3 binding creates a memory of kinase action by stabilizing the modified state of phospholamban
Julia Menzel,Daniel Kownatzki-Danger,Sergiy Tokar,Alice Ballone,Alice Ballone,Kirsten Unthan-Fechner,Markus Kilisch,Christof Lenz,Christof Lenz,Henning Urlaub,Henning Urlaub,Mattia Mori,Christian Ottmann,Michael J. Shattock,Stephan E. Lehnart,Blanche Schwappach,Blanche Schwappach +16 more
TL;DR: It is demonstrated that phosphorylation at either Ser16 or Thr17 converted PLN into a target for the phosphoadaptor protein 14-3-3 with different affinities, and suggest that CaMKII would have a longer-lasting effect on SERCA activity than would PKA and show how different kinases acting on adjacent residues in a substrate can generate distinct biological outcomes.
Journal ArticleDOI
Stable preparations of tyrosine hydroxylase provide the solution structure of the full-length enzyme
Maria Teresa Bezem,Anne Baumann,Anne Baumann,Lars Skjærven,Romain Meyer,Petri Kursula,Aurora Martinez,Marte I. Flydal,Marte I. Flydal +8 more
TL;DR: Improved protocols for purification of recombinant human TH isoform 1 (TH1) are reported, which provide large amounts of pure, stable, active TH1 with an intact N-terminus and reliable structural models of full-length tetrameric TH1.
Journal ArticleDOI
Computational design of mechanically coupled axle-rotor protein assemblies
Alexis Courbet,Jesse M Hansen,Yang Hsia,N. Bethel,Y.-J. Park,Adam Moyer,Scott E. Boyken,George Ueda,Una Nattermann,D. Nagarajan,D. Silva,William Sheffler,J. Quispe,A. Nord,Neil P. King,Philip Bradley,David Veesler,Justin M. Kollman,David Baker +18 more
TL;DR: The de novo construction of protein machinery from designed axle and rotor components with internal cyclic or dihedral symmetry is explored and it is found that the axle-rotor systems assemble in vitro and in vivo as designed.
References
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VMD: Visual molecular dynamics
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David A. Case,Thomas E. Cheatham,Tom Darden,Holger Gohlke,Ray Luo,Kenneth M. Merz,Alexey V. Onufriev,Carlos Simmerling,Bing Wang,Robert J. Woods +9 more
TL;DR: The development, current features, and some directions for future development of the Amber package of computer programs, which contains a group of programs embodying a number of powerful tools of modern computational chemistry, focused on molecular dynamics and free energy calculations of proteins, nucleic acids, and carbohydrates.
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