TITLE OF MANUSCRIPT:
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Multi-scale simulations of the T cell receptor reveal its lipid interactions, dynamics and the arrangement of its cytoplasmic region


AUTHOR LIST & AFFILIATION:
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Dheeraj Prakaash (1,2)
Graham P. Cook (3)
Oreste Acuto (4)
Antreas C. Kalli (1,2)*

1. Leeds Institute of Cardiovascular and Metabolic Medicine, School of Medicine, University of Leeds, Leeds, LS2 9DA, United Kingdom.
2. Astbury Center for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, United Kingdom.
3. Leeds Institute of Medical Research at St Jamesâs, School of Medicine, University of Leeds, Leeds, LS9 7TF, United Kingdom.
4. Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, United Kingdom.


Correspondence: Antreas C. Kalli
Email: a.kalli@leeds.ac.uk

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CONTENTS of ZIP file:

MDP files (Molecular Dynamics Parameters)
GRO files (Final snapshot of simulations - Gromacs format)
XTC files (Trajectories of simulations)

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FILENAME FORMAT + DESCRIPTION for GRO & XTC files:

Format:  [A]-[B]-[C]-[D].[E]
          |   |   |   |   |
Example: CG-5us-TCRfl-r1.xtc


DESCRIPTION:
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[A] = CG / AT resolution
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CG = coarse-grained resolution simulations using Martini 2.2 forcefield.
AT = atomistic resolution simulations using Charmm36 forcefield.

[B] = Timescale of simulation
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5μs (μs=microseconds) : all five CG simulations.
250ns (ns=nanoseconds): three AT simulations which were backmapped from the end of a CG simulation at 5μs simulation time.
100ns (ns=nanoseconds): three AT simulations which started from the initial (extended tails) configuration.

[C] = Protein type (in complex asymmetric bilayer)
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TCRtm   = T cell receptor containing only the transmembrane (TM) region.
TCRectm = T cell receptor containing only the extracellular (EC) and transmembrane (TM) regions.
TCRfl   = entire T cell receptor i.e. consisting of full-length (FL) subunits.
TCRfl-memb2 = entire T cell receptor i.e. consisting of full-length (FL) subunits (simulated in membrane 2, with higher lipid unsaturation).

[D] = Simulation replica number
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(r1 to r5) = 5 replicas for each CG simulation.
(r1 to r3) = 3 replicas for each AT simulation.

[E] = File format (GRO/XTC)

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NOTE:
All XTC trajectories in the ZIP are truncated.
Total frames in trunc. CG simulations = 626 (skipped every 8 nanoseconds)
Total frames in trunc. (250ns) AT simulations = 313 (skipped every 800 picoseconds)
Total frames in trunc. (100ns) AT simulations = 125 (skipped every 800 picoseconds)

Total frames in original CG simulations (not uploaded)         = 25000 (each frame = 400 picoseconds)
Total frames in original (250ns) AT simulations (not uploaded) = 6250 (each frame = 40 picoseconds)
Total frames in original (100ns) AT simulations (not uploaded) = 1000 (each frame = 100 picoseconds)
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2 MDP files are contained in the ZIP i.e. production simulation parameters for CG and AT simulations.

(1) CG-production.mdp
(2) AT-250ns-production.mdp (backmapped)
(3) AT-100ns-production.mdp (from Charmm-GUI)

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# README file updated: 31 May 2021