CHARMM-GUI supports hydrogen mass repartitioning and different protonation states of phosphates in lipopolysaccharides
CHARMM-GUI supports hydrogen mass repartitioning and different protonation states of phosphates in lipopolysaccharides
Hydrogen mass repartitioning (HMR) that permits time steps of all-atom molecular dynamics simulation up to 4 fs by increasing the mass of hydrogen atoms has been used in protein and phospholipid bilayers simulations to improve conformational sampling. Molecular simulation input generation via CHARMM-GUI now supports HMR for diverse simulation programs. In addition, considering ambiguous pH at the bacterial outer membrane surface, different protonation states, either-2e or-1e, of phosphate groups in lipopolysaccharides (LPS) are also supported in CHARMM-GUI LPS Modeler. To examine the robustness of HMR and the influence of protonation states of phosphate groups on LPS bilayer properties, eight different LPS-type all-atom systems with two phosphate protonation states are modeled and simulated utilizing both OpenMM 2-fs (standard) and 4-fs (HMR) schemes. Consistency in the conformational space sampled by standard and HMR simulations shows the reliability of HMR even in LPS, one of the most complex biomolecules. For systems with different protonation states, similar conformations are sampled with a PO41- or PO42- group, but different phosphate protonation states make slight impacts on lipid packing and conformational properties of LPS acyl chains. Systems with PO41- have a slightly smaller area per lipid and thus slightly more ordered lipid A acyl chains compared to those with PO42-, due to more electrostatic repulsion between PO42- even with neutralizing Ca2+ ions. HMR and different protonation states of phosphates of LPS available in CHARMM-GUI are expected to be useful for further investigations of biological systems of diverse origin.
831-839
Gao, Ya
5840c373-d7c9-4503-bbbe-a617bf02f2ab
Lee, Jumin
e7171f0b-bdbe-43c2-b8ef-b47b01c22417
Smith, Iain Peter Shand
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Lee, Hwayoung
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Kim, Seonghoon
18f56ee6-c419-4660-a132-8a5d1d7ae7c5
Qi, Yifei
5151661f-8b67-47c1-aecd-4ff929a1ff0e
Klauda, Jeffery B.
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Widmalm, Göran
0283e306-9ee9-4de4-8a7f-b558a2e9a231
Khalid, Syma
90fbd954-7248-4f47-9525-4d6af9636394
Im, Wonpil
8bf787f4-fc58-4c33-9b54-05afd9e71879
22 February 2021
Gao, Ya
5840c373-d7c9-4503-bbbe-a617bf02f2ab
Lee, Jumin
e7171f0b-bdbe-43c2-b8ef-b47b01c22417
Smith, Iain Peter Shand
16d4b544-dc39-49db-9d14-15b5eb4d295d
Lee, Hwayoung
7dec488a-d26b-4435-ac42-2e4288d1eaee
Kim, Seonghoon
18f56ee6-c419-4660-a132-8a5d1d7ae7c5
Qi, Yifei
5151661f-8b67-47c1-aecd-4ff929a1ff0e
Klauda, Jeffery B.
6b45f1af-d124-419d-a460-363509dd6661
Widmalm, Göran
0283e306-9ee9-4de4-8a7f-b558a2e9a231
Khalid, Syma
90fbd954-7248-4f47-9525-4d6af9636394
Im, Wonpil
8bf787f4-fc58-4c33-9b54-05afd9e71879
Gao, Ya, Lee, Jumin, Smith, Iain Peter Shand, Lee, Hwayoung, Kim, Seonghoon, Qi, Yifei, Klauda, Jeffery B., Widmalm, Göran, Khalid, Syma and Im, Wonpil
(2021)
CHARMM-GUI supports hydrogen mass repartitioning and different protonation states of phosphates in lipopolysaccharides.
Journal of Chemical Information and Modeling, 61 (2), .
(doi:10.1021/acs.jcim.0c01360).
Abstract
Hydrogen mass repartitioning (HMR) that permits time steps of all-atom molecular dynamics simulation up to 4 fs by increasing the mass of hydrogen atoms has been used in protein and phospholipid bilayers simulations to improve conformational sampling. Molecular simulation input generation via CHARMM-GUI now supports HMR for diverse simulation programs. In addition, considering ambiguous pH at the bacterial outer membrane surface, different protonation states, either-2e or-1e, of phosphate groups in lipopolysaccharides (LPS) are also supported in CHARMM-GUI LPS Modeler. To examine the robustness of HMR and the influence of protonation states of phosphate groups on LPS bilayer properties, eight different LPS-type all-atom systems with two phosphate protonation states are modeled and simulated utilizing both OpenMM 2-fs (standard) and 4-fs (HMR) schemes. Consistency in the conformational space sampled by standard and HMR simulations shows the reliability of HMR even in LPS, one of the most complex biomolecules. For systems with different protonation states, similar conformations are sampled with a PO41- or PO42- group, but different phosphate protonation states make slight impacts on lipid packing and conformational properties of LPS acyl chains. Systems with PO41- have a slightly smaller area per lipid and thus slightly more ordered lipid A acyl chains compared to those with PO42-, due to more electrostatic repulsion between PO42- even with neutralizing Ca2+ ions. HMR and different protonation states of phosphates of LPS available in CHARMM-GUI are expected to be useful for further investigations of biological systems of diverse origin.
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Accepted/In Press date: 11 January 2021
e-pub ahead of print date: 14 January 2021
Published date: 22 February 2021
Additional Information:
Funding Information:
This work was supported in part by grants from the NSF MCB-1810695, NSF DBI-1660380, NIH GM138472, XSEDE MCB070009, Friedrich Wilhelm Bessel Research Award from the Humboldt Foundation (to W.I.), the Swedish Research Council 2017-03703 (G.W.), KIAS individual grant (CG080501) (S.K.), the National Natural Science Foundation of China (62072296) (Y.G.), NSF CHE-2003912 and MCB-1951425 (to J.B.K.), and the Engineering and Physical Sciences Research Council, EP/R029407/1 (to S.K.).
Publisher Copyright:
© 2021 American Chemical Society.
Copyright:
Copyright 2021 Elsevier B.V., All rights reserved.
Identifiers
Local EPrints ID: 447442
URI: http://eprints.soton.ac.uk/id/eprint/447442
ISSN: 1549-9596
PURE UUID: 260ec04f-01f8-4188-86b5-0937d09f1140
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Date deposited: 11 Mar 2021 17:36
Last modified: 26 Nov 2024 02:57
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Author:
Ya Gao
Author:
Jumin Lee
Author:
Iain Peter Shand Smith
Author:
Hwayoung Lee
Author:
Seonghoon Kim
Author:
Yifei Qi
Author:
Jeffery B. Klauda
Author:
Göran Widmalm
Author:
Syma Khalid
Author:
Wonpil Im
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