Capturing the multiscale dynamics of membrane protein complexes with all-atom, mixed-resolution, and coarse-grained models
Literature Information
Chenyi Liao, Xiaochuan Zhao, Jiyuan Liu, Severin T. Schneebeli, John C. Shelley, Jianing Li
The structures and dynamics of protein complexes are often challenging to model in heterogeneous environments such as biological membranes. Herein, we meet this fundamental challenge at attainable cost with all-atom, mixed-resolution, and coarse-grained models of vital membrane proteins. We systematically simulated five complex models formed by two distinct G protein-coupled receptors (GPCRs) in the lipid-bilayer membrane on the ns-to-μs timescales. These models, which suggest the swinging motion of an intracellular loop, for the first time, provide the molecular details for the regulatory role of such a loop. For the models at different resolutions, we observed consistent structural stability but various levels of speed-ups in protein dynamics. The mixed-resolution and coarse-grained models show two and four times faster protein diffusion than the all-atom models, in addition to a 4- and 400-fold speed-up in the simulation performance. Furthermore, by elucidating the strengths and challenges of combining all-atom models with reduced resolution models, this study can serve as a guide to simulating other complex systems in heterogeneous environments efficiently.
Recommended Journals

Herald of the Russian Academy of Sciences

Cellulose

Polycyclic Aromatic Compounds

Acta Metallurgica Sinica-English Letters

Biocatalysis and Biotransformation

Atomization and Sprays

Journal of the Indian Institute of Science

Bioorganic & Medicinal Chemistry

Medicinal Chemistry Research

Bioorganic & Medicinal Chemistry Letters
Related Literature
A missing allene of heavy Group 14 elements: 2-germadisilaallene
Takeaki Iwamoto, Takashi Abe, Chizuko Kabuto, Mitsuo Kira
DOI: 10.1039/B509878E
Ferrimagnetic Mn2SnO4nanowires
Chan Woong Na, Doo Suk Han, Jeunghee Park, Younghun Jo, Myung-Hwa Jung
DOI: 10.1039/B601404F
Selective aerobic oxidation in supercritical carbon dioxide catalyzed by the H5PV2Mo10O40 polyoxometalate
Galia Maayan, Benjamin Ganchegui, Ronny Neumann
DOI: 10.1039/B603148J
Metal complexes of selenophosphinates from reactions with (R2PSe)2Se: [M(R2PSe2)n] (M = ZnII, CdII, PbII, InIII, GaIII, CuI, BiIII, NiII; R = iPr, Ph) and [MoV2O2Se2(Se2PiPr2)2]
Chinh Q. Nguyen, Adekunle Adeogun, Mohammad Afzaal, Mohammad A. Malik, Paul O'Brien
DOI: 10.1039/B603198F
ortho-Hydroxylation of benzoic acids with hydrogen peroxide at a non-heme iron center
Sonia Taktak, Margaret Flook, Bruce M. Foxman, Lawrence Que, Jr., Elena V. Rybak-Akimova
DOI: 10.1039/B508004E
Monitoring the formation of TTF dimers by Na+ complexation
Marc Sallé, Jean-Yves Balandier, Franck Le Derf, Eric Levillain, Magali Allain, Pascal Viel, Serge Palacin
DOI: 10.1039/B518275A
Efficient dynamic kinetic resolution of secondary amines with Pd on alkaline earth salts and a lipase
Andrei Parvulescu, Dirk De Vos, Pierre Jacobs
DOI: 10.1039/B509747A
Demonstration of the optical limiting effect for an hemiporphyrazine
Danilo Dini, Mario J. F. Calvete, Michael Hanack, Vincenzo Amendola, Moreno Meneghetti
DOI: 10.1039/B601591C
Construction of superhydrophobic surfaces by fibrous aggregation of perfluoroalkyl chain-containing organogelators
Motoshi Yamanaka, Kazuki Sada, Mikiji Miyata, Kenji Hanabusa, Kazunori Nakano
DOI: 10.1039/B601485B
You might also like
What are the main uses of 1H-Indazole-6-carbonitrile (CAS: 141290-59-7)?
1H-Indazole-6-carbonitrile finds applications in pharmaceuticals, where it serve...
How should waste containing Dioctyl (2E)-2-butenedioate (CAS: 2997-85-5) be handled?
Waste containing Dioctyl (2E)-2-butenedioate (CAS: 2997-85-5) should be collecte...
What industries use Sodium [(1,2-benzoxazol-3-ylmethyl)sulfonyl]azanide (CAS: 68291-98-5)?
Sodium [(1,2-benzoxazol-3-ylmethyl)sulfonyl]azanide is primarily used in pharmac...
Are there alternatives to Dimethyl 4-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-2,6-pyridinedicarboxylate (CAS: 741709-66-0) in synthesis?
Dimethyl 4-(4,4,5,5-tetramethyl-1,3,2-dioxaborolan-2-yl)-2,6-pyridinedicarboxyla...
How should waste containing 2-Fluoro-6-hydrazinopyridine (CAS: 80714-39-2) be handled?
Waste containing 2-Fluoro-6-hydrazinopyridine (CAS: 80714-39-2) should be manage...
What is 6-Formyl-2-pyridinecarboxylic acid (CAS: 499214-11-8)?
6-Formyl-2-pyridinecarboxylic acid is an organic compound with the molecular for...
What is the market or research trend for 3-(3,4-dimethoxyphenyl)-2,5-dimethyl-N-(2-morpholin-4-ylethyl)pyrazolo[1,5-a]pyrimidin-7-amine (CAS: 900874-91-1)?
Research trends for this compound indicate a focus on its potential applications...
How is 9H-Tribenzo[b,d,f]azepine (CAS: 29875-73-8) typically synthesized?
9H-Tribenzo[b,d,f]azepine is typically synthesized via a multi-step process invo...
How is 1-Cyclopropyl-7-ethoxy-6-fluoro-8-methoxy-4-oxo-1,4-dihydro-3-quinolinecarboxylic acid (CAS: 1797982-51-4) typically synthesized?
1-Cyclopropyl-7-ethoxy-6-fluoro-8-methoxy-4-oxo-1,4-dihydro-3-quinolinecarboxyli...
How should waste containing Methyl 3-oxo-1,2,3,4-tetrahydro-6-quinoxalinecarboxylate (CAS: 671820-52-3) be handled?
Waste containing Methyl 3-oxo-1,2,3,4-tetrahydro-6-quinoxalinecarboxylate (CAS: ...
Source Journal
Physical Chemistry Chemical Physics

Physical Chemistry Chemical Physics (PCCP) is an international journal co-owned by 19 physical chemistry and physics societies from around the world. This journal publishes original, cutting-edge research in physical chemistry, chemical physics and biophysical chemistry. To be suitable for publication in PCCP, articles must include significant innovation and/or insight into physical chemistry; this is the most important criterion that reviewers and Editors will judge against when evaluating submissions. The journal has a broad scope and welcomes contributions spanning experiment, theory, computation and data science. Topical coverage includes spectroscopy, dynamics, kinetics, statistical mechanics, thermodynamics, electrochemistry, catalysis, surface science, quantum mechanics, quantum computing and machine learning. Interdisciplinary research areas such as polymers and soft matter, materials, nanoscience, energy, surfaces/interfaces, and biophysical chemistry are welcomed if they demonstrate significant innovation and/or insight into physical chemistry. Joined experimental/theoretical studies are particularly appreciated when complementary and based on up-to-date approaches.



![N-[(9H-Fluoren-9-ylmethoxy)carbonyl]serine structure N-[(9H-Fluoren-9-ylmethoxy)carbonyl]serine structure](https://static.chemtradehub.com/structs/737/73724-45-5-b0dc.webp)
