Preparing Membrane Proteins for Simulation Using CHARMM-GUI

Li, Yupeng; Liu, Jinchan; Gumbart, James C.

doi:10.1007/978-1-0716-1394-8_13

Cited by 14 publications

(11 citation statements)

References 43 publications

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“…This ratio is in agreement with the literature [ 36 ]. Membrane bilayer was built using CHARMM-GUI [ 53 ] or insane script [ 54 ] for all-atom and CG systems, respectively.…”

Section: Methodsmentioning

confidence: 99%

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Towards Molecular Understanding of the Functional Role of UbiJ-UbiK2 Complex in Ubiquinone Biosynthesis by Multiscale Molecular Modelling Studies

Launay

Teppa

Martins

et al. 2022

IJMS

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Ubiquinone (UQ) is a polyisoprenoid lipid found in the membranes of bacteria and eukaryotes. UQ has important roles, notably in respiratory metabolisms which sustain cellular bioenergetics. Most steps of UQ biosynthesis take place in the cytosol of E. coli within a multiprotein complex called the Ubi metabolon, that contains five enzymes and two accessory proteins, UbiJ and UbiK. The SCP2 domain of UbiJ was proposed to bind the hydrophobic polyisoprenoid tail of UQ biosynthetic intermediates in the Ubi metabolon. How the newly synthesised UQ might be released in the membrane is currently unknown. In this paper, we focused on better understanding the role of the UbiJ-UbiK2 heterotrimer forming part of the metabolon. Given the difficulties to gain functional insights using biophysical techniques, we applied a multiscale molecular modelling approach to study the UbiJ-UbiK2 heterotrimer. Our data show that UbiJ-UbiK2 interacts closely with the membrane and suggests possible pathways to enable the release of UQ into the membrane. This study highlights the UbiJ-UbiK2 complex as the likely interface between the membrane and the enzymes of the Ubi metabolon and supports that the heterotrimer is key to the biosynthesis of UQ8 and its release into the membrane of E. coli.

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“…This ratio is in agreement with the literature [ 36 ]. Membrane bilayer was built using CHARMM-GUI [ 53 ] or insane script [ 54 ] for all-atom and CG systems, respectively.…”

Section: Methodsmentioning

confidence: 99%

“…For MD simulations with the lipid membrane, CHARMM-GUI ( , accessed on 27 May 2022) [ 53 ] protocol was used, corresponding to a series of minimisation, 3 NVT and 3 NPT equilibrations with decreasing constraints. The production phase was run without constraint in NPT ensemble at 303 K and a timestep of 2 fs.…”

Section: Methodsmentioning

confidence: 99%

Towards Molecular Understanding of the Functional Role of UbiJ-UbiK2 Complex in Ubiquinone Biosynthesis by Multiscale Molecular Modelling Studies

Launay

Teppa

Martins

et al. 2022

IJMS

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“…For each complex, the 1-palmitoyl-2-oleoyl- glycero -3-phosphocholine (POPC) was selected to generate the lipid bilayer using CHARMM-GUI, 27–29 and a 10 Å thick TIP3P water layer was added on each side of the lipid bilayer, along with 0.1 M NaCl. All cMD simulations were carried out using GPU-accelerated NAMD (version 2.13) 30 with the AMBER force field parameters.…”

Section: Methodsmentioning

confidence: 99%

“…For each complex, the 1-palmitoyl-2-oleoyl-glycero-3-phosphocholine (POPC) was selected to generate the lipid bilayer using CHARMM-GUI, [27][28][29] and a 10 Å thick TIP3P water layer was added on each side of the lipid bilayer, along with 0.1 M NaCl.…”

Section: Conventional Molecular Dynamics Simulationmentioning

confidence: 99%

Assessing the role of residue Phe108 of cytochrome P450 3A4 in allosteric effects of midazolam metabolism

Fu,

Zhang,

Zheng

2024

Phys. Chem. Chem. Phys.

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“…The procedure described in ( 49 ) ( https://www.ks.uiuc.edu/Training/Tutorials - Membrane Protein Tutorials) for membrane-protein system preparation was followed. For both systems, GspDPT/LPS and GspDPT/POPC, the entire procedure was performed using the CHARMM-GUI server ( 50 ).…”

Section: Methodsmentioning

confidence: 99%

Structural characterization and functional insights into the type II secretion system of the poly-extremophile Deinococcus radiodurans

Farci,

Milenkovic,

Iesu

et al. 2024

Journal of Biological Chemistry

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Preparing Membrane Proteins for Simulation Using CHARMM-GUI

Cited by 14 publications

References 43 publications

Towards Molecular Understanding of the Functional Role of UbiJ-UbiK2 Complex in Ubiquinone Biosynthesis by Multiscale Molecular Modelling Studies

Towards Molecular Understanding of the Functional Role of UbiJ-UbiK2 Complex in Ubiquinone Biosynthesis by Multiscale Molecular Modelling Studies

Assessing the role of residue Phe108 of cytochrome P450 3A4 in allosteric effects of midazolam metabolism

Structural characterization and functional insights into the type II secretion system of the poly-extremophile Deinococcus radiodurans

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