Comparative Protein Structure Modeling Using MODELLER

Webb, Benjamin; Šali, Andrej

doi:10.1002/cpbi.3

Cited by 3,261 publications

(2,727 citation statements)

References 273 publications

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“…The three-dimensional model of BRP MBL was built using Modeler v9.16 (28), with the structure of BMLT (PDB code 1EWJ) as the template (13). The structure was constructed as a dimer, with two bleomycin molecules positioned at the interface of the monomers.…”

Section: Methodsmentioning

confidence: 99%

Characterization of BRP _MBL , the Bleomycin Resistance Protein Associated with the Carbapenemase NDM

Dortet

Girlich

Virlouvet

et al. 2017

Antimicrob Agents Chemother

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The metallo-␤-lactamase NDM-1 is among the most worrisome resistance determinants and is spreading worldwide among Gram-negative bacilli. A bleomycin resistance gene, ble MBL , downstream of the bla NDM-1 gene has been associated with resistance almost systematically. Here, we characterized the corresponding protein, BRP MBL , conferring resistance to bleomycin, an antitumoral glycopeptide molecule. We have determined whether the expression of the bla NDM-1 -ble MBL operon is inducible in the presence of carbapenems and/or bleomycin-like molecules using quantitative reverse transcription-PCR (qRT-PCR), determination of imipenem and zeocin MICs, and carbapenemase-specific activity assays. We showed that the bla NDM-1 -ble MBL operon is constitutively expressed. Using electrophoretic mobility shift and DNA protection assays performed with purified glutathione S-transferase (GST)-BRP MBL , we demonstrated that BRP MBL is able to bind and sequester bleomycin-like molecules, thus preventing bleomycin-dependent DNA degradation. In silico modeling confirmed that the mechanism of action required the dimerization of the BRP MBL protein in order to sequester bleomycin and prevent DNA damage. BRP MBL acts specifically on bleomycinlike molecules since cloning and expression of ble MBL in Staphyloccoccus aureus did not confer cross-resistance to any other antimicrobial glycopeptides such as vancomycin and teicoplanin.

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Section: Methodsmentioning

confidence: 99%

Characterization of BRP _MBL , the Bleomycin Resistance Protein Associated with the Carbapenemase NDM

Dortet

Girlich

Virlouvet

et al. 2017

Antimicrob Agents Chemother

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“…All parts were assembled to an overall alignment. Modeller version 9.14 was used to construct the 3D structure of TRPL (Webb and Sali 2016). The pipeline was built up by self-defined python scripts, for which all atom types, except of water molecules, were considered.…”

Section: Methodsmentioning

confidence: 99%

Molecular basis for the sensitivity of TRP channels to polyunsaturated fatty acids

Riehle

Tsvetkov

Gohlke

et al. 2018

Naunyn-Schmiedeberg's Arch Pharmacol

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Transient receptor potential (TRP) channels represent a superfamily of unselective cation channels that are subdivided into seven subfamilies based on their sequence homology and differences in gating and functional properties. Little is known about the molecular mechanisms of TRP channel regulation, particularly of the “canonical” TRP (TRPC) subfamily and their activation by polyunsaturated fatty acids (PUFAs). Here, we analyzed the structure-function relationship of Drosophila fruit fly TRPC channels. The primary aim was to uncover the molecular basis of PUFA sensitivity of Drosophila TRP-like (TRPL) and TRPgamma channels. Amino acid (aa) sequence alignment of the three Drosophila TRPC channels revealed 50 aa residues highly conserved in PUFA-sensitive TRPL and TRPgamma channels but not in the PUFA-insensitive TRP channel. Substitution of respective aa in TRPL by corresponding aa of TRP identified 18 residues that are necessary for PUFA-mediated activation of TRPL. Most aa positions are located within a stretch comprising transmembrane domains S2–S4, whereas six aa positions have been assigned to the proximal cytosolic C-terminus. Interestingly, residues I465 and S471 are required for activation by 5,8,11,14-eicosatetraynoic acid (ETYA) but not 5,8,11-eicosatriynoic acid (ETI). As proof of concept, we generated a PUFA-sensitive TRP channel by exchanging the corresponding aa from TRPL to TRP. Our study demonstrates a specific aa pattern in the transmembrane domains S2–S4 and the proximal C-terminus essential for TRP channel activation by PUFAs.Electronic supplementary materialThe online version of this article (10.1007/s00210-018-1507-3) contains supplementary material, which is available to authorized users.

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“…The final alignment was generated using CLUSTALX (version 2.1) 141-146 , showing a good match in helices S5, S6, and the pore region, with identity about 44% (Figure 2). After automatic model building and loop refinement, candidate models were evaluated based on the DOPE score from MODELLER (version 9.15) 141-145, 147 . The final homology model of the hERG K + channel is shown in Figure 3, which is found to be highly consistent with a previously reported homology model based on a slightly different procedure 143, 148-150 .…”

Section: Methodsmentioning

confidence: 99%

A Continuum Poisson–Boltzmann Model for Membrane Channel Proteins

Xiao¹,

Diao²,

Greene³

et al. 2017

J. Chem. Theory Comput.

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Membrane proteins constitute a large portion of the human proteome and perform a variety of important functions as membrane receptors, transport proteins, enzymes, signaling proteins, and more. Computational studies of membrane proteins are usually much more complicated than those of globular proteins. Here we propose a new continuum model for Poisson-Boltzmann calculations of membrane channel proteins. Major improvements over the existing continuum slab model are as follows:1) The location and thickness of the slab model are fine-tuned based on explicit-solvent MD simulations. 2) The highly different accessibility in the membrane and water regions are addressed with a two-step, two-probe grid labeling procedure, and 3) The water pores/channels are automatically identified. The new continuum membrane model is optimized (by adjusting the membrane probe, as well as the slab thickness and center) to best reproduce the distributions of buried water molecules in the membrane region as sampled in explicit water simulations. Our optimization also shows that the widely adopted water probe of 1.4 Å for globular proteins is a very reasonable default value for membrane protein simulations. It gives the best compromise in reproducing the explicit water distributions in membrane channel proteins, at least in the water accessible pore/channel regions that we focus on. Finally, we validate the new membrane model by carrying out binding affinity calculations for a potassium channel, and we observe a good agreement with experiment results.

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Comparative Protein Structure Modeling Using MODELLER

Cited by 3,261 publications

References 273 publications

Characterization of BRP _MBL , the Bleomycin Resistance Protein Associated with the Carbapenemase NDM

Characterization of BRP _MBL , the Bleomycin Resistance Protein Associated with the Carbapenemase NDM

Molecular basis for the sensitivity of TRP channels to polyunsaturated fatty acids

A Continuum Poisson–Boltzmann Model for Membrane Channel Proteins

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Comparative Protein Structure Modeling Using MODELLER

Cited by 3,261 publications

References 273 publications

Characterization of BRP MBL , the Bleomycin Resistance Protein Associated with the Carbapenemase NDM

Characterization of BRP MBL , the Bleomycin Resistance Protein Associated with the Carbapenemase NDM

Molecular basis for the sensitivity of TRP channels to polyunsaturated fatty acids

A Continuum Poisson–Boltzmann Model for Membrane Channel Proteins

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Product

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Characterization of BRP _MBL , the Bleomycin Resistance Protein Associated with the Carbapenemase NDM

Characterization of BRP _MBL , the Bleomycin Resistance Protein Associated with the Carbapenemase NDM