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      An Arg/Ala-rich helix in the N-terminal region of M. tuberculosis FtsQ is a potential membrane anchor of the Z-ring

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          Abstract

          Mtb infects a quarter of the worldwide population. Most drugs for treating tuberculosis target cell growth and division. With rising drug resistance, it becomes ever more urgent to better understand Mtb cell division. This process begins with the formation of the Z-ring via polymerization of FtsZ and anchoring of the Z-ring to the inner membrane. Here we show that the transmembrane protein FtsQ is a potential membrane anchor of the Mtb Z-ring. In the otherwise disordered cytoplasmic region of FtsQ, a 29-residue, Arg/Ala-rich α-helix is formed that interacts with upstream acidic residues in solution and with acidic lipids at the membrane surface. This helix also binds to the GTPase domain of FtsZ, with implications for drug binding and Z-ring formation.

          Abstract

          The disordered cytoplasmic region of Mtb FtsQ can interact with three partners – the upstream acidic residues in solution, the inner membrane surface, and the GTPase domain of FtsZ – suggesting its role in cell division and as a drug target.

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          Most cited references62

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          Molecular dynamics with coupling to an external bath

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            ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB.

            Molecular mechanics is powerful for its speed in atomistic simulations, but an accurate force field is required. The Amber ff99SB force field improved protein secondary structure balance and dynamics from earlier force fields like ff99, but weaknesses in side chain rotamer and backbone secondary structure preferences have been identified. Here, we performed a complete refit of all amino acid side chain dihedral parameters, which had been carried over from ff94. The training set of conformations included multidimensional dihedral scans designed to improve transferability of the parameters. Improvement in all amino acids was obtained as compared to ff99SB. Parameters were also generated for alternate protonation states of ionizable side chains. Average errors in relative energies of pairs of conformations were under 1.0 kcal/mol as compared to QM, reduced 35% from ff99SB. We also took the opportunity to make empirical adjustments to the protein backbone dihedral parameters as compared to ff99SB. Multiple small adjustments of φ and ψ parameters were tested against NMR scalar coupling data and secondary structure content for short peptides. The best results were obtained from a physically motivated adjustment to the φ rotational profile that compensates for lack of ff99SB QM training data in the β-ppII transition region. Together, these backbone and side chain modifications (hereafter called ff14SB) not only better reproduced their benchmarks, but also improved secondary structure content in small peptides and reproduction of NMR χ1 scalar coupling measurements for proteins in solution. We also discuss the Amber ff12SB parameter set, a preliminary version of ff14SB that includes most of its improvements.
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              CHARMM-GUI: a web-based graphical user interface for CHARMM.

              CHARMM is an academic research program used widely for macromolecular mechanics and dynamics with versatile analysis and manipulation tools of atomic coordinates and dynamics trajectories. CHARMM-GUI, http://www.charmm-gui.org, has been developed to provide a web-based graphical user interface to generate various input files and molecular systems to facilitate and standardize the usage of common and advanced simulation techniques in CHARMM. The web environment provides an ideal platform to build and validate a molecular model system in an interactive fashion such that, if a problem is found through visual inspection, one can go back to the previous setup and regenerate the whole system again. In this article, we describe the currently available functional modules of CHARMM-GUI Input Generator that form a basis for the advanced simulation techniques. Future directions of the CHARMM-GUI development project are also discussed briefly together with other features in the CHARMM-GUI website, such as Archive and Movie Gallery. 2008 Wiley Periodicals, Inc.
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                Author and article information

                Contributors
                timothyacross@gmail.com
                hzhou43@uic.edu
                Journal
                Commun Biol
                Commun Biol
                Communications Biology
                Nature Publishing Group UK (London )
                2399-3642
                23 March 2023
                23 March 2023
                2023
                : 6
                : 311
                Affiliations
                [1 ]GRID grid.481548.4, ISNI 0000 0001 2292 2549, National High Magnetic Field Laboratory, ; Tallahassee, FL 32310 USA
                [2 ]GRID grid.255986.5, ISNI 0000 0004 0472 0419, Department of Chemistry and Biochemistry, , Florida State University, ; Tallahassee, FL 32306 USA
                [3 ]GRID grid.255986.5, ISNI 0000 0004 0472 0419, Institute of Molecular Biophysics, , Florida State University, ; Tallahassee, FL 32306 USA
                [4 ]GRID grid.185648.6, ISNI 0000 0001 2175 0319, Department of Chemistry, , University of Illinois Chicago, ; Chicago, IL 60607 USA
                [5 ]GRID grid.185648.6, ISNI 0000 0001 2175 0319, Department of Physics, , University of Illinois Chicago, ; Chicago, IL 60607 USA
                Author information
                http://orcid.org/0000-0002-4607-2996
                http://orcid.org/0000-0002-4366-5681
                http://orcid.org/0000-0001-9020-0302
                Article
                4686
                10.1038/s42003-023-04686-5
                10036325
                36959324
                defad152-b035-4b49-8e3e-1d8df58fa22b
                © The Author(s) 2023

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 7 December 2022
                : 9 March 2023
                Funding
                Funded by: FundRef https://doi.org/10.13039/100000002, U.S. Department of Health & Human Services | National Institutes of Health (NIH);
                Award ID: AI119187
                Award ID: GM122698
                Award ID: GM118091
                Award Recipient :
                Funded by: U.S. Department of Health & Human Services | National Institutes of Health (NIH)
                Funded by: U.S. Department of Health & Human Services | National Institutes of Health (NIH)
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                © The Author(s) 2023

                intrinsically disordered proteins,membrane biophysics

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