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      Biophysical Characterization of Nucleophosmin Interactions with Human Immunodeficiency Virus Rev and Herpes Simplex Virus US11

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          Abstract

          Nucleophosmin (NPM1, also known as B23, numatrin or NO38) is a pentameric RNA-binding protein with RNA and protein chaperon functions. NPM1 has increasingly emerged as a potential cellular factor that directly associates with viral proteins; however, the significance of these interactions in each case is still not clear. In this study, we have investigated the physical interaction of NPM1 with both human immunodeficiency virus type 1 (HIV-1) Rev and Herpes Simplex virus type 1 (HSV-1) US11, two functionally homologous proteins. Both viral proteins show, in mechanistically different modes, high affinity for a binding site on the N-terminal oligomerization domain of NPM1. Rev, additionally, exhibits low-affinity for the central histone-binding domain of NPM1. We also showed that the proapoptotic cyclic peptide CIGB-300 specifically binds to NPM1 oligomerization domain and blocks its association with Rev and US11. Moreover, HIV-1 virus production was significantly reduced in the cells treated with CIGB-300. Results of this study suggest that targeting NPM1 may represent a useful approach for antiviral intervention.

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          Most cited references 82

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          CHARMM: the biomolecular simulation program.

          CHARMM (Chemistry at HARvard Molecular Mechanics) is a highly versatile and widely used molecular simulation program. It has been developed over the last three decades with a primary focus on molecules of biological interest, including proteins, peptides, lipids, nucleic acids, carbohydrates, and small molecule ligands, as they occur in solution, crystals, and membrane environments. For the study of such systems, the program provides a large suite of computational tools that include numerous conformational and path sampling methods, free energy estimators, molecular minimization, dynamics, and analysis techniques, and model-building capabilities. The CHARMM program is applicable to problems involving a much broader class of many-particle systems. Calculations with CHARMM can be performed using a number of different energy functions and models, from mixed quantum mechanical-molecular mechanical force fields, to all-atom classical potential energy functions with explicit solvent and various boundary conditions, to implicit solvent and membrane models. The program has been ported to numerous platforms in both serial and parallel architectures. This article provides an overview of the program as it exists today with an emphasis on developments since the publication of the original CHARMM article in 1983. Copyright 2009 Wiley Periodicals, Inc.
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            Rho-family GTPases: it's not only Rac and Rho (and I like it).

            The Rho-family proteins make up a major branch of the Ras superfamily of small GTPases. To date, 22 human genes encoding at least 25 proteins have been described. The best known 'classical' members are RhoA, Rac1 and Cdc42. Highly related isoforms of these three proteins have not been studied as intensively, in part because it has been assumed that they are functionally identical to their better-studied counterparts. This now appears not to be the case. Variations in C-terminal-signaled modifications and subcellular targeting cause otherwise highly biochemically related isoforms (e.g. RhoA, RhoB and RhoC) to exhibit surprisingly divergent biological activities. Whereas the classical Rho GTPases are regulated by GDP/GTP cycling, other Rho GTPases are also regulated by other mechanisms, particularly by transcriptional regulation. Newer members of the family possess additional sequence elements beyond the GTPase domain, which suggests they exhibit yet other mechanisms of regulation.
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              Multifaceted activities of the HIV-1 transactivator of transcription, Tat.

               K Jeang,  H. Xiao,  Maria Rich (1999)
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                Author and article information

                Contributors
                Role: Editor
                Journal
                PLoS One
                PLoS ONE
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, CA USA )
                1932-6203
                1 December 2015
                2015
                : 10
                : 12
                Affiliations
                [1 ]Institute of Biochemistry and Molecular Biology II, Medical Faculty, Heinrich-Heine University, Düsseldorf, Germany
                [2 ]Laboratory of Chemical Biology & Institute of Complex Molecular Systems, Department of Biomedical Engineering, Technische Universiteit Eindhoven, Eindhoven, Netherlands
                [3 ]Clinic for Gastroenterology, Hepatology and Infectiology, Medical Faculty, Heinrich-Heine University, Düsseldorf, Germany
                [4 ]Institute of Biochemistry, Heinrich-Heine University, Düsseldorf, Germany
                [5 ]Institute of Complex Systems (ICS-6), Research Centre Jülich, Jülich, Germany
                [6 ]Institute of Physical Biology, Heinrich-Heine University, Düsseldorf, Germany
                [7 ]Institute of Virology, Medical Faculty, Heinrich-Heine University, Düsseldorf, Germany
                [8 ]Institute of Virology, University Medical Center Freiburg, Freiburg, Germany
                University of Regensburg, GERMANY
                Author notes

                Competing Interests: The authors have declared that no competing interests exist.

                Conceived and designed the experiments: KN MRA CM. Performed the experiments: KN JMM AH RD EA ML LNS. Analyzed the data: KN MRA CM LNS RD. Contributed reagents/materials/analysis tools: KN MRA RD EA LGM SH LB HH LS LB SHJS. Wrote the paper: KN MRA.

                PONE-D-15-29879
                10.1371/journal.pone.0143634
                4704560
                26624888

                This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited

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                Figures: 6, Tables: 3, Pages: 22
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                Funding
                This work was funded by the International Graduate School of Protein Science and Technology (iGRASP), Research Commission of the Medical Faculty and the Strategic Research Fund (SFF) of Heinrich-Heine University Düsseldorf, and the German Research Foundation (Deutsche Forschungsgemeinschaft or DFG) through the Collaborative Research Center 974 (SFB 974) “Communication and Systems Relevance during Liver Injury and Regeneration”, the International Research Training Group 1902 (IRTG 1902) “Intra- and interorgan communication of the cardiovascular system”, and GRK 1045 “Modulation of host cell function”. CM is supported by the Heinz Ansmann foundation. AH is supported by the Jürgen Manchot Foundation, Molecules of Infection Graduate School.
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