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      NMR Structure of the Myristylated Feline Immunodeficiency Virus Matrix Protein

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          Abstract

          Membrane targeting by the Gag proteins of the human immunodeficiency viruses (HIV types-1 and -2) is mediated by Gag’s N-terminally myristylated matrix (MA) domain and is dependent on cellular phosphatidylinositol-4,5-bisphosphate [PI(4,5)P 2]. To determine if other lentiviruses employ a similar membrane targeting mechanism, we initiated studies of the feline immunodeficiency virus (FIV), a widespread feline pathogen with potential utility for development of human therapeutics. Bacterial co-translational myristylation was facilitated by mutation of two amino acids near the amino-terminus of the protein (Q5A/G6S; myrMA Q5A/G6S). These substitutions did not affect virus assembly or release from transfected cells. NMR studies revealed that the myristyl group is buried within a hydrophobic pocket in a manner that is structurally similar to that observed for the myristylated HIV-1 protein. Comparisons with a recent crystal structure of the unmyristylated FIV protein [myr(-)MA] indicate that only small changes in helix orientation are required to accommodate the sequestered myr group. Depletion of PI(4,5)P 2 from the plasma membrane of FIV-infected CRFK cells inhibited production of FIV particles, indicating that, like HIV, FIV hijacks the PI(4,5)P 2 cellular signaling system to direct intracellular Gag trafficking during virus assembly.

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          Most cited references 74

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          NMRPipe: a multidimensional spectral processing system based on UNIX pipes.

          The NMRPipe system is a UNIX software environment of processing, graphics, and analysis tools designed to meet current routine and research-oriented multidimensional processing requirements, and to anticipate and accommodate future demands and developments. The system is based on UNIX pipes, which allow programs running simultaneously to exchange streams of data under user control. In an NMRPipe processing scheme, a stream of spectral data flows through a pipeline of processing programs, each of which performs one component of the overall scheme, such as Fourier transformation or linear prediction. Complete multidimensional processing schemes are constructed as simple UNIX shell scripts. The processing modules themselves maintain and exploit accurate records of data sizes, detection modes, and calibration information in all dimensions, so that schemes can be constructed without the need to explicitly define or anticipate data sizes or storage details of real and imaginary channels during processing. The asynchronous pipeline scheme provides other substantial advantages, including high flexibility, favorable processing speeds, choice of both all-in-memory and disk-bound processing, easy adaptation to different data formats, simpler software development and maintenance, and the ability to distribute processing tasks on multi-CPU computers and computer networks.
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            Inference of macromolecular assemblies from crystalline state.

            We discuss basic physical-chemical principles underlying the formation of stable macromolecular complexes, which in many cases are likely to be the biological units performing a certain physiological function. We also consider available theoretical approaches to the calculation of macromolecular affinity and entropy of complexation. The latter is shown to play an important role and make a major effect on complex size and symmetry. We develop a new method, based on chemical thermodynamics, for automatic detection of macromolecular assemblies in the Protein Data Bank (PDB) entries that are the results of X-ray diffraction experiments. As found, biological units may be recovered at 80-90% success rate, which makes X-ray crystallography an important source of experimental data on macromolecular complexes and protein-protein interactions. The method is implemented as a public WWW service.
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              Electrostatics of nanosystems: application to microtubules and the ribosome.

              Evaluation of the electrostatic properties of biomolecules has become a standard practice in molecular biophysics. Foremost among the models used to elucidate the electrostatic potential is the Poisson-Boltzmann equation; however, existing methods for solving this equation have limited the scope of accurate electrostatic calculations to relatively small biomolecular systems. Here we present the application of numerical methods to enable the trivially parallel solution of the Poisson-Boltzmann equation for supramolecular structures that are orders of magnitude larger in size. As a demonstration of this methodology, electrostatic potentials have been calculated for large microtubule and ribosome structures. The results point to the likely role of electrostatics in a variety of activities of these structures.
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                Author and article information

                Contributors
                Role: Academic Editor
                Journal
                Viruses
                Viruses
                viruses
                Viruses
                MDPI
                1999-4915
                30 April 2015
                May 2015
                : 7
                : 5
                : 2210-2229
                Affiliations
                [1 ]Howard Hughes Medical Institute, University of Maryland Baltimore County, 1000 Hilltop Circle, Baltimore, MD 21250, USA; E-Mails: lola.brown@ 123456yale.edu (L.A.B.); cassiah.cox@ 123456nih.gov (C.C.); janaeb@ 123456umbc.edu (J.B.); hsummers@ 123456umbc.edu (H.S.); ryan.button@ 123456umaryland.edu (R.B.); kennedy.bahlow@ 123456temple.edu (K.B.); vspurrier@ 123456uchicago.edu (V.S.); jmk216@ 123456lehigh.edu (J.K.)
                [2 ]Virus-Cell Interaction Section, HIV Drug Resistance Program, National Cancer Institute at Frederick, Frederick, MD 21702-1201, USA; E-Mails: bxl244@ 123456case.edu (B.G.L.); kuols@ 123456mail.nih.gov (L.K.)
                Author notes
                [* ]Authors to whom correspondence should be addressed; E-Mails: efreed@ 123456mail.nih.gov (E.O.F.); summers@ 123456hhmi.umbc.edu (M.F.S.); Tel.: +1-301-846-6223 (E.O.F.); +1-410-455-2527 (M.F.S).
                Article
                viruses-07-02210
                10.3390/v7052210
                4452903
                25941825
                © 2015 by the authors; licensee MDPI, Basel, Switzerland.

                This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution license ( http://creativecommons.org/licenses/by/4.0/).

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