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      Relevance of the protein macrodipole in the membrane-binding process. Interactions of fatty-acid binding proteins with cationic lipid membranes

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          The fatty acid-binding proteins L-BABP and Rep1-NCXSQ bind to anionic lipid membranes by electrostatic interactions. According to Molecular Dynamics (MD) simulations, the interaction of the protein macrodipole with the membrane electric field is a driving force for protein binding and orientation in the interface. To further explore this hypothesis, we studied the interactions of these proteins with cationic lipid membranes. As in the case of anionic lipid membranes, we found that both proteins, carrying a negative as well as a positive net charge, were bound to the positively charged membrane. Their major axis, those connecting the bottom of the β-barrel with the α-helix portal domain, were rotated about 180 degrees as compared with their orientations in the anionic lipid membranes. Fourier transform infrared (FTIR) spectroscopy of the proteins showed that the positively charged membranes were also able to induce conformational changes with a reduction of the β-strand proportion and an increase in α-helix secondary structure. Fatty acid-binding proteins (FABPs) are involved in several cell processes, such as maintaining lipid homeostasis in cells. They transport hydrophobic molecules in aqueous medium and deliver them into lipid membranes. Therefore, the interfacial orientation and conformation, both shown herein to be electrostatically determined, have a strong correlation with the specific mechanism by which each particular FABP exerts its biological function.

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          Most cited references 52

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          Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features.

           C. Sander,  W Kabsch (1983)
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            VMD: visual molecular dynamics.

            VMD is a molecular graphics program designed for the display and analysis of molecular assemblies, in particular biopolymers such as proteins and nucleic acids. VMD can simultaneously display any number of structures using a wide variety of rendering styles and coloring methods. Molecules are displayed as one or more "representations," in which each representation embodies a particular rendering method and coloring scheme for a selected subset of atoms. The atoms displayed in each representation are chosen using an extensive atom selection syntax, which includes Boolean operators and regular expressions. VMD provides a complete graphical user interface for program control, as well as a text interface using the Tcl embeddable parser to allow for complex scripts with variable substitution, control loops, and function calls. Full session logging is supported, which produces a VMD command script for later playback. High-resolution raster images of displayed molecules may be produced by generating input scripts for use by a number of photorealistic image-rendering applications. VMD has also been expressly designed with the ability to animate molecular dynamics (MD) simulation trajectories, imported either from files or from a direct connection to a running MD simulation. VMD is the visualization component of MDScope, a set of tools for interactive problem solving in structural biology, which also includes the parallel MD program NAMD, and the MDCOMM software used to connect the visualization and simulation programs. VMD is written in C++, using an object-oriented design; the program, including source code and extensive documentation, is freely available via anonymous ftp and through the World Wide Web.
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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.

                Author and article information

                [1 ] Universidad Nacional de Córdoba, Facultad de Ciencias Químicas, Departamento de Química Biológica “Ranwel Caputto”, Córdoba, Argentina
                [2 ] CONICET, Universidad Nacional de Córdoba, Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), Córdoba, Argentina
                [3 ] Universidad Nacional de Córdoba, Facultad de Ciencias Químicas, Departamento de Química Teórica y Computacional, Córdoba, Argentina
                [4 ] CONICET, Universidad Nacional de Córdoba. Instituto de Investigaciones en Fisicoquímica de Córdoba (INFIQC), Córdoba, Argentina
                University of Waterloo, CANADA
                Author notes

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


                Current address: CONICET, Facultad de Ciencias Exactas y Naturales, Universidad Nacional de Cuyo, Mendoza, Argentina.

                Role: Conceptualization, Role: Data curation, Role: Formal analysis, Role: Writing – original draft
                Role: Conceptualization
                ORCID:, Role: Conceptualization, Role: Funding acquisition, Role: Project administration, Role: Supervision, Role: Writing – review & editing
                Role: Editor
                PLoS One
                PLoS ONE
                PLoS ONE
                Public Library of Science (San Francisco, CA USA )
                8 March 2018
                : 13
                : 3
                29518146 5843346 10.1371/journal.pone.0194154 PONE-D-17-33567
                © 2018 Galassi et al

                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.

                Figures: 8, Tables: 2, Pages: 15
                Funded by: Consejo Nacional de Investigaciones Científicas y Técnicas (AR)
                Award ID: PIP 2013-2015
                Funded by: funder-id, Fondo para la Investigación Científica y Tecnológica;
                Award ID: PICT 2015-1612
                This work was supported by Consejo Nacional de Investigaciones Científicas y Técnicas (AR), PIP 2013-2015; Fondo para la Investigación Científica y Tecnológica, PICT 2015-1612; and Secretaría de Ciencia y Técnica UNC.
                Research Article
                Biology and Life Sciences
                Biology and Life Sciences
                Biochemical Simulations
                Biology and Life Sciences
                Computational Biology
                Biochemical Simulations
                Biology and Life Sciences
                Protein Interactions
                Biology and Life Sciences
                Cell Biology
                Cellular Structures and Organelles
                Cell Membranes
                Membrane Proteins
                Peripheral Membrane Proteins
                Research and Analysis Methods
                Bioassays and Physiological Analysis
                Electrophysiological Techniques
                Membrane Electrophysiology
                Physical Sciences
                Electric Field
                Physical Sciences
                Physical Sciences
                Physical Chemistry
                Chemical Bonding
                Electrostatic Bonding
                Custom metadata
                All relevant data are within the paper and the Supporting Information files.



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