An Introduction to Biomolecular Graphics

Mura, Cameron; McCrimmon, Colin M.; Vertrees, Jason; Sawaya, M.R.

doi:10.1371/journal.pcbi.1000918

Cited by 50 publications

(57 citation statements)

References 37 publications

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“…Other lipid tails are shown in gray spheres and other phosphates in orange spheres. A thin gray plane shows the average phosphorus position in the upper leaflet [46]. The fusion peptides are membrane-inserted but sit in a local undulation of the bilayer, hence the local abundance of lipids above the average z -position.…”

Section: Introductionmentioning

confidence: 99%

Lipid Tail Protrusion in Simulations Predicts Fusogenic Activity of Influenza Fusion Peptide Mutants and Conformational Models

2013

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Fusion peptides from influenza hemagglutinin act on membranes to promote membrane fusion, but the mechanism by which they do so remains unknown. Recent theoretical work has suggested that contact of protruding lipid tails may be an important feature of the transition state for membrane fusion. If this is so, then influenza fusion peptides would be expected to promote tail protrusion in proportion to the ability of the corresponding full-length hemagglutinin to drive lipid mixing in fusion assays. We have performed molecular dynamics simulations of influenza fusion peptides in lipid bilayers, comparing the X-31 influenza strain against a series of N-terminal mutants. As hypothesized, the probability of lipid tail protrusion correlates well with the lipid mixing rate induced by each mutant. This supports the conclusion that tail protrusion is important to the transition state for fusion. Furthermore, it suggests that tail protrusion can be used to examine how fusion peptides might interact with membranes to promote fusion. Previous models for native influenza fusion peptide structure in membranes include a kinked helix, a straight helix, and a helical hairpin. Our simulations visit each of these conformations. Thus, the free energy differences between each are likely low enough that specifics of the membrane environment and peptide construct may be sufficient to modulate the equilibrium between them. However, the kinked helix promotes lipid tail protrusion in our simulations much more strongly than the other two structures. We therefore predict that the kinked helix is the most fusogenic of these three conformations.

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Section: Introductionmentioning

confidence: 99%

Lipid Tail Protrusion in Simulations Predicts Fusogenic Activity of Influenza Fusion Peptide Mutants and Conformational Models

2013

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“…This function gives the scene settings in a compact format for easy addition to a series of commands in a single row. The horizontal scripts complement and extend the approaches outlined earlier by others . We discuss below how horizontal scripts enable new ways to use PyMOL.…”

Section: Discussionmentioning

confidence: 90%

“…One program that is difficult to master is PyMOL. In spite of this difficulty, PyMOL is used widely in structural biology . PyMOL is often used for molecular visualization by crystallographic, molecular dynamics simulation, and protein modeling software packages .…”

Section: Introductionmentioning

confidence: 99%

Simplifying and enhancing the use of PyMOL with horizontal scripts

Mooers

2016

Protein Science

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Scripts are used in PyMOL to exert precise control over the appearance of the output and to ease remaking similar images at a later time. We developed horizontal scripts to ease script development. A horizontal script makes a complete scene in PyMOL like a traditional vertical script. The commands in a horizontal script are separated by semicolons. These scripts are edited interactively on the command line with no need for an external text editor. This simpler workflow accelerates script development. In using PyMOL, the illustration of a molecular scene requires an 18-element matrix of view port settings. The default format spans several lines and is laborious to manually reformat for one line. This default format prevents the fast assembly of horizontal scripts that can reproduce a molecular scene. We solved this problem by writing a function that displays the settings on one line in a compact format suitable for horizontal scripts. We also demonstrate the mapping of aliases to horizontal scripts. Many aliases can be defined in a single script file, which can be useful for applying costume molecular representations to any structure. We also redefined horizontal scripts as Python functions to enable the use of the help function to print documentation about an alias to the command history window. We discuss how these methods of using horizontal scripts both simplify and enhance the use of PyMOL in research and education.

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“…Helices are depicted as simplified spirals approximating the alpha-carbon tracing, and beta strands are represented as flattened arrows. The ribbon representation mode remains the most frequent method of depiction of structure in scientist-to-scientist peer communication (Mura et al, 2010;Goodsell 2005). Richardson also developed a related cartoon mode using rods instead of spirals to represent helices, a depiction which further simplifies and abstracts protein positional information into recognizable motifs ( Figure 2, (Humphreys et al, 1996); UCSF Chimera (Peterson et al, 2004);and Pymol (The PyMOL Molecular Graphics System, Schrödinger, LLC;http://pymol.org/) (Mura et al, 2010).…”

Section: Protein Representationmentioning

confidence: 99%

“…Papers by O'Donoghue et al (2010), Mura et al (2010), and Johnson and Hertig (2014) serve as practical guides to the visualization of protein structures, reviewing different modes of representation, guidelines as to appropriate level of detail and complexity, and software to produce accurate illustrations. There are several papers that expound upon the importance of choosing a certain representation to match the communication goal of the illustration.…”

Section: Protein Representationmentioning

confidence: 99%

The Science Behind G Protein-Coupled Receptors (GPCRs) and Their Accurate Visual Representation in Scientific Research

Sojka¹,

Brennan²,

Maizels³

et al. 2017

JBC

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IntroductionG Protein-Coupled Receptors (GPCRs) are transmembrane (TM) proteins that span the cell membrane seven times, and contain intracellular and extracellular domains comprised of connecting loops as well as terminal extension sequences. GPCRs bind ligands within their transmembrane and/or extracellular domains. Ligand binding elicits conformational changes that initiate downstream intracellular signaling events through arrestins and G proteins ( Figure 1; Katritch et al., 2013). GPCRs play central roles in many physiological processes from sensory to neurological, cardiovascular, endocrine, and reproductive functions. GPCRs represent one of the largest gene families in the human genome, encoding approximately 800 unique proteins (Fredriksson et al., 2003). GPCRs' unique structure and cell surface location make them ideal targets for various drug therapies, assuring interest from the pharmaceutical and clinical medicine communities (Vischer et al., 2011). It is estimated that roughly 40% of the pharmaceuticals currently marketed, target GPCRs (Vischer et al., 2011). BI-167107, bovine Gs;Rasmussen et al., 2011) Urbana-Champaign (Humphreys et al., 1996). This image was made with Visual Molecular Dynamics (VMD). VMD is developed with NIH support by the Theoretical and Computational Biophysics group at the Beckman Institute, University of Illinois atThe elucidation of x-ray crystallographic structures of GPCRs has been monumental to the research in understanding the function and conformational flexibility of GPCRs (Costanzi 2014;Venkatakrishnan et al., 2014). Understanding how ligand binding alters the structure and function of GPCRs to mediate signaling has undergone an expansion in recent years (Katritch et al., 2013). Concepts such as ligands acting as functionally selective biased agonists to elicit a specific subset of signaling responses are now at the forefront of GPCR research (Andresen 2011). Development of allosteric ligands extends the repertoire of GPCR regulators (Smith 2010). GPCRs were originally considered to be monomeric, but increasing evidence indicates that they can form dimers and oligomers as well (Ferre et al., 2014 Piscitelli et al., 2015), has been described as a "crystallization boom" (Costanzi 2014), with rapid growth emerging due to recent technological advances in both crystallization and structure detection. The availability of growing numbers of experimentally-determined GPCR structures, as well as improved homology-modeling of unknown target proteins based on a wider field of experimentally determined GPCR template structures, allows visual representation of GPCRs to be built upon the basis of known or modeled three-dimensional structures. Nevertheless, several challenges to accurate communication of GPCR structure remain.The goal of this paper is to provide strategies to address common visual representation challenges for GPCRs, and to identify errors that may arise from an incomplete understanding of GPCR structure. GPCRs comprise a subclass of the alpha-helical membrane p...

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An Introduction to Biomolecular Graphics

Cited by 50 publications

References 37 publications

Lipid Tail Protrusion in Simulations Predicts Fusogenic Activity of Influenza Fusion Peptide Mutants and Conformational Models

Lipid Tail Protrusion in Simulations Predicts Fusogenic Activity of Influenza Fusion Peptide Mutants and Conformational Models

Simplifying and enhancing the use of PyMOL with horizontal scripts

The Science Behind G Protein-Coupled Receptors (GPCRs) and Their Accurate Visual Representation in Scientific Research

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