scholarly journals Unveiling the Hidden Rules of Spherical Viruses Using Point Arrays

2020 ◽  
Author(s):  
David Wilson
Keyword(s):  
Double Point ◽  
Solvent Accessibility ◽  
Geometric Constraints ◽  
Asymmetric Unit ◽  
Local Surface ◽  
Bacteriophage Ms2 ◽  
Surface Loops ◽  
Triangulation Number ◽  
Steric Hinderance ◽  
Insight Into

Since its introduction, the Triangulation number has been the most successful and ubiquitous scheme for classifying spherical viruses. However, despite its many successes, it fails to describe the relative angular orientations of proteins, as well as their radial mass distribution within the capsid. It also fails to provide any insight into critical sites of stability, modifications or possible mutations. We show how classifying spherical viruses using icosahedral point arrays, introduced by Keef and Twarock, unveils new geometric rules and constraints for understanding virus stability and key locations for exterior and interior modifications. We present a modified fitness measure which classifies viruses in an unambiguous and rigorous manner, irrespective of local surface chemistry, steric hinderance, solvent accessibility or triangulation number. We then utilize these point arrays to explain the immutable surface loops of bacteriophage MS2, the relative reactivity of surface lysines in CPMV and the non-quasiequivalent flexibility of the HBV dimers. We explain how using sister and double point arrays can function as predictive tools for site directed modifications in other systems. This success builds on our previous work showing that viruses place their protruding features along the great circles of the asymmetric unit, demonstrating that viruses indeed adhere to these geometric constraints.

scholarly journals Unveiling the Hidden Rules of Spherical Viruses Using Point Arrays

Viruses ◽  
2020 ◽  
Vol 12 (4) ◽  
pp. 467
Author(s):  
David P. Wilson
Keyword(s):  
Solvent Accessibility ◽  
Geometric Constraints ◽  
Predictive Tool ◽  
Bacteriophage Ms2 ◽  
Lysine Residues ◽  
Critical Insight ◽  
Surface Loops ◽  
Triangulation Number ◽  
Steric Hinderance ◽  
Insight Into

Since its introduction, the Triangulation number has been the most successful and ubiquitous scheme for classifying spherical viruses. However, despite its many successes, it fails to describe the relative angular orientations of proteins, as well as their radial mass distribution within the capsid. It also fails to provide any critical insight into sites of stability, modifications or possible mutations. We show how classifying spherical viruses using icosahedral point arrays, introduced by Keef and Twarock, unveils new geometric rules and constraints for understanding virus stability and key locations for exterior and interior modifications. We present a modified fitness measure which classifies viruses in an unambiguous and rigorous manner, irrespective of local surface chemistry, steric hinderance, solvent accessibility or Triangulation number. We then use these point arrays to explain the immutable surface loops of bacteriophage MS2, the relative reactivity of surface lysine residues in CPMV and the non-quasi-equivalent flexibility of the HBV dimers. We then explain how point arrays can be used as a predictive tool for site-directed modifications of capsids. This success builds on our previous work showing that viruses place their protruding features along the great circles of the asymmetric unit, demonstrating that viruses indeed adhere to these geometric constraints.

scholarly journals Structural Characterization of Cuta- and Tusavirus: Insight into Protoparvoviruses Capsid Morphology

Viruses ◽  
2020 ◽  
Vol 12 (6) ◽  
pp. 653
Author(s):  
Mario Mietzsch ◽  
Robert McKenna ◽  
Elina Väisänen ◽  
Jennifer C. Yu ◽  
Maria Ilyas ◽  
...  
Keyword(s):  
Sialic Acid ◽  
Structure Evolution ◽  
Cellular Interactions ◽  
Human Pathogens ◽  
Cryo Electron Microscopy ◽  
Cellular Entry ◽  
Surface Loops ◽  
Antigenic Reactivity ◽  
Insight Into

Several members of the Protoparvovirus genus, capable of infecting humans, have been recently discovered, including cutavirus (CuV) and tusavirus (TuV). To begin the characterization of these viruses, we have used cryo-electron microscopy and image reconstruction to determine their capsid structures to ~2.9 Å resolution, and glycan array and cell-based assays to identify glycans utilized for cellular entry. Structural comparisons show that the CuV and TuV capsids share common features with other parvoviruses, including an eight-stranded anti-parallel β-barrel, depressions at the icosahedral 2-fold and surrounding the 5-fold axes, and a channel at the 5-fold axes. However, the viruses exhibit significant topological differences in their viral protein surface loops. These result in three separated 3-fold protrusions, similar to the bufaviruses also infecting humans, suggesting a host-driven structure evolution. The surface loops contain residues involved in receptor binding, cellular trafficking, and antigenic reactivity in other parvoviruses. In addition, terminal sialic acid was identified as the glycan potentially utilized by both CuV and TuV for cellular entry, with TuV showing additional recognition of poly-sialic acid and sialylated Lewis X (sLeXLeXLeX) motifs reported to be upregulated in neurotropic and cancer cells, respectively. These structures provide a platform for annotating the cellular interactions of these human pathogens.

Analytical modeling provides new insight into complex mutual coupling between surface loops at ultrahigh fields

2017 ◽  
Vol 30 (10) ◽  
pp. e3759 ◽  
Author(s):  
N. I. Avdievich ◽  
A. Pfrommer ◽  
I. A. Giapitzakis ◽  
A. Henning
Keyword(s):  
Mutual Coupling ◽  
Analytical Modeling ◽  
Ultrahigh Fields ◽  
Surface Loops ◽  
Insight Into

scholarly journals Perception and misperception of surface opacity

2017 ◽  
Vol 114 (52) ◽  
pp. 13840-13845 ◽  
Author(s):  
Phillip J. Marlow ◽  
Juno Kim ◽  
Barton L. Anderson
Keyword(s):  
Visual System ◽  
Fundamental Problem ◽  
Surface Orientation ◽  
The Body ◽  
Local Surface ◽  
Significant Information ◽  
Scene Structure ◽  
The Relationship ◽  
Opaque Surface ◽  
Insight Into

A fundamental problem in extracting scene structure is distinguishing different physical sources of image structure. Light reflected by an opaque surface covaries with local surface orientation, whereas light transported through the body of a translucent material does not. This suggests the possibility that the visual system may use the covariation of local surface orientation and intensity as a cue to the opacity of surfaces. We tested this hypothesis by manipulating the contrast of luminance gradients and the surface geometries to which they belonged and assessed how these manipulations affected the perception of surface opacity/translucency. We show that (i) identical luminance gradients can appear either translucent or opaque depending on the relationship between luminance and perceived 3D surface orientation, (ii) illusory percepts of translucency can be induced by embedding opaque surfaces in diffuse light fields that eliminate the covariation between surface orientation and intensity, and (iii) illusory percepts of opacity can be generated when transparent materials are embedded in a light field that generates images where surface orientation and intensity covary. Our results provide insight into how the visual system distinguishes opaque surfaces and light-permeable materials and why discrepancies arise between the perception and physics of opacity and translucency. These results suggest that the most significant information used to compute the perceived opacity and translucency of surfaces arise at a level of representation where 3D shape is made explicit.

scholarly journals Crystallization and Preliminary X-Ray Analysis of Rotavirus Protein VP6

1998 ◽  
Vol 72 (9) ◽  
pp. 7615-7619 ◽  
Author(s):  
Isabelle Petitpas ◽  
Jean Lepault ◽  
Patrice Vachette ◽  
Annie Charpilienne ◽  
Magali Mathieu ◽  
...  
Keyword(s):  
Atomic Resolution ◽  
Asymmetric Unit ◽  
Tubular Structures ◽  
Solvent Content ◽  
X Ray ◽  
X Ray Scattering ◽  
A Cell ◽  
Crystallization Conditions ◽  
Insight Into ◽  
Better Than

ABSTRACT As a first step to gain insight into the structure of the rotavirus virion at atomic resolution, we report here the expression, purification, and crystallization of recombinant rotavirus protein VP6. This protein has the property of polymerizing in the form of tubular structures in solution which have hindered crystallization thus far. Using a combination of electron microscopy and small-angle X-ray scattering, we found that addition of Ca2+ at concentrations higher than 100 mM results in depolymerization of the tubes, leading to an essentially monodisperse solution of trimeric VP6 even at high protein concentrations (higher than 10 mg/ml), thereby enabling us to search for crystallization conditions. We have thus obtained crystals of VP6 which diffract to better than 2.4 Å resolution and belong to the cubic space group P4132 with a cell dimension a of 160 Å. The crystals contain a trimer of VP6 lying along the diagonal of the cubic unit cell, resulting in one VP6 monomer per asymmetric unit and a solvent content of roughly 70%.

scholarly journals Substrate-dependent accessibility changes in the Na+-dependent C4-dicarboxylate transporter, VcINDY, suggest differential substrate effects in a multistep mechanism

2020 ◽  
Author(s):  
Connor D. D. Sampson ◽  
Matthew J. Stewart ◽  
Joseph A. Mindell ◽  
Christopher Mulligan
Keyword(s):  
Metabolic Diseases ◽  
Solvent Accessibility ◽  
Substrate Binding ◽  
Body Movement ◽  
Krebs Cycle ◽  
Acid Synthesis ◽  
Age Related ◽  
Krebs Cycle Intermediates ◽  
A Site ◽  
Insight Into

AbstractMembers of the divalent anion sodium symporter (DASS) family (SLC13 in humans) play critical roles in metabolic homeostasis, influencing many processes including fatty acid synthesis, insulin resistance, adiposity, and lifespan determination. DASS transporters catalyse the Na+-driven concentrative uptake of Krebs cycle intermediates and sulfate into cells; disrupting their function can protect against age-related metabolic diseases and can extend lifespan. An inward-facing crystal structure and an outward-facing model of a bacterial DASS family member, VcINDY from Vibrio cholerae, predict an elevator-like transport mechanism involving a large rigid body movement of the substrate binding site. How substrate binding influences the conformational state of VcINDY is currently unknown. Here, we probe the interaction between substrate binding and VcINDY conformation using a site-specific alkylation strategy to probe the solvent accessibility of several broadly distributed positions in VcINDY in the presence and absence of substrates (Na+ and succinate). Our findings reveal that accessibility to all positions tested can be modulated by the presence of substrates, with the majority becoming less accessible in the presence of Na+. Mapping these solvent accessibility changes onto the known structures of VcINDY suggests that Na+ binding drives the transporter into an as-yet-unidentified intermediate state. We also observe substantial, separable effects of Na+ and succinate binding at several amino acid positions suggesting distinct effects of the two substrates. Furthermore, analysis of a solely succinate-sensitive residue indicates that VcINDY binds its substrate with a low affinity and proceeds via an ordered process in which one or more Na+ ions must bind prior to succinate. These findings provide insight into the mechanism of VcINDY, which is currently the only structural-characterised representative of the entire DASS family.

scholarly journals Geometric constraints dominate the antigenic evolution of influenza H3N2 hemagglutinin

2015 ◽  
Author(s):  
Austin G Meyer ◽  
Claus O Wilke
Keyword(s):  
Receptor Binding ◽  
Protein Function ◽  
Influenza A ◽  
Immune Escape ◽  
Solvent Accessibility ◽  
Geometric Constraints ◽  
Binding Region ◽  
Primary Determinant ◽  
Evolutionary Variation ◽  
Receptor Binding Region

We have carried out a comprehensive analysis of the determinants of human influenza A H3 hemagglutinin evolution, considering three distinct predictors of evolutionary variation at individual sites: solvent accessibility (as a proxy for protein fold stability and/or conservation), experimental epitope sites (as a proxy for host immune bias), and proximity to the receptor-binding region (as a proxy for protein function). We found that these three predictors individually explain approximately 15% of the variation in site-wise dN/dS. The solvent accessibility and proximity predictors were largely independent of each other, while the epitope sites were not. In combination, solvent accessibility and proximity explained 32% of the variation in dN/dS. Incorporating experimental epitope sites into the model added only an additional 2 percentage points. We also found that the historical H3 epitope sites, which date back to the 1980s and 1990s, showed only weak overlap with the latest experimental epitope data. Finally, sites with dN/dS>1, i.e., the sites most likely driving seasonal immune escape, are not correctly predicted by either historical or experimental epitope sites, but only by proximity to the receptor-binding region. In summary, proximity to the receptor-binding region, and not host immune bias, seems to be the primary determinant of H3 evolution.

ReX: a computer program for structural analysis using powder diffraction data

2009 ◽  
Vol 42 (3) ◽  
pp. 538-539 ◽  
Author(s):  
Mauro Bortolotti ◽  
Luca Lutterotti ◽  
Ivan Lonardelli
Keyword(s):  
Powder Diffraction ◽  
Diffraction Data ◽  
Degrees Of Freedom ◽  
Nonlinear Least Squares ◽  
Geometric Constraints ◽  
Powder Diffraction Data ◽  
Asymmetric Unit ◽  
Torsion Angles ◽  
Structure Solution ◽  
Definition Of

Multi-platform software has been developed for the analysis of powder diffraction data, with particular focus on structure solution. The program provides a Rietveld optimization engine, with the possibility of refining parameters describing both the sample and the instrument model. Geometric constraints such as rigid fragments and torsion angles can be defined for the atomic structure, to reduce the number of degrees of freedom of the model. An innovative hierarchical description of the asymmetric unit has been adopted, which allows, in principle, the definition of arbitrarily complex geometric relationships. Additionally, global optimization algorithms may be used in place of the standard nonlinear least squares, when particularly challenging problems are being faced.

Expression, crystallization and preliminary X-ray analysis of ligand-free human glutathione S-transferase M2–2

1998 ◽  
Vol 54 (3) ◽  
pp. 458-460 ◽  
Author(s):  
Larysa N. Patskovska ◽  
Alexander A. Fedorov ◽  
Yury V. Patskovsky ◽  
Steven C. Almo ◽  
Irving Listowsky
Keyword(s):  
Escherichia Coli ◽  
Active Site ◽  
Asymmetric Unit ◽  
Glutathione S Transferase ◽  
Crystal Forms ◽  
Space Group ◽  
X Ray ◽  
Ligand Free ◽  
Catalytically Active ◽  
Insight Into

Human glutathione-S-transferase M2–2 (hGSTM2–2) was expressed in Escherichia coli and purified by GSH-affinity chromatography. The recombinant enzyme and the protein isolated from human tissue were indistinguishable based on physicochemical, enzymatic and immunological criteria. The catalytically active dimeric hGSTM2–2 was crystallized without GSH or other active-site ligands in two crystal forms. Diffraction from form A crystals extends to 2.5 Å and is consistent with the space group P21 (a = 53.9, b = 81.5, c = 55.6 Å, β = 109.26 Å) with two monomers in the asymmetric unit. Diffraction from form B crystals extends to 3 Å and is consistent with a space group P212121 (a = 57.2, b = 80.7, c = 225.9 Å) with two dimers in the asymmetric unit. This is the first report of ligand-free mu-class GST crystals, and a comparison with liganded complexes will provide insight into the structural consequences of substrate binding which are thought to be important for catalysis.

scholarly journals Crystallization and preliminary X-ray analysis of a ribokinase fromVibrio choleraeO395

2014 ◽  
Vol 70 (8) ◽  
pp. 1098-1102 ◽  
Author(s):  
Rakhi Paul ◽  
Madhumita Dandopath Patra ◽  
Ramanuj Banerjee ◽  
Udayaditya Sen
Keyword(s):  
Escherichia Coli ◽  
Polyethylene Glycol ◽  
Catalytic Mechanism ◽  
Empty Space ◽  
Adenosine Diphosphate ◽  
Asymmetric Unit ◽  
Solvent Content ◽  
X Ray ◽  
Polyethylene Glycol 6000 ◽  
Insight Into

Ribokinase (RK) is one of the principal enzymes in carbohydrate metabolism, catalyzing the reaction of D-ribose and adenosine triphosphate to produce ribose-5-phosphate and adenosine diphosphate (ADP). To provide further insight into the catalytic mechanism, therbsKgene fromVibrio choleraeO395 encoding ribokinase was cloned and the protein was overexpressed inEscherichia coliBL21 (DE3) and purified using Ni2+–NTA affinity chromatography. Crystals ofV. choleraeRK (Vc-RK) and of its complex with ribose and ADP were grown in the presence of polyethylene glycol 6000 and diffracted to 3.4 and 1.75 Å resolution, respectively. Analysis of the diffraction data showed that both crystals possess symmetry consistent with space groupP1. In the Vc-RK crystals, 16 molecules in the asymmetric unit were arranged in a spiral fashion, leaving a large empty space inside the crystal, which is consistent with its high Matthews coefficient (3.9 Å3 Da−1) and solvent content (68%). In the Vc-RK co-crystals four molecules were located in the asymmetric unit with a Matthews coefficient of 2.4 Å3 Da−1, corresponding to a solvent content of 50%.

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