Viruses

4 pages, 715 KiB

Open AccessObituary

In Memory of Michael G. Rossmann: A Wise Man with a Forever Young Heart

by Chuan (River) Xiao

Viruses 2021, 13(7), 1305; https://0-doi-org.brum.beds.ac.uk/10.3390/v13071305 - 05 Jul 2021

Viewed by 1654

Abstract

Whenever I think about Michael’s passing, a sad feeling still strikes me [...] Full article

(This article belongs to the Special Issue In Memory of Michael Rossmann)

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21 pages, 6340 KiB

Open AccessReview

Conserved and Diverse Traits of Adhesion Devices from Siphoviridae Recognizing Proteinaceous or Saccharidic Receptors

by Adeline Goulet, Silvia Spinelli, Jennifer Mahony and Christian Cambillau

Viruses 2020, 12(5), 512; https://0-doi-org.brum.beds.ac.uk/10.3390/v12050512 - 06 May 2020

Cited by 32 | Viewed by 6944

Abstract

Bacteriophages can play beneficial roles in phage therapy and destruction of food pathogens. Conversely, they play negative roles as they infect bacteria involved in fermentation, resulting in serious industrial losses. Siphoviridae phages possess a long non-contractile tail and use a mechanism of infection [...] Read more.

Bacteriophages can play beneficial roles in phage therapy and destruction of food pathogens. Conversely, they play negative roles as they infect bacteria involved in fermentation, resulting in serious industrial losses. Siphoviridae phages possess a long non-contractile tail and use a mechanism of infection whose first step is host recognition and binding. They have evolved adhesion devices at their tails’ distal end, tuned to recognize specific proteinaceous or saccharidic receptors on the host’s surface that span a large spectrum of shapes. In this review, we aimed to identify common patterns beyond this apparent diversity. To this end, we analyzed siphophage tail tips or baseplates, evaluating their known structures, where available, and uncovering patterns with bioinformatics tools when they were not. It was thereby identified that a triad formed by three proteins in complex, i.e., the tape measure protein (TMP), the distal tail protein (Dit), and the tail-associated lysozyme (Tal), is conserved in all phages. This common scaffold may harbor various functional extensions internally while it also serves as a platform for plug-in ancillary or receptor-binding proteins (RBPs). Finally, a group of siphophage baseplates involved in saccharidic receptor recognition exhibits an activation mechanism reminiscent of that observed in Myoviridae. Full article

(This article belongs to the Special Issue In Memory of Michael Rossmann)

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21 pages, 7420 KiB

Open AccessReview

The Dynamic Life of Virus Capsids

by Michael B. Sherman, Hong Q. Smith and Thomas J. Smith

Viruses 2020, 12(6), 618; https://0-doi-org.brum.beds.ac.uk/10.3390/v12060618 - 05 Jun 2020

Cited by 17 | Viewed by 3928

Abstract

Protein-shelled viruses have been thought as “tin cans” that merely carry the genomic cargo from cell to cell. However, through the years, it has become clear that viruses such as rhinoviruses and caliciviruses are active and dynamic structures waiting for the right environmental [...] Read more.

Protein-shelled viruses have been thought as “tin cans” that merely carry the genomic cargo from cell to cell. However, through the years, it has become clear that viruses such as rhinoviruses and caliciviruses are active and dynamic structures waiting for the right environmental cues to deliver their genomic payload to the host cell. In the case of human rhinoviruses, the capsid has empty cavities that decrease the energy required to cause conformational changes, resulting in the capsids “breathing”, waiting for the moment when the receptor binds for it to release its genome. Most strikingly, the buried N-termini of VP1 and VP4 are transiently exposed during this process. A more recent example of a “living” protein capsid is mouse norovirus (MNV). This family of viruses have a large protruding (P) domain that is loosely attached to the shell via a single-polypeptide tether. Small molecules found in the gut, such as bile salts, cause the P domains to rotate and collapse onto the shell surface. Concomitantly, bile alters the conformation of the P domain itself from one that binds antibodies to one that recognizes receptors. In this way, MNV appears to use capsid flexibility to present one face to the immune system and a completely different one to attack the host tissue. Therefore, it appears that even protein-shelled viruses have developed an impressive array of tricks to dodge our immune system and efficiently attack the host. Full article

(This article belongs to the Special Issue In Memory of Michael Rossmann)

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19 pages, 5033 KiB

Open AccessArticle

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

by Mario Mietzsch, Robert McKenna, Elina Väisänen, Jennifer C. Yu, Maria Ilyas, Joshua A. Hull, Justin Kurian, J. Kennon Smith, Paul Chipman, Yi Lasanajak, David Smith, Maria Söderlund-Venermo and Mavis Agbandje-McKenna

Viruses 2020, 12(6), 653; https://0-doi-org.brum.beds.ac.uk/10.3390/v12060653 - 17 Jun 2020

Cited by 7 | Viewed by 4187

Abstract

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 [...] Read more.

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. Full article

(This article belongs to the Special Issue In Memory of Michael Rossmann)

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18 pages, 8181 KiB

Open AccessArticle

Adeno-Associated Virus (AAV) Capsid Stability and Liposome Remodeling During Endo/Lysosomal pH Trafficking

by Bridget Lins-Austin, Saajan Patel, Mario Mietzsch, Dewey Brooke, Antonette Bennett, Balasubramanian Venkatakrishnan, Kim Van Vliet, Adam N. Smith, Joanna R. Long, Robert McKenna, Mark Potter, Barry Byrne, Sanford L. Boye, Brian Bothner, Regine Heilbronn and Mavis Agbandje-McKenna

Viruses 2020, 12(6), 668; https://0-doi-org.brum.beds.ac.uk/10.3390/v12060668 - 20 Jun 2020

Cited by 28 | Viewed by 8951

Abstract

Adeno-associated viruses (AAVs) are small, non-pathogenic ssDNA viruses being used as therapeutic gene delivery vectors for the treatment of a variety of monogenic diseases. An obstacle to successful gene delivery is inefficient capsid trafficking through the endo/lysosomal pathway. This study aimed to characterize [...] Read more.

Adeno-associated viruses (AAVs) are small, non-pathogenic ssDNA viruses being used as therapeutic gene delivery vectors for the treatment of a variety of monogenic diseases. An obstacle to successful gene delivery is inefficient capsid trafficking through the endo/lysosomal pathway. This study aimed to characterize the AAV capsid stability and dynamics associated with this process for a select number of AAV serotypes, AAV1, AAV2, AAV5, and AAV8, at pHs representative of the early and late endosome, and the lysosome (6.0, 5.5, and 4.0, respectively). All AAV serotypes displayed thermal melt temperatures that varied with pH. The stability of AAV1, AAV2, and AAV8 increased in response to acidic conditions and then decreased at pH 4.0. In contrast, AAV5 demonstrated a consistent decrease in thermostability in response to acidification. Negative-stain EM visualization of liposomes in the presence of capsids at pH 5.5 or when heat shocked showed induced remodeling consistent with the externalization of the PLA₂ domain of VP1u. These observations provide clues to the AAV capsid dynamics that facilitate successful infection. Finally, transduction assays revealed a pH and temperature dependence with low acidity and temperatures > 4 °C as detrimental factors. Full article

(This article belongs to the Special Issue In Memory of Michael Rossmann)

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22 pages, 4469 KiB

Open AccessArticle

Mutagenic Analysis of a DNA Translocating Tube’s Interior Surface

by Aaron P. Roznowski, Julia M. Fisher and Bentley A. Fane

Viruses 2020, 12(6), 670; https://0-doi-org.brum.beds.ac.uk/10.3390/v12060670 - 22 Jun 2020

Cited by 4 | Viewed by 2714

Abstract

Bacteriophage ϕX174 uses a decamer of DNA piloting proteins to penetrate its host. These proteins oligomerize into a cell wall-spanning tube, wide enough for genome passage. While the inner surface of the tube is primarily lined with inward-facing amino acid side chains containing [...] Read more.

Bacteriophage ϕX174 uses a decamer of DNA piloting proteins to penetrate its host. These proteins oligomerize into a cell wall-spanning tube, wide enough for genome passage. While the inner surface of the tube is primarily lined with inward-facing amino acid side chains containing amide and guanidinium groups, there is a 28 Å-long section near the tube’s C-terminus that does not exhibit this motif. The majority of the inward-facing residues in this region are conserved across the three ϕX174-like clades, suggesting that they play an important role during genome delivery. To test this hypothesis, and explore the general function of the tube’s inner surface, non-glutamine residues within this region were mutated to glutamine, while existing glutamine residues were changed to serine. Four of the resulting mutants had temperature-dependent phenotypes. Virion assembly, host attachment, and virion eclipse, defined as the cell’s ability to inactivate the virus, were not affected. Genome delivery, however, was inhibited. The results support a model in which a balance of forces governs genome delivery: potential energy provided by the densely packaged viral genome and/or an osmotic gradient move the genome into the cell, while the tube’s inward facing glutamine residues exert a frictional force, or drag, that controls genome release. Full article

(This article belongs to the Special Issue In Memory of Michael Rossmann)

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17 pages, 2726 KiB

Open AccessReview

Nucleocapsid Structure of Negative Strand RNA Virus

by Ming Luo, James Ross Terrell and Shelby Ashlyn Mcmanus

Viruses 2020, 12(8), 835; https://0-doi-org.brum.beds.ac.uk/10.3390/v12080835 - 30 Jul 2020

Cited by 26 | Viewed by 6693

Abstract

Negative strand RNA viruses (NSVs) include many important human pathogens, such as influenza virus, Ebola virus, and rabies virus. One of the unique characteristics that NSVs share is the assembly of the nucleocapsid and its role in viral RNA synthesis. In NSVs, the [...] Read more.

Negative strand RNA viruses (NSVs) include many important human pathogens, such as influenza virus, Ebola virus, and rabies virus. One of the unique characteristics that NSVs share is the assembly of the nucleocapsid and its role in viral RNA synthesis. In NSVs, the single strand RNA genome is encapsidated in the linear nucleocapsid throughout the viral replication cycle. Subunits of the nucleocapsid protein are parallelly aligned along the RNA genome that is sandwiched between two domains composed of conserved helix motifs. The viral RNA-dependent-RNA polymerase (vRdRp) must recognize the protein–RNA complex of the nucleocapsid and unveil the protected genomic RNA in order to initiate viral RNA synthesis. In addition, vRdRp must continuously translocate along the protein–RNA complex during elongation in viral RNA synthesis. This unique mechanism of viral RNA synthesis suggests that the nucleocapsid may play a regulatory role during NSV replication. Full article

(This article belongs to the Special Issue In Memory of Michael Rossmann)

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17 pages, 2582 KiB

Open AccessArticle

Removing the Polyanionic Cargo Requirement for Assembly of Alphavirus Core-Like Particles to Make an Empty Alphavirus Core

by Julie M. Button and Suchetana Mukhopadhyay

Viruses 2020, 12(8), 846; https://0-doi-org.brum.beds.ac.uk/10.3390/v12080846 - 03 Aug 2020

Cited by 5 | Viewed by 2979

Abstract

The assembly of alphavirus nucleocapsid cores requires electrostatic interactions between the positively charged N-terminus of the capsid protein (CP) and the encapsidated polyanionic cargo. This system differs from many other viruses that can self-assemble particles in the absence of cargo, or form “empty” [...] Read more.

The assembly of alphavirus nucleocapsid cores requires electrostatic interactions between the positively charged N-terminus of the capsid protein (CP) and the encapsidated polyanionic cargo. This system differs from many other viruses that can self-assemble particles in the absence of cargo, or form “empty” particles. We hypothesized that the introduction of a mutant, anionic CP could replace the need for charged cargo during assembly. In this work, we produced a CP mutant, Minus 38 (M38), where all N-terminal charged residues are negatively-charged. When wild-type (WT) and M38 CPs were mixed, they assembled into core-like particles (CLPs). These “empty” particles were of similar size and morphology to WT CLPs assembled with DNA cargo, but did not contain nucleic acid. When DNA cargo was added to the assembly mixture, the amount of M38 CP that was assembled into CLPs decreased, but was not fully excluded from the CLPs, suggesting that M38 competes with DNA to interact with WT CPs. The composition of CLPs can be tuned by altering the order of addition of M38 CP, WT CP, and DNA cargo. The ability to produce alphavirus CLPs that contain a range of amounts of encapsidated cargo, including none, introduces a new platform for packaging cargo for delivery or imaging purposes. Full article

(This article belongs to the Special Issue In Memory of Michael Rossmann)

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16 pages, 19707 KiB

Open AccessArticle

Structure of the Capsid Size-Determining Scaffold of “Satellite” Bacteriophage P4

by James L. Kizziah, Cynthia M. Rodenburg and Terje Dokland

Viruses 2020, 12(9), 953; https://0-doi-org.brum.beds.ac.uk/10.3390/v12090953 - 27 Aug 2020

Cited by 9 | Viewed by 3247

Abstract

P4 is a mobile genetic element (MGE) that can exist as a plasmid or integrated into its Escherichia coli host genome, but becomes packaged into phage particles by a helper bacteriophage, such as P2. P4 is the original example of what we have [...] Read more.

P4 is a mobile genetic element (MGE) that can exist as a plasmid or integrated into its Escherichia coli host genome, but becomes packaged into phage particles by a helper bacteriophage, such as P2. P4 is the original example of what we have termed “molecular piracy”, the process by which one MGE usurps the life cycle of another for its own propagation. The P2 helper provides most of the structural gene products for assembly of the P4 virion. However, when P4 is mobilized by P2, the resulting capsids are smaller than those normally formed by P2 alone. The P4-encoded protein responsible for this size change is called Sid, which forms an external scaffolding cage around the P4 procapsids. We have determined the high-resolution structure of P4 procapsids, allowing us to build an atomic model for Sid as well as the gpN capsid protein. Sixty copies of Sid form an intertwined dodecahedral cage around the T = 4 procapsid, making contact with only one out of the four symmetrically non-equivalent copies of gpN. Our structure provides a basis for understanding the sir mutants in gpN that prevent small capsid formation, as well as the nms “super-sid” mutations that counteract the effect of the sir mutations, and suggests a model for capsid size redirection by Sid. Full article

(This article belongs to the Special Issue In Memory of Michael Rossmann)

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18 pages, 4696 KiB

Open AccessReview

Structural Biology of Influenza Hemagglutinin: An Amaranthine Adventure

by Nicholas C. Wu and Ian A. Wilson

Viruses 2020, 12(9), 1053; https://0-doi-org.brum.beds.ac.uk/10.3390/v12091053 - 22 Sep 2020

Cited by 32 | Viewed by 6008

Abstract

Hemagglutinin (HA) glycoprotein is an important focus of influenza research due to its role in antigenic drift and shift, as well as its receptor binding and membrane fusion functions, which are indispensable for viral entry. Over the past four decades, X-ray crystallography has [...] Read more.

Hemagglutinin (HA) glycoprotein is an important focus of influenza research due to its role in antigenic drift and shift, as well as its receptor binding and membrane fusion functions, which are indispensable for viral entry. Over the past four decades, X-ray crystallography has greatly facilitated our understanding of HA receptor binding, membrane fusion, and antigenicity. The recent advances in cryo-EM have further deepened our comprehension of HA biology. Since influenza HA constantly evolves in natural circulating strains, there are always new questions to be answered. The incessant accumulation of knowledge on the structural biology of HA over several decades has also facilitated the design and development of novel therapeutics and vaccines. This review describes the current status of the field of HA structural biology, how we got here, and what the next steps might be. Full article

(This article belongs to the Special Issue In Memory of Michael Rossmann)

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26 pages, 4799 KiB

Open AccessReview

Solid-State NMR for Studying the Structure and Dynamics of Viral Assemblies

by Lauriane Lecoq, Marie-Laure Fogeron, Beat H. Meier, Michael Nassal and Anja Böckmann

Viruses 2020, 12(10), 1069; https://0-doi-org.brum.beds.ac.uk/10.3390/v12101069 - 24 Sep 2020

Cited by 27 | Viewed by 4580

Abstract

Structural virology reveals the architecture underlying infection. While notably electron microscopy images have provided an atomic view on viruses which profoundly changed our understanding of these assemblies incapable of independent life, spectroscopic techniques like NMR enter the field with their strengths in detailed [...] Read more.

Structural virology reveals the architecture underlying infection. While notably electron microscopy images have provided an atomic view on viruses which profoundly changed our understanding of these assemblies incapable of independent life, spectroscopic techniques like NMR enter the field with their strengths in detailed conformational analysis and investigation of dynamic behavior. Typically, the large assemblies represented by viral particles fall in the regime of biological high-resolution solid-state NMR, able to follow with high sensitivity the path of the viral proteins through their interactions and maturation steps during the viral life cycle. We here trace the way from first solid-state NMR investigations to the state-of-the-art approaches currently developing, including applications focused on HIV, HBV, HCV and influenza, and an outlook to the possibilities opening in the coming years. Full article

(This article belongs to the Special Issue In Memory of Michael Rossmann)

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21 pages, 5033 KiB

Open AccessArticle

Structure and Function of the T4 Spackle Protein Gp61.3

by Shuji Kanamaru, Kazuya Uchida, Mai Nemoto, Alec Fraser, Fumio Arisaka and Petr G. Leiman

Viruses 2020, 12(10), 1070; https://0-doi-org.brum.beds.ac.uk/10.3390/v12101070 - 24 Sep 2020

Cited by 4 | Viewed by 2605

Abstract

The bacteriophage T4 genome contains two genes that code for proteins with lysozyme activity—e and 5. Gene e encodes the well-known T4 lysozyme (commonly called T4L) that functions to break the peptidoglycan layer late in the infection cycle, which is required [...] Read more.

The bacteriophage T4 genome contains two genes that code for proteins with lysozyme activity—e and 5. Gene e encodes the well-known T4 lysozyme (commonly called T4L) that functions to break the peptidoglycan layer late in the infection cycle, which is required for liberating newly assembled phage progeny. Gene product 5 (gp5) is the tail-associated lysozyme, a component of the phage particle. It forms a spike at the tip of the tail tube and functions to pierce the outer membrane of the Escherichia coli host cell after the phage has attached to the cell surface. Gp5 contains a T4L-like lysozyme domain that locally digests the peptidoglycan layer upon infection. The T4 Spackle protein (encoded by gene 61.3) has been thought to play a role in the inhibition of gp5 lysozyme activity and, as a consequence, in making cells infected by bacteriophage T4 resistant to later infection by T4 and closely related phages. Here we show that (1) gp61.3 is secreted into the periplasm where its N-terminal periplasm-targeting peptide is cleaved off; (2) gp61.3 forms a 1:1 complex with the lysozyme domain of gp5 (gp5Lys); (3) gp61.3 selectively inhibits the activity of gp5, but not that of T4L; (4) overexpression of gp5 causes cell lysis. We also report a crystal structure of the gp61.3-gp5Lys complex that demonstrates that unlike other known lysozyme inhibitors, gp61.3 does not interact with the active site cleft. Instead, it forms a “wall” that blocks access of an extended polysaccharide substrate to the cleft and, possibly, locks the enzyme in an “open-jaw”-like conformation making catalysis impossible. Full article

(This article belongs to the Special Issue In Memory of Michael Rossmann)

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7 pages, 836 KiB

Open AccessReview

Perspectives on Viral RNA Genomes and the RNA Folding Problem

by Susan J. Schroeder

Viruses 2020, 12(10), 1126; https://0-doi-org.brum.beds.ac.uk/10.3390/v12101126 - 05 Oct 2020

Cited by 5 | Viewed by 2652

Abstract

Viral RNA genomes change shape as virus particles disassemble, form replication complexes, attach to ribosomes for translation, evade host defense mechanisms, and assemble new virus particles. These structurally dynamic RNA shapeshifters present a challenging RNA folding problem, because the RNA sequence adopts multiple [...] Read more.

Viral RNA genomes change shape as virus particles disassemble, form replication complexes, attach to ribosomes for translation, evade host defense mechanisms, and assemble new virus particles. These structurally dynamic RNA shapeshifters present a challenging RNA folding problem, because the RNA sequence adopts multiple structures and may sometimes contain regions of partial disorder. Recent advances in high resolution asymmetric cryoelectron microscopy and chemical probing provide new ways to probe the degree of structure and disorder, and have identified more than one conformation in dynamic equilibrium in viral RNA. Chemical probing and the Detection of RNA Folding Ensembles using Expectation Maximization (DREEM) algorithm has been applied to studies of the dynamic equilibrium conformations in HIV RNA in vitro, in virio, and in vivo. This new type of data provides insight into important questions about virus assembly mechanisms and the fundamental physical forces driving virus particle assembly. Full article

(This article belongs to the Special Issue In Memory of Michael Rossmann)

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11 pages, 1964 KiB

Open AccessArticle

The Central Spike Complex of Bacteriophage T4 Contacts PpiD in the Periplasm of Escherichia coli

by Sabrina Wenzel, Mikhail M. Shneider, Petr G. Leiman, Andreas Kuhn and Dorothee Kiefer

Viruses 2020, 12(10), 1135; https://0-doi-org.brum.beds.ac.uk/10.3390/v12101135 - 06 Oct 2020

Cited by 3 | Viewed by 3114

Abstract

Infecting bacteriophage T4 uses a contractile tail structure to breach the envelope of the Escherichia coli host cell. During contraction, the tail tube headed with the “central spike complex” is thought to mechanically puncture the outer membrane. We show here that a purified [...] Read more.

Infecting bacteriophage T4 uses a contractile tail structure to breach the envelope of the Escherichia coli host cell. During contraction, the tail tube headed with the “central spike complex” is thought to mechanically puncture the outer membrane. We show here that a purified tip fragment of the central spike complex interacts with periplasmic chaperone PpiD, which is anchored to the cytoplasmic membrane. PpiD may be involved in the penetration of the inner membrane by the T4 injection machinery, resulting in a DNA-conducting channel to translocate the phage DNA into the interior of the cell. Host cells with the ppiD gene deleted showed partial reduction in the plating efficiency of T4, suggesting a supporting role of PpiD to improve the efficiency of the infection process. Full article

(This article belongs to the Special Issue In Memory of Michael Rossmann)

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15 pages, 3736 KiB

Open AccessReview

Superimposition of Viral Protein Structures: A Means to Decipher the Phylogenies of Viruses

by Janne J. Ravantti, Ane Martinez-Castillo and Nicola G.A. Abrescia

Viruses 2020, 12(10), 1146; https://0-doi-org.brum.beds.ac.uk/10.3390/v12101146 - 09 Oct 2020

Cited by 7 | Viewed by 3591

Abstract

Superimposition of protein structures is key in unravelling structural homology across proteins whose sequence similarity is lost. Structural comparison provides insights into protein function and evolution. Here, we review some of the original findings and thoughts that have led to the current established [...] Read more.

Superimposition of protein structures is key in unravelling structural homology across proteins whose sequence similarity is lost. Structural comparison provides insights into protein function and evolution. Here, we review some of the original findings and thoughts that have led to the current established structure-based phylogeny of viruses: starting from the original observation that the major capsid proteins of plant and animal viruses possess similar folds, to the idea that each virus has an innate “self”. This latter idea fueled the conceptualization of the PRD1-adenovirus lineage whose members possess a major capsid protein (innate “self”) with a double jelly roll fold. Based on this approach, long-range viral evolutionary relationships can be detected allowing the virosphere to be classified in four structure-based lineages. However, this process is not without its challenges or limitations. As an example of these hurdles, we finally touch on the difficulty of establishing structural “self” traits for enveloped viruses showcasing the coronaviruses but also the power of structure-based analysis in the understanding of emerging viruses Full article

(This article belongs to the Special Issue In Memory of Michael Rossmann)

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22 pages, 3256 KiB

Open AccessReview

Keeping It Together: Structures, Functions, and Applications of Viral Decoration Proteins

by Corynne L. Dedeo, Carolyn M. Teschke and Andrei T. Alexandrescu

Viruses 2020, 12(10), 1163; https://0-doi-org.brum.beds.ac.uk/10.3390/v12101163 - 14 Oct 2020

Cited by 13 | Viewed by 4810

Abstract

Decoration proteins are viral accessory gene products that adorn the surfaces of some phages and viral capsids, particularly tailed dsDNA phages. These proteins often play a “cementing” role, reinforcing capsids against accumulating internal pressure due to genome packaging, or environmental insults such as [...] Read more.

Decoration proteins are viral accessory gene products that adorn the surfaces of some phages and viral capsids, particularly tailed dsDNA phages. These proteins often play a “cementing” role, reinforcing capsids against accumulating internal pressure due to genome packaging, or environmental insults such as extremes of temperature or pH. Many decoration proteins serve alternative functions, including target cell recognition, participation in viral assembly, capsid size determination, or modulation of host gene expression. Examples that currently have structures characterized to high-resolution fall into five main folding motifs: β-tulip, β-tadpole, OB-fold, Ig-like, and a rare knotted α-helical fold. Most of these folding motifs have structure homologs in virus and target cell proteins, suggesting horizontal gene transfer was important in their evolution. Oligomerization states of decoration proteins range from monomers to trimers, with the latter most typical. Decoration proteins bind to a variety of loci on capsids that include icosahedral 2-, 3-, and 5-fold symmetry axes, as well as pseudo-symmetry sites. These binding sites often correspond to “weak points” on the capsid lattice. Because of their unique abilities to bind virus surfaces noncovalently, decoration proteins are increasingly exploited for technology, with uses including phage display, viral functionalization, vaccination, and improved nanoparticle design for imaging and drug delivery. These applications will undoubtedly benefit from further advances in our understanding of these versatile augmenters of viral functions. Full article

(This article belongs to the Special Issue In Memory of Michael Rossmann)

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15 pages, 4212 KiB

Open AccessArticle

Adeno-Associated Virus (AAV-DJ)—Cryo-EM Structure at 1.56 Å Resolution

by Qing Xie, Craig K. Yoshioka and Michael S. Chapman

Viruses 2020, 12(10), 1194; https://0-doi-org.brum.beds.ac.uk/10.3390/v12101194 - 20 Oct 2020

Cited by 18 | Viewed by 5595

Abstract

Adeno-associated virus is the leading viral vector for gene therapy. AAV-DJ is a recombinant variant developed for tropism to the liver. The AAV-DJ structure has been determined to 1.56 Å resolution through cryo-electron microscopy (cryo-EM). Only apoferritin is reported in preprints at 1.6 [...] Read more.

Adeno-associated virus is the leading viral vector for gene therapy. AAV-DJ is a recombinant variant developed for tropism to the liver. The AAV-DJ structure has been determined to 1.56 Å resolution through cryo-electron microscopy (cryo-EM). Only apoferritin is reported in preprints at 1.6 Å or higher resolution, and AAV-DJ nearly matches the highest resolutions ever attained through X-ray diffraction of virus crystals. However, cryo-EM has the advantage that most of the hydrogens are clear, improving the accuracy of atomic refinement, and removing ambiguity in hydrogen bond identification. Outside of secondary structures where hydrogen bonding was predictable a priori, the networks of hydrogen bonds coming from direct observation of hydrogens and acceptor atoms are quite different from those inferred even at 2.8 Å resolution. The implications for understanding viral assembly mean that cryo-EM will likely become the favored approach for high resolution structural virology. Full article

(This article belongs to the Special Issue In Memory of Michael Rossmann)

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19 pages, 5375 KiB

Open AccessReview

Neutralizing Antibodies Targeting HIV-1 gp41

by Christophe Caillat, Delphine Guilligay, Guidenn Sulbaran and Winfried Weissenhorn

Viruses 2020, 12(11), 1210; https://0-doi-org.brum.beds.ac.uk/10.3390/v12111210 - 23 Oct 2020

Cited by 18 | Viewed by 3377

Abstract

HIV-1 vaccine research has obtained an enormous boost since the discovery of many broadly neutralizing antibodies (bnAbs) targeting all accessible sites on the HIV-1 envelope glycoprotein (Env). This in turn facilitated high-resolution structures of the Env glycoprotein in complex with bnAbs. Here we [...] Read more.

HIV-1 vaccine research has obtained an enormous boost since the discovery of many broadly neutralizing antibodies (bnAbs) targeting all accessible sites on the HIV-1 envelope glycoprotein (Env). This in turn facilitated high-resolution structures of the Env glycoprotein in complex with bnAbs. Here we focus on gp41, its highly conserved heptad repeat region 1 (HR1), the fusion peptide (FP) and the membrane-proximal external region (MPER). Notably, the broadest neutralizing antibodies target MPER. Both gp41 HR1 and MPER are only fully accessible once receptor-induced conformational changes have taken place, although some studies suggest access to MPER in the close to native Env conformation. We summarize the data on the structure and function of neutralizing antibodies targeting gp41 HR1, FP and MPER and we review their access to Env and their complex formation with gp41 HR1, MPER peptides and FP within native Env. We further discuss MPER bnAb binding to lipids and the role of somatic mutations in recognizing a bipartite epitope composed of the conserved MPER sequence and membrane components. The problematic of gp41 HR1 access and MPER bnAb auto- and polyreactivity is developed in the light of inducing such antibodies by vaccination. Full article

(This article belongs to the Special Issue In Memory of Michael Rossmann)

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14 pages, 6773 KiB

Open AccessArticle

Simulations of Phage T7 Capsid Expansion Reveal the Role of Molecular Sterics on Dynamics

by Paul C. Whitford, Wen Jiang and Philip Serwer

Viruses 2020, 12(11), 1273; https://0-doi-org.brum.beds.ac.uk/10.3390/v12111273 - 07 Nov 2020

Cited by 7 | Viewed by 3256

Abstract

Molecular dynamics techniques provide numerous strategies for investigating biomolecular energetics, though quantitative analysis is often only accessible for relatively small (frequently monomeric) systems. To address this limit, we use simulations in combination with a simplified energetic model to study complex rearrangements in a [...] Read more.

Molecular dynamics techniques provide numerous strategies for investigating biomolecular energetics, though quantitative analysis is often only accessible for relatively small (frequently monomeric) systems. To address this limit, we use simulations in combination with a simplified energetic model to study complex rearrangements in a large assembly. We use cryo-EM reconstructions to simulate the DNA packaging-associated 3 nm expansion of the protein shell of an initially assembled phage T7 capsid (called procapsid or capsid I). This is accompanied by a disorder–order transition and expansion-associated externalization displacement of the 420 N-terminal tails of the shell proteins. For the simulations, we use an all-atom structure-based model (1.07 million atoms), which is specifically designed to probe the influence of molecular sterics on dynamics. We find that the rate at which the N-terminal tails undergo translocation depends heavily on their position within hexons and pentons. Specifically, trans-shell displacements of the hexon E subunits are the most frequent and hexon A subunits are the least frequent. The simulations also implicate numerous tail translocation intermediates during tail translocation that involve topological traps, as well as sterically induced barriers. The presented study establishes a foundation for understanding the precise relationship between molecular structure and phage maturation. Full article

(This article belongs to the Special Issue In Memory of Michael Rossmann)

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9 pages, 8100 KiB

Open AccessArticle

Biphasic Packing of DNA and Internal Proteins in Bacteriophage T4 Heads Revealed by Bubblegram Imaging

by Weimin Wu, Naiqian Cheng, Lindsay W. Black, Hendrik Dietz and Alasdair C. Steven

Viruses 2020, 12(11), 1282; https://0-doi-org.brum.beds.ac.uk/10.3390/v12111282 - 10 Nov 2020

Cited by 2 | Viewed by 2252

Abstract

The virions of tailed bacteriophages and the evolutionarily related herpesviruses contain, in addition to highly condensed DNA, substantial quantities of internal proteins. These proteins (“ejection proteins”) have roles in scaffolding, maturational proteolysis, and cell-to-cell delivery. Whereas capsids are amenable to analysis at high [...] Read more.

The virions of tailed bacteriophages and the evolutionarily related herpesviruses contain, in addition to highly condensed DNA, substantial quantities of internal proteins. These proteins (“ejection proteins”) have roles in scaffolding, maturational proteolysis, and cell-to-cell delivery. Whereas capsids are amenable to analysis at high resolution by cryo-electron microscopy, internal proteins have proved difficult to localize. In this study, we investigated the distribution of internal proteins in T4 by bubblegram imaging. Prior work has shown that at suitably high electron doses, radiation damage generates bubbles of hydrogen gas in nucleoprotein specimens. Using DNA origami as a test specimen, we show that DNA does not bubble under these conditions; it follows that bubbles represent markers for proteins. The interior of the prolate T4 head, ~1000 Å long by ~750 Å wide, has a bubble-free zone that is ~100–110 Å thick, underlying the capsid shell from which proteins are excluded by highly ordered DNA. Inside this zone, which is plausibly occupied by ~4 layers of coaxial spool, bubbles are generated at random locations in a disordered ensemble of internal proteins and the remainder of the genome. Full article

(This article belongs to the Special Issue In Memory of Michael Rossmann)

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13 pages, 1348 KiB

Open AccessReview

Spike Glycoprotein-Mediated Entry of SARS Coronaviruses

by Lin Wang and Ye Xiang

Viruses 2020, 12(11), 1289; https://0-doi-org.brum.beds.ac.uk/10.3390/v12111289 - 11 Nov 2020

Cited by 31 | Viewed by 4699

Abstract

Severe acute respiratory syndrome coronavirus (SARS-CoV) and SARS-CoV-2 are enveloped, positive-sense, single-stranded RNA viruses and causes of epidemic diseases that have resulted in public health emergencies worldwide. Angiotensin-converting enzyme 2 (ACE2) is the receptor that allows the entry of these two viruses into [...] Read more.

Severe acute respiratory syndrome coronavirus (SARS-CoV) and SARS-CoV-2 are enveloped, positive-sense, single-stranded RNA viruses and causes of epidemic diseases that have resulted in public health emergencies worldwide. Angiotensin-converting enzyme 2 (ACE2) is the receptor that allows the entry of these two viruses into host cells, a key step in the life cycle of the pathogens. The characterization of the interactions of ACE2 with the viral spike glycoproteins and structural studies of the ACE2-binding-induced conformational changes in the viral spike glycoproteins have furthered our understanding of the entry processes of these two viruses, and these studies provide useful information that will facilitate the development of antiviral agents and vaccines to control the diseases. Full article

(This article belongs to the Special Issue In Memory of Michael Rossmann)

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18 pages, 8442 KiB

Open AccessArticle

The Structure of an AAV5-AAVR Complex at 2.5 Å Resolution: Implications for Cellular Entry and Immune Neutralization of AAV Gene Therapy Vectors

by Mark A. Silveria, Edward E. Large, Grant M. Zane, Tommi A. White and Michael S. Chapman

Viruses 2020, 12(11), 1326; https://0-doi-org.brum.beds.ac.uk/10.3390/v12111326 - 18 Nov 2020

Cited by 16 | Viewed by 4704

Abstract

Adeno-Associated Virus is the leading vector for gene therapy. Although it is the vector for all in vivo gene therapies approved for clinical use by the US Food and Drug Administration, its biology is still not yet fully understood. It has been shown [...] Read more.

Adeno-Associated Virus is the leading vector for gene therapy. Although it is the vector for all in vivo gene therapies approved for clinical use by the US Food and Drug Administration, its biology is still not yet fully understood. It has been shown that different serotypes of AAV bind to their cellular receptor, AAVR, in different ways. Previously we have reported a 2.4Å structure of AAV2 bound to AAVR that shows ordered structure for only one of the two AAVR domains with which AAV2 interacts. In this study we present a 2.5Å resolution structure of AAV5 bound to AAVR. AAV5 binds to the first polycystic kidney disease (PKD) domain of AAVR that was not ordered in the AAV2 structure. Interactions of AAV5 with AAVR are analyzed in detail, and the implications for AAV2 binding are explored through molecular modeling. Moreover, we find that binding sites for the antibodies ADK5a, ADK5b, and 3C5 on AAV5 overlap with the binding site of AAVR. These insights provide a structural foundation for development of gene therapy agents to better evade immune neutralization without disrupting cellular entry. Full article

(This article belongs to the Special Issue In Memory of Michael Rossmann)

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18 pages, 4828 KiB

Open AccessArticle

Structural Basis of Zika Virus Specific Neutralization in Subsequent Flavivirus Infections

by Madhumati Sevvana, Thomas F. Rogers, Andrew S. Miller, Feng Long, Thomas Klose, Nathan Beutler, Yen-Chung Lai, Mara Parren, Laura M. Walker, Geeta Buda, Dennis R. Burton, Michael G. Rossmann and Richard J. Kuhn

Viruses 2020, 12(12), 1346; https://0-doi-org.brum.beds.ac.uk/10.3390/v12121346 - 24 Nov 2020

Cited by 6 | Viewed by 3415

Abstract

Zika virus (ZIKV), a mosquito-borne human flavivirus that causes microcephaly and other neurological disorders, has been a recent focus for the development of flavivirus vaccines and therapeutics. We report here a 4.0 Å resolution structure of the mature ZIKV in complex with ADI-30056, [...] Read more.

Zika virus (ZIKV), a mosquito-borne human flavivirus that causes microcephaly and other neurological disorders, has been a recent focus for the development of flavivirus vaccines and therapeutics. We report here a 4.0 Å resolution structure of the mature ZIKV in complex with ADI-30056, a ZIKV-specific human monoclonal antibody (hMAb) isolated from a ZIKV infected donor with a prior dengue virus infection. The structure shows that the hMAb interactions span across the E protein dimers on the virus surface, inhibiting conformational changes required for the formation of infectious fusogenic trimers similar to the hMAb, ZIKV-117. Structure-based functional analysis, and structure and sequence comparisons, identified ZIKV residues essential for neutralization and crucial for the evolution of highly potent E protein crosslinking Abs in ZIKV. Thus, this epitope, ZIKV’s “Achilles heel”, defined by the contacts between ZIKV and ADI-30056, could be a suitable target for the design of therapeutic antibodies. Full article

(This article belongs to the Special Issue In Memory of Michael Rossmann)

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16 pages, 2242 KiB

Open AccessArticle

An Intracellular Model of Hepatitis B Viral Infection: An In Silico Platform for Comparing Therapeutic Strategies

by Farzad Fatehi, Richard J. Bingham, Eric C. Dykeman, Nikesh Patel, Peter G. Stockley and Reidun Twarock

Viruses 2021, 13(1), 11; https://0-doi-org.brum.beds.ac.uk/10.3390/v13010011 - 23 Dec 2020

Cited by 9 | Viewed by 2908

Abstract

Hepatitis B virus (HBV) is a major focus of antiviral research worldwide. The International Coalition to Eliminate HBV, together with the World Health Organisation (WHO), have prioritised the search for a cure, with the goal of eliminating deaths from viral hepatitis by 2030. [...] Read more.

Hepatitis B virus (HBV) is a major focus of antiviral research worldwide. The International Coalition to Eliminate HBV, together with the World Health Organisation (WHO), have prioritised the search for a cure, with the goal of eliminating deaths from viral hepatitis by 2030. We present here a comprehensive model of intracellular HBV infection dynamics that includes all molecular processes currently targeted by drugs and agrees well with the observed outcomes of several clinical studies. The model reveals previously unsuspected kinetic behaviour in the formation of sub-viral particles, which could lead to a better understanding of the immune responses to infection. It also enables rapid comparative assessment of the impact of different treatment options and their potential synergies as combination therapies. A comparison of available and currently developed treatment options reveals that combinations of multiple capsid assembly inhibitors perform best. Full article

(This article belongs to the Special Issue In Memory of Michael Rossmann)

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26 pages, 1308 KiB

Open AccessReview

Beyond the Surface: Endocytosis of Mosquito-Borne Flaviviruses

by Stephen D. Carro and Sara Cherry

Viruses 2021, 13(1), 13; https://0-doi-org.brum.beds.ac.uk/10.3390/v13010013 - 23 Dec 2020

Cited by 19 | Viewed by 5439

Abstract

Flaviviruses are a group of positive-sense RNA viruses that are primarily transmitted through arthropod vectors and are capable of causing a broad spectrum of diseases. Many of the flaviviruses that are pathogenic in humans are transmitted specifically through mosquito vectors. Over the past [...] Read more.

Flaviviruses are a group of positive-sense RNA viruses that are primarily transmitted through arthropod vectors and are capable of causing a broad spectrum of diseases. Many of the flaviviruses that are pathogenic in humans are transmitted specifically through mosquito vectors. Over the past century, many mosquito-borne flavivirus infections have emerged and re-emerged, and are of global importance with hundreds of millions of infections occurring yearly. There is a need for novel, effective, and accessible vaccines and antivirals capable of inhibiting flavivirus infection and ameliorating disease. The development of therapeutics targeting viral entry has long been a goal of antiviral research, but most efforts are hindered by the lack of broad-spectrum potency or toxicities associated with on-target effects, since many host proteins necessary for viral entry are also essential for host cell biology. Mosquito-borne flaviviruses generally enter cells by clathrin-mediated endocytosis (CME), and recent studies suggest that a subset of these viruses can be internalized through a specialized form of CME that has additional dependencies distinct from canonical CME pathways, and antivirals targeting this pathway have been discovered. In this review, we discuss the role and contribution of endocytosis to mosquito-borne flavivirus entry as well as consider past and future efforts to target endocytosis for therapeutic interventions. Full article

(This article belongs to the Special Issue In Memory of Michael Rossmann)

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18 pages, 33924 KiB

Open AccessArticle

Biochemical and Biophysical Characterization of the dsDNA Packaging Motor from the Lactococcus lactis Bacteriophage Asccphi28

by Emilio Reyes-Aldrete, Erik A. Dill, Cecile Bussetta, Michal R. Szymanski, Geoffrey Diemer, Priyank Maindola, Mark A. White, Wlodzimierz M. Bujalowski, Kyung H. Choi and Marc C. Morais

Viruses 2021, 13(1), 15; https://0-doi-org.brum.beds.ac.uk/10.3390/v13010015 - 23 Dec 2020

Cited by 4 | Viewed by 2455

Abstract

Double-stranded DNA viruses package their genomes into pre-assembled protein procapsids. This process is driven by macromolecular motors that transiently assemble at a unique vertex of the procapsid and utilize homomeric ring ATPases to couple genome encapsidation to ATP hydrolysis. Here, we describe the [...] Read more.

Double-stranded DNA viruses package their genomes into pre-assembled protein procapsids. This process is driven by macromolecular motors that transiently assemble at a unique vertex of the procapsid and utilize homomeric ring ATPases to couple genome encapsidation to ATP hydrolysis. Here, we describe the biochemical and biophysical characterization of the packaging ATPase from Lactococcus lactis phage asccφ28. Size-exclusion chromatography (SEC), analytical ultracentrifugation (AUC), small angle X-ray scattering (SAXS), and negative stain transmission electron microscopy (TEM) indicate that the ~45 kDa protein formed a 443 kDa cylindrical assembly with a maximum dimension of ~155 Å and radius of gyration of ~54 Å. Together with the dimensions of the crystallographic asymmetric unit from preliminary X-ray diffraction experiments, these results indicate that gp11 forms a decameric D5-symmetric complex consisting of two pentameric rings related by 2-fold symmetry. Additional kinetic analysis shows that recombinantly expressed gp11 has ATPase activity comparable to that of functional ATPase rings assembled on procapsids in other genome packaging systems. Hence, gp11 forms rings in solution that likely reflect the fully assembled ATPases in active virus-bound motor complexes. Whereas ATPase functionality in other double-stranded DNA (dsDNA) phage packaging systems requires assembly on viral capsids, the ability to form functional rings in solution imparts gp11 with significant advantages for high-resolution structural studies and rigorous biophysical/biochemical analysis. Full article

(This article belongs to the Special Issue In Memory of Michael Rossmann)

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