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Viruses
Special Issues
Virus Assembly through the Lens of Structural Biology
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Virus Assembly through the Lens of Structural Biology

A special issue of Viruses (ISSN 1999-4915). This special issue belongs to the section "General Virology".

Deadline for manuscript submissions: closed (5 August 2021) | Viewed by 13591

Special Issue Editors

Prof. Dr. Jamil S. Saad

E-Mail Website
Guest Editor
Department of Microbiology, University of Alabama at Birmingham, BBRB 366/15, 845 19th Street South, Birmingham, AL 35294-2170, USA
Interests: HIV; Gag; NMR; cancer; drug design
Prof. Dr. Terje Dokland

E-Mail Website
Guest Editor
Department of Microbiology, University of Alabama at Birmingham, 845 19th St. South, BBRB 311, Birmingham, AL 35294, USA
Interests: electron microscopy; virus structure and assembly; arteriviruses; bacteriophages; Staphylococcus aureus pathogenicity islands; mobile genetic elements

Special Issue Information

Dear Colleagues,

Assembly is a key step in the viral replication cycle that is accompanied by the formation of complexes comprised of viral and cellular factors, including proteins, nucleic acids, and lipid/membranes. Structural biology techniques, including cryo-electron microscopy, X-ray crystallography, NMR, mass spectrometry, and small-angle X-ray scattering (SAXS) are widely used to elucidate mechanisms of assembly at the molecular level. For decades, visualization of macromolecules at the atomic level often relied on X-ray and NMR methods. However, recent advances in cryo-EM techniques, solid-state NMR, mass spectrometry, and computational methods (Rosetta modeling) have revolutionized our approach and allowed for atomic detail characterization of key steps in virus replication.    

For this Special Issue, we invite submissions in the form of original research articles, methodological advances, or reviews that address any aspect of structural biology focused on the viral assembly process. This Special Issue will cover all types of viruses that infect humans, animals, plants, or bacteria. In summary, our aim is to present an inspiring collection of articles covering this vibrant field of structural biology with a focus on virus assembly.

Prof. Dr. Jamil S. Saad
Prof. Dr. Terje Dokland
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Viruses is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • viral assembly
  • viral replication
  • viral structural biology
  • cryo-electron microscopy
  • X-ray crystallography
  • NMR

Published Papers (4 papers)

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Research

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25 pages, 44626 KiB  
Article
Viral Phrenology
by David P. Wilson and Danielle A. Roof
Viruses 2021, 13(11), 2191; https://0-doi-org.brum.beds.ac.uk/10.3390/v13112191 - 30 Oct 2021
Cited by 1 | Viewed by 2832
Abstract
We introduce Viral Phrenology, a new scheme for understanding the genomic composition of spherical viruses based on the locations of their structural protrusions. We used icosahedral point arrays to classify 135 distinct viral capsids collected from over 600 capsids available in the VIPERdb. [...] Read more.
We introduce Viral Phrenology, a new scheme for understanding the genomic composition of spherical viruses based on the locations of their structural protrusions. We used icosahedral point arrays to classify 135 distinct viral capsids collected from over 600 capsids available in the VIPERdb. Using gauge points of point arrays, we found 149 unique structural protrusions. We then show how to use the locations of these protrusions to determine the genetic composition of the virus. We then show that ssDNA, dsDNA, dsRNA and ssRNA viruses use different arrangements for distributing their protrusions. We also found that Triangulation number is also partially dependent on the structural protrusions. This analysis begins to tie together Baltimore Classification and Triangulation number using point arrays. Full article
(This article belongs to the Special Issue Virus Assembly through the Lens of Structural Biology)
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Review

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12 pages, 4050 KiB  
Review
A Structural Perspective of the Role of IP6 in Immature and Mature Retroviral Assembly
by Martin Obr, Florian K. M. Schur and Robert A. Dick
Viruses 2021, 13(9), 1853; https://0-doi-org.brum.beds.ac.uk/10.3390/v13091853 - 17 Sep 2021
Cited by 9 | Viewed by 3175
Abstract
The small cellular molecule inositol hexakisphosphate (IP6) has been known for ~20 years to promote the in vitro assembly of HIV-1 into immature virus-like particles. However, the molecular details underlying this effect have been determined only recently, with the identification of the IP6 [...] Read more.
The small cellular molecule inositol hexakisphosphate (IP6) has been known for ~20 years to promote the in vitro assembly of HIV-1 into immature virus-like particles. However, the molecular details underlying this effect have been determined only recently, with the identification of the IP6 binding site in the immature Gag lattice. IP6 also promotes formation of the mature capsid protein (CA) lattice via a second IP6 binding site, and enhances core stability, creating a favorable environment for reverse transcription. IP6 also enhances assembly of other retroviruses, from both the Lentivirus and the Alpharetrovirus genera. These findings suggest that IP6 may have a conserved function throughout the family Retroviridae. Here, we discuss the different steps in the viral life cycle that are influenced by IP6, and describe in detail how IP6 interacts with the immature and mature lattices of different retroviruses. Full article
(This article belongs to the Special Issue Virus Assembly through the Lens of Structural Biology)
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18 pages, 4264 KiB  
Review
Morphological Diversity and Dynamics of Dengue Virus Affecting Antigenicity
by Guntur Fibriansah, Xin-Ni Lim and Shee-Mei Lok
Viruses 2021, 13(8), 1446; https://0-doi-org.brum.beds.ac.uk/10.3390/v13081446 - 24 Jul 2021
Cited by 5 | Viewed by 3709
Abstract
The four serotypes of the mature dengue virus can display different morphologies, including the compact spherical, the bumpy spherical and the non-spherical clubshape morphologies. In addition, the maturation process of dengue virus is inefficient and therefore some partially immature dengue virus particles have [...] Read more.
The four serotypes of the mature dengue virus can display different morphologies, including the compact spherical, the bumpy spherical and the non-spherical clubshape morphologies. In addition, the maturation process of dengue virus is inefficient and therefore some partially immature dengue virus particles have been observed and they are infectious. All these viral particles have different antigenicity profiles and thus may affect the type of the elicited antibodies during an immune response. Understanding the molecular determinants and environmental conditions (e.g., temperature) in inducing morphological changes in the virus and how potent antibodies interact with these particles is important for designing effective therapeutics or vaccines. Several techniques, including cryoEM, site-directed mutagenesis, hydrogen-deuterium exchange mass spectrometry, time-resolve fluorescence resonance energy transfer, and molecular dynamic simulation, have been performed to investigate the structural changes. This review describes all known morphological variants of DENV discovered thus far, their surface protein dynamics and the key residues or interactions that play important roles in the structural changes. Full article
(This article belongs to the Special Issue Virus Assembly through the Lens of Structural Biology)
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16 pages, 2792 KiB  
Review
Novel Tsg101 Binding Partners Regulate Viral L Domain Trafficking
by Madeleine Strickland, David Nyenhuis, Susan M. Watanabe, Nico Tjandra and Carol A. Carter
Viruses 2021, 13(6), 1147; https://0-doi-org.brum.beds.ac.uk/10.3390/v13061147 - 15 Jun 2021
Cited by 7 | Viewed by 2940
Abstract
Two decades ago, Tsg101, a component of the Endosomal Sorting Complexes Required for Transport (ESCRT) complex 1, was identified as a cellular factor recruited by the human immunodeficiency virus type 1 (HIV-1) to facilitate budding of viral particles assembled at the cell periphery. [...] Read more.
Two decades ago, Tsg101, a component of the Endosomal Sorting Complexes Required for Transport (ESCRT) complex 1, was identified as a cellular factor recruited by the human immunodeficiency virus type 1 (HIV-1) to facilitate budding of viral particles assembled at the cell periphery. A highly conserved Pro-(Thr/Ser)-Ala-Pro [P(T/S)AP] motif in the HIV-1 structural polyprotein, Gag, engages a P(T/S)AP-binding pocket in the Tsg101 N-terminal domain. Since the same domain in Tsg101 that houses the pocket was found to bind mono-ubiquitin (Ub) non-covalently, Ub binding was speculated to enhance P(T/S)AP interaction. Within the past five years, we found that the Ub-binding site also accommodates di-Ub, with Lys63-linked di-Ub exhibiting the highest affinity. We also identified small molecules capable of disrupting Ub binding and inhibiting budding. The structural similarity of these molecules, prazoles, to nucleosides prompted testing for nucleic acid binding and led to identification of tRNA as a Tsg101 binding partner. Here, we discuss these recently identified interactions and their contribution to the viral assembly process. These new partners may provide additional insight into the control and function of Tsg101 as well as identify opportunities for anti-viral drug design. Full article
(This article belongs to the Special Issue Virus Assembly through the Lens of Structural Biology)
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