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Viruses, Volume 4, Issue 3 (March 2012), Pages 325-423

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Research

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Open AccessArticle Mining the Protein Data Bank to Differentiate Error from Structural Variation in Clustered Static Structures: An Examination of HIV Protease
Viruses 2012, 4(3), 348-362; doi:10.3390/v4030348
Received: 5 February 2012 / Revised: 29 February 2012 / Accepted: 1 March 2012 / Published: 5 March 2012
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Abstract
The Protein Data Bank (PDB) contains over 71,000 structures. Extensively studied proteins have hundreds of submissions available, including mutations, different complexes, and space groups, allowing for application of data-mining algorithms to analyze an array of static structures and gain insight about a [...] Read more.
The Protein Data Bank (PDB) contains over 71,000 structures. Extensively studied proteins have hundreds of submissions available, including mutations, different complexes, and space groups, allowing for application of data-mining algorithms to analyze an array of static structures and gain insight about a protein’s structural variation and possibly its dynamics. This investigation is a case study of HIV protease (PR) using in-house algorithms for data mining and structure superposition through generalized formulæ that account for multiple conformations and fractional occupancies. Temperature factors (B-factors) are compared with spatial displacement from the mean structure over the entire study set and separately over bound and ligand-free structures, to assess the significance of structural deviation in a statistical context. Space group differences are also examined. Full article
(This article belongs to the Special Issue HIV Dynamics and Evolution)
Open AccessArticle The Coronavirus E Protein: Assembly and Beyond
Viruses 2012, 4(3), 363-382; doi:10.3390/v4030363
Received: 24 December 2011 / Revised: 18 February 2012 / Accepted: 27 February 2012 / Published: 8 March 2012
Cited by 16 | PDF Full-text (839 KB) | HTML Full-text | XML Full-text
Abstract
The coronavirus E protein is a small membrane protein that has an important role in the assembly of virions. Recent studies have indicated that the E protein has functions during infection beyond assembly, including in virus egress and in the host stress [...] Read more.
The coronavirus E protein is a small membrane protein that has an important role in the assembly of virions. Recent studies have indicated that the E protein has functions during infection beyond assembly, including in virus egress and in the host stress response. Additionally, the E protein has ion channel activity, interacts with host proteins, and may have multiple membrane topologies. The goal of this review is to highlight the properties and functions of the E protein, and speculate on how they may be related. Full article
(This article belongs to the Special Issue Animal Arteriviruses and Coronaviruses)
Figures

Open AccessCommunication Folding and Oligomerization of the gp2b/gp3/gp4 Spike Proteins of Equine Arteritis Virus in Vitro
Viruses 2012, 4(3), 414-423; doi:10.3390/v4030414
Received: 5 January 2012 / Revised: 13 March 2012 / Accepted: 18 March 2012 / Published: 22 March 2012
Cited by 2 | PDF Full-text (1470 KB) | HTML Full-text | XML Full-text
Abstract
Equine arteritis virus (EAV) is a small, positive-stranded RNA virus. The glycoproteins gp2b, gp3 and gp4 form a heterotrimer in the viral envelope, which is required for cell entry of EAV. We describe expression of the ectodomains of the proteins in E. [...] Read more.
Equine arteritis virus (EAV) is a small, positive-stranded RNA virus. The glycoproteins gp2b, gp3 and gp4 form a heterotrimer in the viral envelope, which is required for cell entry of EAV. We describe expression of the ectodomains of the proteins in E. coli and their refolding from inclusion bodies. After extraction of inclusion bodies and dialysis, Gst-, but not His-tagged proteins, refold into a soluble conformation. However, when dialyzed together with Gst-gp3 or with Gst-gp4, His-gp2b and His-gp4 remain soluble and oligomers are obtained by affinity-chromatography. Thus, folding and oligomerization of gp2b, gp3 and gp4 in vitro are interdependent processes. Full article
(This article belongs to the Special Issue Animal Arteriviruses and Coronaviruses)
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Review

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Open AccessReview Nuclear Actin and Lamins in Viral Infections
Viruses 2012, 4(3), 325-347; doi:10.3390/v4030325
Received: 24 January 2012 / Revised: 20 February 2012 / Accepted: 21 February 2012 / Published: 28 February 2012
Cited by 8 | PDF Full-text (528 KB) | HTML Full-text | XML Full-text
Abstract
Lamins are the best characterized cytoskeletal components of the cell nucleus that help to maintain the nuclear shape and participate in diverse nuclear processes including replication or transcription. Nuclear actin is now widely accepted to be another cytoskeletal protein present in the [...] Read more.
Lamins are the best characterized cytoskeletal components of the cell nucleus that help to maintain the nuclear shape and participate in diverse nuclear processes including replication or transcription. Nuclear actin is now widely accepted to be another cytoskeletal protein present in the nucleus that fulfills important functions in the gene expression. Some viruses replicating in the nucleus evolved the ability to interact with and probably utilize nuclear actin for their replication, e.g., for the assembly and transport of capsids or mRNA export. On the other hand, lamins play a role in the propagation of other viruses since nuclear lamina may represent a barrier for virions entering or escaping the nucleus. This review will summarize the current knowledge about the roles of nuclear actin and lamins in viral infections. Full article
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Open AccessReview Feline Immunodeficiency Virus in South America
Viruses 2012, 4(3), 383-396; doi:10.3390/v4030383
Received: 13 February 2012 / Revised: 22 February 2012 / Accepted: 24 February 2012 / Published: 14 March 2012
Cited by 4 | PDF Full-text (300 KB) | HTML Full-text | XML Full-text
Abstract
The rapid emergence of AIDS in humans during the period between 1980 and 2000 has led to extensive efforts to understand more fully similar etiologic agents of chronic and progressive acquired immunodeficiency disease in several mammalian species. Lentiviruses that have gene sequence [...] Read more.
The rapid emergence of AIDS in humans during the period between 1980 and 2000 has led to extensive efforts to understand more fully similar etiologic agents of chronic and progressive acquired immunodeficiency disease in several mammalian species. Lentiviruses that have gene sequence homology with human immunodeficiency virus (HIV) have been found in different species (including sheep, goats, horses, cattle, cats, and several Old World monkey species). Lentiviruses, comprising a genus of the Retroviridae family, cause persistent infection that can lead to varying degrees of morbidity and mortality depending on the virus and the host species involved. Feline immunodeficiency virus (FIV) causes an immune system disease in domestic cats (Felis catus) involving depletion of the CD4+ population of T lymphocytes, increased susceptibility to opportunistic infections, and sometimes death. Viruses related to domestic cat FIV occur also in a variety of nondomestic felids. This is a brief overview of the current state of knowledge of this large and ancient group of viruses (FIVs) in South America. Full article
(This article belongs to the Special Issue Feline Retroviruses)
Open AccessReview Innate Immunity Evasion by Dengue Virus
Viruses 2012, 4(3), 397-413; doi:10.3390/v4030397
Received: 30 January 2012 / Revised: 14 February 2012 / Accepted: 7 March 2012 / Published: 15 March 2012
Cited by 46 | PDF Full-text (880 KB) | HTML Full-text | XML Full-text
Abstract
For viruses to productively infect their hosts, they must evade or inhibit important elements of the innate immune system, namely the type I interferon (IFN) response, which negatively influences the subsequent development of antigen-specific adaptive immunity against those viruses. Dengue virus (DENV) [...] Read more.
For viruses to productively infect their hosts, they must evade or inhibit important elements of the innate immune system, namely the type I interferon (IFN) response, which negatively influences the subsequent development of antigen-specific adaptive immunity against those viruses. Dengue virus (DENV) can inhibit both type I IFN production and signaling in susceptible human cells, including dendritic cells (DCs). The NS2B3 protease complex of DENV functions as an antagonist of type I IFN production, and its proteolytic activity is necessary for this function. DENV also encodes proteins that antagonize type I IFN signaling, including NS2A, NS4A, NS4B and NS5 by targeting different components of this signaling pathway, such as STATs. Importantly, the ability of the NS5 protein to bind and degrade STAT2 contributes to the limited host tropism of DENV to humans and non-human primates. In this review, we will evaluate the contribution of innate immunity evasion by DENV to the pathogenesis and host tropism of this virus. Full article
(This article belongs to the Special Issue Recent Progress in Dengue Virus Research)

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