Interaction of viral proteins with metal ions: role in maintaining the structure and functions of viruses

Chaturvedi, U. C.; Shrivastava, Rahul

doi:10.1016/j.femsim.2004.11.004

Cited by 102 publications

(101 citation statements)

References 73 publications

(77 reference statements)

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“…These bound metal ions are also required for nucleocapsid protein-transactivation response-RNA interactions. Zinc is the most common divalent metal ion that influences a variety of viral infections (3). Proteins from viruses such as human immunodeficiency virus type 1, hepatitis C, hepatitis B, herpes simplex, pox, rubella, influenza, corona, human papilloma, Ebola, picorn, and rotavirus essentially bind with Zn 2ϩ and carry out the host infection (3).…”

Section: Resultsmentioning

confidence: 99%

Identification of a Novel Nonstructural Protein, VP9, from White Spot Syndrome Virus: Its Structure Reveals a Ferredoxin Fold with Specific Metal Binding Sites

Liu¹,

Wu²,

Song

et al. 2006

J Virol

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White spot syndrome virus (WSSV) is a major pathogen in shrimp aquaculture. VP9, a full-length protein of WSSV, encoded by open reading frame wsv230, was identified for the first time in the infected Penaeus monodon shrimp tissues, gill, and stomach as a novel, nonstructural protein by Western blotting, mass spectrometry, and immunoelectron microscopy. Real-time reverse transcription-PCR demonstrated that the transcription of VP9 started from the early to the late stage of WSSV infection as a major mRNA species. The structure of full-length VP9 was determined by both X-ray and nuclear magnetic resonance (NMR) techniques. It is the first structure to be reported for WSSV proteins. The crystal structure of VP9 revealed a ferredoxin fold with divalent metal ion binding sites. Cadmium sulfate was found to be essential for crystallization. The Cd 2؉ ions were bound between the monomer interfaces of the homodimer. Various divalent metal ions have been titrated against VP9, and their interactions were analyzed using NMR spectroscopy. The titration data indicated that VP9 binds with both Zn 2؉ and Cd 2؉ . VP9 adopts a similar fold as the DNA binding domain of the papillomavirus E2 protein. Based on our present investigations, we hypothesize that VP9 might be involved in the transcriptional regulation of WSSV, a function similar to that of the E2 protein during papillomavirus infection of the host cells.Shrimp aquaculture has become an important industry worldwide during the last few decades. Intensive cultivation and massive worldwide trade of the shrimp and other aquaculture industries have led to the emergence and spread of numerous viral pathogens. Out of these viral pathogens, shrimp white spot syndrome virus (WSSV) is the most devastating to crustacean species. To date, there is no effective treatment available for WSSV infection.WSSV belongs to a new virus family, Nimaviridae, under a new genus, Whispovirus, which shares low sequence homology with other DNA viruses (16,24). WSSV is an enveloped virus with a 305-kb double-stranded circular DNA genome. Its genome was completely sequenced, with 180 predicted open reading frames (ORFs) (27). Most of these WSSV genes bear poor sequence homology with other known proteins, and thus the function of these genes cannot be predicted. However, a large amount of work has been carried out on the identification and characterization of WSSV structural proteins, including envelope and other capsid proteins. To date, a total of 39 structural proteins are known from WSSV (12, 23). A structure-based functional study is a promising approach to elucidate the function of such WSSV proteins. Besides the envelope and capsid proteins, nonstructural proteins are required for replication of the viral genome, production of the virus particle, and inhibition of the host cell functions. These proteins are therefore potential candidates for drug design and the development of vaccines.Here we report, for the first time, the identification of a novel, nonstructural WSSV protein, VP9. We have demon...

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Section: Resultsmentioning

confidence: 99%

Identification of a Novel Nonstructural Protein, VP9, from White Spot Syndrome Virus: Its Structure Reveals a Ferredoxin Fold with Specific Metal Binding Sites

Liu¹,

Wu²,

Song

et al. 2006

J Virol

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“…About one third of all proteins contain metal ions as integral components (Chaturvedi & Shrivastava, 2005; Waldron & Robinson, 2009). These metalloproteins—as well as other proteins that transiently bind ions—recognize and associate with only specific types of ions.…”

Section: Modeling Ionic Solutionsmentioning

confidence: 99%

Biomolecular electrostatics and solvation: a computational perspective

Ren

Chun

Thomas

et al. 2012

Quart. Rev. Biophys.

168

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An understanding of molecular interactions is essential for insight into biological systems at the molecular scale. Among the various components of molecular interactions, electrostatics are of special importance because of their long-range nature and their influence on polar or charged molecules, including water, aqueous ions, proteins, nucleic acids, carbohydrates, and membrane lipids. In particular, robust models of electrostatic interactions are essential for understanding the solvation properties of biomolecules and the effects of solvation upon biomolecular folding, binding, enzyme catalysis, and dynamics. Electrostatics, therefore, are of central importance to understanding biomolecular structure and modeling interactions within and among biological molecules. This review discusses the solvation of biomolecules with a computational biophysics view towards describing the phenomenon. While our main focus lies on the computational aspect of the models, we provide an overview of the basic elements of biomolecular solvation (e.g., solvent structure, polarization, ion binding, and nonpolar behavior) in order to provide a background to understand the different types of solvation models.

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“…The regulation of metal ions plays a major role in enzymes to catalyze a range of biological reactions involved in signaling pathways, maintaining the electrochemical gradient for ion transport, and translocation of proteins 1–5. Identification and characterization of the metal ion binding sites and their selectivity have received immense attention in the past few decades 6–9.…”

Section: Introductionmentioning

confidence: 99%