Solution structure of dengue virus capsid protein reveals another fold.

Dengue virus is responsible for approximately 50-100 million infections, resulting in nearly 24,000 deaths annually. The capsid (C) protein of dengue virus is essential for specific encapsidation of the RNA genome, but little structural information on the C protein is available. We report the solution structure of the 200-residue homodimer of dengue 2 C protein. The structure provides, to our knowledge, the first 3D picture of a flavivirus C protein and identifies a fold that includes a large dimerization surface contributed by two pairs of helices, one of which has characteristics of a coiled-coil. NMR structure determination involved a secondary structure sorting approach to facilitate assignment of the intersubunit nuclear Overhauser effect interactions. The dimer of dengue C protein has an unusually high net charge, and the structure reveals an asymmetric distribution of basic residues over the surface of the protein. Nearly half of the basic residues lie along one face of the dimer. In contrast, the conserved hydrophobic region forms an extensive apolar surface at a dimer interface on the opposite side of the molecule. We propose a model for the interaction of dengue C protein with RNA and the viral membrane that is based on the asymmetric charge distribution of the protein and is consistent with previously reported results.

[1]  P. Kraulis.  A program to produce both detailed and schematic plots of protein structures , 1991 .

[2]  D J Barlow,et al.  The distribution of charged groups in proteins , 1986, Biopolymers.

[3]  Christopher T. Jones,et al.  Flavivirus Capsid Is a Dimeric Alpha-Helical Protein , 2003, Journal of Virology.

[4]  Timothy F. Havel,et al.  Protein structures in solution by nuclear magnetic resonance and distance geometry. The polypeptide fold of the basic pancreatic trypsin inhibitor determined using two different algorithms, DISGEO and DISMAN. , 1987, Journal of molecular biology.

[5]  T. Creighton.  Proteins: Structures and Molecular Properties , 1986 .

[6]  S. Harrison,et al.  The envelope glycoprotein from tick-borne encephalitis virus at 2 Å resolution , 1995, Nature.

[7]  S. Grzesiek,et al.  Measurement of homo- and heteronuclear J couplings from quantitative J correlation. , 1994, Methods in enzymology.

[8]  R. Compans,et al.  Formation of the flavivirus envelope: role of the viral NS2B-NS3 protease , 1995, Journal of virology.

[9]  S. Grzesiek,et al.  NMRPipe: A multidimensional spectral processing system based on UNIX pipes , 1995, Journal of biomolecular NMR.

[10]  E A Merritt,et al.  Raster3D: photorealistic molecular graphics. , 1997, Methods in enzymology.

[11]  Paul A. Keifer,et al.  Pure absorption gradient enhanced heteronuclear single quantum correlation spectroscopy with improved sensitivity , 1992 .

[12]  Ying Zhang,et al.  Visualization of membrane protein domains by cryo-electron microscopy of dengue virus , 2003, Nature Structural Biology.

[13]  C. Rice,et al.  NS2B-3 proteinase-mediated processing in the yellow fever virus structural region: in vitro and in vivo studies , 1994, Journal of virology.

[14]  Wei Zhang,et al.  Structure of Dengue Virus Implications for Flavivirus Organization, Maturation, and Fusion , 2002, Cell.

[15]  B. Falgout,et al.  A conserved internal hydrophobic domain mediates the stable membrane integration of the dengue virus capsid protein. , 1997, Virology.

[16]  S D Fuller,et al.  Molecular organization of a recombinant subviral particle from tick-borne encephalitis virus. , 2001, Molecular cell.

[17]  Charles M. Rice,et al.  Mutations in the Yellow Fever Virus Nonstructural Protein NS2A Selectively Block Production of Infectious Particles , 2002, Journal of Virology.

[18]  F. Corpet.  Multiple sequence alignment with hierarchical clustering. , 1988, Nucleic acids research.

[19]  B. Berger,et al.  MultiCoil: A program for predicting two‐and three‐stranded coiled coils , 1997, Protein science : a publication of the Protein Society.

[20]  J. H. Strauss,et al.  Nucleotide sequence of dengue 2 RNA and comparison of the encoded proteins with those of other flaviviruses. , 1988, Virology.

[21]  C. Sander,et al.  Protein structure comparison by alignment of distance matrices. , 1993, Journal of molecular biology.

[22]  C. Mandl,et al.  Spontaneous Mutations Restore the Viability of Tick-Borne Encephalitis Virus Mutants with Large Deletions in Protein C , 2003, Journal of Virology.

[23]  L. Kay,et al.  Simultaneous Acquisition of 15N- and 13C-Edited NOE Spectra of Proteins Dissolved in H2O , 1994 .

[24]  M Nilges,et al.  A calculation strategy for the structure determination of symmetric demers by 1H NMR , 1993, Proteins.

[25]  L. Kay,et al.  Two-dimensional NMR experiments for correlating carbon-13.beta. and proton.delta./.epsilon. chemical shifts of aromatic residues in 13C-labeled proteins via scalar couplings , 1993 .

[26]  D. Wishart,et al.  The 13C Chemical-Shift Index: A simple method for the identification of protein secondary structure using 13C chemical-shift data , 1994, Journal of biomolecular NMR.

[27]  K. Sharp,et al.  Protein folding and association: Insights from the interfacial and thermodynamic properties of hydrocarbons , 1991, Proteins.

[28]  M. Luo,et al.  Structure of a bifunctional membrane-RNA binding protein, influenza virus matrix protein M1 , 1997, Nature Structural Biology.

[29]  C. Mandl,et al.  Capsid Protein C of Tick-Borne Encephalitis Virus Tolerates Large Internal Deletions and Is a Favorable Target for Attenuation of Virulence , 2002, Journal of Virology.

[30]  Peter J. Rossky,et al.  Surface topography dependence of biomolecular hydrophobic hydration , 1998, Nature.

[31]  Shao-Hung Wang,et al.  Intracellular localization and determination of a nuclear localization signal of the core protein of dengue virus. , 2002, The Journal of general virology.

[32]  D. Gubler.  Epidemic dengue/dengue hemorrhagic fever as a public health, social and economic problem in the 21st century. , 2002, Trends in microbiology.