Functional Relevance of Amino Acid Residues Involved in Interactions with Ordered Nucleic Acid in a Spherical Virus*

In the spherical virion of the parvovirus minute virus of mice, several amino acid side chains of the capsid were previously found to be involved in interactions with the viral single-stranded DNA molecule. We have individually truncated by mutation to alanine many (ten) of these side chains and analyzed the effects on capsid assembly, stability and conformation, viral DNA encapsidation, and virion infectivity. Mutation of residues Tyr-270, Asp-273, or Asp-474 led to a drastic reduction in infectivity. Mutant Y270A was defective in capsid assembly; mutant D273A formed stable capsids, but it was essentially unable to encapsidate the viral DNA or to externalize the N terminus of the capsid protein VP2, a connected conformational event. Mutation of residues Asp-58, Trp-60, Asn-183, Thr-267, or Lys-471 led to a moderate reduction in infectivity. None of these mutations had an effect on capsid assembly or stability, or on the DNA encapsidation process. However, those five mutant virions were substantially less stable than the parental virion in thermal inactivation assays. The results with this model spherical virus indicate that several capsid residues that are found to be involved in polar interactions or multiple hydrophobic contacts with the viral DNA molecule contribute to preserving the active conformation of the infectious viral particle. Their effect appears to be mediated by the non-covalent interactions they establish with the viral DNA. In addition, at least one acidic residue at each DNA-binding region is needed for DNA packaging.

[1]  John E. Johnson,et al.  The refined three-dimensional structure of an insect virus at 2.8 A resolution. , 1994, Journal of molecular biology.

[2]  J. Markley,et al.  Thermal stability of cowpea mosaic virus components: differential scanning calorimetry studies. , 1985, Virology.

[3]  Mauricio G. Mateu,et al.  Complete Alanine Scanning of Intersubunit Interfaces in a Foot-and-Mouth Disease Virus Capsid Reveals Critical Contributions of Many Side Chains to Particle Stability and Viral Function* , 2003, Journal of Biological Chemistry.

[4]  John E. Johnson,et al.  Ordered duplex RNA controls capsid architecture in an icosahedral animal virus , 1993, Nature.

[5]  J. Murray,et al.  The three-dimensional structures of two complexes between recombinant MS2 capsids and RNA operator fragments reveal sequence-specific protein-RNA interactions. , 1997, Journal of molecular biology.

[6]  M. Rossmann,et al.  Atomic structure of single-stranded DNA bacteriophage ΦX174 and its functional implications , 1991, Nature.

[7]  M. S. Chapman,et al.  Structure, sequence, and function correlations among parvoviruses. , 1993, Virology.

[8]  P. Ahlquist,et al.  Effects of deletions in the N-terminal basic arm of brome mosaic virus coat protein on RNA packaging and systemic infection , 1989, Journal of virology.

[9]  M. S. Chapman,et al.  Single-stranded DNA-protein interactions in canine parvovirus. , 1995, Structure.

[10]  J. Murray,et al.  Crystal structures of MS2 coat protein mutants in complex with wild-type RNA operator fragments. , 1998, Nucleic acids research.

[11]  Mauricio G Mateu,et al.  Role of interfacial amino acid residues in assembly, stability, and conformation of a spherical virus capsid. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[12]  John E. Johnson,et al.  Nodavirus Coat Protein Imposes Dodecahedral RNA Structure Independent of Nucleotide Sequence and Length , 2004, Journal of Virology.

[13]  Structural refinement of the DNA-containing capsid of canine parvovirus using RSRef, a resolution-dependent stereochemically restrained real-space refinement method. , 1996, Acta crystallographica. Section D, Biological crystallography.

[14]  Y. Li,et al.  Protein-RNA interactions in an icosahedral virus at 3.0 A resolution. , 1989, Science.

[15]  M. Agbandje-McKenna,et al.  A Beta-Stranded Motif Drives Capsid Protein Oligomers of the Parvovirus Minute Virus of Mice into the Nucleus for Viral Assembly , 2000, Journal of Virology.

[16]  D. Peabody,et al.  The RNA binding site of bacteriophage MS2 coat protein. , 1993, The EMBO journal.

[17]  P. Tattersall,et al.  Mapping of the fibrotropic and lymphotropic host range determinants of the parvovirus minute virus of mice , 1988, Journal of virology.

[18]  M S Chapman,et al.  The three-dimensional structure of canine parvovirus and its functional implications. , 1991, Science.

[19]  S. Larson,et al.  Refined structure of satellite tobacco mosaic virus at 1.8 A resolution. , 1998, Journal of molecular biology.

[20]  S. Jones,et al.  Protein-RNA interactions: a structural analysis. , 2001, Nucleic acids research.

[21]  John E. Johnson,et al.  Protein-RNA Interactions and Virus Stability as Probed by the Dynamics of Tryptophan Side Chains* , 2002, The Journal of Biological Chemistry.

[22]  R. McKenna,et al.  Biochemical and physical characterization of parvovirus minute virus of mice virus-like particles. , 2000, Virology.

[23]  O. Uhlenbeck,et al.  Specific interaction between RNA phage coat proteins and RNA. , 1991, Progress in nucleic acid research and molecular biology.

[24]  L. Liljas,et al.  The structure of spherical viruses. , 1986, Progress in biophysics and molecular biology.

[25]  M. G. Mateu,et al.  High Mutant Frequency in Populations of a DNA Virus Allows Evasion from Antibody Therapy in an Immunodeficient Host , 2003, Journal of Virology.

[26]  R A Sayle,et al.  RASMOL: biomolecular graphics for all. , 1995, Trends in biochemical sciences.

[27]  S. Hafenstein,et al.  φX174 Genome-Capsid Interactions Influence the Biophysical Properties of the Virion: Evidence for a Scaffolding-Like Function for the Genome during the Final Stages of Morphogenesis , 2002, Journal of Virology.

[28]  R. Saffrich,et al.  Nuclear Export of the Nonenveloped Parvovirus Virion Is Directed by an Unordered Protein Signal Exposed on the Capsid Surface , 2004, Journal of Virology.

[29]  D. Wild,et al.  The three-dimensional distribution of RNA and protein in the interior of tomato bushy stunt virus: a neutron low-resolution single-crystal diffraction study. , 1994, Structure.

[30]  M G Rossmann,et al.  Functional implications of the structure of the murine parvovirus, minute virus of mice. , 1998, Structure.

[31]  G Vriend,et al.  WHAT IF: a molecular modeling and drug design program. , 1990, Journal of molecular graphics.

[32]  Lars Liljas,et al.  Crystal structure of an RNA bacteriophage coat protein–operator complex , 1994, Nature.

[33]  F. Eiserling,et al.  Studies on the structure, protein composition and aseembly of the neck of bacteriophage T4. , 1977, Journal of molecular biology.

[34]  G. Farr,et al.  A conserved leucine that constricts the pore through the capsid fivefold cylinder plays a central role in parvoviral infection. , 2004, Virology.

[35]  W. Chiu,et al.  Structural biology of viruses , 1997 .

[36]  P. Tattersall,et al.  Controlled conformational transitions in the MVM virion expose the VP1 N-terminus and viral genome without particle disassembly. , 1999, Virology.

[37]  Jerson L. Silva,et al.  Mutations in the hydrophobic core and in the protein-RNA interface affect the packing and stability of icosahedral viruses. , 2003, European journal of biochemistry.

[38]  J. Almendral,et al.  Transcriptional inhibition of the parvovirus minute virus of mice by constitutive expression of an antisense RNA targeted against the NS-1 transactivator protein. , 1995, Virology.

[39]  C. Pleij,et al.  RNA–protein interactions in spherical viruses , 2002, Archives of Virology.

[40]  J. Wells,et al.  High-resolution epitope mapping of hGH-receptor interactions by alanine-scanning mutagenesis. , 1989, Science.

[41]  M. S. Chapman,et al.  Canine parvovirus capsid structure, analyzed at 2.9 A resolution. , 1996, Journal of molecular biology.

[42]  J. Johnson,et al.  Conformations, interactions, and thermostabilities of RNA and proteins in bean pod mottle virus: investigation of solution and crystal structures by laser Raman spectroscopy. , 1992, Biochemistry.

[43]  John E. Johnson,et al.  PRINCIPLES OF VIRUS STRUCTURE , 1999 .

[44]  D I Stuart,et al.  Viral RNA modulates the acid sensitivity of foot-and-mouth disease virus capsids , 1995, Journal of virology.

[45]  M. Rossmann,et al.  Analysis of the single-stranded DNA bacteriophage phi X174, refined at a resolution of 3.0 A. , 1994, Journal of molecular biology.

[46]  T. Hohn Role of RNA in the assembly process of bacteriophage fr. , 1969, Journal of molecular biology.

[47]  John E. Johnson,et al.  Structures of the native and swollen forms of cowpea chlorotic mottle virus determined by X-ray crystallography and cryo-electron microscopy. , 1995, Structure.

[48]  Wei Yang,et al.  Protein–nucleic acid interactions , 2004 .

[49]  M. Rossmann,et al.  The canine parvovirus empty capsid structure. , 1993, Journal of molecular biology.

[50]  G. Vriend,et al.  Role of the N-terminal part of the coat protein in the assembly of cowpea chlorotic mottle virus. A 500 MHz proton nuclear magnetic resonance study and structural calculations. , 1986, Journal of molecular biology.

[51]  J. Johnson,et al.  Differences in pressure stability of the three components of cowpea mosaic virus: implications for virus assembly and disassembly. , 1994, Biochemistry.

[52]  John E. Johnson,et al.  Particle Polymorphism Caused by Deletion of a Peptide Molecular Switch in a Quasiequivalent Icosahedral Virus , 1998, Journal of Virology.

[53]  O. Uhlenbeck,et al.  A thermodynamic analysis of the sequence-specific binding of RNA by bacteriophage MS2 coat protein. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[54]  John E. Johnson,et al.  Icosahedral RNA virus structure. , 1989, Annual review of biochemistry.

[55]  G. Stubbs Protein-nucleic acid interactions in tobacco mosaic virus , 1989 .

[56]  J. Almendral,et al.  Complementary Roles of Multiple Nuclear Targeting Signals in the Capsid Proteins of the Parvovirus Minute Virus of Mice during Assembly and Onset of Infection , 2002, Journal of Virology.

[57]  Alexander McPherson,et al.  Double-helical RNA in satellite tobacco mosaic virus , 1993, Nature.

[58]  P. Tattersall,et al.  DNA sequence of the lymphotropic variant of minute virus of mice, MVM(i), and comparison with the DNA sequence of the fibrotropic prototype strain , 1986, Journal of virology.

[59]  W. R. Wikoff,et al.  Structure determination of minute virus of mice. , 1997, Acta crystallographica. Section D, Biological crystallography.

[60]  Liang Tang,et al.  The structure of Pariacoto virus reveals a dodecahedral cage of duplex RNA , 2000, Nature Structural Biology.

[61]  P. Tattersall,et al.  Reciprocal productive and restrictive virus-cell interactions of immunosuppressive and prototype strains of minute virus of mice , 1983, Journal of virology.

[62]  Viral protein-nucleic acid interactions , 1992 .

[63]  Lars Liljas,et al.  Structural folds of viral proteins. , 2003, Advances in protein chemistry.

[64]  M. Rossmann,et al.  The phiX174 protein J mediates DNA packaging and viral attachment to host cells. , 2004, Journal of molecular biology.

[65]  Mauricio G Mateu,et al.  In Vitro Disassembly of a Parvovirus Capsid and Effect on Capsid Stability of Heterologous Peptide Insertions in Surface Loops* , 2004, Journal of Biological Chemistry.

[66]  P. Tattersall,et al.  The autonomously replicating parvoviruses of vertebrates. , 1987, Advances in virus research.