scholarly journals Cryoelectron Microscopy Structures of Rotavirus NSP2-NSP5 and NSP2-RNA Complexes: Implications for Genome Replication

2006 ◽  
Vol 80 (21) ◽  
pp. 10829-10835 ◽  
Author(s):  
Xiaofang Jiang ◽  
Hariharan Jayaram ◽  
Mukesh Kumar ◽  
Steven J. Ludtke ◽  
Mary K. Estes ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Solution Structure ◽  
Cryoelectron Microscopy ◽  
Genome Replication ◽  
Binding Assays ◽  
Nonstructural Proteins ◽  
Multiple Components ◽  
Rna Complexes ◽  
Fourfold Axis ◽  
Positively Charged

ABSTRACT The replication and packaging of the rotavirus genome, comprising 11 segments of double-stranded RNA, take place in specialized compartments called viroplasms, which are formed during infection and involve a coordinated interplay of multiple components. Two rotavirus nonstructural proteins, NSP2 (with nucleoside triphosphatase, single-stranded RNA [ssRNA] binding and helix-destabilizing activities) and NSP5, are essential in these events. Previous structural analysis of NSP2 showed that it is an octamer in crystals, obeying 4-2-2 crystal symmetry, with a large 35-Å central hole along the fourfold axis and deep grooves at one of the twofold axes. To ascertain that the solution structure of NSP2 is the same as that in the crystals and investigate how NSP2 interacts with NSP5 and RNA, we carried out single-particle cryoelectron microscopy (cryo-EM) analysis of NSP2 alone and in complexes with NSP5 and ssRNA at subnanometer resolution. Because full-length NSP5 caused severe aggregation upon mixing with NSP2, the deletion construct NSP566-188 was used in these studies. Our studies show that the solution structure of NSP2 is same as the crystallographic octamer and that both NSP566-188 and ssRNA bind to the grooves in the octamer, which are lined by positively charged residues. The fitting of the NSP2 crystal structure to cryo-EM reconstructions of the complexes indicates that, in contrast to the binding of NSP566-188, the binding of RNA induces noticeable conformational changes in the NSP2 octamer. Consistent with the observation that both NSP5 and RNA share the same binding site on the NSP2 octamer, filter binding assays showed that NSP5 competes with ssRNA binding, indicating that one of the functions of NSP5 is to regulate NSP2-RNA interactions during genome replication.

scholarly journals NMR structure of a vestigial nuclease provides insight into the evolution of functional transitions in viral dsDNA packaging motors

2020 ◽  
Author(s):  
Bryon P. Mahler ◽  
Pawel J. Bujalowski ◽  
Huzhang Mao ◽  
Erik A. Dill ◽  
Paul J. Jardine ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Molecular Motors ◽  
Solution Structure ◽  
Nuclease Activity ◽  
Structural Basis ◽  
Binding Assays ◽  
Dna Viruses ◽  
Double Stranded Dna ◽  
Fluorescence Binding ◽  
Insight Into

SummaryDouble-stranded DNA viruses use ATP-powered molecular motors to package their genomes. To do so, these motors must efficiently transition between initiation, translocation, and termination modes. Here, we report structural and biophysical analyses of the C-terminal domain of the bacteriophage phi29 ATPase (CTD) that suggest a structural basis for these functional transitions. Sedimentation experiments show that the inter-domain linker in the full-length protein promotes dimerization and thus may play a role in assembly of the functional motor. The NMR solution structure of the CTD indicates it is a vestigial nuclease domain that likely evolved from conserved nuclease domains in phage terminases. Despite the loss of nuclease activity, fluorescence binding assays confirm the CTD retains its DNA binding capabilities and fitting the CTD into cryoEM density of the phi29 motor shows that the CTD directly binds DNA. However, the interacting residues differ from those identified by NMR titration in solution, suggesting that packaging motors undergo conformational changes to transition between initiation, translocation, and termination.

scholarly journals NMR structure of a vestigial nuclease provides insight into the evolution of functional transitions in viral dsDNA packaging motors

2020 ◽  
Vol 48 (20) ◽  
pp. 11737-11749 ◽  
Author(s):  
Bryon P Mahler ◽  
Paul J Bujalowski ◽  
Huzhang Mao ◽  
Erik A Dill ◽  
Paul J Jardine ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Molecular Motors ◽  
Solution Structure ◽  
Nuclease Activity ◽  
Structural Basis ◽  
Binding Assays ◽  
Dna Viruses ◽  
Double Stranded Dna ◽  
Fluorescence Binding ◽  
Insight Into

Abstract Double-stranded DNA viruses use ATP-powered molecular motors to package their genomic DNA. To ensure efficient genome encapsidation, these motors regulate functional transitions between initiation, translocation, and termination modes. Here, we report structural and biophysical analyses of the C-terminal domain of the bacteriophage phi29 ATPase (CTD) that suggest a structural basis for these functional transitions. Sedimentation experiments show that the inter-domain linker in the full-length protein promotes oligomerization and thus may play a role in assembly of the functional motor. The NMR solution structure of the CTD indicates it is a vestigial nuclease domain that likely evolved from conserved nuclease domains in phage terminases. Despite the loss of nuclease activity, fluorescence binding assays confirm the CTD retains its DNA binding capabilities and fitting the CTD into cryoEM density of the phi29 motor shows that the CTD directly binds DNA. However, the interacting residues differ from those identified by NMR titration in solution, suggesting that packaging motors undergo conformational changes to transition between initiation, translocation, and termination. Taken together, these results provide insight into the evolution of functional transitions in viral dsDNA packaging motors.

Solution Structure and Conformational Changes of theStreptomycesChitin-Binding Protein (CHB1)†

Biochemistry ◽  
2000 ◽  
Vol 39 (35) ◽  
pp. 10677-10683 ◽  
Author(s):  
Dmitri I. Svergun ◽  
Ardina Bećirević ◽  
Hildgund Schrempf ◽  
Michel H. J. Koch ◽  
Gerhard Grüber
Keyword(s):  
Conformational Changes ◽  
Solution Structure ◽  
Binding Protein

The D′ domain of von Willebrand factor requires the presence of the D3 domain for optimal factor VIII binding

2018 ◽  
Vol 475 (17) ◽  
pp. 2819-2830 ◽  
Author(s):  
Małgorzata A. Przeradzka ◽  
Henriet Meems ◽  
Carmen van der Zwaan ◽  
Eduard H.T.M. Ebberink ◽  
Maartje van den Biggelaar ◽  
...  
Keyword(s):  
Factor Viii ◽  
Binding Affinity ◽  
Von Willebrand Factor ◽  
Conformational Changes ◽  
Effective Interaction ◽  
Von Willebrand Disease ◽  
Binding Assays ◽  
Surface Plasmon Resonance Analysis ◽  
Von Willebrand ◽  
Willebrand Factor

The D′–D3 fragment of von Willebrand factor (VWF) can be divided into TIL′-E′-VWD3-C8_3-TIL3-E3 subdomains of which TIL′-E′-VWD3 comprises the main factor VIII (FVIII)-binding region. Yet, von Willebrand disease (VWD) Type 2 Normandy (2N) mutations, associated with impaired FVIII interaction, have been identified in C8_3-TIL3-E3. We now assessed the role of the VWF (sub)domains for FVIII binding using isolated D′, D3 and monomeric C-terminal subdomain truncation variants of D′–D3. Competitive binding assays and surface plasmon resonance analysis revealed that D′ requires the presence of D3 for effective interaction with FVIII. The isolated D3 domain, however, did not show any FVIII binding. Results indicated that the E3 subdomain is dispensable for FVIII binding. Subsequent deletion of the other subdomains from D3 resulted in a progressive decrease in FVIII-binding affinity. Chemical footprinting mass spectrometry suggested increased conformational changes at the N-terminal side of D3 upon subsequent subdomain deletions at the C-terminal side of the D3. A D′–D3 variant with a VWD type 2N mutation in VWD3 (D879N) or C8_3 (C1060R) also revealed conformational changes in D3, which were proportional to a decrease in FVIII-binding affinity. A D′–D3 variant with a putative VWD type 2N mutation in the E3 subdomain (C1225G) showed, however, normal binding. This implies that the designation VWD type 2N is incorrect for this variant. Results together imply that a structurally intact D3 in D′–D3 is indispensable for effective interaction between D′ and FVIII explaining why specific mutations in D3 can impair FVIII binding.

scholarly journals Function, Architecture, and Biogenesis of Reovirus Replication Neoorganelles

Viruses ◽  
2019 ◽  
Vol 11 (3) ◽  
pp. 288 ◽  
Author(s):  
Raquel Tenorio ◽  
Isabel Fernández de Castro ◽  
Jonathan J. Knowlton ◽  
Paula F. Zamora ◽  
Danica M. Sutherland ◽  
...  
Keyword(s):  
Protein Complexes ◽  
Host Cells ◽  
Genome Replication ◽  
Nonstructural Proteins ◽  
Particle Assembly ◽  
The Matrix ◽  
Viral Genome Replication ◽  
Pathogenic Viruses ◽  
Infected Cells ◽  
Reovirus Replication

Most viruses that replicate in the cytoplasm of host cells form neoorganelles that serve as sites of viral genome replication and particle assembly. These highly specialized structures concentrate viral proteins and nucleic acids, prevent the activation of cell-intrinsic defenses, and coordinate the release of progeny particles. Reoviruses are common pathogens of mammals that have been linked to celiac disease and show promise for oncolytic applications. These viruses form nonenveloped, double-shelled virions that contain ten segments of double-stranded RNA. Replication organelles in reovirus-infected cells are nucleated by viral nonstructural proteins µNS and σNS. Both proteins partition the endoplasmic reticulum to form the matrix of these structures. The resultant membranous webs likely serve to anchor viral RNA–protein complexes for the replication of the reovirus genome and the assembly of progeny virions. Ongoing studies of reovirus replication organelles will advance our knowledge about the strategies used by viruses to commandeer host biosynthetic pathways and may expose new targets for therapeutic intervention against diverse families of pathogenic viruses.

scholarly journals Architecture and Nucleotide-Dependent Conformational Changes of the Rvb1-Rvb2 AAA+ Complex Revealed by Cryoelectron Microscopy

Structure ◽  
2016 ◽  
Vol 24 (5) ◽  
pp. 657-666 ◽  
Author(s):  
Caroline A. Ewens ◽  
Min Su ◽  
Liang Zhao ◽  
Nardin Nano ◽  
Walid A. Houry ◽  
...  
Keyword(s):  
Conformational Changes ◽  
Cryoelectron Microscopy

scholarly journals Reovirus Nonstructural Protein σNS Acts as an RNA Stability Factor Promoting Viral Genome Replication

2018 ◽  
Vol 92 (15) ◽  
Author(s):  
Paula F. Zamora ◽  
Liya Hu ◽  
Jonathan J. Knowlton ◽  
Roni M. Lahr ◽  
Rodolfo A. Moreno ◽  
...  
Keyword(s):  
Virus Replication ◽  
Viral Genome ◽  
Nonstructural Protein ◽  
Dsrna Virus ◽  
Genome Replication ◽  
Nonstructural Proteins ◽  
Content Type ◽  
The Family ◽  
Viral Genome Replication

ABSTRACTViral nonstructural proteins, which are not packaged into virions, are essential for the replication of most viruses. Reovirus, a nonenveloped, double-stranded RNA (dsRNA) virus, encodes three nonstructural proteins that are required for viral replication and dissemination in the host. The reovirus nonstructural protein σNS is a single-stranded RNA (ssRNA)-binding protein that must be expressed in infected cells for production of viral progeny. However, the activities of σNS during individual steps of the reovirus replication cycle are poorly understood. We explored the function of σNS by disrupting its expression during infection using cells expressing a small interfering RNA (siRNA) targeting the σNS-encoding S3 gene and found that σNS is required for viral genome replication. Using complementary biochemical assays, we determined that σNS forms complexes with viral and nonviral RNAs. We also discovered, usingin vitroand cell-based RNA degradation experiments, that σNS increases the RNA half-life. Cryo-electron microscopy revealed that σNS and ssRNAs organize into long, filamentous structures. Collectively, our findings indicate that σNS functions as an RNA-binding protein that increases the viral RNA half-life. These results suggest that σNS forms RNA-protein complexes in preparation for genome replication.IMPORTANCEFollowing infection, viruses synthesize nonstructural proteins that mediate viral replication and promote dissemination. Viruses from the familyReoviridaeencode nonstructural proteins that are required for the formation of progeny viruses. Although nonstructural proteins of different viruses in the familyReoviridaediverge in primary sequence, they are functionally homologous and appear to facilitate conserved mechanisms of dsRNA virus replication. Usingin vitroand cell culture approaches, we found that the mammalian reovirus nonstructural protein σNS binds and stabilizes viral RNA and is required for genome synthesis. This work contributes new knowledge about basic mechanisms of dsRNA virus replication and provides a foundation for future studies to determine how viruses in the familyReoviridaeassort and replicate their genomes.

Structural analysis of the C-terminal domain of the spliceosomal helicase Prp22

2012 ◽  
Vol 393 (10) ◽  
pp. 1131-1140 ◽  
Author(s):  
Denis Kudlinzki ◽  
Andreas Schmitt ◽  
Henning Christian ◽  
Ralf Ficner
Keyword(s):  
Rna Binding ◽  
Dna Helicase ◽  
Specific Interactions ◽  
Winged Helix ◽  
Dsrna Binding ◽  
Binding Surface ◽  
Rna Complexes ◽  
Positively Charged ◽  
Analogous Function

Abstract Splicing of pre-mRNA requires the activity of at least eight different DEAD/H-box proteins that are involved in distinct steps of the splicing process. These proteins are driving the spliceosomal machinery by ATP-dependent unwinding of dsRNA and/or disrupting protein-RNA complexes. The spliceosomal DEAH-box proteins Prp2, Prp16, Prp22 and Prp43 share homologous C-terminal domains (CTD). We have determined the crystal structure of the CTD of human Prp22 by means of MAD. The fold of the human Prp22-CTD closely resembles that of the yeast Prp43-CTD. The similarity of these helicase-associated CTDs to the winged-helix and ratchet domains of the DNA helicase Hel308 suggests an analogous function in dsRNA binding and unwinding. Here, we also demonstrate that the CTD has a significant impact on the ATPase activity of yPrp22 in vitro. Homology modeling of the CTDs of hPrp2, hPrp16 and hPrp43 suggests that the CTDs of spliceosomal helicases contain conserved positively charged patches on their surfaces representing a common RNA-binding surface as well as divergent regions most likely mediating specific interactions with different proteins of the spliceosome.

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