scholarly journals Structural and Functional Characterization of the Phosphoprotein Central Domain of Spring Viremia of Carp Virus

2020 ◽  
Vol 94 (15) ◽  
Author(s):  
Zhao-Xi Wang ◽  
Shu-Bo Liu ◽  
Hongxin Guan ◽  
Long-Feng Lu ◽  
Jia-Gang Tu ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Functional Characterization ◽  
Oligomeric State ◽  
Hydrophobic Surfaces ◽  
Central Domain ◽  
P Protein ◽  
Homologous Virus ◽  
Β Sheets ◽  
P Proteins

ABSTRACT Spring viremia of carp virus (SVCV) is a highly pathogenic Vesiculovirus in the common carp. The phosphoprotein (P protein) of SVCV is a multifunctional protein that acts as a polymerase cofactor and an antagonist of cellular interferon (IFN) response. Here, we report the 1.5-Å-resolution crystal structure of the P protein central domain (PCD) of SVCV (SVCVPCD). The PCD monomer consists of two β sheets, an α helix, and another two β sheets. Two PCD monomers pack together through their hydrophobic surfaces to form a dimer. The mutations of residues on the hydrophobic surfaces of PCD disrupt the dimer formation to different degrees and affect the expression of host IFN consistently. Therefore, the oligomeric state formation of the P protein of SVCV is an important mechanism to negatively regulate host IFN response. IMPORTANCE SVCV can cause spring viremia of carp with up to 90% lethality, and it is the homologous virus of the notorious vesicular stomatitis virus (VSV). There are currently no drugs that effectively cure this disease. P proteins of negative-strand RNA viruses (NSVs) play an essential role in many steps during the replication cycle and an additional role in immunosuppression as a cofactor. All P proteins of NSVs are oligomeric, but the studies on the role of this oligomerization mainly focus on the process of virus transcription or replication, and there are few studies on the role of PCD in immunosuppression. Here, we present the crystal structure of SVCVPCD. A new mechanism of immune evasion is clarified by exploring the relationship between SVCVPCD and host IFN response from a structural biology point of view. These findings may provide more accurate target sites for drug design against SVCV and provide new insights into the function of NSVPCD.

scholarly journals Role of Intermolecular Interactions of Vesicular Stomatitis Virus Nucleoprotein in RNA Encapsidation

2007 ◽  
Vol 82 (2) ◽  
pp. 674-682 ◽  
Author(s):  
Xin Zhang ◽  
Todd J. Green ◽  
Jun Tsao ◽  
Shihong Qiu ◽  
Ming Luo
Keyword(s):  
Crystal Structure ◽  
Intermolecular Interactions ◽  
Vesicular Stomatitis Virus ◽  
N Protein ◽  
P Protein ◽  
Intermolecular Contacts ◽  
Vesicular Stomatitis ◽  
Nucleoprotein N ◽  
Stable Ring

ABSTRACT The crystal structure of the vesicular stomatitis virus nucleoprotein (N) in complex with RNA reveals extensive and specific intermolecular interactions among the N molecules in the 10-member oligomer. What roles these interactions play in encapsidating RNA was studied by mutagenesis of the N protein. Three N mutants intended for disruption of the intermolecular interactions were designed and coexpressed with the phosphoprotein (P) in an Escherichia coli system previously described (T. J. Green et al., J. Virol. 74:9515-9524, 2000). Mutants N (Δ1-22), N (Δ347-352), and N (320-324, (Ala)5) lost RNA encapsidation and oligomerization but still bound with P. Another mutant, N (Ser290→Trp), was able to form a stable ring-like N oligomer and bind with the P protein but was no longer able to encapsidate RNA. The crystal structure of N (Ser290→Trp) at 2.8 Å resolution showed that this mutant can maintain all the same intermolecular interactions as the wild-type N except for a slight unwinding of the N-terminal lobe. These results suggest that the intermolecular contacts among the N molecules are required for encapsidation of the viral RNA.

scholarly journals A Role for the Sendai Virus P Protein Trimer in RNA Synthesis

1998 ◽  
Vol 72 (5) ◽  
pp. 4274-4280 ◽  
Author(s):  
Joseph Curran
Keyword(s):  
Amino Acids ◽  
Mammalian Cells ◽  
Essential Role ◽  
Rna Synthesis ◽  
Sendai Virus ◽  
Coiled Coil ◽  
The Third ◽  
P Protein ◽  
P Proteins

ABSTRACT The SeV P protein is found as a homotrimer (P3) when it is expressed in mammalian cells, and trimerization is mediated by a predicted coiled-coil motif which maps within amino acids (aa) 344 to 411 (the BoxA region). The bacterially expressed protein also appears to be trimeric, apparently precluding a role for phosphorylation in the association of the P monomers. I have examined the role of P trimerization both in the protein’s interaction with the nucleocapsid (N:RNA) template and in the protein’s function on the template during RNA synthesis. As with the results of earlier experiments (32), I found that both the BoxA and BoxC (aa 479 to 568) regions were required for stable binding of P to the N:RNA. Binding was also observed with P proteins containing less than three BoxC regions, suggesting that trimerization may be required to permit contacts between multiple BoxC regions and the N:RNA. However, these heterologous trimers failed to function in viral RNA synthesis, indicating that the third C-terminal leg of the trimer plays an essential role in P function on the template. We speculate that this function may involve the movement of P (and possibly the polymerase complex) on the template and the maintenance of processivity.

Structure of a hyperthermostable dimeric archaeal Rubisco fromHyperthermus butylicus

2019 ◽  
Vol 75 (6) ◽  
pp. 536-544
Author(s):  
Rudranuj Bundela ◽  
Jeremy Keown ◽  
Serena Watkin ◽  
Frederick Grant Pearce
Keyword(s):  
Crystal Structure ◽  
Thermal Stability ◽  
Electrostatic Interactions ◽  
Thermal Denaturation ◽  
High Thermal Stability ◽  
Enzyme Function ◽  
Oligomeric State ◽  
Bisphosphate Carboxylase ◽  
Hyperthermophilic Archaeon

The crystal structure of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) from the hyperthermophilic archaeonHyperthermus butylicusis presented at 1.8 Å resolution. Previous structures of archaeal Rubisco have been found to assemble into decamers, and this oligomerization was thought to be required for a highly thermally stable enzyme. In the current study,H. butylicusRubisco is shown to exist as a dimer in solution, yet has a thermal denaturation midpoint of 114°C, suggesting that high thermal stability can be achieved without an increased oligomeric state. This increased thermal stability appears to be due to an increased number of electrostatic interactions within the monomeric subunit. As such,H. butylicusRubisco presents a well characterized system in which to investigate the role of assembly and thermal stability in enzyme function.

scholarly journals Functional characterization of ribosomal P1/P2 proteins in human cells

2008 ◽  
Vol 413 (3) ◽  
pp. 527-534 ◽  
Author(s):  
Francisco Martinez-Azorin ◽  
Miguel Remacha ◽  
Juan P. G. Ballesta
Keyword(s):  
Functional Characterization ◽  
Ribosomal Subunit ◽  
Human Cell Line ◽  
Human Cells ◽  
Translation Efficiency ◽  
Ribosomal Stalk ◽  
P Proteins ◽  
Subunit Joining

The ‘stalk’ is a large ribosomal subunit domain that regulates translation. In the present study the role of the ribosomal stalk P proteins in modulating ribosomal activity has been investigated in human cells using RNA interference. A strong down-regulation of P2 mRNA and a drastic decrease in P2 protein in a stable human cell line was achieved using a doxycycline-inducible system. Interestingly, the amount of P1 protein was similarly decreased in these cells, in contrast with the expression of P1 mRNA. The loss of P1/P2 proteins produced a decrease in the growth rate of these cells, as well as an altered polysome pattern with reduced translation efficiency, but without affecting the free 40 S/60 S subunit ratio. A decrease in the ribosomal-subunit joining capacity was also observed. These data indicate that P1/P2 proteins modulate cytoplasmic translation by influencing the interaction between subunits, thereby regulating the rate of cell proliferation.

The Role of Hydrophobicity in the Stability and pH-Switchability of (RXDX)4 and Coumarin-RXDX Conjugate β-Sheets

2020 ◽  
Author(s):  
Ryan Weber ◽  
Martin McCullagh
Keyword(s):  
Biological Imaging ◽  
Ph Sensing ◽  
Hydrophobic Residue ◽  
Ideal Candidate ◽  
Self Assembling ◽  
Sensing Applications ◽  
Β Sheets ◽  
The Stability ◽  
Dynamics Simulations

<p>pH-switchable, self-assembling materials are of interest in biological imaging and sensing applications. Here we propose that combining the pH-switchability of RXDX (X=Ala, Val, Leu, Ile, Phe) peptides and the optical properties of coumarin creates an ideal candidate for these materials. This suggestion is tested with a thorough set of all-atom molecular dynamics simulations. We first investigate the dependence of pH-switchabiliy on the identity of the hydrophobic residue, X, in the bare (RXDX)<sub>4</sub> systems. Increasing the hydrophobicity stabilizes the fiber which, in turn, reduces the pH-switchabilty of the system. This behavior is found to be somewhat transferable to systems in which a single hydrophobic residue is replaced with a coumarin containing amino acid. In this case, conjugates with X=Ala are found to be unstable and both pHs while conjugates with X=Val, Leu, Ile and Phe are found to form stable β-sheets at least at neutral pH. The (RFDF)<sub>4</sub>-coumarin conjugate is found to have the largest relative entropy value of 0.884 +/- 0.001 between neutral and acidic coumarin ordering distributions. Thus, we posit that coumarin-(RFDF)<sub>4</sub> containing peptide sequences are ideal candidates for pH-sensing bioelectronic materials.</p>

scholarly journals Role of Chemistry and Crystal Structure on the Electronic Defect States in Cs-Based Halide Perovskites

Materials ◽  
2021 ◽  
Vol 14 (4) ◽  
pp. 1032
Author(s):  
Anirban Naskar ◽  
Rabi Khanal ◽  
Samrat Choudhury
Keyword(s):  
Crystal Structure ◽  
Density Functional ◽  
Covalent Bond ◽  
Density Functional Theory Calculations ◽  
Antisite Defect ◽  
Defect States ◽  
Functional Theory ◽  
Electronic Defect ◽  
Constituent Elements

The electronic structure of a series perovskites ABX3 (A = Cs; B = Ca, Sr, and Ba; X = F, Cl, Br, and I) in the presence and absence of antisite defect XB were systematically investigated based on density-functional-theory calculations. Both cubic and orthorhombic perovskites were considered. It was observed that for certain perovskite compositions and crystal structure, presence of antisite point defect leads to the formation of electronic defect state(s) within the band gap. We showed that both the type of electronic defect states and their individual energy level location within the bandgap can be predicted based on easily available intrinsic properties of the constituent elements, such as the bond-dissociation energy of the B–X and X–X bond, the X–X covalent bond length, and the atomic size of halide (X) as well as structural characteristic such as B–X–B bond angle. Overall, this work provides a science-based generic principle to design the electronic states within the band structure in Cs-based perovskites in presence of point defects such as antisite defect.

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