pH-dependent polymorphism of the structure of SARS-CoV-2 nsp7

AbstractThe solution structure of SARS-CoV-2 nonstructural protein 7 (nsp7) at pH 7.0 has been determined by NMR spectroscopy. nsp7 is conserved in the coronavirinae subfamily and is an essential co-factor of the viral RNA-dependent RNA polymerase for active and processive replication. Similar to the previously deposited structures of SARS-CoV-1 nsp7 at acidic and basic conditions, SARS-CoV-2 nsp7 has a helical bundle folding at neutral pH. Remarkably, the α4 helix shows gradual dislocation from the core α2-α3 structure as pH increases from 6.5 to 7.5. The protonation state of residue H36 contributes to the change of nsp7’s intramolecular interactions, and thus, to the structural variation near-neutral pH. Spin-relaxation results revealed that all three loop regions in nsp7 possess dynamic properties associated with this structural variation.

Download Full-text

Interfacial dynamic properties of whey protein concentrate/polysaccharide mixtures at neutral pH

Food Hydrocolloids ◽

10.1016/j.foodhyd.2008.08.013 ◽

2009 ◽

Vol 23 (5) ◽

pp. 1253-1262 ◽

Cited By ~ 68

Author(s):

Adrián A. Perez ◽

Carlos R. Carrara ◽

Cecilio Carrera Sánchez ◽

Liliana G. Santiago ◽

Juan M. Rodríguez Patino

Keyword(s):

Whey Protein ◽

Dynamic Properties ◽

Whey Protein Concentrate ◽

Protein Concentrate ◽

Neutral Ph

Download Full-text

The Single Disulfide-Directed β-Hairpin Fold: Role of Disulfide Bond in Folding and Effect of an Additional Disulfide Bond on Stability

Australian Journal of Chemistry ◽

10.1071/ch19386 ◽

2020 ◽

Vol 73 (4) ◽

pp. 312

Author(s):

Balasubramanyam Chittoor ◽

Bankala Krishnarjuna ◽

Rodrigo A. V. Morales ◽

Raymond S. Norton

Keyword(s):

Disulfide Bond ◽

Disulfide Bonds ◽

Solution Structure ◽

Conformational Stability ◽

Disulfide Bridge ◽

Solution Nmr ◽

Peptide Epitope ◽

The Core ◽

Native Fold

Disulfide bonds play a key role in the oxidative folding, conformational stability, and functional activity of many peptides. A few disulfide-rich peptides with privileged architecture such as the inhibitor cystine knot motif have garnered attention as templates in drug design. The single disulfide-directed β-hairpin (SDH), a novel fold identified more recently in contryphan-Vc1, has been shown to possess remarkable thermal, conformational, and chemical stability and can accept a short bioactive epitope without compromising the core structure of the peptide. In this study, we demonstrated that the single disulfide bond is critical in maintaining the native fold by replacing both cysteine residues with serine. We also designed an analogue with an additional, non-native disulfide bridge by replacing Gln1 and Tyr9 with Cys. Contryphan-Vc11–22[Q1C, Y9C] was synthesised utilising orthogonal cysteine protection and its solution structure determined using solution NMR spectroscopy. This analogue maintained the overall fold of native contryphan-Vc1. Previous studies had shown that the β-hairpin core of contryphan-Vc1 was resistant to proteolysis by trypsin and α-chymotrypsin but susceptible to cleavage by pepsin. Contryphan-Vc11–22[Q1C, Y9C] proved to be completely resistant to pepsin, thus confirming our design strategy. These results highlight the role of the disulfide bond in maintaining the SDH fold and provide a basis for the design of more stable analogues for peptide epitope grafting.

Download Full-text

The three-dimensional solution structure and dynamic properties of the human FADD death domain 1 1Edited by A. Fersht

Journal of Molecular Biology ◽

10.1006/jmbi.2000.4011 ◽

2000 ◽

Vol 302 (1) ◽

pp. 171-188 ◽

Cited By ~ 74

Author(s):

Helena Berglund ◽

Dionne Olerenshaw ◽

Andrew Sankar ◽

Matthias Federwisch ◽

Neil Q McDonald ◽

...

Keyword(s):

Solution Structure ◽

Dynamic Properties ◽

Three Dimensional ◽

Death Domain ◽

Dimensional Solution

Download Full-text

Study on the Dynamic Mechanical Properties of Viscoelastic Materials Based on Asymmetrical Sandwich Beams

Applied Sciences ◽

10.3390/app8081359 ◽

2018 ◽

Vol 8 (8) ◽

pp. 1359 ◽

Cited By ~ 1

Author(s):

Qingqing Wu ◽

Minqing Wang

Keyword(s):

Mechanical Properties ◽

Dynamic Properties ◽

Estimation Method ◽

Dynamic Mechanical Properties ◽

Test Method ◽

Core Material ◽

Beam Specimen ◽

Viscoelastic Materials ◽

Dynamic Mechanical ◽

The Core

A modified estimation method for the dynamic mechanical properties of viscoelastic materials via asymmetrical sandwich specimens is presented. In contrast to the traditional vibrating cantilever beam test method (VCBTM), the proposed method allows asymmetrical base beams in sandwich specimens. Based on the complex stiffness method, complex parameters are introduced for general sandwich configurations. Calculation formulas for loss factor and shear modulus of the core material are presented. The effectiveness of this approach is validated numerically and experimentally by analysis of one symmetrical sandwich beam specimen and two specimens with asymmetrical thicknesses and materials. It is shown that dynamic mechanical parameters of the core material can be obtained regardless of sandwiches’ symmetry. The proposed method breaks the symmetrical criteria for sandwich specimens and may provide a wider application to measure viscoelastic materials’ dynamic properties.

Download Full-text

Structural Variation among Retroviral Primer−DNA Junctions: Solution Structure of the HIV-1 (−)-Strand Okazaki Fragment r(gcca)d(CTGC)·d(GCAGTGGC)†,‡

Biochemistry ◽

10.1021/bi9607822 ◽

1996 ◽

Vol 35 (34) ◽

pp. 11070-11080 ◽

Cited By ~ 16

Author(s):

Oleg Yu. Fedoroff ◽

Miguel Salazar ◽

Brian R. Reid

Keyword(s):

Solution Structure ◽

Structural Variation ◽

Okazaki Fragment ◽

Dna Junctions ◽

Hiv 1

Download Full-text

De novo design of a transmembrane Zn2+-transporting four-helix bundle

Science ◽

10.1126/science.1261172 ◽

2014 ◽

Vol 346 (6216) ◽

pp. 1520-1524 ◽

Cited By ~ 183

Author(s):

Nathan H. Joh ◽

Tuo Wang ◽

Manasi P. Bhate ◽

Rudresh Acharya ◽

Yibing Wu ◽

...

Keyword(s):

Membrane Proteins ◽

Metal Binding ◽

De Novo ◽

Dynamic Properties ◽

Transition Metal Ions ◽

Grand Challenge ◽

Conduction Path ◽

Helical Bundle ◽

X Ray Crystallography ◽

Membrane Spanning

The design of functional membrane proteins from first principles represents a grand challenge in chemistry and structural biology. Here, we report the design of a membrane-spanning, four-helical bundle that transports first-row transition metal ions Zn2+ and Co2+, but not Ca2+, across membranes. The conduction path was designed to contain two di-metal binding sites that bind with negative cooperativity. X-ray crystallography and solid-state and solution nuclear magnetic resonance indicate that the overall helical bundle is formed from two tightly interacting pairs of helices, which form individual domains that interact weakly along a more dynamic interface. Vesicle flux experiments show that as Zn2+ ions diffuse down their concentration gradients, protons are antiported. These experiments illustrate the feasibility of designing membrane proteins with predefined structural and dynamic properties.

Download Full-text

The C Terminus of the Core β-Ladder Domain in Japanese Encephalitis Virus Nonstructural Protein 1 Is Flexible for Accommodation of Heterologous Epitope Fusion

Journal of Virology ◽

10.1128/jvi.02057-15 ◽

2015 ◽

Vol 90 (3) ◽

pp. 1178-1189 ◽

Cited By ~ 2

Author(s):

Li-Chen Yen ◽

Jia-Teh Liao ◽

Hwei-Jen Lee ◽

Wei-Yuan Chou ◽

Chun-Wei Chen ◽

...

Keyword(s):

Japanese Encephalitis Virus ◽

Virus Replication ◽

Japanese Encephalitis ◽

Protective Immunity ◽

Nonstructural Protein ◽

Encephalitis Virus ◽

The Core ◽

Nonstructural Protein 1 ◽

C Terminus ◽

Infected Cells

ABSTRACTNS1 is the only nonstructural protein that enters the lumen of the endoplasmic reticulum (ER), where NS1 is glycosylated, forms a dimer, and is subsequently secreted during flavivirus replication as dimers or hexamers, which appear to be highly immunogenic to the infected host, as protective immunity can be elicited against homologous flavivirus infections. Here, by using atrans-complementation assay, we identified the C-terminal end of NS1 derived from Japanese encephalitis virus (JEV), which was more flexible than other regions in terms of housing foreign epitopes without a significant impact on virus replication. This mapped flexible region is located in the conserved tip of the core β-ladder domain of the multimeric NS1 structure and is also known to contain certain linear epitopes, readily triggering specific antibody responses from the host. Despite becoming attenuated, recombinant JEV with insertion of a neutralizing epitope derived from enterovirus 71 (EV71) into the C-terminal end of NS1 not only could be normally released from infected cells, but also induced dual protective immunity for the host to counteract lethal challenge with either JEV or EV71 in neonatal mice. These results indicated that the secreted multimeric NS1 of flaviviruses may serve as a natural protein carrier to render epitopes of interest more immunogenic in the C terminus of the core β-ladder domain.IMPORTANCEThe positive-sense RNA genomes of mosquito-borne flaviviruses appear to be flexible in terms of accommodating extra insertions of short heterologous antigens into their virus genes. Here, we illustrate that the newly identified C terminus of the core β-ladder domain in NS1 could be readily inserted into entities such as EV71 epitopes, and the resulting NS1-epitope fusion proteins appeared to maintain normal virus replication, secretion ability, and multimeric formation from infected cells. Nonetheless, such an insertion attenuated the recombinant JEV in mice, despite having retained the brain replication ability observed in wild-type JEV. Mother dams immunized with recombinant JEV expressing EV71 epitope-NS1 fused proteins elicited neutralizing antibodies that protected the newborn mice against lethal EV71 challenge. Together, our results implied a potential application of JEV NS1 as a viral carrier protein to express a heterologous epitope to stimulate dual/multiple protective immunity concurrently against several pathogens.

Download Full-text

NMR structure note: solution structure of the core domain of MESD that is essential for proper folding of LRP5/6

Journal of Biomolecular NMR ◽

10.1007/s10858-010-9426-8 ◽

2010 ◽

Vol 47 (4) ◽

pp. 283-288 ◽

Cited By ~ 4

Author(s):

Jianglei Chen ◽

Qianqian Li ◽

Chia-Chen Liu ◽

Bei Zhou ◽

Guojun Bu ◽

...

Keyword(s):

Solution Structure ◽

Nmr Structure ◽

Core Domain ◽

The Core

Download Full-text

Reovirus Nonstructural Protein μNS Recruits Viral Core Surface Proteins and Entering Core Particles to Factory-Like Inclusions

Journal of Virology ◽

10.1128/jvi.78.4.1882-1892.2004 ◽

2004 ◽

Vol 78 (4) ◽

pp. 1882-1892 ◽

Cited By ~ 71

Author(s):

Teresa J. Broering ◽

Jonghwa Kim ◽

Cathy L. Miller ◽

Caroline D. S. Piggott ◽

Jason B. Dinoso ◽

...

Keyword(s):

Rna Binding ◽

Core Protein ◽

Nonstructural Protein ◽

Viral Proteins ◽

Surface Proteins ◽

Core Surface ◽

Viral Core ◽

The Core ◽

Infected Cells ◽

Core Particles

ABSTRACT Mammalian reoviruses are thought to assemble and replicate within cytoplasmic, nonmembranous structures called viral factories. The viral nonstructural protein μNS forms factory-like globular inclusions when expressed in the absence of other viral proteins and binds to the surfaces of the viral core particles in vitro. Given these previous observations, we hypothesized that one or more of the core surface proteins may be recruited to viral factories through specific associations with μNS. We found that all three of these proteins—λ1, λ2, and σ2—localized to factories in infected cells but were diffusely distributed through the cytoplasm and nucleus when each was separately expressed in the absence of other viral proteins. When separately coexpressed with μNS, on the other hand, each core surface protein colocalized with μNS in globular inclusions, supporting the initial hypothesis. We also found that λ1, λ2, and σ2 each localized to filamentous inclusions formed upon the coexpression of μNS and μ2, a structurally minor core protein that associates with microtubules. The first 40 residues of μNS, which are required for association with μ2 and the RNA-binding nonstructural protein σNS, were not required for association with any of the three core surface proteins. When coexpressed with μ2 in the absence of μNS, each of the core surface proteins was diffusely distributed and displayed only sporadic, weak associations with μ2 on filaments. Many of the core particles that entered the cytoplasm of cycloheximide-treated cells following entry and partial uncoating were recruited to inclusions of μNS that had been preformed in those cells, providing evidence that μNS can bind to the surfaces of cores in vivo. These findings expand a model for how viral and cellular components are recruited to the viral factories in infected cells and provide further evidence for the central but distinct roles of viral proteins μNS and μ2 in this process.

Download Full-text