scholarly journals Role of N501Y Mutation in SARS-CoV-2 Spike Protein Structure

2021 ◽  
Author(s):  
Urmi Roy
Keyword(s):  
Computer Simulation ◽  
Structural Changes ◽  
Spike Protein ◽  
Wild Type ◽  
Binding Domains ◽  
First Case ◽  
Mutant Variant ◽  
Structural Differences ◽  
Mutant Forms

It has been more than a year since the first case of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was found. This coronavirus has infected more than 110 million people worldwide by the end of February, 2021, and several virulent as well as more spreadable mutant forms of SARS-CoV-2 have emerged subsequently. In the latter group, three variants B.1.1.7, B.1.351, and P1 lineages, have been reported. Using computer simulation, the present paper investigates the structural differences between the wild type SARS-CoV-2 spike protein and its Asn501Tyr (N501Y) mutant variant. Time-based structural changes between the receptor binding domains of these two species are also examined. The N501Y mutation is common to all the three aforesaid mutant variants.

scholarly journals The folate-binding module ofThermus thermophiluscobalamin-dependent methionine synthase displays a distinct variation of the classical TIM barrel: a TIM barrel with a `twist'

2018 ◽  
Vol 74 (1) ◽  
pp. 41-51
Author(s):  
Kazuhiro Yamada ◽  
Markos Koutmos
Keyword(s):  
Tertiary Amine ◽  
Thermus Thermophilus ◽  
Methionine Synthase ◽  
Structural Studies ◽  
Binding Domains ◽  
Methyl Transfer ◽  
Structural Differences ◽  
Tim Barrel ◽  
Eukaryotic Organisms

Methyl transfer between methyltetrahydrofolate and corrinoid molecules is a key reaction in biology that is catalyzed by a number of enzymes in many prokaryotic and eukaryotic organisms. One classic example of such an enzyme is cobalamin-dependent methionine synthase (MS). MS is a large modular protein that utilizes an SN2-type mechanism to catalyze the chemically challenging methyl transfer from the tertiary amine (N5) of methyltetrahydrofolate to homocysteine in order to form methionine. Despite over half a century of study, many questions remain about how folate-dependent methyltransferases, and MS in particular, function. Here, the structure of the folate-binding (Fol) domain of MS fromThermus thermophilusis reported in the presence and absence of methyltetrahydrofolate. It is found that the methyltetrahydrofolate-binding environment is similar to those of previously described methyltransferases, highlighting the conserved role of this domain in binding, and perhaps activating, the methyltetrahydrofolate substrate. These structural studies further reveal a new distinct and uncharacterized topology in the C-terminal region of MS Fol domains. Furthermore, it is found that in contrast to the canonical TIM-barrel β8α8fold found in all other folate-binding domains, MS Fol domains exhibit a unique β8α7fold. It is posited that these structural differences are important for MS function.

scholarly journals Surface-Exposed Adeno-Associated Virus Vp1-NLS Capsid Fusion Protein Rescues Infectivity of Noninfectious Wild-Type Vp2/Vp3 and Vp3-Only Capsids but Not That of Fivefold Pore Mutant Virions

2007 ◽  
Vol 81 (15) ◽  
pp. 7833-7843 ◽  
Author(s):  
Joshua C. Grieger ◽  
Jarrod S. Johnson ◽  
Brittney Gurda-Whitaker ◽  
Mavis Agbandje-McKenna ◽  
R. Jude Samulski
Keyword(s):  
Conformational Changes ◽  
Structural Changes ◽  
Wild Type ◽  
Dot Blot ◽  
Adeno Associated Virus ◽  
N Terminus ◽  
Localization Signal ◽  
Significant Effort

ABSTRACT Over the past 2 decades, significant effort has been dedicated to the development of adeno-associated virus (AAV) as a vector for human gene therapy. However, understanding of the virus with respect to the functional domains of the capsid remains incomplete. In this study, the goal was to further examine the role of the unique Vp1 N terminus, the N terminus plus the recently identified nuclear localization signal (NLS) (J. C. Grieger, S. Snowdy, and R. J. Samulski, J. Virol 80:5199-5210, 2006), and the virion pore at the fivefold axis in infection. We generated two Vp1 fusion proteins (Vp1 and Vp1NLS) linked to the 8-kDa chemokine domain of rat fractalkine (FKN) for the purpose of surface exposure upon assembly of the virion, as previously described (K. H. Warrington, Jr., O. S. Gorbatyuk, J. K. Harrison, S. R. Opie, S. Zolotukhin, and N. Muzyczka, J. Virol 78:6595-6609, 2004). The unique Vp1 N termini were found to be exposed on the surfaces of these capsids and maintained their phospholipase A2 (PLA2) activity, as determined by native dot blot Western and PLA2 assays, respectively. Incorporation of the fusions into AAV type 2 capsids lacking a wild-type Vp1, i.e., Vp2/Vp3 and Vp3 capsid only, increased infectivity by 3- to 5-fold (Vp1FKN) and 10- to 100-fold (Vp1NLSFKN), respectively. However, the surface-exposed fusions did not restore infectivity to AAV virions containing mutations at a conserved leucine (Leu336Ala, Leu336Cys, or Leu336Trp) located at the base of the fivefold pore. EM analyses suggest that Leu336 may play a role in global structural changes to the virion directly impacting downstream conformational changes essential for infectivity and not only have local effects within the pore, as previously suggested.

scholarly journals Fluorescence-Reported Allelic Exchange Mutagenesis-Mediated Gene Deletion Indicates a Requirement for Chlamydia trachomatis Tarp during In Vivo Infectivity and Reveals a Specific Role for the C Terminus during Cellular Invasion

2020 ◽  
Vol 88 (5) ◽  
Author(s):  
Susmita Ghosh ◽  
Elizabeth A. Ruelke ◽  
Joshua C. Ferrell ◽  
Maria D. Bodero ◽  
Kenneth A. Fields ◽  
...  
Keyword(s):  
Chlamydia Trachomatis ◽  
Host Cell ◽  
Host Cells ◽  
Actin Binding ◽  
Wild Type ◽  
Content Type ◽  
Allelic Exchange ◽  
Binding Domains

ABSTRACT The translocated actin recruiting phosphoprotein (Tarp) is a multidomain type III secreted effector used by Chlamydia trachomatis. In aggregate, existing data suggest a role of this effector in initiating new infections. As new genetic tools began to emerge to study chlamydial genes in vivo, we speculated as to what degree Tarp function contributes to Chlamydia’s ability to parasitize mammalian host cells. To address this question, we generated a complete tarP deletion mutant using the fluorescence-reported allelic exchange mutagenesis (FRAEM) technique and complemented the mutant in trans with wild-type tarP or mutant tarP alleles engineered to harbor in-frame domain deletions. We provide evidence for the significant role of Tarp in C. trachomatis invasion of host cells. Complementation studies indicate that the C-terminal filamentous actin (F-actin)-binding domains are responsible for Tarp-mediated invasion efficiency. Wild-type C. trachomatis entry into HeLa cells resulted in host cell shape changes, whereas the tarP mutant did not. Finally, using a novel cis complementation approach, C. trachomatis lacking tarP demonstrated significant attenuation in a murine genital tract infection model. Together, these data provide definitive genetic evidence for the critical role of the Tarp F-actin-binding domains in host cell invasion and for the Tarp effector as a bona fide C. trachomatis virulence factor.

Serving two masters

2013 ◽  
Vol 37 (3) ◽  
pp. 534-565 ◽  
Author(s):  
Hendrik De Smet ◽  
Freek Van de Velde
Keyword(s):  
Word Order ◽  
Contrastive Analysis ◽  
Free Relatives ◽  
Form Function ◽  
First Case ◽  
Structural Differences ◽  
Syntactic Status ◽  
Eventual Outcome

This paper examines two cases of so-called syntactic amalgams. In syntactic amalgams a particular string that is shared by two constructions is exploited to combine them, in such a way that one of the constructions functions as a modifier of the other. Typical examples are after God knows how many years (< after many years + God knows how many years) and a big enough house (< a big house + big enough). In formal theories, these kinds of constructions have been insightfully described as ‘grafts’. However, the exact process through which these amalgams arise remains unexplored. When studied closely, these processes reveal form–function friction not fully accounted for by the graft metaphor. Syntactic amalgams typically serve a subjective function and have been recruited for this purpose. However, because they consist of a syntagm that is still internally parsable, they tend to resist full reanalysis. More precisely, their original syntax continues to constrain their use. As such, amalgams get caught between their original syntax, which remains transparent, and their new function, which suggests a new syntactic status. This appears clearly from contrastive studies of amalgams in Dutch and English that are functionally similar but whose use is constrained in different ways due to structural differences between the two languages. Our first case study deals with the Dutch and English amalgam wie weet / who knows. A contrastive analysis of the development of the respective items shows both the conservative effect of the origin of change and the attraction exerted by the target of change. The second case we discuss in detail involves so-called transparent free relatives. A contrastive analysis shows the role of the overall grammar of a language in licensing change, in this case with Dutch word order posing more difficulties to the new focusing function of transparent free relatives. In general, both case studies show the formation of syntactic amalgams to be sensitive to system pressures both in the course of their development and in the eventual outcome of change.

STUDIES ON THE FLAGELLA OF ALGAE: III. ELECTRON MICROGRAPHS OF CHLAMYDOMONAS MOEWUSII

1953 ◽  
Vol 31 (6) ◽  
pp. 711-717 ◽  
Author(s):  
R. A. Lewin ◽  
Josephine O. Meinhart
Keyword(s):  
Electron Microscopy ◽  
Hollow Cylinder ◽  
Mating Type ◽  
Electron Micrographs ◽  
Structural Changes ◽  
Agglutination Reaction ◽  
Wild Type ◽  
Structural Differences ◽  
Chlamydomonas Moewusii ◽  
Axial Cylinder

Each flagellum of Chlamydomonas moewusii appears to originate at a basal granule beneath the papilla. The intact flagellum is composed of:(a) a central axis, consisting of 9 – 11 dense fibrils, 450 Å wide, fused laterally to form a hollow cylinder;(b) a less dense component, possibly fluid, within the axial cylinder; and(c) a sheath of less dense material, surrounding the axial cylinder, and clearly delimited by a superficial membrane which is believed to be semipermeable. Mating-type specificity seems to reside in this component, since it is involved in the agglutination reaction which precedes copulation.The flagellum terminates in a mucro 0.3 – 0.5 μ long. There is no whiplash filament. Certain structural changes, due to disorganization, disruption, or disintegration of the flagellar components, are described and figured. Possible modes of action of the flagella in cell propulsion are briefly discussed in the light of flagellar structure as revealed by electron microscopy. No structural differences have been observed between the flagella of paralyzed mutants and of wild-type cells.

scholarly journals Structural Insights into GluK3-kainate Receptor Desensitization and Recovery

2019 ◽  
Author(s):  
Jyoti Kumari ◽  
Rajesh Vinnakota ◽  
Janesh Kumar
Keyword(s):  
Structural Changes ◽  
Mutational Analysis ◽  
Receptor Activation ◽  
Kainate Receptors ◽  
Kainate Receptor ◽  
Amino Terminal ◽  
Binding Domains ◽  
Domain Interactions ◽  
Structural Insights

AbstractGluK3-kainate receptors are atypical members of the iGluR family that reside at both the pre- and postsynapse and play key role in regulation of synaptic transmission. For better understanding of structural changes that underlie receptor recovery from desensitized state, GluK3 receptors were trapped in desensitized and resting/closed states and structures analyzed using single particle cryo-electron microscopy. We show that receptor recovery from desensitization requires major rearrangements of the ligand binding domains (LBD) while the amino terminal (ATD) and transmembrane domains remain virtually unaltered. While, the desensitized GluK3 has domain organization as seen earlier for another kainate receptor-GluK2, antagonist bound GluK3 trapped a partially “recovered” state with only two LBD domains in dimeric arrangement necessary for receptor activation. Using these structures as guide, we show that the N-linked glycans at the interface of GluK3 ATD and LBD likely mediate inter-domain interactions and attune receptor-gating properties. Mutational analysis also identifies putative N-glycan interacting residues. These results provide a molecular framework for understanding gating properties unique to GluK3 and identify role of N-linked glycosylation in their modulation.

scholarly journals The Membrane Dynamics of Pexophagy Are Influenced by Sar1p in Pichia pastoris

2008 ◽  
Vol 19 (11) ◽  
pp. 4888-4899 ◽  
Author(s):  
Laura A. Schroder ◽  
Michael V. Ortiz ◽  
William A. Dunn
Keyword(s):  
Pichia Pastoris ◽  
Membrane Dynamics ◽  
Dominant Negative ◽  
Dominant Negative Mutant ◽  
Wild Type ◽  
Guanosine Triphosphate ◽  
Guanosine Diphosphate ◽  
Mutant Forms ◽  
Negative Mutant

Several Sec proteins including a guanosine diphosphate/guanosine triphosphate exchange factor for Sar1p have been implicated in autophagy. In this study, we investigated the role of Sar1p in pexophagy by expressing dominant-negative mutant forms of Sar1p in Pichia pastoris. When expressing sar1pT34N or sar1pH79G, starvation-induced autophagy, glucose-induced micropexophagy, and ethanol-induced macropexophagy are dramatically suppressed. These Sar1p mutants did not affect the initiation or expansion of the sequestering membranes nor the trafficking of Atg11p and Atg9p to these membranes during micropexophagy. However, the lipidation of Atg8p and assembly of the micropexophagic membrane apparatus, which are essential to complete the incorporation of the peroxisomes into the degradative vacuole, were inhibited when either Sar1p mutant protein was expressed. During macropexophagy, the expression of sar1pT34N inhibited the formation of the pexophagosome, whereas sar1pH79G suppressed the delivery of the peroxisome from the pexophagosome to the vacuole. The pexophagosome contained Atg8p in wild-type cells, but in cells expressing sar1pH79G these organelles contain both Atg8p and endoplasmic reticulum components as visualized by DsRFP-HDEL. Our results demonstrate key roles for Sar1p in both micro- and macropexophagy.

scholarly journals Identification of Rhodospirillum rubrum GlnB Variants That Are Altered in Their Ability To Interact with Different Targets in Response to Nitrogen Status Signals

2006 ◽  
Vol 188 (5) ◽  
pp. 1866-1874 ◽  
Author(s):  
Yu Zhu ◽  
Mary C. Conrad ◽  
Yaoping Zhang ◽  
Gary P. Roberts
Keyword(s):  
Hybrid System ◽  
Structural Changes ◽  
Rhodospirillum Rubrum ◽  
Single Copy ◽  
Wild Type ◽  
Yeast Two Hybrid System ◽  
Dinitrogenase Reductase ◽  
Nitrogen Excess ◽  
Two Hybrid

ABSTRACT In Rhodospirillum rubrum, NifA, the transcriptional activator for the nif genes, is posttranslationally activated only by the uridylylated form of GlnB, one of three PII homologs in the organism. We have used the yeast two-hybrid system to detect variants of GlnB that interact better with NifA than does wild-type GlnB. When examined for physiological effects in R. rubrum, these GlnB* variants activated NifA in the presence of NH4 +, which normally blocks NifA activation completely, and in the absence of GlnD, whose uridylylation of GlnB is also normally essential for NifA activation. When these variants were tested in the two-hybrid system for their interaction with NtrB, a receptor that should interact with the nonuridylylated form of GlnB, they were uniformly weaker than wild-type GlnB in that interaction. When expressed in R. rubrum either as single-copy integrants or on multiple-copy plasmids, these variants were also dramatically altered in terms of their ability to regulate several other receptors involved in nitrogen metabolism, including GlnE, NtrB/NtrC, and DRAT (dinitrogenase reductase ADP-ribosyl transferase)-DRAG (dinitrogenase reductase-activating glycohydrolase). The consistent pattern throughout is that these GlnB variants partially mimic the uridylylated form of wild-type GlnB, even under nitrogen-excess conditions and in strains lacking GlnD. The results suggest that the role of uridylylation of GlnB is primarily to shift the equilibrium of GlnB from a “nitrogen-sufficient” form to a “nitrogen-deficient” form, each of which interacts with different but overlapping receptor proteins in the cell. These GlnB variants apparently shift that equilibrium through direct structural changes.

scholarly journals Bioinformatics analysis of SARS-CoV-2 RBD mutant variants and insights into antibody and ACE2 receptor binding

2021 ◽  
Author(s):  
Prashant Ranjan ◽  
Neha   ◽  
Chandra Devi ◽  
Parimal Das
Keyword(s):  
Binding Affinity ◽  
Receptor Binding ◽  
Double Mutant ◽  
Structural Changes ◽  
Protective Efficacy ◽  
Spike Protein ◽  
Wild Type ◽  
Current Vaccine ◽  
New Variant ◽  
The Impact

Prevailing COVID-19 vaccines are based on the spike protein of earlier SARS-CoV-2 strain that emerged in Wuhan, China. Continuously evolving nature of SARS-CoV-2 resulting emergence of new variant/s raise the risk of immune absconds. Several RBD (receptor-binding domain) variants have been reported to affect the vaccine efficacy considerably. In the present study, we performed in silico structural analysis of spike protein of double mutant (L452R & E484Q), a new variant of SARS-CoV-2 recently reported in India along with K417G variants and earlier reported RBD variants and found structural changes in RBD region after comparing with the wild type. Comparison of the binding affinity of the double mutant and earlier reported RBD variant for ACE2 (angiotensin 2 altered enzymes) receptor and CR3022 antibody with the wild-type strain revealed the lowest binding affinity of the double mutant for CR3022 among all other variants. These findings suggest that the newly emerged double mutant could significantly reduce the impact of the current vaccine which threatens the protective efficacy of current vaccine therapy.

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