Biology subjects

Anand, G. S.

Publications and source records attributed to Anand, G. S..

3 recordsLinked to original sources

bioRxiv2021

Dengue virus 2 capsid protein chaperones strand displacement without altering the capsid-coding region hairpin element's structural functionality

By virtue of its chaperone activity, the capsid protein of dengue virus strain 2 (DENV2C) promotes nucleic acid structural rearrangements. However, the role of DENV2C during the interaction of RNA elements involved in stabilizing the 5-3 panhandle structure of DENV RNA is still unclear. Therefore, we determined how DENV2C affects structural functionality of the capsid-coding region hairpin element (cHP) during RNA rearrangement of the 9-nt conserved sequence (5CS) to its complementary 3CS counterpart. The cHP element has two distinct functions: a role in translation start codon selection and a role in RNA synthesis. Our results showed that the cHP hairpin impedes annealing between the 5CS and the 3CS elements. Although DENV2C does not modulate structural functionality of the cHP hairpin, it accelerates annealing and specifically promotes strand displacement of 3CS during 5-3 panhandle formation. Furthermore, DENV2C exerts its chaperone activity by favoring one of the active conformations of the cHP element. Based on our results, we propose mechanisms for annealing and strand displacement involving the cHP element. Thus, our results provide mechanistic insights on how DENV2C regulates RNA synthesis by modulating essential RNA elements in the capsid-coding region, that in turn allow for DENV replication.

molecular biology↗

bioRxiv2020

SARS-CoV-2 S protein ACE2 interaction reveals novel allosteric targets

The Spike (S) protein is the main handle for SARS-CoV-2 to enter host cells through surface ACE2 receptors. How ACE2 binding activates proteolysis of S protein is unknown. Here, we have mapped the S:ACE2 interface and uncovered long-range allosteric propagation of ACE2 binding to sites critical for viral host entry. Unexpectedly, ACE2 binding enhances dynamics at a distal S1/S2 cleavage site and flanking protease docking site ~27 [A] away while dampening dynamics of the stalk hinge (central helix and heptad repeat) regions ~ 130 [A] away. This highlights that the stalk and proteolysis sites of the S protein are dynamic hotspots in the pre-fusion state. Our findings provide a mechanistic basis for S:ACE2 complex formation, critical for proteolytic processing and viral-host membrane fusion and highlight protease docking sites flanking the S1/S2 cleavage site, fusion peptide and heptad repeat 1 (HR1) as allosterically exposed cryptic hotspots for potential therapeutic development. One Sentence SummarySARS-CoV-2 spike protein binding to receptor ACE2 allosterically enhances furin proteolysis at distal S1/S2 cleavage sites

biochemistry↗

bioRxiv2020

Dengue virus strain 2 capsid protein switches the annealing pathway and reduces the intrinsic dynamics of the conserved 5' untranslated region

The capsid protein of Dengue Virus strain 2 (DENV2C) is a structural protein with RNA chaperone activity that promotes multiple nucleic acid structural rearrangements, critical for transcription of the single-stranded positive-sense DENV2 genomic RNA. Annealing of the conserved 5 untranslated region (5UTR) to either its complementary sequence or to the 3 untranslated region (3UTR) occurs during (+)/(-) ds-RNA formation and (+) RNA circularization, respectively, both essential steps during DENV RNA replication. We investigated the effect of DENV2C on the annealing mechanism of two hairpin structures from the 5UTR region (21-nt upstream AUG region (5UAR) and 23-nt capsid-coding hairpin (5cHP)) to their complementary sequences during (+)/(-) ds-RNA formation and (+) RNA circularization. Using fluorescence spectroscopy, DENV2C was found to switch annealing reactions nucleated mainly through kissing-loop intermediates to stem-stem interactions during (+)/(-) ds-RNA formation while it promotes annealing mainly through kissing-loop interactions during the (+) RNA circularization. Using FRET-FCS and trFRET, we determined that DENV2C exerts RNA chaperone activities by modulating intrinsic dynamics and by reducing the kinetically trapped unfavorable conformations of the 5UTR sequence. Thus, DENV2C is likely to facilitate genome folding into functional conformations required for replication, playing a role in modulating (+)/(-) ds-RNA formation and (+) RNA circularization.

molecular biology↗