Binding and structural asymmetry governs ligand sensitivity in a cyclic nucleotide–gated ion channel

Ng, Leo C.T.; Zhuang, Meiying; Petegem, Filip Van; Li, Yue Xian; Accili, Eric A.

doi:10.1085/jgp.201812162

“…It could be shown that mutations G660E, R669E and R710E led to an almost complete loss of whole cell fluorescence. This confirmed that these amino acids, supposed to directly interact with the ligand, are essential for binding [ 56 ]. Additionally, three amino acids not supposed to directly interact with the ligand were mutated.…”

Section: Early Career Researcher Presentationssupporting

confidence: 60%

30th Annual GP2A Medicinal Chemistry Conference

O’Boyle

¹

,

Hélesbeux

²

,

Meegan

³

et al. 2023

Pharmaceuticals

0

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“…Intriguingly, it had been suggested by Watson and Crick that small viral genome is more conducive to attaining protein multi-functionality via protein homooligomerization than by direct translation of large protein units (50). It is further noted that conformational symmetry or breakage is harnessed in several biological processes including ligand binding, nonspecific DNA binding, enzyme activation, and signaling (53)(54)(55)(56)(57).…”

Section: Allosteric Induction Of Homooligomeric Asymmetrymentioning

confidence: 99%

Disulfide Reduction Allosterically Destabilizes the β-Ladder Subdomain Assembly within the NS1 Dimer of ZIKV

Roy

¹

,

Roy

²

,

Sengupta

³

2020

Biophysical Journal

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The Zika virus (ZIKV) was responsible for a recent debilitating epidemic that till date has no cure. A potential way to reduce ZIKV virulence is to limit the action of the non-structural proteins involved in its viral replication. One such protein, NS1, encoded as a monomer by the viral genome, plays a major role via symmetric oligomerization. We examine the homodimeric structure of the dominant b-ladder segment of NS1 with extensive all atom molecular dynamics. We find it stably bounded by two spatially separated interaction clusters (C1 and C2) with significant differences in the nature of their interactions. Four pairs of distal, intramonomeric disulfide bonds are found to be coupled to the stability, local structure, and wettability of the interfacial region. Symmetric reduction of the intra-monomeric disulfides triggers marked dynamical heterogeneity, interfacial wettability and asymmetric salt bridging propensity. Harnessing the model-free Lipari-Szabo based formalism for estimation of conformational entropy (S conf ), we find clear signatures of heterogeneity in the monomeric conformational entropies. The observed asymmetry, very small in the unperturbed state, expands significantly in the reduced states. This allosteric effect is most noticeable in the electrostatically bound C2 cluster that underlies the greatest stability in the unperturbed state.Allosteric induction of conformational and thermodynamic asymmetry is expected to affect the pathways leading to symmetric higher ordered oligomerization, and thereby affect crucial replication pathways.

show abstract

“…Intriguingly, it had been suggested by Watson and Crick that small viral genome is more conducive to attaining protein multi-functionality via protein homooligomerization than by direct translation of large protein units (50). It is further noted that conformational symmetry perturbation or breakage is harnessed in several biological processes including ligand binding, nonspecific DNA binding, enzyme activation, and signaling (53)(54)(55)(56)(57).…”

Section: Allosteric Induction Of Homooligomeric Asymmetrymentioning

confidence: 99%

Disulfide reduction allosterically destabilizes the β-ladder sub-domain assembly within the NS1 dimer of ZIKV

Sengupta

¹

,

Roy

²

,

Roy

³

2020

Preprint

0

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The Zika virus (ZIKV) was responsible for a recent debilitating epidemic that till date has no cure. A potential way to reduce ZIKV virulence is to limit the action of the non-structural proteins involved in its viral replication. One such protein, NS1, encoded as a monomer by the viral genome, plays a major role via symmetric oligomerization. We examine the homodimeric structure of the dominant b-ladder segment of NS1 with extensive all atom molecular dynamics. We find it stably bounded by two spatially separated interaction clusters (C1 and C2) with significant differences in the nature of their interactions. Four pairs of distal, intramonomeric disulfide bonds are found to be coupled to the stability, local structure, and wettability of the interfacial region. Symmetric reduction of the intra-monomeric disulfides triggers marked dynamical heterogeneity, interfacial wettability and asymmetric salt bridging propensity. Harnessing the model-free Lipari-Szabo based formalism for estimation of conformational entropy (S conf ), we find clear signatures of heterogeneity in the monomeric conformational entropies. The observed asymmetry, very small in the unperturbed state, expands significantly in the reduced states. This allosteric effect is most noticeable in the electrostatically bound C2 cluster that underlies the greatest stability in the unperturbed state.Allosteric induction of conformational and thermodynamic asymmetry is expected to affect the pathways leading to symmetric higher ordered oligomerization, and thereby affect crucial replication pathways. Statement of significanceControlling viral pathogenesis remains a challenge in the face of modern-day epidemics.Though cumbersome and fraught with misleads, most therapeutic endeavors lean towards the design of drug molecules targeting specific proteins involved in viral pathogenesis. This work demonstrates an alternative approach, namely the usage of allosteric intervention to disrupt the binding integrity of the primary domain of the non-structural NS1 protein dimer crucially important in ZIKV virulence. The intervention, triggered by symmetric reduction of the internal monomeric disulfide bonds, results in weakening and distortion of the distal binding interfaces. It further introduces marked structural and entropic asymmetry within the homooligomeric unit, precluding the formation of higher ordered oligomers of high symmetry.The results have important ramifications for consolidated efforts at limiting ZIKV virulence.Recent mutational and phylogenetic studies indicate that ZIKV spread is facilitated by the non-structural protein NS1, whose mutations can enhance antigenemia and inhibit the interferon beta-induction (14,15). NS1 is a multifunctional, yet highly conserved protein within the flavivirus family (16). Its general roles include immune evasion and invasion, formation of viral replication complex, and interactions with ribosomal subunits. NS1 spontaneously form multimeric structures that are capable of localization in various cellular regions, and for...

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Binding and structural asymmetry governs ligand sensitivity in a cyclic nucleotide–gated ion channel

Cited by 6 publications

References 59 publications

30th Annual GP2A Medicinal Chemistry Conference

30th Annual GP2A Medicinal Chemistry Conference

Disulfide Reduction Allosterically Destabilizes the β-Ladder Subdomain Assembly within the NS1 Dimer of ZIKV

Disulfide reduction allosterically destabilizes the β-ladder sub-domain assembly within the NS1 dimer of ZIKV

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