The dengue virus NS2B–NS3 protease retains the closed conformation in the complex with BPTI

Chen, Wan-Na; Loscha, Karin V.; Nitsche, Christoph; Graham, Bimbil; Otting, Gottfried

doi:10.1016/j.febslet.2014.05.018

Cited by 47 publications

(64 citation statements)

References 43 publications

(77 reference statements)

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“…On the other hand, even in the context of the complex, the NS2B cofactor has much higher structural fluctuations than NS3pro, implying that the bound NS2B cofactor is still capable to sample a large ensemble of conformations. The high flexibility of NS2B uncovered by MD simulations here is completely consistent with the invisibility of many cofactor residues in crystal structures and also provides a dynamic basis for the conformational exchange of NS2B between open and closed conformations as previously observed [8][9][10][11][12].…”

Section: Molecular Dynamics (Md) Simulationssupporting

confidence: 87%

“…Amazingly, unlike other proteases with a chymotrypsin-like fold, the flavivirus proteases including dengue protease, requires a stretch of approximately 40 amino acids from the cytosolic domain of NS2B for catalytic activity, thus called two-component protease [6][7][8]. Intriguingly, while the protease domains adopt highly similar structures in all crystal structures determined to date, the NS2B cofactors have been found to assume two distinctive structures, namely open (inactive) and closed (active) conformations by X-ray crystallography and NMR spectroscopy [7][8][9][10][11][12].…”

Section: Introductionmentioning

confidence: 99%

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NMR and MD Studies Reveal That the Isolated Dengue NS3 Protease Is an Intrinsically Disordered Chymotrypsin Fold Which Absolutely Requests NS2B for Correct Folding and Functional Dynamics

2015

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Dengue genome encodes a two component protease complex (NS2B-NS3pro) essential for the viral maturation/infectivity, thus representing a key drug target. Previously, due to its “complete insolubility”, the isolated NS3pro could not be experimentally studied and it remains elusive what structure it adopts without NS2B and why NS2B is indispensable. Here as facilitated by our previous discovery, the isolated NS3pro has been surprisingly deciphered by NMR to be the first intrinsically-disordered chymotrypsin-like fold, which exists in a loosely-packed state with non-native long-range interactions as revealed by paramagnetic relaxation enhancement (PRE). The disordered NS3pro appears to be needed for binding a human host factor to trigger the membrane remodeling. Moreover, we have in vitro refolded the NS3pro in complex with either NS2B (48–100) or the full-length NS2B (1–130) anchored into the LMPC micelle, and the two complexes have similar activities but different dynamics. We also performed molecular dynamics (MD) simulations and the results revealed that NS2B shows the highest structural fluctuations in the complex, thus providing the dynamic basis for the observation on its conformational exchange between open and closed states. Remarkably, the NS2B cofactor plays a central role in maintaining the correlated motion network required for the catalysis as we previously decoded for the SARS 3CL protease. Indeed, a truncated NS2B (48–100;Δ77–84) with the flexible loop deleted is able to trap the NS2B-NS3pro complex in a highly dynamic and catalytically-impotent state. Taken together, our study implies potential strategies to perturb the NS2B-NS3pro interface for design of inhibitors for treating dengue infection.

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Section: Molecular Dynamics (Md) Simulationssupporting

confidence: 87%

Section: Introductionmentioning

confidence: 99%

NMR and MD Studies Reveal That the Isolated Dengue NS3 Protease Is an Intrinsically Disordered Chymotrypsin Fold Which Absolutely Requests NS2B for Correct Folding and Functional Dynamics

2015

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“…1B). Amazingly, however, the flaviviral proteases appear to adopt two distinctive conformations: the open and the closed states (Erbel et al, 2006;Noble and Shi, 2012;Noble et al, 2012;Lei et al, 2016;Luo et al, 2015;Chen et al, 2014;de la Cruz et al, 2011;Kim et al, 2013;Gibbs et al, 2018;Mahawaththa et al, 2017;Gupta et al, 2015;Pan et al, 2017;Roy et al, 2017). In both states the NS3 protease domains adopting the chymotrypsin fold remain highly similar while the NS2B co-factors assumes diverse conformations (Fig.…”

Section: The Ns2b-ns3 Two-component Proteases Of Dengue and Zika Virusesmentioning

confidence: 99%

Structurally- and dynamically-driven allostery of the chymotrypsin-like proteases of SARS, Dengue and Zika viruses

Lim

Gupta

Roy

et al. 2019

Progress in Biophysics and Molecular Biology

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Coronavirus 3C-like and Flavivirus NS2B-NS3 proteases utilize the chymotrypsin fold to harbor their catalytic machineries but also contain additional domains/co-factors. Over the past decade, we aimed to decipher how the extra domains/co-factors mediate the catalytic machineries of SARS 3C-like, Dengue and Zika NS2B-NS3 proteases by characterizing their folding, structures, dynamics and inhibition with NMR, X-ray crystallography and MD simulations, and the results revealed: 1) the chymotrypsin fold of the SARS 3C-like protease can independently fold, while, by contrast, those of Dengue and Zika proteases lack the intrinsic capacity to fold without co-factors. 2) Mutations on the extra domain of SARS 3C-like protease can transform the active catalytic machinery into the inactive collapsed state by structurally-driven allostery. 3) Amazingly, even without detectable structural changes, mutations on the extra domain are sufficient to either inactivate or enhance the catalytic machinery of SARS 3C-like protease by dynamically-driven allostery. 4) Global networks of correlated motions have been identified: for SARS 3C-like protease, N214A inactivates the catalytic machinery by decoupling the network, while STI/A and STIF/A enhance by altering the patterns of the network. The global networks of Dengue and Zika proteases are coordinated by their NS2B-cofactors. 5) Natural products were identified to allosterically inhibit Zika and Dengue proteases through binding a pocket on the back of the active site. Therefore, by introducing extra domains/cofactors, nature develops diverse strategies to regulate the catalytic machinery embedded on the chymotrypsin fold through folding, structurally- and dynamically-driven allostery, all of which might be exploited to develop antiviral drugs.

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“…The amino-terminal domain of NS3 is a trypsin-like serine protease 59 that interacts with the core hydrophilic region of NS2B and processes the viral polyprotein 60,61 . In the catalytically active 'closed' form, NS2B contributes to the S 2 and S 3 sub-pockets of the binding site [62][63][64][65][66] . The protease was the first ZIKV target whose structure has been solved in complex with a high-affinity inhibitor 67 .…”

Section: Ns3 Protease Inhibitorsmentioning

confidence: 99%

Broad-spectrum agents for flaviviral infections: dengue, Zika and beyond

Boldescu

Behnam

Vasilakis³

et al. 2017

Nat Rev Drug Discov

238

213

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Infections with flaviviruses, such as dengue, West Nile virus, and the recently re-emerging Zika virus are an increasing and probably lasting global risk. This review summarizes and comments on the opportunities for broad-spectrum agents that are active against a range of flaviviruses. Broad-spectrum activity would be particularly desirable as preparatory measure for the next flaviviral epidemic that could emerge from as-yet-unknown or neglected viruses. Potential target sites for broad-spectrum anti-flaviviral compounds include viral proteins and host mechanisms that are exploited by these viruses during entry and replication. A variety of compounds with broad-spectrum antiviral activity have already been identified by target-specific or phenotypic assays. For some other compound classes, broad-spectrum activity can be anticipated because of their mode of action and molecular target(s).

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The dengue virus NS2B–NS3 protease retains the closed conformation in the complex with BPTI

Cited by 47 publications

References 43 publications

NMR and MD Studies Reveal That the Isolated Dengue NS3 Protease Is an Intrinsically Disordered Chymotrypsin Fold Which Absolutely Requests NS2B for Correct Folding and Functional Dynamics

NMR and MD Studies Reveal That the Isolated Dengue NS3 Protease Is an Intrinsically Disordered Chymotrypsin Fold Which Absolutely Requests NS2B for Correct Folding and Functional Dynamics

Structurally- and dynamically-driven allostery of the chymotrypsin-like proteases of SARS, Dengue and Zika viruses

Broad-spectrum agents for flaviviral infections: dengue, Zika and beyond

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