Dynamically-Driven Inactivation of the Catalytic Machinery of the SARS 3C-Like Protease by the N214A Mutation on the Extra Domain

Shi, Jiahai; Han, Nanyu; Lim, Liangzhong; Lua, Shixiong; Sivaraman, J.; Wang, Lushan; Mu, Yuguang; Song, Jianxing

doi:10.1371/journal.pcbi.1001084

Cited by 50 publications

(115 citation statements)

References 54 publications

(190 reference statements)

Supporting

Mentioning

105

Contrasting

Order By: Relevance

“…It is well established that helices can be stabilized by local interactions while β-sheets are mostly specified by long-range interactions and their presence is, therefore, highly context-dependent. Consequently, loss of long-range interactions usually leads to the chameleon transformation into helical conformations as exemplified by our previous reports [29], [65], [66].…”

Section: Discussionmentioning

confidence: 65%

“…To unravel the intrinsic dynamics of the EphA5 LBD, three independent, 30 ns molecular dynamics simulations were performed as we previously conducted [14], [25], [29]. Briefly, the simulation cell is a periodic cubic box with a minimum distance of 9 Å between the protein and the box walls to ensure the proteins does not directly interact with its own periodic image.…”

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

Unique Structure and Dynamics of the EphA5 Ligand Binding Domain Mediate Its Binding Specificity as Revealed by X-ray Crystallography, NMR and MD Simulations

et al. 2013

Self Cite

View full text Add to dashboard Cite

The 16 EphA and EphB receptors represent the largest family of receptor tyrosine kinases, and their interactions with 9 ephrin-A and ephrin-B ligands initiate bidirectional signals controlling many physiological and pathological processes. Most interactions occur between receptor and ephrins of the same class, and only EphA4 can bind all A and B ephrins. To understand the structural and dynamic principles that enable Eph receptors to utilize the same jellyroll β-sandwich fold to bind ephrins, the VAPB-MSP domain, peptides and small molecules, we have used crystallography, NMR and molecular dynamics (MD) simulations to determine the first structure and dynamics of the EphA5 ligand-binding domain (LBD), which only binds ephrin-A ligands. Unexpectedly, despite being unbound, the high affinity ephrin-binding pocket of EphA5 resembles that of other Eph receptors bound to ephrins, with a helical conformation over the J–K loop and an open pocket. The openness of the pocket is further supported by NMR hydrogen/deuterium exchange data and MD simulations. Additionally, the EphA5 LBD undergoes significant picosecond-nanosecond conformational exchanges over the loops, as revealed by NMR and MD simulations, but lacks global conformational exchanges on the microsecond-millisecond time scale. This is markedly different from the EphA4 LBD, which shares 74% sequence identity and 87% homology. Consequently, the unbound EphA5 LBD appears to comprise an ensemble of open conformations that have only small variations over the loops and appear ready to bind ephrin-A ligands. These findings show how two proteins with high sequence homology and structural similarity are still able to achieve distinctive binding specificities through different dynamics, which may represent a general mechanism whereby the same protein fold can serve for different functions. Our findings also suggest that a promising strategy to design agonists/antagonists with high affinity and selectivity might be to target specific dynamic states of the Eph receptor LBDs.

show abstract

Section: Discussionmentioning

confidence: 65%

Section: Methodsmentioning

confidence: 99%

Unique Structure and Dynamics of the EphA5 Ligand Binding Domain Mediate Its Binding Specificity as Revealed by X-ray Crystallography, NMR and MD Simulations

et al. 2013

Self Cite

View full text Add to dashboard Cite

show abstract

“…This implies that the protein dynamics may play a key role beyond the static structure, as we recently demonstrated on the SARS 3C-like protease [36]. As such here we utilized the molecular dynamics (MD) simulation to explore the dynamical behavior of the MSP domain as well as the consequence of the T46I mutation.…”

Section: Resultsmentioning

confidence: 99%

“…The T46I mutation on the MSP domain was generated by use of site-directed mutagenesis [36]. The vectors were transformed into E. coli BL21 (DE3) cells (Novagen) for protein expression.…”

Section: Methodsmentioning

confidence: 99%

Structural, Stability, Dynamic and Binding Properties of the ALS-Causing T46I Mutant of the hVAPB MSP Domain as Revealed by NMR and MD Simulations

et al. 2011

Self Cite

View full text Add to dashboard Cite

T46I is the second mutation on the hVAPB MSP domain which was recently identified from non-Brazilian kindred to cause a familial amyotrophic lateral sclerosis (ALS). Here using CD, NMR and molecular dynamics (MD) simulations, we characterized the structure, stability, dynamics and binding capacity of the T46I-MSP domain. The results reveal: 1) unlike P56S which we previously showed to completely eliminate the native MSP structure, T46I leads to no significant disruption of the native secondary and tertiary structures, as evidenced from its far-UV CD spectrum, as well as Cα and Cβ NMR chemical shifts. 2) Nevertheless, T46I does result in a reduced thermodynamic stability and loss of the cooperative urea-unfolding transition. As such, the T46I-MSP domain is more prone to aggregation than WT at high protein concentrations and temperatures in vitro, which may become more severe in the crowded cellular environments. 3) T46I only causes a 3-fold affinity reduction to the Nir2 peptide, but a significant elimination of its binding to EphA4. 4) EphA4 and Nir2 peptide appear to have overlapped binding interfaces on the MSP domain, which strongly implies that two signaling networks may have a functional interplay in vivo. 5) As explored by both H/D exchange and MD simulations, the MSP domain is very dynamic, with most loop residues and many residues on secondary structures highly fluctuated or/and exposed to bulk solvent. Although T46I does not alter overall dynamics, it does trigger increased dynamics of several local regions of the MSP domain which are implicated in binding to EphA4 and Nir2 peptide. Our study provides the structural and dynamic understanding of the T46I-causing ALS; and strongly highlights the possibility that the interplay of two signaling networks mediated by the FFAT-containing proteins and Eph receptors may play a key role in ALS pathogenesis.

show abstract

“…Molecular dynamics (MD) simulation represents a powerful tool to gain insights into roles of protein dynamics in the enzymatic catalysis (28), and we have previously utilized it to study the Dengue NS2B-NS3pro in the "open" form (12), as well as the dynamically-driven allosteric mechanisms of the SARS 3C-like protease, which also shares the chymotrypsin fold to host the catalytic machinery (29,30). Here with the exact same protocols we previously used for the Dengue (12), we conducted MD simulations up to 100 ns for Zika and Dengue NS2B-author/funder.…”

Section: Dynamic Behaviors As Revealed By MD Simulations-low Solubilimentioning

confidence: 99%

Unique properties of Zika NS2B-NS3pro complexes as decoded by experiments and MD simulations

Roy

Lim

Srivastava

et al. 2016

Preprint

Self Cite

View full text Add to dashboard Cite

first two authors contribute equally. ABSTRACTZika virus can be passed from a pregnant woman to her fetus, thus leading to birth defects including more than microcephaly. It has been recently estimated that one-third of the world population will be infected by Zika, but unfortunately no vaccine or medicine is available so far. Zika NS2B-NS3pro is essential for its replication and thus represents an attractive target for drug discovery/design. Here we characterized conformation, catalysis, inhibition and dynamics of linked and unlinkedZika NS2B-NS3pro complexes by both experiments and MD simulations. The results unveil the unique properties of Zika NS2B-NS3pro which are very different from Dengue one. Particularly, CD and NMR studies indicate that unlike Dengue, the C-terminal region of Zika NS2B with a significant sequence variation is highly disordered in the open conformation. Indeed, MD simulations reveal that up to 100 ns, the Dengue NS2B C-terminus constantly has close contacts with its NS3pro domain. By a sharp contrast, the Zika NS2B C-terminus loses the contacts with its NS3pro domain after 10 ns, further forming a short β-sheet characteristic of the closed conformation at 30 ns. Furthermore, we found that a small molecule, previously identified as an active site inhibitor for other flaviviral NS2B-NS3pro, inhibited Zika NS2B-NS3pro potently in an allosteric manner. Our study provides the first insight into the dynamics of Zika NS2B-NS3pro and further deciphers that it is susceptible to allosteric inhibition, which thus bears critical implications for the future development of therapeutic allosteric inhibitors.author/funder. All rights reserved. No reuse allowed without permission.

show abstract

Dynamically-Driven Inactivation of the Catalytic Machinery of the SARS 3C-Like Protease by the N214A Mutation on the Extra Domain

Cited by 50 publications

References 54 publications

Unique Structure and Dynamics of the EphA5 Ligand Binding Domain Mediate Its Binding Specificity as Revealed by X-ray Crystallography, NMR and MD Simulations

Unique Structure and Dynamics of the EphA5 Ligand Binding Domain Mediate Its Binding Specificity as Revealed by X-ray Crystallography, NMR and MD Simulations

Structural, Stability, Dynamic and Binding Properties of the ALS-Causing T46I Mutant of the hVAPB MSP Domain as Revealed by NMR and MD Simulations

Unique properties of Zika NS2B-NS3pro complexes as decoded by experiments and MD simulations

Contact Info

Product

Resources

About