Novel mutant of Escherichia coli asparaginase II to reduction of the glutaminase activity in treatment of acute lymphocytic leukemia by molecular dynamics simulations and QM-MM studies

2018 ◽  
Vol 112 ◽  
pp. 7-17 ◽  
Author(s):  
Noeman Ardalan ◽  
Sako Mirzaie ◽  
Abbas Akhavan Sepahi ◽  
Ramazan Ali Khavari-Nejad
2016 ◽  
Vol 68 ◽  
pp. 216-223 ◽  
Author(s):  
Sonia M. Aguilera-Segura ◽  
Vanessa Núñez Vélez ◽  
Luke Achenie ◽  
Oscar Álvarez Solano ◽  
Rodrigo Torres ◽  
...  

2020 ◽  
Vol 6 (29) ◽  
pp. eabb4054 ◽  
Author(s):  
D. Collias ◽  
R. T. Leenay ◽  
R. A. Slotkowski ◽  
Z. Zuo ◽  
S. P. Collins ◽  
...  

CRISPR technologies have overwhelmingly relied on the Streptococcus pyogenes Cas9 (SpyCas9), with its consensus NGG and less preferred NAG and NGA protospacer-adjacent motifs (PAMs). Here, we report that SpyCas9 also recognizes sequences within an N(A/C/T)GG motif. These sequences were identified on the basis of preferential enrichment in a growth-based screen in Escherichia coli. DNA binding, cleavage, and editing assays in bacteria and human cells validated recognition, with activities paralleling those for NAG(A/C/T) PAMs and dependent on the first two PAM positions. Molecular-dynamics simulations and plasmid-clearance assays with mismatch-intolerant variants supported induced-fit recognition of an extended PAM by SpyCas9 rather than recognition of NGG with a bulged R-loop. Last, the editing location for SpyCas9-derived base editors could be shifted by one nucleotide by selecting between (C/T)GG and adjacent N(C/T)GG PAMs. SpyCas9 and its enhanced variants thus recognize a larger repertoire of PAMs, with implications for precise editing, off-target predictions, and CRISPR-based immunity.


2020 ◽  
Vol 295 (17) ◽  
pp. 5785-5794 ◽  
Author(s):  
Javier Aguilera ◽  
Chitra B. Karki ◽  
Lin Li ◽  
Salvador Vazquez Reyes ◽  
Igor Estevao ◽  
...  

The Mycobacterium tuberculosis virulence factor EsxA and its chaperone EsxB are secreted as a heterodimer (EsxA:B) and are crucial for mycobacterial escape from phagosomes and cytosolic translocation. Current findings support the idea that for EsxA to interact with host membranes, EsxA must dissociate from EsxB at low pH. However, the molecular mechanism by which the EsxA:B heterodimer separates is not clear. In the present study, using liposome-leakage and cytotoxicity assays, LC-MS/MS–based proteomics, and CCF-4 FRET analysis, we obtained evidence that the Nα-acetylation of the Thr-2 residue on EsxA, a post-translational modification that is present in mycobacteria but absent in Escherichia coli, is required for the EsxA:B separation. Substitutions at Thr-2 that precluded Nα-acetylation inhibited the heterodimer separation and hence prevented EsxA from interacting with the host membrane, resulting in attenuated mycobacterial cytosolic translocation and virulence. Molecular dynamics simulations revealed that at low pH, the Nα-acetylated Thr-2 makes direct and frequent “bind-and-release” contacts with EsxB, which generates a force that pulls EsxB away from EsxA. In summary, our findings provide evidence that the Nα-acetylation at Thr-2 of EsxA facilitates dissociation of the EsxA:B heterodimer required for EsxA membrane permeabilization and mycobacterial cytosolic translocation and virulence.


2020 ◽  
Vol 22 (17) ◽  
pp. 9518-9533
Author(s):  
Diego S. Vazquez ◽  
Ari Zeida ◽  
William A. Agudelo ◽  
Mónica R. Montes ◽  
Gerardo Ferrer-Sueta ◽  
...  

Temporal acquisition of the fully folded conformational substate of the Escherichia coli thiol peroxidase by accelerated molecular dynamics simulations.


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