Probing the Structure of the Escherichia coli Periplasmic Proteins HdeA and YmgD by Molecular Dynamics Simulations

2016 ◽  
Vol 120 (46) ◽  
pp. 11845-11855 ◽  
Author(s):  
Eileen Socher ◽  
Heinrich Sticht
Keyword(s):  
Escherichia Coli ◽  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Periplasmic Proteins ◽  
Dynamics Simulations

Peptides design based on transmembrane Escherichia coli ’ s OmpA protein through molecular dynamics simulations in water–dodecane interfaces

2016 ◽  
Vol 68 ◽  
pp. 216-223 ◽  
Author(s):  
Sonia M. Aguilera-Segura ◽  
Vanessa Núñez Vélez ◽  
Luke Achenie ◽  
Oscar Álvarez Solano ◽  
Rodrigo Torres ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Ompa Protein ◽  
Dynamics Simulations

scholarly journals A positive, growth-based PAM screen identifies noncanonical motifs recognized by the S. pyogenes Cas9

2020 ◽  
Vol 6 (29) ◽  
pp. eabb4054 ◽  
Author(s):  
D. Collias ◽  
R. T. Leenay ◽  
R. A. Slotkowski ◽  
Z. Zuo ◽  
S. P. Collins ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Molecular Dynamics ◽  
Dna Binding ◽  
Molecular Dynamics Simulations ◽  
Streptococcus Pyogenes ◽  
Human Cells ◽  
Induced Fit ◽  
Positive Growth ◽  
Dynamics Simulations

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.

scholarly journals Nα-Acetylation of the virulence factor EsxA is required for mycobacterial cytosolic translocation and virulence

2020 ◽  
Vol 295 (17) ◽  
pp. 5785-5794 ◽  
Author(s):  
Javier Aguilera ◽  
Chitra B. Karki ◽  
Lin Li ◽  
Salvador Vazquez Reyes ◽  
Igor Estevao ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Molecular Dynamics ◽  
Mycobacterium Tuberculosis ◽  
Molecular Dynamics Simulations ◽  
Virulence Factor ◽  
Low Ph ◽  
Post Translational Modification ◽  
Cytotoxicity Assays ◽  
Host Membrane ◽  
Dynamics Simulations

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.

scholarly journals Data for molecular dynamics simulations of Escherichia coli cytochrome bd oxidase with the Amber force field

Data in Brief ◽  
2021 ◽  
Vol 38 ◽  
pp. 107401
Author(s):  
Surl-Hee Ahn ◽  
Christian Seitz ◽  
Vinícius Wilian D. Cruzeiro ◽  
J. Andrew McCammon ◽  
Andreas W. Götz
Keyword(s):  
Escherichia Coli ◽  
Molecular Dynamics ◽  
Force Field ◽  
Molecular Dynamics Simulations ◽  
Amber Force Field ◽  
Cytochrome Bd ◽  
Dynamics Simulations ◽  
Cytochrome Bd Oxidase

scholarly journals Exploring the conformational transition between the fully folded and locally unfolded substates of Escherichia coli thiol peroxidase

2020 ◽  
Vol 22 (17) ◽  
pp. 9518-9533
Author(s):  
Diego S. Vazquez ◽  
Ari Zeida ◽  
William A. Agudelo ◽  
Mónica R. Montes ◽  
Gerardo Ferrer-Sueta ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Conformational Transition ◽  
Accelerated Molecular Dynamics ◽  
Thiol Peroxidase ◽  
Dynamics Simulations ◽  
Conformational Substate

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

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