Marker residue types at the structural regions of transmembrane alpha‐helical and beta‐barrel interfaces

2021 ◽  
Author(s):  
Sercan Beytur
Keyword(s):  
Beta Barrel

Cupin Variants as Macromolecular Ligand Library for Stereoselective Michael Addition of Nitroalkanes

2019 ◽  
Author(s):  
Nobutaka Fujieda ◽  
Miho Yuasa ◽  
Yosuke Nishikawa ◽  
Genji Kurisu ◽  
Shinobu Itoh ◽  
...  
Keyword(s):  
Michael Addition ◽  
In Silico ◽  
Addition Reaction ◽  
Single Point ◽  
Point Mutations ◽  
Unsaturated Ketone ◽  
Michael Addition Reaction ◽  
Beta Barrel ◽  
Cupin Superfamily ◽  
Single Point Mutations

Cupin superfamily proteins (TM1459) work as a macromolecular ligand framework with a double-stranded beta-barrel structure ligating to a Cu ion through histidine side chains. Variegating the first coordination sphere of TM1459 revealed that H52A and H54A/H58A mutants effectively catalyzed the diastereo- and enantio-selective Michael addition reaction of nitroalkanes to an α,β-unsaturated ketone. Moreover, in silico substrate docking signified C106N and F104W single-point mutations, which inverted the diastereoselectivity of H52A and further improved the stereoselectivity of H54A/H58A, respectively.

Designing an Outer Membrane Protein (Omp-W) Based Vaccine for Immunization against Vibrio and Salmonella: An in silico Approach

2020 ◽  
Vol 14 (4) ◽  
pp. 312-324
Author(s):  
Sadra S. Tehrani ◽  
Abolfazl Jahangiri ◽  
Mortaza Taheri-Anganeh ◽  
Hossein Maghsoudi ◽  
Saeed Khalili ◽  
...  
Keyword(s):  
Infectious Disease ◽  
Vibrio Cholerae ◽  
Gram Negative Bacteria ◽  
B Cell Epitopes ◽  
E Coli ◽  
Beta Barrel ◽  
The World ◽  
Cd4 Cell ◽  
Stimulating Factor ◽  
Topology Prediction

Background: Cholera triggered by Vibrio cholerae remains the main reason for morbidity and mortality all over the world. In addition, salmonellosis is regarded as an infectious disease that makes it essential for the identification and detection of Salmonella. With a beta-barrel structure consisting of eight non-parallel beta strands, OmpW family is widely distributed among gram-negative bacteria. Moreover, OmpW isolated from S. typhimurium and Vibrio cholerae can be used in vaccine design. Methods: Topology prediction was determined. T-cell and B-cell epitopes were selected from exposed areas, and sequence conservancy was evaluated. The remaining loops and inaccessible residues were removed to prepare OmpW-1. High antigenicity peptides were detected to replace inappropriate residues to obtain OmpW-2. Physicochemical properties were assessed, and antigenicity, hydrophobicity, flexibility, and accessibility were compared to the native Omp-W structure. Low score areas were removed from the designed structure for preparing the OmpW-3. To construct OmpW-4, TTFrC was used as T-CD4+ cell-stimulating factor and CTB as adjuvant to the end of the C-terminal of this sequence, which can increase the antigenicity and sequence density. The sequences were re-analyzed to delete the unfavorable residues. Besides, the solubility of the mature OmpW and the designed structure were predicted while overexpressed in E. coli. Results: The designed vaccine is a stable protein which has immune cells recognizing epitopes and is considered as an antigen. The construct can be overexpressed in a E. coli. Conclusion: The multi-epitope vaccine is a suitable stimulator for immune system and would be a candidate for experimental research. Recent patents describing numerous inventions related to the clinical facets of vaccine peptide against human infectious disease.

scholarly journals In Silico Analysis of Potential Outer Membrane Beta-Barrel Proteins in Aeromonas hydrophila Pangenome

2021 ◽  
Author(s):  
Furqan Awan ◽  
Muhammad Muddassir Ali ◽  
Yuhao Dong ◽  
Yong Yu ◽  
Zhenling Zeng ◽  
...  
Keyword(s):  
Outer Membrane ◽  
Aeromonas Hydrophila ◽  
In Silico ◽  
In Silico Analysis ◽  
Beta Barrel ◽  
Silico Analysis

scholarly journals Circular dichroism spectroscopy of membrane proteins

2016 ◽  
Vol 45 (18) ◽  
pp. 4859-4872 ◽  
Author(s):  
A. J. Miles ◽  
B. A. Wallace
Keyword(s):  
Circular Dichroism ◽  
Membrane Proteins ◽  
Circular Dichroism Spectroscopy ◽  
Circular Dichroism Spectra ◽  
Helical Bundle ◽  
Beta Barrel ◽  
Circular Dichroïsm

Circular dichroism spectra of helical bundle (red), beta barrel (blue), and mixed helical/sheet/unordered (green) membrane proteins.

Towards a universal method for protein refolding: The trimeric beta barrel membrane Omp2a as a test case

2012 ◽  
Vol 110 (2) ◽  
pp. 417-423 ◽  
Author(s):  
Guillaume Roussel ◽  
Eric A. Perpète ◽  
André Matagne ◽  
Emmanuel Tinti ◽  
Catherine Michaux
Keyword(s):  
Protein Refolding ◽  
Test Case ◽  
Universal Method ◽  
Beta Barrel
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