Predicting Beta Barrel Transmembrane Proteins Using HMMs

2017 ◽  
pp. 43-61 ◽  
Author(s):  
Georgios N. Tsaousis ◽  
Stavros J. Hamodrakas ◽  
Pantelis G. Bagos
Keyword(s):  
Transmembrane Proteins ◽  
Beta Barrel

scholarly journals 2P311 Amino acid sequence analysis of beta-barrel transmembrane proteins

2005 ◽  
Vol 45 (supplement) ◽  
pp. S197
Author(s):  
A. Ino ◽  
T. Tsuji ◽  
N. Asakawa ◽  
K. Imai ◽  
M. Sonoyama ◽  
...  
Keyword(s):  
Amino Acid ◽  
Sequence Analysis ◽  
Amino Acid Sequence ◽  
Transmembrane Proteins ◽  
Amino Acid Sequence Analysis ◽  
Beta Barrel

scholarly journals The Functional Significance of Hydrophobic Residue Distribution in Bacterial Beta-Barrel Transmembrane Proteins

Membranes ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 580
Author(s):  
Irena Roterman ◽  
Katarzyna Stapor ◽  
Piotr Fabian ◽  
Leszek Konieczny
Keyword(s):  
Membrane Proteins ◽  
Lipid Membrane ◽  
Hydrophobic Interactions ◽  
Transmembrane Proteins ◽  
Soluble Proteins ◽  
Aqueous Environment ◽  
Hydrophobic Core ◽  
Hydrophobic Residues ◽  
Beta Barrel ◽  
Gauss Function

β-barrel membrane proteins have several important biological functions, including transporting water and solutes across the membrane. They are active in the highly hydrophobic environment of the lipid membrane, as opposed to soluble proteins, which function in a more polar, aqueous environment. Globular soluble proteins typically have a hydrophobic core and a polar surface that interacts favorably with water. In the fuzzy oil drop (FOD) model, this distribution is represented by the 3D Gauss function (3DG). In contrast, membrane proteins expose hydrophobic residues on the surface, and, in the case of ion channels, the polar residues face inwards towards a central pore. The distribution of hydrophobic residues in membrane proteins can be characterized by means of 1–3DG, a complementary 3D Gauss function. Such an analysis was carried out on the transmembrane proteins of bacteria, which, despite the considerable similarities of their super-secondary structure (β-barrel), have highly differentiated properties in terms of stabilization based on hydrophobic interactions. The biological activity and substrate specificity of these proteins are determined by the distribution of the polar and nonpolar amino acids. The present analysis allowed us to compare the ways in which the different proteins interact with antibiotics and helped us understand their relative importance in the development of the resistance mechanism. We showed that beta barrel membrane proteins with a hydrophobic core interact less strongly with the molecules they transport.

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 Evidence for an evolutionary relationship between Vmp1 and bacterial DedA proteins

2019 ◽  
Vol 63 (1-2) ◽  
pp. 67-71 ◽  
Author(s):  
Luis-Carlos Tábara ◽  
Olivier Vincent ◽  
Ricardo Escalante
Keyword(s):  
Experimental Approach ◽  
Functional Relationship ◽  
Evolutionary Relationship ◽  
Transmembrane Proteins ◽  
Lipid Homeostasis ◽  
Molecular Function ◽  
Yeast Protein ◽  
Glycine Residue ◽  
Cellular Processes ◽  
Domain Of Unknown Function

VMP1 and DedA proteins are conserved families of transmembrane proteins in eukaryotes and prokaryotes respectively. Despite numerous reports involving these proteins in multiple cellular processes, their molecular function is still unknown. They share the domain of unknown function PF09335, suggesting a possible functional relationship between these protein families. Here we show that VMP1 from different species contain two short motifs conserved in the bacterial DedA proteins and the yeast protein Tvp38. The hallmark of one of these motifs is a glycine residue previously shown to be strictly conserved in all the DedA proteins. Substitution of this residue to leucine, glutamate or arginine in Dictyostelium Vmp1 inactivates the protein, as shown by the inability of the mutants to rescue the phenotypes associated with the lack of Vmp1 including development and lipid homeostasis. This is the first experimental approach that supports an evolutionary relationship between Vmp1 and DedA proteins and highlights the importance of the conserved glycine residue in the PF09335 domain.

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