Bioinformatic Analysis of Protein Families to Select Function-Related Variable Positions

2016 ◽  
pp. 375-410
Keyword(s):  
Bioinformatic Analysis ◽  
Related Variable ◽  
Protein Families ◽  
Select Function

scholarly journals Yosshi: a web-server for disulfide engineering by bioinformatic analysis of diverse protein families

2019 ◽  
Vol 47 (W1) ◽  
pp. W308-W314 ◽  
Author(s):  
Dmitry Suplatov ◽  
Daria Timonina ◽  
Yana Sharapova ◽  
Vytas Švedas
Keyword(s):  
Disulfide Bonds ◽  
Web Server ◽  
Bioinformatic Analysis ◽  
Protein Families ◽  
Sequence Alignments ◽  
Interactive Analysis ◽  
Functionally Diverse ◽  
Available Information ◽  
Related Proteins

Abstract Disulfide bonds play a significant role in protein stability, function or regulation but are poorly conserved among evolutionarily related proteins. The Yosshi can help to understand the role of S–S bonds by comparing sequences and structures of homologs with diverse properties and different disulfide connectivity patterns within a common structural fold of a superfamily, and assist to select the most promising hot-spots to improve stability of proteins/enzymes or modulate their functions by introducing naturally occurring crosslinks. The bioinformatic analysis is supported by the integrated Mustguseal web-server to construct large structure-guided sequence alignments of functionally diverse protein families that can include thousands of proteins based on all available information in public databases. The Yosshi+Mustguseal is a new integrated web-tool for a systematic homology-driven analysis and engineering of S–S bonds that facilitates a broader interpretation of disulfides not just as a factor of structural stability, but rather as a mechanism to implement functional diversity within a superfamily. The results can be downloaded as a content-rich PyMol session file or further studied online using the HTML5-based interactive analysis tools. Both web-servers are free and open to all users at https://biokinet.belozersky.msu.ru/yosshi and there is no login requirement.

Zebra: a web server for bioinformatic analysis of diverse protein families

2013 ◽  
Vol 32 (11) ◽  
pp. 1752-1758 ◽  
Author(s):  
Dmitry Suplatov ◽  
Evgeny Kirilin ◽  
Vakil Takhaveev ◽  
Vytas Švedas
Keyword(s):  
Web Server ◽  
Bioinformatic Analysis ◽  
Protein Families

scholarly journals A unifying mechanism for the biogenesis of prokaryotic membrane proteins co-operatively integrated by the Sec and Tat pathways

2017 ◽  
Author(s):  
Fiona J. Tooke ◽  
Marion Babot ◽  
Govind Chandra ◽  
Grant Buchanan ◽  
Tracy Palmer
Keyword(s):  
Amino Acids ◽  
Membrane Proteins ◽  
Streptomyces Coelicolor ◽  
Bioinformatic Analysis ◽  
Protein Families ◽  
Iron Sulfur Cluster ◽  
Sec Pathway ◽  
Charged Amino Acids ◽  
Loop Region ◽  
Twin Arginine Translocase

AbstractThe vast majority of polytopic membrane proteins are inserted into the cytoplasmic membrane of prokaryotes by the general secretory (Sec) pathway. However, a subset of monotopic proteins that contain non-covalently-bound redox cofactors depend on the twin-arginine translocase (Tat) machinery for membrane integration. Recently actinobacterial Rieske iron-sulfur cluster-containing proteins were identified as an unusual class of membrane proteins that require both the Sec and Tat pathways for the insertion of their three transmembrane domains (TMDs). The Sec pathway inserts the first two TMDs of these proteins co-translationally, but releases the polypeptide prior to the integration of TMD3 to allow folding of the cofactor-containing domain and its translocation by Tat. Here we have investigated features of the Streptomyces coelicolor Rieske polypeptide that modulate its interaction with the Sec and Tat machineries. Mutagenesis of a highly conserved loop region between Sec-dependent TMD2 and Tat-dependent TMD3 shows that it plays no significant role in coordinating the activities of the two translocases, but that a minimum loop length of approximately eight amino acids is required for the Tat machinery to recognise TMD3. Instead we show that a combination of relatively low hydrophobicity of TMD3, coupled with the presence of C-terminal positively-charged amino acids, results in abortive insertion of TMD3 by the Sec pathway and its release at the cytoplasmic side of the membrane. Bioinformatic analysis identified two further families of polytopic membrane proteins that share features of dual Sec-Tat-targeted membrane proteins. A predicted heme-molybdenum cofactor-containing protein with five TMDs, and a polyferredoxin also with five predicted TMDs, are encoded across bacterial and archaeal genomes. We demonstrate that membrane insertion of representatives of each of these newly-identified protein families is dependent on more than one protein translocase, with the Tat machinery recognising TMD5. Importantly, the combination of low hydrophobicity of the final TMD and the presence of multiple C-terminal positive charges that serve as critical Sec-release features for the actinobacterial Rieske protein also dictate Sec release in these further protein families. Therefore we conclude that a simple unifying mechanism governs the assembly of dual targeted membrane proteins.

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