Understanding structure-function relationship in protein families: bioinformatics and molecular modeling provide new concept for enzyme engineeringстатья

Статья опубликована в высокорейтинговом журнале

Информация о цитировании статьи получена из Web of Science
Статья опубликована в журнале из списка Web of Science и/или Scopus
Дата последнего поиска статьи во внешних источниках: 27 мая 2015 г.

Работа с статьей


[1] Suplatov D., Švedas V. Understanding structure-function relationship in protein families: bioinformatics and molecular modeling provide new concept for enzyme engineering // FEBS Journal. — 2013. — Vol. 280, no. 1. — P. 589. Analysis of sequence and structure information in enzyme families provide opportunity to rationalize protein engineering and move away from unguided evolutionary stochastic approaches. Homologous enzymes evolved from a common ancestor to retain a general function but diverged in more specific features and can be divided into subfamilies with different functional properties such as specificity, enantioselectivity, stability, etc. Not all positions can be subjected to mutations as some residues are crucial to maintain structure or function and thus may be constrained in the allowed residue types. Conserved positions can define general properties of the entire family (for example, have direct roles in enzyme catalytic machinery) but they do not explain functional diversity. New method of bioinformatic analysis has been developed [1, 2] to identify subfamily-specific positions (SSPs) – conserved only within protein subfamilies, but different between subfamilies – that seem to play important role in functional discrimination, and used to study how lipase and amidase catalytic activities are implemented into the alpha-beta hydrolase fold. Subfamily-specific positions of α/β-hydrolases with lipase and protease activities were identified and used as hotspots to introduce amidase activity into Candida antarctica lipase B (CALB). Molecular modeling was applied to evaluate influence of selected residues on binding and catalytic conversion of amide substrate by corresponding in silico library of mutants. In silico screening was implemented to select reactive enzyme-substrate complexes that satisfy knowledge-based criteria of amidase catalytic activity. Selected CALB variants were produced and showed significant improvement of experimentally measured amidase activity [3, 4]. Developed method was also applied to study evolution of structure-functional relationship in other enzyme families: Ntn-hydrolases, penicillin-binding proteins, etc. It was shown, that patterns of SSPs can be effectively used to design enzyme mutants with improved functional properties. Based on these results, we suggest that bioinformatic analysis of subfamily-specific positions can be implemented in the laboratory practice to study structure-function relationship and for rational design of advanced biocatalysts. [1] Suplatov, et.al. (2013) J Biomol Struct Dyn, doi:10.1080/07391102.2012.750249. [2] http://biokinet.belozersky.msu.ru/zebra [3] Suplatov, et.al. (2011) Acta naturae, 3(1), 93-98. [4] Suplatov, et.al. (2012) Protein Eng Des Sel, 25(11), 689-697. [ DOI ]

Публикация в формате сохранить в файл сохранить в файл сохранить в файл сохранить в файл сохранить в файл сохранить в файл скрыть