ABSTRACT
Recent computational and bioinformatics advances have enabled the efficient creation of novel biocatalysts by reducing amino acid variability at hot spot regions. To further expand the utility of this strategy, we present here a tool called Multi-site Degenerate Codon Analyzer (MDC-Analyzer) for the automated design of intelligent mutagenesis libraries that can completely cover user-defined randomized sequences, especially when multiple contiguous and/or adjacent sites are targeted. By initially defining an objective function, the possible optimal degenerate PCR primer profiles could be automatically explored using the heuristic approach of Greedy Best-First-Search. Compared to the previously developed DC-Analyzer, MDC-Analyzer allows for the existence of a small amount of undesired sequences as a tradeoff between the number of degenerate primers and the encoded library size while still providing all the benefits of DC-Analyzer with the ability to randomize multiple contiguous sites. MDC-Analyzer was validated using a series of randomly generated mutation schemes and experimental case studies on the evolution of halohydrin dehalogenase, which proved that the MDC methodology is more efficient than other methods and is particularly well-suited to exploring the sequence space of proteins using data-driven protein engineering strategies.
Subject(s)
DNA Primers/genetics , Gene Library , Mutagenesis , Protein Engineering/methods , Proteins/genetics , Amino Acid Sequence , Animals , Base Sequence , Codon , Humans , Protein Engineering/instrumentation , Proteins/chemistryABSTRACT
Described in this paper are concept, characteristics and functions of cloud computing, mobile library and Internet of things and their effect on intelligent, knowledge-based and ubiquitous library service.
ABSTRACT
After a description of the elements in constructing an intelligent library, innovative service, and the role of intelligent librarians, the new ideas the intelligent librarians should have were pointed out with the hormonal development of intelligent library stressed .
ABSTRACT
Unnatural amino acids (UAAs) containing conjugated ring systems are of interest for their optical properties. Until now, such bulky and planar UAAs could not be incorporated into proteins using the pyrrolysyl tRNA/synthetase shuttling system. Using the "small-intelligent" approach to construct a highly diverse library, we evolved novel synthetases specific for two such UAAs and incorporated them into proteins in E. coli and mammalian cells.
