Synthetic biology for the directed evolution of protein biocatalysts: navigating sequence space intelligently

A Currin, N Swainston, PJ Day, DB Kell - Chemical Society Reviews, 2015 - pubs.rsc.org
The amino acid sequence of a protein affects both its structure and its function. Thus, the
ability to modify the sequence, and hence the structure and activity, of individual proteins in …

Bacterial cell‐wall recycling

JW Johnson, JF Fisher… - Annals of the New York …, 2013 - Wiley Online Library
Many Gram‐negative and Gram‐positive bacteria recycle a significant proportion of the
peptidoglycan components of their cell walls during their growth and septation. In many …

Genomic enzymology: web tools for leveraging protein family sequence–function space and genome context to discover novel functions

JA Gerlt - Biochemistry, 2017 - ACS Publications
The exponentially increasing number of protein and nucleic acid sequences provides
opportunities to discover novel enzymes, metabolic pathways, and metabolites/natural …

The structure–function linkage database

E Akiva, S Brown, DE Almonacid… - Nucleic acids …, 2014 - academic.oup.com
Abstract The Structure–Function Linkage Database (SFLD, http://sfld. rbvi. ucsf. edu/) is a
manually curated classification resource describing structure–function relationships for …

Evolutionary and molecular foundations of multiple contemporary functions of the nitroreductase superfamily

E Akiva, JN Copp, N Tokuriki… - Proceedings of the …, 2017 - National Acad Sciences
Insight regarding how diverse enzymatic functions and reactions have evolved from
ancestral scaffolds is fundamental to understanding chemical and evolutionary biology, and …

Discovery and mining of enzymes from the human gut microbiome

B Jia, X Han, KH Kim, CO Jeon - Trends in Biotechnology, 2022 - cell.com
Advances in technological and bioinformatics approaches have led to the generation of a
plethora of human gut metagenomic datasets. Metabolomics has also provided substantial …

Revealing the hidden functional diversity of an enzyme family

K Bastard, AAT Smith, C Vergne-Vaxelaire… - Nature chemical …, 2014 - nature.com
Millions of protein database entries are not assigned reliable functions, preventing the full
understanding of chemical diversity in living organisms. Here, we describe an integrated …

[图书][B] From protein structure to function with bioinformatics

DJ Rigden, DJ Rigden - 2009 - Springer
With the success of an expanding array of genome sequencing projects, the number of
known protein sequences has been increasing exponentially. However, the sequences on …

Revealing unexplored sequence-function space using sequence similarity networks

JN Copp, E Akiva, PC Babbitt, N Tokuriki - Biochemistry, 2018 - ACS Publications
The rapidly expanding number of protein sequences found in public databases can improve
our understanding of how protein functions evolve. However, our current knowledge of …

Evolution of enzyme superfamilies: comprehensive exploration of sequence–function relationships

F Baier, JN Copp, N Tokuriki - Biochemistry, 2016 - ACS Publications
The sequence and functional diversity of enzyme superfamilies have expanded through
billions of years of evolution from a common ancestor. Understanding how protein sequence …