Evolutionary dynamics of natural product biosynthesis in bacteria
Covering: 2008 up to 2019 The forces of biochemical adaptive evolution operate at the level
of genes, manifesting in complex phenotypes and the global biodiversity of proteins and …
of genes, manifesting in complex phenotypes and the global biodiversity of proteins and …
A bird's-eye view of enzyme evolution: chemical, physicochemical, and physiological considerations
Enzymes catalyze a vast range of reactions. Their catalytic performances, mechanisms,
global folds, and active-site architectures are also highly diverse, suggesting that enzymes …
global folds, and active-site architectures are also highly diverse, suggesting that enzymes …
Social network analysis methods for exploring SARS-CoV-2 contact tracing data
K Nagarajan, M Muniyandi, B Palani… - BMC medical research …, 2020 - Springer
Background Contact tracing data of severe acute respiratory syndrome coronavirus 2 (SARS-
CoV-2) pandemic is used to estimate basic epidemiological parameters. Contact tracing …
CoV-2) pandemic is used to estimate basic epidemiological parameters. Contact tracing …
[HTML][HTML] Enzyme evolution: innovation is easy, optimization is complicated
Highlights•Enzyme 'promiscuity space'is vast.•Functional innovation by divergent evolution
is easy.•Gene loss is also an important driver of enzyme evolution.•Evolutionary trajectories …
is easy.•Gene loss is also an important driver of enzyme evolution.•Evolutionary trajectories …
The limits of enzyme specificity and the evolution of metabolism
A Peracchi - Trends in biochemical sciences, 2018 - cell.com
The substrate specificity of enzymes is bound to be imperfect, because of unavoidable
physicochemical limits. In extant metabolic enzymes, furthermore, such limits are seldom …
physicochemical limits. In extant metabolic enzymes, furthermore, such limits are seldom …
How enzyme promiscuity and horizontal gene transfer contribute to metabolic innovation
ME Glasner, DP Truong, BC Morse - The FEBS journal, 2020 - Wiley Online Library
Promiscuity is the coincidental ability of an enzyme to catalyze its native reaction and
additional reactions that are not biological functions in the same active site. Promiscuity …
additional reactions that are not biological functions in the same active site. Promiscuity …
The sphingolipid anteome: implications for evolution of the sphingolipid metabolic pathway
Modern cell membranes contain a bewildering complexity of lipids, among them
sphingolipids (SLs). Advances in mass spectrometry have led to the realization that the …
sphingolipids (SLs). Advances in mass spectrometry have led to the realization that the …
Complex Loop Dynamics Underpin Activity, Specificity, and Evolvability in the (βα)8 Barrel Enzymes of Histidine and Tryptophan Biosynthesis
Enzymes are conformationally dynamic, and their dynamical properties play an important
role in regulating their specificity and evolvability. In this context, substantial attention has …
role in regulating their specificity and evolvability. In this context, substantial attention has …
Distal mutations in the β-clamp of DNA polymerase III* disrupt DNA orientation and affect exonuclease activity
MB Berger, GA Cisneros - Journal of the American Chemical …, 2023 - ACS Publications
DNA polymerases are responsible for the replication and repair of DNA found in all DNA-
based organisms. DNA Polymerase III is the main replicative polymerase of E. coli and is …
based organisms. DNA Polymerase III is the main replicative polymerase of E. coli and is …
Rhodococcus comparative genomics reveals a phylogenomic-dependent non-ribosomal peptide synthetase distribution: insights into biosynthetic gene cluster …
Natural products (NPs) are synthesized by biosynthetic gene clusters (BGCs), whose genes
are involved in producing one or a family of chemically related metabolites. Advances in …
are involved in producing one or a family of chemically related metabolites. Advances in …