Mechanisms of protein evolution

V Jayaraman, S Toledo‐Patiño, L Noda‐García… - Protein …, 2022 - Wiley Online Library
How do proteins evolve? How do changes in sequence mediate changes in protein
structure, and in turn in function? This question has multiple angles, ranging from …

Metabolite–enzyme coevolution: from single enzymes to metabolic pathways and networks

L Noda-Garcia, W Liebermeister… - Annual Review of …, 2018 - annualreviews.org
How individual enzymes evolved is relatively well understood. However, individual enzymes
rarely confer a physiological advantage on their own. Judging by its current state, the …

A bird's-eye view of enzyme evolution: chemical, physicochemical, and physiological considerations

D Davidi, LM Longo, J Jabłońska, R Milo… - Chemical …, 2018 - ACS Publications
Enzymes catalyze a vast range of reactions. Their catalytic performances, mechanisms,
global folds, and active-site architectures are also highly diverse, suggesting that enzymes …

[HTML][HTML] Enzyme evolution: innovation is easy, optimization is complicated

MS Newton, VL Arcus, ML Gerth, WM Patrick - Current Opinion in Structural …, 2018 - Elsevier
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 …

Biotechnological and protein-engineering implications of ancestral protein resurrection

VA Risso, JM Sanchez-Ruiz, SB Ozkan - Current opinion in structural …, 2018 - Elsevier
Highlights•Ancestral environments likely differed from the environments hosting modern
proteins.•Resurrected ancestral protein often display unusual properties and …

Quantifying and understanding the fitness effects of protein mutations: Laboratory versus nature

JI Boucher, DNA Bolon, DS Tawfik - Protein Science, 2016 - Wiley Online Library
The last decade has seen a growing number of experiments aimed at systematically
map** the effects of mutations in different proteins, and of attempting to correlate their …

Crystal structure of 4, 6-α-glucanotransferase supports diet-driven evolution of GH70 enzymes from α-amylases in oral bacteria

Y Bai, J Gangoiti, BW Dijkstra, L Dijkhuizen, T Pijning - Structure, 2017 - cell.com
Food processing and refining has dramatically changed the human diet, but little is known
about whether this affected the evolution of enzymes in human microbiota. We present …

[HTML][HTML] Upper ocean oxygenation, evolution of RuBisCO and the Phanerozoic succession of phytoplankton

REM Rickaby, MRE Hubbard - Free Radical Biology and Medicine, 2019 - Elsevier
Evidence is compiled to demonstrate a redox scale within Earth's photosynthesisers that
correlates the specificity of their RuBisCO with organismal metabolic tolerance to anoxia …

Harnessing underground metabolism for pathway development

J Rosenberg, FM Commichau - Trends in biotechnology, 2019 - cell.com
Fermentative production of valuable substances is an economically competitive and
ecologically sustainable alternative to chemical synthesis, but it is often hampered by …

Frustration can limit the adaptation of promiscuous enzymes through gene duplication and specialisation

M Schmutzer, P Dasmeh, A Wagner - Journal of Molecular Evolution, 2024 - Springer
Virtually all enzymes catalyse more than one reaction, a phenomenon known as enzyme
promiscuity. It is unclear whether promiscuous enzymes are more often generalists that …