Atomic-level design of metalloenzyme-like active pockets in metal–organic frameworks for bioinspired catalysis

W Xu, Y Wu, W Gu, D Du, Y Lin, C Zhu - Chemical Society Reviews, 2024 - pubs.rsc.org
Natural metalloenzymes with astonishing reaction activity and specificity underpin essential
life transformations. Nevertheless, enzymes only operate under mild conditions to keep …

Protein ensembles: how does nature harness thermodynamic fluctuations for life? The diverse functional roles of conformational ensembles in the cell

G Wei, W Xi, R Nussinov, B Ma - Chemical reviews, 2016 - ACS Publications
All soluble proteins populate conformational ensembles that together constitute the native
state. Their fluctuations in water are intrinsic thermodynamic phenomena, and the …

Automated design of efficient and functionally diverse enzyme repertoires

O Khersonsky, R Lipsh, Z Avizemer, Y Ashani… - Molecular cell, 2018 - cell.com
Substantial improvements in enzyme activity demand multiple mutations at spatially
proximal positions in the active site. Such mutations, however, often exhibit unpredictable …

The role of protein dynamics in the evolution of new enzyme function

E Campbell, M Kaltenbach, GJ Correy, PD Carr… - Nature chemical …, 2016 - nature.com
Enzymes must be ordered to allow the stabilization of transition states by their active sites,
yet dynamic enough to adopt alternative conformations suited to other steps in their catalytic …

Comparing proteins by their internal dynamics: Exploring structure–function relationships beyond static structural alignments

C Micheletti - Physics of life reviews, 2013 - Elsevier
The growing interest for comparing protein internal dynamics owes much to the realisation
that protein function can be accompanied or assisted by structural fluctuations and …

From protein engineering to immobilization: promising strategies for the upgrade of industrial enzymes

RK Singh, MK Tiwari, R Singh, JK Lee - International journal of molecular …, 2013 - mdpi.com
Enzymes found in nature have been exploited in industry due to their inherent catalytic
properties in complex chemical processes under mild experimental and environmental …

Conformational dynamics and enzyme evolution

D Petrović, VA Risso, SCL Kamerlin… - Journal of the …, 2018 - royalsocietypublishing.org
Enzymes are dynamic entities, and their dynamic properties are clearly linked to their
biological function. It follows that dynamics ought to play an essential role in enzyme …

The universality of enzymatic rate–temperature dependency

M Elias, G Wieczorek, S Rosenne, DS Tawfik - Trends in Biochemical …, 2014 - cell.com
Organismal adaptation to extreme temperatures yields enzymes with distinct configurational
stabilities, including thermophilic and psychrophilic enzymes, which are adapted to high and …

Diminishing returns and tradeoffs constrain the laboratory optimization of an enzyme

N Tokuriki, CJ Jackson, L Afriat-Jurnou… - Nature …, 2012 - nature.com
Optimization processes, such as evolution, are constrained by diminishing returns—the
closer the optimum, the smaller the benefit per mutation, and by tradeoffs—improvement of …

Pervasive cooperative mutational effects on multiple catalytic enzyme traits emerge via long-range conformational dynamics

CG Acevedo-Rocha, A Li, L D'Amore… - Nature …, 2021 - nature.com
Multidimensional fitness landscapes provide insights into the molecular basis of laboratory
and natural evolution. To date, such efforts usually focus on limited protein families and a …