Loop dynamics and the evolution of enzyme activity

M Corbella, GP Pinto, SCL Kamerlin - Nature Reviews Chemistry, 2023 - nature.com
In the early 2000s, Tawfik presented his 'New View'on enzyme evolution, highlighting the
role of conformational plasticity in expanding the functional diversity of limited repertoires of …

New Insights into the Cooperativity and Dynamics of Dimeric Enzymes

KW Chen, TY Sun, YD Wu - Chemical Reviews, 2023 - ACS Publications
A survey of protein databases indicates that the majority of enzymes exist in oligomeric
forms, with about half of those found in the UniProt database being homodimeric …

The Bio3D packages for structural bioinformatics

BJ Grant, L Skjærven, XQ Yao - Protein Science, 2021 - Wiley Online Library
Bio3D is a family of R packages for the analysis of biomolecular sequence, structure, and
dynamics. Major functionality includes biomolecular database searching and retrieval …

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 …

Generalized correlation-based dynamical network analysis: a new high-performance approach for identifying allosteric communications in molecular dynamics …

MCR Melo, RC Bernardi… - The Journal of …, 2020 - pubs.aip.org
Molecular interactions are essential for regulation of cellular processes from the formation of
multi-protein complexes to the allosteric activation of enzymes. Identifying the essential …

Emerging computational methods for the rational discovery of allosteric drugs

JR Wagner, CT Lee, JD Durrant, RD Malmstrom… - Chemical …, 2016 - ACS Publications
Allosteric drug development holds promise for delivering medicines that are more selective
and less toxic than those that target orthosteric sites. To date, the discovery of allosteric …

Harnessing conformational plasticity to generate designer enzymes

RM Crean, JM Gardner… - Journal of the American …, 2020 - ACS Publications
Recent years have witnessed an explosion of interest in understanding the role of
conformational dynamics both in the evolution of new enzymatic activities from existing …

Allostery without a conformational change? Revisiting the paradigm

R Nussinov, CJ Tsai - Current opinion in structural biology, 2015 - Elsevier
Highlights•Classically, allostery induces a functional switch through a conformational
change.•Lately numerous studies concluded that allostery takes place through …

Time evolution of the millisecond allosteric activation of imidazole glycerol phosphate synthase

C Calvó-Tusell, MA Maria-Solano… - Journal of the …, 2022 - ACS Publications
Deciphering the molecular mechanisms of enzymatic allosteric regulation requires the
structural characterization of functional states and also their time evolution toward the …

[HTML][HTML] NMR tools to detect protein allostery

O Gampp, H Kadavath, R Riek - Current Opinion in Structural Biology, 2024 - Elsevier
Allostery is a fundamental mechanism of cellular homeostasis by intra-protein
communication between distinct functional sites. It is an internal process of proteins to steer …