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 …

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 …

Neural relational inference to learn long-range allosteric interactions in proteins from molecular dynamics simulations

J Zhu, J Wang, W Han, D Xu - Nature communications, 2022 - nature.com
Protein allostery is a biological process facilitated by spatially long-range intra-protein
communication, whereby ligand binding or amino acid change at a distant site affects the …

The role of conformational dynamics and allostery in modulating protein evolution

P Campitelli, T Modi, S Kumar… - Annual review of …, 2020 - annualreviews.org
Advances in sequencing techniques and statistical methods have made it possible not only
to predict sequences of ancestral proteins but also to identify thousands of mutations in the …

Hot spots-making directed evolution easier

H Yu, S Ma, Y Li, PA Dalby - Biotechnology Advances, 2022 - Elsevier
Directed evolution has emerged as a powerful strategy to engineer various properties of
proteins. Traditional methods to construct libraries such as error-prone PCR and DNA …

Integrated computational approaches and tools for allosteric drug discovery

O Sheik Amamuddy, W Veldman, C Manyumwa… - International journal of …, 2020 - mdpi.com
Understanding molecular mechanisms underlying the complexity of allosteric regulation in
proteins has attracted considerable attention in drug discovery due to the benefits and …

Using deep learning and molecular dynamics simulations to unravel the regulation mechanism of peptides as noncompetitive inhibitor of xanthine oxidase

Y He, K Liu, F Cao, R Song, J Liu, Y Zhang, W Li… - Scientific Reports, 2024 - nature.com
Xanthine oxidase (XO) is a crucial enzyme in the development of hyperuricemia and gout.
This study focuses on LWM and ALPM, two food-derived inhibitors of XO. We used …

[HTML][HTML] D3Targets-2019-nCoV: a webserver for predicting drug targets and for multi-target and multi-site based virtual screening against COVID-19

Y Shi, X Zhang, K Mu, C Peng, Z Zhu, X Wang… - … Pharmaceutica Sinica B, 2020 - Elsevier
A highly effective medicine is urgently required to cure coronavirus disease 2019 (COVID-
19). For the purpose, we developed a molecular docking based webserver, namely …

Evolution of conformational dynamics determines the conversion of a promiscuous generalist into a specialist enzyme

T Zou, VA Risso, JA Gavira… - Molecular biology …, 2015 - academic.oup.com
β-lactamases are produced by many modern bacteria as a mechanism of resistance toward
β-lactam antibiotics, the most common antibiotics in use. β-lactamases, however, are ancient …

Principles of allosteric interactions in cell signaling

R Nussinov, CJ Tsai, J Liu - Journal of the American Chemical …, 2014 - ACS Publications
Linking cell signaling events to the fundamental physicochemical basis of the
conformational behavior of single molecules and ultimately to cellular function is a key …