Protein allostery and conformational dynamics

J Guo, HX Zhou - Chemical reviews, 2016 - ACS Publications
The functions of many proteins are regulated through allostery, whereby effector binding at a
distal site changes the functional activity (eg, substrate binding affinity or catalytic efficiency) …

Principles and overview of sampling methods for modeling macromolecular structure and dynamics

T Maximova, R Moffatt, B Ma, R Nussinov… - PLoS computational …, 2016 - journals.plos.org
Investigation of macromolecular structure and dynamics is fundamental to understanding
how macromolecules carry out their functions in the cell. Significant advances have been …

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 …

Precision medicine and driver mutations: computational methods, functional assays and conformational principles for interpreting cancer drivers

R Nussinov, H Jang, CJ Tsai… - PLoS computational …, 2019 - journals.plos.org
At the root of the so-called precision medicine or precision oncology, which is our focus
here, is the hypothesis that cancer treatment would be considerably better if therapies were …

Discovery of multiple hidden allosteric sites by combining Markov state models and experiments

GR Bowman, ER Bolin, KM Hart… - Proceedings of the …, 2015 - National Acad Sciences
The discovery of drug-like molecules that bind pockets in proteins that are not present in
crystallographic structures yet exert allosteric control over activity has generated great …

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 …

Rational design of allosteric modulators: Challenges and successes

A Chatzigoulas, Z Cournia - Wiley Interdisciplinary Reviews …, 2021 - Wiley Online Library
Recent advances in structural biology and computational techniques have revealed
allosteric mechanisms for an abundance of targets leading to the establishment of rational …

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 …

[HTML][HTML] Allostery: allosteric cancer drivers and innovative allosteric drugs

R Nussinov, M Zhang, R Maloney, Y Liu, CJ Tsai… - Journal of molecular …, 2022 - Elsevier
Here, we discuss the principles of allosteric activating mutations, propagation downstream of
the signals that they prompt, and allosteric drugs, with examples from the Ras signaling …

webPSN v2. 0: a webserver to infer fingerprints of structural communication in biomacromolecules

A Felline, M Seeber, F Fanelli - Nucleic acids research, 2020 - academic.oup.com
Abstract A mixed Protein Structure Network (PSN) and Elastic Network Model-Normal Mode
Analysis (ENM-NMA)-based strategy (ie PSN-ENM) was developed to investigate structural …