Allostery: an overview of its history, concepts, methods, and applications

J Liu, R Nussinov - PLoS computational biology, 2016 - journals.plos.org
The concept of allostery has evolved in the past century. In this Editorial, we briefly overview
the history of allostery, from the pre-allostery nomenclature era starting with the Bohr effect …

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 …

Revealing enzyme functional architecture via high-throughput microfluidic enzyme kinetics

CJ Markin, DA Mokhtari, F Sunden, MJ Appel, E Akiva… - Science, 2021 - science.org
INTRODUCTION Enzymes possess extraordinary catalytic proficiency and specificity. These
properties ultimately derive from interactions not just between the active-site residues and …

Efficient generative modeling of protein sequences using simple autoregressive models

J Trinquier, G Uguzzoni, A Pagnani, F Zamponi… - Nature …, 2021 - nature.com
Generative models emerge as promising candidates for novel sequence-data driven
approaches to protein design, and for the extraction of structural and functional information …

Evolution of dynamical networks enhances catalysis in a designer enzyme

HA Bunzel, JLR Anderson, D Hilvert, VL Arcus… - Nature Chemistry, 2021 - nature.com
Activation heat capacity is emerging as a crucial factor in enzyme thermoadaptation, as
shown by the non-Arrhenius behaviour of many natural enzymes. However, its physical …

Learning the pattern of epistasis linking genotype and phenotype in a protein

FJ Poelwijk, M Socolich, R Ranganathan - Nature communications, 2019 - nature.com
Understanding the pattern of epistasis—the non-independence of mutations—is critical for
relating genotype and phenotype. However, the combinatorial complexity of potential …

Coevolution-based inference of amino acid interactions underlying protein function

VH Salinas, R Ranganathan - Elife, 2018 - elifesciences.org
Protein function arises from a poorly understood pattern of energetic interactions between
amino acid residues. Sequence-based strategies for deducing this pattern have been …

Connecting sequence features within the disordered C-terminal linker of Bacillus subtilis FtsZ to functions and bacterial cell division

MK Shinn, MC Cohan, JL Bullock… - Proceedings of the …, 2022 - National Acad Sciences
Intrinsically disordered regions (IDRs) can function as autoregulators of folded enzymes to
which they are tethered. One example is the bacterial cell division protein FtsZ. This includes …

A hotspot for posttranslational modifications on the androgen receptor dimer interface drives pathology and anti-androgen resistance

A Alegre-Martí, A Jiménez-Panizo… - Science …, 2023 - science.org
Mutations of the androgen receptor (AR) associated with prostate cancer and androgen
insensitivity syndrome may profoundly influence its structure, protein interaction network …

An evolutionary hotspot defines functional differences between CRYPTOCHROMES

C Rosensweig, KA Reynolds, P Gao… - Nature …, 2018 - nature.com
Mammalian circadian clocks are driven by a transcription/translation feedback loop
composed of positive regulators (CLOCK/BMAL1) and repressors (CRYPTOCHROME 1/2 …