Physicochemical mechanisms of protein regulation by phosphorylation

H Nishi, A Shaytan, AR Panchenko - Frontiers in genetics, 2014 - frontiersin.org
Phosphorylation offers a dynamic way to regulate protein activity and subcellular
localization, which is achieved through its reversibility and fast kinetics. Adding or removing …

Growth inhibitory signaling of the Raf/MEK/ERK pathway

PK Wu, A Becker, JI Park - International journal of molecular sciences, 2020 - mdpi.com
In response to extracellular stimuli, the Raf/MEK/extracellular signal-regulated kinase (ERK)
pathway regulates diverse cellular processes. While mainly known as a mitogenic signaling …

Entropy transfer between residue pairs and allostery in proteins: quantifying allosteric communication in ubiquitin

A Hacisuleyman, B Erman - PLoS computational biology, 2017 - journals.plos.org
It has recently been proposed by Gunasakaran et al. that allostery may be an intrinsic
property of all proteins. Here, we develop a computational method that can determine and …

Mutations that confer drug-resistance, oncogenicity and intrinsic activity on the ERK MAP kinases—current state of the art

K Smorodinsky-Atias, N Soudah, D Engelberg - Cells, 2020 - mdpi.com
Unique characteristics distinguish extracellular signal-regulated kinases (Erks) from other
eukaryotic protein kinases (ePKs). Unlike most ePKs, Erks do not autoactivate and they …

Molecular modelling and simulations in cancer research

R Friedman, K Boye, K Flatmark - … et Biophysica Acta (BBA)-Reviews on …, 2013 - Elsevier
The complexity of cancer and the vast amount of experimental data available have made
computer-aided approaches necessary. Biomolecular modelling techniques are becoming …

Activation loop dynamics are controlled by conformation-selective inhibitors of ERK2

LM Pegram, JC Liddle, Y Xiao, M Hoh… - Proceedings of the …, 2019 - National Acad Sciences
Conformational selection by small molecules expands inhibitory possibilities for protein
kinases. Nuclear magnetic resonance (NMR) measurements of the mitogen-activated …

Ancestral reconstruction reveals mechanisms of ERK regulatory evolution

D Sang, S Pinglay, RP Wiewiora, ME Selvan, HJ Lou… - Elife, 2019 - elifesciences.org
Protein kinases are crucial to coordinate cellular decisions and therefore their activities are
strictly regulated. Previously we used ancestral reconstruction to determine how CMGC …

Causality, transfer entropy, and allosteric communication landscapes in proteins with harmonic interactions

A Hacisuleyman, B Erman - Proteins: Structure, Function, and …, 2017 - Wiley Online Library
ABSTRACT A fast and approximate method of generating allosteric communication
landscapes in proteins is presented by using Schreiber's entropy transfer concept in …

Activation loop plasticity and active site coupling in the MAP kinase, ERK2

L Pegram, D Riccardi, N Ahn - Journal of Molecular Biology, 2023 - Elsevier
Previous studies of the protein kinase, ERK2, using NMR and hydrogen-exchange
measurements have shown changes in dynamics accompanying its activation by …

Subsets of slow dynamic modes reveal global information sources as allosteric sites

B Altintel, B Acar, B Erman, T Haliloglu - Journal of Molecular Biology, 2022 - Elsevier
Allostery is a key biological control mechanism, and dynamic information flow provides a
perspective to describe allosteric interactions in causal relationships. Here, as a novel …