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 …
forms, with about half of those found in the UniProt database being homodimeric …
Emerging computational methods for the rational discovery of allosteric drugs
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 …
and less toxic than those that target orthosteric sites. To date, the discovery of allosteric …
Dynamic architecture of a protein kinase
CL McClendon, AP Kornev… - Proceedings of the …, 2014 - National Acad Sciences
Protein kinases are dynamically regulated signaling proteins that act as switches in the cell
by phosphorylating target proteins. To establish a framework for analyzing linkages between …
by phosphorylating target proteins. To establish a framework for analyzing linkages between …
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 …
allosteric mechanisms for an abundance of targets leading to the establishment of rational …
Crystal cryocooling distorts conformational heterogeneity in a model Michaelis complex of DHFR
Most macromolecular X-ray structures are determined from cryocooled crystals, but it is
unclear whether cryocooling distorts functionally relevant flexibility. Here we compare …
unclear whether cryocooling distorts functionally relevant flexibility. Here we compare …
Dynamics at the serine loop underlie differential affinity of cryptochromes for CLOCK: BMAL1 to control circadian timing
Mammalian circadian rhythms are generated by a transcription-based feedback loop in
which CLOCK: BMAL1 drives transcription of its repressors (PER1/2, CRY1/2), which …
which CLOCK: BMAL1 drives transcription of its repressors (PER1/2, CRY1/2), which …
The atlas for the aspiring network scientist
M Coscia - arXiv preprint arXiv:2101.00863, 2021 - arxiv.org
Network science is the field dedicated to the investigation and analysis of complex systems
via their representations as networks. We normally model such networks as graphs: sets of …
via their representations as networks. We normally model such networks as graphs: sets of …
Cancer-associated arginine-to-histidine mutations confer a gain in pH sensing to mutant proteins
The intracellular pH (pHi) of most cancers is constitutively higher than that of normal cells
and enhances proliferation and cell survival. We found that increased pHi enabled the …
and enhances proliferation and cell survival. We found that increased pHi enabled the …
Enhancing conformation and protonation state sampling of hen egg white lysozyme using pH replica exchange molecular dynamics
JM Swails, AE Roitberg - Journal of chemical theory and …, 2012 - ACS Publications
We evaluate the efficiency of the pH replica exchange molecular dynamics (pH-REMD)
method proposed by Itoh et al.(Proteins 2011, 79, 3420–3436) by using it to predict the p K a …
method proposed by Itoh et al.(Proteins 2011, 79, 3420–3436) by using it to predict the p K a …
Detecting allosteric networks using molecular dynamics simulation
S Bowerman, J Wereszczynski - Methods in enzymology, 2016 - Elsevier
Allosteric networks allow enzymes to transmit information and regulate their catalytic
activities over vast distances. In principle, molecular dynamics (MD) simulations can be used …
activities over vast distances. In principle, molecular dynamics (MD) simulations can be used …