Elucidating solution structures of cyclic peptides using molecular dynamics simulations

J Damjanovic, J Miao, H Huang, YS Lin - Chemical reviews, 2021 - ACS Publications
Protein–protein interactions are vital to biological processes, but the shape and size of their
interfaces make them hard to target using small molecules. Cyclic peptides have shown …

Computer simulations of intrinsically disordered proteins

SH Chong, P Chatterjee, S Ham - Annual review of physical …, 2017 - annualreviews.org
The investigation of intrinsically disordered proteins (IDPs) is a new frontier in structural and
molecular biology that requires a new paradigm to connect structural disorder to function …

Routine access to millisecond time scale events with accelerated molecular dynamics

LCT Pierce, R Salomon-Ferrer… - Journal of chemical …, 2012 - ACS Publications
In this work, we critically assess the ability of the all-atom enhanced sampling method
accelerated molecular dynamics (aMD) to investigate conformational changes in proteins …

Dynamical network of residue–residue contacts reveals coupled allosteric effects in recognition, catalysis, and mutation

U Doshi, MJ Holliday… - Proceedings of the …, 2016 - National Acad Sciences
Detailed understanding of how conformational dynamics orchestrates function in allosteric
regulation of recognition and catalysis remains ambiguous. Here, we simulate CypA using …

Cyclosporin A: conformational complexity and chameleonicity

S Ono, MR Naylor, CE Townsend… - Journal of chemical …, 2021 - ACS Publications
The chameleonic behavior of cyclosporin A (CsA) was investigated through conformational
ensembles employing multicanonical molecular dynamics simulations that could sample the …

Integration Of Extracellular And Intracellular Signals Via The Calcium Sensing Receptor (CASR)

C Zhang - 2014 - scholarworks.gsu.edu
Abstract The Ca 2+-sensing receptor (CaSR) regulates the calcium homeostasis in the
human body via sensing fluctuations in the extracellular Ca 2+ concentration. Naturally …

Toward protein NMR at physiological concentrations by hyperpolarized water—Finding and mapping uncharted conformational spaces

LM Epasto, K Che, F Kozak, A Selimovic… - Science …, 2022 - science.org
Nuclear magnetic resonance (NMR) spectroscopy is a key method for determining the
structural dynamics of proteins in their native solution state. However, the low sensitivity of …

The cyclophilin A-binding loop of the capsid regulates the human TRIM5α sensitivity of nonpandemic HIV-1

AP Twizerimana, D Becker, S Zhu… - Proceedings of the …, 2023 - National Acad Sciences
The rather few cases of humans infected by HIV-1 N, O, or P raise the question of their
incomplete adaptation to humans. We hypothesized that early postentry restrictions may be …

On the temperature dependence of enzymatic degradation of poly (ethylene terephthalate)

E Akram, Y Cao, H Xing, Y Ding, Y Luo, R Wei… - Chinese Journal of …, 2024 - Elsevier
Enzymatic recycling of poly (ethylene terephthalate), PET, has attracted significant attention
in recent years. Temperature is a governing factor in the enzymatic degradation of PET …

Dissecting the allosteric fine-tuning of enzyme catalysis

XQ Yao, D Hamelberg - JACS Au, 2024 - ACS Publications
Fully understanding the mechanism of allosteric regulation in biomolecules requires
separating and examining all of the involved factors. In enzyme catalysis, allosteric effector …