Analytical methods for structural ensembles and dynamics of intrinsically disordered proteins

M Schor, ASJS Mey, CE MacPhee - Biophysical reviews, 2016 - Springer
Intrinsically disordered proteins, proteins that do not have a well-defined three-dimensional
structure, make up a significant proportion of our proteome and are particularly prevalent in …

Analysis and interpretation of first passage time distributions featuring rare events

EJ Woods, DJ Wales - Physical Chemistry Chemical Physics, 2024 - pubs.rsc.org
In this contribution we consider theory and associated computational tools to treat the
kinetics associated with competing pathways on multifunnel energy landscapes. Multifunnel …

Molecular Insights into Phosphorylation-Induced Allosteric Conformational Changes in a β2-Adrenergic Receptor

MK Madhu, A Debroy, RK Murarka - The Journal of Physical …, 2022 - ACS Publications
The large conformational flexibility of G protein-coupled receptors (GPCRs) has been a
puzzle in structural and pharmacological studies for the past few decades. Apart from …

Structural and Kinetic Characterization of the Intrinsically Disordered Protein SeV NTAIL through Enhanced Sampling Simulations

M Bernetti, M Masetti, F Pietrucci… - The Journal of …, 2017 - ACS Publications
Intrinsically disordered proteins (IDPs) are emerging as an important class of the proteome.
Being able to interact with different molecular targets, they participate in many physiological …

Conformational ensemble of the NSP1 CTD in SARS-CoV-2: Perspectives from the free energy landscape

P Dutta, A Kshirsagar, P Bibekar, N Sengupta - Biophysical Journal, 2023 - cell.com
Abstract The nonstructural protein-1 (NSP1) of the severe acute respiratory syndrome-
associated coronavirus 2 plays a crucial role in the translational shutdown and immune …

Intrinsically disordered landscapes for human CD4 receptor peptide

JA Joseph, DJ Wales - The Journal of Physical Chemistry B, 2018 - ACS Publications
Because of their inherent structural plasticity, intrinsically disordered proteins (IDPs) are
generally difficult to characterize, both experimentally and via simulations. In this work, an …

Molecular Mechanism of Nucleotide-Dependent Allosteric Regulation in AMP-Activated Protein Kinase

N Ahalawat, RK Murarka - The Journal of Physical Chemistry B, 2017 - ACS Publications
The AMP-activated protein kinase (AMPK), a central enzyme in the regulation of energy
homeostasis, is an important drug target for type 2 diabetes, obesity, and cancer. Binding of …

Exploring Kinetics and Drug Residence Time in Biological Systems through Molecular Simulations

M Bernetti - 2018 - amsdottorato.unibo.it
Characterizing thermodynamics and kinetics of molecular systems is the ultimate goal of
biophysics. In drug discovery, this information becomes essential. Understanding local and …