Deciphering the dynamic interaction profile of an intrinsically disordered protein by NMR exchange spectroscopy

E Delaforge, J Kragelj, L Tengo… - Journal of the …, 2018 - ACS Publications
Intrinsically disordered proteins (IDPs) display a large number of interaction modes
including folding-upon-binding, binding without major structural transitions, or binding …

Free-energy landscape of intrinsically disordered proteins investigated by all-atom multicanonical molecular dynamics

J Higo, K Umezawa - Protein Conformational Dynamics, 2014 - Springer
We introduce computational studies on intrinsically disordered proteins (IDPs). Especially,
we present our multicanonical molecular dynamics (McMD) simulations of two IDP-partner …

pH and non-covalent ligand binding modulate Zika virus NS2B/NS3 protease binding site residues: Discoveries from MD and constant pH MD simulations

LH Santos, ER Caffarena… - Journal of Biomolecular …, 2022 - Taylor & Francis
Zika virus (ZIKV) is a global health concern and has been linked to severe neurological
pathologies. Although no medication is available yet, many efforts to develop antivirals and …

Editorial [Hot topic: Structural Disorder in Viral Proteins (Guest Editor: Sonia Longhi)]

S Longhi - Protein and Peptide Letters, 2010 - ingentaconnect.com
The notion that protein function relies on a precise 3D structure constitutes one of the central
paradigms of biochemistry. According to this concept, a protein can perform its biological …

Elucidating the Structural and Dynamical Properties of the Intrinsically Disordered Protein Nrf2 Using Molecular Dynamics Simulations

MN Chang - 2021 - search.proquest.com
The nuclear factor erythroid 2-related factor 2 (Nrf2) protein is a critical transcription factor for
activating the antioxidant response pathway, a primary defense mechanism against …

Coupling supervised molecular dynamics (SuMD) with entropy estimations to shine light on the stability of multiple binding sites

SK Panday, M Sturlese, V Salmaso… - ACS Medicinal …, 2019 - ACS Publications
Exploring at the molecular level, all possible ligand–protein approaching pathways and,
consequently, identifying the energetically favorable binding sites is considered crucial to …

Computational study of conformational changes in nuclear receptors upon ligand binding

A Rashidian - 2023 - tobias-lib.ub.uni-tuebingen.de
The nuclear receptor superfamily (NR), as a major group of intracellular receptors, regulate
broad aspects of cell functions. The activation of these receptors is regulated by …

Elucidating binding mechanisms and dynamics of intrinsically disordered protein complexes using NMR spectroscopy

R Schneider, M Blackledge, MR Jensen - Current opinion in structural …, 2019 - Elsevier
Highlights•Intrinsically disordered proteins (IDPs) employ a variety of binding
mechanisms.•They may form stable folded complex structures or remain highly …

Topology‐based modeling of intrinsically disordered proteins: balancing intrinsic folding and intermolecular interactions

D Ganguly, J Chen - Proteins: Structure, Function, and …, 2011 - Wiley Online Library
Coupled binding and folding is frequently involved in specific recognition of so‐called
intrinsically disordered proteins (IDPs), a newly recognized class of proteins that rely on a …

Impact of Nonnative Interactions on the Binding Kinetics of Intrinsically Disordered p53 with MDM2: Insights from All-Atom Simulation and Markov State Model Analysis

Q Xu, M Yang, J Ji, J Weng, W Wang… - Journal of Chemical …, 2024 - ACS Publications
Intrinsically disordered proteins (IDPs) lack a well-defined tertiary structure but are essential
players in various biological processes. Their ability to undergo a disorder-to-order transition …