Structural and dynamics analysis of intrinsically disordered proteins by high-speed atomic force microscopy

N Kodera, D Noshiro, SK Dora, T Mori, J Habchi… - Nature …, 2021 - nature.com
Intrinsically disordered proteins (IDPs) are ubiquitous proteins that are disordered entirely or
partly and play important roles in diverse biological phenomena. Their structure dynamically …

Visualization of intrinsically disordered regions of proteins by high‐speed atomic force microscopy

A Miyagi, Y Tsunaka, T Uchihashi, K Mayanagi… - …, 2008 - Wiley Online Library
Intrinsically disordered (ID) regions of proteins are recognized to be involved in biological
processes such as transcription, translation, and cellular signal transduction. Despite the …

Visualizing single-molecule conformational transition and binding dynamics of intrinsically disordered proteins

W Liu, L Chen, D Yin, Z Yang, J Feng, Q Sun… - Nature …, 2023 - nature.com
Intrinsically disordered proteins (IDPs) play crucial roles in cellular processes and hold
promise as drug targets. However, the dynamic nature of IDPs remains poorly understood …

Full structural ensembles of intrinsically disordered proteins from unbiased molecular dynamics simulations

UR Shrestha, JC Smith, L Petridis - Communications biology, 2021 - nature.com
Molecular dynamics (MD) simulation is widely used to complement ensemble-averaged
experiments of intrinsically disordered proteins (IDPs). However, MD often suffers from …

Residue-specific force field improving the sample of intrinsically disordered proteins and folded proteins

S Yang, H Liu, Y Zhang, H Lu… - Journal of Chemical …, 2019 - ACS Publications
Intrinsically disordered proteins and regions (IDPs and IDRs) have attracted increasing
interest with their abundance in the human proteome and critical roles in various human …

Structural ensembles of intrinsically disordered proteins depend strongly on force field: a comparison to experiment

S Rauscher, V Gapsys, MJ Gajda… - Journal of chemical …, 2015 - ACS Publications
Intrinsically disordered proteins (IDPs) are notoriously challenging to study both
experimentally and computationally. The structure of IDPs cannot be described by a single …

Artificial intelligence techniques for integrative structural biology of intrinsically disordered proteins

A Ramanathan, H Ma, A Parvatikar… - Current Opinion in …, 2021 - Elsevier
Highlights•Recent successes of artificial intelligence (AI) and machine learning (ML)
techniques can be leveraged to obtain quantitative insights into how intrinsically disordered …

From sequence and forces to structure, function, and evolution of intrinsically disordered proteins

JD Forman-Kay, T Mittag - Structure, 2013 - cell.com
Intrinsically disordered proteins (IDPs), which lack persistent structure, are a challenge to
structural biology due to the inapplicability of standard methods for characterization of folded …

Maximum entropy optimized force field for intrinsically disordered proteins

AP Latham, B Zhang - Journal of chemical theory and …, 2019 - ACS Publications
Intrinsically disordered proteins (IDPs) constitute a significant fraction of eukaryotic
proteomes. High-resolution characterization of IDP conformational ensembles can help …

Recent advances in atomic molecular dynamics simulation of intrinsically disordered proteins

W Wang - Physical Chemistry Chemical Physics, 2021 - pubs.rsc.org
Intrinsically disordered proteins (IDPs) play important roles in cellular functions. The inherent
structural heterogeneity of IDPs makes the high-resolution experimental characterization of …