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Atomistic Molecular Dynamics Simulations of Intrinsically Disordered Proteins

Current Opinion in Structural Biology
Recent years have seen remarkable gains in the accuracy of atomistic molecular dynamics (MD) simulations of intrinsically disordered proteins (IDPs) and expansion in the types of calculated properties that can be directly compared with experimental ...
Fidha Nazreen Kunnath Muhammedkutty, Matthew MacAinsh, Huan-Xiang Zhou   +2 more
semanticscholar   +1 more source

Effects of Sequence Composition, Patterning and Hydrodynamics on the Conformation and Dynamics of Intrinsically Disordered Proteins

International Journal of Molecular Sciences, 2023
Intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) perform diverse functions in cellular organization, transport and signaling.
Andrei Vovk, A. Zilman
semanticscholar   +1 more source

Spontaneous Switching among Conformational Ensembles in Intrinsically Disordered Proteins

Biomolecules, 2019
The common conception of intrinsically disordered proteins (IDPs) is that they stochastically sample all possible configurations driven by thermal fluctuations.
Ucheor B. Choi, Hugo Sanabria, Tatyana Smirnova, Mark E. Bowen, Keith R. Weninger   +4 more
doaj   +1 more source

The roles of intrinsically disordered proteins in neurodegeneration.

Biochimica et Biophysica Acta - General Subjects
Neurodegenerative diseases such as Amyotrophic Lateral Sclerosis, Alzheimer's disease, Parkinson's disease, and Huntington's disease share a common pathological hallmark: the accumulation of misfolded proteins, particularly involving intrinsically ...
K. Utami, Satoru Morimoto, Yasue Mitsukura, Hideyuki Okano   +3 more
semanticscholar   +1 more source

How phosphorylation impacts intrinsically disordered proteins and their function

Essays in Biochemistry, 2022
Phosphorylation is the most common post-translational modification (PTM) in eukaryotes, occurring particularly frequently in intrinsically disordered proteins (IDPs). These proteins are highly flexible and dynamic by nature.
E. Newcombe, Elise Delaforge, R. Hartmann-Petersen, K. Skriver, B. Kragelund   +4 more
semanticscholar   +1 more source

Intrinsically Disordered Proteins (IDPs): Experimental and Computational Approaches in Drug Discovery [PDF]

Drug Designing & Intellectual Properties International Journal, 2018
Intrinsically disordered proteins (IDPs) are proteins that usually do not adopt well-defined native structures when isolated in solution under physiological conditions. Numerous IDPs have close relationships with human diseases such as Parkinson disease, Alzheimer disease, diabetes, and so on.
openaire   +1 more source

Intrinsically disordered proteins: critical components of the wetware

Chemical Reviews, 2022
Despite the wealth of knowledge gained on intrinsically disordered proteins (IDPs) since their discovery, there are several aspects that remain unexplored and hence, poorly understood. A living cell is a complex adaptive system that can be described as a
Prakash Kulkarni, Supriyo Bhattacharya, S. Achuthan, A. Behal, M. Jolly, Sourabh Kotnala, Atish Mohanty, Govindan Rangarajan, Ravi Salgia, V. Uversky   +9 more
semanticscholar   +1 more source

Programming the Optoelectronic Properties of Atomically Precise Gold Nanoclusters Using the Conformational Landscape of Intrinsically Disordered Proteins

Chemistry – A European Journal, EarlyView.
ABSTRACT The rational design of hybrid nanomaterials with precisely controlled properties remains a central challenge in materials science. While atomically precise gold nanoclusters (Au‐NCs) offer molecule‐like control over a metallic core, tuning their optoelectronic behavior via surface engineering is often empirically driven.
Santiago Rodriguez, Sylvain Kumanski, Zeineb Ayed, Aurélie Fournet, Charlène Bouanchaud, Amin Sagar, Frédéric Allemand, Vladimir A. Baulin, Ute Resch‐Genger, Juan Cortés, Nathalie Sibille, Fabien Chirot, Karl David Wegner, Rodolphe Antoine, Xavier Le Guével, Pau Bernadó   +15 more
wiley   +1 more source

IDP-Bert: Predicting Properties of Intrinsically Disordered Proteins Using Large Language Models

The Journal of Physical Chemistry B
22 pages, 5 ...
Parisa Mollaei, Danush Sadasivam, Chakradhar Guntuboina, Amir Barati Farimani   +3 more
openaire   +3 more sources

Impact of Stabilizing Osmolytes on the Conformational Dynamics of Human and Rat Islet Amyloid Polypeptides

Proteins: Structure, Function, and Bioinformatics, EarlyView.
ABSTRACT The aggregation of human islet amyloid polypeptide (hIAPP) into cytotoxic oligomers and amyloid fibrils is a hallmark of type 2 diabetes mellitus (T2DM), leading to pancreatic β‐cell dysfunction. In contrast, rat IAPP (rIAPP) is largely non‐amyloidogenic. Osmolytes such as glucose, glycerol, and sorbitol are known to stabilize globular protein
Kiara A. Kidman, Claudio Pedrick, Cara A. Kreck, Ricardo L. Mancera   +3 more
wiley   +1 more source