From system modeling to system analysis: The impact of resolution level and resolution distribution in the computer-aided investigation of biomolecules

M Giulini, M Rigoli, G Mattiotti, R Menichetti… - Frontiers in Molecular …, 2021 - frontiersin.org
The ever increasing computer power, together with the improved accuracy of atomistic force
fields, enables researchers to investigate biological systems at the molecular level with …

Disorder-to-order transition of the amyloid-β peptide upon lipid binding

H Fatafta, B Kav, BF Bundschuh, J Loschwitz… - Biophysical …, 2022 - Elsevier
There is mounting evidence that Alzheimer's disease progression and severity are linked to
neuronal membrane damage caused by aggregates of the amyloid-β (A β) peptide …

Spontaneous switching among conformational ensembles in intrinsically disordered proteins

UB Choi, H Sanabria, T Smirnova, ME Bowen… - Biomolecules, 2019 - mdpi.com
The common conception of intrinsically disordered proteins (IDPs) is that they stochastically
sample all possible configurations driven by thermal fluctuations. This is certainly true for …

Intrinsically disordered proteins in chronic diseases

P Kulkarni, VN Uversky - Biomolecules, 2019 - mdpi.com
It is now increasingly evident that a large fraction of the human proteome comprises proteins
that, under physiological conditions, lack fixed, ordered 3D structures as a whole or have …

Exploring energy landscapes of intrinsically disordered proteins: Insights into functional mechanisms

AB Oliveira Junior, X Lin, P Kulkarni… - Journal of Chemical …, 2021 - ACS Publications
Intrinsically disordered proteins (IDPs) lack a rigid three-dimensional structure and populate
a polymorphic ensemble of conformations. Because of the lack of a reference conformation …

Intrinsically disordered proteins and conformational noise: The hypothesis a decade later

P Kulkarni, R Salgia, G Rangarajan - Iscience, 2023 - cell.com
Phenotypic plasticity is the ability of individual genotypes to produce different phenotypes in
response to environmental perturbations. We previously postulated how conformational …

Illuminating intrinsically disordered proteins with integrative structural biology

R Evans, S Ramisetty, P Kulkarni, K Weninger - Biomolecules, 2023 - mdpi.com
Intense study of intrinsically disordered proteins (IDPs) did not begin in earnest until the late
1990s when a few groups, working independently, convinced the community that these …

Specific conformational dynamics and expansion underpin a multi-step mechanism for specific binding of p27 with Cdk2/Cyclin A

M Tsytlonok, K Hemmen, G Hamilton, N Kolimi… - Journal of molecular …, 2020 - Elsevier
The protein p27, a prominent regulatory protein in eukaryotes and an intrinsically disordered
protein (IDP), regulates cell division by causing cell cycle arrest when bound in ternary …

Protein structure–function continuum model: Emerging nexuses between specificity, evolution, and structure

MN Gupta, VN Uversky - Protein Science, 2024 - Wiley Online Library
The rationale for replacing the old binary of structure–function with the trinity of structure,
disorder, and function has gained considerable ground in recent years. A continuum model …

Molecular simulations of IDPs: From ensemble generation to IDP interactions leading to disorder-to-order transitions

H Fatafta, S Samantray, A Sayyed-Ahmad… - Progress in molecular …, 2021 - Elsevier
Intrinsically disordered proteins (IDPs) lack a well-defined three-dimensional structure but
do exhibit some dynamical and structural ordering. The structural plasticity of IDPs indicates …