Relating sequence encoded information to form and function of intrinsically disordered proteins

RK Das, KM Ruff, RV Pappu - Current opinion in structural biology, 2015 - Elsevier
Highlights•Compositions of IDPs fall into distinct classes.•Compositional classes encode
preferences for distinct conformational classes.•Functions of disordered proteins are …

Exploring free-energy landscapes of intrinsically disordered proteins at atomic resolution using NMR spectroscopy

MR Jensen, M Zweckstetter, J Huang… - Chemical …, 2014 - ACS Publications
The last 15 years have seen a paradigm shift in our understanding of protein biochemistry,
with the realization that an unexpectedly high fraction of the human genome codes for …

Developing a molecular dynamics force field for both folded and disordered protein states

P Robustelli, S Piana, DE Shaw - Proceedings of the …, 2018 - National Acad Sciences
Molecular dynamics (MD) simulation is a valuable tool for characterizing the structural
dynamics of folded proteins and should be similarly applicable to disordered proteins and …

Water dispersion interactions strongly influence simulated structural properties of disordered protein states

S Piana, AG Donchev, P Robustelli… - The journal of physical …, 2015 - ACS Publications
Many proteins can be partially or completely disordered under physiological conditions.
Structural characterization of these disordered states using experimental methods can be …

PED in 2021: a major update of the protein ensemble database for intrinsically disordered proteins

T Lazar, E Martínez-Pérez, F Quaglia… - Nucleic acids …, 2021 - academic.oup.com
Abstract The Protein Ensemble Database (PED)(https://proteinensemble. org), which holds
structural ensembles of intrinsically disordered proteins (IDPs), has been significantly …

Targeting the disordered C terminus of PTP1B with an allosteric inhibitor

N Krishnan, D Koveal, DH Miller, B Xue… - Nature chemical …, 2014 - nature.com
PTP1B, a validated therapeutic target for diabetes and obesity, has a critical positive role in
HER2 signaling in breast tumorigenesis. Efforts to develop therapeutic inhibitors of PTP1B …

Principles and overview of sampling methods for modeling macromolecular structure and dynamics

T Maximova, R Moffatt, B Ma, R Nussinov… - PLoS computational …, 2016 - journals.plos.org
Investigation of macromolecular structure and dynamics is fundamental to understanding
how macromolecules carry out their functions in the cell. Significant advances have been …

Conformational ensembles of intrinsically disordered proteins and flexible multidomain proteins

FE Thomasen, K Lindorff-Larsen - Biochemical Society …, 2022 - portlandpress.com
Intrinsically disordered proteins (IDPs) and multidomain proteins with flexible linkers show a
high level of structural heterogeneity and are best described by ensembles consisting of …

Liquid–liquid phase separation is driven by large-scale conformational unwinding and fluctuations of intrinsically disordered protein molecules

A Majumdar, P Dogra, S Maity… - The Journal of Physical …, 2019 - ACS Publications
Liquid–liquid phase separation occurs via a multitude of transient, noncovalent, and
intermolecular interactions resulting in phase transition of intrinsically disordered …

Describing intrinsically disordered proteins at atomic resolution by NMR

MR Jensen, RWH Ruigrok, M Blackledge - Current opinion in structural …, 2013 - Elsevier
There is growing interest in the development of physical methods to study the
conformational behaviour and biological activity of intrinsically disordered proteins (IDPs). In …