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 …

Phase separation in biology; functional organization of a higher order

DM Mitrea, RW Kriwacki - Cell Communication and Signaling, 2016 - Springer
Inside eukaryotic cells, macromolecules are partitioned into membrane-bounded
compartments and, within these, some are further organized into non-membrane-bounded …

Intrinsically disordered linkers determine the interplay between phase separation and gelation in multivalent proteins

TS Harmon, AS Holehouse, MK Rosen, RV Pappu - elife, 2017 - elifesciences.org
Phase transitions of linear multivalent proteins control the reversible formation of many
intracellular membraneless bodies. Specific non-covalent crosslinks involving …

Tuning the flexibility of glycine-serine linkers to allow rational design of multidomain proteins

M Van Rosmalen, M Krom, M Merkx - Biochemistry, 2017 - ACS Publications
Flexible polypeptide linkers composed of glycine and serine are important components of
engineered multidomain proteins. We have previously shown that the conformational …

Conserved interdomain linker promotes phase separation of the multivalent adaptor protein Nck

S Banjade, Q Wu, A Mittal… - Proceedings of the …, 2015 - National Acad Sciences
The organization of membranes, the cytosol, and the nucleus of eukaryotic cells can be
controlled through phase separation of lipids, proteins, and nucleic acids. Collective …

Cryptic sequence features within the disordered protein p27Kip1 regulate cell cycle signaling

RK Das, Y Huang, AH Phillips… - Proceedings of the …, 2016 - National Acad Sciences
Peptide motifs embedded within intrinsically disordered regions (IDRs) of proteins are often
the sites of posttranslational modifications that control cell-signaling pathways. How do IDR …

Machine learning generation of dynamic protein conformational ensembles

LE Zheng, S Barethiya, E Nordquist, J Chen - Molecules, 2023 - mdpi.com
Machine learning has achieved remarkable success across a broad range of scientific and
engineering disciplines, particularly its use for predicting native protein structures from …

Toward accurate coarse-grained simulations of disordered proteins and their dynamic interactions

Y Zhang, X Liu, J Chen - Journal of chemical information and …, 2022 - ACS Publications
Intrinsically disordered proteins (IDPs) play crucial roles in cellular regulatory networks and
are now recognized to often remain highly dynamic even in specific interactions and …

Sequence-to-conformation relationships of disordered regions tethered to folded domains of proteins

A Mittal, AS Holehouse, MC Cohan… - Journal of molecular …, 2018 - Elsevier
Intrinsically disordered proteins and regions (IDPs/IDRs) are characterized by well-defined
sequence-to-conformation relationships (SCRs). These relationships refer to the sequence …

Targeting intrinsically disordered proteins through dynamic interactions

J Chen, X Liu, J Chen - Biomolecules, 2020 - mdpi.com
Intrinsically disordered proteins (IDPs) are over-represented in major disease pathways and
have attracted significant interest in understanding if and how they may be targeted using …