Human PCNA structure, function, and interactions

A González-Magaña, FJ Blanco - Biomolecules, 2020 - mdpi.com
Proliferating cell nuclear antigen (PCNA) is an essential factor in DNA replication and repair.
It forms a homotrimeric ring that embraces the DNA and slides along it, anchoring DNA …

Accurate model of liquid–liquid phase behavior of intrinsically disordered proteins from optimization of single-chain properties

G Tesei, TK Schulze, R Crehuet… - Proceedings of the …, 2021 - National Acad Sciences
Many intrinsically disordered proteins (IDPs) may undergo liquid–liquid phase separation
(LLPS) and participate in the formation of membraneless organelles in the cell, thereby …

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 …

Rescaling protein-protein interactions improves Martini 3 for flexible proteins in solution

FE Thomasen, T Skaalum, A Kumar… - Nature …, 2024 - nature.com
Multidomain proteins with flexible linkers and disordered regions play important roles in
many cellular processes, but characterizing their conformational ensembles is difficult. We …

Improved predictions of phase behaviour of intrinsically disordered proteins by tuning the interaction range

G Tesei, K Lindorff-Larsen - Open Research Europe, 2023 - pmc.ncbi.nlm.nih.gov
The formation and viscoelastic properties of condensates of intrinsically disordered proteins
(IDPs) is dictated by amino acid sequence and solution conditions. Because of the …

Towards decoding the sequence-based grammar governing the functions of intrinsically disordered protein regions

S Chong, M Mir - Journal of molecular biology, 2021 - Elsevier
A substantial portion of the proteome consists of intrinsically disordered regions (IDRs) that
do not fold into well-defined 3D structures yet perform numerous biological functions and are …

Improving Martini 3 for disordered and multidomain proteins

FE Thomasen, F Pesce, MA Roesgaard… - Journal of Chemical …, 2022 - ACS Publications
Coarse-grained molecular dynamics simulations are a useful tool to determine
conformational ensembles of proteins. Here, we show that the coarse-grained force field …

A coarse‐grained model for disordered and multi‐domain proteins

F Cao, S von Bülow, G Tesei… - Protein …, 2024 - Wiley Online Library
Many proteins contain more than one folded domain, and such modular multi‐domain
proteins help expand the functional repertoire of proteins. Because of their larger size and …

The PCNA interaction motifs revisited: thinking outside the PIP-box

A Prestel, N Wichmann, JM Martins, R Marabini… - Cellular and Molecular …, 2019 - Springer
Proliferating cell nuclear antigen (PCNA) is a cellular hub in DNA metabolism and a
potential drug target. Its binding partners carry a short linear motif (SLiM) known as the …

Balanced three-point water model OPC3-B for intrinsically disordered and ordered proteins

Z Pan, J Mu, HF Chen - Journal of Chemical Theory and …, 2023 - ACS Publications
Intrinsically disordered proteins (IDPs) play a critical role in many biological processes. Due
to the inherent structural flexibility of IDPs, experimental methods present significant …