Short linear motifs in colorectal cancer interactome and tumorigenesis

C Fasano, V Grossi, G Forte, C Simone - Cells, 2022 - mdpi.com
Colorectal tumorigenesis is driven by alterations in genes and proteins responsible for
cancer initiation, progression, and invasion. This multistage process is based on a dense …

How do disordered regions achieve comparable functions to structured domains?

NS Latysheva, T Flock, RJ Weatheritt… - Protein …, 2015 - Wiley Online Library
The traditional structure to function paradigm conceives of a protein's function as emerging
from its structure. In recent years, it has been established that unstructured, intrinsically …

Human VAPome analysis reveals MOSPD1 and MOSPD3 as membrane contact site proteins interacting with FFAT-related FFNT motifs

B Cabukusta, I Berlin, DM van Elsland, I Forkink… - Cell Reports, 2020 - cell.com
Membrane contact sites (MCS) are intracellular regions where two organelles come closer
to exchange information and material. The majority of the endoplasmic reticulum (ER) MCS …

Systematic prediction of FFAT motifs across eukaryote proteomes identifies nucleolar and eisosome proteins with the predicted capacity to form bridges to the …

JA Slee, TP Levine - Contact, 2019 - journals.sagepub.com
The endoplasmic reticulum (ER), the most pervasive organelle, exchanges information and
material with many other organelles, but the extent of its interorganelle connections and the …

Hammock: a hidden Markov model-based peptide clustering algorithm to identify protein-interaction consensus motifs in large datasets

A Krejci, TR Hupp, M Lexa, B Vojtesek, P Muller - Bioinformatics, 2016 - academic.oup.com
Motivation: Proteins often recognize their interaction partners on the basis of short linear
motifs located in disordered regions on proteins' surface. Experimental techniques that study …

Structural prediction of protein interactions and docking using conservation and coevolution

J Andreani, C Quignot, R Guerois - Wiley Interdisciplinary …, 2020 - Wiley Online Library
Abstract Knowledge of the detailed structure of macromolecular interactions is key to a better
understanding and modulation of essential cellular functions and pathological situations …

LMPID: A manually curated database of linear motifs mediating protein–protein interactions

D Sarkar, T Jana, S Saha - Database, 2015 - academic.oup.com
Linear motifs (LMs), used by a subset of all protein–protein interactions (PPIs), bind to
globular receptors or domains and play an important role in signaling networks. LMPID …

Controllability of protein-protein interaction phosphorylation-based networks: Participation of the hub 14-3-3 protein family

M Uhart, G Flores, DM Bustos - Scientific Reports, 2016 - nature.com
Posttranslational regulation of protein function is an ubiquitous mechanism in eukaryotic
cells. Here, we analyzed biological properties of nodes and edges of a human protein …

Thousands of protein linear motif classes may still be undiscovered

D Bulavka, AA Aptekmann, NA Méndez, T Krick… - Plos one, 2021 - journals.plos.org
Linear motifs are short protein subsequences that mediate protein interactions. Hundreds of
motif classes including thousands of motif instances are known. Our theory estimates how …

K-shell analysis reveals distinct functional parts in an electron transfer network and its implications for extracellular electron transfer

D Ding, L Li, C Shu, X Sun - Frontiers in microbiology, 2016 - frontiersin.org
Shewanella oneidensis MR-1 is capable of extracellular electron transfer (EET) and hence
has attracted considerable attention. The EET pathways mainly consist of c-type …