In this review, we discuss the structural and functional diversity of protein-protein interactions (PPIs) based primarily on protein families for which three-dimensional structural data are available. PPIs play diverse roles in biology and differ based on the composition, affinity and whether the association is permanent or transient. In vivo, the protomer's localization, concentration and local environment can affect the interaction between protomers and are vital to control the composition and oligomeric state of protein complexes. Since a change in quaternary state is often coupled with biological function or activity, transient PPIs are important biological regulators. Structural characteristics of different types of PPIs are discussed and related to their physiological function, specificity and evolution.
Download full-text PDF |
Source |
|---|---|
| http://www.ncbi.nlm.nih.gov/pmc/articles/PMC165629 | PMC |
| http://dx.doi.org/10.1093/emboj/cdg359 | DOI Listing |
Publication Analysis
Top Keywords
Similar Publications
Decoding Plant-Pathogen Interactions: A Comprehensive Exploration of Effector-Plant Transcription Factor Dynamics.
Mol Plant Pathol
January 2025
Faculty of Bioscience Engineering, Ghent University, Gent, Belgium.
In the coevolutionary process between plant pathogens and hosts, pathogen effectors, primarily proteinaceous, engage in interactions with host proteins, such as plant transcription factors (TFs), during the infection process. This review delves into the intricate interplay between TFs and effectors, a key aspect in the prolonged and complex battle between plants and pathogens. Effectors strategically manipulate TFs using diverse tactics.
View Article and Find Full Text PDFEquiRank: Improved protein-protein interface quality estimation using protein language-model-informed equivariant graph neural networks.
Comput Struct Biotechnol J
December 2024
Department of Computer Science, Virginia Tech, Blacksburg, 24061, VA, USA.
Quality estimation of the predicted interaction interface of protein complex structural models is not only important for complex model evaluation and selection but also useful for protein-protein docking. Despite recent progress fueled by symmetry-aware deep learning architectures and pretrained protein language models (pLMs), existing methods for estimating protein complex quality have yet to fully exploit the collective potentials of these advances for accurate estimation of protein-protein interface. Here we present EquiRank, an improved protein-protein interface quality estimation method by leveraging the strength of a symmetry-aware E(3) equivariant deep graph neural network (EGNN) and integrating pLM embeddings from the pretrained ESM-2 model.
View Article and Find Full Text PDFExploration of the mechanism of tetramethoxyflavone in treating osteoarthritis based on network pharmacology and molecular docking.
Tzu Chi Med J
July 2024
Pharmacy College, Gannan Medical University, Ganzhou, Jiangxi, China.
Objectives: This study aimed to explore the potential mechanisms of TMF (5,7,3',4'-tetramethoxyflavone) in treating osteoarthritis (OA) using network pharmacology and molecular docking.
Materials And Methods: Databases including SwissTargetPrediction, BATMAN-TCM, PharmMapper, TargetNet, SuperPred, and SEA were utilized to screen the targets of TMF. "OA" was used as the disease keyword to predict OA-related genes through GeneCards, Therapeutic Target Database, PharmGKB, Online Mendelian Inheritance in Man, and Comparative Toxicogenomics Database.
Genome-wide analysis of TCP family genes and their constitutive expression pattern analysis in the melon (Cucumis melo).
Genes Genomics
January 2025
Plant Molecular Breeding and Bioinformatics Laboratory, Department of Genetics and Plant Breeding, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh.
Background: TCP proteins are plant-specific transcription factors that play essential roles in various developmental processes, including leaf morphogenesis and senescence, flowering, lateral branching, hormone crosstalk, and stress responses. However, a comprehensive analysis of genome-wide TCP genes and their expression patterns in melon is yet to be done.
Objective: The present study aims to identify and analyze the TCP genes in the melon genome and understand their putative functions.
Massively parallel reporter assay investigates shared genetic variants of eight psychiatric disorders.
Cell
January 2025
Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Neuroscience Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA. Electronic address:
A meta-genome-wide association study across eight psychiatric disorders has highlighted the genetic architecture of pleiotropy in major psychiatric disorders. However, mechanisms underlying pleiotropic effects of the associated variants remain to be explored. We conducted a massively parallel reporter assay to decode the regulatory logic of variants with pleiotropic and disorder-specific effects.
View Article and Find Full Text PDFWant AI Summaries of new PubMed Abstracts delivered to your In-box?
Enter search terms and have AI summaries delivered each week - change queries or unsubscribe any time!