𝔖 Bobbio Scriptorium
✦   LIBER   ✦

Protein coadaptation and the design of novel approaches to identify protein–protein interactions

✍ Scribed by Mario A. Fares; Mario X. Ruiz-González; Juan Pablo Labrador

Publisher
John Wiley and Sons
Year
2011
Tongue
English
Weight
134 KB
Volume
63
Category
Article
ISSN
1521-6543

No coin nor oath required. For personal study only.

✦ Synopsis

Abstract

Proteins rarely function in isolation but they form part of complex networks of interactions with other proteins within or among cells. The importance of a particular protein for cell viability is directly dependent upon the number of interactions where it participates and the function it performs: the larger the number of interactions of a protein the greater its functional importance is for the cell. With the advent of genome sequencing and “omics” technologies it became feasible conducting large‐scale searches for protein interacting partners. Unfortunately, the accuracy of such analyses has been underwhelming owing to methodological limitations and to the inherent complexity of protein interactions. In addition to these experimental approaches, many computational methods have been developed to identify protein–protein interactions by assuming that interacting proteins coevolve resulting from the coadaptation dynamics between the amino acids of their interacting faces. We review the main technological advances made in the field of interactomics and discuss the feasibility of computational methods to identify protein–protein interactions based on the estimation of coevolution. As proof‐of‐concept, we present a classical case study: the interactions of cell surface proteins (receptors) and their ligands. Finally, we take this discussion one step forward to include interactions between organisms and species to understand the generation of biological complexity. Development of technologies for accurate detection of protein–protein interactions may shed light on processes that go from the fine‐tuning of pathways and metabolic networks to the emergence of biological complexity. © 2011 IUBMB IUBMB Life, 63(4): 264–271, 2011

📜 SIMILAR VOLUMES

A novel approach to tag and identify ger
A novel approach to tag and identify geranylgeranylated proteins
✍ Lai N. Chan; Courtenay Hart; Lea Guo; Tamara Nyberg; Brandon S.J. Davies; Loren 📂 Article 📅 2009 🏛 John Wiley and Sons 🌐 English ⚖ 274 KB

## Abstract A recently developed proteomic strategy, the “GG‐azide”‐labeling approach, is described for the detection and proteomic analysis of geranylgeranylated proteins. This approach involves metabolic incorporation of a synthetic azido‐geranylgeranyl analog and chemoselective derivatization of

Computational approaches to identifying
Computational approaches to identifying and characterizing protein binding sites for ligand design
✍ Stefan Henrich; Outi M. H. Salo-Ahen; Bingding Huang; Friedrich F. Rippmann; Gab 📂 Article 📅 2009 🏛 John Wiley and Sons 🌐 English ⚖ 457 KB

## Abstract Given the three‐dimensional structure of a protein, how can one find the sites where other molecules might bind to it? Do these sites have the properties necessary for high affinity binding? Is this protein a suitable target for drug design? Here, we discuss recent developments in compu

Peptidic modulators of protein-protein i
Peptidic modulators of protein-protein interactions: Progress and challenges in computational design
✍ Mor Rubinstein; Masha Y. Niv 📂 Article 📅 2009 🏛 Wiley (John Wiley & Sons) 🌐 English ⚖ 161 KB 👁 2 views

## Abstract With the decline in productivity of drug‐development efforts, novel approaches to rational drug design are being introduced and developed. Naturally occurring and synthetic peptides are emerging as novel promising compounds that can specifically and efficiently modulate signaling pathwa