Current Protein and Peptide Science - Volume 10, Issue 2, 2009

Information is going to replace matter and energy as the primary stuff of the universe [1]. Information will provide a new basic unifying conceptual framework for describing and predicting physical events and reality in the 21st century [1]. However biological matter, from atomistic-molecular level to organ-organism level, constitutes the most sophisticated multiscale (in space and time) media in which information is codified, st Read More

Proteins in their native folded states can possess multiple energy minima and they can show constant conformational fluctuations at physiological temperatures. In this article, we discuss the quantitative relationship between ligandinduced perturbation of such fluctuations, modeled as probability distributions of conformational substates, and allosteric coupling of ligand binding to different sites, as defined by linkage ther Read More

The phenomenon of intra-protein communication is fundamental to such processes as allostery and signaling, yet comparatively little is understood about its physical origins despite notable progress in recent years. This review introduces contemporary but distinct frameworks for understanding intra-protein communication by presenting both the ideas behind them and a discussion of their successes and shortcomings. The first f Read More

Allostery forms the basis of intra-molecular communications in various enzymes, however the underlying conformational changes are largely elusive. Recently, we have proposed to employ an elastic model based normal mode analysis to investigate the allosteric transitions in several molecular nanomachines (including myosin II, DNA polymerase and chaperonin GroEL). After combining with bioinformatics analysis of t Read More

Transducing environmental signals from the cell surface to the nucleus in order to evoke appropriate gene regulatory response requires an accurate and robust medium to propagate biological information. The structure of proteins and especially the dynamic properties of these structures allows for the uptake and restitution of biological information from and to the environment. To understand the functioning an Read More

Communication within and across proteins is crucial for the biological functioning of proteins. Experiments such as mutational studies on proteins provide important information on the amino acids, which are crucial for their function. However, the protein structures are complex and it is unlikely that the entire responsibility of the function rests on only a few amino acids. A large fraction of the protein is expected to partici Read More

The network paradigm is increasingly used to describe the dynamics of complex systems. Here we review the current results and propose future development areas in the assessment of perturbation waves, i.e. propagating structural changes in amino acid networks building individual protein molecules and in protein-protein interaction networks (interactomes). We assess the possibilities and critically review the initial attempts Read More

Intramolecular and intermolecular communication is a privileged issue in G protein-Coupled Receptor (GPCR) function as the prominent role of these receptors is to respond to extracellular signals by catalyzing nucleotide exchange in intracellular G proteins. In the last decade or so we have applied much effort in elaborating computational strategies to infer the mechanisms of intramolecular and intermolecular communicati Read More

Ligand-protein and protein-protein interactions play a pivotal role in any cellular process and function by means of complex and dynamic mechanisms that involve sophisticated intra- and intermolecular communication pathways. The deeper understanding of the molecular and structural mechanisms of these pathways of chemical information transfer constitutes the foundations of rational druggable target disc Read More

This is with reference to the article entitled “Branched Peptides as Therapeutics”, by Alessandro Pini*, Chiara Falciani and Luisa Bracci, published in Current Protein and Peptide Science, Vol. 9, No. 5, October 2008, pp. 468-477. Due to an oversight the figures of this paper were interchanged on reproduction in the printing. The correct figures are now being presented below with their corresponding captions.