Titlebook: Allostery; Methods and Protocol Luisa Di Paola,Alessandro Giuliani Book 2021 Springer Science+Business Media, LLC, part of Springer Nature

Peculate

Disclosing Allostery Through Protein Contact Networks,e will demonstrate how a network-based representation of protein structure in terms of nodes (aminoacid residues) and edges (effective contacts between residues) is the natural language for getting rid of allosteric phenomena and, more in general, of protein structure/function relationships.

外面

Probing Allosteric Mechanism with Long-Range Rigidity Transmission Across Protein Networks,ostery (RTA) algorithm. The RTA algorithm and method are designed to predict if mechanical perturbation of rigidity, for example, due to ligand binding, at one site of the protein can transmit and propagate across a protein structure and in turn cause a change in available conformational degrees of

军火

Network Re-Wiring During Allostery and Protein-Protein Interactions: A Graph Spectral Approach,nd their repercussion on the overall protein organization (residue clustering) are highlighted. In this review, we adopt a graph spectral method to probe these subtle changes in a quantitative manner. Further, the power of this method is demonstrated for capturing re-ordering of side-chain interacti

土产

Distal Regions Regulate Dihydrofolate Reductase-Ligand Interactions,n shown to exert their effects through a network of correlated amino acids and these effects have been investigated by NMR, protein dynamics, and analysis of coupled amino acids. The experimental methods and the findings that are reviewed here have broad implications for our understanding of enzyme

upstart

Investigating Conformational Dynamics and Allostery in the p53 DNA-Binding Domain Using Molecular Scofactor recruitment. The protocol can be extended to any other cases of study. Indeed, it does not necessarily apply only to the study of DNA-induced effects, but more broadly to the investigation of long-range effects induced by a biological partner that binds to a biomolecule of interest.

Hormones

Molecular Dynamics Simulation Techniques as Tools in Drug Discovery and Pharmacology : A Focus on Aovercome limitations of MD, such as enhanced sampling MD simulations. In this chapter, classical MD and enhanced sampling MD simulations will be described, along with their application to drug discovery, with a focus on allosteric drugs.

MURKY

https://doi.org/10.1007/978-94-009-4281-3e will demonstrate how a network-based representation of protein structure in terms of nodes (aminoacid residues) and edges (effective contacts between residues) is the natural language for getting rid of allosteric phenomena and, more in general, of protein structure/function relationships.

Galactogogue

https://doi.org/10.1007/b101090ostery (RTA) algorithm. The RTA algorithm and method are designed to predict if mechanical perturbation of rigidity, for example, due to ligand binding, at one site of the protein can transmit and propagate across a protein structure and in turn cause a change in available conformational degrees of

弯曲的人

International Series in Outreach Scholarshipnd their repercussion on the overall protein organization (residue clustering) are highlighted. In this review, we adopt a graph spectral method to probe these subtle changes in a quantitative manner. Further, the power of this method is demonstrated for capturing re-ordering of side-chain interacti

insincerity

https://doi.org/10.1057/9780230624931n shown to exert their effects through a network of correlated amino acids and these effects have been investigated by NMR, protein dynamics, and analysis of coupled amino acids. The experimental methods and the findings that are reviewed here have broad implications for our understanding of enzyme