A structural perspective on protein–protein interactions

Russell, Robert B.; Alber, Frank; Aloy, Patrick; Davis, Fred P.; Korkin, Dmitry; Pichaud, Matthieu; Topf, Maya; Šali, Andrej

doi:10.1016/j.sbi.2004.04.006

Cited by 247 publications

(129 citation statements)

References 186 publications

Supporting

Mentioning

127

Contrasting

Unclassified

Order By: Relevance

“…This loss of water, or desolvation, is generally energetically unfavorable and offsets the favorable interactions formed upon binding. The binding affinities, from an electrostatic point of view, are determined by balance of these two energetic contributions (Xu et al, 1997;Lee and Tidor, 2001;Sheinerman and Honig, 2002;Russell et al, 2004;del Álamo and Mateu, 2005). Systematic studies of protein pairs, such as barnase and barstar Fersht, 1993, 1995;Frisch et al, 1997;Dong et al, 2003), and fasciculin-2 (Radic et al, 1997), as well as protein kinase A and balanol (Wong et al, 2001), have shown that charged and polar residues at the protein-protein interfaces play important roles in binding energetics.…”

Section: Iib Biomolecule-ligand and -Biomolecule Interactionsmentioning

confidence: 99%

Computational Methods for Biomolecular Electrostatics

Dong

Olsen

Baker

2008

Methods in Cell Biology

116

View full text Add to dashboard Cite

An understanding of intermolecular interactions is essential for insight into how cells develop, operate, communicate and control their activities. Such interactions include several components: contributions from linear, angular, and torsional forces in covalent bonds, van der Waals forces, as well as electrostatics. Among the various components of molecular interactions, electrostatics are of special importance because of their long range and their influence on polar or charged molecules, including water, aqueous ions, and amino or nucleic acids, which are some of the primary components of living systems. Electrostatics, therefore, play important roles in determining the structure, motion and function of a wide range of biological molecules. This chapter presents a brief overview of electrostatic interactions in cellular systems with a particular focus on how computational tools can be used to investigate these types of interactions.

show abstract

Section: Iib Biomolecule-ligand and -Biomolecule Interactionsmentioning

confidence: 99%

Computational Methods for Biomolecular Electrostatics

Dong

Olsen

Baker

2008

Methods in Cell Biology

116

View full text Add to dashboard Cite

show abstract

“…However, their transient and conditional nature, which is the very thing that makes them biologically important, can also render them difficult to study. They tend to be under-represented in the large-scale affinity purification assays reported so far [25,26], and may be missed by yeast two-hybrid methods, for example if they require a modification such as tyrosine phosphorylation which is unlikely to occur in yeast. Thus, most interaction networks derived from HTP data are dominated by the more stable domain-domain interactions, and may therefore lack the biochemical and biological complexity imparted by these more evanescent interactions, which likely confer dynamic responsiveness to cellular networks.…”

Section: Identification and Prediction Of Interaction Motifsmentioning

confidence: 99%

Synthetic modular systems – reverse engineering of signal transduction

Pawson

Linding

2005

FEBS Letters

View full text Add to dashboard Cite

During the last decades, biology has decomposed cellular systems into genetic, functional and molecular networks. It has become evident that these networks consist of components with specific functions (e.g., proteins and genes). This has generated a considerable amount of knowledge and hypotheses concerning cellular organization. The idea discussed here is to test the extent of this knowledge by reconstructing, or reverse engineering, new synthetic biological systems from known components. We will discuss how integration of computational methods with proteomics and engineering concepts might lead us to a deeper and more abstract understanding of signal transduction systems. Designing and successfully introducing synthetic proteins into cellular pathways would provide us with a powerful research tool with many applications, such as development of biosensors, protein drugs and rewiring of biological pathways.

show abstract

“…The next step will involve bridging the resolution gap between molecular and cell biology. This implies the accurate modeling of large complexes and their location and fitting in whole cell tomograms, which will place the complexes in their cellular context and provide the quantitative information (e.g., concentration) necessary for an accurate description of the systems behavior [30] (Fig. 1, bottom).…”

Section: Complex Assembly From Binary Interactionsmentioning

confidence: 99%

Structure‐based systems biology: a zoom lens for the cell

Aloy

Russell

2005

FEBS Letters

Self Cite

View full text Add to dashboard Cite

Systems biology seeks to explain complex biological systems, such as the cell, through the integration of many different types of information. Here, we discuss how the incorporation of high-resolution structural data can provide key molecular details often necessary to understand the complex connection between individual molecules and cell behavior. We suggest a process of zooming on the cell, from global networks through pathways to the precise atomic contacts at the interfaces of interacting proteins.

show abstract

A structural perspective on protein–protein interactions

Cited by 247 publications

References 186 publications

Computational Methods for Biomolecular Electrostatics

Computational Methods for Biomolecular Electrostatics

Synthetic modular systems – reverse engineering of signal transduction

Structure‐based systems biology: a zoom lens for the cell

Contact Info

Product

Resources

About