Structural Biochemistry/Analyzing and visualizing residue networks of protein structures

Introduction

To understand structure-function relationships, it is crucial to study the individual amino acid residues and each of their molecular interactions in protein structures. Experiments and work have been conducted, observing that residue networks created by a 3D protein structure provides more insight into structural and functional roles of interacting residues. There are software tools called the RINerator and RINalyzer to see the 2D visualization.

Protein structure visualization and residue networks

Viewing a 3D protein structure has been accessible by using X-ray crystallography and NMR spectroscopy. Although 2D visualization is very important in terms of observing structures of proteins, 2D representations of RINs have started to become popular.
RINs simplify the visual complexity of 3D protein structures and allows the scientist to focus on individual residues and their interactions within the molecular level. RIN is derived from 3D coordinates of a protein model. Each RIN is composed of nodes, representing amino acid residues. RINs can study residue interactions in many application scenarios, like, with regard to protein dynamics.
Recently, RINs have been applied to study protein-ligand interactions and to observe the structural and functional effects of residue changes under drug use or disease.

Visual analysis of RINs

The RINalyzer (http://www.rinalyzer.de) is a software tool that provides versatile structural analysis tools for RINs and one can observe the structure in either 2D or 3D. Residue nodes of interest are automatically highlighted in the RINalyzer.
Cytoscape plugin structureViz (http://www.cgl.ucsf.edu/cytoscape/structureViz/) analyzes and supports the structural analysis of protein-to-protein interactions.

Network approaches to protein structure analysis

One software feature is the ability to perform analysis of residue interactions by comparing the residues with one another by loooking at the similarities and differences between two proteins. One can also observe the binding site similarities.

Generation of RINs

The RINerator module generates RINs from a 3D protein structure. This provides a more realistic visual by sampling contacts on the Van der Waals surface on each atom. By doing this, different residue interaction types can be observed and the strength of the interactions can be determined as well.

References

Doncheva, Nadezhda T, et al. "Analyzing and visualizing residue networks of protein structures" Trends in Biochemical Sciences 36.4 (2011) 179-182. Academic Search Complete. Web. 05 December. 2012.