Software to Visualize Proteins and Perform Structural Alignments

Area of Science:

• Structural Biology
• Bioinformatics
• Evolutionary Biology

Background:

• Protein structural data availability is rapidly increasing, enabling advanced in silico analyses.
• Structural model comparisons offer refined functional and evolutionary insights.
• Free and open-source software facilitates protein structure interrogation.

Purpose of the Study:

• To describe three structural alignment protocols for investigating protein structure evolution.
• To utilize freely available software for analyzing protein structure at different levels.
• To demonstrate the application of these methods on specific protein families.

Main Methods:

• Utilized Swiss-PDBViewer and PyMOL for structural alignment and visualization.
• Applied protocols to analyze quaternary structure in PfpI/DJ-1 superfamily.
• Investigated tertiary structure evolution in cytochrome c proteins.
• Visualized allosteric mechanisms and dynamics in winged helix-turn-helix proteins.

Main Results:

• Quaternary structure variations in PfpI/DJ-1 proteins correlate with distinct enzyme activities.
• Cytochrome c proteins exhibit conserved structures with species-specific substitutions influencing interactions.
• Evolution of allosteric mechanisms and protein dynamics were revealed in DNA-binding proteins.

Conclusions:

• Freely available software enables detailed investigation of protein structure evolution.
• Structural comparisons provide insights into protein function, evolution, and mechanism.
• These methods are valuable for understanding protein family diversification and adaptation.