An Integrated Sequence-Structure Database incorporating matching mRNA sequence, amino acid sequence and protein...

Area of Science:

• Bioinformatics
• Structural Biology
• Computational Biology

Background:

• Integrating diverse biological data is crucial for comprehensive analysis.
• Existing databases may lack integrated sequence and structure information for non-homologous proteins.
• Understanding the relationship between nucleotide sequences and protein structures is fundamental.

Purpose of the Study:

• To develop a comprehensive database (ISSD) integrating gene sequences, protein sequences, secondary structures, and 3D coordinates.
• To provide a resource for analyzing the correlation between synonymous codon usage and protein structure.
• To facilitate research in protein expression, structure prediction, and evolutionary analysis.

Main Methods:

• Construction of a non-homologous database (ISSD) containing coding sequences, amino acid sequences, secondary structure assignments, and backbone coordinates.
• Alignment of nucleotide sequences, amino acid sequences, and Protein Data Bank (PDB) 3D structure data for each protein entry.
• Selection of sequences based on exact matches of source organism and cell environment.

Main Results:

• The Integrated Sequence-Structure Database (ISSD) version 1.0 is available online.
• The database currently includes 107 non-homologous mammalian proteins, with 80 human proteins.
• Analysis revealed correlations between synonymous codon usage patterns in mRNA and 3D structure features of encoded proteins.

Conclusions:

• The ISSD provides a valuable resource for studying sequence-structure relationships.
• The database can be applied to optimize protein expression and improve protein structure prediction.
• ISSD facilitates the investigation of evolutionary aspects linking nucleotide sequences and protein structures.