GDAP

GDAP predicts disulfide bonds in proteins from user-supplied sequences and across bacterial and archaeal genomes to support analysis of protein stability and evolutionary patterns.

Key Features:

• Predictive scope: Predicts disulfide bonds for user-supplied protein sequences and across over one hundred microbial genomes encompassing bacterial and archaeal species.
• Homology mapping: Maps sequences of unknown structure to homologous structures in the Protein Data Bank (PDB).
• PDB sequence search: Searches the PDB sequence database to identify the best structural matches for query sequences.
• Distance-criterion prediction: Applies specific distance criteria to mapped structures to predict potential disulfide bonds.
• Structure scanning and reporting: Scans matched structures for candidate disulfide bond formations and returns detailed predictions.
• Biological insight generation: Has revealed a pronounced preference for intracellular disulfide bonds among certain thermophilic archaea and bacteria.
• Protein engineering support: Provides data used to design site-directed mutants aimed at enhancing protein thermal stability.

Scientific Applications:

• Intracellular disulfide profiling: Identification of intracellular disulfide bond prevalence in thermophilic archaea and bacteria.
• Protein stability engineering: Informing site-directed mutagenesis strategies to enhance thermal stability via disulfide introduction.
• Comparative structural and evolutionary analysis: Comparative analysis of disulfide bond distribution across bacterial and archaeal proteomes for structural biology and evolutionary biochemistry studies.
• Molecular genetics investigations: Guiding experiments that probe the role of disulfide bonds in protein function and stability.

Methodology:

Maps query sequences to homologous PDB structures by searching the PDB sequence database, scans matched structures and applies specific distance criteria to identify candidate disulfide bonds, and returns detailed predictions.