The Protein Crystallisation Construct Designer

The Protein Crystallisation Construct Designer streamlines design of truncated protein constructs for structural biology by integrating sequence-based feature predictions and generating PCR oligonucleotides from DNA input.

Key Features:

• Multiple truncation construct design: Allows specification of start and end points to design multiple truncated protein constructs.
• Integration of prediction servers: Aggregates results from secondary structure prediction servers to inform construct boundaries.
• Feature detection: Identifies disorder regions, coiled coils, transmembrane segments, domains, and domain linkers from prediction outputs.
• Condensed sequence-aligned view: Presents prediction results condensed and aligned with the protein sequence to support boundary selection.
• DNA-sequence-based input: Accepts DNA sequences rather than protein sequences to preserve nucleotide context for oligonucleotide design.
• Automated oligonucleotide design: Generates PCR oligonucleotide sequences tailored to each designed construct.
• Construct and oligo output: Produces detailed summaries of designed constructs with corresponding oligonucleotide sequences.

Scientific Applications:

• Protein crystallography construct design: Design and evaluate truncated constructs for X-ray crystallography and structural studies.
• Construct optimization: Select truncation boundaries that avoid disorder, coiled coils, and transmembrane regions to improve construct stability and crystallizability.
• Cloning and PCR preparation: Generate PCR oligonucleotide sequences for cloning and expression of designed truncation constructs.

Methodology:

Aggregates outputs from secondary structure prediction servers (disorder, coiled coils, transmembrane segments, domains, linkers), aligns these results with the protein sequence, and generates PCR oligonucleotide sequences from the provided DNA sequence.