Tspred

TSpred predicts temperature-sensitive (Ts) mutants in proteins to enable conditional gene expression studies and functional analysis of proteins.

Key Features:

• Rational design approach: Predictively designs Ts mutants instead of relying on random mutagenesis and extensive screening.
• Hydrophobicity and hydrophobic moment analysis: Computes hydrophobicity and hydrophobic moment from the primary amino acid sequence.
• Residue depth inference: Infers residue depth based on 3D structures to identify buried hydrophobic residues.
• Hydrophobic residue identification: Identifies buried hydrophobic residues that, when mutated, are likely to destabilize protein structure at elevated temperatures and produce a Ts phenotype.
• Amino acid substitution suggestions: Proposes specific amino acid substitutions for candidate residues to generate Ts mutants.
• Sequence-only operation: Can operate using only the primary amino acid sequence without requiring homologous sequence information.
• High precision mutation proposals: Proposes a limited number of mutations with reported high precision and efficiency.

Scientific Applications:

• Experimental validation: Methodology has been experimentally validated across 36 positions in six different proteins.
• Conditional functional studies: Enables in vivo and cell culture studies of protein function by generating reversible Ts mutants for conditional gene expression.
• Validated predictions in specific proteins: Successfully predicted known Ts and partially active mutants in T4 lysozyme, lambda repressor, gene V protein, and staphylococcal nuclease.
• Hydrophobic core identification: Accurately identified residues forming hydrophobic cores in proteins such as myoglobin and cytochrome b562.

Methodology:

TSpred computes hydrophobicity and hydrophobic moment from the primary sequence, infers residue depth from 3D structures to identify buried hydrophobic residues, and suggests amino acid substitutions for candidate residues.