DeltaG prediction

DeltaG prediction predicts the apparent free energy difference of potential transmembrane helices in integral membrane proteins to assess their recognition and co-translational insertion by the Sec61 translocon into the endoplasmic reticulum lipid bilayer.

Key Features:

• Quantitative Analysis: Provides a quantitative framework linking amino acid sequences to apparent free energy values that correlate with membrane insertion efficiency.
• Position-Dependent Contributions: Evaluates the contributions of all 20 standard amino acids as a function of their position within the transmembrane segment.
• Segment Length and Flanking Effects: Accounts for transmembrane segment length and the influence of flanking amino acids on insertion propensity.
• Physical Properties Correlation: Aligns sequence characteristics with the physical properties of the lipid bilayer to reflect biophysical requirements for helix assembly in the membrane.

Scientific Applications:

• Membrane Protein Engineering: Enables design and optimization of synthetic transmembrane segments with predicted insertion efficiencies for protein engineering and therapeutic development.
• Structural Biology Studies: Supports interpretation of how sequence features influence membrane integration relevant to structural models of membrane proteins.
• Biophysical Research: Facilitates studies of the biophysics of Sec61 translocon–mediated helix assembly by quantifying sequence-dependent insertion energetics.

Methodology:

Derived from in vitro translation experiments using model proteins and dog pancreas rough microsomes with systematic analysis of hydrophobic segments to obtain quantitative data on how sequence features affect membrane insertion efficiency.