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A potential function for conformational analysis of proteins.

G M Crippen, V N Viswanadhan

    International Journal of Peptide and Protein Research
    |September 1, 1984
    PubMed
    Summary
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    Researchers developed a new residue-residue potential function for protein structure prediction. This empirical function accurately models protein folding, maintaining secondary structures and overall shape for small proteins.

    Area of Science:

    • Computational Biology
    • Structural Biology
    • Biophysics

    Background:

    • Protein structure prediction is crucial for understanding biological function.
    • Low-resolution models are valuable for large-scale conformational searches.
    • Accurate potential functions are essential for reliable protein modeling.

    Purpose of the Study:

    • To develop a novel residue-residue potential function for low-resolution protein conformational calculations.
    • To incorporate both short-range and long-range interactions governing protein structure.
    • To create an empirically derived potential function applicable to small proteins.

    Main Methods:

    • Calculated short-range terms by comparing observed C-alpha atom distance distributions in 35 protein crystal structures to expected distributions.

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  • Modeled discrepancies using a Boltzmann distribution and an effective potential.
  • Adjusted long-range terms to ensure native conformations have lower energy than perturbed states, implicitly including solvation and entropy effects.
  • Tested the potential on bovine pancreatic trypsin inhibitor and other small proteins.

    • Main Results:

    • The devised potential function effectively maintains correct secondary structure through short-range interactions.
    • Long-range terms accurately govern larger packing features and overall protein globularity.
    • The empirical potential implicitly includes solvation and conformational entropy effects.
    • Testing confirmed general applicability to small proteins, preserving native conformations without artificial compression or expansion.

    Conclusions:

    • The developed residue-residue potential function is a robust tool for low-resolution protein conformational calculations.
    • The potential accurately models key aspects of protein folding, including secondary structure and tertiary packing.
    • It provides a reliable method for exploring conformational landscapes of small proteins, maintaining structural integrity.