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|2ptc, resolution 1.90Å ()|
THE GEOMETRY OF THE REACTIVE SITE AND OF THE PEPTIDE GROUPS IN TRYPSIN, TRYPSINOGEN AND ITS COMPLEXES WITH INHIBITORS
We present a new computational method of docking pairs of proteins by using spherical polar Fourier correlations to accelerate the search for candidate low-energy conformations. Interaction energies are estimated using a hydrophobic excluded volume model derived from the notion of "overlapping surface skins," augmented by a rigorous but "soft" model of electrostatic complementarity. This approach has several advantages over former three-dimensional grid-based fast Fourier transform (FFT) docking correlation methods even though there is no analogue to the FFT in a spherical polar representation. For example, a complete search over all six rigid-body degrees of freedom can be performed by rotating and translating only the initial expansion coefficients, many unfeasible orientations may be eliminated rapidly using only low-resolution terms, and the correlations are easily localized around known binding epitopes when this knowledge is available. Typical execution times on a single processor workstation range from 2 hours for a global search (5 x 10(8) trial orientations) to a few minutes for a local search (over 6 x 10(7) orientations). The method is illustrated with several domain dimer and enzyme-inhibitor complexes and 20 large antibody-antigen complexes, using both the bound and (when available) unbound subunits. The correct conformation of the complex is frequently identified when docking bound subunits, and a good docking orientation is ranked within the top 20 in 11 out of 18 cases when starting from unbound subunits. Proteins 2000;39:178-194.
Protein docking using spherical polar Fourier correlations., Ritchie DW, Kemp GJ, Proteins. 2000 May 1;39(2):178-94. PMID:010737939
From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine.
About this Structure
2ptc is a 2 chain structure with sequence from Bos taurus. This structure supersedes the now removed PDB entry 1ptc. The October 2003 RCSB PDB Molecule of the Month feature on Trypsin by David S. Goodsell is 10.2210/rcsb_pdb/mom_2003_10. Full crystallographic information is available from OCA.
- Ritchie DW, Kemp GJ. Protein docking using spherical polar Fourier correlations. Proteins. 2000 May 1;39(2):178-94. PMID:10737939
- Liang S, Li L, Hsu WL, Pilcher MN, Uversky V, Zhou Y, Dunker AK, Meroueh SO. Exploring the molecular design of protein interaction sites with molecular dynamics simulations and free energy calculations. Biochemistry. 2009 Jan 20;48(2):399-414. PMID:19113835 doi:10.1021/bi8017043