David: In my experience most people don't put a lot of thought into an upper limit for van der Waals (VDW) contacts and use a "hard", arbitrary upper value of 4 Angstrom.
In the mid-1980's, Wayne Hendrickson and I proposed that one should use: · Atom type dependent cutoffs · As an approximation to the asymptote to zero energy at infinite distance, an upper bound that was as much above the distance of minimum energy (Rmin) as Rmin was above the zero energy, Rzero, which is the point at which the repulsive forces exceed the attractive forces. Using a form of a 6-12 potential, we calculated that Rlimit = 1.11 x Rmin (and that Rzero = 0.89 x Rmin). I have used that in all my succeeding work, e.g. on antibodies, although during a stint in David Davies' group at NIH following working with Wayne at the Naval Research Laboratory, I switched from using the very simple 4 atom types that PROTIN used to a somewhat more complex set of values that I was introduced to based on a paper by Gelin & Karplus (1979). Here are some references: S. Sheriff, W. A. Hendrickson & J. L. Smith (1987). The Structure of Myohemerythrin in the Azidomet State at 1.7/1.3 Å Resolution. J. Mol. Biol. 197, 273-296. S. Sheriff (1993). Some Methods for Examining the Interaction between Two Molecules. Immunomethods 3, 191-196. B. R. Gelin & M. Karplus (1979). Side-Chain Torsional Potentials: Effect of Dipeptide, Protein, and Solvent Environment. Biochemistry 18, 1256-1268. And here are some reviews that used that used this calculation to compare structures: D. R. Davies, E. A. Padlan & S. Sheriff (1990). Antibody-Antigen Complexes. Annu. Rev. Biochem. 59, 439-473. S. Sheriff (1993). Antibody - Protein Complexes. Immunomethods 3, 222-227. Papers on antibody/antigen complexes that were edited by Ian Wilson in his capacity as an editor of J. Mol. Biol. were often requested to use the methodology as well. Unfortunately [ ;) ], too many papers appeared outside of J. Mol. Biol. that were ignorant of the methodology put in place by me and used by Ian's group at Scripps as evidenced by (although these report on buried surface area calculations): I. A. Wilson & R. L. Stanfield (1993). Antibody-antigen interactions (1993). Curr. Opin. Struct. Biol. 3, 113-118. I. A. Wilson & R. L. Stanfield (1994). Antibody-antigen interactions: new structures and new conformational changes (1994). Curr. Opin. Struct. Biol. 4, 857-867. for these methods to remain the standard in the field. In the department of totally shameless self-promotion (as opposed to the above shameless self-promotion), I have published a recent paper, where I have used this methodology for the field of 10Fn3-based variants, when used as binding proteins in a manner analogous to antibodies, or more similarly, VHH domains (Camelid-like VH domains): V. Ramamurthy, S. R. Krystek, Jr., A. Bush, A. Wei, S. Emanuel, R. DasGupta, A. Janjua, Z. Lin, L. Cheng, M. Murdock, D. Cohen, P. Morin, J. H. Davis, M. Dabritz, D. C. McLaughlin, K. A. Russo, G. Chao, M. C. Wright, V. A. Jenny, L. J. Engle, E. Furfine & S. Sheriff (2012). Structures of Adnectin/Protein complexes reveal an expanded binding footprint. Structure, 20, 259-269. Steven ________________________________ This message (including any attachments) may contain confidential, proprietary, privileged and/or private information. The information is intended to be for the use of the individual or entity designated above. If you are not the intended recipient of this message, please notify the sender immediately, and delete the message and any attachments. Any disclosure, reproduction, distribution or other use of this message or any attachments by an individual or entity other than the intended recipient is prohibited.
