D. Janezic et Br. Brooks, HARMONIC-ANALYSIS OF LARGE SYSTEMS .2. COMPARISON OF DIFFERENT PROTEIN MODELS, Journal of computational chemistry, 16(12), 1995, pp. 1543-1553
A series of normal mode analyses of bovine pancreatic trypsin inhibito
r (BPTI) has been performed. The results of modifying the long-range t
runcation of electrostatics, reducing the conformational spate of the
system (reduced basis normal mode analysis), and using different param
eter sets and models for the potential function are reported. Both exp
licit (904 atoms) and polar hydrogen (580 atoms) representations of BP
TI were examined and produced nearly identical normal mode vectors but
slightly modified vibrational frequencies. The truncation methods-no
cutoff, shift, and switch-were examined, and the use of a short switch
ing function was found to alter harmonic motion greatly. A table relat
ing the different cutoff methods to several previously published frequ
encies for BPTI indicates that the diversity of published lowest frequ
encies is due to the use of different electrostatic models rather than
to inherent differences in the models or energy parameters. Examining
reduced basis results demonstrates that a dihedral basis yields simil
ar normal mode vectors, though the vibrational frequencies are shifted
to higher values. The analysis of BPTI harmonic dynamics using a sphe
rical harmonic reduced basis set yields significantly altered dynamics
, indicating that BPTI is not well represented as a homogeneous object
at low temperatures. (C) 1995 by John Wiley & Sons, Inc.double dagger