Ab Initio Geometry Determinations of Proteins. 1. Crambin

Abstract

The geometry of crambin, a protein with 46 residues, was determined by ab initio HF/4-21G geometry optimization. The results are compared with the crystal structure of the compound and with HF/4-21G φ,ψconformational geometry maps calculated for the model dipeptide N-acetyl-N′-methylalaninamide. Rootmean-square (rms) deviations between calculated and crystallographic backbone structural parameters are 1.5°for N-C(R)-C′ and 0.013 and 0.017 Å, respectively, for N-C(R) and C(R)-C′. In the case of N-C(R)-C′ the rms deviations are small compared to the observed range of values, which is from <108°to >118°, confirming a definite conformational dependence of peptide backbone structural parameters on φ and ψ. In contrast, the deviations in bond lengths are of the same magnitude as the overall variations. The considerable nonplanarity of the peptide units found in the crystal structure is well reproduced by the calculations. When the calculated and crystal structures are superimposed, the rms positional deviation is 0.6 Å for the heavy atom framework and 0.4 Å for the backbone chain. The phenomenon of helix compression is confirmed that is found in elongated helical chains compared to isolated residues or smaller oligomers.

Comment onStereochemical restraints revisited: how accurate are refinement targets and how much should protein structures be allowed to deviate from them?by Jaskolski, Gilski, Dauter & Wlodawer (2007)

“…The planar angles as obtained from a model of crambin refined at 0.83 Å resolution by the full-matrix least-squares method without constraints (the disordered elements were minimally constrained; Stec et al, 1995). The N-C -C theoretical curve represents the result of ab inito quantum-mechanical optimization as obtained by Van Alsenoy et al (1998). There is a remarkable agreement between the high-resolution crystal structure and the result of the quantum-mechanical optimization.…”

Ab initio quality properties for macromolecules using the ADMA approach

“…This protein was already used in a number of different quantum chemical investigations including an ab initio geometry optimization. 29,[41][42][43] Crambin is a small protein composed of 642 atoms. The threedimensional structure was taken from the Protein Data Bank 44 (pdb-entry 1CNR 45 ).…”

Towards the charge-density study of proteins: a room-temperature scorpion-toxin structure at 0.96 Å resolution as a first test case

“…In the case of crambin, the averaging of residual electron density over the peptide bonds of the protein clearly shows some non-modelled bonding density when using a spherical atom model. Also, quantummechanics calculations are now being performed on whole protein structures such as crambin (Van Alsenoy et al, 1998;Fernandez-Serra et al, 1999). This joint approach will enable the calculation of reliable protein electrostatics in the near future.…”