Amino acids torsion angles

Fig. 10.5 The torsion angles that define the eonformation of an amino acid.

HyperChem uses the improper dihedral angle formed by central atom - neighbor 1 - neighbor 2 - neighbor 3, where the order of neighbors is how they appear in a HIN file. Not all planar atoms customarily have associated improper torsions. The order of atoms is arbitrary but has been consistently chosen by the original authors of the CHARMM force field. The templates contain equivalent CHARMM definitions of improper torsions for amino acids. Improper dihedral angles cannot be defined that do not have a central atom, as is sometimes done in CHARMM calculations. 

The secondary stmcture elements are then identified, and finally, the three-dimensional protein stmcture is obtained from the measured interproton distances and torsion angle parameters. This procedure requites a minimum of two days of nmr instmment time per sample, because two pulse delays are requited in the 3-D experiment. In addition, approximately 20 hours of computing time, using a supercomputer, is necessary for the calculations. Nevertheless, protein stmcture can be assigned using 3-D nmr and a resolution of 0.2 nanometers is achievable. The largest protein characterized by nmr at this writing contained 43 amino acid units (51). However, attempts ate underway to characterize the stmcture of interleukin 2 [85898-30-2] which has over 150 amino acid units. 

As a consequence of their different turn geometry a 10-membered turn closed by H-bonds between NH and C=0 +i and a 12-membered turn closed by Id-bonds between C=0 and NH +3, antiparallel hairpins formed by y9-peptides 121 and 122 display opposite sheet polarities (see Fig. 2.30A and B). Comparison of backbone torsion angles (X-ray and NMR) for selected y9-amino acids residues within extended strand segments of peptides 117-122 are shown in Tab. 2.7. The observed values are close to ideal values for y9-peptide pleated sheets =-120° (or 120°), 01 = 180°, (/ =120°(or-120°). 

Murphy et al. [34,45] have parameterized and extensively tested a QM/MM approach utilizing the frozen orbital method at the HF/6-31G and B3LYP/6-31G levels for amino acid side chains. They parameterized the van der Waals parameters of the QM atoms and molecular mechanical bond, angle and torsion angle parameters (Eq. 3, Hqm/mm (bonded int.)) acting across the covalent QM/MM boundary. High-level QM calculations were used as a reference in the parameterization and the molecular mechanical calculations were performed with the OPLS-AA force... 

Fig. 11.9 D iagram showing the homonuclear distance measurements necessary to define the torsion angle

amino acid of an arbitary amino acid, i. 

The P-tetralin amino acid induces the a-helical conformation by fixing the torsional angles along the peptide backbone at about -60° (< >) and -50° ( p).109 P-Tetralin amino acids may be regarded as cyclic-constrained phenylalanine analogues. As shown in Section II.A, this class of unnatural amino acids is known to stabilize distinct conformations in peptides since the two substituents at the a-cen-ter restrict the available conformational space. Cyclic a,a-dialkylated glycines and a-substituted alanines preferentially adopt a-helical conformations.205... 

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