Protein torsion angle

In another GA study, Le Grand and Merz encoded protein torsional angles as binary numbers in each individual, Unfortunately problems were encountered with the knowledge-based... 

Example Yon can monitor improper torsion angles to determine wh ich side of a substrate m olecn le faces the active site of a protein. Select three atoms on the substrate molecule and a fourth in the active site. These atom s define an improper torsion angle. Save th is selection as a named selection. Then observe a plot of this improper torsion angle (in the Molecular Dynam ics Results dialog... 

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. 

To understand the function of a protein at the molecular level, it is important to know its three-dimensional stmcture. The diversity in protein stmcture, as in many other macromolecules, results from the flexibiUty of rotation about single bonds between atoms. Each peptide unit is planar, ie, oJ = 180°, and has two rotational degrees of freedom, specified by the torsion angles ( ) and /, along the polypeptide backbone. The number of torsion angles associated with the side chains, R, varies from residue to residue. The allowed conformations of a protein are those that avoid atomic coUisions between nonbonded atoms. 

Standard calculation methods developed for small proteins are sufficiently powerful to solve protein structures and complexes in the 30 kDa range and beyond [97,98] and protein-nucleic acid complexes [99]. Torsion angle dynamics offers increased conver-... 

Oldfield TJ. A number of real-space torsion-angle refinement techniques for proteins, nucleic acids, ligands and solvent. Acta Cryst 2001 057 82-94. 

Schaumann T, Braun W, Wilthrich K. The program FANTOM for energy refinement of polypeptides and proteins using a Newton-Raphson minimizer in torsion angle space. Biopolymers 1990 29 679-694. 

Many of the conformational properties of peptide systems, including protein conformation, can be approximated in terms of the local interactions encountered in dipeptides, where the two torsional angles 4> (N-C(a)) and < i (C(a)-C ) are the main conformational variables. N-acetyl N -methyl alanine amide, shown in Fig. 7.11, is a model dipeptide that has been the subject of numerous computational studies. 

Fig. 7.17 Bend structure resulting from the HF/4-21G geometry refinement of a type-II bend of N-formyl pentaglycine amide. The torsional angles in this structure are not common in proteins due to the effects of the end groups on the dihedral angles in the bend.

Figure 4.1 represents the typical free energy profile or potential of mean force (PMF) along a reaction coordinate. The rc-axis is the reaction coordinate, which could be the distance between two molecules, a torsion angle along the backbone of a protein, or the relative orientation of an a-helix with respect to a membrane. 

---