SECONDARY STRUCTURE PREDICTION AND SUMMARY

                   Secondary Structure refers to the local folding pattern of the polypeptide chain and are are predominantly stabilized by hydrogen bonds. The most common type of secondary structures in proteins,
are the alpha helices, beta sheets, and turns. That which cannot be classified as one of the standard three classes is usually grouped into a category called "other" or "random coil"(1).
With the use of Anthreprot software the secondary structure of a protein can be predicted. Anthepreot provided a combination of different methods such as  Garnier
(GOR 1),Levin, DPM, Predator  etc. The aim of secondary structure prediction is to provide the location of alpha helices, and beta strands within a protein or protein family. The GOR(Garnier, Osguthorpe and Robson) method assumes that amino acids up to 8 residues on each side influence the secondary structure of central residue(2)

                                NH2	A G T F H N D  S  H I K N M D A		COOH
                                      -8              0            +8

The frequency of amino acids at the central position in the window, and at -1, .... -8 and +1,....+8 is determined for a, b and turns (later other or coils) to give three 17 x 20 scoring matrices. The GOR method uses information theory and the values in these tables to calculate the probabilities that the central residue is one type of secondary structure not another(2). Fig 1 below shows the result of the GOR 1 method use to  prediction the secondary structure  of papain(1cvz)

Fig. 1 Secondary structure prediction of papain(pdb 1cvz) using the Garnier(GOR 1) method available in Antheprot.

Fig. 3 BELOW PROVIDES A SUMMARY OF THE SECONDARY STRCTURES OF PAPAIN(7) , (8)

Pepetide torsion angles                       Peptide Torsion Angles(3) The figure below shows the three main chain torsion angles of a polypeptide. These are phi , psi , and omega . In a polypeptide the main chain N-C alpha  and C alpha -C bonds relatively are free to rotate.. These rotations are represented by the torsion angles phi and psi , respectively.	Fig.3           ( 7 ) , ( 8 )
RAMCHANDRAN PLOT Fig. 4 on the right shows the Ramchandran plot for Papain(1cvz). GN Ramachandran used computer models of small polypeptides to systematically vary and with the objective of finding stable conformations. For each conformation, the structure was examined for close contacts between atoms. Atoms were treated as hard spheres with dimensions corresponding to their van der Waals radii. Therefore, an angles, which cause spheres to collide correspond to sterically disallowed conformations of the polypeptide backbone(4).   In the diagram on the right, the light yellow areas correspond to conformations where atoms in the polypeptide come closer than the sum of their van der Waals radii. These regions are sterically disallowed for all amino acids except glycine which is unique in that it lacks a side chain(notice glycine is shown as a small blue triangle). Disallowed regions generally involve steric hindrance between the side chain C methylene group and main chain atoms. Glycine has no side chain and therefore can adopt phi and psi angles in all four quadrants of the Ramachandran plot. Hence it frequently occurs in turn regions of proteins where any other residue would be sterically hindered. The red regions are the most favored region which contains(154 residues).Additional allowed region is shown in brown(18 residues). The generously allowed region is shown in bright yellow.  SUMMARY                                                                                   No. of                                                                                 residues     %-tage                                                                               ------             ------ Most favoured regions      [A,B,L]                                154            89.5%*  Additional allowed regions [a,b,l,p]                               18             10.5%          Generously allowed regions [~a,~b,~l,~p]                        0              0.0%          Disallowed regions         [XX]                                      0               0.0%                                                                                       ----              ------ Non-glycine and non-proline residues                          172             100.0% End-residues (excl. Gly and Pro)                                   2 Glycine residues                                                       28 Proline residues                                                        10                                                                             ---- Total number of residues                                        212	RAMCHANDRAN PLOT [PAPAIN (PDB CODE 1CVZ)](12)                            Fig.4
	Inside/Outside RMS Z-score plot The Inside/Outside distribution normality RMS Z-score over a 15 residue window is plotted as function of the residue number. High areas in the plot (above 1.5) indicate unusual inside/outside  patterns. (13)                                                                                                                                       RMS Z-score for papain(1cvz)