homepage Introduction Secondary structure Hydrophobicity of papain Papain compared to A.thaliana sequence-alignment Homology Modelling Spreadsheet Animation

INTRODUCTION:                                     Papain is an endolytic cysteine protease which is isolated from papaya latex. It belongs to the peptidase family - C1, and is noted for its wide specificity. It preferentially cleaves peptide bonds involving basic amino acids, particularly arginine, lysine and residues following phenylalanine(1). A three-dimensional structure has been indicated by Wolthers et al (1970). The molecule consists of a single, folded polypeptide chain of 212 amino acid residues(Fig. 1a,b below), containing 3 disulphide bonds(Fig.8) and one free functional -SH group at the active site( Smith et al. 1975).                              Many other plants contain cysteine endopeptidases, all of which seem to be homologs of papain, often with similar specificity. Examples are calotropin from the madar plant (Calotropis gigantea), phytolacin from the pokeweed (Phytolacca americana) and mexicanain from Pileus mexicanus (2). The uses for papain are diverse and thus it makes it an extremely valuable enzyme(3). Table 1, below provides classification and structural summary of papain(pdb1cvz)(4)                                    Organism:                   Carica Papaya Compound:                  Papain Type :                          Protein     Molecular Weight :    23410     Number of Alpha:          5           Content of Alpha 23.11 Number of Beta ;           9          Content of Beta   16.51 Number of disulfide Bridges ... 3 Number of Turns ..... 0 Number of Strands ... 10 Number of Helices ... 7 Number of Bonds ..... 1730 Number of Atoms ..... 1655 (159) Number of Groups .... 212 (130) Classification ...... HYDROLASE                                                                                                Table . 1              Papain is well known for it's hydrolase activity at the hinge site of immunoglobin. This is an interesting activity considering it is found in the juice and leaves of an unripe papaya (Carcia papaya). This enzyme is believed to be produced as a defense against having the fruit eaten before its seeds have matured(5). Fig. 1 a Protein: 1CVZ:A PAPAIN Length = 212 amino acids Molecular Weight = 23424.27 Daltons Amino Acid  Number   Mol%   Ala     A       14         6.60   Cys     C        7          3.30   Asp     D       6          2.83   Glu     E       7          3.30   Phe      F       4          1.89   Gly     G      28         13.21   His     H        2         0.94   Ile       I       12          5.66   Lys     K      10          4.72   Leu     L      11          5.19   Met     M      0           0.00   Asn     N      13          6.13   Pro      P      10          4.72   Gln     Q      13         6.13   Arg      R      12         5.66   Ser      S       13         6.13   Thr     T        8          3.77   Val     V       18          8.49   Trp     W       5          2.36   Tyr     Y      19           8.96               Fig. 1 b Figure1a,  shows a graphical representation of the amino acid composition of papain(1cvz).  Fig. 1b shows the tabulated values.   Glycine is present in the highest percentage, while histidine the lowest.(3)                                                                                                                                                                       Fig2 shows a 3D model (surface view of papain(pdb 1cvz)(5).                                                                          Fig. 2               3D Surface View Model of Papain(1CVZ) Fig. 3 below shows the 212 residues of papain(1cvz) .(4)                                   Fig. 3  shows the sequence of the residues in chain A, along with the seven helices(red spiral) (6) The PDB structure of papain was determined by x-ray diffraction(ray crystallography) (7). Figure 4a  shows the secondary structure of papain(pdb1cvz) and the amino acids(Cys 25, His 159 and Asn 175) which are part of the catalytic center.  Fig. 3b shows both 2D and 3D structure of these amino acids.       Fig. 4 a Backbone structure of Papain(1cvz) showing locations of His 159( blue), Asn 175 ( yellow ) and Cys 25 ( cyan) (Quickpdb) Fig. 4b Shows 2D and 3D structures of the amino acids at the catalytic center .  ( Chemsketch/ACD)                                                     Figure 5a and 5b below, shows the secondary structure of papain (1cvz) , in which the alpha helices, and beta sheets are colored red and yellow respectively(5).

Fig. 5 a The amino acids at the catalytic center are shown space filled Fig 5b Shows the ligand (C48) at the catalytic center Fig. 6. Shows the interaction of the ligand(C48) with the amino acids at the catalytic site ( 9)                                                           Fig. 7 Wireframe model of papain(pdb1cvz) showing the three disulfide bridges(yellow) and inhibitor(C48 ) in the active site .        '                    Fig. 8  Strand model of papain showing water molecules(red sphere). The Disulfide bridges are shown in yellow.                                                               Fig.9 Papain(pdb 1cvz) structure as backbones colored in a spectral rainbow sequence as follows:  Amino/5' ------------------ Carboxy/3   the ligand(C48) is shown space filled PREVIOUS PAGE NEXT PAGE

formatic enough,
>maybe they should start new threads.
>
>Here's one:
>
>If we're going to talk about "what bioinformatics needs" (quoting
>Jon), it seems that we should attempt to nail down what
>"bioinformatics" _is_.
>
>I'll offer a starting point[1]: "bioinformatics" is really just
>computational biology under a newer, more media-friendly name -- that
>is, it's a largely content-free buzz-phrase invoked to describe some
>combination of something to do with computers, and something to do
>with biology.
>
>Dissenting opinions welcome. 8^)=
>
>john.
>

Papain is an



References
http://www.d-trends.com/webs/ics_preface.html