 
PFRMAT TS 
TARGET T0052 
AUTHOR 5529-3140-9255 
REMARK Prediction team BENNER-COHEN has two group leaders, 
REMARK but we will consistently use Steven Benner's predictor 
REMARK number to avoid confusion concerning a second team 
REMARK connected with Fred Cohen (called Cohen, Fred). 
REMARK (Fred Cohen's number as a group leader is 6140-7890-6093). 
REMARK Prediction team members: D.L.Gerloff, G.Cannarozzi, 
REMARK M.Joachimiak, M.Cueto, F.E.Cohen & S.A.Benner. 
METHOD Important comment: We submit T0052 as a "modeling 
METHOD exercise" as the lack of homologous sequences in the 
METHOD databases precluded the use of the systematic methods 
METHOD developed by members of our team. In particular, the 
METHOD prediction is NOT based on the SAINT secondary structure 
METHOD prediction system (Benner et al., U.of Florida). 
METHOD To illustrate this fact, we submit coordinates only. 
METHOD 
METHOD Methodology used in this prediction for T0052 (CN-V): 
METHOD The prediction process was mostly manual and based on 
METHOD different, sometimes contradicting, clues found through  
METHOD sequence analysis and in the literature, as described 
METHOD below.  
METHOD Firstly, we inspected the automated secondary structure 
METHOD predictions available to us and potentially useful even 
METHOD if used in the absence of homologous sequence information 
METHOD (PHD and J.M.Chandonia, personal communication). The in- 
METHOD consistencies between the outputs by different methods 
METHOD prompted us to disregard the predicted secondary structure 
METHOD in this case! Instead, we attempted to conclude from the 
METHOD position of the DISULFIDE BRIDGES and the indications in  
METHOD the sequence on the number and approximate position of  
METHOD SEGMENTS OF POSSIBLE SECONDARY STRUCTURE. On these grounds,  
METHOD we favor a model with a total of up to 7 short segments, or half- 
METHOD segments, probably separated only by a bend in the protein chain  
METHOD (in contrast to a sharp turn). Thus the 7 short segments are  
METHOD likely to be found in approximately five stretches of secondary 
METHOD structure. Further, like others before us, we found a putative  
METHOD INTERNAL REPEAT in the target sequence (#1-50, 51-101).  
METHOD Interestingly, this piece of information was IN CONFLICT 
METHOD WITH A POSSIBLE, DISTANT HOMOLOGY TO 1PMD that was found through 
METHOD "second frame" homology searches. 
METHOD With this information, wea ttempted to perform an EXHAUSTIVE 
METHOD COMBINATORIAL ANALYSIS of the possible folding topology of T0052, 
METHOD assuming that the repeated domains are superimposable and contain 
METHOD predominately (exclusively) beta-sheet structure. 
METHOD However, the analysis using a similar scheme as we applied 
METHOD quite successfully in CASP1 on synaptotagmin (Proteins 
METHOD 1995, 22:299-310), FAILED TO REDUCE THE NUMBER OF POSSIBLE 
METHOD FOLDING TOPOLOGIES to the desired level for submission at 
METHOD at CASP3. This is because we could not find sufficiently 
METHOD strong and reliable "filters", for example a prediction 
METHOD of tight turns vs. wide turns/connections as is often 
METHOD possible with the help of multiple sequence information. 
METHOD 
METHOD Therefore, and due to time pressure, we submit our model 
METHOD as an "educated guess", illustrating that we decided to 
METHOD rely on the postulated internal repeat rather than on the 
METHOD the conflicting secondary structures. Further, we disre- 
METHOD garded the output of the UCLA-DOE fold recognition server 
METHOD programs as no significant matches were returned.  
METHOD Instead, the packing constraints for the putative 50 res. 
METHOD domains seem to FAVOR AN ALL-BETA FOLD PREDICTION. 
METHOD The possible homology to 1pmd (163-263) was, again,  
METHOD conflicting with an internally repeated structure made of 
METHOD two lobes. Intriguingly, however, we are able to propose 
METHOD a model predicting partial structural similarity of T0052 
METHOD with a small domain in 1prc (photosythetic react. center) 
METHOD which, if duplicated as putatively in T0052, has some 
METHOD resemblance in shape with the domain of interest in 1pmd. 
METHOD As the crystal structure 1pmd is at low resolution and 
METHOD undoubtedly faulty, this could be an indication for how 
METHOD to correct 1pmd, if correct. However, according to our 
METHOD combinatorial analysis (see above), there are several 
METHOD other topologies that would meet all the "filtering" 
METHOD constraints we could bring forward. For example, a  
METHOD model made of two symmetry-equivalent SH3-like domains 
METHOD would also be conceivable. 
METHOD 
METHOD Both of the lobes of our model are constructed partly 
METHOD onto the topology of 1prc (res. 155h-196h). The remaining 
METHOD parts of the model, and the possible ROTATIONAL SYMMETRY 
METHOD between the two lobes was modeled manually, ab initio.  
METHOD (coordinates generated using SYBYL, Tripos). The ab initio 
METHOD fragments are mostly to accommodate the necessary changes 
METHOD in the structure for adopting a two-lobe structure with 
METHOD a shared part of the core. As such, the overall folding 
METHOD arrangement (topology) is more important in our prediction  
METHOD than the detail conformation of the polypeptide  
METHOD chain of the shortfragments, in the case of T0052! 
METHOD Backbone and C-beta coordinate are submitted, but the 
METHOD model is to be considered at the resolution equivalent 
METHOD to not more than a wire model... 
MODEL 1 
REMARK     T0052 Cyanovirin-N, Nostoc ellipsosporum 
PARENT 1prc_H 
ATOM     73  N   ASN    10      16.160  -3.408   3.972  1.00 10.00               
ATOM     74  CA  ASN    10      16.649  -3.133   2.627  1.00 10.00               
ATOM     75  C   ASN    10      16.047  -4.114   1.658  1.00 10.00               
ATOM     76  O   ASN    10      16.564  -5.212   1.532  1.00 10.00               
ATOM     77  CB  ASN    10      18.189  -3.199   2.519  1.00 10.00               
ATOM     81  N   SER    11      14.954  -3.688   0.986  1.00 10.00               
ATOM     82  CA  SER    11      14.215  -4.544   0.060  1.00 10.00               
ATOM     83  C   SER    11      12.738  -4.296   0.232  1.00 10.00               
ATOM     84  O   SER    11      12.034  -5.135   0.772  1.00 10.00               
ATOM     85  CB  SER    11      14.516  -6.059   0.128  1.00 10.00               
ATOM     87  N   ALA    12      12.249  -3.129  -0.232  1.00 10.00               
ATOM     88  CA  ALA    12      10.837  -2.831  -0.047  1.00 10.00               
ATOM     89  C   ALA    12       9.956  -3.816  -0.767  1.00 10.00               
ATOM     90  O   ALA    12       9.995  -3.896  -1.985  1.00 10.00               
ATOM     91  CB  ALA    12      10.553  -1.399  -0.533  1.00 10.00               
ATOM     92  N   ILE    13       9.165  -4.577   0.017  1.00 10.00               
ATOM     93  CA  ILE    13       8.364  -5.646  -0.560  1.00 10.00               
ATOM     94  C   ILE    13       6.930  -5.304  -0.862  1.00 10.00               
ATOM     95  O   ILE    13       6.183  -5.087   0.078  1.00 10.00               
ATOM     96  CB  ILE    13       9.091  -6.638  -1.491  1.00 10.00               
ATOM    100  N   GLN    14       6.518  -5.261  -2.146  1.00 10.00               
ATOM    101  CA  GLN    14       5.129  -4.908  -2.403  1.00 10.00               
ATOM    102  C   GLN    14       4.216  -6.086  -2.623  1.00 10.00               
ATOM    103  O   GLN    14       3.481  -6.403  -1.701  1.00 10.00               
ATOM    104  CB  GLN    14       4.938  -3.788  -3.443  1.00 10.00               
ATOM    109  N   GLY    15       4.216  -6.736  -3.810  1.00 10.00               
ATOM    110  CA  GLY    15       3.272  -7.825  -3.985  1.00 10.00               
ATOM    111  C   GLY    15       4.040  -9.058  -4.361  1.00 10.00               
ATOM    112  O   GLY    15       3.802  -9.587  -5.434  1.00 10.00               
ATOM    113  N   SER    16       4.978  -9.496  -3.491  1.00 10.00               
ATOM    114  CA  SER    16       5.872 -10.593  -3.843  1.00 10.00               
ATOM    115  C   SER    16       7.118 -10.091  -4.519  1.00 10.00               
ATOM    116  O   SER    16       8.183 -10.579  -4.182  1.00 10.00               
ATOM    117  CB  SER    16       5.229 -11.719  -4.682  1.00 10.00               
ATOM    119  N   VAL    17       7.031  -9.146  -5.480  1.00 10.00               
ATOM    120  CA  VAL    17       8.250  -8.698  -6.133  1.00 10.00               
ATOM    121  C   VAL    17       8.989  -7.719  -5.264  1.00 10.00               
ATOM    122  O   VAL    17       8.360  -6.939  -4.567  1.00 10.00               
ATOM    123  CB  VAL    17       7.993  -8.108  -7.537  1.00 10.00               
ATOM    126  N   LEU    18      10.335  -7.736  -5.305  1.00 10.00               
ATOM    127  CA  LEU    18      11.053  -6.715  -4.562  1.00 10.00               
ATOM    128  C   LEU    18      10.966  -5.417  -5.316  1.00 10.00               
ATOM    129  O   LEU    18      11.350  -5.359  -6.474  1.00 10.00               
ATOM    130  CB  LEU    18      12.527  -7.119  -4.374  1.00 10.00               
ATOM    134  N   THR    19      10.435  -4.372  -4.653  1.00 10.00               
ATOM    135  CA  THR    19      10.216  -3.124  -5.364  1.00 10.00               
ATOM    136  C   THR    19      11.340  -2.152  -5.149  1.00 10.00               
ATOM    137  O   THR    19      11.904  -1.670  -6.118  1.00 10.00               
ATOM    138  CB  THR    19       8.888  -2.492  -4.905  1.00 10.00               
ATOM    141  N   SER    20      11.645  -1.845  -3.873  1.00 10.00               
ATOM    142  CA  SER    20      12.665  -0.844  -3.608  1.00 10.00               
ATOM    143  C   SER    20      13.667  -1.388  -2.629  1.00 10.00               
ATOM    144  O   SER    20      13.830  -2.596  -2.564  1.00 10.00               
ATOM    145  CB  SER    20      11.972   0.417  -3.060  1.00 10.00               
ATOM    147  N   THR    21      14.349  -0.517  -1.857  1.00 10.00               
ATOM    148  CA  THR    21      15.363  -1.050  -0.963  1.00 10.00               
ATOM    149  C   THR    21      15.419  -0.377   0.382  1.00 10.00               
ATOM    150  O   THR    21      16.510  -0.158   0.884  1.00 10.00               
ATOM    151  CB  THR    21      16.741  -1.149  -1.650  1.00 10.00               
ATOM    154  N   CYS    22      14.236  -0.074   0.960  1.00 10.00               
ATOM    155  CA  CYS    22      14.162   0.396   2.343  1.00 10.00               
ATOM    156  C   CYS    22      15.293   1.329   2.719  1.00 10.00               
ATOM    157  O   CYS    22      16.205   0.935   3.428  1.00 10.00               
ATOM    158  CB  CYS    22      14.034  -0.818   3.296  1.00 10.00               
ATOM    160  N   GLU    23      15.255   2.585   2.237  1.00 10.00               
ATOM    161  CA  GLU    23      16.416   3.446   2.422  1.00 10.00               
ATOM    162  C   GLU    23      16.501   4.165   3.744  1.00 10.00               
ATOM    163  O   GLU    23      17.265   3.747   4.600  1.00 10.00               
ATOM    164  CB  GLU    23      16.508   4.465   1.272  1.00 10.00               
ATOM    169  N   ARG    24      15.745   5.273   3.881  1.00 10.00               
ATOM    170  CA  ARG    24      15.953   6.139   5.029  1.00 10.00               
ATOM    171  C   ARG    24      14.653   6.395   5.745  1.00 10.00               
ATOM    172  O   ARG    24      13.666   5.730   5.472  1.00 10.00               
ATOM    173  CB  ARG    24      16.530   7.462   4.480  1.00 10.00               
ATOM    180  N   THR    25      14.652   7.371   6.674  1.00 10.00               
ATOM    181  CA  THR    25      13.423   7.635   7.406  1.00 10.00               
ATOM    182  C   THR    25      13.240   9.107   7.656  1.00 10.00               
ATOM    183  O   THR    25      14.203   9.853   7.729  1.00 10.00               
ATOM    184  CB  THR    25      13.394   6.839   8.728  1.00 10.00               
ATOM    187  N   ASN    26      11.963   9.515   7.782  1.00 10.00               
ATOM    188  CA  ASN    26      11.665  10.916   8.040  1.00 10.00               
ATOM    189  C   ASN    26      11.107  11.040   9.434  1.00 10.00               
ATOM    190  O   ASN    26      11.387  10.176  10.250  1.00 10.00               
ATOM    191  CB  ASN    26      10.602  11.335   7.007  1.00 10.00               
ATOM    195  N   GLY    27      10.305  12.093   9.720  1.00 10.00               
ATOM    196  CA  GLY    27       9.658  12.141  11.023  1.00 10.00               
ATOM    197  C   GLY    27       8.856  10.880  11.200  1.00 10.00               
ATOM    198  O   GLY    27       9.205  10.075  12.048  1.00 10.00               
ATOM    199  N   GLY    28       7.801  10.690  10.382  1.00 10.00               
ATOM    200  CA  GLY    28       7.126   9.403  10.386  1.00 10.00               
ATOM    201  C   GLY    28       7.204   8.739   9.035  1.00 10.00               
ATOM    202  O   GLY    28       6.348   7.917   8.753  1.00 10.00               
ATOM    203  N   TYR    29       8.210   9.092   8.210  1.00 10.00               
ATOM    204  CA  TYR    29       8.202   8.560   6.860  1.00 10.00               
ATOM    205  C   TYR    29       9.157   7.428   6.637  1.00 10.00               
ATOM    206  O   TYR    29      10.273   7.452   7.129  1.00 10.00               
ATOM    207  CB  TYR    29       8.416   9.648   5.792  1.00 10.00               
ATOM    215  N   ASN    30       8.695   6.431   5.858  1.00 10.00               
ATOM    216  CA  ASN    30       9.631   5.420   5.405  1.00 10.00               
ATOM    217  C   ASN    30      10.046   5.775   4.007  1.00 10.00               
ATOM    218  O   ASN    30       9.198   6.022   3.163  1.00 10.00               
ATOM    219  CB  ASN    30       9.040   3.998   5.428  1.00 10.00               
ATOM    223  N   THR    31      11.370   5.818   3.768  1.00 10.00               
ATOM    224  CA  THR    31      11.807   6.212   2.440  1.00 10.00               
ATOM    225  C   THR    31      12.611   5.110   1.805  1.00 10.00               
ATOM    226  O   THR    31      13.202   4.300   2.501  1.00 10.00               
ATOM    227  CB  THR    31      12.532   7.582   2.473  1.00 10.00               
ATOM    230  N   SER    32      12.607   5.073   0.460  1.00 10.00               
ATOM    231  CA  SER    32      13.362   4.029  -0.214  1.00 10.00               
ATOM    232  C   SER    32      13.597   4.355  -1.664  1.00 10.00               
ATOM    233  O   SER    32      12.941   5.225  -2.215  1.00 10.00               
ATOM    234  CB  SER    32      12.661   2.660  -0.087  1.00 10.00               
ATOM    236  N   SER    33      14.558   3.634  -2.276  1.00 10.00               
ATOM    237  CA  SER    33      14.810   3.847  -3.691  1.00 10.00               
ATOM    238  C   SER    33      14.365   2.645  -4.471  1.00 10.00               
ATOM    239  O   SER    33      14.510   1.529  -3.998  1.00 10.00               
ATOM    240  CB  SER    33      16.312   4.117  -3.907  1.00 10.00               
ATOM    242  N   ILE    34      13.801   2.885  -5.671  1.00 10.00               
ATOM    243  CA  ILE    34      13.235   1.776  -6.416  1.00 10.00               
ATOM    244  C   ILE    34      14.281   0.927  -7.081  1.00 10.00               
ATOM    245  O   ILE    34      15.445   1.292  -7.129  1.00 10.00               
ATOM    246  CB  ILE    34      12.244   2.353  -7.441  1.00 10.00               
ATOM    250  N   ASP    35      13.832  -0.226  -7.615  1.00 10.00               
ATOM    251  CA  ASP    35      14.756  -1.069  -8.350  1.00 10.00               
ATOM    252  C   ASP    35      14.461  -0.914  -9.816  1.00 10.00               
ATOM    253  O   ASP    35      13.345  -1.187 -10.232  1.00 10.00               
ATOM    254  CB  ASP    35      14.586  -2.553  -7.954  1.00 10.00               
ATOM    258  N   LEU    36      15.477  -0.486 -10.592  1.00 10.00               
ATOM    259  CA  LEU    36      15.301  -0.351 -12.036  1.00 10.00               
ATOM    260  C   LEU    36      15.116   1.067 -12.491  1.00 10.00               
ATOM    261  O   LEU    36      15.150   1.288 -13.691  1.00 10.00               
ATOM    262  CB  LEU    36      14.296  -1.299 -12.736  1.00 10.00               
ATOM    266  N   ASN    37      14.919   2.026 -11.564  1.00 10.00               
ATOM    267  CA  ASN    37      14.778   3.401 -12.020  1.00 10.00               
ATOM    268  C   ASN    37      15.299   4.406 -11.025  1.00 10.00               
ATOM    269  O   ASN    37      15.978   4.033 -10.083  1.00 10.00               
ATOM    270  CB  ASN    37      13.349   3.749 -12.482  1.00 10.00               
ATOM    274  N   SER    38      14.995   5.701 -11.246  1.00 10.00               
ATOM    275  CA  SER    38      15.700   6.730 -10.501  1.00 10.00               
ATOM    276  C   SER    38      15.031   7.248  -9.257  1.00 10.00               
ATOM    277  O   SER    38      15.485   6.922  -8.172  1.00 10.00               
ATOM    278  CB  SER    38      16.105   7.887 -11.434  1.00 10.00               
ATOM    280  N   VAL    39      13.982   8.086  -9.402  1.00 10.00               
ATOM    281  CA  VAL    39      13.457   8.801  -8.245  1.00 10.00               
ATOM    282  C   VAL    39      13.058   7.957  -7.058  1.00 10.00               
ATOM    283  O   VAL    39      12.861   6.759  -7.184  1.00 10.00               
ATOM    284  CB  VAL    39      12.588  10.035  -8.596  1.00 10.00               
ATOM    287  N   ILE    40      12.967   8.608  -5.881  1.00 10.00               
ATOM    288  CA  ILE    40      12.747   7.856  -4.654  1.00 10.00               
ATOM    289  C   ILE    40      11.331   7.930  -4.148  1.00 10.00               
ATOM    290  O   ILE    40      10.457   8.397  -4.861  1.00 10.00               
ATOM    291  CB  ILE    40      13.779   8.293  -3.595  1.00 10.00               
ATOM    295  N   GLU    41      11.101   7.447  -2.908  1.00 10.00               
ATOM    296  CA  GLU    41       9.726   7.276  -2.467  1.00 10.00               
ATOM    297  C   GLU    41       9.485   7.604  -1.017  1.00 10.00               
ATOM    298  O   GLU    41      10.409   7.634  -0.222  1.00 10.00               
ATOM    299  CB  GLU    41       9.361   5.790  -2.641  1.00 10.00               
ATOM    304  N   ASN    42       8.198   7.834  -0.688  1.00 10.00               
ATOM    305  CA  ASN    42       7.802   8.021   0.702  1.00 10.00               
ATOM    306  C   ASN    42       6.530   7.249   0.920  1.00 10.00               
ATOM    307  O   ASN    42       5.560   7.496   0.223  1.00 10.00               
ATOM    308  CB  ASN    42       7.477   9.501   0.982  1.00 10.00               
ATOM    312  N   VAL    43       6.509   6.295   1.871  1.00 10.00               
ATOM    313  CA  VAL    43       5.377   5.383   1.889  1.00 10.00               
ATOM    314  C   VAL    43       4.255   5.737   2.830  1.00 10.00               
ATOM    315  O   VAL    43       3.112   5.564   2.438  1.00 10.00               
ATOM    316  CB  VAL    43       5.862   3.924   2.018  1.00 10.00               
TER 
END 
