 
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    450  N   ASN    60     -10.593   8.087  -2.431  1.00 10.00               
ATOM    451  CA  ASN    60     -11.472   6.990  -2.817  1.00 10.00               
ATOM    452  C   ASN    60     -10.919   6.413  -4.098  1.00 10.00               
ATOM    453  O   ASN    60     -10.963   7.136  -5.078  1.00 10.00               
ATOM    454  CB  ASN    60     -12.927   7.468  -3.028  1.00 10.00               
ATOM    458  N   THR    61     -10.386   5.166  -4.054  1.00 10.00               
ATOM    459  CA  THR    61      -9.607   4.552  -5.135  1.00 10.00               
ATOM    460  C   THR    61      -8.242   4.067  -4.675  1.00 10.00               
ATOM    461  O   THR    61      -7.250   4.698  -5.007  1.00 10.00               
ATOM    462  CB  THR    61      -9.416   5.366  -6.435  1.00 10.00               
ATOM    465  N   ASN    62      -8.115   2.941  -3.937  1.00 10.00               
ATOM    466  CA  ASN    62      -6.774   2.507  -3.556  1.00 10.00               
ATOM    467  C   ASN    62      -5.983   2.059  -4.753  1.00 10.00               
ATOM    468  O   ASN    62      -6.306   1.038  -5.339  1.00 10.00               
ATOM    469  CB  ASN    62      -6.642   1.422  -2.468  1.00 10.00               
ATOM    473  N   LEU    63      -4.937   2.832  -5.108  1.00 10.00               
ATOM    474  CA  LEU    63      -4.104   2.464  -6.239  1.00 10.00               
ATOM    475  C   LEU    63      -3.020   1.487  -5.870  1.00 10.00               
ATOM    476  O   LEU    63      -2.102   1.905  -5.184  1.00 10.00               
ATOM    477  CB  LEU    63      -4.870   2.275  -7.568  1.00 10.00               
ATOM    481  N   ALA    64      -3.070   0.207  -6.297  1.00 10.00               
ATOM    482  CA  ALA    64      -1.973  -0.686  -5.950  1.00 10.00               
ATOM    483  C   ALA    64      -0.840  -0.591  -6.940  1.00 10.00               
ATOM    484  O   ALA    64      -1.000   0.044  -7.970  1.00 10.00               
ATOM    485  CB  ALA    64      -2.444  -2.145  -5.791  1.00 10.00               
ATOM    486  N   GLY    65       0.316  -1.224  -6.637  1.00 10.00               
ATOM    487  CA  GLY    65       1.443  -1.178  -7.558  1.00 10.00               
ATOM    488  C   GLY    65       1.115  -1.670  -8.945  1.00 10.00               
ATOM    489  O   GLY    65       1.778  -1.240  -9.875  1.00 10.00               
ATOM    490  N   SER    66       0.098  -2.545  -9.114  1.00 10.00               
ATOM    491  CA  SER    66      -0.278  -2.985 -10.455  1.00 10.00               
ATOM    492  C   SER    66      -0.596  -1.867 -11.416  1.00 10.00               
ATOM    493  O   SER    66      -0.589  -2.138 -12.606  1.00 10.00               
ATOM    494  CB  SER    66      -1.569  -3.835 -10.425  1.00 10.00               
ATOM    496  N   SER    67      -0.905  -0.635 -10.949  1.00 10.00               
ATOM    497  CA  SER    67      -1.488   0.359 -11.837  1.00 10.00               
ATOM    498  C   SER    67      -2.964   0.103 -12.028  1.00 10.00               
ATOM    499  O   SER    67      -3.548   0.686 -12.927  1.00 10.00               
ATOM    500  CB  SER    67      -0.757   0.535 -13.185  1.00 10.00               
ATOM    502  N   GLU    68      -3.594  -0.762 -11.200  1.00 10.00               
ATOM    503  CA  GLU    68      -5.018  -0.993 -11.353  1.00 10.00               
ATOM    504  C   GLU    68      -5.696  -0.572 -10.079  1.00 10.00               
ATOM    505  O   GLU    68      -5.086  -0.658  -9.024  1.00 10.00               
ATOM    506  CB  GLU    68      -5.272  -2.492 -11.618  1.00 10.00               
ATOM    511  N   LEU    69      -6.961  -0.117 -10.163  1.00 10.00               
ATOM    512  CA  LEU    69      -7.654   0.224  -8.934  1.00 10.00               
ATOM    513  C   LEU    69      -7.878  -1.032  -8.141  1.00 10.00               
ATOM    514  O   LEU    69      -8.578  -1.916  -8.605  1.00 10.00               
ATOM    515  CB  LEU    69      -8.983   0.965  -9.170  1.00 10.00               
ATOM    519  N   ALA    70      -7.266  -1.118  -6.943  1.00 10.00               
ATOM    520  CA  ALA    70      -7.435  -2.319  -6.140  1.00 10.00               
ATOM    521  C   ALA    70      -8.674  -2.257  -5.288  1.00 10.00               
ATOM    522  O   ALA    70      -9.382  -3.250  -5.230  1.00 10.00               
ATOM    523  CB  ALA    70      -6.199  -2.575  -5.254  1.00 10.00               
ATOM    524  N   ALA    71      -8.954  -1.116  -4.622  1.00 10.00               
ATOM    525  CA  ALA    71     -10.119  -1.065  -3.748  1.00 10.00               
ATOM    526  C   ALA    71     -10.601   0.361  -3.585  1.00 10.00               
ATOM    527  O   ALA    71     -10.271   1.163  -4.444  1.00 10.00               
ATOM    528  CB  ALA    71      -9.689  -1.731  -2.426  1.00 10.00               
ATOM    529  N   GLU    72     -11.355   0.734  -2.524  1.00 10.00               
ATOM    530  CA  GLU    72     -11.780   2.124  -2.433  1.00 10.00               
ATOM    531  C   GLU    72     -11.648   2.823  -1.103  1.00 10.00               
ATOM    532  O   GLU    72     -12.587   2.805  -0.324  1.00 10.00               
ATOM    533  CB  GLU    72     -13.076   2.449  -3.194  1.00 10.00               
ATOM    538  N   CYS    73     -10.465   3.452  -0.906  1.00 10.00               
ATOM    539  CA  CYS    73     -10.139   4.290   0.248  1.00 10.00               
ATOM    540  C   CYS    73     -11.326   4.549   1.147  1.00 10.00               
ATOM    541  O   CYS    73     -12.044   5.511   0.927  1.00 10.00               
ATOM    542  CB  CYS    73      -9.445   5.589  -0.255  1.00 10.00               
ATOM    544  N   LYS    74     -11.569   3.676   2.150  1.00 10.00               
ATOM    545  CA  LYS    74     -12.837   3.748   2.870  1.00 10.00               
ATOM    546  C   LYS    74     -12.832   4.461   4.197  1.00 10.00               
ATOM    547  O   LYS    74     -13.422   5.526   4.275  1.00 10.00               
ATOM    548  CB  LYS    74     -13.441   2.350   3.086  1.00 10.00               
ATOM    553  N   THR    75     -12.213   3.890   5.254  1.00 10.00               
ATOM    554  CA  THR    75     -12.275   4.538   6.557  1.00 10.00               
ATOM    555  C   THR    75     -10.896   4.698   7.140  1.00 10.00               
ATOM    556  O   THR    75      -9.932   4.347   6.480  1.00 10.00               
ATOM    557  CB  THR    75     -13.228   3.780   7.513  1.00 10.00               
ATOM    560  N   ARG    76     -10.780   5.211   8.381  1.00 10.00               
ATOM    561  CA  ARG    76      -9.459   5.281   8.979  1.00 10.00               
ATOM    562  C   ARG    76      -9.433   4.693  10.362  1.00 10.00               
ATOM    563  O   ARG    76     -10.415   4.794  11.081  1.00 10.00               
ATOM    564  CB  ARG    76      -8.874   6.704   8.941  1.00 10.00               
ATOM    571  N   ALA    77      -8.300   4.066  10.734  1.00 10.00               
ATOM    572  CA  ALA    77      -8.190   3.519  12.075  1.00 10.00               
ATOM    573  C   ALA    77      -7.212   4.344  12.868  1.00 10.00               
ATOM    574  O   ALA    77      -6.716   5.331  12.347  1.00 10.00               
ATOM    575  CB  ALA    77      -7.712   2.054  12.000  1.00 10.00               
ATOM    576  N   GLN    78      -6.916   3.948  14.126  1.00 10.00               
ATOM    577  CA  GLN    78      -5.930   4.691  14.901  1.00 10.00               
ATOM    578  C   GLN    78      -4.667   4.864  14.102  1.00 10.00               
ATOM    579  O   GLN    78      -4.146   5.966  14.067  1.00 10.00               
ATOM    580  CB  GLN    78      -5.523   3.968  16.198  1.00 10.00               
ATOM    585  N   GLN    79      -4.168   3.796  13.443  1.00 10.00               
ATOM    586  CA  GLN    79      -2.982   3.980  12.621  1.00 10.00               
ATOM    587  C   GLN    79      -3.042   3.262  11.299  1.00 10.00               
ATOM    588  O   GLN    79      -2.006   2.852  10.798  1.00 10.00               
ATOM    589  CB  GLN    79      -1.736   3.460  13.354  1.00 10.00               
ATOM    594  N   PHE    80      -4.234   3.073  10.703  1.00 10.00               
ATOM    595  CA  PHE    80      -4.264   2.280   9.489  1.00 10.00               
ATOM    596  C   PHE    80      -5.262   2.824   8.509  1.00 10.00               
ATOM    597  O   PHE    80      -6.161   3.537   8.923  1.00 10.00               
ATOM    598  CB  PHE    80      -4.680   0.847   9.861  1.00 10.00               
ATOM    605  N   VAL    81      -5.135   2.498   7.208  1.00 10.00               
ATOM    606  CA  VAL    81      -6.212   2.882   6.316  1.00 10.00               
ATOM    607  C   VAL    81      -7.175   1.741   6.164  1.00 10.00               
ATOM    608  O   VAL    81      -6.769   0.591   6.222  1.00 10.00               
ATOM    609  CB  VAL    81      -5.863   3.602   4.999  1.00 10.00               
ATOM    612  N   SER    82      -8.470   2.062   5.993  1.00 10.00               
ATOM    613  CA  SER    82      -9.452   0.999   5.902  1.00 10.00               
ATOM    614  C   SER    82     -10.012   0.993   4.512  1.00 10.00               
ATOM    615  O   SER    82     -10.410   2.044   4.037  1.00 10.00               
ATOM    616  CB  SER    82     -10.556   1.206   6.953  1.00 10.00               
ATOM    618  N   THR    83     -10.025  -0.172   3.836  1.00 10.00               
ATOM    619  CA  THR    83     -10.405  -0.138   2.440  1.00 10.00               
ATOM    620  C   THR    83     -11.371  -1.204   2.005  1.00 10.00               
ATOM    621  O   THR    83     -11.369  -2.284   2.571  1.00 10.00               
ATOM    622  CB  THR    83      -9.149  -0.133   1.553  1.00 10.00               
ATOM    625  N   LYS    84     -12.206  -0.890   0.990  1.00 10.00               
ATOM    626  CA  LYS    84     -13.121  -1.896   0.471  1.00 10.00               
ATOM    627  C   LYS    84     -12.527  -2.555  -0.745  1.00 10.00               
ATOM    628  O   LYS    84     -12.278  -1.867  -1.721  1.00 10.00               
ATOM    629  CB  LYS    84     -14.486  -1.276   0.110  1.00 10.00               
ATOM    634  N   ILE    85     -12.307  -3.886  -0.698  1.00 10.00               
ATOM    635  CA  ILE    85     -11.661  -4.547  -1.825  1.00 10.00               
ATOM    636  C   ILE    85     -12.522  -4.631  -3.060  1.00 10.00               
ATOM    637  O   ILE    85     -13.719  -4.838  -2.943  1.00 10.00               
ATOM    638  CB  ILE    85     -11.046  -5.912  -1.446  1.00 10.00               
ATOM    642  N   ASN    86     -11.910  -4.466  -4.254  1.00 10.00               
ATOM    643  CA  ASN    86     -12.696  -4.532  -5.479  1.00 10.00               
ATOM    644  C   ASN    86     -12.978  -5.950  -5.895  1.00 10.00               
ATOM    645  O   ASN    86     -12.164  -6.821  -5.635  1.00 10.00               
ATOM    646  CB  ASN    86     -12.035  -3.809  -6.670  1.00 10.00               
ATOM    650  N   LEU    87     -14.142  -6.178  -6.541  1.00 10.00               
ATOM    651  CA  LEU    87     -14.501  -7.521  -6.972  1.00 10.00               
ATOM    652  C   LEU    87     -14.419  -8.544  -5.869  1.00 10.00               
ATOM    653  O   LEU    87     -14.049  -9.680  -6.126  1.00 10.00               
ATOM    654  CB  LEU    87     -13.746  -7.929  -8.253  1.00 10.00               
ATOM    658  N   ASP    88     -14.762  -8.142  -4.625  1.00 10.00               
ATOM    659  CA  ASP    88     -14.683  -9.078  -3.512  1.00 10.00               
ATOM    660  C   ASP    88     -15.671  -8.720  -2.432  1.00 10.00               
ATOM    661  O   ASP    88     -16.262  -7.654  -2.484  1.00 10.00               
ATOM    662  CB  ASP    88     -13.275  -9.069  -2.883  1.00 10.00               
ATOM    666  N   ASP    89     -15.857  -9.611  -1.435  1.00 10.00               
ATOM    667  CA  ASP    89     -16.739  -9.270  -0.328  1.00 10.00               
ATOM    668  C   ASP    89     -15.994  -8.568   0.785  1.00 10.00               
ATOM    669  O   ASP    89     -16.547  -7.667   1.395  1.00 10.00               
ATOM    670  CB  ASP    89     -17.388 -10.527   0.300  1.00 10.00               
ATOM    674  N   HIS    90     -14.745  -8.995   1.065  1.00 10.00               
ATOM    675  CA  HIS    90     -14.044  -8.553   2.265  1.00 10.00               
ATOM    676  C   HIS    90     -13.515  -7.141   2.263  1.00 10.00               
ATOM    677  O   HIS    90     -13.628  -6.433   1.275  1.00 10.00               
ATOM    678  CB  HIS    90     -12.880  -9.518   2.598  1.00 10.00               
ATOM    684  N   ILE    91     -12.913  -6.747   3.407  1.00 10.00               
ATOM    685  CA  ILE    91     -12.261  -5.448   3.490  1.00 10.00               
ATOM    686  C   ILE    91     -10.886  -5.620   4.089  1.00 10.00               
ATOM    687  O   ILE    91     -10.707  -6.545   4.866  1.00 10.00               
ATOM    688  CB  ILE    91     -13.122  -4.463   4.310  1.00 10.00               
ATOM    692  N   ALA    92      -9.895  -4.771   3.743  1.00 10.00               
ATOM    693  CA  ALA    92      -8.562  -5.016   4.264  1.00 10.00               
ATOM    694  C   ALA    92      -8.025  -3.794   4.953  1.00 10.00               
ATOM    695  O   ALA    92      -8.533  -2.706   4.738  1.00 10.00               
ATOM    696  CB  ALA    92      -7.599  -5.502   3.163  1.00 10.00               
ATOM    697  N   ASN    93      -6.996  -3.971   5.801  1.00 10.00               
ATOM    698  CA  ASN    93      -6.441  -2.819   6.492  1.00 10.00               
ATOM    699  C   ASN    93      -5.068  -2.599   5.932  1.00 10.00               
ATOM    700  O   ASN    93      -4.515  -3.596   5.514  1.00 10.00               
ATOM    701  CB  ASN    93      -6.321  -3.209   7.979  1.00 10.00               
ATOM    705  N   ILE    94      -4.492  -1.379   5.890  1.00 10.00               
ATOM    706  CA  ILE    94      -3.098  -1.277   5.469  1.00 10.00               
ATOM    707  C   ILE    94      -2.153  -1.037   6.626  1.00 10.00               
ATOM    708  O   ILE    94      -1.595   0.040   6.757  1.00 10.00               
ATOM    709  CB  ILE    94      -2.779  -0.799   4.030  1.00 10.00               
TER 
END 
