REMARK  ---------------------------------------------------------- 
REMARK  Molecule : T0074AL156_2_1 
REMARK  Alignment model prepared for CASP3 experiment 
REMARK  by group : BENNER-COHEN 
REMARK  ---------------------------------------------------------- 
TARGET T0074  
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, F.E.Cohen & S.A.Benner.  
REMARK  
REMARK This threading alignment prediction is not accompanied by  
REMARK a separate secondary structure submission.  
METHOD  
METHOD The PROSITE motif for EF-hand proteins (Bairoch/Cox/Kretsinger)  
METHOD revealed the most probable fold for this target. Further, we used  
METHOD the UCLA-DOE Fold Recognition server (Eisenberg/Fischer/Rice) which  
METHOD returned a number of different structures of this fold as top ranked,  
METHOD some above significance threshold. We also ran ProCyon (Sippl), which  
METHOD did not seem to return a conclusive match in our hands; finally, we  
METHOD looked at the predicted secondary structures by the PredictProtein-  
METHOD Server (PHD, Rost) and by a new method by Chandonia in our laboratory,  
METHOD besides our own. The latter two methods in the list were applied on  
METHOD a multiple sequence alignment including 28 sequences, uniting homologous  
METHOD sequence fragments to all three EH-domains found in EP15_HUMAN. The  
METHOD width and balanced distribution of this master alignment has certainly  
METHOD had an effect on our prediction.   
METHOD   
METHOD Departing from the assumption that T0074 folds into a EF-hand-like  
METHOD structure still leaves open a wide variety in 3D-structures, as the  
METHOD members of the fold/motif family display variation in the relative  
METHOD orientation of the two EF-hands as well as in the dihedral angle   
METHOD between the two helices composing one EF-hand, and in the mode of  
METHOD calcium-binding per se. Therefore, we attempted to find the most  
METHOD suitable candidates for parent structures by a manual approach that  
METHOD could be summarized as a "knowledge-enhanced profile threading" which   
METHOD is explained below.  
METHOD  
METHOD We considered 10 representative structures covering the (6) families  
METHOD of EF-hand-like proteins classified in the SCOP database (Murzin/  
METHOD Brenner/Chothia), and studied which positions in the corresponding   
METHOD HSSP-alignments (Sander) seemed to play important structural roles  
METHOD in each protein family. Notably, we tried to (a) distinguish between  
METHOD positions that appeared to be conserved for structural and functional  
METHOD reasons, respectively, and (b) to also identify structurally important  
METHOD positions which were not absolutely conserved in the alignment, simply  
METHOD by looking at the structures. Then, applied a manual equivalent to a   
METHOD profile-based threading method with primary emphasis on patterns of   
METHOD variation and conservation of residues in the target and reference  
METHOD multiple sequence alignments. However, we attributed very much higher  
METHOD weight to matching the positions we had identified/predicted as  
METHOD structurally essential in this procedure. In short, this would include  
METHOD to ask "WHY" is a position conserved in the reference sequence alignment,  
METHOD and to avoid unexplained conserved positions in the target sequence  
METHOD alignment. In the first EF-hand, for example, we noted the uncommon  
METHOD conservation of Gly 144 within the EF-hand motif region. One possible  
METHOD explanation for conservation of this Gly (or Ala) could be to make  
METHOD space, or a sharp turn, because another part of the protein is near,  
METHOD and rigid. We found an example for this in the 3nd (pseudo-)EF-hand of  
METHOD 1scm_C, and have modeled the first EF-hand of T0074 based on this  
METHOD structure. The fix points in all EF-hands is the beta-bridge, and  
METHOD this will be the case for T0074 as well. However, we had difficulties  
METHOD to propose an unambiguous alignment for the 2nd EF-hand in T0074  
METHOD with the 1scm_C coordinates, because of the mandatory short connection  
METHOD between the two modules (T0074 158-163 approximately). To generate   
METHOD a structure for the entire T0074 based on 1scm would require moving  
METHOD the first helix in the second EF-hand of T0074, or, rather, tilting  
METHOD it differently. As the second EF-hand motif in T0074 seems nicely  
METHOD intact, however, we expect a "classic" calcium-binding site, like  
METHOD the one found in 4icb, for example.  
METHOD  
METHOD Thus, we submit two different models, one pieced together using  
METHOD the 3rd EF-hand of 1scm_C and the 2nd EF-hand of 4icb (the relative  
METHOD orientation would be determined by conserving the beta bridge  
METHOD between T0074 residues 146 and 180), the other based on the 3rd  
METHOD and 4th EF-and-pseudo-EF-hands in 1scm_C but omitting the sequence  
METHOD fragments corresponding to the first helix in the 2nd EF-hand of T0074.  
METHOD  
METHOD Through this prediction, we hope to provide an appreciation for  
METHOD discriminating between globally similar parent structures that  
METHOD do, however, differ in the relative orientation of individual   
METHOD secondary structural elements (segment contacts). While the applied  
METHOD method is entirely experimental at this point, we strongly believe  
METHOD that manual, or automated, assignment of "roles" (e.g. hydrophobic  
METHOD anchor") to particular positions in the fold would prove useful  
METHOD with further development. For example, it is our understanding that  
METHOD the profficiency demonstrated by A.Murzin's submissions at CASP2  
METHOD can, in part, be attributed to such "knowledge-based" assignments.  
METHOD  
REMARK   
REMARK WE HAVE GENERATED A COORDINATE MODEL FOR T0074 ALSO (WHICH IS MODEL1).  
REMARK THE COORDINATE MODEL WILL BE A COMPOSITE OF 2 EF-HANDS TAKEN FROM THE  
REMARK PDB STRUCTURES 1SCM_C(1.EF-HAND) AND 4ICB(2.EF-HAND). MODEL 2 IS THUS  
REMARK THE INTENDED SAME MODEL IN AL SUBMISSION FORMAT (WE WANTED TO AVOID  
REMARK THE FRAGMENTATION OF OUR MODEL, PROVIDED AL FORMAT WILL BE TRANSLATED  
REMARK TO TS FORMAT AND ACTUALLY REPLACE THE SAME MODEL NUMBER! MODEL 3  
REMARK IS BASED ONLY ON ONE PARENT STRUCTURE, WITH ONE OF THE HELICES  
REMARK MISSING AS WE WOULD HAVE HAD TO REORIENT IT (SEE ABOVE).  
REMARK IN BRIEF: MODEL 1 (TS) IS WHAT WE THOUGHT MODEL 2 (AL) WOULD  
REMARK LOOK LIKE IF TRANSLATED INTO COORDINATES *AS A WHOLE*.  
REMARK   
REMARK OUR TRUE FAVORITE IS MODEL 1.  
REMARK  
MODEL  2  
REMARK  ---------------------------------------------------------- 
REMARK  AL2TS service [v. 08/06/1998]: Adam Zemla, adamz@llnl.gov 
REMARK  ---------------------------------------------------------- 
REMARK  Coordinates assigned from PDB entry: 1scm_C 
ATOM      1  N   LYS   129     -30.042  22.862  80.388  1.00  0.00              
ATOM      2  CA  LYS   129     -29.989  23.671  81.593  1.00  0.00              
ATOM      3  C   LYS   129     -30.734  23.000  82.731  1.00  0.00              
ATOM      4  O   LYS   129     -30.298  23.031  83.885  1.00  0.00              
ATOM      5  N   ALA   130     -31.836  22.329  82.398  1.00  0.00              
ATOM      6  CA  ALA   130     -32.630  21.664  83.403  1.00  0.00              
ATOM      7  C   ALA   130     -31.873  20.576  84.121  1.00  0.00              
ATOM      8  O   ALA   130     -31.965  20.447  85.340  1.00  0.00              
ATOM      9  N   LYS   131     -31.086  19.825  83.356  1.00  0.00              
ATOM     10  CA  LYS   131     -30.353  18.704  83.905  1.00  0.00              
ATOM     11  C   LYS   131     -29.322  19.216  84.885  1.00  0.00              
ATOM     12  O   LYS   131     -29.200  18.755  86.020  1.00  0.00              
ATOM     13  N   TYR   132     -28.625  20.243  84.394  1.00  0.00              
ATOM     14  CA  TYR   132     -27.526  20.835  85.097  1.00  0.00              
ATOM     15  C   TYR   132     -27.980  21.402  86.423  1.00  0.00              
ATOM     16  O   TYR   132     -27.345  21.275  87.472  1.00  0.00              
ATOM     17  N   ASP   133     -29.160  21.972  86.427  1.00  0.00              
ATOM     18  CA  ASP   133     -29.638  22.539  87.660  1.00  0.00              
ATOM     19  C   ASP   133     -30.303  21.513  88.536  1.00  0.00              
ATOM     20  O   ASP   133     -30.233  21.773  89.727  1.00  0.00              
ATOM     21  N   ALA   134     -30.902  20.373  88.092  1.00  0.00              
ATOM     22  CA  ALA   134     -31.451  19.416  89.059  1.00  0.00              
ATOM     23  C   ALA   134     -30.283  18.625  89.627  1.00  0.00              
ATOM     24  O   ALA   134     -30.279  18.298  90.815  1.00  0.00              
ATOM     25  N   ILE   135     -29.223  18.423  88.824  1.00  0.00              
ATOM     26  CA  ILE   135     -27.973  17.772  89.248  1.00  0.00              
ATOM     27  C   ILE   135     -27.262  18.608  90.294  1.00  0.00              
ATOM     28  O   ILE   135     -26.976  18.149  91.392  1.00  0.00              
ATOM     29  N   PHE   136     -27.023  19.875  90.004  1.00  0.00              
ATOM     30  CA  PHE   136     -26.495  20.772  90.987  1.00  0.00              
ATOM     31  C   PHE   136     -27.481  21.093  92.101  1.00  0.00              
ATOM     32  O   PHE   136     -27.078  21.839  93.002  1.00  0.00              
ATOM     33  N   ASP   137     -28.740  20.614  92.154  1.00  0.00              
ATOM     34  CA  ASP   137     -29.549  20.914  93.344  1.00  0.00              
ATOM     35  C   ASP   137     -28.931  20.061  94.417  1.00  0.00              
ATOM     36  O   ASP   137     -28.403  20.695  95.309  1.00  0.00              
ATOM     37  N   SER   138     -29.040  18.724  94.359  1.00  0.00              
ATOM     38  CA  SER   138     -28.417  17.743  95.227  1.00  0.00              
ATOM     39  C   SER   138     -27.453  18.249  96.295  1.00  0.00              
ATOM     40  O   SER   138     -27.580  17.990  97.485  1.00  0.00              
ATOM     41  N   LEU   139     -26.473  19.035  95.861  1.00  0.00              
ATOM     42  CA  LEU   139     -25.412  19.547  96.701  1.00  0.00              
ATOM     43  C   LEU   139     -25.794  20.849  97.438  1.00  0.00              
ATOM     44  O   LEU   139     -24.987  21.432  98.166  1.00  0.00              
ATOM     45  N   SER   140     -27.054  21.293  97.353  1.00  0.00              
ATOM     46  CA  SER   140     -27.532  22.518  97.956  1.00  0.00              
ATOM     47  C   SER   140     -28.323  22.037  99.153  1.00  0.00              
ATOM     48  O   SER   140     -29.534  21.802  99.116  1.00  0.00              
ATOM     49  N   ASN   143     -30.723  27.937  98.929  1.00  0.00              
ATOM     50  CA  ASN   143     -30.445  29.198  98.248  1.00  0.00              
ATOM     51  C   ASN   143     -29.355  28.625  97.400  1.00  0.00              
ATOM     52  O   ASN   143     -28.535  27.860  97.903  1.00  0.00              
ATOM     53  N   GLY   144     -29.349  28.984  96.137  1.00  0.00              
ATOM     54  CA  GLY   144     -28.548  28.358  95.101  1.00  0.00              
ATOM     55  C   GLY   144     -27.035  28.351  95.197  1.00  0.00              
ATOM     56  O   GLY   144     -26.404  28.625  94.181  1.00  0.00              
ATOM     57  N   PHE   145     -26.511  27.807  96.311  1.00  0.00              
ATOM     58  CA  PHE   145     -25.117  27.746  96.692  1.00  0.00              
ATOM     59  C   PHE   145     -24.633  26.321  96.951  1.00  0.00              
ATOM     60  O   PHE   145     -25.227  25.480  97.637  1.00  0.00              
ATOM     61  N   LEU   146     -23.467  26.124  96.353  1.00  0.00              
ATOM     62  CA  LEU   146     -22.664  24.919  96.465  1.00  0.00              
ATOM     63  C   LEU   146     -21.336  25.567  96.807  1.00  0.00              
ATOM     64  O   LEU   146     -20.890  26.506  96.137  1.00  0.00              
ATOM     65  N   SER   147     -20.692  25.091  97.873  1.00  0.00              
ATOM     66  CA  SER   147     -19.491  25.749  98.331  1.00  0.00              
ATOM     67  C   SER   147     -18.381  25.599  97.328  1.00  0.00              
ATOM     68  O   SER   147     -18.545  24.999  96.263  1.00  0.00              
ATOM     69  N   GLY   148     -17.257  26.207  97.671  1.00  0.00              
ATOM     70  CA  GLY   148     -16.105  26.096  96.826  1.00  0.00              
ATOM     71  C   GLY   148     -15.695  24.634  96.778  1.00  0.00              
ATOM     72  O   GLY   148     -15.853  23.957  95.765  1.00  0.00              
ATOM     73  N   ASP   149     -15.243  24.158  97.929  1.00  0.00              
ATOM     74  CA  ASP   149     -14.772  22.815  98.087  1.00  0.00              
ATOM     75  C   ASP   149     -15.692  21.823  97.407  1.00  0.00              
ATOM     76  O   ASP   149     -15.246  21.179  96.465  1.00  0.00              
ATOM     77  N   LYS   150     -16.988  21.830  97.758  1.00  0.00              
ATOM     78  CA  LYS   150     -17.984  20.916  97.193  1.00  0.00              
ATOM     79  C   LYS   150     -18.083  20.921  95.687  1.00  0.00              
ATOM     80  O   LYS   150     -18.284  19.879  95.066  1.00  0.00              
ATOM     81  N   VAL   151     -17.890  22.083  95.096  1.00  0.00              
ATOM     82  CA  VAL   151     -17.943  22.169  93.661  1.00  0.00              
ATOM     83  C   VAL   151     -16.785  21.491  92.962  1.00  0.00              
ATOM     84  O   VAL   151     -17.066  20.768  92.013  1.00  0.00              
ATOM     85  N   LYS   152     -15.507  21.652  93.331  1.00  0.00              
ATOM     86  CA  LYS   152     -14.487  20.923  92.609  1.00  0.00              
ATOM     87  C   LYS   152     -14.347  19.512  93.142  1.00  0.00              
ATOM     88  O   LYS   152     -13.582  18.733  92.587  1.00  0.00              
ATOM     89  N   PRO   153     -15.034  19.104  94.222  1.00  0.00              
ATOM     90  CA  PRO   153     -15.054  17.697  94.547  1.00  0.00              
ATOM     91  C   PRO   153     -16.055  17.187  93.598  1.00  0.00              
ATOM     92  O   PRO   153     -15.558  16.407  92.799  1.00  0.00              
ATOM     93  N   VAL   154     -17.311  17.658  93.467  1.00  0.00              
ATOM     94  CA  VAL   154     -18.210  17.016  92.498  1.00  0.00              
ATOM     95  C   VAL   154     -17.813  17.081  91.012  1.00  0.00              
ATOM     96  O   VAL   154     -18.476  16.507  90.147  1.00  0.00              
ATOM     97  N   LEU   155     -16.735  17.762  90.655  1.00  0.00              
ATOM     98  CA  LEU   155     -16.320  17.820  89.279  1.00  0.00              
ATOM     99  C   LEU   155     -15.161  16.905  89.016  1.00  0.00              
ATOM    100  O   LEU   155     -14.967  16.539  87.864  1.00  0.00              
ATOM    101  N   LEU   156     -14.371  16.565  90.042  1.00  0.00              
ATOM    102  CA  LEU   156     -13.163  15.748  89.908  1.00  0.00              
ATOM    103  C   LEU   156     -13.266  14.364  90.548  1.00  0.00              
ATOM    104  O   LEU   156     -12.504  13.466  90.213  1.00  0.00              
ATOM    105  N   ASN   157     -14.173  14.185  91.504  1.00  0.00              
ATOM    106  CA  ASN   157     -14.399  12.934  92.222  1.00  0.00              
ATOM    107  C   ASN   157     -15.439  12.032  91.589  1.00  0.00              
ATOM    108  O   ASN   157     -15.552  10.858  91.966  1.00  0.00              
ATOM    109  N   SER   158     -16.184  12.617  90.638  1.00  0.00              
ATOM    110  CA  SER   158     -17.362  12.010  90.027  1.00  0.00              
ATOM    111  C   SER   158     -17.392  12.110  88.513  1.00  0.00              
ATOM    112  O   SER   158     -16.511  12.656  87.833  1.00  0.00              
END
