REMARK  ---------------------------------------------------------- 
REMARK  Molecule : T0074AL156_2_2 
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: 4icb 
ATOM      1  N   ARG   167      17.869   9.070  18.110  1.00  0.00              
ATOM      2  CA  ARG   167      17.938   7.699  17.723  1.00  0.00              
ATOM      3  C   ARG   167      17.653   7.441  16.281  1.00  0.00              
ATOM      4  O   ARG   167      18.318   6.633  15.594  1.00  0.00              
ATOM      5  N   VAL   168      16.636   8.130  15.770  1.00  0.00              
ATOM      6  CA  VAL   168      16.296   8.010  14.345  1.00  0.00              
ATOM      7  C   VAL   168      17.562   8.520  13.526  1.00  0.00              
ATOM      8  O   VAL   168      17.962   7.836  12.638  1.00  0.00              
ATOM      9  N   TRP   169      18.050   9.670  13.871  1.00  0.00              
ATOM     10  CA  TRP   169      19.255  10.173  13.123  1.00  0.00              
ATOM     11  C   TRP   169      20.387   9.139  13.092  1.00  0.00              
ATOM     12  O   TRP   169      20.985   8.905  12.040  1.00  0.00              
ATOM     13  N   GLU   170      20.673   8.610  14.296  1.00  0.00              
ATOM     14  CA  GLU   170      21.747   7.590  14.428  1.00  0.00              
ATOM     15  C   GLU   170      21.485   6.398  13.610  1.00  0.00              
ATOM     16  O   GLU   170      22.389   5.800  12.999  1.00  0.00              
ATOM     17  N   LEU   171      20.234   5.973  13.457  1.00  0.00              
ATOM     18  CA  LEU   171      19.909   4.821  12.639  1.00  0.00              
ATOM     19  C   LEU   171      20.063   5.017  11.147  1.00  0.00              
ATOM     20  O   LEU   171      20.409   4.107  10.389  1.00  0.00              
ATOM     21  N   SER   172      19.668   6.216  10.671  1.00  0.00              
ATOM     22  CA  SER   172      19.691   6.604   9.289  1.00  0.00              
ATOM     23  C   SER   172      21.165   6.846   8.776  1.00  0.00              
ATOM     24  O   SER   172      21.445   6.528   7.632  1.00  0.00              
ATOM     25  N   ASP   173      21.889   7.420   9.736  1.00  0.00              
ATOM     26  CA  ASP   173      23.315   7.751   9.417  1.00  0.00              
ATOM     27  C   ASP   173      24.194   6.494   9.524  1.00  0.00              
ATOM     28  O   ASP   173      24.962   6.337  10.489  1.00  0.00              
ATOM     29  N   ILE   174      24.188   5.664   8.542  1.00  0.00              
ATOM     30  CA  ILE   174      24.929   4.424   8.493  1.00  0.00              
ATOM     31  C   ILE   174      26.445   4.599   8.528  1.00  0.00              
ATOM     32  O   ILE   174      27.153   3.846   9.302  1.00  0.00              
ATOM     33  N   ASP   175      26.958   5.540   7.729  1.00  0.00              
ATOM     34  CA  ASP   175      28.424   5.705   7.705  1.00  0.00              
ATOM     35  C   ASP   175      28.878   6.517   8.866  1.00  0.00              
ATOM     36  O   ASP   175      30.137   6.712   8.888  1.00  0.00              
ATOM     37  N   HIS   176      28.083   7.028   9.738  1.00  0.00              
ATOM     38  CA  HIS   176      28.546   7.774  10.884  1.00  0.00              
ATOM     39  C   HIS   176      29.279   9.064  10.609  1.00  0.00              
ATOM     40  O   HIS   176      30.069   9.475  11.509  1.00  0.00              
ATOM     41  N   ASP   177      28.954   9.718   9.489  1.00  0.00              
ATOM     42  CA  ASP   177      29.582  10.999   9.140  1.00  0.00              
ATOM     43  C   ASP   177      28.826  12.233   9.642  1.00  0.00              
ATOM     44  O   ASP   177      29.283  13.378   9.381  1.00  0.00              
ATOM     45  N   GLY   178      27.739  12.039  10.351  1.00  0.00              
ATOM     46  CA  GLY   178      26.944  13.099  10.931  1.00  0.00              
ATOM     47  C   GLY   178      26.000  13.689   9.875  1.00  0.00              
ATOM     48  O   GLY   178      25.439  14.770  10.232  1.00  0.00              
ATOM     49  N   MET   179      25.831  13.085   8.783  1.00  0.00              
ATOM     50  CA  MET   179      24.956  13.659   7.728  1.00  0.00              
ATOM     51  C   MET   179      24.062  12.582   7.198  1.00  0.00              
ATOM     52  O   MET   179      24.502  11.415   7.222  1.00  0.00              
ATOM     53  N   LEU   180      22.857  12.921   6.782  1.00  0.00              
ATOM     54  CA  LEU   180      21.981  11.861   6.165  1.00  0.00              
ATOM     55  C   LEU   180      21.865  12.166   4.703  1.00  0.00              
ATOM     56  O   LEU   180      21.365  13.216   4.243  1.00  0.00              
ATOM     57  N   ASP   181      22.352  11.237   3.831  1.00  0.00              
ATOM     58  CA  ASP   181      22.295  11.466   2.376  1.00  0.00              
ATOM     59  C   ASP   181      20.881  11.041   1.861  1.00  0.00              
ATOM     60  O   ASP   181      20.127  10.431   2.645  1.00  0.00              
ATOM     61  N   ARG   182      20.625  11.348   0.594  1.00  0.00              
ATOM     62  CA  ARG   182      19.302  10.909   0.057  1.00  0.00              
ATOM     63  C   ARG   182      19.229   9.371   0.065  1.00  0.00              
ATOM     64  O   ARG   182      18.160   8.822   0.366  1.00  0.00              
ATOM     65  N   ASP   183      20.385   8.748  -0.142  1.00  0.00              
ATOM     66  CA  ASP   183      20.374   7.216  -0.151  1.00  0.00              
ATOM     67  C   ASP   183      20.008   6.670   1.218  1.00  0.00              
ATOM     68  O   ASP   183      19.334   5.677   1.453  1.00  0.00              
ATOM     69  N   GLU   184      20.564   7.326   2.268  1.00  0.00              
ATOM     70  CA  GLU   184      20.350   6.916   3.626  1.00  0.00              
ATOM     71  C   GLU   184      18.884   7.149   4.070  1.00  0.00              
ATOM     72  O   GLU   184      18.334   6.406   4.883  1.00  0.00              
ATOM     73  N   PHE   185      18.384   8.256   3.610  1.00  0.00              
ATOM     74  CA  PHE   185      16.991   8.696   3.889  1.00  0.00              
ATOM     75  C   PHE   185      15.948   7.686   3.371  1.00  0.00              
ATOM     76  O   PHE   185      14.834   7.629   3.935  1.00  0.00              
ATOM     77  N   ALA   186      16.282   6.934   2.355  1.00  0.00              
ATOM     78  CA  ALA   186      15.339   5.922   1.781  1.00  0.00              
ATOM     79  C   ALA   186      14.768   4.974   2.815  1.00  0.00              
ATOM     80  O   ALA   186      13.719   4.403   2.567  1.00  0.00              
ATOM     81  N   VAL   187      15.531   4.683   3.848  1.00  0.00              
ATOM     82  CA  VAL   187      15.020   3.743   4.864  1.00  0.00              
ATOM     83  C   VAL   187      13.687   4.272   5.396  1.00  0.00              
ATOM     84  O   VAL   187      12.831   3.470   5.874  1.00  0.00              
ATOM     85  N   ALA   188      13.397   5.568   5.372  1.00  0.00              
ATOM     86  CA  ALA   188      12.153   6.114   5.916  1.00  0.00              
ATOM     87  C   ALA   188      10.957   6.014   5.003  1.00  0.00              
ATOM     88  O   ALA   188       9.825   6.244   5.474  1.00  0.00              
ATOM     89  N   MET   189      11.199   5.783   3.741  1.00  0.00              
ATOM     90  CA  MET   189      10.065   5.793   2.797  1.00  0.00              
ATOM     91  C   MET   189       9.050   4.741   3.138  1.00  0.00              
ATOM     92  O   MET   189       7.857   5.022   2.877  1.00  0.00              
ATOM     93  N   PHE   190       9.400   3.572   3.624  1.00  0.00              
ATOM     94  CA  PHE   190       8.294   2.557   3.897  1.00  0.00              
ATOM     95  C   PHE   190       7.344   3.184   4.905  1.00  0.00              
ATOM     96  O   PHE   190       6.107   3.264   4.657  1.00  0.00              
ATOM     97  N   LEU   191       7.865   3.774   5.951  1.00  0.00              
ATOM     98  CA  LEU   191       7.151   4.472   7.036  1.00  0.00              
ATOM     99  C   LEU   191       6.248   5.585   6.526  1.00  0.00              
ATOM    100  O   LEU   191       5.083   5.725   6.972  1.00  0.00              
ATOM    101  N   VAL   192       6.778   6.371   5.615  1.00  0.00              
ATOM    102  CA  VAL   192       6.096   7.493   4.978  1.00  0.00              
ATOM    103  C   VAL   192       4.977   7.089   4.002  1.00  0.00              
ATOM    104  O   VAL   192       3.974   7.789   3.876  1.00  0.00              
END
