REMARK  ---------------------------------------------------------- 
REMARK  Molecule : T0073AL019_1_3 
REMARK  Alignment model prepared for CASP3 experiment 
REMARK  by group : UCSC-COMPBIO 
REMARK  ---------------------------------------------------------- 
TARGET T0073  
AUTHOR 9070-5088-8627  
REMARK   
REMARK Prediction date: Monday June 22, 1998  
REMARK Group name: UCSC-compbio  
REMARK Authors: Christian Barrett, Melissa Cline, Mark Diekens, Kevin Karplus,  
REMARK 	 David Haussler and Richard Hughey  
REMARK University of California, Santa Cruz  
REMARK   
METHOD Overview  
METHOD   
METHOD Fold recognition was performed using the Target98 (SAM-T98) method  
METHOD [3] using SAM version 2.1.1 [1], a refinement of the methods developed  
METHOD by this group for CASP2 [2].  This method attempts to find and multiply   
METHOD align a set of homologs to a given sequence, then create an HMM from that   
METHOD multiple alignment.  
METHOD   
METHOD First, a set of sequence weights is determined from the alignment.  Next,   
METHOD Modelfromalign is used to build the model from the alignment and the   
METHOD sequence weights.  Finally, hmmscore performs a local, all-paths scoring   
METHOD of the sequences, using a reversed-sequence normalization feature.  
METHOD   
METHOD The weighting method, detailed in upcoming publications [3,4],  
METHOD combines the Henikoffs' scheme [5], Dirichlet mixtures [6], and an  
METHOD entropy method to set the final weights.  
METHOD   
METHOD Alignment generation  
METHOD   
METHOD The initial step uses BLASTP to search NRP twice: once to produce a set  
METHOD of very close homologs, and once to produce a set of possible homologs.  
METHOD   
METHOD The method then uses multiple iterations of a selection, training, and   
METHOD alignment procedure.  Each iteration involves an initial alignment, a set   
METHOD of search sequences, a threshold value, and a transition regularizer.   
METHOD   
METHOD The first iteration uses a single sequence (or seed alignment) as the   
METHOD initial alignment and the close homologs found by BLASTP are used as the   
METHOD search set.  The threshold is set very strictly, so that only good matches   
METHOD to the sequence are considered.  This iteration uses a transition regularizer   
METHOD that was designed to match the gap costs used by BLASTP.  
METHOD   
METHOD On subsequent iterations the input alignment is the output from the  
METHOD previous iteration, the search set is the larger set of possible  
METHOD homologs found by BLASTP, and the thresholds are gradually loosened.  
METHOD The second through second-from-last iteration use a ``long-match''  
METHOD transition regularizer, and the final iteration uses a transition regularizer   
METHOD trained on FSSP alignments.  
METHOD   
METHOD References  
METHOD [1] R. Hughey and A. Krogh, CABIOS 12(2): 95-107, 1996.  
METHOD     http://www.cse.ucsc.edu/research/compbio/sam.html.    
METHOD [2] K. Karplus, K. Sjolander, C. Barrett, M. Cline, D. Haussler, R.  
METHOD     Hughey, L. Holm, and C. Sander, Proteins: Structure, Function, and   
METHOD     Genetics, Suppl. 1, 134-9, 1997.  
METHOD [3] K. Karplus, C. Barrett, and R. Hughey, Technical Report UCSC-CRL-98-06,  
METHOD     Department of Computer Engineering, Univ. of California, Santa Cruz, 1998.  
METHOD [4] J. Park, K. Karplus, C. Barrett, R. Hughey, D. Haussler, T. Hubbard,  
METHOD     and C. Chothia, http://cyrah.med.harvard.edu/~jong/assess_final.html, 1998.  
METHOD [5] S. Henikoff and J. C. Henikoff, JMB, vol 243, pp 574-578, Nov 1994.  
METHOD [6] K. Sjolander, K. Karplus, M. P. Brown, R. Hughey, A. Krogh, I. S.  
METHOD    Mian, and D. Haussler, CABIOS 12(4):327-345, 1996.  
METHOD   
METHOD   
METHOD T0073 obviously has 2 heptads of helix, a hexad GFSPEE, and 4  
METHOD more heptads of helix.  The helices are classic coiled-coil formers,  
METHOD with leucines in both the a and d positions of the heptad.  
METHOD   
METHOD The questions are  
METHOD         1) what happens with the GFSPEE?  
METHOD         2) is this a dimer, trimer, tetramer, ...?  
METHOD         3) if this is a single coild-coil, how do the peptides stack?  
METHOD   
METHOD Our first guess was that the GFSPEE would form a 3-10 helix, with the  
METHOD whole sequence forming a single dimeric, parallel coiled-coil with 180  
METHOD degrees of twist around the superhelical axis, so that the peptides  
METHOD could stack along that axis.  However, we were uncomfortable with the  
METHOD proline in the middle of a helix in solution, and looked for other  
METHOD possibilities.  
METHOD   
METHOD After consulting with Glenn Millhauser, whose first reaction was that  
METHOD the GFSPEE would form a turn, we found a similar turn in 1ETC  
METHOD (GYPTEEL), in which the ring of the tyrosine packs nicely against the  
METHOD leucine that starts a helix coming out of the turn.  The length of the  
METHOD turn is about right for going from the exposed side of one helix to  
METHOD the buried side of the other in an anti-parallel coiled-coil.  Glenn  
METHOD pointed out that substituting F for Y would make it more hydrophobic,  
METHOD and subsituting S for T would make that exposed residue more  
METHOD hydrophilic, further stabilizing the turn.  
METHOD   
METHOD This lead us to the conjecture that the structure is a long and a  
METHOD short helix packed as a coiled-coil with a turn between them.  The  
METHOD peptides could dimerize with the long helices of one extending the  
METHOD short helices of the other (like sticky tails in DNA double helices).  
METHOD This arrangement nicely balances the dipole moments, and buries all  
METHOD the leucines in coiled-coils.  
METHOD   
METHOD Based on Woolfson and Alber's method for predicting oligomerization  
METHOD states of coiled coils, we expect two helices in the coiled-coil, not  
METHOD three or more.  
METHOD   
METHOD   
METHOD   
METHOD   
METHOD   
METHOD   
METHOD   
METHOD   
MODEL 1  
REMARK  ---------------------------------------------------------- 
REMARK  AL2TS service [v. 08/06/1998]: Adam Zemla, adamz@llnl.gov 
REMARK  ---------------------------------------------------------- 
REMARK  Coordinates assigned from PDB entry: 1coi 
ATOM      1  N   LEU    22      12.314   7.592  11.042  1.00  0.00              
ATOM      2  CA  LEU    22      12.560   8.879  11.668  1.00  0.00              
ATOM      3  C   LEU    22      11.393   9.351  12.532  1.00  0.00              
ATOM      4  O   LEU    22      11.605   9.727  13.674  1.00  0.00              
ATOM      5  N   ALA    23      10.164   9.258  12.038  1.00  0.00              
ATOM      6  CA  ALA    23       9.009   9.675  12.815  1.00  0.00              
ATOM      7  C   ALA    23       8.919   8.854  14.101  1.00  0.00              
ATOM      8  O   ALA    23       8.545   9.378  15.158  1.00  0.00              
ATOM      9  N   ALA    24       9.240   7.567  14.001  1.00  0.00              
ATOM     10  CA  ALA    24       9.205   6.693  15.151  1.00  0.00              
ATOM     11  C   ALA    24      10.251   7.151  16.151  1.00  0.00              
ATOM     12  O   ALA    24       9.982   7.221  17.331  1.00  0.00              
ATOM     13  N   LEU    25      11.437   7.501  15.686  1.00  0.00              
ATOM     14  CA  LEU    25      12.463   7.986  16.599  1.00  0.00              
ATOM     15  C   LEU    25      12.037   9.273  17.260  1.00  0.00              
ATOM     16  O   LEU    25      12.400   9.523  18.415  1.00  0.00              
ATOM     17  N   GLU    26      11.314  10.105  16.513  1.00  0.00              
ATOM     18  CA  GLU    26      10.838  11.388  17.028  1.00  0.00              
ATOM     19  C   GLU    26       9.940  11.186  18.240  1.00  0.00              
ATOM     20  O   GLU    26      10.048  11.913  19.224  1.00  0.00              
ATOM     21  N   SER    27       9.022  10.229  18.140  1.00  0.00              
ATOM     22  CA  SER    27       8.117   9.925  19.240  1.00  0.00              
ATOM     23  C   SER    27       8.841   9.371  20.457  1.00  0.00              
ATOM     24  O   SER    27       8.526   9.748  21.564  1.00  0.00              
ATOM     25  N   GLU    28       9.814   8.497  20.242  1.00  0.00              
ATOM     26  CA  GLU    28      10.589   7.914  21.332  1.00  0.00              
ATOM     27  C   GLU    28      11.411   8.974  22.012  1.00  0.00              
ATOM     28  O   GLU    28      11.620   8.918  23.207  1.00  0.00              
ATOM     29  N   LEU    29      11.992   9.869  21.233  1.00  0.00              
ATOM     30  CA  LEU    29      12.796  10.924  21.804  1.00  0.00              
ATOM     31  C   LEU    29      11.974  11.937  22.598  1.00  0.00              
ATOM     32  O   LEU    29      12.412  12.372  23.673  1.00  0.00              
ATOM     33  N   GLN    30      10.789  12.294  22.101  1.00  0.00              
ATOM     34  CA  GLN    30       9.917  13.243  22.797  1.00  0.00              
ATOM     35  C   GLN    30       9.456  12.636  24.151  1.00  0.00              
ATOM     36  O   GLN    30       9.310  13.341  25.145  1.00  0.00              
ATOM     37  N   ALA    31       9.162  11.337  24.157  1.00  0.00              
ATOM     38  CA  ALA    31       8.749  10.630  25.375  1.00  0.00              
ATOM     39  C   ALA    31       9.897  10.650  26.385  1.00  0.00              
ATOM     40  O   ALA    31       9.694  10.957  27.557  1.00  0.00              
ATOM     41  N   LEU    32      11.107  10.335  25.923  1.00  0.00              
ATOM     42  CA  LEU    32      12.266  10.341  26.795  1.00  0.00              
ATOM     43  C   LEU    32      12.495  11.713  27.387  1.00  0.00              
ATOM     44  O   LEU    32      12.784  11.813  28.566  1.00  0.00              
ATOM     45  N   GLU    33      12.413  12.772  26.593  1.00  0.00              
ATOM     46  CA  GLU    33      12.617  14.108  27.133  1.00  0.00              
ATOM     47  C   GLU    33      11.626  14.415  28.242  1.00  0.00              
ATOM     48  O   GLU    33      11.968  15.043  29.233  1.00  0.00              
ATOM     49  N   LYS    34      10.392  13.969  28.060  1.00  0.00              
ATOM     50  CA  LYS    34       9.341  14.180  29.041  1.00  0.00              
ATOM     51  C   LYS    34       9.661  13.435  30.356  1.00  0.00              
ATOM     52  O   LYS    34       9.595  14.008  31.440  1.00  0.00              
ATOM     53  N   LYS    35      10.072  12.173  30.235  1.00  0.00              
ATOM     54  CA  LYS    35      10.420  11.349  31.384  1.00  0.00              
ATOM     55  C   LYS    35      11.656  11.868  32.112  1.00  0.00              
ATOM     56  O   LYS    35      11.750  11.789  33.323  1.00  0.00              
ATOM     57  N   LEU    36      12.646  12.310  31.358  1.00  0.00              
ATOM     58  CA  LEU    36      13.860  12.814  31.947  1.00  0.00              
ATOM     59  C   LEU    36      13.624  14.133  32.677  1.00  0.00              
ATOM     60  O   LEU    36      14.203  14.352  33.733  1.00  0.00              
ATOM     61  N   ALA    37      12.757  14.987  32.157  1.00  0.00              
ATOM     62  CA  ALA    37      12.479  16.245  32.840  1.00  0.00              
ATOM     63  C   ALA    37      11.754  15.934  34.154  1.00  0.00              
ATOM     64  O   ALA    37      12.028  16.537  35.177  1.00  0.00              
ATOM     65  N   ALA    38      10.831  14.986  34.146  1.00  0.00              
ATOM     66  CA  ALA    38      10.136  14.656  35.385  1.00  0.00              
ATOM     67  C   ALA    38      11.136  14.036  36.399  1.00  0.00              
ATOM     68  O   ALA    38      11.195  14.448  37.556  1.00  0.00              
ATOM     69  N   LEU    39      11.974  13.102  35.948  1.00  0.00              
ATOM     70  CA  LEU    39      12.961  12.484  36.819  1.00  0.00              
ATOM     71  C   LEU    39      13.881  13.504  37.423  1.00  0.00              
ATOM     72  O   LEU    39      14.218  13.383  38.579  1.00  0.00              
ATOM     73  N   LYS    40      14.368  14.442  36.614  1.00  0.00              
ATOM     74  CA  LYS    40      15.270  15.483  37.080  1.00  0.00              
ATOM     75  C   LYS    40      14.669  16.233  38.277  1.00  0.00              
ATOM     76  O   LYS    40      15.353  16.518  39.251  1.00  0.00              
ATOM     77  N   SER    41      13.382  16.546  38.196  1.00  0.00              
ATOM     78  CA  SER    41      12.689  17.282  39.259  1.00  0.00              
ATOM     79  C   SER    41      12.447  16.446  40.508  1.00  0.00              
ATOM     80  O   SER    41      12.580  16.956  41.630  1.00  0.00              
ATOM     81  N   LYS    42      12.107  15.172  40.296  1.00  0.00              
ATOM     82  CA  LYS    42      11.875  14.244  41.390  1.00  0.00              
ATOM     83  C   LYS    42      13.141  14.181  42.218  1.00  0.00              
ATOM     84  O   LYS    42      13.108  14.348  43.423  1.00  0.00              
ATOM     85  N   LEU    43      14.262  13.908  41.570  1.00  0.00              
ATOM     86  CA  LEU    43      15.536  13.816  42.264  1.00  0.00              
ATOM     87  C   LEU    43      15.951  15.133  42.907  1.00  0.00              
ATOM     88  O   LEU    43      16.480  15.122  44.017  1.00  0.00              
ATOM     89  N   GLN    44      15.661  16.257  42.256  1.00  0.00              
ATOM     90  CA  GLN    44      15.993  17.577  42.788  1.00  0.00              
ATOM     91  C   GLN    44      15.385  17.760  44.209  1.00  0.00              
ATOM     92  O   GLN    44      15.961  18.427  45.073  1.00  0.00              
ATOM     93  N   ALA    45      14.191  17.211  44.421  1.00  0.00              
ATOM     94  CA  ALA    45      13.539  17.291  45.713  1.00  0.00              
ATOM     95  C   ALA    45      14.343  16.502  46.761  1.00  0.00              
ATOM     96  O   ALA    45      14.340  16.840  47.944  1.00  0.00              
ATOM     97  N   LEU    46      15.011  15.437  46.326  1.00  0.00              
ATOM     98  CA  LEU    46      15.781  14.602  47.236  1.00  0.00              
ATOM     99  C   LEU    46      17.151  15.123  47.528  1.00  0.00              
ATOM    100  O   LEU    46      17.644  14.940  48.627  1.00  0.00              
ATOM    101  N   LYS    47      17.805  15.680  46.520  1.00  0.00              
ATOM    102  CA  LYS    47      19.146  16.204  46.714  1.00  0.00              
ATOM    103  C   LYS    47      19.448  17.414  45.852  1.00  0.00              
ATOM    104  O   LYS    47      18.921  17.556  44.752  1.00  0.00              
ATOM    105  N   GLY    48      20.337  18.249  46.383  1.00  0.00              
ATOM    106  CA  GLY    48      20.783  19.530  45.840  1.00  0.00              
ATOM    107  C   GLY    48      19.654  20.469  45.435  1.00  0.00              
ATOM    108  O   GLY    48      19.198  20.462  44.301  1.00  0.00              
END
