REMARK  ---------------------------------------------------------- 
REMARK  Molecule : T0073AL019_1_1 
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   SER     1       9.814   8.497  20.242  1.00  0.00              
ATOM      2  CA  SER     1      10.589   7.914  21.332  1.00  0.00              
ATOM      3  C   SER     1      11.411   8.974  22.012  1.00  0.00              
ATOM      4  O   SER     1      11.620   8.918  23.207  1.00  0.00              
ATOM      5  N   LEU     2      11.992   9.869  21.233  1.00  0.00              
ATOM      6  CA  LEU     2      12.796  10.924  21.804  1.00  0.00              
ATOM      7  C   LEU     2      11.974  11.937  22.598  1.00  0.00              
ATOM      8  O   LEU     2      12.412  12.372  23.673  1.00  0.00              
ATOM      9  N   ALA     3      10.789  12.294  22.101  1.00  0.00              
ATOM     10  CA  ALA     3       9.917  13.243  22.797  1.00  0.00              
ATOM     11  C   ALA     3       9.456  12.636  24.151  1.00  0.00              
ATOM     12  O   ALA     3       9.310  13.341  25.145  1.00  0.00              
ATOM     13  N   ALA     4       9.162  11.337  24.157  1.00  0.00              
ATOM     14  CA  ALA     4       8.749  10.630  25.375  1.00  0.00              
ATOM     15  C   ALA     4       9.897  10.650  26.385  1.00  0.00              
ATOM     16  O   ALA     4       9.694  10.957  27.557  1.00  0.00              
ATOM     17  N   LEU     5      11.107  10.335  25.923  1.00  0.00              
ATOM     18  CA  LEU     5      12.266  10.341  26.795  1.00  0.00              
ATOM     19  C   LEU     5      12.495  11.713  27.387  1.00  0.00              
ATOM     20  O   LEU     5      12.784  11.813  28.566  1.00  0.00              
ATOM     21  N   LYS     6      12.413  12.772  26.593  1.00  0.00              
ATOM     22  CA  LYS     6      12.617  14.108  27.133  1.00  0.00              
ATOM     23  C   LYS     6      11.626  14.415  28.242  1.00  0.00              
ATOM     24  O   LYS     6      11.968  15.043  29.233  1.00  0.00              
ATOM     25  N   SER     7      10.392  13.969  28.060  1.00  0.00              
ATOM     26  CA  SER     7       9.341  14.180  29.041  1.00  0.00              
ATOM     27  C   SER     7       9.661  13.435  30.356  1.00  0.00              
ATOM     28  O   SER     7       9.595  14.008  31.440  1.00  0.00              
ATOM     29  N   GLU     8      10.072  12.173  30.235  1.00  0.00              
ATOM     30  CA  GLU     8      10.420  11.349  31.384  1.00  0.00              
ATOM     31  C   GLU     8      11.656  11.868  32.112  1.00  0.00              
ATOM     32  O   GLU     8      11.750  11.789  33.323  1.00  0.00              
ATOM     33  N   LEU     9      12.646  12.310  31.358  1.00  0.00              
ATOM     34  CA  LEU     9      13.860  12.814  31.947  1.00  0.00              
ATOM     35  C   LEU     9      13.624  14.133  32.677  1.00  0.00              
ATOM     36  O   LEU     9      14.203  14.352  33.733  1.00  0.00              
ATOM     37  N   GLN    10      12.757  14.987  32.157  1.00  0.00              
ATOM     38  CA  GLN    10      12.479  16.245  32.840  1.00  0.00              
ATOM     39  C   GLN    10      11.754  15.934  34.154  1.00  0.00              
ATOM     40  O   GLN    10      12.028  16.537  35.177  1.00  0.00              
ATOM     41  N   ALA    11      10.831  14.986  34.146  1.00  0.00              
ATOM     42  CA  ALA    11      10.136  14.656  35.385  1.00  0.00              
ATOM     43  C   ALA    11      11.136  14.036  36.399  1.00  0.00              
ATOM     44  O   ALA    11      11.195  14.448  37.556  1.00  0.00              
ATOM     45  N   LEU    12      11.974  13.102  35.948  1.00  0.00              
ATOM     46  CA  LEU    12      12.961  12.484  36.819  1.00  0.00              
ATOM     47  C   LEU    12      13.881  13.504  37.423  1.00  0.00              
ATOM     48  O   LEU    12      14.218  13.383  38.579  1.00  0.00              
ATOM     49  N   LYS    13      14.368  14.442  36.614  1.00  0.00              
ATOM     50  CA  LYS    13      15.270  15.483  37.080  1.00  0.00              
ATOM     51  C   LYS    13      14.669  16.233  38.277  1.00  0.00              
ATOM     52  O   LYS    13      15.353  16.518  39.251  1.00  0.00              
ATOM     53  N   LYS    14      13.382  16.546  38.196  1.00  0.00              
ATOM     54  CA  LYS    14      12.689  17.282  39.259  1.00  0.00              
ATOM     55  C   LYS    14      12.447  16.446  40.508  1.00  0.00              
ATOM     56  O   LYS    14      12.580  16.956  41.630  1.00  0.00              
ATOM     57  N   GLU    15      12.107  15.172  40.296  1.00  0.00              
ATOM     58  CA  GLU    15      11.875  14.244  41.390  1.00  0.00              
ATOM     59  C   GLU    15      13.141  14.181  42.218  1.00  0.00              
ATOM     60  O   GLU    15      13.108  14.348  43.423  1.00  0.00              
END
