REMARK  ---------------------------------------------------------- 
REMARK  Molecule : T0073AL019_1_2 
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: 1etc 
ATOM      1  N   GLY    16      -7.461  14.376  -9.719  1.00  0.00              
ATOM      2  CA  GLY    16      -6.735  15.556 -10.269  1.00  0.00              
ATOM      3  C   GLY    16      -6.586  16.620  -9.179  1.00  0.00              
ATOM      4  O   GLY    16      -7.060  17.731  -9.314  1.00  0.00              
ATOM      5  N   PHE    17      -5.934  16.288  -8.099  1.00  0.00              
ATOM      6  CA  PHE    17      -5.757  17.279  -7.000  1.00  0.00              
ATOM      7  C   PHE    17      -4.784  18.374  -7.444  1.00  0.00              
ATOM      8  O   PHE    17      -3.583  18.234  -7.326  1.00  0.00              
ATOM      9  N   SER    18      -5.291  19.465  -7.947  1.00  0.00              
ATOM     10  CA  SER    18      -4.390  20.567  -8.387  1.00  0.00              
ATOM     11  C   SER    18      -4.611  21.792  -7.493  1.00  0.00              
ATOM     12  O   SER    18      -3.752  22.144  -6.708  1.00  0.00              
ATOM     13  N   PRO    19      -5.760  22.402  -7.632  1.00  0.00              
ATOM     14  CA  PRO    19      -6.097  23.588  -6.826  1.00  0.00              
ATOM     15  C   PRO    19      -6.408  23.169  -5.386  1.00  0.00              
ATOM     16  O   PRO    19      -6.280  23.946  -4.461  1.00  0.00              
ATOM     17  N   GLU    20      -6.820  21.945  -5.192  1.00  0.00              
ATOM     18  CA  GLU    20      -7.144  21.474  -3.816  1.00  0.00              
ATOM     19  C   GLU    20      -5.876  21.474  -2.958  1.00  0.00              
ATOM     20  O   GLU    20      -4.780  21.303  -3.453  1.00  0.00              
ATOM     21  N   GLU    21      -6.020  21.663  -1.674  1.00  0.00              
ATOM     22  CA  GLU    21      -4.826  21.671  -0.782  1.00  0.00              
ATOM     23  C   GLU    21      -4.703  20.313  -0.088  1.00  0.00              
ATOM     24  O   GLU    21      -5.135  20.137   1.034  1.00  0.00              
END
