PFRMAT TS 
TARGET T0084 
AUTHOR 3363-3494-1306 
METHOD During the last year, we developed a new approach to reduced  
METHOD representation and Monte Carlo simulation of protein structures.   
METHOD It builds on the very well known fact that intra-protein  
METHOD interactions are rather specific for amino acid side chains and  
METHOD rather generic for the main chain units.  Thus, the proposed lattice  
METHOD model of polypeptides assumes explicit representation only for  
METHOD the side chains, where particular side groups are represented  
METHOD as clusters of occupied points on the underlying simple cubic  
METHOD lattice (1,2).  A new, knowledge-based force field has been  
METHOD developed for this model based on local distance geometry,  
METHOD statistics of side chain contacts in known protein structures  
METHOD and some multibody correlations observed in real proteins.   
METHOD The model is a purely lattice type and in spite of the same  
METHOD level of resolution as more complex reduced models, allows for  
METHOD about hundred times faster Monte Carlo sampling, thereby enabling  
METHOD the study of much larger protein systems. 
METHOD The important part of this methodology is the development of  
METHOD potentials that are characteristic for a given protein sequence.  
METHOD First, from the structural database, the collection of sequence  
METHOD fragments that are most similar to particular (overlapping)  
METHOD sequence fragments of the query protein are selected.  These  
METHOD fragments, presumably also similar structurally, are then used to  
METHOD build statistical potentials describing secondary propensities  
METHOD of the query sequence.  In a somewhat similar fashion, the  
METHOD long-range potentials could be derived.  
METHOD The model force filed is supplemented with theoretically predicted  
METHOD tertiary restraints derived from multiple sequence alignments  
METHOD and a combination of correlated mutation analysis and fragment  
METHOD threading procedures (3).  A number of folds (20-40) were generated  
METHOD and the  lowest energy structure from the best defined clusters  
METHOD were selected for all atom reconstruction. 
METHOD (1) A.Kolinski and J. Skolnick,  
METHOD Assembly of protein structure from sparse experimental data:  
METHOD An efficient Monte Carlo model, Proteins, 32, 475-494 (1998). 
METHOD (2) A.Kolinski, L. Jaroszewski, P. Rotkiewicz, J. Skolnick,  
METHOD An efficient Monte Carlo model of protein chains. Modeling  
METHOD the short-range correlations between side group centers  
METHOD of mass, J. Chem. Phys., in press (1998). 
METHOD (3) A.Ortiz, A. Kolinski, J. Skolnick,  
METHOD Fold assembly of small proteins using Monte Carlo simulations  
METHOD driven by restraints derived from multiple sequence alignments,  
METHOD J. Mol. Biol., 277:419-448 (1998). 
REMARK STRUCTURE PREDICTED AS A PARALLEL COILED-COIL 
REMARK THIS IS MONOMER STRUCTURE (HALF OF MOLECULE) 
MODEL  1 
PARENT N/A 
ATOM      1  N   CYS     1      24.152  -0.189  -4.448  1.00  5.00 
ATOM      2  CA  CYS     1      23.122   0.184  -5.405  1.00  5.00 
ATOM      3  C   CYS     1      23.004   1.669  -5.682  1.00  5.00 
ATOM      4  O   CYS     1      21.951   2.254  -5.484  1.00  5.00 
ATOM      6  N   GLY     2      23.861   2.129  -6.311  1.00  5.00 
ATOM      7  CA  GLY     2      23.965   3.572  -6.493  1.00  5.00 
ATOM      8  C   GLY     2      22.687   4.199  -7.011  1.00  5.00 
ATOM      9  O   GLY     2      22.320   5.299  -6.624  1.00  5.00 
ATOM     10  N   GLY     3      22.100   3.545  -7.808  1.00  5.00 
ATOM     11  CA  GLY     3      20.850   4.048  -8.359  1.00  5.00 
ATOM     12  C   GLY     3      19.798   3.608  -7.381  1.00  5.00 
ATOM     13  O   GLY     3      18.769   3.853  -7.559  1.00  5.00 
ATOM     14  N   ARG     4      20.059   3.023  -6.447  1.00  5.00 
ATOM     15  CA  ARG     4      19.164   2.527  -5.441  1.00  5.00 
ATOM     16  C   ARG     4      19.519   3.148  -4.073  1.00  5.00 
ATOM     17  O   ARG     4      20.521   2.879  -3.393  1.00  5.00 
ATOM     19  N   GLU     5      18.795   4.343  -3.662  1.00  5.00 
ATOM     20  CA  GLU     5      18.720   5.504  -2.771  1.00  5.00 
ATOM     21  C   GLU     5      17.846   6.393  -3.524  1.00  5.00 
ATOM     22  O   GLU     5      17.055   7.153  -2.983  1.00  5.00 
ATOM     24  N   GLY     6      18.066   6.108  -5.190  1.00  5.00 
ATOM     25  CA  GLY     6      17.266   6.636  -6.218  1.00  5.00 
ATOM     26  C   GLY     6      16.175   5.546  -6.076  1.00  5.00 
ATOM     27  O   GLY     6      14.983   5.967  -6.174  1.00  5.00 
ATOM     28  N   VAL     7      16.354   4.603  -5.795  1.00  5.00 
ATOM     29  CA  VAL     7      15.421   3.556  -5.541  1.00  5.00 
ATOM     30  C   VAL     7      14.892   3.390  -4.121  1.00  5.00 
ATOM     31  O   VAL     7      14.014   2.563  -3.819  1.00  5.00 
ATOM     33  N   LEU     8      15.526   3.944  -3.221  1.00  5.00 
ATOM     34  CA  LEU     8      14.974   3.766  -1.891  1.00  5.00 
ATOM     35  C   LEU     8      14.525   5.246  -1.971  1.00  5.00 
ATOM     36  O   LEU     8      13.399   5.493  -1.443  1.00  5.00 
ATOM     38  N   LYS     9      15.046   5.953  -2.406  1.00  5.00 
ATOM     39  CA  LYS     9      14.607   7.289  -2.636  1.00  5.00 
ATOM     40  C   LYS     9      13.310   7.293  -3.472  1.00  5.00 
ATOM     41  O   LYS     9      12.320   7.866  -3.063  1.00  5.00 
ATOM     43  N   LYS    10      13.073   6.094  -4.958  1.00  5.00 
ATOM     44  CA  LYS    10      11.842   5.724  -5.675  1.00  5.00 
ATOM     45  C   LYS    10      10.910   5.050  -4.678  1.00  5.00 
ATOM     46  O   LYS    10       9.707   5.281  -4.701  1.00  5.00 
ATOM     48  N   LEU    11      11.571   4.073  -3.406  1.00  5.00 
ATOM     49  CA  LEU    11      10.826   3.537  -2.272  1.00  5.00 
ATOM     50  C   LEU    11      10.069   4.649  -1.560  1.00  5.00 
ATOM     51  O   LEU    11       8.925   4.464  -1.163  1.00  5.00 
ATOM     53  N   ARG    12      10.659   5.683  -1.525  1.00  5.00 
ATOM     54  CA  ARG    12      10.067   6.794  -0.788  1.00  5.00 
ATOM     55  C   ARG    12       8.916   7.479  -1.522  1.00  5.00 
ATOM     56  O   ARG    12       8.207   8.307  -0.949  1.00  5.00 
ATOM     58  N   ALA    13       8.672   7.252  -2.988  1.00  5.00 
ATOM     59  CA  ALA    13       7.505   7.601  -3.784  1.00  5.00 
ATOM     60  C   ALA    13       6.571   6.450  -3.444  1.00  5.00 
ATOM     61  O   ALA    13       5.340   6.605  -3.427  1.00  5.00 
ATOM     63  N   VAL    14       7.231   5.478  -3.185  1.00  5.00 
ATOM     64  CA  VAL    14       6.594   4.224  -2.779  1.00  5.00 
ATOM     65  C   VAL    14       6.064   4.280  -1.361  1.00  5.00 
ATOM     66  O   VAL    14       4.993   3.769  -1.065  1.00  5.00 
ATOM     68  N   GLU    15       6.774   4.797  -0.549  1.00  5.00 
ATOM     69  CA  GLU    15       6.336   4.942   0.832  1.00  5.00 
ATOM     70  C   GLU    15       5.578   6.170   1.026  1.00  5.00 
ATOM     71  O   GLU    15       4.894   6.373   2.019  1.00  5.00 
ATOM     73  N   ASN    16       5.825   7.126   0.094  1.00  5.00 
ATOM     74  CA  ASN    16       5.037   8.283  -0.027  1.00  5.00 
ATOM     75  C   ASN    16       3.813   7.646  -0.699  1.00  5.00 
ATOM     76  O   ASN    16       2.658   7.998  -0.546  1.00  5.00 
ATOM     78  N   GLU    17       4.196   6.555  -1.244  1.00  5.00 
ATOM     79  CA  GLU    17       3.227   5.816  -2.013  1.00  5.00 
ATOM     80  C   GLU    17       2.464   4.888  -1.119  1.00  5.00 
ATOM     81  O   GLU    17       1.285   4.864  -1.185  1.00  5.00 
ATOM     83  N   LEU    18       3.063   4.024  -0.524  1.00  5.00 
ATOM     84  CA  LEU    18       2.355   3.163   0.400  1.00  5.00 
ATOM     85  C   LEU    18       1.920   3.798   1.636  1.00  5.00 
ATOM     86  O   LEU    18       1.105   3.285   2.390  1.00  5.00 
ATOM     88  N   HIS    19       2.664   4.910   1.913  1.00  5.00 
ATOM     89  CA  HIS    19       2.210   5.777   2.922  1.00  5.00 
ATOM     90  C   HIS    19       0.914   6.156   2.164  1.00  5.00 
ATOM     91  O   HIS    19      -0.123   6.243   2.888  1.00  5.00 
ATOM     93  N   TYR    20       1.015   5.895   1.030  1.00  5.00 
ATOM     94  CA  TYR    20      -0.101   5.953   0.146  1.00  5.00 
ATOM     95  C   TYR    20      -1.103   4.846   0.443  1.00  5.00 
ATOM     96  O   TYR    20      -2.291   5.086   0.498  1.00  5.00 
ATOM     98  N   ASN    21      -0.620   3.788   0.647  1.00  5.00 
ATOM     99  CA  ASN    21      -1.498   2.646   0.855  1.00  5.00 
ATOM    100  C   ASN    21      -2.048   2.696   2.272  1.00  5.00 
ATOM    101  O   ASN    21      -3.242   2.524   2.466  1.00  5.00 
ATOM    103  N   LYS    22      -1.074   3.099   3.627  1.00  5.00 
ATOM    104  CA  LYS    22      -1.506   3.427   4.983  1.00  5.00 
ATOM    105  C   LYS    22      -2.458   4.623   4.903  1.00  5.00 
ATOM    106  O   LYS    22      -3.498   4.659   5.574  1.00  5.00 
ATOM    108  N   SER    23      -2.045   5.461   4.175  1.00  5.00 
ATOM    109  CA  SER    23      -2.786   6.729   4.031  1.00  5.00 
ATOM    110  C   SER    23      -4.025   6.341   3.242  1.00  5.00 
ATOM    111  O   SER    23      -5.081   6.864   3.465  1.00  5.00 
ATOM    113  N   LEU    24      -3.852   5.476   2.411  1.00  5.00 
ATOM    114  CA  LEU    24      -4.947   5.056   1.554  1.00  5.00 
ATOM    115  C   LEU    24      -5.839   4.057   2.267  1.00  5.00 
ATOM    116  O   LEU    24      -7.055   4.151   2.171  1.00  5.00 
ATOM    118  N   LEU    25      -5.235   2.928   3.147  1.00  5.00 
ATOM    119  CA  LEU    25      -6.004   2.021   3.985  1.00  5.00 
ATOM    120  C   LEU    25      -6.791   2.810   5.040  1.00  5.00 
ATOM    121  O   LEU    25      -7.819   2.378   5.531  1.00  5.00 
ATOM    123  N   GLU    26      -6.300   4.080   5.406  1.00  5.00 
ATOM    124  CA  GLU    26      -6.939   5.033   6.284  1.00  5.00 
ATOM    125  C   GLU    26      -8.037   5.643   5.409  1.00  5.00 
ATOM    126  O   GLU    26      -9.177   5.833   5.851  1.00  5.00 
ATOM    128  N   GLU    27      -7.579   5.981   4.357  1.00  5.00 
ATOM    129  CA  GLU    27      -8.506   6.555   3.363  1.00  5.00 
ATOM    130  C   GLU    27      -9.462   5.382   3.110  1.00  5.00 
ATOM    131  O   GLU    27     -10.656   5.475   2.893  1.00  5.00 
ATOM    133  N   VAL    28      -8.877   3.821   3.208  1.00  5.00 
ATOM    134  CA  VAL    28      -9.591   2.569   3.225  1.00  5.00 
ATOM    135  C   VAL    28     -10.393   2.410   4.503  1.00  5.00 
ATOM    136  O   VAL    28     -11.492   1.913   4.461  1.00  5.00 
ATOM    138  N   LYS    29      -9.907   2.825   5.500  1.00  5.00 
ATOM    139  CA  LYS    29     -10.561   2.583   6.780  1.00  5.00 
ATOM    140  C   LYS    29     -11.632   3.586   7.192  1.00  5.00 
ATOM    141  O   LYS    29     -12.259   3.505   8.262  1.00  5.00 
ATOM    143  N   ASP    30     -11.737   4.635   6.554  1.00  5.00 
ATOM    144  CA  ASP    30     -12.768   5.553   7.001  1.00  5.00 
ATOM    145  C   ASP    30     -13.758   5.175   5.910  1.00  5.00 
ATOM    146  O   ASP    30     -14.981   5.286   6.086  1.00  5.00 
ATOM    148  N   GLU    31     -13.116   4.630   4.607  1.00  5.00 
ATOM    149  CA  GLU    31     -13.793   3.967   3.491  1.00  5.00 
ATOM    150  C   GLU    31     -14.587   2.767   4.013  1.00  5.00 
ATOM    151  O   GLU    31     -15.761   2.577   3.668  1.00  5.00 
ATOM    153  N   LEU    32     -13.884   1.897   4.745  1.00  5.00 
ATOM    154  CA  LEU    32     -14.491   0.750   5.447  1.00  5.00 
ATOM    155  C   LEU    32     -15.347   1.449   6.512  1.00  5.00 
ATOM    156  O   LEU    32     -16.431   1.069   6.912  1.00  5.00 
ATOM    158  N   GLN    33     -14.856   2.681   7.091  1.00  5.00 
ATOM    159  CA  GLN    33     -15.539   3.528   8.036  1.00  5.00 
ATOM    160  C   GLN    33     -16.776   4.158   7.419  1.00  5.00 
ATOM    161  O   GLN    33     -17.799   3.991   8.073  1.00  5.00 
ATOM    163  N   LYS    34     -16.548   4.847   6.237  1.00  5.00 
ATOM    164  CA  LYS    34     -17.587   5.456   5.411  1.00  5.00 
ATOM    165  C   LYS    34     -18.428   4.317   4.818  1.00  5.00 
ATOM    166  O   LYS    34     -19.602   4.469   4.528  1.00  5.00 
ATOM    168  N   MET    35     -17.806   3.263   4.718  1.00  5.00 
ATOM    169  CA  MET    35     -18.453   2.080   4.198  1.00  5.00 
ATOM    170  C   MET    35     -18.858   1.212   5.388  1.00  5.00 
ATOM    171  O   MET    35     -19.606   0.246   5.238  1.00  5.00 
ATOM    173  N   ARG    36     -18.359   1.495   6.392  1.00  5.00 
ATOM    174  CA  ARG    36     -18.757   0.772   7.590  1.00  5.00 
ATOM    175  C   ARG    36     -19.442   1.951   8.295  1.00  5.00 
ATOM    176  O   ARG    36     -19.476   1.999   9.534  1.00  5.00 
ATOM    178  N   GLN    37     -19.926   2.902   7.329  1.00  5.00 
ATOM    179  CA  GLN    37     -20.611   3.873   8.148  1.00  5.00 
ATOM    180  C   GLN    37     -20.090   3.816   9.582  1.00  5.00 
ATOM    181  O   GLN    37     -19.964   4.925  10.078  1.00  5.00 
TER 
END 
