PFRMAT TS 
TARGET T0052 
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, in press (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). 
MODEL  1 
PARENT N/A 
ATOM      2  CA  LEU     1     104.363  99.825  91.675  1.00  4.00 
ATOM     10  CA  GLY     2     101.583 102.262  92.006  1.00  4.00 
ATOM     14  CA  LYS     3     103.610 105.079  93.421  1.00  4.00 
ATOM     23  CA  PHE     4     103.284 108.484  92.120  1.00  4.00 
ATOM     34  CA  SER     5     103.518 112.202  93.000  1.00  4.00 
ATOM     40  CA  GLN     6     104.641 112.488  96.537  1.00  4.00 
ATOM     49  CA  THR     7     102.329 109.642  97.634  1.00  4.00 
ATOM     56  CA  CYS     8     102.698 106.908 100.188  1.00  4.00 
ATOM     62  CA  TYR     9     100.295 104.186 100.358  1.00  4.00 
ATOM     74  CA  ASN    10      98.926 102.747 103.261  1.00  4.00 
ATOM     82  CA  SER    11      97.027 100.478 101.180  1.00  4.00 
ATOM     88  CA  ALA    12      93.793  98.574 101.873  1.00  4.00 
ATOM     93  CA  ILE    13      93.762  96.329 104.981  1.00  4.00 
ATOM    101  CA  GLN    14      90.575  95.469 106.495  1.00  4.00 
ATOM    110  CA  GLY    15      89.334  93.297 109.222  1.00  4.00 
ATOM    114  CA  SER    16      92.356  91.150 108.556  1.00  4.00 
ATOM    120  CA  VAL    17      95.588  92.963 109.501  1.00  4.00 
ATOM    127  CA  LEU    18      97.137  96.109 107.879  1.00  4.00 
ATOM    135  CA  THR    19      98.982  97.163 104.725  1.00  4.00 
ATOM    142  CA  SER    20     101.085  99.160 102.284  1.00  4.00 
ATOM    148  CA  THR    21     102.125 102.433 103.314  1.00  4.00 
ATOM    155  CA  CYS    22     104.890 102.820 100.724  1.00  4.00 
ATOM    161  CA  GLU    23     106.255 106.460 100.799  1.00  4.00 
ATOM    170  CA  ARG    24     107.063 108.760  97.761  1.00  4.00 
ATOM    181  CA  THR    25     108.719 112.295  98.096  1.00  4.00 
ATOM    188  CA  ASN    26     106.938 115.477  98.443  1.00  4.00 
ATOM    196  CA  GLY    27     105.352 117.664  96.001  1.00  4.00 
ATOM    200  CA  GLY    28     101.806 116.544  95.596  1.00  4.00 
ATOM    204  CA  TYR    29      98.825 115.483  97.620  1.00  4.00 
ATOM    216  CA  ASN    30      98.040 111.976  98.804  1.00  4.00 
ATOM    224  CA  THR    31      96.673 108.645  97.762  1.00  4.00 
ATOM    231  CA  SER    32      95.923 105.234  98.961  1.00  4.00 
ATOM    237  CA  SER    33      94.860 104.783 102.556  1.00  4.00 
ATOM    243  CA  ILE    34      91.505 103.585 103.281  1.00  4.00 
ATOM    251  CA  ASP    35      89.770 101.937 106.117  1.00  4.00 
ATOM    259  CA  LEU    36      89.468  98.844 104.348  1.00  4.00 
ATOM    267  CA  ASN    37      86.338  97.633 105.825  1.00  4.00 
ATOM    275  CA  SER    38      86.975  94.237 104.496  1.00  4.00 
ATOM    281  CA  VAL    39      88.054  93.052 101.069  1.00  4.00 
ATOM    288  CA  ILE    40      90.074  89.898 101.738  1.00  4.00 
ATOM    296  CA  GLU    41      93.551  88.419 100.661  1.00  4.00 
ATOM    305  CA  ASN    42      96.646  86.670 101.898  1.00  4.00 
ATOM    313  CA  VAL    43      99.833  88.812 102.323  1.00  4.00 
ATOM    320  CA  ASP    44     102.283  85.890 102.226  1.00  4.00 
ATOM    328  CA  GLY    45     100.565  82.725 101.849  1.00  4.00 
ATOM    332  CA  SER    46      98.332  84.276 104.337  1.00  4.00 
ATOM    338  CA  LEU    47      98.958  87.723 105.694  1.00  4.00 
ATOM    346  CA  LYS    48     101.298  86.728 108.506  1.00  4.00 
ATOM    355  CA  TRP    49     100.545  89.845 110.330  1.00  4.00 
ATOM    369  CA  GLN    50     100.217  93.191 112.023  1.00  4.00 
ATOM    378  CA  PRO    51     101.569  95.893 113.105  1.00  4.00 
ATOM    385  CA  SER    52      99.756  99.201 112.767  1.00  4.00 
ATOM    391  CA  ASN    53     100.472 100.101 109.111  1.00  4.00 
ATOM    399  CA  PHE    54     102.776  97.825 106.868  1.00  4.00 
ATOM    410  CA  ILE    55     105.747  98.235 104.085  1.00  4.00 
ATOM    418  CA  GLU    56     108.056 100.395 106.048  1.00  4.00 
ATOM    427  CA  THR    57     107.115  99.946 109.631  1.00  4.00 
ATOM    434  CA  CYS    58     110.118 101.484 108.736  1.00  4.00 
ATOM    440  CA  ARG    59     111.602 100.883 105.260  1.00  4.00 
ATOM    451  CA  ASN    60     113.440 101.896 102.078  1.00  4.00 
ATOM    459  CA  THR    61     113.237 104.612  99.516  1.00  4.00 
ATOM    466  CA  ASN    62     110.986 104.129  96.191  1.00  4.00 
ATOM    474  CA  LEU    63     108.213 101.341  94.761  1.00  4.00 
ATOM    482  CA  ALA    64     106.959 101.907  91.229  1.00  4.00 
ATOM    487  CA  GLY    65     108.398 102.533  87.962  1.00  4.00 
ATOM    491  CA  SER    66     111.268 100.929  89.630  1.00  4.00 
ATOM    497  CA  SER    67     111.213  97.318  90.752  1.00  4.00 
ATOM    503  CA  GLU    68     113.823  95.640  92.963  1.00  4.00 
ATOM    512  CA  LEU    69     111.939  97.058  95.971  1.00  4.00 
ATOM    520  CA  ALA    70     108.630  96.117  94.841  1.00  4.00 
ATOM    525  CA  ALA    71     110.986  93.074  95.186  1.00  4.00 
ATOM    530  CA  GLU    72     111.547  93.601  98.899  1.00  4.00 
ATOM    539  CA  CYS    73     108.708  95.787  99.963  1.00  4.00 
ATOM    545  CA  LYS    74     106.117  94.514  97.578  1.00  4.00 
ATOM    554  CA  THR    75     107.275  91.366  99.166  1.00  4.00 
ATOM    561  CA  ARG    76     106.262  94.142 101.416  1.00  4.00 
ATOM    572  CA  ALA    77     103.087  94.638  99.638  1.00  4.00 
ATOM    577  CA  GLN    78     101.763  91.067  99.852  1.00  4.00 
ATOM    586  CA  GLN    79     103.459  90.228 102.978  1.00  4.00 
ATOM    595  CA  PHE    80     102.488  93.886 103.830  1.00  4.00 
ATOM    606  CA  VAL    81      99.567  93.973 101.371  1.00  4.00 
ATOM    613  CA  SER    82      98.742  97.113  98.946  1.00  4.00 
ATOM    619  CA  THR    83      95.633  96.780  96.628  1.00  4.00 
ATOM    626  CA  LYS    84      94.389  98.940  93.713  1.00  4.00 
ATOM    635  CA  ILE    85      90.869  97.750  92.751  1.00  4.00 
ATOM    643  CA  ASN    86      88.426  96.293  95.173  1.00  4.00 
ATOM    651  CA  LEU    87      88.990  99.769  96.360  1.00  4.00 
ATOM    659  CA  ASP    88      89.749 102.700  94.117  1.00  4.00 
ATOM    667  CA  ASP    89      87.113 101.114  92.535  1.00  4.00 
ATOM    675  CA  HIS    90      85.796  99.692  95.659  1.00  4.00 
ATOM    685  CA  ILE    91      86.866 102.512  97.053  1.00  4.00 
ATOM    693  CA  ALA    92      84.159 104.130  95.326  1.00  4.00 
ATOM    698  CA  ASN    93      82.629 101.026  96.575  1.00  4.00 
ATOM    706  CA  ILE    94      83.940 102.077  99.816  1.00  4.00 
ATOM    714  CA  ASP    95      82.499 104.733  97.763  1.00  4.00 
ATOM    722  CA  GLY    96      82.373 108.280  98.361  1.00  4.00 
ATOM    726  CA  THR    97      83.830 107.436 101.696  1.00  4.00 
ATOM    733  CA  LEU    98      87.068 109.187 102.809  1.00  4.00 
ATOM    741  CA  LYS    99      89.956 110.992 101.058  1.00  4.00 
ATOM    750  CA  TYR   100      90.751 114.616 100.417  1.00  4.00 
ATOM    762  CA  GLU   101      89.833 116.586  97.401  1.00  4.00 
TER 
END 
