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  3 
PARENT N/A 
ATOM      2  CA  LEU     1     111.848 109.373 106.613  1.00  4.00 
ATOM     10  CA  GLY     2     109.253 109.362 109.350  1.00  4.00 
ATOM     14  CA  LYS     3     108.578 106.438 111.730  1.00  4.00 
ATOM     23  CA  PHE     4     106.829 103.546 109.805  1.00  4.00 
ATOM     34  CA  SER     5     107.286 101.595 106.446  1.00  4.00 
ATOM     40  CA  GLN     6     104.915  99.723 104.011  1.00  4.00 
ATOM     49  CA  THR     7     105.914  98.157 100.564  1.00  4.00 
ATOM     56  CA  CYS     8     104.726  99.955  97.309  1.00  4.00 
ATOM     62  CA  TYR     9     105.278  99.951  93.332  1.00  4.00 
ATOM     74  CA  ASN    10     108.149 102.273  92.398  1.00  4.00 
ATOM     82  CA  SER    11     108.234 105.971  93.076  1.00  4.00 
ATOM     88  CA  ALA    12     106.410 107.640  95.912  1.00  4.00 
ATOM     93  CA  ILE    13     107.506 108.426  99.361  1.00  4.00 
ATOM    101  CA  GLN    14     105.540 108.218 102.592  1.00  4.00 
ATOM    110  CA  GLY    15     105.093 110.102 105.771  1.00  4.00 
ATOM    114  CA  SER    16     103.735 108.780 109.030  1.00  4.00 
ATOM    120  CA  VAL    17     103.609 105.497 107.081  1.00  4.00 
ATOM    127  CA  LEU    18     105.585 105.428 103.849  1.00  4.00 
ATOM    135  CA  THR    19     104.953 102.837 101.072  1.00  4.00 
ATOM    142  CA  SER    20     108.064 102.902  98.813  1.00  4.00 
ATOM    148  CA  THR    21     108.668 100.012  96.473  1.00  4.00 
ATOM    155  CA  CYS    22     108.989  98.889  93.223  1.00  4.00 
ATOM    161  CA  GLU    23     107.486  96.479  91.347  1.00  4.00 
ATOM    170  CA  ARG    24     105.504  95.062  88.648  1.00  4.00 
ATOM    181  CA  THR    25     106.404  95.308  85.206  1.00  4.00 
ATOM    188  CA  ASN    26     102.738  95.076  84.107  1.00  4.00 
ATOM    196  CA  GLY    27      99.815  92.942  85.223  1.00  4.00 
ATOM    200  CA  GLY    28      96.253  93.549  86.295  1.00  4.00 
ATOM    204  CA  TYR    29      94.059  91.986  88.900  1.00  4.00 
ATOM    216  CA  ASN    30      91.382  92.308  91.291  1.00  4.00 
ATOM    224  CA  THR    31      92.222  91.085  94.630  1.00  4.00 
ATOM    231  CA  SER    32      91.267  89.401  97.685  1.00  4.00 
ATOM    237  CA  SER    33      94.811  90.317  97.147  1.00  4.00 
ATOM    243  CA  ILE    34      96.247  90.010  93.662  1.00  4.00 
ATOM    251  CA  ASP    35      97.428  91.024  90.216  1.00  4.00 
ATOM    259  CA  LEU    36     101.130  91.757  89.578  1.00  4.00 
ATOM    267  CA  ASN    37     104.358  90.696  91.000  1.00  4.00 
ATOM    275  CA  SER    38     106.540  93.711  91.726  1.00  4.00 
ATOM    281  CA  VAL    39     110.260  93.707  90.815  1.00  4.00 
ATOM    288  CA  ILE    40     111.119  96.402  93.468  1.00  4.00 
ATOM    296  CA  GLU    41     114.045  98.342  92.556  1.00  4.00 
ATOM    305  CA  ASN    42     114.546 101.470  94.433  1.00  4.00 
ATOM    313  CA  VAL    43     116.674 103.015  96.884  1.00  4.00 
ATOM    320  CA  ASP    44     116.835 104.717 100.101  1.00  4.00 
ATOM    328  CA  GLY    45     116.899 100.958 100.664  1.00  4.00 
ATOM    332  CA  SER    46     115.305  97.896  98.696  1.00  4.00 
ATOM    338  CA  LEU    47     112.700  95.335 100.166  1.00  4.00 
ATOM    346  CA  LYS    48     112.271  91.898  98.061  1.00  4.00 
ATOM    355  CA  TRP    49     109.328  90.815  95.811  1.00  4.00 
ATOM    369  CA  GLN    50     106.974  88.115  94.425  1.00  4.00 
ATOM    378  CA  PRO    51     103.558  89.703  93.730  1.00  4.00 
ATOM    385  CA  SER    52     102.684  92.010  96.556  1.00  4.00 
ATOM    391  CA  ASN    53     102.548  95.549  97.940  1.00  4.00 
ATOM    399  CA  PHE    54     100.223  98.175  99.620  1.00  4.00 
ATOM    410  CA  ILE    55      97.915  99.650  96.747  1.00  4.00 
ATOM    418  CA  GLU    56      97.206 102.869  95.089  1.00  4.00 
ATOM    427  CA  THR    57      99.642 105.667  96.066  1.00  4.00 
ATOM    434  CA  CYS    58     102.259 103.115  95.597  1.00  4.00 
ATOM    440  CA  ARG    59     101.698 100.497  92.757  1.00  4.00 
ATOM    451  CA  ASN    60     100.304 103.599  91.551  1.00  4.00 
ATOM    459  CA  THR    61     102.340 106.542  92.074  1.00  4.00 
ATOM    466  CA  ASN    62     102.516 109.678  93.913  1.00  4.00 
ATOM    474  CA  LEU    63     105.439 110.459  95.712  1.00  4.00 
ATOM    482  CA  ALA    64     103.948 112.232  98.657  1.00  4.00 
ATOM    487  CA  GLY    65     105.670 113.839 101.559  1.00  4.00 
ATOM    491  CA  SER    66     102.498 113.887 103.440  1.00  4.00 
ATOM    497  CA  SER    67      99.183 115.465 103.024  1.00  4.00 
ATOM    503  CA  GLU    68      95.842 113.988 102.980  1.00  4.00 
ATOM    512  CA  LEU    69      97.416 110.732 102.172  1.00  4.00 
ATOM    520  CA  ALA    70      99.172 108.933 104.789  1.00  4.00 
ATOM    525  CA  ALA    71      95.549 108.417 105.261  1.00  4.00 
ATOM    530  CA  GLU    72      95.280 108.021 101.564  1.00  4.00 
ATOM    539  CA  CYS    73      97.845 105.728 102.725  1.00  4.00 
ATOM    545  CA  LYS    74      94.941 105.122 105.297  1.00  4.00 
ATOM    554  CA  THR    75      92.327 104.609 102.699  1.00  4.00 
ATOM    561  CA  ARG    76      95.145 103.156 100.468  1.00  4.00 
ATOM    572  CA  ALA    77      96.299 100.329 102.415  1.00  4.00 
ATOM    577  CA  GLN    78      93.467 100.609 104.889  1.00  4.00 
ATOM    586  CA  GLN    79      92.222  98.970 101.822  1.00  4.00 
ATOM    595  CA  PHE    80      95.383  97.091 100.770  1.00  4.00 
ATOM    606  CA  VAL    81      99.052  96.924 102.359  1.00  4.00 
ATOM    613  CA  SER    82     101.793  94.768 104.091  1.00  4.00 
ATOM    619  CA  THR    83     102.582  96.748 107.233  1.00  4.00 
ATOM    626  CA  LYS    84     105.976  97.515 108.596  1.00  4.00 
ATOM    635  CA  ILE    85     106.529  98.265 112.130  1.00  4.00 
ATOM    643  CA  ASN    86     110.011  99.172 111.806  1.00  4.00 
ATOM    651  CA  LEU    87     109.330 102.821 112.139  1.00  4.00 
ATOM    659  CA  ASP    88     111.872 105.600 111.425  1.00  4.00 
ATOM    667  CA  ASP    89     115.582 105.369 112.181  1.00  4.00 
ATOM    675  CA  HIS    90     115.871 103.322 109.113  1.00  4.00 
ATOM    685  CA  ILE    91     112.530 103.909 107.841  1.00  4.00 
ATOM    693  CA  ALA    92     113.671 107.067 106.616  1.00  4.00 
ATOM    698  CA  ASN    93     115.550 104.746 104.332  1.00  4.00 
ATOM    706  CA  ILE    94     112.265 102.774 104.183  1.00  4.00 
ATOM    714  CA  ASP    95     113.812  99.443 103.199  1.00  4.00 
ATOM    722  CA  GLY    96     111.205  97.140 104.458  1.00  4.00 
ATOM    726  CA  THR    97     111.704  93.579 104.223  1.00  4.00 
ATOM    733  CA  LEU    98     110.077  91.513 101.731  1.00  4.00 
ATOM    741  CA  LYS    99     109.302  88.107 102.928  1.00  4.00 
ATOM    750  CA  TYR   100     108.275  87.654  99.448  1.00  4.00 
ATOM    762  CA  GLU   101     109.154  84.041  99.209  1.00  4.00 
TER 
END 
