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  2 
PARENT N/A 
ATOM      2  CA  LEU     1      94.372 108.063 102.775  1.00  5.00 
ATOM     10  CA  GLY     2      95.359 111.550 103.890  1.00  5.00 
ATOM     14  CA  LYS     3      99.031 112.038 104.435  1.00  5.00 
ATOM     23  CA  PHE     4     101.041 109.203 106.077  1.00  5.00 
ATOM     34  CA  SER     5     103.875 106.639 105.980  1.00  5.00 
ATOM     40  CA  GLN     6     104.300 103.085 105.083  1.00  5.00 
ATOM     49  CA  THR     7     104.647 101.059 102.322  1.00  5.00 
ATOM     56  CA  CYS     8     105.396  97.531 102.036  1.00  5.00 
ATOM     62  CA  TYR     9     103.956  94.692 103.961  1.00  5.00 
ATOM     74  CA  ASN    10     106.401  91.809 104.737  1.00  5.00 
ATOM     82  CA  SER    11     107.860  88.374 104.425  1.00  5.00 
ATOM     88  CA  ALA    12     108.658  85.287 102.236  1.00  5.00 
ATOM     93  CA  ILE    13     105.236  83.616 102.250  1.00  5.00 
ATOM    101  CA  GLN    14     102.976  82.484  99.407  1.00  5.00 
ATOM    110  CA  GLY    15     104.225  84.315  96.445  1.00  5.00 
ATOM    114  CA  SER    16     105.954  86.062  99.388  1.00  5.00 
ATOM    120  CA  VAL    17     106.985  89.935  99.951  1.00  5.00 
ATOM    127  CA  LEU    18     109.717  90.957 102.755  1.00  5.00 
ATOM    135  CA  THR    19     108.254  94.309 104.330  1.00  5.00 
ATOM    142  CA  SER    20     110.184  97.290 103.450  1.00  5.00 
ATOM    148  CA  THR    21     108.618 100.271 105.178  1.00  5.00 
ATOM    155  CA  CYS    22     108.676 103.410 103.104  1.00  5.00 
ATOM    161  CA  GLU    23     107.051 106.669 103.417  1.00  5.00 
ATOM    170  CA  ARG    24     106.711 110.238 104.227  1.00  5.00 
ATOM    181  CA  THR    25     103.971 112.831 104.921  1.00  5.00 
ATOM    188  CA  ASN    26     101.367 115.236 103.371  1.00  5.00 
ATOM    196  CA  GLY    27      98.049 115.572 101.726  1.00  5.00 
ATOM    200  CA  GLY    28      95.266 115.797 104.279  1.00  5.00 
ATOM    204  CA  TYR    29      96.380 113.945 107.409  1.00  5.00 
ATOM    216  CA  ASN    30      95.167 111.084 109.303  1.00  5.00 
ATOM    224  CA  THR    31      98.455 109.418 109.665  1.00  5.00 
ATOM    231  CA  SER    32      98.836 105.617 108.815  1.00  5.00 
ATOM    237  CA  SER    33     101.731 103.307 108.105  1.00  5.00 
ATOM    243  CA  ILE    34      99.631 102.189 105.361  1.00  5.00 
ATOM    251  CA  ASP    35      99.948  98.584 104.646  1.00  5.00 
ATOM    259  CA  LEU    36     100.552  97.901 101.082  1.00  5.00 
ATOM    267  CA  ASN    37      99.936  94.409 101.878  1.00  5.00 
ATOM    275  CA  SER    38     100.491  91.499  99.572  1.00  5.00 
ATOM    281  CA  VAL    39     102.445  88.898  97.449  1.00  5.00 
ATOM    288  CA  ILE    40     106.138  88.883  96.409  1.00  5.00 
ATOM    296  CA  GLU    41     109.264  88.797  94.141  1.00  5.00 
ATOM    305  CA  ASN    42     112.480  87.031  95.195  1.00  5.00 
ATOM    313  CA  VAL    43     114.125  87.623  98.483  1.00  5.00 
ATOM    320  CA  ASP    44     116.260  85.283 100.433  1.00  5.00 
ATOM    328  CA  GLY    45     114.745  85.778 103.667  1.00  5.00 
ATOM    332  CA  SER    46     113.838  89.106 102.109  1.00  5.00 
ATOM    338  CA  LEU    47     116.753  89.323 102.842  1.00  5.00 
ATOM    346  CA  LYS    48     117.795  89.344 106.062  1.00  5.00 
ATOM    355  CA  TRP    49     115.791  91.768 107.568  1.00  5.00 
ATOM    369  CA  GLN    50     116.398  92.005 104.127  1.00  5.00 
ATOM    378  CA  PRO    51     119.146  92.142 105.483  1.00  5.00 
ATOM    385  CA  SER    52     118.587  95.023 107.657  1.00  5.00 
ATOM    391  CA  ASN    53     115.229  96.450 108.612  1.00  5.00 
ATOM    399  CA  PHE    54     113.348  96.894 105.158  1.00  5.00 
ATOM    410  CA  ILE    55     114.109 100.003 102.860  1.00  5.00 
ATOM    418  CA  GLU    56     112.197 103.397 102.692  1.00  5.00 
ATOM    427  CA  THR    57     110.353 105.781 100.247  1.00  5.00 
ATOM    434  CA  CYS    58     109.254 104.528  96.875  1.00  5.00 
ATOM    440  CA  ARG    59     106.899 107.393  96.266  1.00  5.00 
ATOM    451  CA  ASN    60     106.423 110.728  94.813  1.00  5.00 
ATOM    459  CA  THR    61     106.908 112.043  91.408  1.00  5.00 
ATOM    466  CA  ASN    62     110.064 112.722  93.124  1.00  5.00 
ATOM    474  CA  LEU    63     110.048 109.652  94.929  1.00  5.00 
ATOM    482  CA  ALA    64     111.369 109.568  91.535  1.00  5.00 
ATOM    487  CA  GLY    65     114.705 110.914  91.781  1.00  5.00 
ATOM    491  CA  SER    66     115.297 108.083  93.982  1.00  5.00 
ATOM    497  CA  SER    67     113.746 105.137  92.359  1.00  5.00 
ATOM    503  CA  GLU    68     115.835 102.135  93.202  1.00  5.00 
ATOM    512  CA  LEU    69     114.397 102.706  96.501  1.00  5.00 
ATOM    520  CA  ALA    70     111.007 101.634  95.589  1.00  5.00 
ATOM    525  CA  ALA    71     113.023  99.172  93.435  1.00  5.00 
ATOM    530  CA  GLU    72     114.244  98.298  96.534  1.00  5.00 
ATOM    539  CA  CYS    73     110.735  98.326  97.676  1.00  5.00 
ATOM    545  CA  LYS    74     109.538  97.987  94.185  1.00  5.00 
ATOM    554  CA  THR    75     110.782  94.755  92.738  1.00  5.00 
ATOM    561  CA  ARG    76     111.781  94.870  96.231  1.00  5.00 
ATOM    572  CA  ALA    77     108.397  96.058  97.087  1.00  5.00 
ATOM    577  CA  GLN    78     107.659  93.920  94.316  1.00  5.00 
ATOM    586  CA  GLN    79     108.401  91.853  97.262  1.00  5.00 
ATOM    595  CA  PHE    80     105.961  94.406  99.121  1.00  5.00 
ATOM    606  CA  VAL    81     104.036  96.688  96.753  1.00  5.00 
ATOM    613  CA  SER    82     102.811 100.294  96.652  1.00  5.00 
ATOM    619  CA  THR    83      99.022 100.801  96.400  1.00  5.00 
ATOM    626  CA  LYS    84      98.697 104.405  95.250  1.00  5.00 
ATOM    635  CA  ILE    85      95.529 104.470  97.253  1.00  5.00 
ATOM    643  CA  ASN    86      94.076 107.909  97.130  1.00  5.00 
ATOM    651  CA  LEU    87      91.123 108.361  99.395  1.00  5.00 
ATOM    659  CA  ASP    88      87.576 107.720  98.219  1.00  5.00 
ATOM    667  CA  ASP    89      86.654 104.457  96.761  1.00  5.00 
ATOM    675  CA  HIS    90      89.076 102.012  95.291  1.00  5.00 
ATOM    685  CA  ILE    91      91.429 103.866  97.463  1.00  5.00 
ATOM    693  CA  ALA    92      89.709 101.875 100.083  1.00  5.00 
ATOM    698  CA  ASN    93      88.323  98.915  98.401  1.00  5.00 
ATOM    706  CA  ILE    94      91.906  98.572  97.396  1.00  5.00 
ATOM    714  CA  ASP    95      93.298  96.849 100.139  1.00  5.00 
ATOM    722  CA  GLY    96      95.438  97.826 102.841  1.00  5.00 
ATOM    726  CA  THR    97      93.095 100.633 102.776  1.00  5.00 
ATOM    733  CA  LEU    98      90.163  99.143 103.147  1.00  5.00 
ATOM    741  CA  LYS    99      92.696  96.707 104.698  1.00  5.00 
ATOM    750  CA  TYR   100      94.361  99.331 106.583  1.00  5.00 
ATOM    762  CA  GLU   101      90.755  99.838 107.497  1.00  5.00 
TER 
END 
