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  5 
PARENT N/A 
ATOM      2  CA  LEU     1     106.549  99.795  86.325  1.00  5.00 
ATOM     10  CA  GLY     2     103.414  97.982  85.294  1.00  5.00 
ATOM     14  CA  LYS     3     100.060  97.952  87.008  1.00  5.00 
ATOM     23  CA  PHE     4      99.749 100.481  89.678  1.00  5.00 
ATOM     34  CA  SER     5      96.895 101.433  91.984  1.00  5.00 
ATOM     40  CA  GLN     6      98.121 103.769  94.727  1.00  5.00 
ATOM     49  CA  THR     7      97.827 102.785  98.228  1.00  5.00 
ATOM     56  CA  CYS     8      97.600 105.388 100.785  1.00  5.00 
ATOM     62  CA  TYR     9      98.332 103.833 103.937  1.00  5.00 
ATOM     74  CA  ASN    10      97.427 106.138 106.719  1.00  5.00 
ATOM     82  CA  SER    11      98.281 104.262 109.860  1.00  5.00 
ATOM     88  CA  ALA    12     100.351 101.445 110.977  1.00  5.00 
ATOM     93  CA  ILE    13     103.611 103.034 109.619  1.00  5.00 
ATOM    101  CA  GLN    14     102.507 106.098 111.445  1.00  5.00 
ATOM    110  CA  GLY    15     102.742 103.567 114.081  1.00  5.00 
ATOM    114  CA  SER    16     105.193 102.083 111.675  1.00  5.00 
ATOM    120  CA  VAL    17     103.944  98.502 110.842  1.00  5.00 
ATOM    127  CA  LEU    18     100.636  97.301 109.302  1.00  5.00 
ATOM    135  CA  THR    19      97.090  97.771 110.118  1.00  5.00 
ATOM    142  CA  SER    20      94.548  99.003 107.673  1.00  5.00 
ATOM    148  CA  THR    21      91.805 101.682 107.184  1.00  5.00 
ATOM    155  CA  CYS    22      92.956 102.257 103.749  1.00  5.00 
ATOM    161  CA  GLU    23      92.554 105.135 101.448  1.00  5.00 
ATOM    170  CA  ARG    24      93.762 104.707  98.061  1.00  5.00 
ATOM    181  CA  THR    25      93.021 105.642  94.555  1.00  5.00 
ATOM    188  CA  ASN    26      94.159 103.492  91.645  1.00  5.00 
ATOM    196  CA  GLY    27      94.233 104.447  88.030  1.00  5.00 
ATOM    200  CA  GLY    28      94.232 101.344  86.014  1.00  5.00 
ATOM    204  CA  TYR    29      95.172  98.131  87.434  1.00  5.00 
ATOM    216  CA  ASN    30      93.539  94.900  87.987  1.00  5.00 
ATOM    224  CA  THR    31      95.251  91.636  87.255  1.00  5.00 
ATOM    231  CA  SER    32      98.670  90.984  88.850  1.00  5.00 
ATOM    237  CA  SER    33     100.205  93.548  91.236  1.00  5.00 
ATOM    243  CA  ILE    34     103.153  95.738  92.060  1.00  5.00 
ATOM    251  CA  ASP    35     102.071  97.535  95.197  1.00  5.00 
ATOM    259  CA  LEU    36     104.108 100.644  95.930  1.00  5.00 
ATOM    267  CA  ASN    37     102.254 101.575  99.164  1.00  5.00 
ATOM    275  CA  SER    38     103.730 104.783 100.357  1.00  5.00 
ATOM    281  CA  VAL    39     102.753 105.415 104.148  1.00  5.00 
ATOM    288  CA  ILE    40     104.141 108.368 106.489  1.00  5.00 
ATOM    296  CA  GLU    41     107.307 108.292 108.919  1.00  5.00 
ATOM    305  CA  ASN    42     109.569 105.051 108.541  1.00  5.00 
ATOM    313  CA  VAL    43     109.208 101.201 108.699  1.00  5.00 
ATOM    320  CA  ASP    44     112.612 100.577 110.204  1.00  5.00 
ATOM    328  CA  GLY    45     113.949  98.014 112.466  1.00  5.00 
ATOM    332  CA  SER    46     110.297  98.052 113.128  1.00  5.00 
ATOM    338  CA  LEU    47     108.940  96.109 110.440  1.00  5.00 
ATOM    346  CA  LYS    48     112.157  94.354 110.693  1.00  5.00 
ATOM    355  CA  TRP    49     109.556  93.837 113.337  1.00  5.00 
ATOM    369  CA  GLN    50     105.745  93.571 113.224  1.00  5.00 
ATOM    378  CA  PRO    51     103.326  92.276 114.852  1.00  5.00 
ATOM    385  CA  SER    52      99.619  92.999 115.024  1.00  5.00 
ATOM    391  CA  ASN    53      96.316  92.841 113.357  1.00  5.00 
ATOM    399  CA  PHE    54      94.819  95.536 111.054  1.00  5.00 
ATOM    410  CA  ILE    55      91.118  94.790 111.009  1.00  5.00 
ATOM    418  CA  GLU    56      89.756  95.415 107.383  1.00  5.00 
ATOM    427  CA  THR    57      88.029  98.713 106.308  1.00  5.00 
ATOM    434  CA  CYS    58      88.191 101.340 103.585  1.00  5.00 
ATOM    440  CA  ARG    59      86.901 102.434 100.279  1.00  5.00 
ATOM    451  CA  ASN    60      88.527 104.760  97.962  1.00  5.00 
ATOM    459  CA  THR    61      90.100 105.582  94.814  1.00  5.00 
ATOM    466  CA  ASN    62      89.169 107.997  92.264  1.00  5.00 
ATOM    474  CA  LEU    63      86.006 106.167  91.435  1.00  5.00 
ATOM    482  CA  ALA    64      85.097 102.970  93.126  1.00  5.00 
ATOM    487  CA  GLY    65      82.838 102.246  96.006  1.00  5.00 
ATOM    491  CA  SER    66      83.954 100.136  98.924  1.00  5.00 
ATOM    497  CA  SER    67      83.440  96.345  98.799  1.00  5.00 
ATOM    503  CA  GLU    68      86.533  94.662  97.650  1.00  5.00 
ATOM    512  CA  LEU    69      89.003  96.887  99.062  1.00  5.00 
ATOM    520  CA  ALA    70      88.827  96.046 102.584  1.00  5.00 
ATOM    525  CA  ALA    71      88.198  92.647 101.293  1.00  5.00 
ATOM    530  CA  GLU    72      91.204  93.978  99.430  1.00  5.00 
ATOM    539  CA  CYS    73      92.464  95.715 102.227  1.00  5.00 
ATOM    545  CA  LYS    74      91.893  92.306 102.910  1.00  5.00 
ATOM    554  CA  THR    75      94.782  90.367 101.416  1.00  5.00 
ATOM    561  CA  ARG    76      95.883  93.856 101.000  1.00  5.00 
ATOM    572  CA  ALA    77      95.535  94.368 104.521  1.00  5.00 
ATOM    577  CA  GLN    78      96.508  91.134 105.852  1.00  5.00 
ATOM    586  CA  GLN    79      99.462  92.159 103.779  1.00  5.00 
ATOM    595  CA  PHE    80     100.617  95.489 104.930  1.00  5.00 
ATOM    606  CA  VAL    81     103.339  97.430 106.227  1.00  5.00 
ATOM    613  CA  SER    82     104.869 100.253 104.148  1.00  5.00 
ATOM    619  CA  THR    83     107.718 101.930 102.358  1.00  5.00 
ATOM    626  CA  LYS    84     107.664 105.220 104.524  1.00  5.00 
ATOM    635  CA  ILE    85     106.860 108.673 103.185  1.00  5.00 
ATOM    643  CA  ASN    86     108.435 111.664 105.050  1.00  5.00 
ATOM    651  CA  LEU    87     107.506 114.821 103.263  1.00  5.00 
ATOM    659  CA  ASP    88     108.830 116.857 100.497  1.00  5.00 
ATOM    667  CA  ASP    89     107.903 115.610  97.190  1.00  5.00 
ATOM    675  CA  HIS    90     110.543 113.049  97.132  1.00  5.00 
ATOM    685  CA  ILE    91     107.763 111.447  98.546  1.00  5.00 
ATOM    693  CA  ALA    92     106.388 112.469  95.365  1.00  5.00 
ATOM    698  CA  ASN    93     109.141 109.989  94.699  1.00  5.00 
ATOM    706  CA  ILE    94     107.542 107.938  97.204  1.00  5.00 
ATOM    714  CA  ASP    95     105.216 108.665  94.669  1.00  5.00 
ATOM    722  CA  GLY    96     104.179 105.304  94.024  1.00  5.00 
ATOM    726  CA  THR    97     107.021 104.139  96.231  1.00  5.00 
ATOM    733  CA  LEU    98     108.296 100.668  95.490  1.00  5.00 
ATOM    741  CA  LYS    99     108.842  97.803  93.274  1.00  5.00 
ATOM    750  CA  TYR   100     109.404  94.060  93.335  1.00  5.00 
ATOM    762  CA  GLU   101     111.560  92.667  96.089  1.00  5.00 
TER 
END 
