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  4 
PARENT N/A 
ATOM      2  CA  LEU     1     103.248 106.015 115.256  1.00  5.00 
ATOM     10  CA  GLY     2     105.202 108.586 113.385  1.00  5.00 
ATOM     14  CA  LYS     3     107.576 106.453 111.391  1.00  5.00 
ATOM     23  CA  PHE     4     106.707 103.535 109.039  1.00  5.00 
ATOM     34  CA  SER     5     108.062 103.152 105.533  1.00  5.00 
ATOM     40  CA  GLN     6     105.244 101.855 103.318  1.00  5.00 
ATOM     49  CA  THR     7     106.761 101.816 100.023  1.00  5.00 
ATOM     56  CA  CYS     8     104.252 101.666  97.080  1.00  5.00 
ATOM     62  CA  TYR     9     104.180 102.941  93.326  1.00  5.00 
ATOM     74  CA  ASN    10     107.099 105.330  92.217  1.00  5.00 
ATOM     82  CA  SER    11     108.926 108.149  93.895  1.00  5.00 
ATOM     88  CA  ALA    12     107.390 110.632  96.188  1.00  5.00 
ATOM     93  CA  ILE    13     106.178 109.805  99.437  1.00  5.00 
ATOM    101  CA  GLN    14     107.690 112.115 102.120  1.00  5.00 
ATOM    110  CA  GLY    15     106.704 111.338 105.589  1.00  5.00 
ATOM    114  CA  SER    16     107.785 109.876 108.823  1.00  5.00 
ATOM    120  CA  VAL    17     106.041 106.988 107.275  1.00  5.00 
ATOM    127  CA  LEU    18     107.011 106.083 103.690  1.00  5.00 
ATOM    135  CA  THR    19     107.668 107.646 100.667  1.00  5.00 
ATOM    142  CA  SER    20     109.801 105.262  98.958  1.00  5.00 
ATOM    148  CA  THR    21     108.788 103.366  96.046  1.00  5.00 
ATOM    155  CA  CYS    22     109.687 101.035  93.385  1.00  5.00 
ATOM    161  CA  GLU    23     108.307 101.243  89.789  1.00  5.00 
ATOM    170  CA  ARG    24     106.643  98.710  87.735  1.00  5.00 
ATOM    181  CA  THR    25     109.029  98.827  84.929  1.00  5.00 
ATOM    188  CA  ASN    26     107.049  96.033  83.729  1.00  5.00 
ATOM    196  CA  GLY    27     103.466  96.661  83.893  1.00  5.00 
ATOM    200  CA  GLY    28     101.882  95.281  86.985  1.00  5.00 
ATOM    204  CA  TYR    29      99.043  95.771  89.434  1.00  5.00 
ATOM    216  CA  ASN    30      95.562  94.325  89.363  1.00  5.00 
ATOM    224  CA  THR    31      93.133  94.319  92.335  1.00  5.00 
ATOM    231  CA  SER    32      91.416  92.940  95.406  1.00  5.00 
ATOM    237  CA  SER    33      94.774  91.438  96.150  1.00  5.00 
ATOM    243  CA  ILE    34      97.136  92.765  93.826  1.00  5.00 
ATOM    251  CA  ASP    35      99.766  94.777  92.295  1.00  5.00 
ATOM    259  CA  LEU    36     103.265  95.500  91.547  1.00  5.00 
ATOM    267  CA  ASN    37     106.118  93.013  90.663  1.00  5.00 
ATOM    275  CA  SER    38     109.855  93.013  89.764  1.00  5.00 
ATOM    281  CA  VAL    39     112.845  94.798  91.553  1.00  5.00 
ATOM    288  CA  ILE    40     113.999  98.438  91.535  1.00  5.00 
ATOM    296  CA  GLU    41     117.143  99.245  93.722  1.00  5.00 
ATOM    305  CA  ASN    42     118.816 100.954  96.739  1.00  5.00 
ATOM    313  CA  VAL    43     119.458  99.433 100.188  1.00  5.00 
ATOM    320  CA  ASP    44     117.981  99.602 103.752  1.00  5.00 
ATOM    328  CA  GLY    45     115.161  97.482 103.984  1.00  5.00 
ATOM    332  CA  SER    46     115.775  97.729 100.348  1.00  5.00 
ATOM    338  CA  LEU    47     113.058  98.575  98.000  1.00  5.00 
ATOM    346  CA  LYS    48     112.902  95.160  96.333  1.00  5.00 
ATOM    355  CA  TRP    49     109.798  94.778  94.138  1.00  5.00 
ATOM    369  CA  GLN    50     107.545  91.822  93.824  1.00  5.00 
ATOM    378  CA  PRO    51     104.771  91.367  93.502  1.00  5.00 
ATOM    385  CA  SER    52     101.761  93.432  94.484  1.00  5.00 
ATOM    391  CA  ASN    53     101.821  95.338  97.821  1.00  5.00 
ATOM    399  CA  PHE    54     100.356  99.046  97.801  1.00  5.00 
ATOM    410  CA  ILE    55      98.246 100.703  94.910  1.00  5.00 
ATOM    418  CA  GLU    56     100.138 103.978  93.670  1.00  5.00 
ATOM    427  CA  THR    57     100.990 105.773  96.814  1.00  5.00 
ATOM    434  CA  CYS    58      97.842 105.463  98.301  1.00  5.00 
ATOM    440  CA  ARG    59      95.609 105.761  95.420  1.00  5.00 
ATOM    451  CA  ASN    60      94.101 109.328  95.184  1.00  5.00 
ATOM    459  CA  THR    61      95.195 112.700  93.739  1.00  5.00 
ATOM    466  CA  ASN    62      97.834 113.081  96.440  1.00  5.00 
ATOM    474  CA  LEU    63      97.579 111.840  99.798  1.00  5.00 
ATOM    482  CA  ALA    64     100.532 113.303 101.474  1.00  5.00 
ATOM    487  CA  GLY    65     100.558 113.902 105.220  1.00  5.00 
ATOM    491  CA  SER    66     102.453 112.196 108.067  1.00  5.00 
ATOM    497  CA  SER    67     101.102 109.142 109.698  1.00  5.00 
ATOM    503  CA  GLU    68      97.380 108.914 109.399  1.00  5.00 
ATOM    512  CA  LEU    69      98.865 108.680 106.232  1.00  5.00 
ATOM    520  CA  ALA    70     100.005 105.853 108.252  1.00  5.00 
ATOM    525  CA  ALA    71      96.241 105.499 108.621  1.00  5.00 
ATOM    530  CA  GLU    72      95.676 105.608 104.856  1.00  5.00 
ATOM    539  CA  CYS    73      97.677 102.857 103.325  1.00  5.00 
ATOM    545  CA  LYS    74      97.419 100.123 105.790  1.00  5.00 
ATOM    554  CA  THR    75      93.942  99.235 105.508  1.00  5.00 
ATOM    561  CA  ARG    76      94.387 101.297 102.660  1.00  5.00 
ATOM    572  CA  ALA    77      95.864  98.438 101.348  1.00  5.00 
ATOM    577  CA  GLN    78      92.719  97.699 103.359  1.00  5.00 
ATOM    586  CA  GLN    79      92.662  95.589 100.506  1.00  5.00 
ATOM    595  CA  PHE    80      95.896  96.020  98.695  1.00  5.00 
ATOM    606  CA  VAL    81      98.146  93.408 100.140  1.00  5.00 
ATOM    613  CA  SER    82     101.075  94.485 102.588  1.00  5.00 
ATOM    619  CA  THR    83     102.731  97.701 103.814  1.00  5.00 
ATOM    626  CA  LYS    84     106.066  97.985 105.934  1.00  5.00 
ATOM    635  CA  ILE    85     105.967  98.892 109.741  1.00  5.00 
ATOM    643  CA  ASN    86     108.327  97.549 112.271  1.00  5.00 
ATOM    651  CA  LEU    87     110.702  97.353 115.127  1.00  5.00 
ATOM    659  CA  ASP    88     112.997 100.106 114.428  1.00  5.00 
ATOM    667  CA  ASP    89     116.580 100.079 113.184  1.00  5.00 
ATOM    675  CA  HIS    90     115.261  97.104 111.472  1.00  5.00 
ATOM    685  CA  ILE    91     113.921 100.125 110.339  1.00  5.00 
ATOM    693  CA  ALA    92     116.123 102.812 110.992  1.00  5.00 
ATOM    698  CA  ASN    93     117.208 100.660 108.178  1.00  5.00 
ATOM    706  CA  ILE    94     115.639  97.379 107.188  1.00  5.00 
ATOM    714  CA  ASP    95     113.295  94.939 105.552  1.00  5.00 
ATOM    722  CA  GLY    96     110.836  95.753 102.924  1.00  5.00 
ATOM    726  CA  THR    97     112.092  93.716 100.148  1.00  5.00 
ATOM    733  CA  LEU    98     108.423  92.738  99.585  1.00  5.00 
ATOM    741  CA  LYS    99     107.188  89.222  99.807  1.00  5.00 
ATOM    750  CA  TYR   100     103.643  88.299  98.832  1.00  5.00 
ATOM    762  CA  GLU   101     103.049  85.936 101.566  1.00  5.00 
TER 
END 
