protein-dna/rna interfaces by MolSurfer
Instructions:
  • Use menu File--Open to switch between the interfaces;
  • Use menu View to switch between the properties to be displayed on the 2D map;
  • Use Mouse to move/drag/click across the map to navigate in the 3D structure;
  • To adjust the range for displaying properties on 2D map, click left/right mouse button on the color bar;
  • Use features of WebMol while viewing 3D - stereo, colouring, selecting etc;
  • Use menu File--Quit when done.

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    Details of interface mapping for a demo:
  • Each PDB file was split into 2 parts giving coordinates of the first (proterin) and the second (dna/rna) molecules forming the interface, according to the table from "Nadassy K, Wodak SJ, Janin J, Structural features of protein-nucleic acid recognition sites. Biochemistry 1999 Feb 16;38(7):1999-2017", see also  http://www.ebi.ac.uk/~nadassy/table_list.htm.
  • A quasi rectangular mesh of ca 1 Å spacing was generated on the analytically defined interface between these 2 macromolecules;
  • Points for which the sum of the distances to the closest atoms of macromolecules 1 and 2 exceeds 6 Å were deleted;
  • The properties of each molecule were projected onto every point of the interface; these are the properties assigned to the closest atom to the point;
  • Electrostatic potential of each (isolated) macromolecule was computed with the UHBD program by solving FD LPBE and the potential values were interpolated at each interface point.

    • Residue hydrophobicities are assigned according to the residue name and following the parameters in "Eisenberg D., Weiss R.M., Terwilliger T.C. and Wilcox W. (1982) Farad. Symp. Chem. Soc., 17, 109-120", and nucleic acid hydrophobicities were derived from the data in "P.Shih, L.G.Pedersen, P.R.Gibbs, R.Wolfensen, JMB (1998) 280, 421-430", namely:
      ALA   0.25       GLN  -0.69       LEU   0.53       SER  -0.26
      ARG  -1.80       GLU  -0.62       LYS  -1.10       THR  -0.18
      ASN  -0.64       GLY   0.16       MET   0.26       TRP   0.37
      ASP  -0.72       HIS  -0.40       PHE   0.61       TYP   0.02
      CYS   0.04       ILE   0.73       PRO  -0.07       VAL   0.54
        A   0.82         G  -1.35         C  -0.99       T     1.18
        U   0.35
      none of the above                 0.00
  • Atomic hydrophobicities are assigned according to the atom name and follow  Eisenberg D., Wesson M., Yamashita M. (1989) Chem. Scrip., 29A, 217-221, namely:

    •   'NZ  LYS'  -38       'OE1 GLU'  -37         'C'    18
      'NH1 ARG'  -38       'OE2 GLU'  -37         'S'     5
      'NH2 ARG'  -38       'OD1 ASP'  -37         'O'    -9
                           'OD2 ASP'  -37         'N'    -9
                           'O1P'      -37
                           'O2P'      -37
                           'P'        -37
    none of the above    0
  • Atomic radii are also from the previous reference, namely:

    •   'C'    1.9 A
      'S'    1.8 A
      'O'    1.4 A
      'N'    1.7 A
      'P'    1.6 A
      none of the above    1.9 A

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