Table 1 The initial amino acid sequences including binding sites and folding energies (RT units) are shown for the 10 proteins. Additionally, the three ligands for each protein are shown with their initial binding energies (also RT units) at the two sites (A in italics and B in bold). It should be noted that the two binding sites are adjacent in three dimensions and overlap by one amino acid.
From: Subfunctionalization of duplicated genes as a transition state to neofunctionalization
| Â | Sequences | Conf. Eng. | Binding Site A | Ligand A | Ligand Eng. at A | Binding Site B | Ligand B | Ligand Eng. at B | Ligand C | Ligand Eng. at A | Ligand Eng. at B |
|---|---|---|---|---|---|---|---|---|---|---|---|
1 | MSK TAQK R LLKELQQLIKDSPPGIVAGPKSEN NIFI WDCLIQGPPDTPYA DGV FNAKLEFP KDY | -0.78 | R PAV | YRGM | -0.84 | R KIK | YSMD | -1.42 | YLEG | +0.59 | +0.40 |
2 | MSTP ARRRLMRDFKRMKEDAPPGVSASPL PDN VMVWNAMI IGPA DTPYE DGTFR LLLEFDEEYP | -0.73 | E ALI | EIIL | -1.07 | E RTP | EERQ | -1.54 | EKEP | +0.79 | +0.58 |
3 | MTTSKERHSVSKRLQQELRT LL MSGDPGITAF PD GDN LFKWVATLDGPKDTVYES LKYKLTLEF | -0.68 | T LLS | SILL | -0.51 | T NDP | SDEW | -0.81 | STYL | +0.61 | +0.23 |
4 | MNM SGIALSRLAQERKAW RKDHPFGFVAVPT K NPD G TMNL MNWECAIPGKKGTPWEGGLFKLRM | -0.88 | D LTW | GFHW | -0.83 | D GMN | GTFE | -1.22 | GEEC | +0.29 | +0.60 |
5 | MSTPARKRLMRDFKRLQQDPPAGISGAPQD N N IMLWNAV IFGPDDTPWDGG TFKLS LQFSEDYP | -0.66 | D NSG | GTDD | -0.86 | D NAV | GTWF | -0.64 | GIFH | +0.80 | +0.53 |
6 | MIV PYNLPLPGGVVPRMLITILGTVKP NANRI ALDFQ R GNDV AFHFNPRFNENNRRVIVCNTKL | -1.00 | R VKP | YLEE | -1.61 | R QVV | YKII | -1.13 | YQRD | +0.78 | +0.92 |
7 | MT EENSKSEALLDIPMLEQYLELVG PKL I TDG LAVFEKMMPGYVSVLES NLTAQDKKGIVEEGH | -0.96 | I GSE | ATEY | -0.84 | I LGT | AIPG | -1.00 | AEFF | +0.59 | +0.90 |
8 | MEAVIKVISSACK TYCGKTSPS KKEIGAM LS L LQ KEGLLMSPSDLYSPGSWDPITAALSQ RAMI | -0.64 | Q MSK | YWQY | -1.22 | Q SQS | YEPG | -1.04 | YRFF | +0.84 | +0.75 |
9 | MDE PPA DGALKRAEELK TQA ND Y FKAKDYENA IKFYSQAIELNPSNAIYYGNRSLAYLRTECYG | -0.37 | Y AKL | EITF | -0.71 | Y DED | EKKT | -1.92 | EMVR | +0.94 | +1.32 |
10 | MKSR RWFHPNIT GVE AENLLLTRGVDGSFLAR P SKSNPGDLTLSVRRNGAVTHIKIQNTGDYY D | -1.45 | T ERP | ASER | -1.47 | T YRS | AMDD | -1.25 | ALIL | +1.18 | +0.82 |