Visualization of molecules with JMol

Visualization of protein Fructose-1,6-bisphosphatase

Organism: Lentibacillus amyloliquefaciens

Texts of the scripts:

Tasks

Answers and conclusions:

1. There is 10 hydrophobic cores in this protein (PDB ID: 1NI9) (by CluD). Three of them include from 120 to 180 atoms - it is 21% of the total number of atoms. And others cores account for only 2.3% (see table 1). So you can see core 1, 4, 6 (the first type) on the representation.
   Hydrophobic cores locate inside the protein globule and only a few atoms stick out. Indeed, fructose-1,6-bisphosphatase is enzyme (attaches phosphate groups to 1 and 6 fructose's atoms) and it functions in the solution, so it does not need to connect to the membrane by big hydrophobic sites on the surface.

   Table 1. Information about hydrophobic cores.

   Hydrophobic core	Number of atoms	% of the total number of atoms
   core 4	177	8.1%
   core 1	164	7.5%
   core 6	120	5.5%
   core 10, 2, 3, 8, 9, 7, 5	51	2.3%
   all cores	512	23.4%

2. To explore core density I chose the amino acid phenylalanine (PHE280, chain :a, core 4). You can see it at the first visualization (script 2), then atoms at a distance of not more than 7Å are shown. The next representation shows atoms at a distance of not more than 1Å, than 2Å, and so on to 7Å (see table 2).

   Table 2. The number of atoms at different distances from PHE280:A.

   Distance from PHE280:A (Å)	Number of atoms
   1	0
   2	14
   3	22
   4	84
   5	103
   6	177
   7	231

   1. PHE280 begins to disappear from sight of from a distance 4Å and it disappears entirely of from a distance 6Å.
   2. As you can see the number of the atoms surrounding PHE280 increases at the distance = 4Å. I think it is typical distance between neighboring atoms which are not linked covalently.
   3. The typical distance between neighboring atoms = 4Å. It is the distance between nucleus. So if these atoms are the smallest (see table 3), for example - oxygen, free part of this distance is: 4 - 1.4*2 = 1.2 - it is less than Van der Waals radii of the oxygen. Therefore one more atom will not fit between neighboring atoms even more so the water molecule.

      Table 3. Van der Waals radii of chemical elements (John Elmslie, "Elements", 1993).

      Atom	Van der Waals radii (Å)
      O	1.4
      C	1.85
      N	1.54
      S	1.85

3. The third script shows the human DNA polymerase (protein-DNA complex). PDB ID: 5KFM. DNA polymerase eta is a eukaryotic DNA polymerase involved in the DNA repair by translesion synthesis. Polymerase eta is particularly important for allowing accurate translesion synthesis of DNA damage resulting from ultraviolet radiation or UV.It copies undamaged DNA with a lower fidelity than other DNA-directed polymerases. However, it accurately replicates UV-damaged DNA; when thymine dimers are present, this polymerase inserts the complementary nucleotides in the newly synthesized DNA, thereby bypassing the lesion and suppressing the mutagenic effect of UV-induced DNA damage. This polymerase is thought to be involved in hypermutation during immunoglobulin class switch recombination. (Wiki: DNA polymerase eta)

   The piece of the DNA is in the active site of the protein. DNA retains it's structure of the double helix. Both chains of DNA connect with protein, but one of them are longer then other one.

   There are many types of the protein operate with DNA:

   • Proteins support the structure of DNA (histones).
   • Proteins synthes DNA with matrix of DNA and RNA with matrix of DNA (and even DNA with matrix of RNA - found in the viruses); and other proteins take part in DNA-synthesis like helicase and topoisomerase.
   • Proteins are controllers of replication and transcription.
   • Proteins destroys DNA (endonuclease and exonuclease).
   And many others, I think...

4. The gap :(
5. The second gap :( :(