DNA-protein complexes

Task 1

Exercises 1 and 2

According the task I compared forecast of secondary structure of tRNA (1h3e) made by programe "einverted" (EMBOSS. Minimum score threshold = 5) and by the Zucker's algorithm with forecast mabe by "find_pair" and "analyze" 3DNA package (see pr2). The result you can see in table 1.
* For einverted: Minimum score threshold = 5, "---" means that nothing were find.

Figure 1. tRNA.

Table 1.

Part of structure Forecast by "find_pair" Forecast by "einverted" Forecast by Zucker's algorithm

Acceptor stem 5'-1-72 -3'
5'-2-71 -3'
5'-3-70 -3'
5'-4-69 -3'
5'-5-68 -3'
5'-6-67 -3'
5'-7-66 -3'
7 pairs 7 pairs 7 pairs

D arm 5'-10-25 -3'
5'-11-24 -3'
5'-12-23 -3'
5'-13-22 -3'
5'-14-21 -3'
5 pairs --- 5 pairs

Anticodon arm 5'-39-31 -3'
5'-40-30 -3'
5'-41-29 -3'
5'-42-28 -3'
5'-43-27 -3'
5'-44-26 -3'
6 pairs --- 6 pairs

T arm 5'-49-65 -3'
5'-50-64 -3'
5'-51-63 -3'
5'-52-62 -3'
5'-53-61 -3'
5 pairs --- 3 pairs of 5

Number of canonical nucleotide pairs 24 7

* There are another 3 complementary pairs in variable arm forecasted by Zucker's algorithm. (see fig. 2)

Figure 2. Forecast of secondary structure of tRNA by the Zucker's algorithm.

Task 2

Exercise 1

According the task I defined three sets of atoms in my DNA-protein complex (1PP7):

Set1 - the oxygen atoms of 2'-desoxyribose;
Set2 - the oxygen atoms in phosphates;
Set3 - the nitrogen atoms in nitrogen bases.

To see these sets one by one press "Start script". You can see the text of the script here: script 1.

Press "Start script" and then "Resume", please.

Exercise 2

Here oxygen and nitrogen atoms are called polar, and carbon, phosphorus and sulfur atoms are called nonpolar. So I define situation, in which the distance between the polar atom and a polar protein atom DNA less than 0.35 nm, as a polar contact. Similarly, as a nonpolar contact, we will consider a pair of nonpolar atoms at a distance less than 0.45 nm.
The list of contacts you can see in table 2. According pr2 I defined atoms of bases are facing minor or major groove.
To see the visualisation of contacts press "Start script 2" (the text of the script you can see here: script 2. Polar atoms of DNA colored green, polar atoms of protein colored blue, nonpolar atoms of DNA colored purple, nonpolar atoms of protein colored orange.

Table 2.

There is the contact between protein's atom and ... Polar Nonpolar Sum

... atoms of 2'-desoxyribose 5 contacts:
5 protein's atoms
4 DNA's atoms
23 contacts:
23 protein's atoms
23 DNA's atoms
28 contacts

... atoms of phosphate 9 contacts:
9 protein's atoms
8 DNA's atoms
14 contacts:
14 protein's atoms
7 DNA's atoms
23 contacts

... atoms of atoms in nitrogen bases in major groove 2 contacts:
2 protein's atoms
2 DNA's atoms
7 contacts:
7 protein's atoms
5 DNA's atoms
9 contacts

... atoms of atoms in nitrogen bases in minor groove 3 contacts:
2 protein's atoms
3 DNA's atoms
1 contacts:
1 protein's atoms
1 DNA's atoms
4 contacts

Exercise 3

To get a diagram of the DNA-protein contacts I used the program nucplot.
Syntax:

remediator --old ''1pp7.pdb'' > ''1pp7_old.pdb''
nucplot 1pp7_old.pdb

Then I regained the diagram from .ps-file. The result you can see on the figure 3 or here: contacts.pdf.

Figure 3. DNA-protein contacts diagram.

Exercise 4

4.1) The amino acid residue which forms the greatest number of hydrogen bonds is Asn81(U): it conects with 33 C and 7 T. The amino acid residue which forms the greatest number of nonbonded contact is Ser27: it conects with 29 A by two bonds. (see fig. 3 and fig. 4)

Figure 4. The amino acid residue which forms the greatest number of contacts.

4.2) I think the protein recognizes the region 30-CTT-32 (chain E) of DNA by aminoacids: Arg33(U), Phe34(U), Asn86(U), Lys79(U), Thr82(U). I consider so, because every phosphate of these nucleotides is linked with amino acids: 33 C - Arg33(U) and Phe34(U), 31 T - Asn86(U), 32 T - Lys79(U) and Thr82(U) (see fig. 3 and fig. 5).

Figure 5. The aminoacid residues which recognize DNA.

Term 3

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