GNU nano 5.4 pr2.html Practise 3

DNA and protein complexes

Task 1. Predicting the secondary structure of a given tRNA

The exercise was performed using the program einverted from the EMBOSS package.

the obtained complementary sites were compared with their descriptions obtained in the find_pair program

The following parameters were given as input to the program:

! einverted -sequence rna.seq -gap 5 -threshold 1 -match 2 -mismatch -3 -outfile tRNA3.inv -outseq seqout

The data obtained do not correspond to the real RNA structure. It was not possible to select parameters that reflect the real structure. This is probably due to the fact that the algorithms designed for DNA are not suitable for working with RNA.

Next, the secondary structure of tRNA was predicted using the Zucker algorithm (with ViennaRNA).

the resulting structure is shaped like a coverleaf

Sorry!
Structure of tRNA constructed using ViennaRNA.

The results of the comparison of the find_pair and einverted programs are shown in the table below

Structure section Coordinates in the structure(find_pair results) Prediction with einverted Results of Zucker's algorithm prediction
Acceptor stem

5' 2-7 3'

5' 66-71 3'

 6 pairs predicted 6 pairs predicted
D-stable

5' 10-12 3'

5' 23-25 3'

 - 3 pairs predicted
T-stable

5' 49-53 3'

5' 61-65 3'

 - 5 pairs predicted
Anticodone stem

5' 37-44 3'

5' 26-33 3'

 - 5 pairs predicted
Total number of canonical nucleotide pairs 19 19 6

Task 3

Coordinates of tRNA stems:
Strand 1 Strand 2
2-7 66-71
49-53 61-65
37-44 26-33
10-12 23-25
Non-canonical base pairs:

55U-18G

38U-32U

44C-26A

13A-45A

14A-21A

19G-56C is additional hydrogen bond that maintains the tertiary structure of tRNA

Searching for DNA-protein contacts in a given structure

Reference to a script highlighting the oxygen atoms of 2'-deoxyribose, phosphoric acid residues, and nitrogen atoms of nitrogenous base residues in JMol.

Reference to a script whose call to JMol will give a sequential image of the whole structure, only DNA in a wire model, the same model, but with the selected beads set1, then set2 and set3 atoms.

We will consider the oxygen and nitrogen atoms as polar and the carbon, phosphorus, and sulfur atoms as non-polar. We will call as polar contact the situation in which the distance between the polar protein atom and the polar DNA atom is less than 3.5 Å. Similarly, we will consider a pair of non-polar atoms at a distance less than 4.5 Å as a non-polar contact. Below is a table comparing the number of contacts of different types:

Table 2 - Contacts of different types in the complex 1gtr.pdb
Contacts of protein atoms withPolarNon-polarTotal
2'-deoxyribose residues42226
phosphoric acid residue101222
residual nitrogenous bases on the side of the large furrow358
residual nitrogenous bases on the side of the small furrow101


Obtaining a DNA-protein contact diagram using the nucplot program

link to the .ps file

Fig.2 Visualization of DNA-protein contacts using nucplot software
Fig.3

Based on this scheme were selected:

The amino acid residue with the greatest number of contacts with DNA shown in the diagram is Ser17(B) (2 contacts)
The amino acid residue most important for DNA sequence recognition is Arg23(B), which is bound to two nitrogenous base residues, not to the DNA backbone

Fig.4 Contact Ser17(B) (N, OG) with P

Fig.5 Contact Arg23(B) with T (NH2), G(NH1)