DNA-protein complexes

Task 1

For the first task I took my tRNA nucleic sequence and compared results of 3 different algorithms, which help predict pairs in tRNA structure.
Results are presented below:

Table 1. Results of find_pair EMBOSS command from pr2, einverted EMBOSS command and Zuker algorithm.

Stem	Results of using find_pair	Einverted results	Zuker algorithm results
Acceptor stem	5'-1-7-3' 5'-66-72-3' 7 pairs	7/7	8/7
T-stem	5'-49-53-3' 5'-61-65-3' 5 pairs	2/5	4/5
Anticodon stem	5'-39-43-3' 5'-27-31-3' 5 pairs	5/5	5/5
D-stem	5'-10-13-3' 5'-22-25-3' 4 pairs	2/4	4/4
Amount of Watson-Crick base-pairs	21	17	21

Einverted results

: Score 72: 24/24 (100%) matches, 23 gaps
 1 gccgaggta-gc----tcagtt----g-gtagagca-tgcgac---t 33
   |||||||   ||    || |      | |  || || |||||    |
72 cggctcc--gcgccttag-c--ttggcgc--ct-gtgacgct-aaaa 35

Zuker algorithm results

Figure 1. Structure predicted by Zuker algorithm

Task 2

Applet and scripts are presented below:

Download script: pr3.spt

Download script: script.spt

Table 2. Atomic contacts in DNA-protein structures

Atomic protein contacts with the..	Polar (N, O, < 3.5Å)	Nonpolar (P, S, C < 4.5Å)	Total amount of contacts
..2'-deoxyribose residues	7 protein, 7 dna (7 contacts)	38 protein, 47 dna (38 contacts)	45
..phosphoric acid residues	12 protein, 11 dna (14 contacts)	23 protein, 10 dna (23 contacts)	37
..nitrogenous bases residues (major groove)	7 protein, 8 dna (8 contacts)	7 protein, 8 dna (10 contacts)	18
..nitrogenous bases residues (minor groove)	7 protein, 7 dna (8 contacts)	12 protein, 13 dna (12 contacts)	20

Task 3

Images i got by using nucplot

Figure 2. Map of connections, part 1

Figure 3. Map of connections, part 1

Task 4

Figure 4. Arg49 bonds to a phosphate between 7 and 8 Gs of chain D (according to the nuclprot figure above, it has more connections than any other aa).

I've considered His65 (A,B), Thr46 (A), Arg35(A), Arg49(B), Lys67(A) as the most important amino acids in DNA-protein recognition because each of them has a direct bond with a nucleotide.

Figure 5. DNA D chain and 3 amino acids.

Figure 6. DNA E chain and 3 amino acids.

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