Упражнение 1
С помощью команды fiber я получила 3 формы ДНК последовательности "GATCGATCGATCGATCGATC" в виде файлов gatc-a.pdb, gatc-b.pdb и gatc-z.pdb
Упражнение 2
Молекула ДНК в 1bna:
В большую бороздку смотрят атомы: N1, N2, N3, N4, C2, C4, C5, C6
В малую бороздку смотрят атомы: O3', OP1, OP2, O5', P, C3' C4', C5'
| А-форма | B-форма | Z-форма | |
|---|---|---|---|
| Тип спирали | Правая | Правая | Левая |
| Шаг спирали | 28,03 | 33,75 | 43,5 |
| Число оснований на виток | 11 | 10 | 12 |
| Ширина большой бороздки | 16,81 (A14:A-G29:B) | 17,21 (C8:A-A30:B) | 18,30 (C14:A-C24:B) |
| Ширина малой бороздки | 7,98 (G5:A-A30:B) | 11.69 (C8:A-G37:B) | 8,68 (G19:A-G27:B) |
Упражнение 3.1 - Поиск торсионных углов
С помощью команды find_pair -t 1f7v.pdb stdout | analyze получили на выход файл f7v.out.
base alpha beta gamma delta epsilon zeta chi 1 P --- 129.3 45.6 87.4 -152.5 -76.1 -158.7 2 U -70.7 -178.3 51.0 84.1 -156.3 -72.8 -165.2 3 C -68.9 174.2 56.4 83.2 -157.5 -73.7 -160.4 4 C -66.9 177.6 56.3 83.2 -154.1 -69.9 -161.1 5 U -60.7 173.2 49.9 84.0 -160.5 -73.9 -156.4 6 C -79.9 177.9 62.5 87.9 -150.4 -81.9 -160.4 7 G -42.8 167.1 57.4 143.8 -91.2 -54.0 -132.7 8 c 73.7 137.8 34.2 82.8 -151.5 -77.0 -167.2 9 C -63.0 -174.9 47.6 86.0 -158.4 -68.7 -162.0 10 A -67.0 -168.7 41.8 82.5 -162.7 -74.2 -146.4 11 G 142.6 -155.8 -179.7 82.3 -140.6 -79.3 -175.7 12 G -53.1 159.5 57.5 84.8 -150.5 -73.2 179.1 13 t -69.6 -170.8 47.2 82.4 -149.1 -57.0 -153.4 14 P -74.8 -174.3 50.2 88.5 -146.2 -68.2 -149.5 15 C -63.0 -173.8 60.0 84.7 -155.9 -73.9 -170.9 16 C -59.6 170.0 60.4 83.5 -152.3 -73.8 -170.9 17 A -69.8 -176.3 48.9 83.9 -147.3 -68.2 -165.0 18 G -67.9 170.3 56.3 77.6 -160.7 -69.1 -170.9 19 A -57.8 -176.7 51.5 81.4 -149.8 -77.1 -165.3 20 A -64.3 170.2 54.3 83.9 -145.9 -67.3 -154.4 21 g -179.2 147.9 55.3 86.7 -132.1 -79.5 172.6 22 C -68.9 -179.3 48.7 84.1 -153.1 -74.0 -168.6 23 C -76.0 -170.3 54.1 81.8 -148.9 -62.9 -162.0 24 C -67.3 169.6 65.0 84.8 -174.1 -81.9 -163.7 25 A -63.5 -170.3 57.4 85.8 -155.2 -66.0 -163.2 26 A -64.0 180.0 60.7 144.0 -103.2 -48.0 -126.7 27 G -71.3 -158.1 41.1 144.4 -85.1 145.4 -76.3
| α | β | γ | δ | ε | ζ | ξ |
|---|---|---|---|---|---|---|
| -56,68 | 2,85 | 44,13 | 90,72 | -146,11 | -62,82 | -131,68 |
Молекула тРНК 1F7V больше похожа на А-форму ДНК.
Упражнение 3.2
Стебли тРНК:
- (902-907) - (966-971)
- (949-953) - (961-965)
- (939-942) - (928-917)
- (910-913) - (922-925)
Strand I Strand II Helix
1 (0.043) ....>B:.901_:[PSU]P-**--A[..A]:.972_:B<.... (0.002) |
2 (0.002) ....>B:.902_:[..U]U-----A[..A]:.971_:B<.... (0.004) |
3 (0.004) ....>B:.903_:[..C]C-----G[..G]:.970_:B<.... (0.004) |
4 (0.005) ....>B:.904_:[..C]C-----G[..G]:.969_:B<.... (0.004) |
5 (0.003) ....>B:.905_:[..U]U-*---G[..G]:.968_:B<.... (0.008) |
6 (0.003) ....>B:.906_:[..C]C-----G[..G]:.967_:B<.... (0.011) |
7 (0.004) ....>B:.907_:[..G]G-----C[..C]:.966_:B<.... (0.004) |
8 (0.013) ....>B:.949_:[5MC]c-----G[..G]:.965_:B<.... (0.005) |
9 (0.004) ....>B:.950_:[..C]C-----G[..G]:.964_:B<.... (0.007) |
10 (0.006) ....>B:.951_:[..A]A-----U[..U]:.963_:B<.... (0.005) |
11 (0.010) ....>B:.952_:[..G]G-----C[..C]:.962_:B<.... (0.006) |
12 (0.010) ....>B:.953_:[..G]G-----C[..C]:.961_:B<.... (0.004) |
13 (0.005) ....>B:.954_:[5MU]t-**--a[1MA]:.958_:B<.... (0.009) |
14 (0.044) ....>B:.955_:[PSU]P-**+-G[..G]:.917_:B<.... (0.009) x
15 (0.008) ....>B:.939_:[..C]C-----G[..G]:.931_:B<.... (0.010) |
16 (0.003) ....>B:.940_:[..C]C-----G[..G]:.930_:B<.... (0.007) |
17 (0.006) ....>B:.941_:[..A]A-----U[..U]:.929_:B<.... (0.005) |
18 (0.010) ....>B:.942_:[..G]G-----C[..C]:.928_:B<.... (0.004) |
19 (0.003) ....>B:.943_:[..A]A-**--P[PSU]:.927_:B<.... (0.044) |
20 (0.008) ....>B:.944_:[..A]A-*---g[M2G]:.926_:B<.... (0.013) |
21 (0.007) ....>B:.910_:[2MG]g-----C[..C]:.925_:B<.... (0.008) |
22 (0.003) ....>B:.911_:[..C]C-----G[..G]:.924_:B<.... (0.010) |
23 (0.004) ....>B:.912_:[..C]C-----G[..G]:.923_:B<.... (0.012) |
24 (0.010) ....>B:.913_:[..C]C-**--C[..C]:.922_:B<.... (0.005) |
25 (0.003) ....>B:.914_:[..A]A-**--U[..U]:.908_:B<.... (0.004) |
26 (0.005) ....>B:.915_:[..A]A-**+-U[..U]:.948_:B<.... (0.006) x
27 (0.010) ....>B:.918_:[..G]G-----C[..C]:.956_:B<.... (0.003) +
Неканонические пары оснований:
- U-G
- С-С
- t-a
- P-G
- A-P
Дополнительные водородные связи:
Strand I Strand II Helix
13 (0.005) ....>B:.954_:[5MU]t-**--a[1MA]:.958_:B<.... (0.009) |
14 (0.044) ....>B:.955_:[PSU]P-**+-G[..G]:.917_:B<.... (0.009) x
19 (0.003) ....>B:.943_:[..A]A-**--P[PSU]:.927_:B<.... (0.044) |
20 (0.008) ....>B:.944_:[..A]A-*---g[M2G]:.926_:B<.... (0.013) |
25 (0.003) ....>B:.914_:[..A]A-**--U[..U]:.908_:B<.... (0.004) |
26 (0.005) ....>B:.915_:[..A]A-**+-U[..U]:.948_:B<.... (0.006) x
27 (0.010) ....>B:.918_:[..G]G-----C[..C]:.956_:B<.... (0.003) +