BSDB

PDB: 1pmx
Chain: A

Unfolding scenario

What is unfolding scenario?

The conformational change and the identification of the mechanical clamp for proteins can be derived by looking at the unfolding scenario. A unfolding scenario shows distance d_u at which a given native contact is broken for the last time. Contacts in the scenario diagrams are identified by the sequential distance |j - i|. A contact is said to be broken if the distance between amino acids i and j exceeds 1.5σ_ij. An accumulation of many contacts unfolding events at a value of d_u indicates emergence of a force peak. In such figure the y-axis shows the sequential separation between two amino acids that make a native contact. The x-axis indicates at which displacement of the pulling tip the contact is broken for the last time. Notice that thermal fluctuations may reinstate a broken contact temporarily and that’s why we seek the last, and thus definitive, rupture event.

As an example we show the unfolding diagram for the first chain of protein 1c4p. This protein contains an α helix (196-210), denoted as I, and eight β strands, denoted as A through H, as labelled consecutively from the N to C termini. These β strands form three β sheets: a, b, and c. The a sheet comprises four strands (A, B, G, E), b sheet two ( C, F), and c-sheet also two ( D, H). These letters are indicated on the unfolding scenario figure and show which secondary structures are involved in a contact that is broken at the distance d_u. The data symbols marked by asterisks correspond to contacts which do not involve any secondary structures. The remaining symbols are diversified and have a meaning identified by the letter symbols placed next to them. The force peak at about 140 Å involves a near simultaneous rupture of the contacts which relate to the terminal strands A and G: A+G (meaning between A and G), A+I, G+I (i.e. with the helix) as well as D+H, A+B, E+G, D+G, C+G, and A+C. Breaking these contacts results in destroying the a β-sheet. Later on, the remaining contacts, such as C+F in the b sheet are broken and the helix is the last to unravel.

ICN - number that counts native contacts
I, J - sequential locations of amino acids forming a contact
| I-J | - sequential distance between amino acids forming a contact
Displacement - tip displacement, at which given contact is observed during stretching for the last time (for v_p=0.005 Å/τ).
error - standard deviation of Displacement across saveral trajectories

ICN   I    J   |I-J| Displacement error
1     4    48   44       54.12    2.39
2     5    9    4        51.30    0.01
3     5    10   5        43.79    0.34
4     5    13   8        43.61    0.25
5     5    47   42       64.60    0.25
6     5    48   43       81.58    0.09
7     5    57   52       43.62    0.24
8     6    9    3        83.52    1.32
9     6    10   4        60.50    2.15
10    7    10   3        84.05    1.06
11    7    11   4        69.30    2.23
12    8    11   3        76.87    1.55
13    8    12   4        67.11    2.20
14    9    12   3        74.08    0.15
15    9    13   4        72.95    0.70
16    10   13   3        72.97    0.71
17    10   14   4        72.95    0.72
18    10   25   15       68.72    0.04
19    11   14   3        77.73    2.04
20    11   15   4        72.70    0.83
21    11   23   12       67.25    0.56
22    12   15   3        84.94    1.27
23    12   16   4        76.11    0.51
24    13   16   3        77.58    0.23
25    13   17   4        74.48    0.31
26    14   17   3        80.75    1.80
27    14   18   4        73.76    0.66
28    14   19   5        74.50    0.32
29    14   23   9       104.67   13.72
30    14   25   11      189.31    0.10
31    14   60   46       81.92    0.33
32    15   19   4        73.78    0.68
33    15   23   8       188.98    0.26
34    17   57   40      189.49    0.01
35    18   21   3       189.50    0.00
36    18   57   39      124.67    3.48
37    20   64   44      189.48    0.01
38    20   66   46       21.25    0.60
39    21   64   43      183.19    0.04
40    23   60   37      189.47    0.01
41    24   60   36      189.49    0.01
42    25   42   17       61.30    0.66
43    25   43   18       60.67    0.41
44    25   44   19       60.66    0.42
45    25   60   35      189.50    0.00
46    26   40   14       66.72    1.03
47    41   45   4       189.50    0.01
48    42   60   18       61.31    0.66
49    43   46   3       189.50    0.00
50    43   57   14       61.98    0.99
51    43   60   17       60.23    0.21
52    52   56   4        70.42    0.12
53    53   56   3        74.81    0.10
54    54   57   3        73.59    0.70
55    55   58   3        80.66    0.59
56    56   59   3        78.30    0.58
57    56   60   4        76.62    0.26
58    57   60   3        82.26    0.32
59    57   61   4        78.30    0.58
60    58   61   3        82.26    0.32