Secondary Structure of Proteins - I
Using space-filling models, G. N. Ramachandran [Adv. Protein Chem., 1968, 23, 283 explored the sterically accessible conformation space of some simple peptides.
- He described his results in the form of what is now called a Ramachandran diagram, a graph of y against f.
- Molecular dynamics simulations more recently have been applied to refine the contours [Anderson and Hermans, Proteins, 1988, 3, 262; Scully and Hermans, J. Mol. Biol., 1994, 235, 682].
- The medium blue in this diagram represents regions of "no steric hindrance"
- The lighter blue areas are "allowed", but have "some hindrance".
- The white areas are the "badlands" - disfavored for most amino acids
- Positions corresponding to some typical protein secondary structures are indicated, and also tabulated below
| Structure |
f |
y |
| Fully extended |
180 |
180 |
| Antiparallel b-sheet |
-139 |
135 |
| Parallel b-sheet |
-119 |
113 |
| Right-handed a-helix |
-57 |
-47 |
| Left-handed a-helix |
60 |
60 |
| 310 helix |
-49 |
-26 |
| p-helix |
-57 |
-70 |
| Table from Fersht, Structure and Mechanism in Protein Science, p. 18 |
These ranges are not absolute, nor are the outlying territories "forbidden" in any sense.
- We should regard the colored areas as "basins", within which rotation is relatively easy
- The white areas are simply "badlands", a little more difficult to explore
The graph below is a Ramachandran plot for the enzyme chorismate mutase, prepared using VMD.
- The yellow squares are the data points; you will notice that many of them fall outside the "allowed" contours.
- Some of these correspond to sharp turns in the chain.
OK, now, what are a-helices and b-sheets? That's secondary structure.
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