Alpha helix: Difference between revisions
No edit summary |
No edit summary |
||
| Line 4: | Line 4: | ||
===Which amino acids are found in alpha helices?=== | ===Which amino acids are found in alpha helices?=== | ||
Proline is a helix breaker because its main chain nitrogen is not available for hydrogen bonding. Amino acid side chains whose movement is largely restricted in an alpha helix (branched at beta carbon like threonine or valine) are disfavored, as is glycine. Here is an example of a <scene name='77/778341/Proline/1'>kink in a helix</scene> at the position of a <scene name='77/778341/Proline/2'>proline</scene>. | Proline is a helix breaker because its main chain nitrogen is not available for hydrogen bonding. Amino acid side chains whose movement is largely restricted in an alpha helix (branched at beta carbon like threonine or valine) are disfavored, as is glycine. Here is an example of a <scene name='77/778341/Proline/1'>kink in a helix</scene> at the position of a <scene name='77/778341/Proline/2'>proline</scene>. Prolines are often found at the beginning or end of an alpha helix, as in this example of <scene name='77/778341/Proline_cap/1'>the helix in crambin</scene> (this is an ultra high resolution structure where hydrogen atoms - white - are resolved and some atoms are shown in multiple positions). | ||
| Line 12: | Line 12: | ||
===Alpha helices in transmembrane proteins=== | ===Alpha helices in transmembrane proteins=== | ||
opioid | A common fold found in transmembrane proteins are alpha-helical bundles running from one side to the other side of the membrane. An alpha helix of 19 amino acids (with a length of about 30 angstroms) has the right size to cross the double-layer of a typical membrane. If the helix runs at an angle instead of perfectly perpendicular to the membrane, it has to be a bit longer. There is a write-up on opioid receptiors in the Molecule of the Month series by David Goodsell (http://pdb101.rcsb.org/motm/217). | ||
===Alpha helices in filamentous proteins=== | ===Alpha helices in filamentous proteins=== | ||
Revision as of 21:24, 16 January 2018
Structure and hydrogen bondingStructure and hydrogen bonding
The following 4 scenes are inspired by a nice set of figures in Stryer's biochemistry textbook (https://www.ncbi.nlm.nih.gov/books/NBK22580/figure/A322/?report=objectonly). In an alpha helix, the main chain arranges in a with the side chains (green) pointing away from the helical axis. The alpha helix is stabilized by from amino acid n to n+4. There are . In space filling depiction, you can see how the main chain is (no space in the middle). Which amino acids are found in alpha helices?Proline is a helix breaker because its main chain nitrogen is not available for hydrogen bonding. Amino acid side chains whose movement is largely restricted in an alpha helix (branched at beta carbon like threonine or valine) are disfavored, as is glycine. Here is an example of a at the position of a . Prolines are often found at the beginning or end of an alpha helix, as in this example of (this is an ultra high resolution structure where hydrogen atoms - white - are resolved and some atoms are shown in multiple positions).
Alpha helices in soluble (globular) proteinsExample: myoglobin Example: DNA binding Alpha helices in transmembrane proteinsA common fold found in transmembrane proteins are alpha-helical bundles running from one side to the other side of the membrane. An alpha helix of 19 amino acids (with a length of about 30 angstroms) has the right size to cross the double-layer of a typical membrane. If the helix runs at an angle instead of perfectly perpendicular to the membrane, it has to be a bit longer. There is a write-up on opioid receptiors in the Molecule of the Month series by David Goodsell (http://pdb101.rcsb.org/motm/217). Alpha helices in filamentous proteins |
| ||||||||||
Experimental evidenceExperimental evidence
a) CD spectroscopy b) NMR chemical shifts c) Fiber diffraction
Role of alpha helices in the history of structural biologyRole of alpha helices in the history of structural biology
a) Pauling predicts it http://onlinelibrary.wiley.com/doi/10.1111/febs.12796/full
b) Determination of hand: There are several methods in X-ray crystallography where crystallographers obtain an electron density, but don't know whether it or its mirror image is correct. Historically, finding electron density that fits a helix was used to break this ambiguity. If the helix was right-handed, the electron density was used as is, but if the helix was left-handed, the mirror image was used.
c) Tracing the chain: When building a model into electron density, the first step was to place continguous C-alpha atoms into the density (with proper spacing). To see in which direction an alpha helix goes, you look at the side chain density. If it points up, the N-terminus is on top, otherwise on the bottom.