October 23, 2007

Ramachandran Plots and the Alpha Helix

Posted in Biochemistry tagged , , , , at 7:28 am by D. Borst

Structure = Function. This is the creed of the biochemist. However, there are many levels of structure for the biochemist–four is the classical number. We will start in this posted review of my biochemistry class at PSU with discussing how primary structure (the sequence of amino acids in a protein) gives rise to secondary structure (local conformation of the Carbon-nitrogen backbone.)

Amino acids are generally thought of as starting with a amino group (the N terminus) and ending with a carboxilic acid (the C terminus). However, for purposes of thinking about secondary structure, it is more conveinent to think of the peptide backbone as jumping from α-carbon to α-carbon. This is because the conformation of the peptide bond is very rigid, due to it having partial double bond character. The double bonded oxygen shares some of its electrons with the nitrogen, making the Cα to Cα stretch unusually rigid. This makes it possible to think of the peptide as a series of planes that meet at the alpha carbons. In each plane are the atoms between each α-carbon. The planes meet corner to corner at the alpha carbons, not including the R groups.

There are other generalizations that we can make about local structure: Generally the peptide bond assumes a trans-conformation relative to the placement of the R-groups on the α-carbons. This leads to the one-up, one down general representation of the peptide backbone.

If we make the assumption that all the amino acids are in these rigid structures (that there is little to no torsion over the peptide bond due to its possible double character), and that the peptide bonds are generally in trans-conformation, we can describe how the peptide backbone moves by describing two angles, Φ and Ψ, respectively the torsion over the alpha carbon of the amide plane after the alpha carbon and the amide plane before. This can be rather hard to grasp from the text, so here are a few things to help. Try tutorial, which has a few lame drawings. You can also look at this image:

In any case, using this convention, we can represent the conformation of the chain around a single α-carbon by representing it as a point in a plane, along the x axis we can put the φ angle, and on the y axis we can put the ψ angle. This represents the torsional angles of the α-carbon’s bonds in the peptide backbone.

G.N. Ramachandran realized that if one imposed upon all of the atoms in the protein their vanDerWalls radius the area of much of this two dimensional plot may be revealed to be energetically unlikely–certain angles would cause the different atoms to intrude upon each others’ boundaries. Ramachandran thus developed plots that demonstrated which areas in this 2D space were open to the peptide backbone, yielding the plot to the right (for two Alanine residues, other chiral amino acids have similar results).

Only a few area of the plot result in being suitable for protein structure, and the two major structural forms of secondary structure both fall within these two major islands of allowed conformation. The first, the α-helix, falls within the lower island, and the second, the β-sheet, falls within the upper region.

The α-helix is also known as the 3.613 helix, for each turn of the helix takes 3.6 amino acids, and involves a loop of 13 atoms. The loop begins at the carboxyl oxygen on one residue, and ends at the Hydrogen on a nitrogen 3.6 residues away. This helix is right handed, and has all the R groups facing out of the helix. Were they to face in (as they would if the helix was left handed), their VanderWalls radii would be deeply violated. The α-helix is stabilized by intra-chain hydrogen bonding–each loop described earlier is finished by a hydrogen bond between the hydrogen and oxygen. Below is an image of the α-helix.

The Alpha Helix

The β-sheet does not have intra-chain bonding, but rather is stabilized by inter-chain bonding. There are two flavors of β sheet–antiparallel and parallel. β-sheets are often referred to as “pleated” sheets, because the amide planes tend to ripple up and down like a pleated skirt. The antiparallel β sheet is slightly more energetically favorable than the parallel β sheet, since the inter strand hydrogen bonds line up at a more ideal angle. Below is a diagram of the β sheet. The top two strands are in parallel conformation, the second two are in antiparallel conformation.


The Beta Sheets

The α-helix and the β-sheets form the basis of recognized secondary structure. The rest of the polypeptide backbone is generally arranged in complex patterns that we cannot readily identify. It should be stressed that these conformations are not random–there is a lot of structure to them–however as humans we have not been able to impose much understandable regular order upon these sections.

β sheets and α helices are grouped together to form complex patterns that form the basis of tertiary structure.

To remember:

  • The structure of the polypeptide backbone can be described by the φ and ψ torsional angles around the α-carbon.
  • Plotting out the vanDerWalls allowed regions on a 2D plot of φ and ψ yields 2 major and 1 small island of allowed conformations–most protein structures fall within these islands.
  • The α helix is the 3.613 helix, and has all of its R groups arrayed on its outside. It is stabilized by intra-strand hydrogen bonding.
  • The β-sheet is either parallel or anti-parallel. It is stabilized by inter-strand hydrogen bonding.
  • The parts of the protein that are neither β-sheets nor α-helices have definite order–just not regular order that we can easily categorize.
  • Thats all for now. The information in this post came from Biochemistry by Voet and Voet, and from the Monday the 8th and Wednesday the 17th Biochemistry lecture by Dr. Peyton at Portland State University. Most of the images came from Stryer’s Biochemistry textbook, availible via NCBI.


    1 Comment »

    1. Thanks for information.
      many interesting things

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