Which is complex angle or backbone
The basic building blocks of proteins are the amino acids. During protein synthesis, these are combined to form a peptide chain with the formation of covalent bonds, which usually has a well-defined spatial structure. The 3D structure is conditioned on the one hand by the physico-chemical properties of the amino acids involved in the peptide chain and on the other hand by the degrees of freedom that result from the chemical bonds. Successive amino acids are linked to one another via the peptide bond. You should be familiar with the resulting dependencies from the chapter "Biological Basics".
The 3D structure of a protein is essentially determined by non-covalent bonds between atoms different Amino acid residues. This also includes hydrogen bonds. Such bonds between atoms of the backbone (backbones) are responsible for the formation of the secondary structural elements. The most important 2D structures are α-helices and β-sheets. You will study these two in more detail below. Finally, you will get to know clusters of secondary structural elements, so-called super-secondary structures.
|After working the exercise you should |
|Consider the structural formula and the three-dimensional structure of the amino acid phenylalanine. |
Rotate of Mouse wheel changes the size of the model.
As long as the left mouse button is held down, each movement of the mouse pointer changes the spatial orientation of the model.
Clicking the right mouse button brings up a menu that we will ignore in these exercises.
Please practice aligning the model.
Align the structure so that you can see all the atoms clearly. If you position the mouse pointer over an atom, you will see the atom number and the chemical symbol. Can you identify the elements of the amino and carboxyl groups?
In the following figure, which you know from Chapter 1, the peptide bond is shown schematically. You can see that the atoms involved in the bond lie rigidly in one plane and that each peptide bond is determined by specifying two angles (phi and psi). The angle ω does not play a role when describing proteins, as it only has two Values (0 ° and 180 °) and the second value occurs extremely rarely in proteins.
|Conformation of the peptide bond.|
The six atoms involved in a peptide bond (the two shown here are marked in red) are each in one plane. The amino acid residue at the position under consideration (here in green) is labeled R. The spatial arrangement of the main chain of a polypeptide ..- Cα-C-N-Cα-C-N-Cα- .. is determined by the pair of angles (Φ, Ψ) to be specified for each position (each residue) with which the position of the surfaces spanned by the peptide bond relative to the Cα -Atom is set.
In the following model, two amino acids linked by a peptide bond are shown in their spatial position, the amino acid residues have been omitted. Please familiarize yourself with this spatial arrangement:
|Which atoms belong to each amino acid residue?|
Where are the phi and psi angles?
You can use the buttons marked Phi and Psi to mark the axes of the associated angles in yellow.
|Get to know the alpha helix: |
Which atoms are hydrogen bonds formed between?
- parallel; the direction given by the N and C terminus in adjacent strands is the same
- antiparallel; the direction of adjacent β-strands changes alternately.
Inside the protein, the β-sheets are mostly parallel. They are mostly antiparallel on the protein surface. There, the amino acid residues on one side protrude into the (hydrophilic) environment, while those on the other are oriented towards the hydrophobic core. In the ideal case, this results in a characteristic alternation of hydrophobic and hydrophilic amino acids in the sequence.
β-Faltblatt from the B1 domain of the
|Familiarize yourself with leaflets: |
In which direction do the amino acid side chains extend?
Which amino acids protrude into the protein interior, which into the surrounding medium?
Can you make out a conspicuous sequence of hydrophilic and hydrophobic amino acid residues?
Can you roughly describe the 3D structure of β sandwiches? Are they planar?
Generate rough statistics on the length of the individual β strands.
A nice example of a regular sequence of 2D elements can be found in the following illustration.
|The TIM barrel protein fructose bisphosphate aldolase |
belongs to the convolution type of (βα)8-Barrel.
|Determine the sequence of the secondary structural elements. |
Can you see some periodicity?
There the sequence of the secondary structural elements is graphically presented.
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