Which is complex angle or backbone

Why is this knowledge important?

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.

reference These exercises supplement Chapter 1 "Biological Basics".     

Learning objective

After working the exercise you should
  • the main properties of amino acids,
  • the peptide bond,
  • the most important secondary structural elements

be familiar.

 ÜexerciseProt_Str_1, amino acids In protein sequences, the consecutive amino acids are usually noted in one-letter or three-letter code. This simplest of all protein models is also the most abstract. However, it has its justification and is therefore sufficient for many applications because the sequence determines the spatial structure of a protein, although it is generally not possible to predict the structure from the sequence using an algorithm. In this exercise, you should understand that each symbol in a string (sequence) means a complex chemical molecule, an amino acid. This molecule can be divided into two parts, one part which is the same in all amino acids and which forms the main chain (the backbone or backbone) and a side chain that has a different structure in each amino acid molecule and that determines the physical and chemical properties of the entire amino acid. This side chain is often toorest or residuum called.
Consider the structural formula and the three-dimensional structure of the amino acid phenylalanine.
  • Make it clear to yourself that the amino and carboxyl groups in protein sequences result in a clear strand direction.
  • Study the spatial arrangement of the individual groups.
  • What degrees of freedom does the side chain have?
Structure of
amino acids
Structural formula (left) and 3D structure (right) of the amino acid phenylalanine.

The proportion, which is the same in all amino acids, is highlighted in gray in the structural formula. In each amino acid, a hydrogen atom (bottom), an amino group (left), a carboxyl group and a side group are linked to the central carbon atom.

Hints If you move the mouse pointer over the window labeled Jmol and click once, the visualization program Jmol interprets the following mouse movements and clicks.

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?
 ÜexerciseProt_Str_2, peptide bond

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?
 
  

Topology of
Peptide bond

      
     
labeling
Residual 2
   
      
Red angle
at C
α
   
 
   HintsTo make it easier for you to find your way around, you can use the buttons on the right to highlight residue 2.
You can use the buttons marked Phi and Psi to mark the axes of the associated angles in yellow.  ÜexerciseProt_Str_3, alpha helices If the (Φ, Ψ) angles of successive residuals are constant, then helical structures result. Among these, the most common is the α-helix. In the α-helix there is a hydrogen bond between the CO group of one amino acid and the NH group of the fourth next. 3.6 amino acids each make a complete rotation.
Get to know the alpha helix:

Which atoms are hydrogen bonds formed between?

 
 
      

α-Helix made from karyopherin alpha

      
 Rod-
model
 secondary
structure
 Baking
bone
    
α-Helix  
      
Hydrogen-
bridges-
ties
   
 
 Please study now the structure of this protein, which consists almost entirely of α-helices. Please also compare and analyze the secondary structure and how it is presented.

 

exerciseProt_Str_4, beta leaflets The second, important secondary structural element is the β-sheet. A β-sheet consists of individual β-strands, which are usually 5-10 residues long. Between the residuals different Strands form hydrogen bonds. The C = O groups of one strand are linked to the NH groups of the next strand. In this way, several strands can be connected to form one sheet. The Cα-Atoms of successive residuals come to lie alternately above or below the plane that is spanned by the leaflet. The strands can go in two directions:
  • 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
Proteins G from
Streptococcus

 Rod-
model
 secondary
structure
 
   
β strand  
β-sheet  
Total
domain
  
     
Hydrogen-
bridges-
ties
  
 
 Often, β-sheets are sandwiched on top of one another. Please consider the following structure, which consists almost entirely of leaflets.
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.

exerciseProt_Str_5, super secondary structure elementsRegular arrangements of secondary structural elements can be found in many proteins. These serve z. B. in the SCOP database to categorize proteins, i. H. to be classified in families and superfamilies.
A nice example of a regular sequence of 2D elements can be found in the following illustration.The (βα)8-Barrel
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?

 

HintsTo answer these questions, use the corresponding entry in the PDB-SUM database at the EBI.
There the sequence of the secondary structural elements is graphically presented.
  

What you should have understood by now

Proteins are macromolecules made up of a chain of amino acids joined together. The peptide bond links the individual amino acids. Proteins are often characterized by the spatial distribution of the main chain atoms. Hydrogen bonds between main chain atoms determine two important secondary structural elements, the α-helices and β-sheets. The variable part of the amino acid is called the residue.