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Protein Structure


Different Levels of Protein Structure

The wide variety of 3-dimensional protein structures corresponds to the diversity of functions proteins fulfill.

Proteins fold in three dimensions. Protein structure is organized hierarchically from so-called primary structure to quaternary structure. Higher-level structures are motifs and domains.

Above all the wide variety of conformations is due to the huge amount of different sequences of amino acid residues. The primary structure is the sequence of residues in the polypedptide chain.

Secondary structure is a local regulary occuring structure in proteins and is mainly formed through hydrogen bonds between backbone atoms. So-called random coils, loops or turns don't have a stable secondary structure. There are two types of stable secondary structures: Alpha helices and beta-sheets (see Figure 3 and Figure 4). Alpha-helices and beta-sheets are preferably located at the core of the protein, whereat loops prefer to reside in outer regions.



Figure 3: An alpha helix:
The backbone is formed as a helix.
An ideal alpha helix consists
of 3.6 residues per complete turn.
The side chains stick out.
There are hydrogen bonds
between the carboxy group of amino acid n
and the amino group of another amino acid n+4 [1][2].
The mean phi angle is -62 degrees
and the mean psi angle is -41 degrees [3].
(see also section on Helical Wheels)






Figure 4: An antiparallel beta sheet.
Beta sheets are created,
when atoms of beta strands are hydrogen bound.
Beta sheets may consist of parallel strands,
antiparallel strands or out of a mixture
of parallel and antiparallel strands [4].


Tertiary structure describes the packing of alpha-helices, beta-sheets and random coils with respect to each other on the level of one whole polypeptide chain. Figure 5 shows the tertiary structure of Chain B of Protein Kinase C Interacting Protein.



Figure 5: Chain B of Protein Kinase C Interacting Protein.
Helices are visualized as ribbons and
extended strands of betasheets by broad arrows.
(the figure was obtained by using rasmol
and the PDB-file corresponding to PDB-ID 1AV5
stored at PDB, the Brookhaven Protein Data Bank)


Quaternary structure only exists, if there is more than one polypeptide chain present in a complex protein. Then quaternary structure describes the spatial organization of the chains. Figure 6 shows both, Chain A and Chain B of Protein Kinase C Interacting Protein forming the quaternary structure.



Figure 6: Quaternary structure of
Protein Kinase C Interacting Protein.
(the figure was obtained by using rasmol
and the PDB-file corresponding to PDB-ID 1AV5
stored at PDB, the Brookhaven Protein Data Bank)




exercise 1
exercise 1


Motifs and domains are combinations of secondary structures. Motifs only consist out of few secondary structures. They may but need not have a function. A domain is more complex. It is usually defined as a modular functional unit folding independently.


Comments are very welcome.
luz@molgen.mpg.de