Protein
structure
Number of
amino acids involved
Small peptides are referred to as oligopeptides, whereby
dipeptides are made up of only two amino acids, tripeptides of three,
tetrapeptides of four amino acids, etc. Larger peptides with more than ten
amino acids are called polypeptides. Most proteins are
chains of 100 to 300 amino acids, rarely more than a thousand (see bar graph).
The largest known protein consists of a chain of over 30,000 peptidically
linked amino acids and is found in muscle cells: titin.
Proteins need a specific size to function. Oligopeptides can be used as signal substances - for example, like hormones or neurotransmitters - but more than 50 amino acids are usually required for an enzyme function. A protein cannot contain an unlimited number of amino acids, if only because only a limited amount of amino acids is available. Also, the time it takes to assemble an amino acid chain depends on the number of amino acids (see protein biosynthesis ). Nanobiztech
Spatial
structure
The spatial structure determines how the proteins work. The
protein structure can be described on four levels:
The sequence of the individual amino acids in a polypeptide
chain is called the primary structure. Put simply; one could imagine a chain in
which each chain link represents an amino acid (notation from the amino / N- to
the carboxy / C-terminus: AS 1 –AS 2 –AS 3 –AS 4 -…). The primary structure
only describes the amino acid sequence but not the protein's spatial structure.
This also includes the signal sequence.
As a secondary structure, the protein's composition from the
most frequently occurring motifs is referred to for the spatial arrangement of
amino acids. A distinction is made between the following structure types:
α-helix, β-sheet, β-loop, β-helix, and disordered, so-called random-coil
structures. These structures result from hydrogen bonds between the peptide
bonds of the polypeptide backbone. Every amino acid in a protein has
characteristic angles between the backbone's atoms ( dihedral angle). The pitch
(N-terminal) in front of the C-atom with the side chain of an amino acid is
called the φ-angle, the one after that as the ψ-angle. These can be numbered
and plotted against each other in a Ramachandran plot to display secondary
structures. Alternatively, a Janin plot can be used.
The tertiary construction is the spatial arrangement of the
polypeptide chain that is superordinate to the secondary structure. It is
determined by the forces and bonds between the residues (i.e., the amino acids'
side chains). The binding forces that stabilize this three-dimensional
structure are, for example, disulfide bridges ( covalent bonds between the
sulfur atoms of two cysteine residues ) or, above all, non-covalent
interactions such as the hydrogen above bonds. Also, hydrophobic, ionic, and
van der Waals forces play an essential role. Because of these forces and bonds,
the protein continues to fold.
To function, many proteins have to assemble into a protein
complex, the so-called quaternary structure. This can be either an assembly of
different proteins or an association of two or more polypeptide chains from the
same polypeptide chain, the precursor protein (Engl. Precursor emerged) (cf .:
insulin ). The pre-proteins (with signal or activation sequences to be
proteolyzed) and preproproteins (with signal and activation sequences to be
proteolyzed) are called precursor proteins. The individual proteins are often
linked by hydrogen and salt bridges and related to one another by covalent
bonds. The individual subunits of such a complex are called protomers. Some
protomers can also function as independent proteins, but many only achieve
their complexes' functionality. The immunoglobulins ( antibodies ), in which
two identical fatty and two similar light proteins are linked via a total of
four disulfide bridges to form a functional antibody, can serve as an example
of complexes made up of several proteins.
Some proteins are arranged in a "superstructure"
or "superstructure" that goes beyond the quaternary structure but is also
molecularly predetermined, such as collagen in the collagen fibril or actin,
myosin, and titin in the sarcomere.
The division into primary to quaternary structure makes it
easier to understand and describe proteins' folding. Under physiological
conditions, a defined primary structure unfolds into a specific tertiary
structure. In other words: the content of information that is already contained
in the primary system as a linear amino acid sequence is expressed in the form
of a specific three-dimensional protein structure.
For this folding of the polypeptide chain into the
characteristic three-dimensional shape of the native protein, exceptional
environmental conditions are required - such as an aqueous medium, a pH value
in a specific narrow range, a temperature within certain limits. They are
fulfilled in the environment of the cell within its membrane. Nevertheless,
many complex proteins would not spontaneously fold into the functional
structure in the cell but instead need folding aids, so-called chaperones. The
chaperones bind to newly formed ( nascent) Polypeptides - or denatured or
damaged amino acid chains - and help them achieve a physiologically functional
structure by consuming chemical energy.
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