Secondary structure of protein

 Secondary structure of protein 

The term "protein secondary structure" (SS) describes the local configuration of a protein's polypeptide backbone. Pauling13 proposed more than 60 years ago that there are two regular states of supersymmetry (SS): alpha-helix (H) and beta-strand (E), and one irregular form of SS called coil region (C).

There are four layers of organization in the structure of proteins. The polypeptide chain's primary structure is its amino acid sequence, which is linear. 

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The primary sequence is written according to convention, starting with the amino acid at the N-terminus (which is typically on the left) and ending with the amino acid at the C-terminus. Stretches of adjacent amino acid sequences assume a local conformation that makes up the second level of protein structure, or secondary structure. The two primary forms of secondary structures seen in proteins are beta (β) sheets and alpha (α) helices. 

Tertiary structure, or the three-dimensional folded architecture of a polypeptide chain, is the third level. Regions of secondary structure interact with one another in specific ways to form tertiary structure.

Lastly, the interaction of separate folded polypeptide chains to create a higher order complex is known as quaternary structure. 

Peptide bond hydrogen bonding produces secondary structure.

 Peptide bonds have a resonance form that gives the carbonyl oxygen in the bond a partial negative charge and the hydrogen atom in the N-H bond a partial positive charge. This resonance form is what makes peptide bonds polar. These atoms tend to establish hydrogen bonds with other atoms that are oppositely charged because they are charged. Many times, these atoms only make thermodynamically advantageous hydrogen bonds with water.
An even more advantageous energy configuration for these atoms is the formation of hydrogen bonds with one another. This is because interactions involving more charge are stronger, and the atoms in peptide bonds carry a greater charge than the hydrogen and oxygen atoms in water molecules.

Consequently, a hydrogen bond forming between two peptide bonds is more powerful than one forming between a peptide bond and water. The hydrogen atom linked to the amide nitrogen is donated to the carbonyl oxygen, which functions as the hydrogen bond acceptor, when peptide bonds create hydrogen bonds with one another.

Since hydrogen bonds have a 180° bond angle, they are directed, meaning that for the atoms in peptide bonds to generate hydrogen bonds, the peptide backbone must take on particular shapes. A recurring motif in protein structure is hydrogen bonding between atoms in peptide bonds, which serves as the foundation for all secondary structure.

The renowned chemist of the 20th century, Linus Pauling, made significant advances to our knowledge of the composition and properties of biomolecules, such as enzymes.

Amino acid β-strands are abrupt segments that collaborate through hydrogen bonding to create β-sheets. 

Stretches of amino acids called β-strands contained in a single polypeptide chain make up a β-sheet. By arranging the dipoles of their peptide backbones so that complimentary charges engage through hydrogen bonds, β-strands associate intramolecularly. In order to achieve this, the β-sheet strands adopt an elongated, zigzag conformation where the amides and carbonyls of subsequent residues point in opposing directions.

β-sheets can have either a parallel or antiparallel orientation. The β-strands in parallel sheets are oriented so that their N-termini and C-termini point in the same direction . The N-termini and C-termini of neighboring strands are oriented in opposition to one another in antiparallel sheets.

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α-helices have peptide bonds that point in the same direction

The α-helix is an additional secondary structure that enhances the creation of hydrogen bonds inside a single polypeptide chain. The polypeptide chain is arranged in a right-handed corkscrew in α-helical areas of secondary structure, with all amide hydrogen atoms pointing toward the N-terminus and all carbonyl oxygen atoms along the helix pointing towards the C-terminus.The angles that the bonds in the peptide backbone can take on determine how the carbonyls and amide hydrogens are arranged in relation to the helix's axis.

With the exception of the carbonyl oxygen atoms at the C-terminal and amide hydrogen atoms at the N-terminal of the helix, every backbone amide and carbonyl within a stretch of the α-helix forms hydrogen bonds with one another.

Different types of secondary structure can be found in proteins. 

While α-helices and β-sheets are found in most proteins, certain proteins only have one kind of secondary structure .
Loops are peptide backbone segments that do not create secondary structure. Regions of secondary structure are connected by loops, which act as linkers.
A protein's structure is depicted in cartoon form as β-helices as coils and β-sheets as flat arrows, respectively. An uninterrupted sequence of amino acids is represented by each coil and arrow. Cartoon depictions of loops consist of lines joining secondary structural sections. It should be mentioned that proline is not preferred in secondary structures since hydrogen bonding cannot occur between its amide.

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