The secondary structure of proteins refers to the local three-dimensional conformation of the polypeptide chain. It is an important aspect of protein structure that determines the shape and function of the protein.
The secondary structure of a protein is formed by the interactions between the amino acids that make up the polypeptide chain, such as hydrogen bonding, hydrophobic interactions, and ionic bonding.
There are several common types of secondary structure, including the alpha helix, beta sheet, and turn and loop structures. In this article, we will explore the different types of secondary structure and their importance in protein function.
- The term secondary structure refers to the interaction of the hydrogen bond donor and acceptor residues of the repeating peptide unit.
- The two most important secondary structure of proteins, the alpha helix, and the beta sheet were predicted by the American chemist Linus Pauling in the early 1950s.
- Pauling and his associates recognized that folding of peptide chains, among other criteria, should preserve the bond angles and planar configuration of the peptide bond, as well as keep atoms from coming together so closely that they repelled each other through van der Waal’s interactions.
- Finally, Pauling predicted that hydrogen bonds must be able to stabilize the folding of the peptide backbone.
- Two secondary structure of proteins, the alpha helix, and the beta pleated sheet fulfill these criteria well.
- Pauling was correct in his prediction.
- Most defined secondary structures found in proteins are one or the other type.
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Secondary Structure of Proteins
1. Alpha helix
- The alpha helix involves regularly spaced Hydrogen bonds between residues along a chain.
- The amide hydrogen and the carbonyl oxygen of the peptide bond are forming hydrogen bond donors and acceptors respectively:
- The alpha helix is a common type of secondary structure found in proteins.
- It is a spiral-shaped structure held together by hydrogen bonds.
- The alpha helix has a regular, repeating pattern with a pitch of 5.4 Å (angstroms) per turn, and a rise of 1.5 Å per amino acid.
- The structure is stabilized by hydrophobic interactions between the nonpolar side chains of the amino acids.
- The alpha helix is a stable, compact structure that is found in many proteins, including structural proteins and enzymes.
- The alpha helix is right-handed when the chain is followed from the amino to the carboxyl direction. (The helical nomenclature is easily visualized by pointing the thumb of the right hand upwards—this is the amino to carboxyl direction of the helix. The helix then turns in the same direction as the fingers of the right-hand curve.)
- As the helix turns, the carbonyl oxygens of the peptide bond point upwards toward the downward-facing amide protons, making the hydrogen bond.
- The R groups of the amino acids point outwards from the helix.
- Helices are characterized by the number of residues per turn.
- In the alpha helix, there is not an integral number of amino acid residues per turn of the helix.
- There are 3.6 residues per turn in the alpha helix; in other words, the helix will repeat itself every 36 residues, with ten turns of the helix in that interval.
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- The beta sheet is a common type of secondary structure found in proteins.
- It is a flat structure formed by hydrogen bonds between adjacent strands of the polypeptide chain.
- The beta sheet can be either parallel or antiparallel, depending on the direction of the peptide bonds in the strands.
- The beta sheet is stabilized by hydrophobic interactions between the nonpolar side chains of the amino acids.
- The beta sheet is a flexible structure that is found in many proteins, including structural proteins and enzymes.
- The beta sheet involves H-bonding between backbone residues in adjacent chains.
- In the beta sheet, a single chain forms H-bonds with its neighboring chains, with the donor (amide) and acceptor (carbonyl) atoms pointing sideways rather than along the chain, as in the alpha helix.
- Beta sheets can be either parallel, where the chains point in the same direction when represented in the amino- to carboxyl- terminus, or anti-parallel, where the amino- to carboxyl- directions of the adjacent chains point in the same direction.
- Different amino acids favor the formation of alpha helices, beta pleated sheets, or loops.
- The primary sequences and secondary structures are known for over 1,000 different proteins.
- Correlation of these sequences and structures revealed that some amino acids are found more often in alpha helices, beta sheets, or neither.
- Helix formers include alanine, cysteine, leucine, methionine, glutamic acid, glutamine, histidine, and lysine.
- Beta formers include valine, isoleucine, phenylalanine, tyrosine, tryptophan, and threonine.
- Serine, glycine, aspartic acid, asparagine, and proline are found most often in turns.
- No relationship is apparent between the chemical nature of the amino acid side chain and the existence of amino acid in one structure or another.
- For example, Glu and Asp are closely related chemically (and can often be interchanged without affecting a protein’s activity), yet the former is likely to be found in helices and the latter in turns.
- Rationalizing the fact that Gly and Pro are found in turns is somewhat easier.
- Glycine has only a single hydrogen atom for its side chain. Because of this, a glycine peptide bond is more flexible than those of the other amino acids.
- This flexibility allows glycine to form turns between secondary structural elements.
- Conversely, proline, because it contains a secondary amino group, forms rigid peptide bonds that cannot be accommodated in either alpha or beta helices.
3. Fibrous and globular proteins
- Fibrous proteins and globular proteins are two major classes of proteins based on their overall shape and function.
- Fibrous proteins are long and slender, and often have a structural role in the body. Examples include keratin, which is found in hair and nails, and collagen, which is a major component of connective tissue.
- Globular proteins are more compact and spherical in shape, and often have catalytic or regulatory functions. Examples include enzymes, hormones, and transport proteins.
- The formation and structure of fibrous and globular proteins is determined by a combination of their primary, secondary, and tertiary structures.
- The primary structure of a protein is its amino acid sequence, while the secondary and tertiary structures are the local and global three-dimensional conformations of the protein, respectively.
- The structure of a protein is determined by the interactions between the amino acids that make up the polypeptide chain, such as hydrogen bonding, hydrophobic interactions, and ionic bonding.
- The large-scale characteristics of proteins are consistent with their secondary structures. Proteins can be either fibrous (derived from fibers) or globular (meaning, like a globe).
- Fibrous proteins are usually important in forming biological structures. For example, collagen forms part of the matrix upon which cells are arranged in animal tissues.
- The fibrous protein keratin forms structures such as hair and fingernails.
- The structures of keratin illustrate the importance of secondary structure in giving proteins their overall properties.
- Alpha keratin is found in sheep wool. The springy nature of wool is based on its composition of alpha helices that are coiled around and cross-linked to each other through cysteine residues.
- Chemical reduction of the cysteine in keratin to form cysteine breaks the cross-links.
- Subsequent oxidation of the cysteines allows new cross-links to form.
- This simple chemical reaction sequence is used in beauty shops and home permanent products to restructure the curl of the human hair—the reducing agent accounts for the characteristic odor of these products.
- Beta-keratin is found in bird feathers and human fingernails. The more brittle, flat structure of these body parts is determined by beta keratin being composed of beta sheets almost exclusively.
- The combination of the two secondary structures—with important exceptions. For example, hemoglobin is almost entirely alpha-helical, and antibodies are composed almost entirely of beta structures.
- The secondary structures of proteins are often depicted in ribbon diagrams, where the helices and beta sheets of a protein are shown by corkscrews and arrows respectively, as shown in the given Figure.
Importance of secondary structure in protein function
- The secondary structure of a protein plays a crucial role in its overall function.
- It determines the shape and stability of the protein, which is necessary for the protein to perform its specific function in the body.
- The secondary structure also determines the accessibility of the protein’s active site, which is the region of the protein responsible for its catalytic or regulatory activity.
- Changes in the secondary structure of a protein can alter its function, and this can have significant consequences for the overall function of the protein.
- For example, changes in the secondary structure of an enzyme can affect its catalytic activity, while changes in the secondary structure of a structural protein can affect its mechanical properties.
- The stability and function of a protein can also be affected by the presence of other molecules, such as ligands or other proteins, which can bind to specific sites on the protein and alter its conformation.
Techniques for studying secondary structure
The shape and function of a protein are based on its secondary structure, which is an important part of its structure. There are several techniques that can be used to study the secondary structure of proteins, including spectroscopic techniques, X-ray crystallography, and nuclear magnetic resonance (NMR) spectroscopy.
- Infrared spectroscopy and circular dichroism are spectroscopic techniques that measure the absorption of light by the protein. These techniques can provide information about the secondary structure and conformation of the protein by analyzing the vibrations and rotations of the bonds within the protein.
- X-ray crystallography is a powerful technique that involves crystallizing the protein and using X-rays to determine its three-dimensional structure. This technique can provide highly detailed information about the secondary structure of the protein, as well as its tertiary and quaternary structures.
- NMR spectroscopy is another technique that can be used to study the secondary structure of proteins. It works by measuring the magnetic properties of the nuclei of the atoms in the protein, and can provide detailed information about the structure and conformation of the protein.
- In addition to these methods, biochemical assays and computational modeling can also be used to study the secondary structure of proteins. Biochemical assays, like enzyme assays, can give information about how enzymes work, while computational modeling can use computer simulations to predict the structure and conformation of the protein.
Overall, these methods help us learn about the secondary structure of proteins and how that structure affects how they work.
- There are various techniques that can be used to study the secondary structure of proteins.
- Spectroscopic techniques, such as infrared spectroscopy and circular dichroism, measure the absorption of light by the protein and can provide information about the secondary structure and conformation of the protein.
- X-ray crystallography is a powerful technique that involves crystallizing the protein and using X-rays to determine the three-dimensional structure of the protein.
- Nuclear magnetic resonance (NMR) spectroscopy is another technique that can be used to study the secondary structure of proteins. It measures the magnetic properties of the nuclei of the atoms in the protein and can provide detailed information about the structure and conformation of the protein.
- Other techniques that can be used to study the secondary structure of proteins include biochemical assays, such as enzyme assays for enzymes, and computational modeling, which uses computer simulations to predict the structure and conformation of the protein.
In conclusion, the secondary structure of proteins is a key part of their structure that affects how they look and what they do.
The secondary structure is formed by the interactions between the amino acids in the polypeptide chain, and there are several common types of secondary structure, including the alpha helix, beta sheet, and turn and loop structures.
The stability and function of a protein can be affected by changes in its secondary structure, and understanding the secondary structure of a protein can help us better understand its overall function in the body.
There are several techniques that can be used to study the secondary structure of proteins, including spectroscopic techniques, X-ray crystallography, and NMR spectroscopy.
Understanding the secondary structure of proteins is crucial for understanding their role in the body and how they can be used in various applications, such as drug design and industrial processes.