Three Dimensional Structures of Proteins

Introduction

Proteins are the polymers of the amino acids which appear in many sizes and shapes. The three dimensional structures of proteins reflects the underlying structures basically on the variations on the sequences and the length of amino acids. Even the numbers of the disulfides bond and the attachments of the small molecules also differ. Protein consists of long polypeptide chains to determine the sequences of the amino acids. Most protein is folded in defined structures which are maintained by a large number of relatively weak non-covalent bond and the biological activities of the protein depend on the correctly folded conformation. (Lodish, 2008).

The relationship between structure and function is evident in proteins, which exhibits diversity of function. The sequence of amino acids produce a strong, fibrous structure found in hair, wool and some protein that transport oxygen in the blood. The amino acids sequence is a form that diverts the folding of the protein into its unique three dimensional structures and ultimately determines the function protein. (Lehinger, 1995).

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The sequences of amino acids in a polypeptide chain determine the final three dimensional structure of the protein which ultimately functions for various biological activities in the living organisms.

Hierarchical structures of protein:

A protein chain folds into a distinct three dimensional shape that is stabilized by non-covalent interactions between the regions of linear sequences of amino acid and is specified by amino acid sequences. Because the folding of protein is very complex, different elements of structure are considered separately. The structures include primary, secondary, tertiary and the quaternary structures of the proteins.

1. Primary structures of protein:

It is just a sequence of amino acids in a polypeptide chain. It is also a linear arrangement of amino acids. It indicates the covalent structures of the protein, sequences of amino acid residues and position of the any interchange links such as disulfide bond. It is a sequence which determines the further level of organization of the protein molecule. To represent the primary structures of the protein, the N-terminus is always written on the left sides and the C-terminus is on the right end of the chain.

A short chain of amino acid linked by peptide bond is referred as oligopeptide and long chain is polypeptide.

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2. Secondary structure.

It referred to the regular folding of polypeptide chains without reference to the side chains. Polypeptide chains are hold together by the hydrogen bond between amine and carboxyl backbone. A single peptide may contain multiple types of secondary structures in various protein of the chain depending on its structures.

a. Alpha (α) helix: it is a cylindrical rod like helical arrangement of the amino acid in the polypeptide chain which is maintained by the hydrogen bond parallel to it. Each turn of the helix contains 3.6 amino acid residues and is 5.4Ǻ long with a diameter of 6Ǻ. (Lehninger, A.L 1995)

B. β-sheet: in this type the molecules is almost completely extended and hydrogen bonds form between peptide group of polypeptide segments lying adjacent and parallel with one another. The side chain lies alternately above and below the main chain. Two segments of a polypeptide chain can result in the formation of the two types of the β-structure which solely depends on the orientation of the segments. In β-conformation the backbone of the polypeptide chain is extended into a zigzag rather than the helical structure. The adjacent polypeptide chain in a β-sheet can be either parallel or antiparallel. (Lehninger, A.L 1995)

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3. Tertiary structure.

It is referred to overall folding of the polypeptide chain. The polypeptide may be regular which is maintained by hydrogen bonding. The folding includes secondary structures in such a way to expose polar group to the surface and non-polar groups toward interior. The structure is primarily stabilized by the hydrophobic interactions non-polar side chain together with hydrogen bond between the polar sides’ chain and peptides side chains. (Ottaway, J.H. 1984).

What holds protein into secondary structures?

1. Hydrophobic interaction: In most globular protein half of the amino acids have hydrophobic side chains which are internally clustered in folded protein while hydrophobic polar side chain are external.
2. Hydrogen bonding: many of the amino acid side chain can form the hydrogen bond which contributes to the protein folding. Since many polar groups are on the surfaces of the protein folded
3. Ionic bonding: side chains of opposite charge attract each other. The strength of such bonds decreases with increase in the dielectric constant on the surface of the protein, where most ionic groups are situated the dielectric constant is high and the bonding is weak.
4. Covalent bond: the only type of interchain bond is the disulphide bond is cysteine. Disulphide bond are common in structural protein and in extracellular enzymes.

(Ottaway, J.H.1984)

De-naturation of protein:

The three dimensional structures is characteristics of a native proteins. This conformation can be organized without the breakage of any peptide linkage, only by the rupture of the linkages which enable the structure to maintain its conformation in the space. The denaturation of the protein can be triggered by diverse physical and chemical agents such as heat, detergents, organic solvents and PH value. (Weil, 1990)

None of the agents break the peptide bonds, so the primary structure remains contact, when it is denatured. When a protein is denatured it only loses its function. After gently denatured, it returned to the normal condition of temperature, PH, salt concentration, which spontaneously regains it function. So its amino acid sequence ultimately helps in protein structure. Fig: Renaturation (The rules of protein structure)

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Diversity of protein structure:

While studying the three dimensional conformation of protein. They are of two types:

1) Fibrous protein is also called as scleroprotein. As they indicate by the name fibers, Fibrous protein is invariably insoluble. This includes silk fibrous, collagen found in conjunctive tissues, cartilage, tendon and keratin present in the skin and superficial body growth (hairs, nails, horns, feather etc).

α-keratin: the α-keratin has evolved mainly to provide strength. The protein in case of the mammals constitutes almost the entire dry weight of hairs, wool, nails, claws and many of the outer layers of the skin. The α-keratin is right handed α-helixes. Francis and Linnus Pauling in 1950s have suggested that helixes of keratin were arranged in coiled coil. When α-keratin is exposed to the moist heat and stretched, it is converted to different conformation form, namely β-keratin. The hydrogen bonds stabilizing the α-helical structure are broken under these conditions result in the extended parallel β-pleated sheet. (Conn, Eric E.1985)

b.Collagen: triple helical structure exhibited by collagen, a protein found in the skin, cartilage and bone which provide strength. Collagen consists of parallel bundle of individual linear fibrils that are highly soluble in water. The amino acid composition of collagen is unusual, being composed of 25% of glycine and 25% of proline and hydroxyproline. Because of this, no α-helix occurs. Each linear fibrils is capable of consisting of three polypeptide chains. Each chain is twisted into left handed helix and held by interchain hydrogen bond. (Conn, Erie E. 1985).

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Globular protein: is also called as the spheroprotein. On the account of their spherical and ovoid shape. These proteins are easily soluble. This group includes mainly albumins and globulins. (Weil.1990). The albumins which are soluble even in distilled water. The iso-electric point is generally less than that of the 7.hence they are acidic in nature. The globulins which are insoluble in pure water and soluble in dilute saline solutions (eg.5% of NaCL). They are often glycoprotein or lipoprotein.

Myoglobin: is a protein which is unusual in having high contents of α-helix, but no β-sheet. The nine α-helical regions contain are 80% of the amino acid, many of which contain are proline. It is a single chain protein found in muscles fiber, structurally similar to a single subunit of hemoglobin and having higher affinity for oxygen than the hemoglobin in blood. It is oxygen carrying protein in vertebrates which facilitates the transport of oxygen in muscles and serves as the reserve store of oxygen in the tissues. It is a single polypeptide chain of 153 residues which has a compact shape. Internally, non-polar residues are present. Externally both polar and the non-polar residues are present. About 75% of polypeptide chain is α-helical. There are 8 helical segments in total. (Stryer,1981)

b.Hamoblobin: the oxygen carrying protein of the blood contains two α and two β subunits arranged with a quaternary structure in the form α2β2, hemoglobin is therefore a hetero-oligomeric protein.

References:

1. Conn, E.E, & Stumpt, P.K, (1976). Outlines of Biochemistry. 4th edition. New Delhi: Wiley& Eastern Ltd.
2. Lehninger, A.L (1995). Biochemistry. (2nd edition). New Delhi: Kalyani Publishers.
3. Lodish, H. et al. (2008) Molecular cell Biology. (6th edition). New York: W.H.Freeman and Company.
4. Ottawway, J.H. et al. (1984) Biochemistry. (4th edition). UK: The English languages book society and Bailliere Tindall.
5. Ophardt, C.E. (2003). Protein structure.Retrieved from HYPERLINK “http://wlow.elmhurst.edu.-chm/vchebook/563reactions.html” http://wlow.elmhurst.edu.-chm/vchebook/563reactions.html on 24/3/2010.
6. Stryer, L. (1981). Biochemistry. (2nd edition). New Yolk: W.H Freeman and company San Francisco.
7. Weil,J.H. (1990). General Biochemistry. (6th edition). New Delhi: New age international publishers.
8. Wenjia’s, (2007). Myoglobin. Retrieved from http/:www.chemeng.tsinghua.edu.cn/…/luowj.htmon 27/3/2010.

Rules of protein structure.(n.d).Retrieved from HYPERLINK “http://www.friedli.com/herbs/phytochem/proteins.html#denaturation” http://www.friedli.com/herbs/phytochem/proteins.html#denaturation on 24/3/2010.

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Structure of the collagen.(n.d).Retrieved from HYPERLINK “http://openlearn.openac.uk/file.php/1605/SK183_1_005i.jpg on 24/3/2010” http://openlearn.openac.uk/file.php/1605/SK183_1_005i.jpg on 24/3/2010.

Structure of the α-keratin,(n.d). Retrieved from HYPERLINK “http://www.chemistryexplained.com/images/chfa_02_img0322.jpg” http://www.chemistryexplained.com/images/chfa_02_img0322.jpg on 23/3/2010.

Secondary structures of the protein.(n.d). Retrieved from HYPERLINK “http://www.chemguide.co.uk/organicprops/aminoacids/proteinstruct.html” http://www.chemguide.co.uk/organicprops/aminoacids/proteinstruct.html on 23/3/2010.