BiochemistryChapter 6 The Three-Dimensional Structure of Proteins Mak Oi Tong
Introduction This chapter is devoted to an examination of: • the several levels of protein structure – their geometry • how they are stabilized and • their importance in protein function.
Structure of proteins • Primary structure : the amino acid sequence of protein molecules. • Secondary structure : the local regular folding (direction) of protein molecules. • Tertiary structure : the final 3-dimensional (folded) form of protein molecules. • Quaternary structure : the arrangement of several polypeptide chains (subunits). • Conformation and configuration.
Secondary StructureRegular Ways to Fold the Polypeptide Chain Discovery of Regular Polypeptide Structures (Figure 5.12b, Figure 6.2, Figure 6.3, Figure 6.4) • Bond lengths and bond angles should be distorted (changed) as little as possible shown in Fig. 5.12b. • No two atoms should approach one another more closely than is allowed by their van der Waals radius. • The amide group must remain planer and in the trans configuration. • Hydrogen bonds are most probably used to stabilize the peptide folding between amide protons and carbonyl oxygen.
Molecular Helices and Pleated Sheets • (Figure 6.5, Figure 6.6, Table 6.1)
α-Helix • Only right-handed helix found. • Hydrogen bonds are found between the amide hydrogen and carbonyl oxygen. • A loop of 13 atoms is formed between the hydrogen bond. • 3.6 amino acids per turn of helix. • The repeat (c) is 18 amino acid residues. • The (p), distance per turn, is 0.54 nm, and the rise, distance between each atom is 0.15 (0.54/3.6). • α-Helix is also called 3.613 helix, compared to π-helix 4.416 and 310 helix. • Proline is the α-breaker.
β-sheet (pleated sheet) • Two types of β-sheet, parallel (same N to C direction) and anti-parallel (opposite N to C direction) between polypeptide chains. • β-Sheet contains 2 amino acid residues per turn, and cannot form hydrogen bond between amide hydrogen and carboxyl oxygen. • Hydrogen bonds can only formed between adjacent polypeptide chains. • Anti-parallel form is more stable than parallel form.
Ramachandran Plots(Figure 6.2, Figure 6.8, Figure 6.9, Figure 6.10) • A map (Fig. 6.8) describes the backbone conformation of any particular residue in a protein corresponding to the angle Φ (phi) and Ψ (psi) • Rotation of the corresponding angle Φ and Ψ are given by the arrow in clockwise for +180° when looking in either direction from the α-carbon. • This is called Ramachandran plot after the biochemist who first found it. • If all AA residues in a protein have the same secondary structure (e.g. α-helix), the points for all residues would superimpose (come together at one single point).
Because of the steric effect and van der Waals radii, only a relatively small fraction of conformations is possible, the uncolored areas of the plot in Fig. 6.8. • Only right-hand helix is favoured because all AAs are L-form. • Some points of proteins will fall in the non-allowed regions because of the glycine residue. • The conformation Φ = 0, Ψ = 0 is not allowed in any polypeptide chain because of the steric clash between the carbonyl oxygen and amino proton.
Fibrous Proteins Structural Materials of Cells and Tissues (Table 6.2) • More than 1/3 or more of the body protein in large vertebrates. • Functions include: • External protection such as skin, hair, feather and nail. • Structure and support, shape and form, tendons, cartilage and bone. • Native conformations of fibrous proteins are stable proteins after isolated and will not be denatured or unfolded.
Keratins • Two classes of keratin, α- and β-keratins. • α- Keratins is the major fibrous proteins of hair and wool. • Each α-keratin molecule contains over 300 residues in length and all are α-helical. • Two α-keratin helices bond together by their hydrophobic R-side groups. • The higher amounts of AAs are serine, glutamine, glutamic acid and cysteine. • Disulfide cross-links are found in nail and hair (fewer), and human hair for permanent wave.
β-Keratin • Contains β-sheet structure. • Are found mostly in birds and reptiles for feather and scales.
Fibroin • They areall anti-parallel pleated sheet structure. • Comprise almostglycine, alanineand serine AA. Gly-ala-gly-ala-gly-serine-gly-ala-ala- gly- This alternation allows the β-sheet to fit together. • The structure is strong and inextensible. • No intrachain hydrogen bond, only interchain hydrogen bonds. • No cystine cross-linkage presence. • The fibers are very flexible, e.g. silk.
Collagen (Figure 6.13) • Collagen is about one third of total protein in large animals, and is the major constituent of tendons and skin. • Basic unit is tropocollagen which consists of three polypeptide chains in left-handed helix tightly coiled into a three-strand rope in right-handed helix, arranged in head to tail. • Tropocollagen have total about 3000 AA residues (each polypeptide has 1000 AA residues), having of molecule weight of 300,000. • Every third residue can be only glycine because of the bulky effect.
Proline or 4-hydroxyproline is found in tropocollagen molecule, and a repetitive sequence is present of the form gly-X-Y, where X is often proline and Y is proline or hydroxyproline. • Hydrogen bonds are present among the polypeptides of tropocollagen. • Vitamin C is required for the enzyme to catalyze the hydroxylation of proline to hydroxyproline. • Scurvy, a disease which is the weakening of collagen fibers caused by the failure to hydroxylate proline, is a symptom of extreme vitamin C deficiency.
Collagen cannot be stretched. • The toughness of collagen is due to the cross-linking of tropocollagen molecules to one another by a reaction involving lysine side chains. • This process continues through life, and the accumulation cross-links make the collagen steadily less elastic and more brittle, the signs of aging.
Collagen Synthesis (Figure 6.14) • Posttraslational modification is present in the collagen synthesis. • Procollagen is yield having about 1500 residues of which 500 are in N- and C-terminals regions that do not have the typical collagen fiber sequence. • The procollagen triplexes are exported into the extracellular space and the N- and C-terminals regions are cleaved off by specific proteases. • See Fig. 6.14 for further discussion.
Elastin • Basic component of connective tissue of blood arteries and ligaments. • Structure is similar to collagen. • The basic unit of elastin fibrils is tropoelastin. • It contains rich in glycine and alanine, and also high % of lysine but fewer of proline. • The ability for stretch in elastin is caused by the special structure of desmosine cross-linked by four lysine residues to become a form of highly interconnected, rubbery network.
Different Folding for Different Functions (Figure 6.1, 6.15 and 6.16) • Globular proteins which are named because their polypeptide chains are folded into compact structures. • They are the important structures for all kinds of enzymes, hormones and other functional proteins. • Their tightly folded conformations are referred as the tertiary structure and are the crucial factor for the biological functions. • Many globular proteins carry prosthetic groups, the non-amino acid small molecules that may be noncovalently or covalently bonded to the proteins to fulfill special functions. • Every globular protein has a unique tertiary structure that is made up of secondary structure elements such as helics, β -sheet.
Varieties of Globular Protein Structure: Patterns of Folding Figure 6.16, 6.17, 6.18, and 6.19) • Although there will be infinite number of globular protein folding, some principles of protein folding are found. • Many proteins are made up of a number of domains, a compact locally folded region of tertiary structure, which perform different functions of proteins. • Two major kinds of folding patterns, α-helic and β-sheet.
General rules of globular proteins • All globular proteins have a defined inside and outside structure, hydrophobic AAs inside and hydrophilic AAs outside. • β-Sheets are usually twisted and wrapped into barrel structure. • The polypeptide chains can turn corner in a number of ways, to go from one β segment or a helix to the next. • Not all parts of globular proteins can be conveniently classified as helix, β sheet, or turn.
The Information for Protein Folding (Figure 6.20) • The information for determining the 3-dimensional structureofa protein is carried entirely in the amino acid sequence of that protein. • Native structure is the natural 3-dimensional structure of a protein. • Denaturation is a process for the lost of natural structure of a protein, along with many of its specific properties. • In a cell, a newly synthesized polypeptide chain will spontaneously fold into the proper conformation.