Chapter 6 Notes: Protein Structure PDF

Chapter 6- up to quiz 2: Proteins: three-dimensional structure The **primary** structure of the protein is its linear sequence of amino acids. The **secondary** structure is the local spatial arrangement of polypeptide's backbone atoms without regard to the conformations of its side chains. The...

Chapter 6- up to quiz 2: Proteins: three-dimensional structure The **primary** structure of the protein is its linear sequence of amino acids. The **secondary** structure is the local spatial arrangement of polypeptide's backbone atoms without regard to the conformations of its side chains. The **tertiary** structure refers to the three-dimensional structure of an entire polypeptide, including its side chains. Many proteins composed of two or more polypeptide chains, loosely referred to as [subunits]. A protein's **quaternary** structure refers to the spatial arrangement of its subunits. **Levels of protein structure.** a. Primary structure (The unique sequence of amino acids), b. secondary structure (Coils and folds in the polypeptide chain, local) , c. tertiary structure (Overall shape of a polypeptide due to interactions between side chains, local or at a distance), and d. quaternary structure (For proteins that exist as multiple polypeptide chains). Amino acids are connected by peptide bond. The peptide group has a rigid, planar structure because of resonance interactions that give the peptide bond \~40% double bond character. Peptide group, with few exceptions assume the **trans conformation,** in which successive C~α~ atoms are on opposite sides of the peptide bond joining them. Figure: The trans peptide group. The bond lengths (in angstroms) and angles (in degrees) are derived from X-ray crystal structures. This is extended confirmation of a polypeptide. The backbone (atoms that participate in peptide bonds) is shown as a series of planar peptide groups. The confirmation of the backbone can therefore be described by the [torsion angles] (also called [dihedral angles] or [rotation angles] ) around the C~α~--N (Φ) (Phi) and C~α~-C (ψ) (Psi) of each residue. These angles Φ and ψ are both defined 180 ◦ when the polypeptide chain is in fully extended conformation. Figure shows torsion angles of the polypeptide backbone. Two planar peptide groups are shown. The only reasonably free movements are rotations around the C~α~--N bond and C~α~--C bond, by convention both Φ and ψ are 180 ◦ in the conformation shown and increase as indicated when peptide plane is rotated in the clockwise direction as viewed from C~α~ Steric interference between adjacent peptide groups: Rotation can result in a conformation in which the amide hydrogen of one residue and the carbonyl oxygen of the next are closer than their Van der Waals distance. The **Ramachandran diagram** indicates [allowed conformations of polypeptides]. The **blue** shaded regions indicate the **sterically allowed Φ and ψ angles for all residues except Gly and Pro.** The [green] shaded regions indicate the [more crowded (outer limit) Φ and ψ angles]. The yellow circles represent conformational angles of several secondary structures: α, right-handed α helix; ↑↑, parallel ϐ sheet; ↑↓, antiparallel ϐ sheet ; C, collagen helix; α~L~ left-handed α helix. Most area represents forbidden conformation, only three small regions are physically accessible to most residues. The observed values of accurately determined structures nearly always fall within these allowed regions. Except, the cyclic side chain of Pro; and Glycine, the only residue without a C~ϐ~ atom, which is less sterically hindered. The **α Helix** and **ϐ sheet** are called [as regular secondary structures] because they are composed of sequences of [residues with repeating Φ and ψ values]. **The α Helix** was discovered by Linus Pauling , it has a regularly repeating structure. It has both favorable hydrogen bonding pattern and Φ and ψ values that fall within the fully allowed regions of the Ramachandran diagram. **The α Helix**. This right-handed helical conformation has 3.6 residues per turn. Dashed lines indicate hydrogen bonds between C=O groups and N-H groups that are four residues farther along the polypeptide chain. It has Φ = -57◦ and ψ = -47◦ ,and a pitch (the distance the helix rises along its axis per turn) of 5.4 A◦. **ϐ sheets** are formed from extended chains. Pauling and Corey postulated the existence of ϐ sheets. In ϐ sheets hydrogen bonding occurs between neighboring polypeptide chains rather than within one as in an α Helix. If hydrogen-bonded polypeptide chains run in opposite directions, it is called as **antiparallel** ϐ sheets. If hydrogen-bonded chains extend in the same direction, it is called as **parallel** ϐ sheets. In figure dashed lines indicates hydrogen bonds between polypeptide strands. Side chains are omitted for clarity. a) is antiparallel and b) is parallel ϐ sheets. The conformations in which these ϐ structures are optimally hydrogen bonded [vary somewhat from fully extended] (Φ = ψ = ± 180◦), therefore they [have a rippled or pleated edge] on appearance called pleated sheets. [Side chains] in ϐ sheets (its C~α~ --C~ϐ~ bonds) [extend perpendicularly] to the plane of the sheet. With successive side chains located on opposite sides. Each strand of ϐ sheet has a two residue repeat with a repeat distance of 7.0 A◦. Dashed line in figure represents hydrogen bonds. The R groups (purple) alternatively extend to opposite sides of the sheet. Connection between adjacent strands in ϐ sheets. A) antiparallel strands may be connected by a small loop. B) Parallel strands require a more extensive crossover connection that almost always has a right-handed helical sense, as is shown, because it better accommodates a ϐ sheet's inherent right-handed twist. Α helix and ϐ sheets are often joined by stretches of polypeptide that abruptly change direction. Such reverse turns or ϐ bends almost always occur at protein surfaces. They usually involve four successive amino acid residues arranged in one of two ways , type I and type II that differ by 180◦ flip of the peptide unit linking residues 2 and 3. dashed line represents hydrogen bonds. The normal 5.4 A◦ repeat distance of each α helix in the pair is thereby tilted relative to the axis of this assembly, yielding the observed 5.1 A◦ spacing. The assembly is called **coiled coil**. The conformation of **α keratin's** (protein found in hair, nail, horns, skin etc) coiled coil is a consequence of its primary structure. Figure view down the coil axis showing the alignment of nonpolar residues along one side of each α helix. The central 310 residue segment of each polypeptide chain, the helices have the pseudo repeating sequence a-b-c-d-e-f-g in which residues a and d are predominantly nonpolar. Because the 3.5 residue repeat in α keratin is slightly smaller than the 3.6 residues per turn of a standard α helix, the two keratin helices are inclined about 18 ◦ relative to one another, resulting in the coiled coil arrangement. At left is the side view of the polypeptide and at right space-filling form. The 81 residue chains are parallel with their N-terminal ends above. In space-filling the side chains of 2 polypeptides contact each other. Higher order structure of α keratin: A\) Two keratin polypeptides form a dimeric coiled coil. B\) Protofilaments are formed from two staggered rows of head to tail associated coiled coils. C\) Protofilaments dimerize to form a protofibril, four of which forms a microfibril **Collagen** which is a most abundant vertebrae protein. Its strong, insoluble fibers are major stress-bearing component of connective tissues such as bones, teeth, cartilage, tendons and the fibrous matrices of skin and blood vessels. It consists of three polypeptide chains. It has a molecular mass of \~285 kDa , a width of 1.4 A◦. The figure shows collagen **triple helix** structure. Left-handed polypeptides are twisted ropelike together to form a right-handed super helical structure. Collagen has distinct amino acid composition: Nearly one third of its residues are Glycine, another 15-30% are proline and 4-hydroxyprolyl, 3-hydroxyprolyl and 5-hydroxylysyl residues are also present in collagen but in smaller amounts. These nonstandard residues are formed after collagen polypeptide are synthesized. Proline residues are converted to hydroxyprolyl in a reaction catalyzed **by prolyl hydroxylase**. This enzyme requires **ascorbic acid (Vitamin C)** to maintain its activity. The disease **scurvy** results from dietary deficiency of vitamin C. **Sequence Affects 2º Structure:** Variations in amino acid sequence, as well as the overall structure of the folded protein, can distort the regular conformations of secondary structural elements. Like α-helix frequently deviates from its ideal conformation in the initial and final turns of the helix. Β sheet may contain an extra residue that is not hydrogen bonded to a neighboring strand, producing a distortion known as **β bulge**. Analysis of known protein structures by Chou and Fasman revealed the propensity of a residue to occur in an α helix and β sheet. They discovered that certain residues not only have a high propensity for a particular secondary structure, but they tend to disrupt or break other secondary structures.. Such data are useful for predicting the secondary structures of proteins with known amino acid sequences.