Primary Structure
Secondary Structure
PEPTIDE is:s
- Planar
- 40% double bond character
● 10% if Pro residues follow cis
● Torsion angles (dihedral angles) → describe the conformation of the backbone around the alpha C-N bond(phi)
and alpha C-C(si) bond
● Ramahandran diagram → only three areas are physically accessible to the residues
1. The cyclic side chain of Pro limits its range of phi values to 60 degrees, which makes it most
restricted
2. Gly much less sterically hindered
MOST COMMON REGULAR 2NDARY STRUCTURE → composed of sequences of residues with repeated phi
and si angles
1. Alpha helix → favorable H-bonding pattern, phi and si values fall in the allowed of ramachandran
● Right-handed
● Phi: -57 degrees, si: -47 degrees
● 3.6 residues per turn
● Pitch of 5.4 A
● Average length of ~12 residues (3 helical turns) and length of ~18 A
● Backbone H-bonds arranged such that the peptide C=O bond of the nth residue points along
the helix axis toward the peptide N-H group of the (n+4)th residue
● Results into a strong H-bond with distance of 2.8 A
● AA side chains project outward and downward from the helix
2. Beta sheets → formed from extended chains, H-bonding occurs between neigboring polypeptide chains
1. Antiparallel → run in opposite direction
2. Parallel → extend in the same direction, less stable bcos of distorted H-bonds
● Fully extended: 180 degrees
● Side chains extend perpendicularly to the plane of the sheet
● Each strand of beta sheet has 2-residue repeat with repeat distance of 7.0 A
● May contain 2- 22 strands ave. of 6 strands.
● Each strand may contain up to 15 residues
● Geometry is a compromise between optimizing conform. Energies and preserving the chain
● Connections between 2 antiparallel → small loop
● Connections between 2 parallel → out of the plane
→ Reverse turns aka beta bends - occur in the protein surface to join some units of secondary
structure; involve 4 succesive AA residues arranged in two ways: Type I and Type II (differ b a
180 degree flip of the peptide linking residues 2 and 3)
→ both type stabilized by H-bond
→ Type II- oxygen of residue 2 crowds the beta C of residue 3 which is Gly, residue 2 of both
types can be Pro
● Fibrous proteins have repeating secondary structure
1. Keratin
- Coiled coil
- Unreactive protein occurs in all higher vertebrates
- Principal comp. Of the skin layer and hair nails and feather
- Alpha-keratin → mammals; beta-keratin → birds/reptiles
- Humans have more than 50 keratin genes
→ Alpha-keratin: 5.1 A pitch due to the two alpha-keratin forming an alpha-helix to form
a left-handed coil; the original 5.4 A is tilted
- Consequence of primary structure
- Central ~310 residue segment has a 7-residue pseudorepeat, a-b-c-d-e-f-g, w/
nonpolar residues in positions a and d
- Due to the 3.6 residues per turn, the a and d line up in the side which forms the
hydrophobic strip
- 3.5-residue repeat results inclination of 18 degrees
- N and C-term domains facilitate assembly of coiled coils into protofilaments 2 of
which constitutes a protofibril
- Four protofibrils → microfibril which associates with other microfibril to form
macrofibril
- alpha -keratin- rich in Cys residues forming disulfide bonds that crosslink
adjacent polypeptide chains
- Classified into hard (nails, horn and hair) disulfide bonds that desist deformation
or soft (skin and callus)
- Disulfide bonds canbe reductively cleaved by mercaptans
- If disulfide have been cleaved, it can be stretched thus the chain assumes a beta
sheet conformation
→ Beta-keratin: feathers, can be stretched
2. Collagen
- Triple helix
- Occurs in all multicellular animals; most abundant vertebrate protein
- Strong, insoluble fibers major stress-bearing components of connective tissues
such as bone, teeth,
- Single collagen molecule consists of three polypeptide chains assembled into 28
collagen varieties
→ Type I- consists of two alpha 1 (I) chains and one alpha 2 (I) chain; mass of 285 kD,
width of ~14 A and length of ~3000 A
- One-third of residues are Gly, another 15-30% are Pro and 4-hydroxyprolyl
(Hyp) and 5-Hydroxylysly (Hyl)
- Pro residues are converted to Hyp in a reaction catayzed by prolyl hydroxylase
which requires ascorbic acid to maintain its activity
- Scurvy → results from vitamin C deficiency
- Collagen has repeating triplets sequence of Gly-X-Y over a segment of ~1000
residues where X is often Pro and Y is often Hyp but sometimes Hyl
- Because of the collagen’s Pro residue it prevents from forming the alpha-helix,
lacking of the backbone N-H groups which form the intrahelical H-bonds
- Collagen instead assumes a left-handedn helix with about three residues per
turn
- Three parallel chains wind around each other with gentle, right-handed,
ropelike twist
- Every 3rd residue is Gly bcos of crowding in the center of the triple helix
- Three polypeptide chains are staggered so that Gly, X, and Y occurs at each
level
- Collagen molecules in fibrils are staggered arrays stabilized by hydrophobic
interactions
- Covalently crosslinked that account for poor solubility
- Almost devoid of Cys residues , but up to four Lys, Hyl and His chains to form
histidineodehydrohydroxymerodesmosine
- Lysyl oxidase→ converts Lys to aldehyde allysinel is the only enzyme implicated
in the process
● Most proteins include nonrepitetive structure
- Globular proteins
- Random coil → totally disordered and rapidly fluctuating conformations of denatured (fully
folded) proteins
- Native (folded) - simply irregular and difficult to describe
- Sequence affects secondary structure
- Beta bulge → results from an extra residue taht is not H-bonded to the neighboring strand
- Many limits on the AA comp and sequence is due to conformational straints of 3D structure,
also steric clashes between large side chains destabilize alpha-helix
- Helix capping → the residues Asn and Gln can fold back to form H-bonds with one of the
terminal residue of the helix
Tertiary structure
- Describes the folding of its secondary structural elements and specific the positions of each atom
including side chains
- Determined by x-ray crystallography, NMR, and cryo-electron microscopy
- Side chain location varies with polarity
Globular proteins:
1. NONPOLAR (Val, Ile, Leu, Met and Phe) → INTERIOR
2. CHARGED POLAR (Arg, His, Lys, Asp, Glu) → SURFACE
3. UNCHARGED POLAR (Ser, Thr, Asn, Gln, Tyr) → SURFACE/INTERIOR
● Globular proteins - built from combinations of secondary structural elements
- Certain combinations form motifs or supersecondary structures
1. βαβ motif → alpha helix connects two parallel beta sheet
2. β hairpin → antiparallel strands connected by relatively tight reverse turns
3. αα motif → two successive antiparallel helices pack against each other with axes
inclined
4. Greek key motif → a beta hairpin is folded over to form a 4-stranded antiparallel beta
sheet
- Most proteins can be classified as α, β, α/β.
- cytochrome b562 → only alpha-helices
- immunoglobulin fold → beta proteins
-most proteins such as lactate dehydrogenase and carboxypeptidase A → contain mixture of alpha and
beta
- Alpha and beta can be further classified by topology → how their secondary structural elements are
connected
- extended beta sheets can roll up to form beta barrels
- Large polypeptides form domains
→ ~200 residues fold into two or more globular cluster known as domains
→ have ave. diameter of ~25 A
→ two layers are needed to seal off the hydrophobic core of a domain
→ performs a function like dinucleotide binding fold aka the Rossman fold
Quaternary Structure
- Proteins contain multiple subunits arranged symmetrically (rotational symmetry)
1. Cyclic symmetry → protomers related by a single axis of rotation (C2 symmetry)
2. Dihedral symmetry → generated when an n-fold rotation axis intersects a twofold rotation axis at
right angles (D2 symmetry)
- Molecular masses >100 kD associate with a specific geometry
- Increasing the size of an enzyme through association of identical subunits is more efficient
- Subunits usually associate noncovalently
- Proteins with more than one subunit is called oligomer and their identical units are called protomers
- Contact regions bet. Subunits resemble the interior of a single subunit protein
Protein Stability
- Depends primarily on the hydrophobic effects and electrostatic interactions
- Proteins marginally stable under physiological condtns.
● Proteins stabilized by several forces
1. Hydrophobic effect → greatest influence; causes nonpolar substances to minimize contact with
water
→ hydropathy - expresses the combined hydrophobic and hydrophilic tendencies of AA
residues; the greater the hydropathy, more likely to occupy the interior of protein
Factors affecting stability accdg. to site-directed mutagenesis
1. Hydrophobicity
2. Steric compatibility
3. Volume of side chain
2. Electrostatic Interactions → H-bonds make minor contributions to stability, only fine tunes
the tertiary structure by selecting the unique native structure of protein
Ion pair/Salt bridge → association of two protein groups of opp. Charge
3. Disulfide Bonds crosslink extracellular proteins → not essential for stabilization but important for
locking in the backbone
4. Metal ions stabilize small domains → internally crosslink proteins
→ zinc fingers: at least ten motifs described in nucleic acid-binding proteins
