Protein Structure Flashcards
Structure of Proteins
• Unlike most organic polymers, protein molecules adopt a specific three- dimensional conformation.
• This structure
–> is able to fulfil a specific biological function
–> is called the native fold.
–> has a large number of favourable interactions within the protein
The polypeptide chain
polypeptide chain consists of a constant backbone (periódico) and variable side chains
The structure of the protein is partially dictated by the properties of the peptide bond
Primary Structure: The peptide bond
The peptide bond is a resonance hybrid of two canonical structures! (Ligeira deslocalização dos e- no plano –> caráter parcialmente duplo)
The peptide bond is essentially planar –> constrangimento estérico, não há rotação livre
–> Six atoms (Cα, C, O, N, H, and Cα) lie in a plane. Thus rotation about the bond is prohibited.
Polypeptide chain (rotation)
The Polypeptide Is Made Up of a Series of Planes Linked at α Carbons
Rotation around bonds connected to the α carbon is permitted.
(phi) : angle around the α carbon — amide nitrogen bond
(psi) : angle around the α carbon — carbonyl carbon bond
The rotation about the Φ and ψ bonds, called the torsion angle, determines the secondary structure
Distribution of phi and psi Dihedral Angles
Not all torsion angles are permitted!!
Some phi and psi combinations are more favourable because of chance to form favourable H-bonding interactions along the backbone
Some phi and psi combinations are very unfavourable because of steric crowding of backbone atoms with other atoms in the backbone or side chains. (ex: phi= 90, psi=-90 disfavoured)
Ramachandran plot
A Ramachandran plot (mapa de densidade) shows the distribution of phi and psi dihedral angles that are found in a protein:
• shows the common secondary structure elements
• reveals regions with unusual backbone structure
Secondary Structures
Secondary structure is the 3D structure formed by hydrogen bonds between peptide NH and CO groups of amino acids that are near one another in the primary structure.
Two regular arrangements are common
• the alpha helix stabilized by hydrogen bonds between nearby residues
• the beta sheet stabilized by hydrogen bonds between adjacent segments that may not be nearby
Irregular arrangement of the polypeptide chain is called the random coil.
The alpha helix
• Helical backbone is held together by hydrogen bonds between the backbone amides of an n and n + 4 amino acids (In the α helix, the CO group of residue i forms a hydrogen bond with the NH group of residue I + 4)
• It is a right-handed helix with 3.6 residues (5.4 Å) per turn (essentially all α helices in proteins are right-handed)
• Peptide bonds are aligned roughly parallel with the helical axis.
• Side chains point out and are roughly perpendicular with the helical axis.
Amino acids #1 and #8 align nicely on top of each other.
The inner diameter of the helix (no side chains) is about 4–5 Å- too small for anything to fit “inside”
The outer diameter of the helix (with side chains)is 10–12Å.- Happens to fit well into the major groove of dsDNA
Sequence Affects Helix Stability
- Not all polypeptide sequences adopt alpha-helical structures.
- Small hydrophobic residues such as Ala and Leu are strong helix formers.
- Pro acts as a helix breaker because the rotation around the N-Calpha (φ-angle) bond is impossible.
- Gly acts as a helix breaker because the tiny R group supports other conformations.
- Attractive or repulsive interactions between side chains 3 to 4 amino acids apart will affect formation.
The Helix Dipole
- Recall that the peptide bond has a strong dipole moment.
- C−O (carbonyl) negative
- N−H (amide) positive
- All peptide bonds int he alpha helix have a similar orientation.
- The alpha helix has a large macroscopic dipole moment that is enhanced by unpaired amides and carbonyls near the ends of the helix.
- Negatively charged residues often occur near the positive end of the helix dipole.
beta sheets
- The planarity of the peptide bond and tetrahedral geometry of the alpha carbon create a pleated sheet-like structure! (Resulta das caraterísticas planares da cadeia polipeptídica)
- Sheet-like arrangement of the backbone is held together by hydrogen bonds between the backbone amides in different strands.
- Side chains protrude from the sheet, alternating in an up-and- down direction.
- antiparallel
- parallel
- mixed
An antiparallel β sheet
Adjacent β strands run in opposite directions.
Hydrogen bonds between NH and CO groups connect each amino acid to a single amino acid on an adjacent strand, stabilizing the structure. Hydrogen bonds between strands are linear (stronger)
A parallel β sheet
Adjacent β strands run in the same direction
Hydrogen bonds connect each amino acid on one strand with two different amino acids on the adjacent strand. Hydrogen bonds between strands are bent (weaker).
Beta Turns
- β turns occur frequently whenever strands in β sheets change the direction.
- The 180 turn is accomplished over four amino acids.
- The turn is stabilized by a hydrogen bond from a carbonyl oxygen to amide proton three residues down the sequence (interação do backbone! Não da cadeia lateral!)
- Proline in position 2 (type I β turn: occurs more than twice as frequently as type II) or glycine in position 3 (type II β turn)
Protein Tertiary Structure
Tertiary structure refers to the overall spatial arrangement of atoms in a protein.
The tertiary structure of a protein is the 3-dimensional shape of the protein chain. This shape is determined by the characteristics of the AA making up the chain.
Favorable Interactions in Proteins
Stabilized by numerous weak interactions between AA side chains:
Hydrophobic interactions (reorganização da cadeia peptídica --> AA apolares no interior) Hydrogen bonds London dispersion Electrostatic interactions
Interacting AA are not necessarily next to each other in the primary sequence
Major classes of Proteins
2: fibrous & globular
Fibrous proteins
In fibrous proteins the fundamental structural unit is a simple repeating element of secondary structure. (–> Proteínas fibrosas resultam da repetição de uma unidade estrutural secundária.)
insoluble in water (because of high number of interior/surface hydrophobic residues–> força de coesão –> resistência)
hydrophobic surfaces are buried by packing many similar polypeptide chains into elaborate supramolecular complexes
Ex:
• Collagen
• Keratin
• Silk Fibroin
Fibrous proteins- function
Fibrous proteins provide structural support or cells and tissues, because of their structural properties
Properties of fibrous proteins dictate structural roles:
(structure – characteristics – exs)
alpha- Helix, cross-linked by disulphide bons – tough, insoluble protective structures of varying hardness and flexibility – alpha-keratin of hair feathers, nails
beta conformation – soft, flexible filaments – silk fibroin
collagen triple helix – high tensile strength, without stretch – collagen of tendons, bone matrix
Collagen
fibrous proteins
• Collagen is an important constituent of connective tissue: tendons, cartilage, bones, cornea of the eye.
[Gelatin is derived from collagen taken from animal body parts, has little nutritional value as it lacks essential AA]
- Three collagen chains form a triple helix (The triple helix has higher tensile strength than a steel wire of equal cross section)
- Many triple-helices assemble into a collagen fibril. (Aumento de resistência: Fibrila –> Fibra –> Fascículo –> Feixe de fibras)
Collagen- structure
fibrous proteins
Collagen consists of three intertwined left-handed (incostume!) helical polypeptide chains (with 3 residues per turn) that form a superhelical cable with a right- handed twist.
The helical polypeptide chains of collagen are not α-helices (mas chamam-se cadeias alfa)
Collagen has a unique repeating secondary structure:
Glycine appears at every third residue and the sequences Gly-Pro- Hyp and Gly-Pro-Pro are common. Glycine, because of its small size, is required at the tight junction where the three chains are in contact. (–> Gly: alinhamento estrutural)
(nº limitado de AA: ex gelatina não tem grande valor nutricional)
The center of the three-stranded superhelix is not hollow, as it appears here, but very tightly packed.
4-Hydroxyproline in Collagen
fibrous proteins
- Forces the proline ring into a favourable pucker
- Offers more hydrogen bonds between the three strands of collagen
- The post-translational processing is catalysed by prolyl hydroxylase and requires α-ketoglutarate, molecular oxygen, and ascorbate (vitamin C).
Collagen fibrils- structure
fibrous proteins
Collagen (Mr 300,000) is a rod- shaped molecule, ~ 3000 Å long and only 15 Å thick
- Collagen superstructures are formed by cross-linking of collagen triple-helices to form collagen fibrils.
- Each chain has about 1,000 AA residues
- Crosslinks are covalent bonds between Lys or HyLys, or His AA residues.
Human genetic defects in collagen structure
fibrous proteins
Some human genetic defects in collagen structure illustrate the close relationship between amino acid sequence and three-dimensional structure in this protein.
Osteogenesis imperfecta
is characterized by abnormal bone formation in babies;
Ehlers-Danlos syndrome
is characterised by loose joints.
Caused by mutations in the Gly residue by an AA with a larger R group (such as Cys or Ser)
These single-residue substitutions have a catastrophic effect on collagen function because they disrupt the Gly–X–Y repeat that gives collagen its unique helical structure –> altera propriedades mecânicas
