Protein secondary structure Flashcards
What is secondary structure?
Secondary structure is the occurrence of regular repetitive patterns, such as ⍺-helix, over short sections of the polypeptide chain.
The polypeptide chain forms a backbone that appears to be linked by C-C and C-N single bonds
Single bonded structures are flexible due to bond rotation
Bond rotation in secondary structures…
Groups connected by single bonds can rotate about bond axis
Chain flexibility arises from bond rotation, not bond bending
Normal 109° tetrahedral or 120° trigonal planar bond angles are present
Bond rotation allows the peptide chain to adopt a variety of shapes
Conformations vs. configurations
- Conformations represent states of a molecule that can be interconverted by bond rotations, without breaking covalent bonds
- e.g. different shapes of a polypeptide chain
- Configurations can only be interchanged by breaking covalent bonds, not by bond rotation
- e.g. cis- and trans- forms of molecules with a -C=C- double bond
- two chiral forms of amino acids (D- and L-)
- For macromolecules such as proteins, we are usually concerned with conformations
What does X-ray diffraction measure?
- X-ray diffraction measures regular repeating patterns on the molecular scale
- Atoms and molecules have similar dimensions to the wavelength of X-rays
- when X-rays reflect off a regular repetitive structure, e.g.molecular crystal or fibre, they are deflected by an angle, dependent on wavelength of X-ray and spacing of pattern
- If X-ray wavelength is known, dimensions of the repeating pattern of molecules can be calculated
What are crystals?
Crystals are ordered arrays of molecules
X-ray diffraction measures regular patterns in fibrous proteins
What is the ⍺-keratin and β-keratin or fibroin major and minor pattern?
What is the ångstrom unit?
The ångstrom unit, 1 Å = 1x10-10 meter, is commonly used to measure atomic structures; H atom and C–H bond are about 1 Å in size
Who were the fibre patterns interpreted by?
- The fibre patterns were interpreted by Linus Pauling, a physical chemist, who was an expert in molecular structure and bonding
- Pauling built precise scale models of peptide chains with accurate bond lengths, bond angles and atomic radii
- He found that the single-bonded peptide chain seemed too flexible, and no regular patterns would be stable
One key finding is that the peptide bond has a double bond character.
Explain this.
- The peptide bond has two resonance forms, one with a double bond
- Pauling compared lengths of C-N bonds to correlate bond length with bond order
- Normal C–N is 1.49 Å
- Peptide C–N is 1.32 Å
- Normal C=N is 1.27 Å
- A peptide bond is rigid, fixed in trans-geometry because it behaves more like a double bond than a single bond
What do peptide bonds form?
Peptide bonds form rigid planes connecting tetrahedral ⍺-C atoms
In normal peptide chain, ⍺-amino and ⍺-carboxylate are locked in rigid planar peptide bonds, only the two bonds to a ⍺-carbon can rotate freely
What does restricted bond rotation lead to?
Restricted bond rotation leads to only a few possible structures
- Restricted bond rotation limits freedom of motion, so that only a few regular structures can form
- The peptide backbone changes direction by 109° at each tetrahedral ⍺-C, defining two possible regular repeating patterns:
- in a helical shape, every ⍺-C bond down the peptide chain turns in same direction (e.g. clockwise)
- in an extended shape, the ⍺-C bonds turn in alternate directions down the peptide chain
- If there is no regular, repeating structure, get random coil
What is the alpha-helix?
- Helix forms when amino acids all have same orientation, and ⍺-C bonds turn in same direction (i.e. all clockwise)
- Pauling’s models showed a very stable structure with 3.6 amino acids per turn of helix
- # 1 C=O lines up with H–N #5 to form hydrogen bonds that make ⍺-helix stable
- Distance between each turn of helix is 5.4 Å; 5.4 ÷ 3.6 = 1.5 Å is distance along the helix per amino acid
- These distances match ⍺-keratin patterns exactly, hence the name ⍺-helix
When do the extended β-strand and β-sheet occur?
The extended β-strand and β-sheet occur when amino acids alternate in orientation
- strands in the same direction make a parallel β-sheet
- H-bonds connect strand to strand
- strands in opposite directions make antiparallel β-sheet
- H-bonds align better in antiparallel mode
Dimensions of β-sheet match β-keratin patterns
Which amino acids are associated?
maximum space available for bulky or awkward shaped side chains
Trp, Tyr, (Phe) are big
Val, Ile, Thr have a branch on β-C
Cys has a large S atom on β-C
Formation of secondary structure is based on consensus of amino acids in immediate vicinity
Which amino acids tend to form which structure?
-
Ala, Arg, Gln, Glu, His, Leu, Lys, Met, (Phe) tend to form ⍺-helix
- Default behaviour of amino acids
- Trp, Tyr, (Phe), Val, Ile, Thr, Cys need room, prefer β-sheet structure
- Local majority determines which secondary structure forms
- Preference of each amino acid for ⍺ or β secondary structure can be estimated
- Allows secondary structure of sections of a protein to be predicted using software programs
What are secondary structure breakers?
- Gly, Pro, Asn, Asp, Ser have side chains which interfere with secondary structure H-bonds
- GPNDS
- may disrupt secondary structure – secondary structure breakers
- 2 breakers in a group of 4 amino acids interrupts the secondary structure
- forms a turn or flexible loop, allows the polypeptide main chain to change direction drastically (can be 180°)
What are native and denatured states of protein?
- Most proteins are folded into a unique 3D tertiary structure, which is required for their function
- Native state
- Denaturation unfolds proteins; unfolded form may be unstructured or aggregated
- often irreversible
- Protein’s function is typically lost on denaturation
- Ways to denature proteins include:
- heat
- disruptive solvents
- harsh detergents (e.g. SDS)
- When purifying proteins to study them, we usually try to avoid denaturation
