Protein structure Flashcards
types of side chains
- Non-polar e.g. glycine - have alkyl group.
- Uncharged polar e.g. cysteine - has S, N or OH in side chain.
- Negatively charged polar e.g. aspartic acid - has carboxylic acid group.
- Positively charged polar e.g. histidine - has amine group
peptide bond features
- Joins amino acids.
- 40% double bond character.
- Planar.
- Predominantly trans.
- Display resonance structures
peptide
short stretch of amino acids joined by peptide bonds
protein
long chain of amino acids joined by peptide bonds
primary structure
amino acid sequence of a protein
secondary structure
specific coiling or folding of amino acid residues over a short stretch of sequence into beta strand or alpha helix
tertiary structure
3D structure of a complete protein chain
quaternary structure
3D arrangement and structure of multiple chains within a protein
properties of alpha helix
- Interaction between residues that are 4 apart in the protein sequence.
- 3.6 residues/turn; 5.4Å/turn.
- Spiral is “right handed” (turns clockwise as it goes up).
- Side chains point out from the helix.
- stabilised by H bonds
- often have one side polar residues, other side non-polar
properties of beta strand/sheet
- Hydrogen-bonding occurs between adjacent chains.
- B-sheet = 2 or more B strands (typically 2-10 strands/sheet).
- Can be parallel or antiparallel.
- Sheets have right-handed twist
- often alternating polar and non-polar residues
properties of turns
- Hairpin-like, usually involve 3-4 residues.
- High Gly and Pro content.
- 30% of residues involved in turns.
- Normally have H bond across turn.
- More than 16 types, type I and II are common
bond angles limiting protein flexibility
- phi Φ angle = rotation angle around the N–Ca bond
- psi (Ψ) angle = rotation angle around the Ca–C’ bond (C’ = carbonyl carbon)
- omega (ω) angle = rotation angle around peptide bond, not very flexible
These angles take on values from 0 to +/-180 degrees
Phi-Psi angles have restrictions in their values because of steric hinderance
- Phi rotation can lead to O-O collision
- Psi rotation can lead to NH-NH collisions
why are most peptide bonds trans
Steric hinderance is increased for cis peptide bonds
side chain angles
called chi and usually staggered
ramachandran plot of parallel B sheet, antiparallel B sheet, alpha helix and left-handed alpha helix
which amino acids are not found in alpha helices
glycine and proline
afinsen experiment
denatured and reduced ribonuclease and then it reformed into its original shape - showed that only instructions needed for folding are embedded in the sequence
stabilisation of protein folding
- Non-covalent interactions, while individually weak in proteins, collectively make a significant contribution to protein conformational stability
- In some proteins additional covalent bonds (eg. disulfide bonds)
- Hydrophobic core contributes most to protein stability in aqueous solution
folding pathway of proteins
- Formation of short secondary structure segments
- Nuclei come together, growing cooperatively to form a domain
- Domains come together (but tertiary structure still partly disordered)
- Small conformational adjustments to give compact native structure
what assists with protein folding
- chaperones help with folding of some proteins
- About 85% of proteins are either chaperone-independent or need a chaperone e.g. Hsp70
- Other 15% need special type of chaperone called chaperonin e.g. GroEL-GroES
unfolding of proteins
Weakening of non-covalent interactions can lead to unfolding and loss of biological function (denaturation). Can result from:
- Change in pH
- Heat
- Detergent
- Organic solvents
- Urea
misfolding of proteins
- Cause problems e.g. in brain, abnormal form of prion protein PrP causes normal PrP protein to change shape, causing brain damage. Cannot be treated
- Alzheimers disease
- Type 2 diabetes
what is phosphorylation, where can it occur and what does it do
- can occur on the side chains of Ser, Thr and Tyr
- catalysed by kinase enzymes and involves ATP
- addition of the larger charged phosphate to a hydroxyl group induces localised conformation changes in the protein
- These changes affect function e.g., the activation of a catalytic activity
phosphorylation of insulin receptor
- Insulin binds to the extracellular protein subunits of the insulin receptor
- conformation change that is communicated to the intracellular side protein subunits
- activates tyrosine kinase domains on the b-subunits
- Specific Tyr residues are then phosphorylated on the b-subunits which then leads to phosphorylation of ‘insulin receptor substrate’ proteins, which act as second messengers in the cell
- transfer of GLUT4 glucose transporter proteins to the cell membrane to enable uptake of glucose
phosphorylation of Na+/K+ pump
- When the ion pump protein complex is phosphorylated a protein conformation change enables three Na+ to bind and be translocated out of the cell
- When the ion pump is dephosphorylated a protein conformation change enables two K+ to bind and be translocated into the cell
- phosphorylation is achieved as a result of the hydrolysis of a high energy phosphate bond in ATP
hydroxylation PTM
- addition of hydroxyl groups to Pro at 3’ and 4’, and Lys at 5’
- Present in collagen to hold skin and muscles together, strengthen bones and stabilise joints
- facilitates H bonding
- the more hydroxylation, the stronger the higher order collagen structure
- enzyme required is hydroxylase and cofactors Fe2+ and vit C
10 nonpolar amino acids
- glycine (Gly)
- Cysteine (Cys)
- Proline (Pro)
- Valine (Val)
- alanine (Ala)
- phenylalanine (Phe)
- leucine (Leu)
- isoleucine (Ile)
- tryptophan (Trp)
- Methionine (Met)
5 uncharged polar amino acids
- serine (Ser)
- Tyrosine (Tyr)
- Glutamine (Gln)
- Asparagine (Asn)
- Threonine (Thr)
2 negatively charged acidic amino acids
- aspartic acid (Asp)
- Glutamic acid (Glu)
3 positively charged basic amino acids
- lysine (Lys)
- Arginine (Arg)
- histidine (His)
supersecondary structure
- combinations of secondary structures
- e.g. helix-turn-helix, greek key
- form domains/motifs
- often have hydrophobic core, hydrophilic on outside
fibrinogen structure and function
- made up of 2 alpha, 2 beta and 2 gamma subunits linked by disulfide bonds
- thrombin hydrolyses parts of protein to make fibrin which forms mesh to form clot
what does warfarin do
has similar structure to vitamin K so interferes with gamma-carboxylation of blood clotting proteins, causing clotting disorders
gamma carboxylation
- leads to formation of gamma-carboxy glutamic acid (Gla)
- uses carboxylase enzyme with vitamin K cofactor
gamma carboxylation in blood coagulation pathway
- Glu to Gla leads to formation of bidentate Ca2+ binding sites
- allows blood coagulation proteins to interact with platelets as part of blood clot formation process
- e.g. factor IX, factor X and prothrombin
amino acid side chains that can form ionic bonds
Arg, Lys, His, Glu, Asp
amino acid side chains that can form hydrogen bonds
Arg, His, Glu, Asp, Thr, Ser, Tyr, Asn, Gln
