Week 8 (Proteins II) Flashcards
What is the tertiary structure?
The tertiary structure of a protein is the overall 3-dimensional arrangement of all atoms in a polypeptide chain.
- The way in which the α-helices and β-sheets fold up together to form a compact structure.
- Amino acids which are far apart in the amino acid sequence may end up close to each other in the final folded structure.
- Stabilised by multiple weak interactions.
What is the main factor in driving folded structure?
- The main factor in driving folded structure is the hydrophobic effect.
- Most proteins are in aqueous environment.
- Hydrophilic side chains stick out into the water.
- Hydrophobic side chains bury in the core away from the water.
What determines protein folding?
Proteins fold into the lowest energy conformation (shape)
Describe Non-covalent stabilising interactions
- Van der Waals between hydropjobic side chains
- Ionic bonds (electrostatic attraction) between oppositely charged side chains
- Hydrogen bonds between polar side chains
What are prosthetic groups?
A non-protein group forming part of or combined with a protein
- termed prosthetic groups, co-factors or co-enzymes
- Tightly bound into the 3-D structure of the protein
- Can be critical for function
- Examples include haem groups, metal ions, lipids
Hydrophobic effect example – horse heart cytochrome C
Hydrophobic residues burried inside the protein core whereas the hydrophilc residues produe outward
Hydrophobic effect example – myoglobin
Again, hydrophobic residues burried inside the protein core whereas the hydrophilc residues produe outward
What are protein motifs?
A motif or fold is a recognisable folding pattern involving 2 or more secondary structure (supersecondary) elements for example:
- helix loop helix→The motif is characterized by two α-helices connected by a loop
- coiled coiled → in which 2–7 alpha-helices are coiled together like the strands of a rope
- Helical bundle → composed of several alpha helices that are usually nearly parallel or antiparallel to each other
- Beta-alpha-beta (β-α-β) → parallel beta-strands are connected by longer regions of chain which cross the beta-sheet and frequently contain alpha-helical segments
- Beta hairpins → short loop regions between antiparallel hydrogen bonded beta-strands
- Greek key → four adjacent antiparallel strands and their linking loops
- β-meander→ 2 or more consecutive antiparallel β-strands linked together by hairpin loops
What kind of protein motifs are there?
- Ranges from very simple motifs such as β-α-β loop to elaborate structures such as the β-barrel
- Can represent only a small part of the protein or the whole structure.
- Several motifs can join together to create larger common folds.
What are protein domain?
- A conserved part of a given protein sequence and tertiary structure that can evolve, function, and exist independently of the rest of the protein chain.
- Each domain forms a compact three-dimensional structure and often can be independently stable and folded into a compact structure.
What are large single polypeptide proteins that often fold into two or more domains joined together by?
flexible linkers
Do different domains may have distinct functions?
Yes
Describe the domains of cell surface protein CD4?
Cell surface protein with as 4 similarly folded immunoglobulin (Ig) domains (D1-D4), a transmembrane domain and a cytoplasmic tail domain
Src, comprises a C-terminal protein kinase domain. How many regulatory domains does it have?
Two
Example protein structures: α + β
α and β regions somewhat segregated
Example protein structures: α/β
α and β segments interspersed or alternating
What are protein families?
Give an example
- Many proteins can be grouped into families, having similarities in amino acid sequence and structure, yet distinct functions.
- Folded stable proteins with useful properties have been modified during evolution to enable new functions to be carried out.
Elastase and chymotrypsin are members of the serine protease family therefore have very similar structures.
What is the Quaternary structure?
The quaternary structure of a protein is when multiple polypeptide chains join together to form multisubunit structures.
- Can range from two polypeptides to hundreds.
- Often termed oligomers.
- Each separate chain is called a subunit.
- Stabilised by the same types of multiple weak interactions as tertiary structure.
From dimers to huge multisubunit assemblies
Simplest form of quaternary structure is a dimer.
- Can be homo-oligomers or hetero-oligomers.
- Can often form symmetrical or repeating structures.
Describe the quaternary structure of Haemoglobin
A tetramer comprising two α subunits and two β subunits
Describe the nature of disulphide bonds
- Cysteine residues have unique chemistry.
- Two cysteines in close proximity will form a disulphide bond.
- Disulphide bonds are covalent cross-links between the sulfhydryl (SH) side chains.
- An S− anion from one sulfhydryl group acts as a nucleophile, attacking the side chain of a second cysteine to create a disulfide bond
- They significantly stabilise protein structure and facilitate folding progression toward the native state by limiting unfolded or improperly folded conformations
What are intrachain disulphide bonds?
Between two cysteines in the same polypeptide chain
What are interchain disulphide bonds?
Between cysteines in different polypeptide chains
Why does Protein denaturation occur?
Protein folded structure held together predominantly by many weak forces
What factors can cause protein denaturation?
Heat, extreme pH, detergents, urea or guanidium chloride can all disrupt these interactions and cause denaturation of your protein
What can protein denaturation result in?
Results in loss of function – because function is dependent on 3D folded shape
What can break disulphide bonds?
Disulphide bonds can be broken using reducing agents such as dithiothreitol or β-mercaptoethanol
When you remove the denaturant, can the protein re-fold back into its structure and regain biological activity?
Yes and this is called renaturation
Is denaturation always permanent?
No
Protein folding
- Polypeptides fold rapidly by a stepwise process.
- Polypeptides fold into their 3D structure whilst still on the ribosome, co-translational.
Define co-translational
Polypeptides fold into their 3D structure whilst still on the ribosome, co-translational
Amino acid sequence defines structure – genetic disease: Cystic fibrosis
Small mutations in genetic sequence can have quite dramatic effects on the protein produced
One of the most common genetic diseases
- 70% of cases results from deletion of the codon for F508 of the cystic fibrosis protein
- A single amino acid missing form a protein of 1480 amino acids
- Mutation affects the way the protein folds, it isn’t at all stable, and just gets degraded in the ER.
- No functional protein – patient gets ill
Amino acid sequence defines structure – genetic disease: Sickle cell anaemia
A single nucleotide mutation (A→T) in the gene encoding Haemoglobin
- Results in substitution of a hydrophilic amino acid (E- Glutamic acid) for a hydrophobic amino acid (V-Valine)
- Causes the haemoglobin proteins to aggregate
- Distorts the shape of red blood cells – they get destroyed more quickly than usual.
