Lecture 5 - protein structure and function 2 Flashcards
what is an Alpha helix?
A common structural motif.
Hydrogen bonds between every N-H group and the C=O group in the turn of the helix, four amino acids down the chain.
3.6 residues/turn.
Always right-handed.
R-groups point outwards - cf. later.
Proline residues are helix-breakers
what is a beta-sheet?
Unlike the α helix, the ß sheet is formed by hydrogen bonds between protein strands, rather than within a strand.
The amino acids are more extended than in an α-helix.
The R-groups alternate above and below the plane of the sheet.
Hydrogen bonds are formed across the strands.
Sheets may be parallel or anti-parallel.
what is a beta turn?
These allow polypeptide chains to turn abruptly and go in the opposite direction.
Allows proteins to attain a compact (globular) shape.
Pro and Gly are commonly found in such turns, proline because of its cyclic structure and glycine by virtue of its small size making it flexible
what is a tertiary structure?
The overall three-dimensional structure of a polypeptide is called its tertiary structure. The tertiary structure is primarily due to interactions between the R groups of the amino acids that make up the protein.
R group interactions that contribute to tertiary structure include hydrogen bonding, ionic bonding and van der Waals forces.
Also important to tertiary structure are hydrophobic interactions, in which amino acids with nonpolar, hydrophobic R groups cluster together on the inside of the protein, leaving hydrophilic amino acids on the outside to interact with surrounding water molecules.
Disulphide bonds are covalent linkages between the sulphur-containing side chains of Cys; much stronger than the other types of bonds that contribute to tertiary structure (and sometimes quaternary).
how and why does a protein fold?
Anfinsen showed that a protein can re-fold into its active configuration after denaturation, without any external guidance.
Amino acid sequence (primary structure) contains all the information required for a protein to fold.
Proteins fold to the lowest free energy conformation.
Linear chains of amino acids have multiple possible conformations so high entropy. As folding proceeds, both free energy and the entropy decrease to a minimum
It is thought that hydrophobic interactions and hydrophilic interactions drive the early steps in folding. Proteins bury hydrophobic residues in an interior ‘core’.
Most proteins begin to fold during translation (more in a moment).
Molten Globule - a partially folded protein state.
van der Waals forces help the atoms in a protein pack together.
Natural selection has strongly favoured protein sequences that have a single conformation that form easily and seldom makes mistakes (think α-helix, ß-sheet)
what is a molten globule?
a partially folded protein state: conserves a native-like secondary structure content but without the tightly packed protein interior
what is the hydrophobic effect?
The hydrophobic effect is the observed tendency of non-polar molecules to aggregate in water.
The hydrophobic effect is an indirect effect resulting from a peculiarity of water structure. Water molecules exchange hydrogen bonds with neighbours at a rate of about 1011 s-1.
At the interface between water and a non-H-bonding group such as a methyl group, CH3, water molecules have fewer opportunities for H-bond exchange leading to longer than usual lifetime of H-bonds, an ice-like state at the interface, and consequent decrease in entropy.
Thus water at the interface is rotationally and translationally constrained.
is myoglobin hydrophobic or hydrophilic?
the protein core consists of primarily hydrophobic residues
Water molecules adjacent to this would be rotationally constrained - entropically bad news!
what happens when protein folding goes wrong?
Amyloid plaques
Aberrant protein folding
eg alzheimers
what is a domain?
Domains are a conserved part of a protein structure that can evolve, function and exist independently.
They are an independently folding unit of a polypeptide chain that usually carries specific function. Vary from 25 - 500 amino acids in length.
Many proteins consist of different domains linked together.
Because they fold independently, it is ‘easy’ to move these between different proteins either by evolution or genetic engineering.
In molecular evolution such domains may have been utilised as building blocks, and may have been recombined in different arrangements to modulate protein function through evolution.
what is a protein domain?
A protein domain is 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.
Many proteins have multiple domains linked together. ~75% of eukaryotic proteins have multiple structural domains.
Each domain forms a compact three-dimensional structure and often can be independently stable and folded.
Genome sequencing information and structural studies have revolutionised our understanding of protein structure - bioinformatics.
Domains begin to fold as soon as they have been synthesised.
what are outliers, oddities and scientific curiosity?
Known for years that chickens get cancer.
Mechanism unknown, but Rous identified a virus that can cause this cancer.
He studied this (for years) despite the fact that the kind of cancer it formed (sarcoma’s) are incredibly rare in humans.
His view (paraphrasing) is that outliers can teach us ‘stuff’. We tend as biologists to look at populations (with good reason), his thesis is that outliers can sometimes tell you far more
what are SH2 domains?
Structural studies of proteins in the late 1980’s revealed an unexpected similarity in protein primary sequence between the proto-oncogene, Src kinase, and a number of other proteins of different functions.
This similarity was observed in three domains, the kinase domain (more on this later), and two other domains called Src-homology-2 and Src-homology-3 domains: SH2 and SH3 domains.
Analysis of the sequences using bioinformatics began to reveal similarities…SH2 (and SH3) domains found in many other proteins!
>110 proteins in humans contain an SH2 domain
SH2 domains are structurally conserved…
SH2 domains can autonomously fold
Every known SH2 domain exhibits this arrangement of α-helix and ß-sheet
SH2 also exhibit regions of primary sequence conservation.
These characteristics apply to most protein domains and give rise to some important consequences
what is bromodomain?
Binds acetylate lysine residues
Characteristic protein fold
Structure allows us to identify key residues in addition to the acetylated lysine
Key residues identified from structural determination
A small molecule inhibitor of a bromodomain was identified in a drug screen.
Based on the structure of the inhibitor and the structure of the bromodomain it is possible to then model other molecules that might bind, since we know the arrangement of atoms at the AcK binding site (and nearby).
Possible to then predict other compounds that might bind, and which might be selective for variants of the bromodomain (i.e. different bromodomains in different proteins that control different aspects of histone reading activity).
This shows examples of drugs that target the Bromodomain family of proteins to make the point that domains, although having similar protein folds and recognisable homologous structures, are still sufficiently different to be selectively targeted
what is the structural hierarchy?
Folding of a monomeric protein follows the structural hierarchy of primary - secondary - tertiary.
The formation of the secondary structures and structural motifs occurs early in the folding process, followed by the assembly of more complex domains, which then associate into the tertiary structure.
what is the hydrophobic effect?
Hence, a key driver of protein folding is the minimising of entropy loss; clustering of hydrophobic residues (Ala, Trp, Val, Ile, etc.) within the ‘core’ of a protein is an important force in protein folding.
Forces to keep away from water can be as powerful as those attracting to water
the folded protein has hydrophobic core region contains non polar side chains and a polar side on the outside of the molecule can form hydrogen bonds to water
what is Varmus and Bishop won the Nobel in 1989?
They identified the viral oncogene - Src.
Src is only 1% of cancers…so whats the big deal?
First oncogene identified
The proto-oncogene is a tyrosine kinase!
c-Src (the viral form is known as v-Src)
Whole new area of biology
All came from studies of outliers, oddities and a burning curiosity
