Module 2 - Protein Structures Flashcards
Where would you expect to find polar and nonpolar amino acids in a folded globular protein?
Polar side chains are exposed on the surface, while nonpolar side chains are buried in the core
Where would you expect to find Gly and Pro in a folded protein?
Proline has a fixed bind angle, while Glycine without an R group offers a lot of flexibility. Hence, both amino acids can be found both in turns of the chain.
List features of folded proteins:
- Proteins are compact
- Water is generally excluded from the interior
- Nonpolar side chains are usually located inside the protein
- Polar side chains are usually located outside of the protein.
- if it’s inside, it usually forms a H bond
Explain why protein folding is said to be cooperative.
Protein folding is cooperative, in the sense that it is an all or none event (2 equilibrium states). If any part of the protein fold is disrupted, interactions with the rest of the protein structure are disrupted and will be lost. However, it should be noted that protein folding are reversible.
What forces drive protein folding? What are the role of these interactions?
- electrostatic forces
- van der Waals interactions
- hydrogen bonds
- hydrophobic interaction
These interactions combine to stabilise the folded state (native) to make it favoured compared to the unfolded (denatured) state.
Explain how Christian Anfinsen’s experiments showed that under appropriate conditions protein folding are reversible.
First, by adding 8M urea and beta-mercaptoethanol, the native ribonuclease becomes denatured with the sulfide bonds sites being reduced due to the beta-mercaptoethanol. Then, in the next experiment, he removes the urea first causing the protein to refold but without the sulfide bond rebinding, which only rebinds when the beta-mercapethanol is removed. In the final experiment, he switched the order at which the chemicals are removed, which cause the sulfide bonds to rebind randomly causing the protein tp re-fold in multiple possible variations. Hence, he showed that only under specific conditions (lab) protein folding can be reversed. He also discovered that disulfide bonds does not direct protein folding, where the opposite is found to true.
Describe the role of disulfide bonds in protein folding.
Disulfide bonds increase the relative stability of the folded state over the unfolded state (locking it into place). However, disulfide bonds don’t ‘direct’ protein folding, but rather the act of folding itself is directing disulphide bond formation.
Explain the role of protein folding chaperones in protecting unfolded proteins from ‘misfolding’.
Chaperones help avoid misfolding *by binding to temporarily exposed hydrophobic regions of the protein chain* to prevent them from interacting with the wrong partners/molecules.
Explain why protein is very vulnerable to misfolding.
Nascent polypeptide may misfolded as they comes off the ribosome, as the chain grows by sequential addition of amino acid residues to the C-terminal end of the chain. Due to this nature of chain elongation, uncompleted sections of the protein may bind with compounds in the cytoplasm or fold itself incorrectly.
List the forces driving the protein folding and explain.
Electrostatic Interaction:
- Ionic interactions between oppositely charged groups in proteins are called “salt bridges’
- Part due to electrostatic interaction, part due to hydrogen bonding - Exp. Arg and Glu
Van der Waals:
- Optimal distance (Where the interactive energy is minimum)
Hydrogen bonds:
- occurs when two electronegative atoms compete for the same hydrogen atom
- main component is electrostatic, as the dipole caused by the differing electronegativity between the H and the donor atom caused a partial positive charge in the H atom, which attracts with partial negative charged acceptor atom.
Hydrophobic interactions:
- interactions/attractions between non-polar groups/side chains
- case the removal of hydrophobic interactions with ordered water molecule (which is a favorable entropy state), increasing entropy (due to the unordered water molecule)
Explain the thermodynamic basis of the hydrophobic interaction and protein folding.
A favorable Gibbs free energy (negative) would be given by a negative enthalpy change and a positive entropy change. However, it turns out that the hydrogen bonding of polar residues and the backbone is satisfied both in an unfolded state (by water) and in a folded state (by each other), therefore in most cases, enthalpy change is negligible. As a consequence, entropy must be the force that drives protein folding. Positive entropy change is a result of hydrophobic interactions between the hydrophobic side chains. When these side chains bind, the ordered water molecules that bind with them are released becoming unordered, increasing entropy. Hence, it can be concluded that hydrophobic interactions (ergo, entropy) drives protein folding.
List the different regions of the Ramachandran plot.
- alpha, beta, left handed turn (L), disallowed (D)
Mention the two most common secondary structures and explain them in respect to the Ramachandran plot region.
Alpha helix: made up of consecutive residues (amino acids) in the alpha region of the Ramachandran plot & stabilized by H-bond between residues nearby in the sequence
Beta sheet: made up of consecutive residues in the beta region & stabilized by H bind between adjacent segments that may not be nearby in the sequence.
How can a protein exposed to high concentrations of urea become unfolded?
Urea (CO(NH2)2) is a very polar molecule that can act as both a hydrogen bond donor and acceptor. Hence, it disrupts the hydrogen bonds between the amino acid chain itself by attaching to the sites instead causing it unfold.
List the structural properties of alpha-helices
- 3.6 residues per turn
- 0.54 nm per turn
- side chains project outwards from helix axis
- right-handed abundantly -
- NH (residue i) to CO (residue i-4)
- phi= -57 degrees
- psi= -47 degrees
- peptide bond dipoles add together giving a macrodipole
The macrodipole in the alpha-helix cause a partial _______ in the amino terminus and a partial ________ in the carboxyl terminus.
positive charge, negative charge
Explain how amino acid sequence (residues) affects helix stability.
- Small hydrophobic residues such as Ala and Leu are strong helix formers
- Pro acts as a helix breaker because it lacks the NH hydrogen bond donor
- Gly acts as a helix breaker because the tiny R group doesn’t contribute to stability of helix -
- Interactions (attractive or repulsions) between side chains 3 or 4 amino acids apart will affect formation.
Explain the difference between a beta-strand and a beta-sheet.
Beta-sheets consists of two or more beta-strands. The strand is the element.
List the structural properties of beta-sheets.
- Planarity of the peptide bind and tetrahedral geometry of the alpha carbon create a pleated sheet-like structure
- Strands are either parallel or antiparallel to neighbouring strands - can be pure or mixed
- phi= -130 degrees
- psi= 130 degrees
- Twisted sheets are abundant
- H-bonds between the NH and CO of neighbouring strands
Explain how a beta-sheet can have a hydrophilic and hydrophobic face.
An example of a conformation of beta sheets that allow this property is a beta barrel. Hydrophobic side chains are packed into the core of the barrel, while the hydrophilic side chains project outwards into the solvent. This is obtained through alternating hydrophobic/hydrophilic residues.
Hydrogen bonds between the antiparallel beta strands are _____ compared to the parallel strands because they are linear.
stronger
List the structural properties of reverse turns.
- Turn occurs frequently when β sheets change direction
- 180 degrees turn accomplished over four amino acids.
- Turn is stabilized by a hydrogen bond from a carbonyl oxygen of position 1 to amide hydrogen of position 4 in the turn (i and i+3)
- Proline in position 2, glycine in position 3 are common
Explain the difference between type-I and type-II turns.
Type-I beta turn :
- proline in position 2 (phi= -60 degrees matches requirement of most beta-turns)
- right-handed turns
Type-2 beta turn:
- glycine in position 3 (positive phi)
- since R group in position 2 is pointed upwards, glycine is the most sterically accessible amino acid with only H as its side chain.
- left-handed turns
- direction of i+1 carbonyl differ from type 1
Define regular and irregular structures.
Regular structures:
- is defined as residues that have repeating phi and psi angles (consecutive residues).
- stabilized by a repeating pattern of H-bonds.
Irregular structure often:
- links regular elements - is termed ‘loop’ or ‘random coil’ structure.
- residues that do not have repeating phi and psi angles (consecutive residues).
List the structural properties of proteins.
- peptide bonds is usually trans, planar, and rigid
- limitations on the dihedral angles that the main chain can adopt (Ramachandran Plot)
- repeating phi, psi angles are characteristics of observed secondary structures
- all buried polar groups forms hydrogen bonds
- proteins are compact because of favorable VDW contacts and hydrogen bonds
Describe the three common super-secondary structures.
A supersecondary structure is a compact three-dimensional protein structure of several adjacent elements of a secondary structure that is smaller than a protein domain or a subunit.
Explain the difference between the primary, secondary, tertiary, and quaternary protein structure.
Primary: amino acid residues
Secondary: alpha helixes, beta sheets, turns
Tertiary: polypeptide fold chain (domain, folds, modules) & refers to the overall spatial arrangement of atoms in protein
Quaternary: assembled subunits of polypeptide chains
What is a domain?
It is a region within the native tertiary structure that can fold independently with a corresponding function.
What is a protein fold?
It is defined by the arrangement of secondary structure elements relative to each other in space. The same protein fold group may consist of multiple domains.
Domains may be grouped according to their fold type.
What’s unique about a module?
Modules have one or more repeating fold type within their overall structure. Each fold group consists of multiple domains. It should be noted that protein domains are considered modular units at which proteins are built.
Define domain in terms of structure and evolution
Domain can be defined as an evolutionary unit rather than a structural unit, where no new domains are being created, only modified and readjusted. This implies that domain can have a common protein ancestor.
Describe the generic processes that create protein with different functional properties using existing domain structures
- Intragenic Mutation: point mutations, insertions, deletions
- Gene duplication: whole or part of gene is duplicated
- DNA segment shuffle: two or more existing genes can be broken and recombined
- Gene lateral transfer: one organism acquires parts of the genome of another
Explain what is meant by the statement that protein sequences can be optimally aligned.
Protein sequences can be aligned based on identical and similar residues. Alignments can be improved by introducing gaps that account for past residue insertions and deletions.
Explain the link between sequence identity, ancestry, and structural similarity
Structure changes more slowly than sequence. If two protein sequences show more than 25% identity similarity (homologues), it will be structurally similar. This also implies that homologues share a common ancestor noted the fact that they have a similar fold.
Define homologue, orthologue, and paralogue
If two sequences show >25% identity, the protein domain are considered as homologues.
Homologues can be divided into two groups:
- Orthologue: homologous protein that performs the same function in different species
- Paralogue: homologous proteins that perform different but related functions within one organisms.
Explain how alpha helixes can be amphipathic.
Alpha helixes can be amphipathic in the sense that one side contains mainly hydrophilic amino acids and the other side contains mainly hydrophobic amino acids. This is possible due to the alternating sequence between hydrophilic and hydrophobic residues every 3 to 4 residues, since the α helix makes a turn for every 3.6 residues.
