L3: Determinants of Protein Structure Flashcards
What sort of shapes and sizes can proteins come in?
Globular, linear, porous, associated with other molecules etc
Why can protein shape differ?
All different proteins have different functions to carry out in a cell - need to interact with different things, so shape varies to fit a specific function
What is an example of two common, but different environments a protein may need to work within?
- Intracellular = primarily aqueous but has different proteins, salts, etc
- Extracellular = salts and other molecules different to the ones intracellularly
Name 3 examples of where specificity of function is related to shape
- Receptor-ligand interaction
- Antibody-antigen interaction
- Enzyme-substrate interaction
What determines the shape of a protein?
- The sequence of amino acids is the main determinant of a protein’s shape - encoded within the nucleic acid
- This is driven by the DNA and the gene the protein sequence comes from
What are the levels of protein structure?
What characteristic is determined by the Levinthal Paradox?
- Proteins must always fold in ‘pre-arranged’ pathways and in a cooperative manner
- Must be limitation in folding geometry and hydrophobic interactions
- Otherwise a limitless number of potential folding possibilities
What restricts the shapes that can form from an amino acid structure?
- The chemical properties of the atoms and the peptide bond restricts the number of possible shapes
- Non-covalent bonds/interactions between amino acid side chains constrain the folding of the protein
How do hydrophobic associations drive protein folding?
- Non-polar (hydrophobic) amino acid side chain are repelled by water and cluster together in the centre of a protein
- The polar (hydrophilic) amino acids conform on the outside of the non-polar centre - attracted to water
- H bonds form between the polar side chain on the outside of the molecule
- Hydrophobic interactions drive (spontaneous) folding of proteins in aqueous environment
How does clustering of the hydrophobic side chains drive further interactions and folding?
Clustering of hydrophobic side chains in the centre of the protein allows residues involved in non-covalent and covalent interactions to come close enough for these interaction to occur (between amino acid side chains)
What are the two types of secondary protein folding?
- Alpha helix
- Beta pleated sheet
Describe the structure of the alpha helix
- Folding pattern resulting in a helical shape
- Hydrophilic side chains on the outside and available to interact with water with hydrophobic in the centre
- Stabilised by interactions between molecules close enough to form a bond e.g. H bonding
- Intra-strand interactions of amino acid backbone
Describe the structure of beta pleated sheet
- Folding pattern resulting in a kinked sheet structure
- Hydrophilic side chains on the outside and available to interact with water with hydrophobic in the centre
- Stabilised by interactions between molecules close enough to form a bond e.g. H bonding
- Inter-strand interactions of amino acid backbone
What structure can form from the association of many alpha-helices?
- BAR domains
- Binds to curved membranes
What structure can form from the association of many beta-sheets?
- Beta-barrels
- Often associated with membranes and insertion into membranes
What are the 4 types of non-covalent interaction?
- H bonding
- Ionic bonding
- Van der Waals interactions
- Hydrophobic interactions
What is a H bond?
A hydrogen bond is the electrostatic attraction between two adjacent polar molecules
- Directional (impart geometry ) to drive secondary structure
Which two elements can form hydrogen bonding? Why?
-Nitrogen and oxygen
- More electronegative than hydrogen so the electron cloud is shifted slightly more towards the N or O than H (decentralisation of the electron cloud)
- Forms a slight positive charge on H and a slight negative charge on N or O
- Means the slight positive charge on the H is attracted to the lone pair on the N or O
Why do lots of H bonds form between amino acids in protein folding?
High volume of N and O in amino acids - perfect for H bonding
What is an ionic bond?
Electrostatic attraction between a metal and non-metal, formed from the transfer of electrons, to form a giant ionic lattice structure
How do the ionic bonds form in protein folding?
- Some amino acids have side chains containing carboxylic acids groups (e.g. Glutamic acid &
Aspartic acid) - Some amino acids have side chains containing amine groups (e.g. Lysine & Arginine)
- An ionic bond can form between these by transfer of the H from negatively charged carboxylic acid (COOH) and the positively charged amine group (NH2)
- Forms an electrostatic attraction
- Ionic bonds stabilise the structure
What is important to remember about groups involved in ionic bonding?
Because these are ionisable groups, with a defined pKa, the pH of the environment is important for their formation
What are Van der Waal interactions?
- Electron cloud around an atom is constantly fluctuating
- Means a fluctuation in the charge distribution around an atom (both positive and negative charges)
- These small/slight charge difference between atoms gives rise to attraction or repulsion between atoms
- Weak intermolecular forces on their own, but when combined these form a strong electrostatic attraction which helps maintain and stabilise protein structure
What can hydrophobic interactions allow the formation of?
- Multiple protein subunits can combine together to form multimeric proteins
- Regions of hydrophobic amino acid side chains on the exterior of a folded protein may form the contact sites for other proteins
- Once the subunits come together the hydrophobic regions are protected from the cytosolic regions
What is a leucine zipper?
- A non-covalent way of helping the protein monomers come together to facilitate DNA binding
- The alpha-helices form with a leucine residue all on one axis of the helix (leucine every second turn of the helix [every 7th amino acid])
-Able to bind to another protein that is also hydrophobic along that leucine binding site - Forms a structure which DNA can bind to
What are the covalent bonds which can form in proteins?
- Disulphide bridges
- Formed between adjacent amino acids that have a sulphur atom in their side chains
- The oxidation of sulfhydryl groups on the amino acid cysteine gives rise to the formation of a disulphide bridge
Why can disulphide bridges form?
The sulphur atom can either be in a reduced or an oxidised state, either have a hydrogen bonded to it, or not have a hydrogen bonded to it
What biological structure is heavily reliant on disulphide bridges?
Antibodies -hold the light and dark chains together and helps form the binding sites
What is the benefit of having multiple weak non-covalent interactions cooperating?
- Strong electrostatic attraction within a protein or between proteins/binding sites, resulting in an increase in stability
- Allows a high specificity of the interaction, to be selective on what can interact within the binding site
How does temperature affect the bonding in a protein?
Increased thermal energy disrupts the H bonds and other weak interactions, increasing the overall kinetic energy in the system, and disrupting the bonds; denaturing the protein
How does pH affect the binding in a protein?
Changing the pH, changes the ionisation state of the sidechains, meaning the charge of the amino acids changes. This prevents sidechains interacting, disrupting the ionic bonds and the binding of the protein
How does salt concentration affect the binding in a protein?
- A high salt concentration replaces the interactions between side chains with interactions with the salts, disrupting the electrostatic interactions like H bonding and the hydrophobic effect, denaturing the protein.
- Chaotropic agents that can do this are urea, imidazole and guanidinium
How do these different factors affect the structure of the protein?
Interfere with the side chains, and disrupt protein structure and shape, denaturing the protein. These do not break the peptide bonds and leave the primary structure unaffected
What is the second law of thermodynamics?
The Law of increasing entropy
What does the second law of thermodynamics state?
The universe is always moving towards a greater state of disorder (or entropy)
Anything that happens spontaneously (without energy input) results in molecules becoming more spread out or disordered
What is Gibbs free energy?
The maximum useful work obtainable from any reaction e.g. the change in the free energy of a particular process
What endergonic and exergonic?
- Endergonic is when energy is required in a reaction/process or work is done - energetically unfavourable e.g. pushing a weight up a hill
- Exergonic is when energy is not required in a reaction/process and there is loss of potential energy of the position - energetically favourable e.g. a weight falling down a hill
How does the favorability of a process change when delta G changes?
What is the equation for Gibbs free energy?
Define enthalpy
- Energy content of a system
- Sum of all of the bonds holding a particular structure in place or need to be in place for a structure to form
- Energy released or required due to non-covalent interactions
What non-covalent interactions does enthalpy include?
- Ionic bonds (peptide bonds, S-S)
- Electrostatic bonds (-COOH—NH2)
- Hydrogen bonds
- van der Waals interactions
Define entropy
Change in molecular freedom (disorder)
associated with process (+ve AS = disorder)
What processes drive entropy?
Hydrophobic effect (water)
What is the temperature in gibbs free energy?
The temperature at which the reaction occurs - at an absolute temperature (K)
How do the amino acids on the disordered protein chain avoid interaction with water?
- Form hydration spheres around the hydrophobic non-polar amino acid side chains
- These are water molecules which align around the non-polar amino acid side chains to lower the energy - still a fairly ordered structure
Why is a folded protein in a more disordered state than the unfolded protein chain?
- The water interacting with non-polar amino acid side chains are released from the hydration spheres - the hydrophobic amino acids are clustered together in regions that are not interacting with water
- Water molecules gain entropy as they are more ‘disorganised’ - means overall entropy of the system (protein and solvent) increases
Is the enthalpy positive or negative for protein folding?
- Negative - energy is released
- Forming the non-covalent interactions
Is Gibbs free energy (delta G) positive or negative for protein folding?
- Positive
- Overall entropy increases as the protein folds (S is positive)
- Energy is released by the formation of non-covalent bonds (H is negative)
- When combined the enthalpy is greater than entropy, so delta G is negative (Favourable system)
If delta G is negative what does this mean?
Protein folding can occur spontaneously
What value of delta G will proteins aim for?
Aim to fold to the lowest free energy so delta G is negative
