Protein Folding 1 Flashcards
What does secondary structure allow for protein folding?
Very efficient packing
What are the 4 determinants of protein folding?
Secondary structure, hierarchical folding, context dependent folding, and hydrophobic effect
How is folding hierarchical?
When an amino acid chain is formed, the amino acids near wash other will interact and form structures. Those amino acids that are far from each other will not form a structure together. There is an order of folding.
How does hydrophobic effect determine protein folding?
Non polar residues in the folding process go on the inside. There are crystalline molecules around the hydrophobic residues. When those hydrophobic molecules come together, it frees the water molecules and they go crazy (entropy) and cause delta G to be present. Provides the energy of associating and the energy for protein folding
What does the folding funnel depict?
Thermodynamics of protein folding. The top of the funnel represents all possible denatured conformations. As energy decreases the percentage of residues of protein in native conformation increases. As energy is low the protein is in its native structure
What are molten globules?
They are collapsed proteins and generally have some native-like secondary structure. All the secondary structure elements, motifs and to some degree the domains will be completely formed in milliseconds. Not complete functionally and some fine tuning still needs to be done
What formations happen as a protein goes down the folding funnel?
Rapid formation of secondary structure.
Formation of domains through cooperate aggregation (folding nucleus)
Formation of assembled domains (molten globule)
Adjustment of conformation
what is metamorphic (ensemble)?
one protein can be in two confrmations
What are IUPs?
Intrinsically unstructured proteins. They possess little or no ordered structure, having instead an extended conformation with high intra-molecular flexibility, lacking any tightly packed core.
Define the Chou-Fasman method
Empirical technique for the prediction of secondary structures in proteins
What is the Chou-Fasman method based on?
Method is based on analyses of the relative frequencies of each amino acid in alpha helices, beta sheets, and turns based on known protein structures solved with X-ray crystallography.
How are the frequencies used in the Chou- Fasman method?
A set of probability parameters were derived for the appearance of each amino acid in each secondary structure type, and these parameters are used to predict the probability that a given sequence of amino acids would form a helix, a beta strand, or a turn in a protein
A value greater than one represents the probability for what?
Strong tendency to form the corresponding structure/turn
What are the 5 amino acids that cause a reverse turn and why?
Glycine-has no substantial R group therefore it can rotate freely about the Phi and Psi torsional angles
Asp, Asn, and Ser have hydrogens that can hydrogen bond with other main chain hydrogens. Pro-does not have an amide bonding to participate in the backbone H bonding
What is the equation for relative frequency?
# of an amino acid appearance in a structure/ number of that amino acid in data base Example # alanine in alpha helix/# of alanine in data base
