What is denaturation in proteins?
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Loss of three-dimensional structure with loss of activity.
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What is denaturation in proteins?
Loss of three-dimensional structure with loss of activity.
What are fibrous proteins?
Proteins that have elongated structures and are typically involved in structural functions.
What can some protein domains do in relation to the entire protein?
Undergo movements as a single entity.
What is ribonuclease?
A small protein that contains 8 cysteines linked via four disulfide bonds.
Does the C-terminus of p53 adopt the same fold for each interactor?
No, it adopts a different fold for each interactor.
What does AlphaFold2 identify among proteins?
Evolutionary signals across many species.
How does Computational Structure Prediction differ from experimental methods?
It uses algorithms and computational models rather than physical experiments to determine structures.
What type of conformation is silk produced by spiders primarily composed of?
Beta conformation.
What is an example of a protein with multiple binding domains?
Troponin C, which has 2 Ca++ binding domains.
What is Computational Structure Prediction?
A method used to predict the three-dimensional structure of proteins based on their amino acid sequences.
What are some methods for structure determination of proteins?
Techniques such as X-ray crystallography, NMR spectroscopy, and cryo-electron microscopy.
Why is the ribonuclease refolding experiment significant?
It earned Chris Anfinsen the 1972 Chemistry Nobel Prize.
What provides tensile strength in collagen?
Cross-linked triple-helixes.
What limitation does X-Ray Crystallography have concerning hydrogen atoms?
Cannot see hydrogens.
How are the properties of fibrous proteins related to their function?
The properties of fibrous proteins are directly related to their structural characteristics, which determine their functional roles.
Which amino acids are rich in the structure of spider silk?
Alanine (Ala) and Glycine (Gly).
What is a domain in the context of proteins?
An independently stable part of a protein.
What is a characteristic of the C-terminus of p53?
It is disordered but interacts with multiple different binding partners.
What are the major classes of proteins?
Fibrous proteins and globular proteins.
What is an oligomer?
A protein composed of a few subunits.
What are disordered proteins or domains?
Proteins that do not have a fixed or stable structure.
What type of interaction holds silk fibroin together?
Van der Waals interaction.
What type of tissue is collagen primarily found in?
Connective tissue such as tendons.
What are the tripeptide repeats in collagen?
G-X-P or G-X-Y (where Y is hydroxyproline).
What significant challenge does AlphaFold2 address?
It solves a 50-year-old grand challenge in protein structure prediction.
What is denaturation in proteins?
The alteration of a protein's structure, leading to loss of function.
Why is Computational Structure Prediction important in biology?
It helps in understanding protein functions, interactions, and the design of drugs.
To what types of proteins is AlphaFold2 applied?
Proteins without known structure.
What is calculated after collecting diffraction data?
Electron density.
What are the two most important secondary structures in proteins?
α helixes and β sheets.
What is the secondary structure of collagen?
Left-handed helical structure.
What are some factors that can denature proteins?
Heat or cold, pH extremes, organic solvents, chaotropic agents like urea and guanidinium hydrochloride.
What is protein folding?
The process by which a protein assumes its functional three-dimensional shape.
On what type of data was AlphaFold2 trained?
Experimental structures.
What determines the native conformation of ribonuclease?
The sequence alone.
What is a trimer?
A protein consisting of three subunits.
What is an example of a soft, flexible fibrous protein?
Silk fibroin (found in egg sacs, nests, webs).
Why doesn’t silk stretch?
Due to its tightly packed beta conformation.
What are chaotropic agents?
Substances like urea and guanidinium hydrochloride that can denature proteins.
What agents are used to fully denature ribonuclease?
Urea in the presence of 2-mercaptoethanol.
What type of regions are involved in the binding of p53's C-terminus?
Intrinsically disordered regions.
What is the first step in X-Ray Crystallography for protein structure determination?
Purify the protein.
What is the structure of silk fibroin?
Non-covalently held β-sheets.
What does protein function depend on?
Three-dimensional structure.
How many helices form a superhelix in collagen?
Three helices.
What does the term 'tertiary structure' refer to in proteins?
The overall spatial arrangement of atoms in a polypeptide chain.
What role does AlphaFold2 play in Computational Structure Prediction?
AlphaFold2 is an advanced AI system that predicts protein structures with high accuracy.
What is a dimer?
A protein made up of two subunits.
What is the second step in the X-Ray Crystallography process?
Crystallize the protein.
What is a major advantage of X-Ray Crystallography?
No size limits.
What is the structural hierarchy in proteins?
It refers to the organization of protein structure from primary to quaternary levels.
What technology does AlphaFold2 utilize?
Deep learning (AI).
What term describes a protein with multiple subunits?
Multimer.
What are globular proteins?
Water-soluble proteins that can also include lipid-soluble membranous proteins.
What is an example of a tough, rigid fibrous protein?
α-keratin (found in nails, horns, hair, and feathers).
What type of linker is found in collagen?
Flexible linker (Lys-HyLys).
What happens to the C-terminus of p53 upon binding to its partners?
It becomes ordered.
What happens when urea and 2-mercaptoethanol are removed from ribonuclease?
The protein spontaneously refolds, and the correct disulfide bonds are reformed.
What are the main challenges in Computational Structure Prediction?
The complexity of protein folding and the vast number of possible conformations.
What is a tetramer?
A protein composed of four subunits.
What is a disadvantage of X-Ray Crystallography regarding membrane proteins?
It is difficult for membrane proteins.
What is the quaternary structure of a protein?
The assembly of individual polypeptides into a larger functional cluster.
What are the characteristics of fibrous proteins?
Typically insoluble and made from a single secondary structure.
What is the structure of α-keratin?
Cross-linked α-helixes.
What is collected after crystallizing the protein in X-Ray Crystallography?
Diffraction data.
What is the final step in fitting the protein structure using X-Ray Crystallography?
Fit residues into density.
