Tutorial 7 Protein Folding Flashcards
Protein folding is a thermodynamically favored reaction which will result a stable protein. Comment on the above statement
Protein folding must be thermodynamically stable within a cell. Protein folding must be thermodynamically favorable within a cell in order for it to be a spontaneous reaction. Since it is known that protein folding is a spontaneous reaction, then it must assume a negative Gibbs free energy value.
Unfolded state: it is there thermodynamically unstable. there are unfavored interaction. It has high energy and unstable,
Folded state: low energy state, stable state, less interaction, arrangement is at hydrophilic from outside and hydrophobic from inside.
What is the use of sharp transition state during the protein folding process?
The sharp transition suggests that protein folding and unfolding is an “all or none” process that results from a cooperative transition.
Most protein show a sharp transition from the folded to the unfolded form with a froward equilibrium because reaction is spontaneous and transient
Protein is half folded, 50% folded and 50% unfolded are there. Protein cannot switch from completely unfolded state to native state in one step, hence there is a transient intermediate that is existing between native and denatured state.
Describe the importance of Levinthal’s paradox in protein folding?
This paradox clearly reveals that proteins do not fold by trying every possible conformation, instead they follow a least a partly defined folding pathway consisting intermediates between the fully denatured protein and its native structure.
Differentiate the prediction models of 3-D structure of proteins for the ab initio model and the comparative model?
Ab initio model predict the folding of an amino acid sequence without prior knowledge about similar sequences in known protein structures unlike comparative model. Comparative model uses an amino acid sequence of unknown structure and is examined for compatibility with known protein structures. If a significant match is detected, the known structure can be used as an initial model.
What type of bonds are found in the primary structure of a protein?
Peptide binds
Disulfide bonds
When a protein is transferred to a solution with a pH that is much lower than its optimal range, what are the levels of protein structure that could affect to its native structure
Ionic interaction, protein shape will change. Decreasing the pH by adding an acid converts the –COO- ion to a neutral -COOH group. In each case the ionic attraction disappears, and the protein shape unfolds.
What is the fate of unstructured proteins in the human body?
- Protein aggregation
- Pathological conditions, diseases
There are some diseases that are associated with the misfolding of the proteins. Select one disease condition and mention its physiological characteristics?
Bovine spongiform encephalopathy:
The agents causing these diseases are termed prions.
Prions are composed largely of a cellular protein called PrP which is normally present in the brain.
The infectious prions are aggregated forms of the PrP protein termed PrP SC.
Briefly mention the steps of the protein folding studies using the x-ray crystallography?
Step 01 - Protein crystallization: Preparation of a protein or protein complex in crystal form.
Step 02- X-ray exposure: When a narrow beam of x-rays is directed at the protein crystal, most of the beam passes directly through the crystal while a small part is scattered in various directions. These scattered x-rays can be detected by x-ray film/solid state electronic detector. The scanning pattern provides abundant information about protein structure and its folding.
Step 03- Reconstruct an image of the protein
In electron microscopy, diffracted beams are focused by lenses to directly form an image. As there is no appropriate lenses for focusing x-rays, the image is formed by applying a mathematical relation called Fourier transform.
The image obtained is referred to as electron density map.
Proteins that have a particularly complicated or unstable conformation that have difficulty of achieving their native state. What are the natural mechanisms present in the human body on assisting the protein to achieve the native folding? Explain its function?
Specialized proteins called molecular chaperones help these proteins find their native functional conformation. Chaperones interact with the unfolded proteins or partially folded proteins and they are assisting these proteins to their native state.
Energy funnel describes the energy changes occurred during the protein folding processes. Briefly explain the concept of energy funnel model starting from unfolded protein to native folded protein
The energetic funnel limit the conformational space that the unfolded protein has to explore and force the protein to follow a funnel-like energy landscape that allows it to fold quickly. Hydrophobic interactions are going to be interior, remaining side chains are going to stabilize from the outside. The information needed for proteins to fold in their correct minimal-energy configuration is coded in the physiochemical properties of their amino acid sequence. The proteins follow the correct funnel and fold rapidly because amino acids interact locally and are able to find its native state.
For the protein studies, a trending new technology is used which is MALDI-TOF. Mention the use of this technology on identification of protein?
One of the main uses of MALDI-TOF-MS is in the identification of proteins, by peptide mass fingerprinting (PMF) which is protein identification method.
