Proteins and carbohydrates 4 Flashcards
What effect does applying an external force have on the energy landscape of a protein?
It reduces the activation energy of unfolding (of a protein) or unbinding (of multiple bonded proteins).
Describe the freely jointed chain (FJC) model used for understanding the force-extension behaviour of proteins.
Polymer is a chain of N perfectly rigid segments of length b.
No restriction on angles between adjacent segments; no energy is required to change the angles.
No interactions between segments (except end-to-end connectivity).
A tensile force tends to align the segments in the direction of the force.
Opposing the stretching is the tendency of the chain to maximise its entropy (a stretched-out chain has lower conformational entropy).
Describe the force range(s) at which the FJC model is accurate for describing protein backbones and the reasons for any inaccuracy.
The FJC model is accurate at low and high forces but inaccurate at intermediate forces. This is due to the following simplifications:
- Each Kuhn segment has a fixed length, is unstretchable and completely straight.
- No thermal fluctuations away from the straight line.
Describe the worm-like chain (WLC) model used for understanding the force-extension behaviour of proteins.
Like FJC but:
The polymer is semi-flexible.
The entropic elasticity of the polymer involves small deviations of the molecular axis due to thermal fluctuations.
Certain propensity of the chain to bend on the local scale (rather than rigid segments like in FJC). Amount of bending is limited.
How does the WLC model compare to the FJC in terms of accuracy in proteins?
The WLC is more accurate than the FJC for the whole range of applied forces.
What impact does the protein domain size (for proteins) or protein size (for polyprotein mechanical stability investigations) have on the force-extension graph?
A smaller protein domain or protein will have a F-e graph more squished in the x-axis (i.e. contour length decreases (if a protein)).
What effect will protein domain strength or protein strength have on the force-extension graph?
If the protein is weaker, the peaks will be shorter (i.e. the magnitude of the force peaks will be reduced) and vice versa.
What effect does applying a force on a protein have on its lifetime and the unfolding activation energy?
It reduces them (except for catch bonds). As the applied force on a protein increases, the lifetime and unfolding activation energy of the protein decreases.
What is the hydrophobic collapse model? Describe it.
The hydrophobic collapse model is the most accurate model for protein folding.
Folding begins by an initial fast clustering of hydrophobic residue side chains which prefer to be excluded from an aqueous environment (hydrophobic effect). The formation of an ensemble of collapsed structures drastically reduces the available conformational search-space. The ensemble of intermediate states then relatively slowly form into the folded protein.
The protein folding process only takes a few seconds.
Why do some proteins not follow the Bell model?
Due to the presence of catch bonds in some proteins. The dissociation lifetime increases with force until the force reaches a critical maximum where the dissociation lifetime starts to decrease with applied force. At a certain critical force, the system reaches its maximum stability and switches to an alternative dissociation (separation/splitting) path (slip dissociation path).
What are kinesins and dyneins?
Motor proteins that move and pull vesicles along microtubules using ATP as fuel.
What method is used to measure motor protein step length and duration at 0 or higher forces and why?
Optical tweezers due to their high sensitivity to low forces.
What is the amount of steps, step size and maximum speed of motor proteins?
Motor proteins take about 100 steps (all in the same direction) before detaching.
About 8nm (few nm-10nm).
800nm/s (very fast).
How do kinesin respond to mechanical load?
Kinesins can walk against mechanical load but are slowed down by it.
Motor stops at 7pN load. Larger load (≥7pN) causes motion in the opposite direction.
What are catch bonds?
A type of bond whose dissociation lifetime increases with applied tensile force.
