Topic 0: Intro Flashcards
1
Q
- Why do we care about dynamics?
A
- Molecular motions connect chemistry and physics to biology
- Evolution of molecular structure in time is key to understanding many complex biological processes
2
Q
- Describe the difference between overall and local motion in terms of a protein
A
- Overall motion is characterised by how local motion interact and depend on one another
- Examples of local motion might be a side chain flip, NH bond liberation of helix motion
- These in would all contribute to the Brownian motion of the molecule
- Assigning local contribution to the overall motion is very difficult
3
Q
- Explain the link between dynamics and thermodynamics of a molecule
A
- Motion connects the energy of the states of a molecule and the barriers between them
- A change in structure can will lead to these barriers shifting
- These barriers have an associated time scale
- Faster processes generally involve lighter species
4
Q
- Highlight some of the timescales that exist for various processes occurring in proteins and some of the methods that can be used to characterise them. Do this only for the ones we are concerned with in this sub-module
A
- Large timescale of motion accessible with many different methods required to access various regimes/processes
5
Q
- Give two examples of the importance of understanding the dynamics of a system
A
- Signalling: proteins take advantage of intrinsic dynamic properties to respond to incoming signal
- Allosteric regulation: binding elicits response far away in molecule at another site for a further reaction. Means distant sites within a protein can be energetically coupled, often dynamically
- Enzymatic catalysis: rate limiting step of an enzymatic process may be a loop blocking/opening active site. Knowing the dynamics of this may be key to understanding the reaction
6
Q
- Dynamics affect … and pathway of … folding as well as misfolding and … , which can catalyse an array of fatal neurodegenerative diseases.
- E.g. … misfolding in Alzheimer’s
A
- Dynamics affect rate and pathway of protein folding as well as misfolding and aggregation, which can catalyse an array of fatal neurodegenerative diseases.
- E.g. Aβ misfolding in Alzheimer’s
7
Q
- Give examples of NMR interactions affected by motion in size order (don’t need to know)
A
8
Q
(IMP) WHat are examples of anisotropic interactions? Describe the effect reorientation has on anisotropic effects
A
- CSA, dipolar, and quadrupolar coupling are anisotropic interactions
- They all depend on orientation of the molecule with respects to Bo
- This interaction is proportional to ½(3cos2x -1)
- Reorientation motion will affect what is measured in terms of anisotropic interactions
9
Q
- What are the methods of probing dynamical processes with NMR?
A
- Averaging of anisotropic interactions
- Chemical exchange (chemical reaction, conformational change)
- Modulation of anisotropic exchange, resulting in relaxation
- These are the three topics covered in this sub module
10
Q
Lecture 1 summary
- Molecular motions (how structure evolves in … ) are important for many biological processes, … … likely the most
- Interconversion between molecular conformations separated by large … … are typically slower (lower probability)
- NMR gives information about motions from …-…
- Different methods required to access … occurring on different time scales
- Motion can be characterised by time scale (… time), amplitude and …
A
Lecture 1 summary
- Molecular motions (how structure evolves in time) are important for many biological processes, enzymatic catalysis likely the most
- Interconversion between molecular conformations separated by large energy barriers are typically slower (lower probability)
- NMR gives information about motions from ps-s
- Different methods required to access motions occurring on different time scales
- Motion can be characterised by time scale (correlation time), amplitude and direction
