PHYS 051 Physics Of Biological Sys

Question 1

13 Oct, 2017

9:40am-10:30am

Answer 1

• Assistant Professor
• Department of Physics
• Juan Vanega

Question 2

Physics / mechanic of biological sys @ nano-scale

Answer 2

• Cytoskeletal - structural proteins

- Lipid membrane - membrane proteins

Question 3

Computational “microscopy”

Answer 3

• Discover biological function - observe & interact w/ biomolecules
• Molecular dynamics (MD) simulations
  
  • Accurate physics-based models (QM & classical)
  • Explore dynamic processes + ensemble properties
  • High-performance computing for large sys
• Complex interaction: electrostatic force etc.
  > Understand the 1st principle: interaction btw individual molecules
  > Simulate to interaction btw a brunch of molecules

Question 4

MD in action: surfactant self-assembly

Answer 4

• CG surfactant: greasy part + hydrophilic head
• CG water
• W/ KE: greasy part attract each other;
  hydrophilic part attract each other

Question 5

Surfactant self-assembly vs. molecule geometry

Answer 5

1. Bilayer; 2. Michelle, 3. H-phase (cone shape)
   - PEG4 (simple)
   - PEG12 (cone)

Question 6

Essential roles of mechanosensation

Answer 6

• Conversion of external mechanical stimuli into electrochemical signals
• Mechanosensation is critical
  
  • Vascular pressure control
  • Osmotic regulation
  • Touch, hearing, mvt
  • Sensing changes in cell volume / shape
• Sensor @membrane > closed > membrane stretch > opened

Question 7

MscL: Bacteria’s emergency valve

Answer 7

• MscL regulates osmolarity
• Cell’s last resort before lysis
• Model sys for more complex MS channels
• Ref. Naismith & Booth. Annu Rev. Biophys, 41, 157-77 (2012)

Question 8

Stress & traction on MscL

Answer 8

• Simulate a small portion of the membrane
  > Protein: mechanical sensitive > stress observation
  > Protein behaviors under stress

Question 9

Stress “hot-spots” under tension

Answer 9

• Membrane stretch:

> Tension stress in diff parts

Question 10

MscL gated by pulling on bound lipids

Answer 10

• Ref: Vanega & Arroyo. PloS ONE, 9, e113947 (2014)

Question 11

Coiled-coil intermediate filaments

Answer 11

• Cell > cytoskeleton > full length filaments > unit-length filaments > tetramers > dimer > coiled-coil protein domain > alpha-helix domain > alpha-helical turn (H-bond clusters) > H-bond
• Cell is dead when temp changed in a few degrees
  > Pick particular lv of proteins> coiled-coils

Question 12

Coiled-coil pulling simulations

Answer 12

• Undergo phase transition

- Absorb lots of energy > temp does NOT change