Download Protein conformation and energetics

20 amino acids
Deceptive---packing is critical
Solution crystal structure of the prion monomer
…to Discovery Studio
monomer
Dimer (domain swapped)
Expression and crystallization.Human prion protein (90–231)was expressed in E. coli,
refolded and purified as described.Crystals, obtained at 20 °C by vapor diffusion with
protein at 5 mg/ml and reservoir consisting of 0.1 M Tris-HCl, pH 8, 3 M NaCl and 5
mM CdCl2, were stabilized with 2,4-dimethyl-2,4-pentanediol prior to data collection
at –180 °C.
Energy and Stability
A
B
If A is favored over B then A is at lower energy…how much lower?
𝑎𝑚𝑜𝑢𝑛𝑡 𝑜𝑓 𝐴 −∆𝑒𝑛𝑒𝑟𝑔𝑦
=𝑒 𝑅𝑇
𝑎𝑚𝑜𝑢𝑛𝑡 𝑜𝑓 𝐵
RT is thermal energy…the temperature converted into energy units by “R”
𝑎𝑚𝑜𝑢𝑛𝑡 𝑜𝑓 𝐴 −∆𝑒𝑛𝑒𝑟𝑔𝑦
=𝑒 𝑅𝑇
𝑎𝑚𝑜𝑢𝑛𝑡 𝑜𝑓 𝐵
RT is thermal energy…the temperature converted into energy units by “R”
Our body temperature: 37C or 310 Kelvin or 2600 Joules
𝑎𝑚𝑜𝑢𝑛𝑡 𝑜𝑓 𝐴 −∆𝑒𝑛𝑒𝑟𝑔𝑦
=𝑒 𝑅𝑇
𝑎𝑚𝑜𝑢𝑛𝑡 𝑜𝑓 𝐵
RT is thermal energy…the temperature converted into energy units by “R”
Our body temperature: 37C or 310 Kelvin or 2600 Joules
If the energy difference is zero, 𝑒 0 =1 so both are in equal amounts…at equilibrium
If the energy difference is 2600 Joules then B is 2.7 times greater than A
𝑎𝑚𝑜𝑢𝑛𝑡 𝑜𝑓 𝐴 −∆𝑒𝑛𝑒𝑟𝑔𝑦
=𝑒 𝑅𝑇
𝑎𝑚𝑜𝑢𝑛𝑡 𝑜𝑓 𝐵
RT is thermal energy…the temperature converted into energy units by “R”
Our body temperature: 37C or 310 Kelvin or 2600 Joules/mole
If the energy difference is zero, 𝑒 0 =1 so both are in equal amounts… at equilibrium
If the energy difference is 2600 J/mole then B is 2.7 times greater than A
If the energy difference is 10 times 2600 J/mole then B is 20,000 times greater than A
𝑎𝑚𝑜𝑢𝑛𝑡 𝑜𝑓 𝐴 −∆𝑒𝑛𝑒𝑟𝑔𝑦
=𝑒 𝑅𝑇
𝑎𝑚𝑜𝑢𝑛𝑡 𝑜𝑓 𝐵
RT is thermal energy…the temperature converted into energy units by “R”
Our body temperature: 37C or 310 Kelvin or 2600 Joules
If the energy difference is zero, 𝑒 0 =1 so both are in equal amounts… at equilibrium
If the energy difference is 2600 Joules then B is 2.7 times greater than A
If the energy difference is 10 times 2600 Joules then B is 20,000 times greater than A
If the energy difference is very big then it seems that all of A goes to B
How big is 2600 Joules/mole? …2.6 kJ/mole
The heat needed to melt water molecules: 6 kJ/mole
To break a hydrogen bond: 18-24 kJ/mole
Events happen spontaneously when energy needed is “close” to thermal energy
Energy barrier:
Events happen spontaneously when energy needed is “close” to thermal energy
Energy barrier:
A
C
B
C
Energy
A
Energy to
get change
Energy
change
Activation energy
B
For a rate of 1 in 109 sec:
energy of 132kJ/mole
For probability of 1 in a
million: energy=166kJ/mole
uncatalyzed
catalyzed
catalyzed plus bound changes energy
Different species
…must be stable for multiple animal lifetimes
Thus very low energy states…deep wells or
high energy barriers
…protein must pack very well (low energy) in
many different forms or transition structures
are highly unstable