Rerun of essentials of week one - PowerPoint Presentation

Slide1

Rerun of essentials of week one

From Rotamers to Models and back via the Entropy of WaterSlide2

Protein structure bioinformatics

Predict mutations

Analyse mutations

Understand biology

Design medicines (

etc

)

Homology modelling for the aboveSlide3

Mutations and rotamers

‘Rotamer’ is an abused word. It both means any side chain conformation and preferred side chain conformation.Slide4
Slide5
Slide6

Improbable thingsSlide7

©CMBI 2006

β

-branched prefers

β

-strandSlide8

Common sense and tau…

Valine, Isoleucine, and Threonine are

β

-branched. Common sense dictates to treat their tau angles special. Their

γ

-atoms bulldozer into their own backbone, and that is why

β

-branched residues prefer

β

-strandsSlide9

Tau

angleSlide10

Rotamers

So, there is much we don’t understandSlide11

Rotamers

Predict mutations

Analyse mutations

Help with docking

Homology modelling

Structure validationSlide12

Model!

1: Template recognition and initial alignment

2: Alignment correction

3: Backbone generation

4: Loop modeling

5: Sidechain modeling

6: Model optimization

7: Model validation

8: Iteration

8: Iteration

8: Iteration

8: IterationSlide13

MUTANT DESIGN

BIO-

INFORMATICS

QUESTION

‘MOLECULAR

BIOLOGY’

BIOPHYSICSSlide14

Mutations

Protein stability

Enzyme activity

Enzyme specificity

Antigenicity

Validate/falsify hypotheses

EtceteraSlide15

PROTEIN STABILITY

Δ

G

=

Δ

H - T

Δ

S

Δ

G

= -RT ln(K)

K = [Folded] / [Unfolded]

So, you can interfere either with the folded, or with the unfolded form.

Choosing between

Δ

H and

Δ

S will be much more difficult, because

Δ

G is a property of the complete system, including H

2O….Slide16

There is a natural tendency for all things (even atoms & molecules) to roll downhill - to fall to lower energy.



H wants to be negative

This is opposed (at the molecular level) by the equally natural tendency for thermal/Brownian motion (otherwise known as “entropy”) to make things go the other way…

…and this effect gets bigger as the temperature increases.

T.



S wants to be positive

A bluffer’s guide to Thermodynamic

Equilibrium, by Alan CooperSlide17

Thermodynamic Equilibrium, expressed in terms of the Gibbs Free Energy change, reflects just the balance between these opposing tendencies…



G =



H - T



S

Equilibrium is reached when these two forces just balance (



G = 0).

The

standard

free energy change,



G



, is just another way of expressing the equilibrium constant, or affinity (K) for any process, on a logarithmic scale…G

 = -RTlnKSlide18

Both enthalpy and entropy are integral functions of heat capacity...

….from which

D

G =

D

H - T.

D

S

So

D

C

p

is the key - if we can understand heat capacity effects, then we can understand everything else.Slide19

So, what is the role of water?

So

D

C

p

is the key - if we can understand heat capacity effects, then we can understand everything else. And

D

C

p

is largely determined by the interactions between water and the macromolecule(s).

In figure b many more waters are free than in a. And free waters are happy waters!Slide20

Stability engineering

Entropic versus enthalpic

Folded versus unfolded form

Thermodynamic versus kinetic

Always compensatory