Reading from the NCBI

Transcription

1 Reading from the NCBI amics&rid=stryer.section.156#167 otein&rid=stryer.section.365#371 Section&rid=stryer.chapter &rid=stryer.section.1687

2 Web resources dynam2.html

3 Moc/Bio and Nano/Micro Lee and Stowell Moc/Bio-Lecture 2 Bit O review Thermodynamics of Biomolecules DNA RNA Proteins Lipids

4 Biology obeys all the laws of thermodynamics 1) Energy is Neither Created or Destroyed 2) In a closed system the potential energy always decreases (entropy)

5 Activation energy

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7 Performing useful work

8 The currency of the Cell

9 Nanomolecular Trains Kinesin Step size 8 nm

10 Nanomolecular rotors Song et al Science 290, 1554, 2000.

11 The order of the cell requires energy DNA/RNA synthesis Protein synthesis Lipid formation (membranes) etc

12 Stability and Thermo of Biomolecules DNA H-bonding Pi-stacking Tm s calculated from thermo parameters T m = H/( S+RlnC t ) R= eu H in cal/mol C t is total molar strand concentration

13 DNA energetics Delta H (kcal/mol) Delta S (eu) Delta G (kcal/mol) Neighbor Seq AA/TT AT/TA TA/AT CA/GT GT/CA CT/GA GA/CT CG/GC GC/CG GG/CC

14 Example G-C-T-A-G-C/C-G-A-T-C-G G t = 2 G(GC/CG) + 2 G(CT/GA) + G(TA/AT) H t = 2 H(GC/CG) + 2 H(CT/GA) + H(TA/AT) S t = 2 S(GC/CG) + 2 S(CT/GA) + S(TA/AT) T m = H t /( S t +RlnC t )

15 DNA summary Highly specific base pairing Nearest neighbor effects only GC content governs melting temp

16 Example: SNP analysis Single nucleotide polymorphisms Looking for mutations that correlate with disease A) Oligonucleotides with flurophores that FRET (fluorescence resonance energy transfer

17 Example: Gold nanoparticle assembly

18 Protein structure and stability

19 Peptide bond again

20 Polypeptide

21 And now what?

22 Timescales of interest bond vibration proton transfer hydrogen bonding elastic vibration of globular region sugar repuckering rotation of side chains at surface torsional vibration of buried group hinge bending at domain interfaces water structure reorganization helix breakdown/formation allosteric transitions local denaturation Motion rotation of medium-sized interior sidechains Time Scale - log(s) -14 to to to to to to to to -7-5 to 0-5 to 1-4 to 0

23 The route to folded proteins

24 Levinthal s paradox and others 100 amino acids 2 conformations for each AA possible conformations sec for conformational interconversion So sec to sample all conformations ~4x10 16 years (age of universe ~10 10 years)

25 Peptide bond

26 Arg Pro Asn Asp Ser Gly Thr Trp Tyr Phe Ile Val Lys His Gln Glu Met Leu Cys Ala Turn β sheet α helix Amino acid

27 Intramolecular forces

28 Ionic interactions F= (q 1 q 2 )/ (d 2 ε) ε the dialectric (water 85) Weak in water << -kcal/mol Van der Waales Lennard-Jones potential F = D 0 [ (R eq /R) 12-2 (R eq /R) 6 ] 1.3 kcal/mol/ch 2 Hydrogen bond Vapor phase about -6 kcal/mol Water about -0.5 to -1.5 kcal/mol F = D 0 [ 5(R eq /R) 12-6(R eq /R) 6 ]cos 2 DHA

29 The hydrophobic effect Oil in water G = H T S Enthalpy of transfer from oil to water is negligible Entropy is largely due to the ordering of water The main driving force in protein folding is entropic But see temperature dependence.

30 Cooperatively of Folding Movie

31 Protein summary H-bond, I-bonds marginal for overall stability Important for secondary conformations Van der Waals/ hydrophobic effect drive folding and stability Overall stability about kcal/mol Highly cooperative Sequence to fold prediction poor

32 Example:Temp Sensitive Enzyme Half life at 100C Native <0.5 min Mutant 170 min Thermolysin like protein

33 Workshop We learned that the melting temperature of DNA depends on the base content and nearest neighbor effects. What types of forces are responsible for changes due to base content and changes due to neighbor effects?

34 Lipids and membranes

35 Look familiar Ionic interactions F= (q 1 q 2 )/ (d 2 ε) ε the dialectric (water 85) Weak in water << -kcal/mol Van der Waales Lennard-Jones potential F = D 0 [ (R eq /R) 12-2 (R eq /R) 6 ] 1.3 kcal/mol/ch 2 Hydrogen bond Vapor phase about -6 kcal/mol Water about -0.5 to -1.5 kcal/mol F = D 0 [ 5(R eq /R) 12-6(R eq /R) 6 ]cos 2 DHA

36 Lipid phases main effectors Water content Salt concentration Small organic molecules Temperature Nature of the lipid Head group Tail group

37 Phase diagram for CTAB

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39 For each lipid remember the following Below the melting temp bilayers are rigid, tightly packed, and immobile Above they are flexible and mobile The transition temperature is a characteristic of the lipids The more pure the lipid system the sharper the transition.

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42 Example: Lipid templates for ordered array assembly

43 Lipids summary Clear phase transitions Tm of phase transition is lipid dependent and environment dependent Tm is broadened by addition of other lipids