1. Origins of life

4. Miller-Urey experiment 1953

7. A.M. Saittaa, F. Saijac,Miller experiments in atomistic computer simulations
PNAS,111,38 (2014) 13768
Molecular Dynamics DFT – plane-wave/PBE method
a reactants box MS01: 8 H2O, 8 NH3, 8 CH4, 10 CO, and 5 N2 molecules;
intermediate MS02 box: containing nine molecules each of water, ammonia, formaldehyde, and hydrogen cyanide;
the final products MS03 box: nine glycine and nine ammonia molecules
Zero-field evolution
MS01, MS03 no new compounds
MS02 H2CO formaldehide + NH3 ammonia  HCONH2 formamide
Electric field 0.35 V/Å
MS01  HCOOH formic acid,
HCONH2 formamide

8. MetD01 box: 1 CO, 1 NH3, 30 H2O  HCONH2 formamide

9. Miller-Urey experiment
H2O, NH3, CH4, CO2, CO, H2, N2 glycine
MS01: 8 H2O, 8 NH3, 8 CH4, 10 CO, and 5 N2 molecules
MF01: 8 HCOOH formic acid, HCONH2 formamide, 8 H2O, 8 NH3, 8 CO
(no inert CH4, N2)  glycine

10. NH=CH-(OH)3 Hydroxyglycine  NH=CH–COOH dehydroglycine
 NH2-CH2–COOH glycine

11. THEORETICAL STUDY OF GLYCINE CONFORMERS,
Journal of Theoretical and Computational Chemistry, Vol. 7, No. 4 (2008) 889
B3LYP/631+G*
∆E(kcal/mol)
7.63

12. Phys. Chem. Chem. Phys., 2004,6, 2563
MP2/ G** kcal=4.2 kJ

13. Phys. Chem. Chem. Phys., 2013,15, 10094
hybrid CC/DFT

15. RNA World

16. Guanine, Adenine, and Hypoxanthine Production in UV-Irradiated
Formamide Solutions: Relaxation of the Requirements for Prebiotic Purine
Nucleobase Formation
ChemBioChem 2010, 11, 1240

17. RNA or DNA
Protein coating
Viroid
RNA don’t code any protein
No protein coating
RNA structurefunction
1971 Potato spindle disease viroid
In humans Hepatitis D viroid
enclosed in Hepatitis B virus capsid
attacks liver cell 7S RNA
RNA enzime or rybozyme
(2006) 3D structure of the full-length hammerhead ribozyme

18. Self-cleaving RNA enzime

19. Prions – mad cow disease
Stanley Prusiner, Nobel Prize in Physiology/Medicine in 1997
Challenged dogma DNA  RNA protein folding

20. Alzheimer’s disease
Plaques are made up of small peptides, 39–43 amino acids in length, called beta-amyloid (Aβ). Beta-amyloid is a fragment from a larger protein called amyloid precursor protein (APP)

24. Amyloid β protein loop. The broken red  lines indicate a loop in the amyloid-B  protein that enables it to attach to  other proteins and form clumps that kill  brain cells.

25. Towards a Pharmacophore for Amyloid PNAS 2011

26. Short peptides self-assemble to produce catalytic amyloids,
Nature Chemistry 6 (2014) 303–309
7 aminoacid short peptide
Ac-IHIHIQI-CONH2
with Zn ions aggregate in prion-like fibrils
can catalyze its self-ansembling and chemical reactions
Enzyme for a model ester, p-nitrophenyl acetate

27. All 12 aminoacid short peptides - 20 at power 12
Chemical substances recognition
Specific binding
HFTFPQQQPPRP peptide binds to napthalene
34 times better than to benzene, or anthracene

28. molecular recognition

29. From short peptides to nanofibers to macromolecular assemblies in biomedicine
Yihua Loo, Shuguang Zhang, Charlotte A.E. Hauser, Biotechnology Advances 30 (2012) 593

31.  Ho BK, Dill KA (2006) Folding Very Short Peptides Using Molecular Dynamics. PLoS Comput Biol 2(4)
133 peptide 8-mer peptides
Amber 7 force field
Mesostate [a] corresponds to a helical conformation, including the α helix,
310 helix, or π helix.
Mesostate [b] corresponds to an extended
β-strand conformation.
Mesostate [l] corresponds to a left-handed helical conformation.
 3^8 = 6,561 conformers 

32. Structure of the gas-phase glycine tripeptide
Phys. Chem. Chem. Phys., 2010,12, 3463
B3LYP/6-31G(d)
20 most stable Gly–Gly–Gly conformers