Origin of amino acid homo chirality Chemistry. Oxford University Press. Homochirality Homochirality...
67
Origin of Homochirality of Amino Acids Rafida Nossoni Feb 25 th , 2009
Transcript of Origin of amino acid homo chirality Chemistry. Oxford University Press. Homochirality Homochirality...
Origin of Homochiralityof Amino Acids
Rafida Nossoni
Feb 25th, 2009
“g{x zÄÉäx Éy ÉÇx {tÇw vtÇÇÉà ux âáxw ÉÇ à{x Éà{xÜg{x zÄÉäx Éy ÉÇx {tÇw vtÇÇÉà ux âáxw ÉÇ à{x Éà{xÜg{x zÄÉäx Éy ÉÇx {tÇw vtÇÇÉà ux âáxw ÉÇ à{x Éà{xÜg{x zÄÉäx Éy ÉÇx {tÇw vtÇÇÉà ux âáxw ÉÇ à{x Éà{xÜÊÊÊÊ
\ÅÅtÇâxÄ ^tÇà ;DJEG@DKCG<
Discovery of Chirality
Discovered in 1848 by Lewis Pasteur
Introduced in 1884 by Lord Kelvin
What is Chirality ?
Atropisomerism
HelicityAxial Chiraly
Point Chirality
Clayden, J; Greeves , N; Warren. S; Worthers . P. Organic Chemistry. Oxford University Press
Thalidomide Tragedy
N
O
O
H
HN
O
O
R-Thalidomide(sleep inducing)
N
O
O
H
NH
O
O
S-Thalidomide(teratogenic)
http://globalphilosophy.blogspot.com/2008/04/thalidomide-was-one-of-greatest-cases.html
Amino Acids Chirality
Clayden, J; Greeves , N; Warren. S; Worthers . P. Organic Chemistry. Oxford University Press
Homochirality
� Homochirality is a term to describe a group of molecules that possess the same sense of chirality.
Cohen, J. European Review, 2005, 13, 49–59.
Biological Homochirality
Enzyme DNA RNA
Cohen, J. European Review, 2005, 13, 49–59
Outline
� Origin of life
� Physical suggestion
� RNA World hypothesis
� Origin of D-ribose
� Synthesis of protein in biological systems
� Two Different methods to approach homochirality
� Model on the mineral surface
� Minihelix as a progenitor of tRNA
Outline
� Origin of life
� Physical suggestion
� RNA World hypothesis
� Origin of D-ribose
� Synthesis of protein in biological systems
� Two Different methods to approach homochirality
� Model on the mineral surface
� Minihelix as a progenitor of tRNA
Origin of Life
� It is not clear how cool the earth surface had to be before organic compounds were formed.
� It is reasonable to presume that life was a consequent of organic chemistry.
http://www.truthandscience.net/Old%20earth.jpg
UREY-MILLER Experiment
Synthesis of Amino Acids Under Primitive Earth Condition
Ancient ocean
primitive atmosphere
NH3, CH4, H2, CO, H2O
electrical spark
condenser
Miller, S. Science. 1953, 17, 528-529.
Physical Suggestion
� Two main Hypothesis
� Parity Violation
� Synchrotron Radiation
Parity Violation
� Parity Violation Energy Difference (PVED):
� In one mole of racemic mixture, excess of L-alanine is just 106
molecules.
Bonner, W. Physical Origin of Homochirality in Life, American Institute of Physics, 1996, New York
Synchrotron Radiation Destroyed D?
� Circular polarization of synchrotron radiation from the neutron stars which selectively destroyed opposite handed enantiomers.
Interstellar Molecular Cloud
Bailey, M. FASEB, 1998, 12, 503-507
Outline
� Origin of life
� Physical suggestion
� RNA World hypothesis
� Origin of D-ribose
� Synthesis of protein in biological systems
� Two Different methods to approach homochirality
� Model on the mineral surface
� Minihelix as a progenitor of tRNA
From DNA to Protein
http://ucsdnews.ucsd.edu/graphics/images/2006/factory%20copy_lg.jpg
Which One Is First? Egg or Chicken!
� How was the first protein produced?
� Did the nucleic acids or the proteins originate first?
http://www.thelonelyrider.com/uploaded_images/Chicken=egg.big-768486.jpg
RNA World Hypothesis
� Before: informational and
catalytic properties were
combined in RNA, which
synthesized proteins.
� RNA chiral moiety:
D-ribose.
Gilbert, W. Nature, 1986, 319, 618
http://evolution.berkeley.edu/evolibrary/images/interviews/rnaworld2.gif
Walter Gilbert, 1986
Origin of D-ribose
� RNA can be made by oligomerization of nucleotides.
N
NN
N
NH2
O
OHO
PO
O
O-NH
N
N
O
NH2N
O
OHO
PO
O
O-
N
NH2
ON
O
OHO
PO
O
O-NH
O
ON
O
OHO
PO
O
O-
5'
2'3'
Uracil
Guanine
Cytosine
Adenine
Oligomerization of Nucleotides
� Dimerization of racemic mixture of adenosine.
� (D,D & L,L) : (L,D & D,L ) is 94 : 6
Joshi. P.C; Pitsch. S; Ferris. J. P. Chem. Commun, 2000, 2497–2498
L-Adenosine
N
N N
N
NH2
O
OH OH
O P
O-
O
NN
D-Adenosine
N
NN
N
NH2
O
OHOH
OP
O-
O
NN
Oligomerization of Nucleotides
� Homochiralityincreases as the chain length increases.
http://tainano.com/Molecular%20Biology%20Glossary.files/image006.gif
Chiral Selection in Poly (C) Directed Synthesis
� Absence of Template:racemic mixture of poly D and Poly L.
O
PO
O
O-
OH
OO
N
NH2
ONP O
-O
O OH
O
N
NH2
ON
Poly(C), template
Joyce,G.F; Visser. G. M, Nature, 1984, 310, 602-604
Chiral Selection in Poly (C) Directed Synthesis (cont’d)
� Presence of Template:
highly efficient oligomerizationof D-Guanosine
Joyce,G.F; Visser.G.M, Nature, 1984, 310, 602-604
O
PO
O
O-
C
OH
OO
P O-O
C
O OH
O
O
P O-O
C
O OH
O
O
O
P O
O-O
G
HO
OO
PO O-
G
OHO
O
O
PO O-
G
OHO
O
O
Poly C
Chiroselective Ligation
D-nucleotidesL-nucleotides
Racemic mixture of
L& D oligonucleotides
and short oligomers
Tamura, K. Biosystems, 2008, 92, 91-98
Chiroselective Ligation
Formation of D& L libraries
Tamura, K. Biosystems, 2008, 92, 91-98
Origin of D-ribose
Origin of the Universe
Origin of the Earth
RNA World
D-riboseL-ribose
Outline
� Origin of life
� Physical suggestion
� RNA World hypothesis
� Origin of D-ribose
� Synthesis of protein in biological systems
� Two Different methods to approach homochirality
� Model on the mineral surface
� Minihelix as a progenitor of tRNA
Enzymatic Synthesis of protein in biological systems
Two major steps:
� 1- Aminoacylation of tRNA
� 2- Peptide bond formation
Pierce. B, Genetics a Conceptual Approach, third edition, Freeman
Pierce. B, Genetics a Conceptual Approach, third edition, Freeman http://www.budapeststudent.com/notes/biochemistry/images/2/2A09a-tRNA.gif
Acceptor arm
Anti codon arm
Structure of tRNA
Aminoacylation of tRNA
HO OH
O
N
NN
N
NH2
OP
O
O
O-P
O-O
O-
ATP
-OR
O
NH3+
amino acid
O-POP
O O
O-
-O
O-
inorganicpyrophosphate
HO OH
O
N
NN
N
NH2
aminoacyl adenylate
OP
O
O- OP
O
OR
NH3+
O
O-
Pierce. B, Genetics a Conceptual Approach, third edition, Freeman
Aminoacyl tRNA Synthetase (Enzyme)
� Class I aaRs:
� Class II aaRs:
Adenine
HO OH
O
OP
O
O
-OC C
3'-OHtRNA
Pierce. B, Genetics a Conceptual Approach, third edition, Freeman
Mechanism of Aminoacylation
Pierce. B, Genetics a Conceptual Approach, third edition, Freeman
Mechanism of Aminoacylation:Class I Enzyme
Pierce. B, Genetics a Conceptual Approach, third edition, Freeman
Mechanism of Aminoacylation:Class II Enzyme
Pierce. B, Genetics a Conceptual Approach, third edition, Freeman
Class II aminoacyl tRNAsynthetase
Adenine
HO OH
O
Adenine
HO OH
O
OP
O
O
O-
O
R
NH3+
OP
O
O
O-
tRNA
Adenine
O OH
OOP
O
O
O-
AMP
3'
O
R
+H3N
Non-Enzymatic Aminoacylation of Dinucleotides
� Aminoacylation of diinosine
monophosphate.
Profy, A. T; Usher, D. A. J. Mol. Evol. 1984, 20, 147-156
NH
NN
N
O
OHO
HO
P O-O
O
O
NH
NN
N
O
OHOH
external 3' external 2'
internal 2' O
D-inosinylyl-(3'-5')-inosine
O
NH
CH3
OH
O
N-(tert-butoxylcarbonyl)-D,L-alanine
Non-Enzymatic Aminoacylation: Result
L-AlanineNH
NN
N
O
OHO
HO
P O-O
O
O
NH
NN
N
O
OHOH
3' 2'
internal 2' O
Diinosine
DiinosineD-Alanine
Profy, A. T; Usher, D. A. J. Mol. Evol, 1984, 20, 147-156
3’
3’
2’
2’
Internal 2’
Internal 2’
� At 2’-OH : ee for aminoacylation with L-alanine isomer is 40%.
� Without Boc- protecting group : ee for aminoacylation for
D-alanine is 40%.
Non-Enzymatic Aminoacylation: Result
NH
NN
N
O
OHO
HO
P O-O
O
O
NH
NN
N
O
OHOH
3' 2'
internal 2' O
5'
Profy, A. T; Usher, D. A. J. Mol. Evol. 1984, 20, 147-156
Outline
� Origin of life
� Physical suggestion
� RNA World hypothesis
� Origin of D-ribose
� Synthesis of protein in biological systems
� Two Different methods to approach homochirality
� Model on the mineral surface
� Minihelix as a progenitor of tRNA
N
NN
N
NH2
O
OHO
PO
O
O
O-NH
N
N
O
NH2N
O
OHO
PO
O
O-
OH-O
OO
O
NH
N
N
O
NH2N
O
OHO
PO
O
O-
P O--OO
N
NN
N
NH2
O
OO
O
P
O-O
2', 3'-cyclic phosphodiester
NH
N
N
O
NH2N
O
OHO
HO
N
NN
N
NH2
O
OHO
PO
O
O-NH
N
N
O
NH2N
O
OHO
PO
O
O-
N
NH2
ON
O
OHO
PO
O
O-NH
O
ON
O
OHO
PO
O
O-
5'
2'3'
RNA Stability
RNA is hydrolyzed
3 billion times fasterThan DNA
Pierce. B, Genetics a Conceptual Approach, third edition, Freeman
Oligomerization of nucleotides on Mineral Surface
� 30-60 monomers are needed to make a genetic system.
� Hydrolysis competes with oligomerization.
� Montmorillonite is a soft phyllosilicate mineral that typically forms in microscopic crystals.
Ferris .J . P; Hill. A. R. Science, 1996, 381, 59-61
Model on the Flat Surface
Organic Surface
Mineral Layer
Bailey. M. FASEB, 1998, 12, 503-507
Model on the Flat Surface
Bailey. M. FASEB, 1998, 12, 503-507
Mineral Layer
Organic Surface
Model on the Flat Surface
Bailey. M. FASEB, 1998, 12, 503-507
O O
Base
2'-OH3'-OH
D-ribose D- amino acid
O
NO C
Mineral Layer
Organic Surface
Model on the Flat Surface: Results
� Aminoacylation of tRNA at 2’-OH arose first.
� Ribosomal peptidyl transferase is specific for 3’-aminoacylated tRNA.
Bailey. M. FASEB, 1998, 12, 503-507
Modern tRNA
amino acidacceptor end
Amino
acid acceptor end
Anti codon Anti codon
http://www.stkate.edu/physics/Astrobiology/Transfer%20RNA.jpg
The Top Half of tRNA Is Ancient
� It may have simply consisted of a coaxial stack TΨC arm on the CCA acceptor arm.
� The top half of modern tRNA is an independent structural domain.
Maizels, N; Weiner, A. Proc. Nati. Acad. Sci, USA, 1994, 6729-6734
Anti codon Anti codon
Bottom half
Top half
Top half originally
a genometic tag
CCAOH
TΨCDHU
DHU TΨC
OH
A
CC
Evolution of tRNA:
Minihelix might have existedas a part of ancient tRNA.
Minihelix has evolved to the present day by addinganother arm of tRNA andcorresponding aaRS moiety.
Amino acid
Attachment site
Primitive tRNA
Primitive aaRs
Aminoacyl-tRNA synthetaseaaRS
Minihelix
Amino acid
Amino acid
Amino acid
Tamura, K. Biosystems, 2008, 92, 91-98
Real Mimic of tRNA: Minihelix
� Contemporary systems use aminoacyladenylate as an intermediate.
� Minihelix as a progenitor of modern tRNA.
Minihelix
OPO- dTdTdTdTdTdTdAdA
O
O-
O
NH2
R
Aminoacyl-p-oligonucleotide
Tamura, K; Schimmel, P.Science, 2004, 305, 1253
Minihelix Used for Aminoacylation
Minihelix
Aminoacyl-p-oligonucleotide
Bridging oligonucleotide
Tamura, K; Schimmel, P.Science, 2004, 305, 1253
ACCAUGGU
OH3'Minihelix
Aminoacylation Is Specific For 3’-OH
Normal sugar 2’-deoxyadenosine 3’-deoxyadenosine
L-Ala-minihelix
Tamura, K; Schimmel, P.Science, 2004, 305, 1253
PAGE GEL
ee For L & D- Amino Acids
5’-L-Ala-p-dT6dA2 Vs 5’-D-Ala-p-dT6dA2
Ala-minihelix
(D-ribose)
Reaction Time
(min)
L-Ala D-Ala
Tamura, K; Schimmel, P.Science, 2004, 305, 1253
L-Ala : D-Ala
4 : 1
Minihelix as Progenitor of tRNA: Result
� Aminoacylation is specific
at 3’-OH.
� Yield of Aminoacylation
mini helix with L-amino
acid is four time higher
than D.
Tamura, K; Schimmel, P.Science, 2004, 305, 1253
O OH
O
N
NN
N
NH2
O
tRNA
3'
+H3N
R
Mechanism
Tamura, K; Scimmel, P. Proc. Natl. Acad. Sci. USA. 2006, 103, 13750-13752
Aminoacyl-p-oligonucleotide
Bridging oligonucleotide
Minihelix
Watson-Crick Base Pairs
DNA
RNA
Pierce. B, Genetics a Conceptual Approach, third edition, Freeman
Chiral Suppression
� The approach of a nucleophileto the carbonyl carbon can be describe by the Burgi-Dunitzangle, ~105º.
Tamura, K. Biosystems, 2008, 92, 91-98
Minihelix
Chiral Suppression
Aminoacyl-p-oligonucleotide Bridging oligonucleotide
Tamura, K; Scimmel, P. Proc. Natl. Acad. Sci. USA, 2006, 103, 13750-13752
O
O
P O-O
NNH
OH3C
O
HN
Thymine
P O-O
O
O
P O-O
NNH
OH3C
O
H
NN
N
N
O
Adenine
O
PO O-
ON
N
N
NN
H
O
O
P O-O
PO O-
H
Comparison of Aminoacylation with
Different Base Pair
L-Ala > D-Ala L-Ala < D-Ala L-Ala > D-Ala L-Ala > D-Ala
Y = dT
X = GY = dU
X = GY = dT
X = I
Y = dT
X = A
NH
N
O
OHN
N
N
NO
H2N
Tamura, K. Biosystems, 2008, 92, 91-98
Perturbation of Reaction
� The potential clash of the CH3 in dT with the CH3 of L-Ala is avoided in the Watson-Crick dT-A pair.
Tamura, K., Scimmel, P. Proc. Natl. Acad. Sci. USA. 2006, 103, 13750-13752
Minihelix Minihelix
dT-A dT-A
L-Ala D-Ala
Chiral Suppression
� The CH3 in thymine shifts its position toward the outside of the helix.
� The potential clash of the CH3
of L-Ala and the CH3 of thymine in the dT-G increased.
N
NN
NH2N
NH
N
O
O
H3C
Adenine
Thymine
NH
N
O
O
H3C
HN
N
NH
NO
H2N
Guanine
Thymine
Tamura, K. Biosystems, 2008, 92, 91-98
Role of Sugar Pucker
� The potential clash of the CH3 of L-Ala could be avoided through a 3’-endo pucker of dT.
Tamura, K; Scimmel, P. Proc. Natl. Acad. Sci. USA. 2006, 103, 13750-13752Issacs, R; Rayenes, W; Spielman, H. J. Mol. Biol, 2002. 319, 191-2007
Role of Sugar Pucker
Arnott, S; Chandrasekaran, R. J. Mol. Biol. 1986, 188, 631-640Tamura, K. Biosystems, 2008, 92, 91-98
� The RNA bridging oligonucleotide and the aminoacyl phosphate deoxyribonucleotide exist as an A-form double helix.
C
H2N
CH3
H
5'
NH
N
O
O
3'-endo
O
OHOH4'
Role of Sugar Pucker in Chiroselectivity
Tamura, K. Biosystems, 2008, 92, 91-98
Origin of L-Amino Acids
Origin of the Universe
Origin of the Earth
RNA World
D-riboseL-ribose
Aminoacylation of Primitive
tRNA
Primitive ribosome
Protein World
Tamura, K. Biosystems, 2008, 92, 91-98
Conclusion
� Homochirality is necessary for life.
� Selection of RNA occurred by chance and necessity.
� Aminoacylation of tRNA is the key step of homochirality of amino acids.
� Homochirality of amino acid is a consequence of homochirality of
D-ribose in RNA
� Aminoacylation of poly nucleotides aren't chiroselective.
� Chiral selectivity occurs by spatial constraints of molecules.
Acknowledgments
� Professor James Geiger
� Professor Babak Borhan
� Dr. Chrysoula Vasileiou
My Labmates:
� Remie , Susan, Camille, Lei
My Friends:
� Afra, Aman, Arvind, Atefeh, Behnaz, Farid, Mark, Merci, Ramin, Rouzbeh.
Stochastic Symmetry Breaking
Tamura, K. Biosystems, 2008, 92, 91-98
