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N.M. Emanuel Institute of Biochemical Physics, RAS, Moscow, Russia
Prebiological synthesis and evolution of macromolecules
Sergey Varfolomeyev
Origin of Life = Origin of self Proliferating Macromolecules
Life phenomena from point of view of polymer chemistry
Polycondensation – the same reaction for all biopolymers
Three-functional monomers Immense decrease of number of
macromolecules comparing to the number of possible variants
Decrease of macromolecules number
Biological systems implemented the extreme low part of possible macromolecular structures
Human genome 3.104 genes
Possible variants of protein structures (20 amino acids, 100 monomers in chain)
20 100 ~ 10 130
Natural (biological) polymers – products of polycondensation of three-functional monomers
Amino acids - polyamides (proteins)
Nucleotides - polyesters (DNA, RNA)
N
NN
N
NH2
O
HO
HH
HH
PO
O-
HO
O-
H2N CH C
CH2
OH
O
CH2
C
OH
O
N
NH2
ON
O
OHO
HH
HH
PO
O-
HO
O-
Copolymerization of three-functional monomers
A
YX
B
X
A
YX
B
YX+
- Interaction of A and B
minimum two types (A, B)
- electrostatic
- hydrophobic
- hydrogen bonds
Y -H2O
All biomacromolecules (products of polycondensation) are unstable in water
Is it possible to have polycondensation process in water?
Thermocycling
Thermocycle – natural global cycle
ΔT - 200 - +200 - 20 - + 150 0 - + 120
Polymerization at high temperatures 120 – 200 OC (statistical number of polymers with different structures
and size) Reduction of temperature, solubilization in water
condensate Macromolecular selection of monomers by polymer
matrix Temperature increasing, polymerization, monomers on
matrix (template), formation of partly complementary chain
Natural (biological) polymers – productsof polycondensation of three-functional monomers
Amino acids - polyamides (proteins)
Nucleotides - polyesters (DNA, RNA)
"Кинетика как наука о законах и механизме развития различных процессов в природе находит в области биологии почти неограниченные перспективы для теоретических исследований и практического применения."
Н.М. Эмануэль, 1966
Copolymerization of three-functional monomers
Kinetic theory describing and explain the dramatic reduction of the number of polymer structures in systems.
S.D.Varfolomeyev,Kinetic models of the prebiological evolution of macromolecules.Thermocycle as motive force of the process,Mendeleev Communications,2007,17,7-9
Copolymerization of three-functional monomers
dNi\dt =kiNiki=kfi-kdi
ki >0 автоселекцияki <0 деградация
Комплексообразование мономера с полимером,как правило,стабилизирует макромолекулу против термической деструкции и гидролитического расщепления
Copolymerization of three-functional monomers
Copolymerization of three-functional monomers
Copolymerization of three-functional monomers
1
2
3
- segregation
- evolution
- autocatalysis, convergence explosion
part of the "positive" molecules
Copolymerization of three-functional monomers
Thermocycle is a method to change absolutelyimprobable events (probability 10 -50) to absolutely certain ones
(probability 1).S.Varfolomeyev,Mendeleev Comm.2007,17,7-9
Adsorption of monomers over polymer Formation of a complex between
monomer and polymer tends to stabilize macromolecule against thermal destruction and hydrolysis
Synthesis of new polymer is selective
Synthesis
BA A+H2O
BA
A
Hydrolysis
Selection of monomers on polymer and synthesis of partly complementary chain
Polymerization
Hydrolysis
Triads of two monomers
Synthesis on polymer
Reactions
Equations
Equations
Increased stability of certain triplets
AAA
BBB
BBB
Accumulation of AAA and BBB, no monomer competition
BBA
AAB
AAA
AAA
BBA
Depletion of AAB due to monomer competition with more stable BBA
Selection principles(competitive advantages)
Greater thermodynamical stability
Greater hydrolysis resistanceVelocity of catalytic processes:
The most stable and «quick» wins!
Experiments
Thermogravimetric analysis (TGA)
Kinetics of weight reduction (water elimination) during the L-asp polycondensation
time, s
wei
gh
t, %
Unique for Russia combined mass-spectrometer ICR + ionic trap Finnigan LTQ-FT
Линейная ионная ловушка
FTMS Data
Магнит7 T
Электронная пушка
ИК-лазер
F = q(E + v x B)
F F
v
Bv
ω = qB/m –циклотронная частота
F = q(E + v x B)
F F
v
Bv
ω = qB/m –циклотронная частота
FT_time_domane2_FFT_FT #1 RT: 65.39 AV: 1 NL: 2.13E5T: FTMS + p ESI Full ms [ 110.00-2000.00]
200 400 600 800 1000 1200 1400 1600 1800 2000
m/z
0
5
10
15
20
25
30
35
40
45
50
55
60
65
70
75
80
85
90
95
100
Re
lative
Ab
un
da
nce
648.85
432.90
338.34
679.811296.67
998.96
784.41508.26
619.36
908.75324.43 1859.03
716.80
216.45 1028.53 1358.601237.09 1632.901453.75
World of polypeptidesneg-F8p_10e3_200-2000_FT #1 RT: 18.02 AV: 1 NL: 3.84E3T: FTMS - p ESI Full m s [ 200.00-2000.00]
300 400 500 600 700 800 900 1000 1100 1200 1300
m /z
0
5
10
15
20
25
30
35
40
45
50
55
60
65
70
75
80
85
90
95
100
Re
lativ
e A
bu
nd
an
ce
592.138z=0
477.112z=0
707.165z=1
822.192z=1
574.128z=2
513.861z=0
937.218z=1358.841
z=0689.154
z=2459.101z=2
804.182z=2 959.200
z=1919.207
z=0380.823
z=0729.147
z=0
844.174z=0
614.120z=0
1052.245z=1
1074.226z=0755.674
z=0866.156
z=0 981.181z=0306.879
z=0 1167.273z=0
1096.212z=0
1233.624z=0
MS/MS approach
Sequencing of products of polycondensation
H2N CH C
(CH2)4
O
NH2
HN CH C
(CH2)4
OH
O
NH2
HN CH C
(CH2)4
N
O
NH2O
O
N
O
O
CCHNH2
(CH2)4
O
NH2 n
n = 7, 8
H2N CH C
(CH2)4
N
O
NH2O
O
NH
4O
O
HO
N
O
O
N
O
O
4
H2N CH C
(CH2)4
N
O
NH2O
O
4
NH
CH C
(CH2)4
O
NH2
HN CH C
CH2
N
OO
OO OH
H2N CH C
(CH2)4
N
O
NH2O
O
5
NH
N
O
O
3
N
O
OO
HO
O
H2N CH C
(CH2)4
N
O
NH2O
O
5
NH
N
O
O
NH
HC COOH
CH2
HOOC
O
O
HO
H2N CH C
(CH2)4
N
O
NH2O
O
NH
O
N
O
O
N
O
O
2
6
O
HO
H2N CH C
(CH2)4
N
O
NH2O
O
N
O
O
8
Sample G1
H2N CH C
(CH2)4
OH
O
NH2
L-Lys
H2N CH C
CH2
OH
O
C
OH
O
+
L-Asp
104 hours, H2SO4
1920 possible variants of structures, 9 possible structures were realized.
H2N CH C
(CH2)4
OH
O
NH2
H2N CH C
(CH2)4
O
NH2
HN CH C
(CH2)4
OH
O
NH2
L-Lys
Sample G1
HN CH C
(CH2)4
N
O
NH2O
O
N
O
O
CCHNH2
(CH2)4
O
NH2 n
n = 9
H2N CH C
(CH2)4
N
O
NH2O
O
N
O
O
13
H2N CH C
CH2
OH
O
C
OH
O
+
L-Asp
HN CH C
(CH2)4
N
O
NH2O
O
N
O
O
CCHNH2
(CH2)4
O
NH2 n
n = 8
19456 Possible variants of structures , 4 possible structures were realized.
278 hours, H2SO4
World of polypeptides
World of polypeptides
Sample G3
H2N CH C
(CH2)4
OH
O
NH2
L-Lys
H2N CH C
CH2
OH
O
C
OH
O
+
L-Asp
860 Possible variants of structures , 11 possible structures were realized.
104 hours, HCl H2N CH C
(CH2)4
N
O
NH2O
O
N
O
O
3H2N CH C
(CH2)4
NH
O
NH2
NHO
O
HO
N
O
O
N
O
O
6O
O
HO
H2N CH C
(CH2)4
NH
O
NH2
N
O
O
N
O
O
6
O
O
HO
H2N CH C
(CH2)4
N
O
NH2O
O
NHO
O
HO
NH
O
O
N
O
OHO
NH
OHO
O OH
H2N CH C
(CH2)4
N
O
NH2O
O
NHO
O
HO
NHHC
O
OH(CH2)4
NH2
NH2-Lys-Asp-Asp-Lys-Asp-Asp-Asp-Lys-Asp-CO2H NH2-Lys-Lys-Asp-Asp-Asp-Asp-Asp-Lys-Asp-CO2H
NH2-Lys-Asp-CO2H
NH2-Lys-Asp-Asp-CO2H
NH2-Lys-Lys-Asp-CO2H
NH2-Lys-Lys-Asp-Asp-CO2H
Sample G3
H2N CH C
(CH2)4
OH
O
NH2
L-Lys
H2N CH C
CH2
OH
O
C
OH
O
+
L-Asp
128 Possible variants of structures , 4 possible structures were realized.
278 hours, HCl
H2N CH C
(CH2)4
N
O
NH2O
O
N
O
O
6
H2N CH C
(CH2)4
NH
O
NH2
N
O
O
N
O
O
5
O
O
HO
H2N CH C
(CH2)4
N
O
NH2O
O
NH
O
O
2
HO
N
O
O
2
NH
HC COOH
(CH2)4 NH2
NH2-Lys-Asp-COOH
Lys-Asp, basic solution
Chain 5 monomers: 9 structures of 60 possible
Chain 7 monomers: 11 structures of 252 possible
World of polypeptides
KK DK
DDK KDK KKK
DKDK KDKK DKDD
DKDDK DKKDK KDKKK
All structures are closely related
Complimentary structures or intermediates
NH2-AspAspLys-COOH NH2-Asp-Asp-Lys-Asp-Asp-Asp-COOH
NH2-Asp-Asp-COOH NH2-Asp-Asp-Asp-Asp-COOH
NH2-Lys-Lys-COOH NH2-Lys-Lys-Lys-COOH
General principles of evolution of multifunctional macromolecules
Non-statistical distribution of monomers along the polymeric chain
The primary synthesized polymers works as a template for sorption and subsequent polymerization
Selection factors (stability, catalysis, etc.)
A
X Y
B
X Y,
Termocycling
Evolution to unique structure, dramatic reduction of the number
of structural variants.
Globular peptides and proteins
Flexible polyanion RNA
Rigid-linear polyanion DNA
Interdependent coexistence of three worlds of pre-biopolymers
++
++
-
-
-
- -
-
-
-
-
-
-
-
-
In the regime of hydrolytic degradation, system accumulates peptides and nucleic acids affine to each other and forming stable supramolecule complexes
Formation of stable suprmolecule complexes is a selective factor
k1 k2k3
Degradation
k1,k2> k3
Interdependent coexistence of three worlds of pre-biopolymers
Accumulation of selected limited repertoire of peptides (pre-proteins)
Accumulation of selected set of complexes of peptides with RNA
Transfer of structural information from RNA to peptide (and vice versa) and fixation in form of double-stranded DNA, molecular hieroglyphs
Polymer-RNAcomplex
RNA DNA DNA
Interdependent coexistence of three worlds of pre-biopolymers
The same pattern for three main groups of biopolymers
Thermocycle (phase transfer (- H2O)) is a driving energetic force of the process and provides thermodynamics possibility of polycondensation
Autoselection of polymers composed of three-functional monomers. Polymer always makes influence on the products composition due to supramolecular interactions of monomers and polymers
This drives switch from statistical to evolutionary-driven synthesis
Proteins and peptides
RNA
DNA
General principles of evolution of multifunctional macromolecules
(1) Non-statistical distribution of monomers along the polymeric chain
(2) The primary synthesized polymers work as the template for sorption and subsequent polymerization
(3) Selection (stability, catalysis, etc.)
A
X Y
B
X Y,
Termocycling
(4) Evolution to unic structure, dramatic reduction of the number
of structural variants.
Трифункциональные мономеры (X Y, X Y)
Предбиологическая эволюция биополимеров
Поликонденсация - базовый химический процесс (- H2O), образование амидов, пептидов, белков, фосфодиэфирной (РНК, ДНК) связи
Термоцикл (фазовый переход (- H2O)) – движущая энергитическая сила процесса – обеспечение термодинамической возможности поликонденсации
Предбиологическая эволюция биополимеров
Автоселекция полимеров из трифункциональных мономеров
Полимер ВСЕГДА оказывает влияние на состав продуктов в силу супрамолекулярного взаимодействия мономера с полимером
Переход от чисто статистического к эволюционно-направленному синтезу
Общие закономерности для всех трех основных классов биополимеров
- Пептиды и белки О , рибонуклеиновые кислоты (), дезоксирибонуклеиновые кислоты ( I I )
Большая термодинамическая устойчивость Большая устойчивость к гидролитической деструкции Каталитические свойства
Гидролиз пептидов Гидролиз полинуклеотидов Гидролиз пирофосфата Получение мономеров Поликонденсация аминокислот Поликонденсация нуклеотидов
Предбиологическая эволюция биополимеров
Принципы отбора(конкурентные преимущества)
Побеждает наиболее стабильный и «быстрый»
Подвижно – линейные - РНК
Жестко - линейные - ДНК
Взаимозависимое сосуществование трех «миров» предбиополимеров
Глобулярные – пептиды, белки
+ +
++-
--
-
--
-
--
--
-
-
Взаимозависимое сосуществование трех «миров» предбиополимеров
В режиме гидролитической
деградации в системе
накапливаются пептиды и
нуклеиновые кислоты, которые
афинны друг к другу, то есть
образуют устойчивые
супрамолекулярные комплексыОбразование стабильных супрамолекулярных комплексов как фактор отбора
+
k1
k2 k3
деградация
k1,k2> k3
Накапливается «отселектированный» ограниченный набор структур пептидов (предбелков)
Накапливается «отселектированный» набор комплексов пептидов – РНК
Перенос структурной информация от пептида к РНК, и «фиксация» этой информации в ДНК - форме
Взаимозависимое сосуществование трех «миров» предбиополимеров
+
Комплекс Полимер - РНК
РНК Цепь ДНК
ДвойнаяСпираль ДНК
Молекулярные иероглифы
Ферменты и активные центры ферментов Антитела Рецепторы Малые РНК
The great paradox of enzymes origin
Very restricted number of catalytical sites structures
2 Metal ions (2 Zn)\HDB Parathion hydrolase (1DPM)
Chymotrypsin and Streptogrisin
: Primary structures are absolutely different
Catalytical sites are the same
Organophosphatehydrolase
(EC 3..1.8.1)X
R2
P
R2
ZR3R1 O P OHR1 O + HZR3
H2O
Organophosphate hydrolase
O
X = O, S Z = O, S and F, when R3 is absent
Reaction catalyzed by
organophosphate hydrolase (EC 3.1.8.1)
An important conclusion: The role of Asp from catalytic triad is to orient His, but not to serve as a proton relay
2.69Å
2.62Å
2.62Å
2.72Å
Asp102
Ser214
Ala55
Ser195
His57
X-ray structure 2PTC
Переход от гидролитических реакций к синтетическим-
Одни и те же каталитические структуры осуществляют гидролиз и синтез
Structural Unity of catalytical sites
Pyrophosphatase Exonuclease DNA- polymerase
N.M. Emanuel Institute of Biochemical Physics, RAS, Moscow, Russia
Prebiological synthesis and evolution of macromolecules
S.D. Varfolomeev