Isotopic Resonance –the first 10 years

Xueshu Xie, Alexander R. Zubarev, Sergei Rodin, Xupei Zhang and Roman A. Zubarev

Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Scheeles väg 2, S-171 77 Stockholm, Sweden

Roman.Zubarev@ki.se

able Isotopes affect Kinet

ofopic composition of Eart is beneficial for Life

Life on Mars is unlikely

Isotope Mass Abundance

1H 1.007825102H (D) 2.01410222 0.0148%

12C 12.0(0)13C 13.0033544 1.108%

14N 14.0030743915N 15.0001077 0.365%

16O 15.9949150217O 16.9991329 0.037%18O 17.99916002 0.204%

Masses and abundances of stable isotopes

Πυθαγόρας

c. 570 – c. 495 BC

• “All things are numbers”

• “Harmony of the spheres” (Musica universalis)

π = 3.1415926…

Is π a random number?Or is there hidden harmon

there?

Finding π from Pythagoras's Theoremhttp://www.physicsinsights.org/pi_from_pythagoras-1.html

Proper mapping revealsorder (symmetry) hidden in number π

Puent C.E., DNA, π and the Bell, Complexity, 2001, 6, 16-22

Randomization of every 10,000th bit destroys this picture

π = 3.1415926…

Isotope Mass Abundance1H 1.007825102H (D) 2.01410222 0.0148%

12C 12.0(0)13C 13.0033544 1.108%

14N 14.0030743915N 15.0001077 0.365%

16O 15.9949150217O 16.9991329 0.037%18O 17.99916002 0.204%

Masses and abundances of stable isotopes

Lots of numbers…

Where is the music?

Frog skin peptides

Peptide cocktail

Electric stimulation

Rana ridibundaRana arvalis

Rana temporaria

De novo MS sequencing

Hundreds of peptides5-6 families of peptides

with A. Lebedev and T. Samgina, Moscow State University

3 4903 4853 480

100

90

80

70

60

50

40

30

20

10

0

average massC=12.011N=14.03

…

monoisotopic mass

C=12.000(0)N=14.00307439

…

nominal massC=12N=14

…

C153H224N42O50

Molecular mass is the isotopic distribution!

3450 3455 3460

Massdefect

Isotopicshift

Molecular mass, Da

Introducing two mass parameters:

Normalized mass defect, NMD = 1000*(Mmono - Mnominal)/Mnominal

Normalized isotopic shift, NIS = 1000*(Maverage - Mmono)/Mnominal

Mnominal

MaverageMmono

2D mass mapping

NMD - refers to binding energy of the nucleusNMD = 1000*(Mmono - Mnominal)/Mnominal

14N = 14.00307439 Da

NIS - refers to abundances of other isotopesNIS = 1000*(Maverage - Mnmono)/Mnominal

A(14N) = 99.625%

Mnominal

MaverageMmono

2D mass mapping

R. arvalis 2D mass map

FVPLLVSKLVC*VVTKKC*PLLVSKLVC*VVTKKC*

Artemenko et al. Anal. Chem. 2009, 81, 3738–3745

R. temporaria 2D mass map

Artemenko et al. Anal. Chem. 2009, 81, 3738–3745

Masses and abundances of stable isotopes

What is this?...

August 2008

Central line

Molecules satisfying:

S = 0H = 2C - N;

O - any

z = C - (N + H)/2z = 0 - on-Line

On-Line as residues On-Line in free form

Basic

Aromatic

z = C - (N + H)/2

√√√√

√√√√√

√ -√ -√ -√ -

---

√√

√

√√√

√√√

√√√

NANA

Not all amino acids are equally abundant on-Line

Alanine, C3H5NO

0

Asparagine, C4H6N2O2

0

Glutamine, C5H8N2O2

0

Glycine, C2H3NO

0

Isoleucine C6H11NO

0

Leucine C6H11NO

0

Serine, C3H5NO2

0

Threonine, C4H7NO2

0

Valine, C5H9NO

0

Aspartic Acid, C4H5NO3

1

Glutamic Acid, C5H7NO3

1

Histidine, C6H7N3O

1

Proline, C5H7NO

1

Arginine, C6H12N4O

-2

Lysine, C6H12N2O

-1

Phenylalanine, C9H9NO

4

Tryptophan, C11H10N2O

5

Tyrosine, C9H9NO

4

19

Reducing/Oxidizing Environment

Conditions: Electric spark

13 amino acids essential for life were produced

Most of them have Z = 0

Stanley Miller ( 1930 - 2007)

Raw materials: CH4, NH3, H2O, H2

The Miller-Urey Experiment (1953)

Isotopic Resonance Now and Then

Early Life

Probably,

70-80% of all AAs (by abundance) had Z = 0

Modern LifeRelict Line

57% of all AAs (by abundance) have Z = 0

Z-value

Z = 0

Data of Norbert Hertkorn

CHN molecules in meteorites

Z=0 is a singular valuefor small organic molecules

z = C - (N + H)/2z = 0 - on-Line

1. An isotopic resonance reduces the complexityof a molecular system with Z=0.

2. Complexity reduction leads to faster kinetics.

3. Z=0 represents the simplest and the most abundant class of molecules formed spontaneously.

4. If so, early Life could have been helped bythe terrestrial isotopic resonance to emerge

or take root on Earth.Zubarev R. et al. Cent. Eur. J. Biol. 2010, 190-196

Isotopic resonance hypothesis

Less complex systems are in general faster

Simpler = Faster

At the core of the Isotopic Resonance hypothesis:

Symmetry reduces complexity

System A System B

The same number of Parts and Links

What is symmetry?

Nobel laureate PW Anderson wrote in his 1972 article More is Different:

"it is only slightly overstating the case to say that Physics is the study of symmetry."

In Quantum Mechanics:symmetry leads to degeneracy of QM states.

Symmetry = Reduction of complexity

W – number of QM states

Symmetry leads to instability: Jahn-Teller effect

• Symmetry-> degeneracy of energy levels

• Degenerate systems -> instability (higher in energy than the corresponding asymmetric system)

• Symmetric systems -> undergo distortions (“Jahn-Teller distortions”) tobecome lower-energy asymmetric systems

16O17O16O -> 676

Mass independent isotope fractionation:effect of compositional symmetry

O2 + O2* -> O3* + O

Symmetry & Kinetics

A more complex system(less symmetric)

A less complex system(more symmetric)

Otherwiseidentical

Hotter molecules –Faster chemistry

No isotopic resonance Isotopic resonance

Isotope Mass Abundance

1H 1.007825102H (D) 2.01410222 0.0148%

12C 12.0(0)13C 13.0033544 1.108%

14N 14.0030743915N 15.0001077 0.365%

16O 15.9949150217O 16.9991329 0.037%18O 17.99916002 0.204%

14 parameters

Without a linear dependence

Average molecular mass

3 4903 4853 480

100

90

80

70

60

50

40

30

20

10

0

Isotope Mass

1H 1.00782510

12C 12.0(0)

14N 14.00307439

16O 15.99491502

a

b

6 parameters (if a ≠ 0, b ≠ 0)

y = 0.3613x + 0.3978R² = 0.99989

0,56

0,57

0,58

0,59

0,6

0,61

0,62

0,63

0,64

0,4 0,45 0,5 0,55 0,6 0,65 0,7

Maverage = a • Mmono + b

32

13C, %

Reac

tion

rate

Re

acti

onra

te

Conventional theory

Isotopic resonance hypothesis

Isotopic resonance hypothesis: predictions

13C, %

BioScreen

Isotopic resonance hypothesis: testing

E. coli stock in glycerol (-700C)

Agar plate

Media for 3-4 h

Measure the growth curve

E. coli growth curve

34

E. Coli growth parameters

Effect of 15N content on E. Coli growth

3.5% 15N

Normal 0.37% 15N

“Flat line” resonance for z=0

Effect of 13C content on E. Coli growth

Effect of 15N content on E. Coli growthRe

lati

ve m

axim

um d

ensi

ty

% 15N

Effect of 15N content on E. Coli growth

Higgs boson evidence from Atlas experiment

0.35% 13C

Normal 1.1% 13C

“Flat line” resonance for all molecules

Effect of 13C content on E. Coli growth

Effect of 13C content on E. Coli growth

Normal 1.1% 13C

“Thin line” resonance for all moleculesAverage mass ≈ to nominal mass

2H – Normal; 13C, 15N and 18O ≤ 13%

Effect of “Super resonance” on E. Coli growth

Effect of “Super resonance” on E. Coli growth

Deuterium content effect - predictions

D content, %

Com

plex

ity re

duct

ion,

arb

. uni

ts

Z=0 Resonance

Earth, 0.015%

Abundances of C, N, O isotopes –normal

Deuterium content – 150 ppm

1/6000

≈300-400 ppm

0.1% 1% 10% 100%

Normal concentration, 150 ppm

Fast water

Slow water

Rela

tive

grow

th ra

te

Deuterium concentration, parts per million (ppm)

Natural range, 90-160 ppm

Deuterium content effect - predictions

150 ppm

200 ppm

300 ppm

400 ppm

Lobyshev V.I. et al., Biophysics, 1978, N2, 390-391.

ValentinLobyshev

Deuterium content effect - experimentsN

a, K

-ATP

ase

activ

ity, a

rb. u

nits

Deuterium concentration in water, %

Deuterium content effect on luciferase activity

≈30%

Rodin, S.; Rebellato, P.; Lundin, A. Isotopic resonance at 370 ppm deuterium negatively affects kinetics of luciferin oxidation by luciferase, Sci. Rep. 2018, art. 16249.

IsoRes confirmation by other groups

3.5% 15N

What is the strongest resonance?

A more complex system(less symmetric)

A less complex system(more symmetric)

Otherwiseidentical

Faster chemistry

Natural isotopic abundance

Monoisotopic: all carbons – 12C, all hydrogens – 1H, etc.

Monoisotopic

Predictions of the isotopic resonancehypothesis

• Monoisotopic molecules will possess beneficial properties, such as:

- Faster kinetics (enzymes) (?)

- Stronger binding (antibodies) (??)

- Better protein crystals for X-ray structures (?)

- Higher resolution in neutron spectroscopy (?)

16O17O16O -> 676

Mass independent isotope fractionation:effect of compositional symmetry

O2 + O2* -> O3* + O

Example:Silicon: 28Si – 92%, 29Si – 5%, 30Si – 3%Monoisotopic silicon 28Si has 60% higher thermal conductivity than silicon with natural isotopic composition.

Same with GaAs

69Ga≈60%71Ga≈40%

Example:

Monoisotopic diamond 12C (99.98 %):The thermal conductivity exceeds that of natural diamond (12C = 98.9%)by 1.5 times at 300 K.

T.R. Anthony, W.R. Banholzer, J.F. Fleischer, L. Wei, P.K. Kuo, R.L. Thomas, and R.W. Prior, Phys. Rev. B 42, 1104 (1990)

Nature Materials 11, 203–207 (2012)

Thermal conductivity of isotopically modified graphene

Monoisotopic proteins do not exist in nature.E. Coli bacteria can be grown in monoisotopic media.

Monoisotopic: all carbons – 12C, all hydrogens – 1H, etc.

Cytochrome c – 12.4 kDa

Average mass

E. Coli growth in minimal media

0

0,1

0,2

0,3

0,4

0,5

0,6

0,7

0,8

0 500 1000 1500 2000 2500 3000

OD,

AU

Time (min)

Monoisotopic

Normal

Monoisotopic E. Coli and their proteins are less stable thermally

-0.3 -0.2 -0.1 0.0 0.1 0.2 0.3 0.40

2

4

6

p

Mono

Poly

Towards monoisotopic biology

• Grow E. coli in monoisotopic media

• Extract proteins, hydrolyze them into free amino acids

• Formulate mammalian cell monoisotopic growth media

• Grow hybridoma cells in it, extract monoclonal antibodies

• Test the prediction of faster binding kinetics compared topoly-isotopic antibodies

There is no monoisotopic media for mammalian cells, so…

W o r k i n p r o g r e s s …

D/H on other planets

∂13C: 46±4‰ ∂18O: 48±5‰

Curiosity Rover

Mars

∂D = 5880±80 ‰ from evolved water∂15N: 680 ‰

Resonance 1: C + 2(N - H) + 5O = 0

Resonance 2: 2N - H + 4O = 0

Earth Mars

Mars does not contain stroisotopic resonances

Life on Mars is unlikely

Will Martian soil be good for growing

human food?

BYOES – a semi-closed ecosystem

BYOES Experiment:November 2014-February 2016

Earth

Mars

IsoRes predicts life on other planets?

Harmony of the worldFrom Sibly, Ebenezer: “Astrology” (1806).

Conclusions• CHON isotopic compositions on Earth are close to the resonance values for z = 0; z = C -( N + H)/2

• z=0 is a singularly important value for simple organic molecules.

• Isotopic resonances alter (often, increase) the speed of biological and biochemical processes.

• Terrestrial isotopic resonance has likely facilitated Lifeemergence/taking root on our planet.

• Other planets are less lucky. Martian isotopic compositions may not be optimal for humans. IsoRes can evaluate the likelihood

of life on other planets.

• Isotopic resonances affect chemistry and biology, whichcan be used in science, medicine and technology.

• Monoisotopic resonance is the strongest isotopic resonance.

IsoRes in Sci Art

Science and Art - SciArt

AcknowledgementsKim HaselmannBogdan BudnikFrank Kjeldsen

Michael Lund NielsenJesper OlsenIgor IvoninOleg Silivra

Christopher AdamsAlexander Misharin

Mikhail SavitskiThomas Köcher

Corina MayrhoferY.M. Eva Fung

Konstantin ArtemenkoTherése Hemström

Pierre Le GrevèsAtim EnyenihiDavid Good

Ernesto GonzalesConsuelo Marin VicenteMarta Guerrero Valero

Constantin ChinginYaroslav LyutvinskiyAleksandr Manoilov

Hongqian YangPiliang Hao

Mohammad PirmoradianNataliya Tarasova

Alexandra BernadotteBo Zhang

Luciano di Stefano

ThermoFisher ScientificBiomotif AB

Swedish Research CouncilKAW foundation, VINNOVA

European UnionCancerfonden

Alexander MakarovYury Tsybin

Dimitris PapanastasiuThorleif LavoldJuan Astorga-Wells

Molecules

Isotopes

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