IRENA MAMAJANOV FROM MESSY CHEMISTRY TO THE ORIGINS OF …

FROM MESSY CHEMISTRY TO THE ORIGINS OF LIFE

IRENA MAMAJANOV

Habitability: Producing Conditions Conducive to Life LPI “First Billion Years” Conference Series

September 9 2019

PLANETARY HABITABILITY AS PERCEIVED BY A CHEMIST

WHAT IS HABITABILITY ANYWAY?Planetary habitability is the measure of a planet's or a natural satellite's potential to develop and sustain life.

EARTH-CENTRIC?

LIFE IS A SELF-SUSTAINING SYSTEM CAPABLE OF DARWINIAN EVOLUTION

NASA Working Definition

DEFINITION OF LIFE

HOW WE STUDY ORIGINS OF LIFE

TWO APPROACHES IN THE BROADEST SENSE

▸ More Earth biology-centric

▸ Prebiotic synthesis of biological building blocks

▸ Setting biological processes in abiotic environments

▸ Evolution of biological structures

▸ More open-ended: Building a chemical system capable of Darwinian Evolution

▸ Selectivity

▸ Replication

▸ Heredity

MORE EARTH BIOLOGY-CENTRIC: UNSATISFYING?

TV PARADOX ?

?

“MORE OPEN ENDED” APPROACH

MESSY CHEMISTRY

Small fraction of the Organic Chemistry Network (~0.001%).

M. Kowalik, C.M. Gothard, A.M. Drews, N.A. Gothard, B.A. Grzybowski, K.J.M. Bishop, Parallel optimization of synthetic pathways within the network of organic chemistry. Angew. Chem. Int. Ed. 51, 7928-7932 (2012).

▸ Looking at systems level processes.

▸ “Systems Chemistry” usually = small defined networks

▸ “Messy Chemistry” = the network chemistry of large, “intractable”, prebiotically plausible systems.

▸ Sloppy biological processes

▸ Processes resembling biological but inefficient

EVOLUTION OF THE CHEMOSPHERE AND BIOCHEMICAL NETWORKS

SmallfractionoftheOrganicChemistryNetwork(~0.001%).

M.Kowalik,C.M.Gothard,A.M.Drews,N.A.Gothard,B.A.Grzybowski,K.J.M.

Bishop(2012)Angew.Chem.Int.Ed.51:7928-7932

MetabolicPathways:http://pathview.r-forge.r-project.org/

BiomimeticSystems

Open-EndedSystems

Systemsapproximatingbiological function• Protoenzymes

• Protocells

Systemshavingnopredetermined limitorboundary

• Autocatalyticsystems

MODEL SYSTEM

POLYESTERS IN PREBIOTIC CONTEXT

FUNCTIONAL POLYMERS

Chandru K, Guttenberg N, Giri C, Hongo Y, Butch C, Mamajanov I, Cleaves HJ. (2018). Simple prebioticsynthesis of high diversity dynamic combinatorial polyester libraries. Communications Chemistry 1:30

POLYESTER LIBRARY

GlcLac Iso MetPhe

+ + + + 520Uniquesequences

Wet/drycycle

Intensityx106

M/ZpH3,80C,POSmode(FTICR-MS)

Glc1-Lac1-Phe4-Iso0-Met10

Glc0-Lac1-Phe2-Iso0-M

et3






43500uniquesequences identified

FUNCTIONAL POLYMERS

ORGANIZATION THROUGH COMPARTMENTALIZATION

▸ Fatty acid vesicles (Szostak lab, Deamer lab)

▸ Coacervates (Oparin, Haldane)

▸ Membraneless polymer microdroplets

FUNCTIONAL POLYMERS

POLYESTER MICRODOPLETS

Scalebars100µm,insets10µmJia,Chandru,etal.inpress

Tony Jia

KuhanChandru

FUNCTIONAL POLYMERS

POLYESTER MICRODOPLETS

Scalebar100µmJia,Chandru,etal.inpress

sfGFP

FUNCTIONAL POLYMERS

Fox SW & Harada K (1958), Science 128:1214Fox SW & Harada (1960), JACS 82: 3745- 51Fox SW (1989), J.Mol.Struct. 199: 183-8

CAN MESSY POLYMERS BE FUNCTIONAL?• The Good

• Few papers describe the catalytic activity of the microspheres, mostly towards hydrolysis reactions

• The Bad

• The catalytic activity demonstrated was only marginal

• No mechanistic explanation was provided

• The Ugly

• Unsubstantiated claims of

• Non-random incorporation of amino acids

• Linearity

• Life-like behavior and consciousness

Catalytic Microspheres

Glutamic Acid

FUNCTIONAL POLYMERS

Protoenzymatic Functions of Messy Polymers: Few Old Ideas

Eumelanin

Part of the structural formula of eumelanin. The arrow denotes where the polymer continues

Blois M (1965), In: The Origin of Prebiological Systems and their Molecular Matrices (ed. Fox SW)

Prebiotic melanin

PREBIOTICALLY PLAUSIBLE POLYMERS

PLAUSIBLE POLYMERIC ARCHITECTURES IN PREBIOTIC “TARS”

Mamajanov I and Herzfeld J. (2009) J Chem Phys 130, 134503

http://www.looking-glass-blog.com/2016/07/callister-chapter-14-polymer-structure.html

HYPERBRANCHED POLYMERS

PROPERTIES AND APPLICATIONS OF HYPERBRANCHED POLYMERS

▸ Properties

▸ Abundance of Functional Groups

▸ Intramolecular Cavities

▸ Low Viscosity

▸ High Solubility

▸ Applications (only to mention a few)

▸ Additives (e.g. in polymer coatings)

▸ Supramolecular encapsulation agents

▸ Nanoparticle supports

▸ Drug/gene delivery agents

FUNCTIONAL MESSY POLYMERS: PROTOENZYMES

Biology: Enzymes

Synthetic chemistry: Dendrizymes

Prebiotic chemistry: Hyperbranched Polymers

MICROENVIRONMENTS

“PROTOENZYME ASSAY”: KEMP ELIMINATION

T = 30˚C; base: tetramethylguanadine

Kemp DS, Casey ML (1973), JACS 95: 6670-6674

Kemp elimination is a base catalyzed reaction sensitive to solvent polarity. An assay based on Kemp elimination will therefore probe the microenvironment provided by the proto-enzymes.

BUILDING A PROTO-ENZYME

Mamajanov I and Cody GD. (2017) Phil. Trans. R. Soc. A 2017 375 2016035

Methylsuccinic Acid Adipic Acid

ASSAYING A PROTO-ENZYME

Monomeric TEA

Citric Acid/Glycerol/TEA Polymer

Adipic Acid/Glycerol/TEA Polymer

Me-Succinic Acid/Glycerol/TEA Polymer

Mamajanov I and Cody GD. (2017) Phil. Trans. R. Soc. A 2017 375 2016035

METAL SULFIDES IN PREBIOTIC CHEMISTRY

THE IMPORTANCE OF CONSIDERING METAL SULFIDE PROTOENZYMES

▸ Iron-Sulfur Clusters in Modern enzymes

▸ Ferredoxins, hydrogenases, nitrogenases.

▸ In Prebiotic Chemistry

▸ Iron-Sulfur World Hypothesis (G. Wachtershauser)

▸ Zinc World Hypothesis

▸ The hypothesis suggests that life emerged within compartmentalized, photosynthesizing ZnS formations of hydrothermal origin (the Zn world), assembled in sub-aerial settings on the surface of the primeval Earth. (A. Mulkidjanian)

▸ rTCA cycle driven by photocatalytic ZnS minerals (S. Martin)

ENCAPSULATION OF NANOPARTICLES BY MESSY POLYMERS

SYNTHESIS OF NANOPARTICLES SUPPORTED BY A HYPERBRANCHED POLYMER

Polyethyleneimine (PEI)

Procedure:

1)Prepare an aqueous solution of the polymer

2)Add Zn/Co Cl2 solution, stir

3)Add Na2S solution, stir Tony JiaRehana Afrin

METAL SULFIDE NANOPARTICLE ENCAPSULATION BY MESSY POLYMERS

COS AND ZNS FORM STABLE CLEAR WATER SOLUTIONS IN THE PRESENCE OF PEI

CoS CoS/PEI CoCl2/PEI CoCl2

ZnS

ZnS/PEI

Particle size (polymer/cluster nanocomposite) < 100nm by DLS

METAL SULFIDE NANOPARTICLE ENCAPSULATION BY MESSY POLYMERS

TEM ANALYSIS OF ZNS PARTICLE/HYPERBRANCHED POLYMER COMPOSITES

Fresh Sample 2 week old sample

200nm 200nm

MESSY PROTOENZYME

“PROTOENZYME ASSAY”: EOSIN B PHOTODEGRADATION

TiO2 21nm NPs

ZnS/PEI

high-pressure Hg lamp (125 W) Eosin B 5.0x10-5

5M Total volume 30mL ZnS - 10mg/ PEI (Mw= 800Da) - 280mg

Irradiation w/o catalyst

Eosin B

Photo degradation monitoring

Norm

alize

d Eos

in B

Conc

entra

tion

0min

15min

30min

45min

120min

ZnS/G2C

NETWORK PROPERTIES

CONSTRUCTING AN EVOLVABLE CHEMICAL SYSTEMS

EVOLUTION

SELECTION CERTAIN TRAITS, PROPERTIES

REPLICATION AUTOCATALYSIS

HEREDITY HERITABLE VARIATIONS

HYPOTHESIS FOR AN EVOLVABLE CHEMICAL SYSTEM

RNA WORLD

NUCLEOTIDES SELECTIVELY BIND TO TEMPLATE

RNA GETS REPLICATED

MISMATCHES CAN HAPPEN

RNA WORLD?

RNA WORLD: PROBLEMS TO BE ADDRESSED (1)

▸ Formation of nucleotides

I. Nam, H.G. Nam, R.N. Zare, PNAS Jan 2018, 115 (1) 36-40 M.W. Powner,,B. Gerland, J.D. Sutherland, Nature 459: 239–242

RNA WORLD?

RNA WORLD: PROBLEMS TO BE ADDRESSED (2)

▸ Formation of RNA

▸ Nucleotide coupling

▸ Strand separation

Aldersley, M.F.; Joshi, P.C.; Price, J.D.; Ferris, J.P. The role of montmorillonite in its catalysis of RNA synthesis. Appl. Clay Sci. 2011, 54, 1–14.

NETWORK PROPERTIES


EVOLUTION




SELECTIVE FORMOSE REACTION

BY A. RICARDO, M. A. CARRIGAN, A. N. OLCOTT, S. A. BENNER (2004) SCIENCE 303 : 196

–Steve Benner

“Organic molecules given energy and left to themselves devolve into complex mixtures,

“asphalts” better suited for paving roads than supporting Darwinian evolution.”

TAR PROBLEM

IS IT POSSIBLY TO SELECTIVELY SYNTHESIZE FUNCTIONAL POLYMERS AND AVOID TAR FORMATION?

HCN polymer (polymerization

initiated with Rose bengal)

Polymer formed upon thermal

decomposition of diaminomaleonitrile

(DAMN)Titan as seen by Cassini-Huygens.

Brown color attributed to polymeric material (tholin)

Black polymer formed in Miller-Urey System

SELECTION IN HYPERBRANCHED POLYMERS

Hyperbranched Polymers

Flory (1952)One-pot polycondensation reaction

• Not perfectly branched

• Low control over mass and size

• Broad molar mass distribution

• Irregular shape (globular, amorphous

structure, low viscosity)

• No gelation (high solubility)

Types of units present:

• Dendritic unit (both B reacted)

• Linear unit (one B reacted)

• Terminating unit (only A reacted)

• Focal unit (A did not react, but

both B units) Æ present only once

Multifunctional

monomers

Polymerization

Increasing

Degree of

Polymerization (DP)

Gelation (solidification,

decreased solubility)A2 + B3 - Approach

Used when AB2-Monomer is difficult to synthesise (e.g. reactivity too high)

Danger of

crosslinking

(sol and gel

formation)

Very little control

over molar mass

and topology!

No focal unit is present

Monomers are often

commercially available!

Hyperbranched Polymers

Flory (1952)One-pot polycondensation reaction

• Not perfectly branched

• Low control over mass and size

• Broad molar mass distribution

• Irregular shape (globular, amorphous

structure, low viscosity)

• No gelation (high solubility)

Types of units present:

• Dendritic unit (both B reacted)

• Linear unit (one B reacted)

• Terminating unit (only A reacted)

• Focal unit (A did not react, but

both B units) Æ present only once

2,2-Bis(hydroxymethyl)propionic acid

HYPERBRANCHED POLYESTER SYSTEM

citric acid

OH

O

OH

O OHO

HO

OH

OH

HO

OHO

OO

OH

OHO

OH

O

OH

O

O

HO

O

OH

OH

O

HO

O OH

O

O

OH

HO

O

O

O

glycerol

A3B2

21 :

TAR PROBLEM

CAN GELATION BE PREVENTED IN HYPERBRANCHED POLYESTERS BY SUBJECTING THEM TO THE WET-DRY CYCLE?

▸ Continuously dried sampled gelated after 48 hours of drying

▸ Cycled samples remained soluble after at least 8 cycles (32 days)

▸ NMR, SEC and MS analyses consistent with branched structure in the cycled sample and cross-linked in the continuously dried one

Irena Mamajanov (2019) Life, 9(3): 56

NETWORK PROPERTIES


EVOLUTION




AUTOCATALYTIC SETS

AUTOCATALYSIS IN MESSY NETWORKS

▸ A single chemical reaction is said to be autocatalytic if one of the reaction products is also a catalyst for the same or a coupled reaction.

▸ An autocatalytic set is a collection of entities, each of which can be created catalytically by other entities within the set, such that as a whole, the set is able to catalyze its own production. In this way the set as a whole is said to be autocatalytic.

Nathaniel Virgo Jim Cleaves

SELF-ORGANIZING AUTOCATALYSIS IN ARTIFICIAL CHEMISTRY

Nathaniel Virgo

2A1 ��*)�� A2

A1 +A2 ��*)�� A3

A1 +A3 ��*)�� A4

...

2A2 ��*)�� A4

A2 +A3 ��*)�� A5

time

conc

entra

tion A1 +A1 ��! A2

A2 +A1 ��! A3

2A2 ��! A4

A3 +A1 ��! A4

A3 +A2 ��! A5

A4 +A1 ��! A5

...

final

con

cent

ratio

n

oligomer length

2A1 ��*)�� A2

A1 +A2 ��*)�� A3

A1 +A3 ��*)�� A4

...

2A2 ��*)�� A4

A2 +A3 ��*)�� A5

A4

A5

A6

A7A8 A9 A10 A11

A12

A4

A5

A6

A8 A9 A10 A11A12

A7

A

A4 A5

A

A7 A8

A

A10 A11

A

A13 A14

time

conc

entra

tion

Virgo N. et al. (2016), Artificial Life 22(2):138-152

THE SEARCH FOR AUTOCATALYTIC SETS

What we know so far:

1) Samples with the metal salt cocktail and not individual salts exhibit this behavior.

2) The color change is associated with aqueous HCN chemistry

3) Inoculating fresh solutions with a small fraction from the “autocatalytic” sample results in much faster color change.

4) Work in progress: analysis is extremely challenging

No Cations

Transition Metal

Cation Cocktail

Simple Nitrogen SourcesSi

mpl

e Ca

rbon

Sou

rces

NETWORK PROPERTIES


EVOLUTION




HEREDITY - AN IDEA

MOLECULAR IMPRINTING

HEREDITY IN MESSY CHEMISTRY

Molecular Imprinting: The missing piece in the puzzle of abiogenesis? K. Eric Drexler Future of Humanity Institute, Oxford University [email protected]

July 20, 2018

Abstract

In a neglected 2005 paper, Nobel Laureate Paul Lauterbur proposed that molecular imprinting in amorphous materials—a phenomenon with an extensive experimental literature—played a key role in abiogenesis. The present paper builds on Lauterbur’s idea to propose imprint-mediated templating (IMT), a mechanism for prebiotic peptide replication that could potentially avoid a range of difficulties arising in classic gene- first and metabolism-first models of abiogenesis. Unlike models that propose prebiotic RNA synthesis, activation, and polymerization based on unknown chemistries, peptide/IMT models are compatible with demonstrably realistic prebiotic chemistries: synthesis of dilute mixtures of racemic amino acids from atmospheric gases, and polymerization of unactivated amino acids on hot, intermittently-wetted surfaces. Starting from a peptide/IMT-based genetics, plausible processes could support the elaboration of genetic and metabolic complexity in an early-Earth environment, both explaining the emergence of homochirality and providing a potential bridge to nucleic acid metabolism. Peptide/IMT models suggest directions for both theoretical and experimental inquiry.

AN IDEA

IMPRINT MEDIATED PEPTIDE REPLICATION

Amino acid/small peptide

Peptide template

Drying Wetting

Drexler, K.E. Molecular Imprinting: The Missing Piece in the Puzzle of Abiogenesis? arXiv, 2018; 1807.07065v1.

EVOLUTION IN CHEMICAL SYSTEMS

FEW CONCLUDING THOUGHTS

▸ Stepping away from tracing biology might give us universal life principles

▸ Messy chemical systems are where interesting, possibly emergent processes happen

▸ Bottleneck: Analytical chemistry is challenging

ACKNOWLEDGEMENTS*Photo credit Nerissa Escanlar

Nathaniel Virgo* Jim Cleaves*Tony Jia*

Riquin Yi*Kuhan Chandru*

Nicholas Guttenberg*Rehana Afrin* Melina Caudan

Ajay Verma

Masahiko Hara

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IRENA MAMAJANOV FROM MESSY CHEMISTRY TO THE ORIGINS OF …