IRENA MAMAJANOV FROM MESSY CHEMISTRY TO THE ORIGINS OF LIFE 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? DEFINITION OF LIFE LIFE IS A SELF-SUSTAINING SYSTEM CAPABLE OF DARWINIAN EVOLUTION NASA Working Definition 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 ▸ Looking at systems level processes. MESSY CHEMISTRY ▸ “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 Small fraction of the Organic Chemistry 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. Network (~0.001%). Chem. Int. Ed. 51, 7928-7932 (2012). EVOLUTION OF THE CHEMOSPHERE AND BIOCHEMICAL NETWORKS Biomimetic Systems Systems approximating biological fUnction • Protoenzymes • Protocells Open-Ended Systems Systems having no predetermined limit or boundary • Autocatalytic systems 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 Small fraction of the Organic Chemistry Network (~0.001%). Metabolic Pathways: http://pathview.r-forge.r-project.org/ MODEL SYSTEM POLYESTERS IN PREBIOTIC CONTEXT FUNCTIONAL POLYMERS POLYESTER LIBRARY Lac Iso Phe Met Glc 20 + + + + 5 Wet/ dry cycle Unique sequences 43500 unique Glc2-Lac0-Phe0-Iso1-Met5 sequences identified Met3 - Glc3-Lac9-Phe2-Iso0-Met5 Iso0 - 6 Glc3-Lac1-Phe0-Iso1-Met2 Phe2 - Lac1 - 0 Glc Glc0-Lac6-Phe0-Iso0-Met7 Intensity x 10 Glc1-Lac7-Phe2-Iso2-Met7 Glc1-Lac1-Phe4-Iso0-Met10 Chandru K, Guttenberg N, Giri C, Hongo Y, Butch C, Mamajanov I, Cleaves HJ. (2018). Simple prebiotic synthesis of high diversity dynamic combinatorial pH 3, 80 C, POS mode (FTICR-MS) M/Z polyester libraries. Communications Chemistry 1:30 FUNCTIONAL POLYMERS ORGANIZATION THROUGH COMPARTMENTALIZATION ▸ Fatty acid vesicles (Szostak lab, ▸ Coacervates (Oparin, Haldane) Deamer lab) ▸ Membraneless polymer microdroplets FUNCTIONAL POLYMERS POLYESTER MICRODOPLETS Tony Jia Kuhan Chandru Scale bars 100 µm, insets 10 µm Jia, Chandru, et al. in press FUNCTIONAL POLYMERS POLYESTER MICRODOPLETS sfGFP Scale bar 100 µm Jia, Chandru, et al. in press FUNCTIONAL POLYMERS CAN MESSY POLYMERS BE FUNCTIONAL? • The Good • Few papers describe the catalytic activity Catalytic Microspheres 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 Glutamic Acid • Non-random incorporation of amino acids • Linearity Fox SW & Harada K (1958), Science 128:1214 Fox SW & Harada (1960), JACS 82: 3745- 51 • Life-like behavior and consciousness Fox SW (1989), J.Mol.Struct. 199: 183-8 FUNCTIONAL POLYMERS Protoenzymatic Functions of Messy Polymers: Few Old Ideas Prebiotic melanin 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) 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: Synthetic Prebiotic Enzymes chemistry: chemistry: Dendrizymes Hyperbranched Polymers MICROENVIRONMENTS “PROTOENZYME ASSAY”: KEMP ELIMINATION Kemp elimination is a base catalyzed reaction sensitive to T = 30˚C; base: tetramethylguanadine solvent polarity. An assay based on Kemp elimination will therefore probe the microenvironment provided by the proto- enzymes. Kemp DS, Casey ML (1973), JACS 95: 6670-6674 BUILDING A PROTO-ENZYME Methylsuccinic Acid Adipic Acid Mamajanov I and Cody GD. (2017) Phil. Trans. R. Soc. A 2017 375 2016035 ASSAYING A PROTO-ENZYME Me-Succinic Acid/Glycerol/TEA Polymer Adipic Acid/Glycerol/TEA Polymer Citric Acid/Glycerol/TEA Polymer Monomeric TEA 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 Jia Rehana 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/PEI ZnS Particle size (polymer/cluster nanocomposite) < 100nm by DLS METAL SULFIDE NANOPARTICLE ENCAPSULATION BY MESSY POLYMERS TEM ANALYSIS OF ZNS PARTICLE/HYPERBRANCHED POLYMER COMPOSITES 200nm 200nm Fresh Sample 2 week old sample MESSY PROTOENZYME “PROTOENZYME ASSAY”: EOSIN B PHOTODEGRADATION Irradiation w/o catalyst Eosin B Photo degradation monitoring TiO2 21nm NPs 0min ZnS/G2C 15min Normalized Eosin B Concentration Normalized ZnS/PEI 30min high-pressure Hg lamp (125 W) 45min -5 Eosin B 5.0x10 5M Total volume 30mL 120min ZnS - 10mg/ PEI (Mw= 800Da) - 280mg NETWORK PROPERTIES CONSTRUCTING AN EVOLVABLE CHEMICAL SYSTEMS EVOLUTION SELECTION REPLICATION HEREDITY CERTAIN TRAITS, PROPERTIES AUTOCATALYSIS 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 M.W.I. Nam,Powner, H.G.,B. Nam, Gerland, R.N. J.D. Zare Sutherland,, PNAS Jan Nature 2018, 115459: (1) 239–242 36-40 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 CONSTRUCTING AN EVOLVABLE CHEMICAL SYSTEMS EVOLUTION SELECTION REPLICATION HEREDITY CERTAIN TRAITS, PROPERTIES AUTOCATALYSIS HERITABLE VARIATIONS SELECTIVE FORMOSE REACTION BY A. RICARDO, M. A. CARRIGAN, A. N. OLCOTT, S. A. BENNER (2004) SCIENCE 303 : 196 “Organic molecules given energy and left to themselves devolve into complex mixtures, “asphalts” better suited for paving roads than supporting Darwinian evolution.” –Steve Benner TAR PROBLEM IS IT POSSIBLY TO SELECTIVELY SYNTHESIZE FUNCTIONAL POLYMERS AND AVOID TAR FORMATION? HCN polymer (polymerization initiated with Rose bengal) Black polymer formed Polymer formed in Miller-Urey System upon thermal decomposition of diaminomaleonitrile Titan as seen by (DAMN) Cassini-Huygens. Brown color attributed to polymeric material (tholin) SELECTION IN HYPERBRANCHED POLYMERS Increasing Degree of Multifunctional Polymerization Polymerization (DP) monomers Hyperbranched Polymers One-pot polycondensation reaction Flory (1952) • Not perfectly branched Hyperbranched Polymers • Low control over mass and size Gelation (solidification, • Broad molar mass distribution A2 + B3 - Approach One-pot polycondensation reaction • Irregular shape (globular, amorphousFlory (1952) decreased solubility) • Not perfectly branched structure, low viscosity) Used when AB -Monomer is difficult to synthesise (e.g. reactivity too high) 2 • Low control over mass and size • No gelation (high solubility) • Broad molar mass distribution Types of units present: • Irregular shape (globular, amorphous • Dendritic unit (both B reacted) structure, low viscosity) Danger of • Linear unit (one B reacted) • No gelation (high solubility) crosslinking Monomers• Terminating are often unit (only A reacted) Types(sol of and units gel present: commercially• Focal unit available! (A did not react, but • Dendriticformation) unit (both B reacted) both B units) ‰ present only once • Linear unit (one B reacted) •VeryTerminating little control unit (only A reacted) 2,2-Bis(hydroxymethyl)propionic