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Hazra B, Mandal R, Sahu J, Das S, Prasad M, Tarafdar PK. Self-immolation Assisted Morphology Transformation of Prebiotic Lipidated-cationic Amino Acids: Electro-droplet Mediated C-C Coupling Reaction to Synthesize Macromolecules. Chemistry 2024; 30:e202303555. [PMID: 38205907 DOI: 10.1002/chem.202303555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 12/22/2023] [Accepted: 01/08/2024] [Indexed: 01/12/2024]
Abstract
Compartmentalization protected biomolecules from the fluctuating environments of early Earth. Although contemporary cells mostly use phospholipid-based bilayer membranes, the utility of non-bilayer compartments was not ruled out during the prebiotic and modern eras. In the present study, we demonstrated the prebiotic synthesis of lipidated cationic amino acid-based amphiphiles [lauryl ester of lysine (LysL); ornithine (OrnL); and 2,4-diamino butyric acid (DabL)] using model dry-down reaction. These amphiphiles self-assemble into micellar membranes. However, the OrnL and DabL-based micelles undergo pH-responsive transformation to lipid droplet-like morphologies, a modelcompartment in the prebiotic Earth. These cationic droplets encapsulated prebiotic molecules (isoprene) and assisted electron transfer reaction to synthesize isoprenoid derivatives at primitive Earth conditions. The self-assembly of prebiotic amphiphiles, their transformation to droplet compartments, and droplet-assisted C-C bond formation reaction might have helped the evolution to synthesize various biomolecules required for the origin of life.
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Affiliation(s)
- Bibhas Hazra
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, 741 246, Mohanpur, Nadia, West Bengal, India
| | - Raki Mandal
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, 741 246, Mohanpur, Nadia, West Bengal, India
| | - Jayati Sahu
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, 741 246, Mohanpur, Nadia, West Bengal, India
| | - Subrata Das
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, 741 246, Mohanpur, Nadia, West Bengal, India
| | - Mahesh Prasad
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, 741 246, Mohanpur, Nadia, West Bengal, India
| | - Pradip K Tarafdar
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, 741 246, Mohanpur, Nadia, West Bengal, India
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Hazra B, Prasad M, Das S, Mandal R, Sardar A, Dewangan N, Tarafdar PK. Phosphate-Based Amphiphile and Lipidated Lysine Assemble into Superior Protocellular Membranes over Carboxylate and Sulfate-Based Systems: A Potential Missing Link between Prebiotic and the Modern Era? LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:17031-17042. [PMID: 37984966 DOI: 10.1021/acs.langmuir.3c01617] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Amphiphiles are among the most extensively studied building blocks that self-assemble into cell-like compartments. Most literature suggested that the building blocks/amphiphiles of early Earth (fatty acid-based membrane) were much simpler than today's phospholipids. To establish the bridge between the prebiotic fatty acid era and the modern phospholipid era, the investigation and characterization of alternate building blocks that form protocellular membranes are necessary. Herein, we report the potential prebiotic synthesis of alkyl phosphate, alkyl carboxylate, and alkyl sulfate amphiphiles (anionic) using dry-down reactions and demonstrate a more general role of cationic amino acid-based amphiphiles to recruit the anionic amphiphiles via ion-pair, hydrogen bonding, and hydrophobic interactions. The formation and self-assembly of the catanionic (mixed) amphiphilic system to vesicular morphology were characterized by turbidimetric, dynamic light scattering, transmission electron microscopy, fluorescence lifetime imaging microscopy, and glucose encapsulation experiments. Further experiments suggest that the phosphate-based vesicles were more stable than the alkyl sulfate and alkyl carboxylate-based systems. Moreover, the alkyl phosphate system can form vesicles at prebiotically relevant acidic pH (5.0), while alkyl carboxylate mainly forms cluster-type aggregates. An extended supramolecular polymer-type network formation via H-bonding and ion-pair interactions might order the membrane interface and stabilize the phosphate-based vesicles. The results suggest that phosphate-based amphiphiles might be a superior successor to fatty acids as early compartment building blocks. The work highlights the importance of previously unexplored building blocks that participate in protocellular membrane formation to encapsulate important precursors required for the functions of early life.
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Affiliation(s)
- Bibhas Hazra
- Indian Institute of Science Education and Research Kolkata, Nadia, Mohanpur 741246, West Bengal, India
| | - Mahesh Prasad
- Indian Institute of Science Education and Research Kolkata, Nadia, Mohanpur 741246, West Bengal, India
| | - Subrata Das
- Indian Institute of Science Education and Research Kolkata, Nadia, Mohanpur 741246, West Bengal, India
| | - Raki Mandal
- Indian Institute of Science Education and Research Kolkata, Nadia, Mohanpur 741246, West Bengal, India
| | - Avijit Sardar
- Indian Institute of Science Education and Research Kolkata, Nadia, Mohanpur 741246, West Bengal, India
| | - Nikesh Dewangan
- Indian Institute of Science Education and Research Kolkata, Nadia, Mohanpur 741246, West Bengal, India
| | - Pradip K Tarafdar
- Indian Institute of Science Education and Research Kolkata, Nadia, Mohanpur 741246, West Bengal, India
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Prasad M, Hazra B, Mandal R, Das S, Tarafdar PK. ATP-Assisted Protocellular Membrane Formation with Ethanolamine-Based Amphiphiles. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023. [PMID: 37421360 DOI: 10.1021/acs.langmuir.3c00600] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2023]
Abstract
Prebiotic membranes are one of the essential elements of the origin of life because they build compartments to keep genetic materials and metabolic machinery safe. Since modern cell membranes are made up of ethanolamine-based phospholipids, prebiotic membrane formation with ethanolamine-based amphiphiles and phosphates might act as a bridge between the prebiotic and contemporary eras. Here, we report the prebiotic synthesis of O-lauroyl ethanolamine (OLEA), O-lauroyl methyl ethanolamine (OLMEA), and O-lauroyl dimethylethanolamine (OLDMEA) under wet-dry cycles. Turbidimetric, NMR, DLS, fluorescence, microscopy, and glucose encapsulation studies highlighted that OLEA-ATP and OLMEA-ATP form protocellular membranes in a 3:1 ratio, where ATP acts as a template. OLDMEA with a dimethyl group did not form any membrane in the presence of ATP. ADP can also template OLEA to form vesicles in a 2:1 ratio, but the ADP-templated vesicles were smaller. This suggests the critical role of the phosphate backbone in controlling the curvature of supramolecular assembly. The mechanisms of hierarchical assembly and transient dissipative assembly are discussed based on templated-complex formation via electrostatic, hydrophobic, and H-bonding interactions. Our results suggest that N-methylethanolamine-based amphiphiles could be used to form prebiotic vesicles, but the superior H-bonding ability of the ethanolamine moiety likely provides an evolutionary advantage for stable protocell formation during the fluctuating environments of early earth.
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Affiliation(s)
- Mahesh Prasad
- Indian Institute of Science Education and Research Kolkata, Mohanpur, Nadia 741246, West Bengal, India
| | - Bibhas Hazra
- Indian Institute of Science Education and Research Kolkata, Mohanpur, Nadia 741246, West Bengal, India
| | - Raki Mandal
- Indian Institute of Science Education and Research Kolkata, Mohanpur, Nadia 741246, West Bengal, India
| | - Subrata Das
- Indian Institute of Science Education and Research Kolkata, Mohanpur, Nadia 741246, West Bengal, India
| | - Pradip K Tarafdar
- Indian Institute of Science Education and Research Kolkata, Mohanpur, Nadia 741246, West Bengal, India
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Mandal R, Ghosh A, Rout NK, Prasad M, Hazra B, Sar S, Das S, Datta A, Tarafdar PK. Self-assembled prebiotic amphiphile-mixture exhibits tunable catalytic properties. Org Biomol Chem 2023; 21:4473-4481. [PMID: 37194351 DOI: 10.1039/d3ob00606a] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Protocellular surface formation via the self-assembly of amphiphiles, and catalysis by simple peptides/proto-RNA are two important pillars in the evolution of protocells. To hunt for prebiotic self-assembly-supported catalytic reactions, we thought that amino-acid-based amphiphiles might play an important role. In this paper, we investigate the formation of histidine-based and serine-based amphiphiles under mild prebiotic conditions from amino acid : fatty alcohol and amino acid : fatty acid mixtures. The histidine-based amphiphiles were able to catalyze hydrolytic reactions at the self-assembled surface (with a rate increase of ∼1000-fold), and the catalytic ability can be tuned by linkage of the fatty carbon part to histidine (N-acylated vs. O-acylated). Moreover, the presence of cationic serine-based amphiphiles on the surface enhances the catalytic efficiency by another ∼2-fold, whereas the presence of anionic aspartic acid-based amphiphiles reduces the catalytic activity. Ester partitioning into the surface, reactivity, and the accumulation of liberated fatty acid explain the substrate selectivity of the catalytic surface, where the hexyl esters were found to be more hydrolytic than other fatty acyl esters. Di-methylation of the -NH2 of OLH increases the catalytic efficacy by a further ∼2-fold, whereas trimethylation reduces the catalytic ability. The self-assembly, charge-charge repulsion, and the H-bonding to the ester carbonyl are likely to be responsible for the superior (∼2500-fold higher rate than the pre-micellar OLH) catalytic efficiency of O-lauryl dimethyl histidine (OLDMH). Thus, prebiotic amino-acid-based surfaces served as an efficient catalyst that exhibits regulation of catalytic function, substrate selectivity, and further adaptability to perform bio-catalysis.
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Affiliation(s)
- Raki Mandal
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur-741246, India.
| | - Anupam Ghosh
- Indian Association for the Cultivation of Science, Raja S. C. Mullick Road, Kolkata 700032, India
| | - Nilesh K Rout
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur-741246, India.
| | - Mahesh Prasad
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur-741246, India.
| | - Bibhas Hazra
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur-741246, India.
| | - Sanu Sar
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur-741246, India.
| | - Subrata Das
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur-741246, India.
| | - Ayan Datta
- Indian Association for the Cultivation of Science, Raja S. C. Mullick Road, Kolkata 700032, India
| | - Pradip K Tarafdar
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur-741246, India.
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Thoma B, Powner MW. Selective Synthesis of Lysine Peptides and the Prebiotically Plausible Synthesis of Catalytically Active Diaminopropionic Acid Peptide Nitriles in Water. J Am Chem Soc 2023; 145:3121-3130. [PMID: 36700882 PMCID: PMC9912261 DOI: 10.1021/jacs.2c12497] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Why life encodes specific proteinogenic amino acids remains an unsolved problem, but a non-enzymatic synthesis that recapitulates biology's universal strategy of stepwise N-to-C terminal peptide growth may hold the key to this selection. Lysine is an important proteinogenic amino acid that, despite its essential structural, catalytic, and functional roles in biochemistry, has widely been assumed to be a late addition to the genetic code. Here, we demonstrate that lysine thioacids undergo coupling with aminonitriles in neutral water to afford peptides in near-quantitative yield, whereas non-proteinogenic lysine homologues, ornithine, and diaminobutyric acid cannot form peptides due to rapid and quantitative cyclization that irreversibly blocks peptide synthesis. We demonstrate for the first time that ornithine lactamization provides an absolute differentiation of lysine and ornithine during (non-enzymatic) N-to-C-terminal peptide ligation. We additionally demonstrate that the shortest lysine homologue, diaminopropionic acid, undergoes effective peptide ligation. This prompted us to discover a high-yielding prebiotically plausible synthesis of the diaminopropionic acid residue, by peptide nitrile modification, through the addition of ammonia to a dehydroalanine nitrile. With this synthesis in hand, we then discovered that the low basicity of diaminopropionyl residues promotes effective, biomimetic, imine catalysis in neutral water. Our results suggest diaminopropionic acid, synthesized by peptide nitrile modification, can replace or augment lysine residues during early evolution but that lysine's electronically isolated sidechain amine likely provides an evolutionary advantage for coupling and coding as a preformed monomer in monomer-by-monomer peptide translation.
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Viveiros R, Pinto JJ, Costa N, Heggie W, Casimiro T. Development of affinity polymeric particles for the removal of 4-dimethylaminopyridine (DMAP) from Active Pharmaceutical Ingredient crude streams using a green technology. J Supercrit Fluids 2023. [DOI: 10.1016/j.supflu.2023.105853] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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Hazra B, Mondal A, Prasad M, Gayen S, Mandal R, Sardar A, Tarafdar PK. Lipidated Lysine and Fatty Acids Assemble into Protocellular Membranes to Assist Regioselective Peptide Formation: Correlation to the Natural Selection of Lysine over Nonproteinogenic Lower Analogues. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:15422-15432. [PMID: 36450098 DOI: 10.1021/acs.langmuir.2c02849] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
The self-assembly of prebiotically plausible amphiphiles (fatty acids) to form a bilayer membrane for compartmentalization is an important factor during protocellular evolution. Such fatty acid-based membranes assemble at relatively high concentrations, and they lack robust stability. We have demonstrated that a mixture of lipidated lysine (cationic) and prebiotic fatty acids (decanoic acid, anionic) can form protocellular membranes (amino acid-based membranes) at low concentrations via electrostatic, hydrogen bonding, and hydrophobic interactions. The formation of vesicular membranes was characterized by dynamic light scattering (DLS), pyrene and Nile Red partitioning, cryo-transmission electron microscopy (TEM) images, and glucose encapsulation studies. The lipidated nonproteinogenic analogues of lysine (Lys), such as ornithine (Orn) and 2,4-diaminobutyric acid (Dab), also form membranes with decanoate (DA). Time-dependent turbidimetric and 1H NMR studies suggested that the Lys-based membrane is more stable than the membranes prepared from nonproteinogenic lower analogues. The Lys-based membrane embeds a model acylating agent (aminoacyl-tRNA mimic) and facilitates the colocalization of substrates to support regioselective peptide formation via the α-amine of Lys. These membranes thereby assist peptide formation and control the positioning of the reactants (model acylating agent and -NH2 of amino acids) to initiate biologically relevant reactions during early evolution.
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Affiliation(s)
- Bibhas Hazra
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, Nadia 741246, West Bengal, India
| | - Anoy Mondal
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, Nadia 741246, West Bengal, India
| | - Mahesh Prasad
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, Nadia 741246, West Bengal, India
| | - Soumajit Gayen
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, Nadia 741246, West Bengal, India
| | - Raki Mandal
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, Nadia 741246, West Bengal, India
| | - Avijit Sardar
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, Nadia 741246, West Bengal, India
| | - Pradip K Tarafdar
- Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, Nadia 741246, West Bengal, India
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