Small and Random Peptides: An Unexplored Reservoir of Potentially Functional Primitive Organocatalysts. The Case of Seryl-Histidine

Wieczorek, Rafal; Adamala, Katarzyna P.; Gasperi, Tecla; Polticelli, Fabio; Stano, Pasquale

doi:10.3390/life7020019

Cited by 41 publications

(40 citation statements)

References 136 publications

(184 reference statements)

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“…In an example, the dipeptide catalyst seryl-histidine has been shown to catalyse the formation of a covalent peptide bond, generating another dipeptide [ 182 ]. This peptide exemplifies the general phenomenon of catalytic small peptides [ 199 ]. Thus, the lipid derivative in which seryl-histidine is a headgroup, linked to any appropriate hydrocarbon tail, would also likely serve as an effective catalyst, perhaps even better than the soluble version, due to facilitated proximity and reduced dimensionality.…”

Section: Lipid Worldmentioning

confidence: 99%

Systems protobiology: origin of life in lipid catalytic networks

Lancet

Zidovetzki

Markovitch

2018

J. R. Soc. Interface.

127

183

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Life is that which replicates and evolves, but there is no consensus on how life emerged. We advocate a systems protobiology view, whereby the first replicators were assemblies of spontaneously accreting, heterogeneous and mostly non-canonical amphiphiles. This view is substantiated by rigorous chemical kinetics simulations of the graded autocatalysis replication domain (GARD) model, based on the notion that the replication or reproduction of compositional information predated that of sequence information. GARD reveals the emergence of privileged non-equilibrium assemblies (composomes), which portray catalysis-based homeostatic (concentration-preserving) growth. Such a process, along with occasional assembly fission, embodies cell-like reproduction. GARD pre-RNA evolution is evidenced in the selection of different composomes within a sparse fitness landscape, in response to environmental chemical changes. These observations refute claims that GARD assemblies (or other mutually catalytic networks in the metabolism first scenario) cannot evolve. Composomes represent both a genotype and a selectable phenotype, anteceding present-day biology in which the two are mostly separated. Detailed GARD analyses show attractor-like transitions from random assemblies to self-organized composomes, with negative entropy change, thus establishing composomes as dissipative systems—hallmarks of life. We show a preliminary new version of our model, metabolic GARD (M-GARD), in which lipid covalent modifications are orchestrated by non-enzymatic lipid catalysts, themselves compositionally reproduced. M-GARD fills the gap of the lack of true metabolism in basic GARD, and is rewardingly supported by a published experimental instance of a lipid-based mutually catalytic network. Anticipating near-future far-reaching progress of molecular dynamics, M-GARD is slated to quantitatively depict elaborate protocells, with orchestrated reproduction of both lipid bilayer and lumenal content. Finally, a GARD analysis in a whole-planet context offers the potential for estimating the probability of life's emergence. The invigorated GARD scrutiny presented in this review enhances the validity of autocatalytic sets as a bona fide early evolution scenario and provides essential infrastructure for a paradigm shift towards a systems protobiology view of life's origin.

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Section: Lipid Worldmentioning

confidence: 99%

Systems protobiology: origin of life in lipid catalytic networks

Lancet

Zidovetzki

Markovitch

2018

J. R. Soc. Interface.

127

183

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“…Enzymatic hydrolysis with the aid of proteases, such as papain, neutrase, flavorzyme, thermolysin, alcalase, pronase, and ficin, is the most reliable and effective method for producing peptides with functional properties as compared with microbial fermentation and hydrolysis by either acid or alkali (Najafian & Babji, ). Protein degradation that leads to peptides with increased charge density contributes to increased solubility (Wieczorek, Adamala, Gasperi, Polticelli, & Stano, ). Peptides with different biological activities have been recently produced from fish proteins, including seabass (Sae‐leaw et al., ; Sae‐Leaw et al., ), kilka (Zamani, Madani, Rezaei, & Benjakul, ), tilapia (Yarnpakdee, Benjakul, Kristinsson, & Kishimura, ), yellow stripe trevally (Klompong, Benjakul, Kantachote, & Shahidi, ), and sardine (Bougatef et al., ), by enzymatic hydrolysis.…”

Section: Bioactive Peptidesmentioning

confidence: 99%

Natural Preservatives for Extending the Shelf‐Life of Seafood: A Revisit

Olatunde

Benjakul

2018

Comp Rev Food Sci Food Safe

181

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Consumer demand for minimally processed seafood that retains its sensory and nutritional properties after handling and storage is increasing. Nevertheless, quality loss in seafood occurs immediately after death, during processing and storage, and is associated with enzymatic, microbiological, and chemical reactions. To maintain the quality, several synthetic additives (preservatives) are promising for preventing the changes in texture and color, development of unpleasant flavor and rancid odor, and loss of nutrients of seafood during storage at low temperature. However, the use of these preservatives has been linked to potential health hazards. In this regard, natural preservatives with excellent antioxidant and antimicrobial properties have been extensively searched and implemented as safe alternatives in seafood processing, with the sole purpose of extending shelf‐life. Natural preservatives commonly used include plants extracts, chitosan and chitooligosaccharide, bacteriocins, bioactive peptides, and essential oils, among others. This review provides updated information about the production, mode of action, applications, and limitations of these natural preservatives in seafood preservation.

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“…Histidyl-histidine (His-His) catalyzes the dephosphorylation of deoxyribonucleoside monophosphate, the hydrolysis of oligo (A) 12 , and the oligomerization of 2',3'-cAMP under cyclic wet-dry reaction conditions [ 25 ]. More recent studies have shown that seryl-histidine (Ser-His) catalyzes the oligomerization of trimers of imidazole-activated nucleotides [ 26 , 27 ], and catalyze peptide bond formation between two amino acids, an activity also found in seryl-histidyl-glycine (Ser-His-Gly) [ 28 , 29 ].…”

Section: Introductionmentioning

confidence: 99%

Evolutionary convergence in the biosyntheses of the imidazole moieties of histidine and purines

2018

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BackgroundThe imidazole group is an ubiquitous chemical motif present in several key types of biomolecules. It is a structural moiety of purines, and plays a central role in biological catalysis as part of the side-chain of histidine, the amino acid most frequently found in the catalytic site of enzymes. Histidine biosynthesis starts with both ATP and the pentose phosphoribosyl pyrophosphate (PRPP), which is also the precursor for the de novo synthesis of purines. These two anabolic pathways are also connected by the imidazole intermediate 5-aminoimidazole-4-carboxamide ribotide (AICAR), which is synthesized in both routes but used only in purine biosynthesis. Rather surprisingly, the imidazole moieties of histidine and purines are synthesized by different, non-homologous enzymes. As discussed here, this phenomenon can be understood as a case of functional molecular convergence.ResultsIn this work, we analyze these polyphyletic processes and argue that the independent origin of the corresponding enzymes is best explained by the differences in the function of each of the molecules to which the imidazole moiety is attached. Since the imidazole present in histidine is a catalytic moiety, its chemical arrangement allows it to act as an acid or a base. On the contrary, the de novo biosynthesis of purines starts with an activated ribose and all the successive intermediates are ribotides, with the key β-glycosidic bondage joining the ribose and the imidazole moiety. This prevents purine ribonucleotides to exhibit any imidazole-dependent catalytic activity, and may have been the critical trait for the evolution of two separate imidazole-synthesizing-enzymes. We also suggest that, in evolutionary terms, the biosynthesis of purines predated that of histidine.ConclusionsAs reviewed here, other biosynthetic routes for imidazole molecules are also found in extant metabolism, including the autocatalytic cyclization that occurs during the formation of creatinine from creatine phosphate, as well as the internal cyclization of the Ala-Ser-Gly motif of some members of the ammonia-lyase and aminomutase families, that lead to the MIO cofactor. The diversity of imidazole-synthesizing pathways highlights the biological significance of this key chemical group, whose biosyntheses evolved independently several times.

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Small and Random Peptides: An Unexplored Reservoir of Potentially Functional Primitive Organocatalysts. The Case of Seryl-Histidine

Cited by 41 publications

References 136 publications

Systems protobiology: origin of life in lipid catalytic networks

Systems protobiology: origin of life in lipid catalytic networks

Natural Preservatives for Extending the Shelf‐Life of Seafood: A Revisit

Evolutionary convergence in the biosyntheses of the imidazole moieties of histidine and purines

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