Continuous growth of autocatalytic sets

We investigated a topology of the reaction network for polymerization of amino acids as the emergence and the continuous growth of autocatalytic sets. Reaction networks including transpeptidation reaction can yield newer and longer peptides with time having higher concentrations. Conditions necessary for the occurrence of transpeptidation can be met in actual amino acid/peptide systems.     

Autocatalytic Sets and Biological Specificity

A universal feature of the biochemistry of any living system is that all the molecules and catalysts that are required for reactions of the system can be built up from an available food source by repeated application of reactions from within that system. RAF (reflexively autocatalytic and food-generated) theory provides a formal way to study such processes. Beginning with Kauffman’s notion of “collectively autocatalytic sets,” this theory has been further developed over the last decade with the discovery of efficient algorithms and new mathematical analysis. In this paper, we study how the behaviour of a simple binary polymer model can be extended to models where the pattern of catalysis more precisely reflects the ligation and cleavage reactions involved. We find that certain properties of these models are similar to, and can be accurately predicted from, the simple binary polymer model; however, other properties lead to slightly different estimates. We also establish a number of new results concerning the structure of RAFs in these systems.     

Detecting autocatalytic, self-sustaining sets in chemical reaction systems

The ability of systems of molecular reactions to be simultaneously autocatalylic and sustained by some ambient 'food source' of simple molecules may have been an essential step in the origin of life. In this paper we first describe a polynomial-time algorithm that determines whether any given set of molecules, reactions and catalysations contains a subsystem that is both autocatalytic and able to be sustained from a given subset of the molecules. We also describe some combinatorial properties of this algorithm, and show how it can be used to find irreducible auto-catalysing and sustaining subsystems. In the second part of the paper we use the algorithm to investigate random catalytic networks-in particular, a model described by Kauffman. Using simulations and some analytic techniques we investigate the rate of catalysis that is required for the emergence of autocatalytic and sustaining subsystems.     

Synthesis and assembly of membrane glycoproteins. Membrane anchoring COOH-terminal domain of vesicular stomatitis virus envelope glycoprotein G contains fatty acids

Two polypeptides associated with the envelope of vesicular stomatitis virus are obtained by exhaustive proteolytic digestion of the virion. Analysis of the tryptic peptides and determination of the partial amino acid sequence show that the larger membrane-anchoring peptide is derived from the hydrophobic COOH terminus of the viral transmembrane glycoprotein G. The smaller peptide is, however, derived from the nonglycosylated matrix protein M. Analysis of the membrane-anchoring peptide fragments obtained from virus labeled with [3H]palmitic acid shows that the larger peptide fragment contained all the fatty acid present in G, suggesting that the fatty acids in conjunction with the hydrophobic domain may be involved in the binding of G protein to the membrane.     

Angiotensin and bradykinin interactions with phospholipids.

Reversible interactions were demonstrated between some phospholipids and some polypeptides related to angiotensin and bradykinin. The extent of the interaction was dependent on the structures of the lipid and peptide. The naturally occurring compounds that interacted most avidly were cardiolipin and (des-Asp1)-angiotensins. The apparent dissociation constant of this complex in chloroform was 10(-5) M. The complex contained more than one cardiolipin molecule/molecule of peptide. Kinins interacted most strongly with lecithin. The phospholipids altered the chromatographic behavior of radioiodinated derivatives of the polypeptides, and solubilized radioactive and unlabeled polypeptides in chloroform. In aqueous media, cardiolipin suspensions preferentially bound (des-Asp1)-angiotensin II, and inhibited its binding by antibody. The interactions were sensitive to pH and cations in the aqueous phase, and were reversed by some reagents added to the organic phase. These interactions have direct implications for binding reactions of peptides in vitro, and may bear upon the actions of the hormones in vivo.     

Steps Towards the Formation of A Protocell: The Possible Role of Short Peptides

The paper deals with molecular self-organization leading to formation of a protocell. Plausible steps towards a protocell include: polymerization of peptides and oligonucleotides on mineral surfaces; coevolution of peptides and oligonucleotides with formation of collectively autocatalytic sets; self-organization of short peptides into vesicles; entrapment of the peptide/oligonucleotide systems in mixed peptide and simple amphiphile membranes; and formation of functioning protocells with metabolism and cell division. The established propensity of short peptides to self-ordering and to formation of vesicles makes this sequence plausible. We further suggest that evolution of a protocell produced cellular ancestors of viruses as well as ancestors of cellular organisms.     

The Structure of Autocatalytic Sets: Evolvability, Enablement, and Emergence

This paper presents new results from a detailed study of the structure of autocatalytic sets. We show how autocatalytic sets can be decomposed into smaller autocatalytic subsets, and how these subsets can be identified and classified. We then argue how this has important consequences for the evolvability, enablement, and emergence of autocatalytic sets. We end with some speculation on how all this might lead to a generalized theory of autocatalytic sets, which could possibly be applied to entire ecologies or even economies.     

Genetic diversity in natural populations of mammalian reoviruses: tryptic peptide analysis of outer capsid polypeptides of murine, bovine, and human type 1 and 3 reovirus strains.

We have studied the structural relationships between the outer capsid polypeptides of eight murine, bovine, and human isolates of type 1 and 3 mammalian reoviruses. Our results show that the outer capsid polypeptides of reoviruses isolated from different mammalian species, in different years and different geographical areas, have both conserved and unique methionine-containing tryptic peptides. We found that tryptic peptides from mu 1C polypeptides of two human, one murine, and two bovine type 3 isolates and one human and two bovine type 1 reoviruses are highly conserved. Our data show that only one tryptic peptide pattern of the mu 1C polypeptide (encoded by the M2 gene) was present in reoviruses isolated from the three different mammalian species. The mu 1C polypeptide of the type 3 Dearing strain contained one tryptic peptide not found in any other reovirus isolate examined. In marked contrast to the mu 1C polypeptides, the sigma 3 polypeptides (encoded by the S4 gene) of three type 1 and three type 3 isolates were divided into two patterns based on significant differences in their tryptic peptides. In addition, at least seven tryptic peptides were conserved among the sigma 3 polypeptides of all virus strains examined. The sigma 3 polypeptide of the type 3 Dearing strain was distinguishable from the sigma 3 polypeptides of all other strains examined. The one mu 1C and two sigma 3 tryptic peptide patterns were found to occur interchangeably in isolates of type 1 or type 3. About 1/3 of the tyrosine-containing tryptic peptides of sigma 1 polypeptides of four type 3 isolates examined were conserved. Comparison of peptide differences in sigma 1 polypeptides of these isolates showed that each had one or more unique tryptic peptides, suggesting that the S1 genes coding for these polypeptides had undergone genetic drift or, alternatively, that there are at least two tryptic peptide patterns present among the sigma 1 polypeptides of these isolates. Our results suggest that genetic drift and reassortment are the most likely explanation for the extensive genetic diversity found in natural populations of mammalian reoviruses.     

Angiotensin and bradykinin interactions with phospholipids

Reversible interactions were demonstrated between some phospholipids and some polypeptides related to angiotensin and bradykinin. The extent of the interaction was dependent on the structures of the lipid and peptide. The naturally occurring compounds that interacted most avidly were cardiolipin and (des-Asp¹)-angiotensins. The apparent dissociation constant of this complex in chloroform was 10^?5 M. The complex contained more than one cardiolipin molecule/molecule of peptide. Kinins interacted most strongly with lecithin. The phospholipids altered the chromatographic behavior of radioiodinated derivatives of the polypeptides, and solubilized radioactive and unlabeled polypeptides in chloroform. In aqueous media, cardiolipin suspensions preferentially bound (des-Asp¹)-angiotensin II, and inhibited its binding by antibody. The interactions were sensitive to pH and cations in the aqueous phase, and were reversed by some reagents added to the organic phase. These interactions have direct implications for binding reactions of peptides in vitro, and may bear upon the actions of the hormones in vivo.     

In the Beginning was a Mutualism - On the Origin of Translation

The origin of translation is critical for understanding the evolution of life, including the origins of life. The canonical genetic code is one of the most dominant aspects of life on this planet, while the origin of heredity is one of the key evolutionary transitions in living world. Why the translation apparatus evolved is one of the enduring mysteries of molecular biology. Assuming the hypothesis, that during the emergence of life evolution had to first involve autocatalytic systems which only subsequently acquired the capacity of genetic heredity, we propose and discuss possible mechanisms, basic aspects of the emergence and subsequent molecular evolution of translation and ribosomes, as well as enzymes as we know them today. It is possible, in this sense, to view the ribosome as a digital-to-analogue information converter. The proposed mechanism is based on the abilities and tendencies of short RNA and polypeptides to fold and to catalyse biochemical reactions. The proposed mechanism is in concordance with the hypothesis of a possible chemical co-evolution of RNA and proteins in the origin of the genetic code or even more generally at the early evolution of life on Earth. The possible abundance and availability of monomers at prebiotic conditions are considered in the mechanism. The hypothesis that early polypeptides were folding on the RNA scaffold is also considered and mutualism in molecular evolutionary development of RNA and peptides is favoured.     

Analysis of the major polypeptides of spectrin by tryptic digestion

The two major polypeptides of erythrocyte membrane spectrin have been isolated by preparative polyacrylamide gel electrophoresis in the presence of sodium dodecyl sulfate. The tryptic peptide maps of the two polypeptides have been prepared by thin-layer chromatography and electrophoresis. Radioactive peptides have been prepared by ¹⁴C-carboxymethylation and chloramine T-catalysed ¹²⁵I iodination. Maps of both sets of peptides demonstrate a marked similarity between the two parent polypeptides.     

Oxidase reactions of tomato anionic peroxidase

Tomato (Lycopersicon esculentum Mill) anionic peroxidase was found to catalyze oxidase reactions with NADH, glutathione, dithiothreitol, oxaloacetate, and hydroquinone as substrates with a mean activity 30% that of horseradish peroxidase; this is in contrast to the negligible activity of the tomato enzyme as compared to the horseradish enzyme in catalyzing an indoleacetic acid-oxidase reaction with only Mn²⁺ and a phenol as cofactors. Substitution of Ce³⁺ for Mn²⁺ produced an 18-fold larger response with the tomato enzyme than with the horseradish enzyme, suggesting a significant difference in the autocatalytic indoleacetic acid-oxidase reactions with these two enzymes. In attempting to compare enzyme activities with 2,4-dichlorophenol as a cofactor, it was found that reaction rates increased exponentially with both increasing cofactor concentration and increasing enzyme concentration. While the former response may be analogous to allosteric control of enzyme activity, the latter response is contrary to the principle that reaction rate is proportional to enzyme concentration, and additionally makes any comparison of enzyme activity difficult.     

Stability of transformation systems representable by tree graphs: Extension to structures of biological importance

It is known that systems representable by tree graphs have entirely real eigenvalues near a steady state (Hyver, 1973). Here it is shown that the eigenvalues are negative, thus ensuring local stability.The method used in the proof allows some extensions which may be of considerable biological importance in certain cases, for example where linear systems containing circuits are involved, or enzymatic reactions, or autocatalytic reactions.     

Comparisons of the peptide maps of Kunjin virus proteins smaller than the envelope protein.

We analyzed the maps of [35S]methionine-labeled tryptic peptides of the Kunjin virus-specified proteins NV2 1/2, NV2, V2, NV1 1/2, NV1, and V1. The peptides of NV1 1/2 are identical to those of V2, except for one peptide contained only in the latter. The maps of each of the other proteins are unique and, consequently there is no evidence of any one protein being derived from another by proteolytic cleavage. The tryptic peptide maps of the above polypeptides were also compared with those of the larger Kunjin proteins, NV5, NV4, and V3. The resolution of the peptides of NV2 1/2 and NV1 is adequate to exclude any relationships with NV5 and NV4, but a possible relationship with V3 remains, although it seems unlikely in the light of other evidence. Since the peptide map of V1 is comprised of only two methionine-containing peptides similar in mobilities to two peptides found in the maps of NV5, NV4, and V3, a precursor, if any, of V1 has not been positively identified. The peptides of NV2 and V2 (NV1 1/2) are not contained in digests of NV5, NV4, or V3, and therefore, like the latter, NV2 and V2 (NV1 1/2) are independent products of translation from the positive-strand genome.     

Propensity for spontaneous succinimide formation from aspartyl and asparaginyl residues in cellular proteins

One mechanism for the spontaneous degradation of polypeptides is the intramolecular attack of the peptide bond nitrogen on the side chain carbonyl carbon atom of aspartic acid and asparagine residues. This reaction results in the formation of succinimide derivatives and has been shown to be largely responsible for the racemization, isomerization, and deamidation of these residues in several peptides under physiological conditions (Geiger, T. & Clarke, S. J. Biol. Chem. 262, 785-794 (1987]. To determine if similar reactions might occur in proteins, I examined the sequence and conformation about aspartic acid and asparagine residues in a sample of stable, well-characterized proteins. There did not appear to be any large bias against dipeptide sequences that readily form succinimides in small peptides. However, it was found that aspartyl and asparaginyl residues generally exist in native proteins in conformations where the peptide bond nitrogen atom cannot approach the side chain carbonyl carbon to form a succinimide ring. These orientations also represent energy minimum states, and it appears that this factor may account for a low rate of spontaneous damage to proteins by succinimide-linked reactions. The presence of aspartic acid and asparagine residues in other conformations, such as those in partially denatured, conformationally flexible regions, may lead to more rapid succinimide formation and contribute to the degradation of the molecule. The possible role of isoimide intermediates, formed by the attack of the peptide oxygen atom on the side chain carboxyl group, in protein racemization, isomerization, and deamidation is also considered.     

Structure of the hepatitis A virion: peptide mapping of the capsid region.

Milligram amounts of highly purified hepatitis A virus (HAV) were obtained from persistently infected cell cultures. The HAV polypeptides were separated by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and transferred to nitrocellulose for detection by an enzyme-linked immunotransfer blot procedure. The HAV nucleotide-derived amino acid sequence was subjected to computer analysis to identify potential immunogenic regions within the HAV capsid polypeptides. Synthetic peptides corresponding to selected regions of each of the larger putative capsid polypeptides were coupled to keyhole limpet hemocyanin and used to immunize rabbits. Four of six anti-HAV peptide sera were strongly reactive. Antipeptide serum generated against amino acids (a.a.) 75 through 82 reacted with the 27,000-molecular-weight (MW) polypeptide; serum against a.a. 279 through 285 reacted with the 29,000-MW HAV polypeptide; and sera against a.a. 591 through 602 and 606 through 618 reacted with the 33,000-MW HAV polypeptide. These reactions enabled the identification of the gene order of the larger HAV P1 region gene products. Our data indicate the following molecular weights: HAV VP2 or 1B, 27,000; HAV VP3 or 1C, 29,000; and HAV VP1 or 1D, 33,000.     

A hierarchical statistical model to assess the confidence of peptides and proteins inferred from tandem mass spectrometry

MOTIVATION: Statistical evaluation of the confidence of peptide and protein identifications made by tandem mass spectrometry is a critical component for appropriately interpreting the experimental data and conducting downstream analysis. Although many approaches have been developed to assign confidence measure from different perspectives, a unified statistical framework that integrates the uncertainty of peptides and proteins is still missing. RESULTS: We developed a hierarchical statistical model (HSM) that jointly models the uncertainty of the identified peptides and proteins and can be applied to any scoring system. With data sets of a standard mixture and the yeast proteome, we demonstrate that the HSM offers a reliable or at least conservative false discovery rate (FDR) estimate for peptide and protein identifications. The probability measure of HSM also offers a powerful discriminating score for peptide identification. AVAILABILITY: The algorithm is available upon request from the authors.     

Specificity of peptide binding by the HLA-A2.1 molecule

The HLA-A2 molecule contains a putative peptide binding site that is bounded by two alpha-helices and a beta-pleated sheet floor. Previous studies have demonstrated that the influenza virus matrix peptide M1 55-73 can sensitize target cells for lysis by HLA-A2.1-restricted virus-immune CTL and can induce CTL that can lyse virus-infected target cells. To assess the specificity of peptide binding by the HLA-A2.1 molecule, we examined the ability of seven variant M1 peptides to be recognized by a panel of M1 55-73 peptide-specific HLA-A2.1-restricted CTL lines. The results demonstrate that five out of the seven variant M1 55-73 peptides could be recognized by A2.1-restricted M1 55-73 peptide-specific CTL lines. The two variant peptides that were not recognized by any CTL could bind to HLA-A2.1 as indicated by their ability to compete for presentation of the M1 55-73 peptide. In addition, 5 of a panel of 24 unrelated peptides tested could also compete for M1 55-73 presentation by HLA-A2.1. One peptide derived from the sequence of a rotavirus protein could sensitize HLA-A2.1+ targets for lysis by M1 55-73 peptide-specific CTL. We conclude from these studies that: 1) the HLA-A2.1 molecule can bind a broad spectrum of peptides; 2) T cells selected for the ability to recognize one peptide plus a class I molecule can actually recognize an unrelated peptide presented by that same class I molecule; and 3) a stretch of three adjacent hydrophobic amino acids may be an important common feature of peptides that can bind to HLA-A2.1.     

Small organic compounds enhance antigen loading of class II major histocompatibility complex proteins by targeting the polymorphic P1 pocket

Major histocompatibility complex (MHC) molecules are a key element of the cellular immune response. Encoded by the MHC they are a family of highly polymorphic peptide receptors presenting peptide antigens for the surveillance by T cells. We have shown that certain organic compounds can amplify immune responses by catalyzing the peptide loading of human class II MHC molecules HLA-DR. Here we show now that they achieve this by interacting with a defined binding site of the HLA-DR peptide receptor. Screening of a compound library revealed a set of adamantane derivatives that strongly accelerated the peptide loading rate. The effect was evident only for an allelic subset and strictly correlated with the presence of glycine at the dimorphic position beta86 of the HLA-DR molecule. The residue forms the floor of the conserved pocket P1, located in the peptide binding site of MHC molecule. Apparently, transient occupation of this pocket by the organic compound stabilizes the peptide-receptive conformation permitting rapid antigen loading. This interaction appeared restricted to the larger Gly(beta86) pocket and allowed striking enhancements of T cell responses for antigens presented by these "adamantyl-susceptible" MHC molecules. As catalysts of antigen loading, compounds targeting P1 may be useful molecular tools to amplify the immune response. The observation, however, that the ligand repertoire can be affected through polymorphic sites form the outside may also imply that environmental factors could induce allergic or autoimmune reactions in an allele-selective manner.     

Catalysis of peptide bond formation by histidyl-histidine in a fluctuating clay environment

Summary The condensation of glycine to form oligoglycines during wet-dry fluctuations on clay surfaces was enhanced up to threefold or greater by small amounts of histidyl-histidine. In addition, higher relative yields of the longer oligomers were produced. Other specific dipeptides tested gave no enhancement, and imidazole, histidine, and N-acetylhistidine gave only slight enhancements. Histidyl-histidine apparently acts as a true catalyst (in the sense of repeatedly catalyzing the reaction), since up to 52 nmol of additional glycine were incorporated into oligoglycine for each nmol of catalyst added. This is the first known instance of a peptide or similar molecule demonstrating a catalytic turnover number greater than unity in a prebiotic oligomer synthesis reaction, and suggests that histidyl-histidine is a model for a primitive prebiotic protoenzyme. Catalysis of peptide bond synthesis by a molecule which is itself a peptide implies that related systems may be capable of exhibiting autocatalytic growth.