Peptide self-replication enhanced by a proline kink

The effect of a proline substitution within a self-replicating coiled-coil peptide was investigated. Substitutions at either the d (hydrophobic, XL-1) or e (hydrophilic, XL-2) positions within the coiled-coil led to remarkable self-replication differences. The fragments of XL-1 showed little propensity for ligation even in the presence of template, whereas XL-2 demonstrated a high catalytic efficiency for self-replication. These results may be due to intrinsic differences in the bend of the helical axis within the two peptides away from the side with the proline residue, resulting in the loss of the continuous hydrophobic interface within XL-1.     

Chemical Oscillations: The Templator Model

Recently, Rebek has synthesized self-replicating molecules in the laboratory. Given the importance of such molecules, we are introducing a simple model of self-replicating molecules for the first time. The model mimics the experimental template mechanism and is an important new dynamical model with cubic nonlinearity. This nonlinearity is modeled after the self-replicating mechanism recently reported in the literature. Here we consider the full templator model and a minimal model, which disregard the uncatalyzed step in the mechanism. For the minimal model, we find an exact analytical expression for the locations of the bifurcation points. For the full model, however, we obtain analytical approximations for the bifurcation points that compare very well with the exact numerical solutions.     

Coupled Metabolic Cycles Allow Out-of-Equilibrium Autopoietic Vesicle Replication

We report chemically fuelled out-of-equilibrium self-replicating vesicles based on surfactant formation. We studied the vesicles’ autocatalytic formation using UPLC to determine monomer concentration and interferometric scattering microscopy at the nanoparticle level. Unlike related reports of chemically fuelled self-replicating micelles, our vesicular system was too stable to surfactant degradation to be maintained out of equilibrium. The introduction of a catalyst, which introduces a second catalytic cycle into the metabolic network, was used to close the first cycle. This shows how coupled catalytic cycles can create a metabolic network that allows the creation and perseverance of fuel-driven, out-of-equilibrium self-replicating vesicles.     

Loading of Amino Acids onto RNA in a Putative RNA-Peptide World

RNA is a molecule that can both store genetic information and perform catalytic reactions. This observed dualism places RNA into the limelight of concepts about the origin of life. The RNA world concept argues that life started from self-replicating RNA molecules, which evolved toward increasingly complex structures. Recently, we demonstrated that RNA, with the help of conserved non-canonical nucleosides, which are also putative relics of an early RNA world, had the ability to grow peptides covalently connected to RNA nucleobases, creating RNA-peptide chimeras. It is conceivable that such molecules, which combined the information-coding properties of RNA with the catalytic potential of amino acid side chains, were once the structures from which life emerged. Herein, we report prebiotic chemistry that enabled the loading of both nucleosides and RNAs with amino acids as the first step toward RNA-based peptide synthesis in a putative RNA-peptide world.     

Complex dynamics in a cross-catalytic self-replication mechanism

The authors consider a minimal cross-catalytic self-replicating system of only two cross-catalytic templates that mimics the R3C ligase ribozyme system of Dong-Eu and Joyce [Chem. Biol. 11, 1505 (2004)]. This system displays considerably more complex dynamics than its self-replicating counterpart. In particular, the authors discuss the Poincare-Andronov-Hopf bifurcation, canard transitions, excitability, and hysteresis that yield birhythmicity between simple and complex oscillations.     

Canard explosion of limit cycles in templator models of self-replication mechanisms

Templators are differential equation models for self-replicating chemical systems. Beutel and Peacock-Lo?pez [J. Chem. Phys. 126, 125104 (2007)] have numerically analyzed a model for a cross-catalytic self-replicating system and found two cases of canard explosion, that is, a substantial change of amplitude of a limit cycle over a very short parameter interval. We show how the model can be reduced to a two-dimensional system and how canard theory for slow-fast equations can be applied to yield analytic information about the canard explosion. In particular, simple expressions for the parameter value where the canard explosion occurs are obtained. The connection to mixed-mode oscillations also observed in the model is briefly discussed.     

Sol-gel synthesis on self-replicating single-cell scaffolds: applying complex chemistries to nature's 3-D nanostructured templates

A sol-gel process was used, for the first time, to apply a multi-component, nanocrystalline, functional ceramic compound (BaTiO3) to a three-dimensional, self-replicating scaffold derived from a single-celled micro-organism (a diatom).     

18O labeling: a tool for proteomics.

An evaluation of the proteolytic labeling and quantification of proteins for diagnostic purposes using trypsin and 18O-enriched H2O is presented. We demonstrate that comparative or relative quantitation can be performed effectively with this approach. We have developed a protocol that allows the conservation of the labeled peptides in natural abundance water without fear of back-exchange providing that pH is sufficiently low to quench the catalytic activity of trypsin, but not so low as to promote chemical back-exchange. Because the labeling efficiency depends on the nature of the peptide, a simple linear relationship between the relative 16O/18O digest buffer mixture content (x) and labeling efficiency (y) does not exist; rather it follows a probability based y = x(2) relationship. As such, the extent of peptide labeling using 16O/18O digest buffer mixture ratios may deviate significantly from that expected based on a linear relationship. The evaluation of the relative Ziptip efficiency indicated a loss in sample recovery as the peptide concentration was reduced using normal conditions, suggesting that there is a limit below which there are diminishing returns. In addition, the adsorptive losses due to Speedvac dry down and recovery indicated modest (20%) losses that may vary widely (0-50%) from peptide to peptide. The in-solution digestion efficiency of standard protein mixtures as a function of concentration revealed a linear decrease with decreasing concentration. This is consistent with enzyme kinetic effects and emphasizes a potential quantitation error that could arise when evaluating differential expression based on peptide detection. The results from our studies demonstrate the power of 18O labeling as an optimization tool for proteomics process development.     

Transfer of stereochemical information in a minimal self-replicating system

[structure: see text]. The rational design, synthesis, and characterization of a minimal self-replicating system based on a 1,3-dipolar cycloaddition between a nitrone and a maleimide is presented. The importance of molecular recognition in this system is demonstrated using a competitive inhibitor. Doping experiments demonstrate that only one of the two diastereoisomeric products of the cycloaddition reaction is capable of acting as an efficient template for its own formation, accelerating the reaction between the nitrone and maleimide and controlling the stereochemical outcome of the reaction.     

Design of Ligands for Affinity Purification of G-CSF Based on Peptide Ligands Derived from a Peptide Library

Introduction　　 Affinity chromatography is of great interest in pharmaceutical industry as it is simple,fast and is of a high efficiency to purify proteins from a complicated mixture to homogenousones in a single step. The most common affinity ligands are monoclonal antibodies,smallmolecules such as biotin and those specific to the bio-function of the protein of interest,suchas substrates and inhibitors. Although m Ab is less limited by the bioactivity of proteins,itspreparation is a complex …     

"Kinetic NMR titration": including chemical shift information in the kinetic analysis of supramolecular reaction systems such as organic replicators

Efficient harvesting of kinetic and thermodynamic information in supramolecular reaction systems comes from kinetic NMR titration, that is, the combined analysis of NMR integrals and chemical shifts. The method is introduced using a minimal self-replicating system studied at various temperatures.     

化学标记与蛋白质/多肽的识别检测

化学标记技术可以实现选择性地标记蛋白质/多肽分子,从而极大地提高了对蛋白质/多肽的识别效率和检测灵敏度,是突破蛋白质/多肽化学组成局限和仪器分析检测能力瓶颈的有效途径.本文对目前这一领域的研究现状扼要地进行了综述,主要包括针对蛋白质/多肽分子中内源氨基酸残基的标记策略、蛋白质/多肽分子中翻译后修饰基团的标记策略、基因编码表达肽段的标记策略以及配体/抗体亲和标记策略.透过这些研究所取得的成果,可以断定化学标记技术将会不断发展并将在蛋白质及蛋白质组学研究中发挥重要作用.     

Sustainable Peptide Synthesis Enabled by a Transient Protecting Group

The growing interest in synthetic peptides has prompted the development of viable methods for their sustainable production. Currently, large amounts of toxic solvents are required for peptide assembly from protected building blocks, and switching to water as a reaction medium remains a major hurdle in peptide chemistry. We report an aqueous solid‐phase peptide synthesis strategy that is based on a water‐compatible 2,7‐disulfo‐9‐fluorenylmethoxycarbonyl (Smoc) protecting group. This approach enables peptide assembly under aqueous conditions, real‐time monitoring of building block coupling, and efficient postsynthetic purification. The procedure for the synthesis of all natural and several non‐natural Smoc‐protected amino acids is described, as well as the assembly of 22 peptide sequences and the fundamental issues of SPPS, including the protecting group strategy, coupling and cleavage efficiency, stability under aqueous conditions, and crucial side reactions.     

Molecular Recognition with Model Systems

How structures fit together is the principal domain of molecular recognition, and current studies are evolving from the host–guest chemistry of ions to interactions between two molecules. Recent advances in the synthesis of sizable concave molecules, especially those featuring convergent functional groups, make it possible to bind smaller convex structures with considerable selectivity. One result is that hydrogen bonding can be addressed in model systems. The present review emphasizes the use of cleftlike structures as a means of probing the forces involved in nucleic acid recognition. The application of such molecules to the catalysis of chemical reactions, particularly those involved in self-replicating systems, is also described. Some implications for future pharmaceutical agents are suggested as a result of access to synthetic receptors for biologically relevant targets.     

Electrical behavior of molecular junctions incorporating alpha-helical peptide

We synthesized an alpha-helical peptide containing two terminal thiol groups and demonstrated the method of preparation of a self-assembled monolayer (SAM) on gold with uniform orientation of the molecules on the surface. The monolayers were employed as model systems for the investigations of mediated electron transfer. The measurements of electron transfer efficiency through the peptide were performed using scanning tunneling spectroscopy (STS). The molecules were trapped between the gold tip and the substrate using a Au-S linkage. The electron transfer behavior of the peptide was examined as a function of the tip-substrate distance at fixed bias voltage and as a function of bias voltage at a fixed distance between the tip and the substrate. The data obtained from these experiments indicated that the electron transfer through alpha-helical peptide is very efficient, and its conductivity is comparable to those observed for dodecanedithiol. There is also a directional dependence of electron transmission through the peptide, which is connected with the electric field generated by the molecular dipole of the helix.     

From Prebiotic Chemistry to Supramolecular Biomedical Materials: Exploring the Properties of Self-Assembling Nucleobase-Containing Peptides

Peptides and their synthetic analogs are a class of molecules with enormous relevance as therapeutics for their ability to interact with biomacromolecules like nucleic acids and proteins, potentially interfering with biological pathways often involved in the onset and progression of pathologies of high social impact. Nucleobase-bearing peptides (nucleopeptides) and pseudopeptides (PNAs) offer further interesting possibilities related to their nucleobase-decorated nature for diagnostic and therapeutic applications, thanks to their reported ability to target complementary DNA and RNA strands. In addition, these chimeric compounds are endowed with intriguing self-assembling properties, which are at the heart of their investigation as self-replicating materials in prebiotic chemistry, as well as their application as constituents of innovative drug delivery systems and, more generally, as novel nanomaterials to be employed in biomedicine. Herein we describe the properties of nucleopeptides, PNAs and related supramolecular systems, and summarize some of the most relevant applications of these systems.     

The charge ratio between O and N on amide bonds: a new approach to the mobile proton model

The influence of charge distribution on the cleavage of the peptides was investigated by fragmentation efficiency curves and quantum chemical calculations in order to clarify the fragmentation mechanism in this paper. The peptide Arg-Gly-Asp-Cys (RGDC) was oxidized to change the charge distribution, but its main sequence was retained. Under this study, it was illustrated that the fragmentation of the peptide RGDC became easier with each addition of an O atom to the Cys hydrosulfide group and the relative charge ratios between O and N (QO/QN) in the amide bonds had much to do with the cleavage of the peptide RGDC. For each amide bond, the situations coincided with overall conclusion: the increase of the QO/QN values results in a higher fragmentation efficiency and vice versa. The methods which combined fragmentation efficiency curves with the charge distribution of peptides provided a way to refine the mobile proton model for peptide fragmentation and to probe the discrepant fragmentation of peptides in peptide/protein identification.     

Cross-catalytic replication of an RNA ligase ribozyme

A self-replicating RNA ligase ribozyme was converted to a cross-catalytic format whereby two ribozymes direct each other's synthesis from a total of four component substrates. Each ribozyme binds two RNA substrates and catalyzes their ligation to form the opposing ribozyme. The two ribozymes are not perfectly complementary, as is the case for replicating nucleic acid genomes in biology. Rather, the ribozymes contain both template elements, which are complementary, and catalytic elements, which are identical. The specificity of the template interactions allows the cross-catalytic pathway to dominate over all other reaction pathways. As the concentration of the two ribozymes increases, the rate of formation of additional ribozyme molecules increases, consistent with the overall autocatalytic behavior of the reaction system.     

Peptide o‐Aminoanilides as Crypto‐Thioesters for Protein Chemical Synthesis

Fully unprotected peptide o‐aminoanilides can be efficiently activated by NaNO₂ in aqueous solution to furnish peptide thioesters for use in native chemical ligation. This finding enables the convergent synthesis of proteins from readily synthesizable peptide o‐aminoanilides as a new type of crypto‐thioesters. The practicality of this approach is shown by the synthesis of histone H2B from five peptide segments. Purification or solubilization tags, which are sometimes needed to improve the efficiency of protein chemical synthesis, can be incorporated into the o‐aminoanilide moiety, as demonstrated in the preparation of the cyclic protein lactocyclicin Q.     

Effects of peptide acetylation and dimethylation on electrospray ionization efficiency

Peptide acetylation and dimethylation have been widely used to derivatize primary amino groups (peptide N‐termini and the ε‐amino group of lysines) for chemical isotope labeling of quantitative proteomics or for affinity tag labeling for selection and enrichment of labeled peptides. However, peptide acetylation results in signal suppression during electrospray ionization (ESI) due to charge neutralization. In contrast, dimethylated peptides show increased ionization efficiency after derivatization, since dimethylation increases hydrophobicity and maintains a positive charge on the peptide under common LC conditions. In this study, we quantitatively compared the ESI efficiencies of acetylated and dimethylated model peptides and tryptic peptides of BSA. Dimethylated peptides showed higher ionization efficiency than acetylated peptides for both model peptides and tryptic BSA peptides. At the proteome level, peptide dimethylation led to better protein identification than peptide acetylation when tryptic peptides of mouse brain lysate were analyzed with LC‐ESI‐MS/MS. These results demonstrate that dimethylation of tryptic peptides enhanced ESI efficiency and provided up to two‐fold improved protein identification sensitivity in comparison with acetylation. Copyright © 2016 John Wiley & Sons, Ltd.