The Alanine World Model for the Development of the Amino Acid Repertoire in Protein Biosynthesis

A central question in the evolution of the modern translation machinery is the origin and chemical ethology of the amino acids prescribed by the genetic code. The RNA World hypothesis postulates that templated protein synthesis has emerged in the transition from RNA to the Protein World. The sequence of these events and principles behind the acquisition of amino acids to this process remain elusive. Here we describe a model for this process by following the scheme previously proposed by Hartman and Smith, which suggests gradual expansion of the coding space as GC–GCA–GCAU genetic code. We point out a correlation of this scheme with the hierarchy of the protein folding. The model follows the sequence of steps in the process of the amino acid recruitment and fits well with the co-evolution and coenzyme handle theories. While the starting set (GC-phase) was responsible for the nucleotide biosynthesis processes, in the second phase alanine-based amino acids (GCA-phase) were recruited from the core metabolism, thereby providing a standard secondary structure, the α-helix. In the final phase (GCAU-phase), the amino acids were appended to the already existing architecture, enabling tertiary fold and membrane interactions. The whole scheme indicates strongly that the choice for the alanine core was done at the GCA-phase, while glycine and proline remained rudiments from the GC-phase. We suggest that the Protein World should rather be considered the Alanine World, as it predominantly relies on the alanine as the core chemical scaffold.TU Berlin, Open-Access-Mittel - 201

Promotion of the collagen triple helix in a hydrophobic environment

In contrast to many other water-soluble peptide arrangements, the formation of a triple helix in collagen proceeds inside out: polar glycyl residues form the interior, whereas nonpolar prolyl side chains constitute the exterior. In our work, we decided to exploit this aspect of the peptide architecture in order to create hyperstable collagen mimicking peptides (CMPs). The key element of this study is the environment. Given that the peptide assembles in a nonpolar medium, the collapse of the polar peptide backbone into the triple helix should become more favorable. Following this idea, we prepared CMPs based on hydrophobic proline analogues. The synthesis was performed by a combination of liquid- and solid-phase approaches: first, hexapeptides were prepared in solution, and then these were launched into conventional Fmoc-based peptide synthesis on a solid support. The resulting peptides showed an excellent signal of the triple helix in the model nonpolar solvent (octanol) according to circular dichroism observations. In a study of a series of oligomers, we found that the minimal length of the peptides required for triple helical assembly is substantially lower compared to water-soluble CMPs. Our results suggest further explorations of the CMPs in hydrophobic media; in particular, we highlight the suggestion that collagen could be converted into a membrane protein.DFG, 207100805, FOR 1805: Einfluss der Ribosomendynamik auf Regulation der Geschwindigkeit und Genauigkeit der TranslationTU Berlin, Open-Access-Mittel - 201

Construction of a polyproline structure with hydrophobic exterior using octahydroindole-2-carboxylic acid

The proline analogue (2S,3aS,7aS)-octahydroindole-2-carboxylic acid (Oic) has been previously applied as a proline substitute in pharmocologically active peptides and as a structural component of the antihypertensive drug Perindopril. Herein, we describe the formation of an oligoproline structure by an Oic oligomer. A series of Oic oligomers were investigated to show the structural and energetic contribution of appended residues to the structure. NMR investigation of these oligomers revealed an all-trans amide bond structure, and we provide evidence that a cascade-like mechanism is responsible for the all-trans folding cooperativity. X-ray crystallography of the Oic-hexapeptide clearly demonstrates that the all-trans structure of the Oic oligomer is a polyproline II helix. Thus, as a hydrophobic proline analog with a highly stable trans-amide bond, Oic represents an ideal building block for hydrophobic sites of polyproline II structures in biologically relevant contexts.DFG, FOR 1805, Einfluss der Ribosomendynamik auf Regulation der Geschwindigkeit und Genauigkeit der Translatio

Energetic contribution to both acidity and conformational stability in peptide models

The acidity of N-acyl amino acids is dependent upon the rotameric state of the amide bond. In this work we systematically investigated the acidity difference of the rotamers (Delta pK(a)) in the frames of various acetylated amino acids. Our results indicated a mutual interaction of two carbonyl groups of an attractive type. We observed conservative Delta pK(a)s for acyclic amino acids (2.2-3.0 kJ mol(-1)), whereas in the case of alicyclic amino acids, the experimental values revealed a strong dependency on the structural context (1.5-4.4 kJ mol(-1)). In homologous amino acids (alpha-, beta-, gamma-, etc.), the strength of the attraction decays in an exponential fashion. Furthermore, the interaction can accumulate through a chain of amide bonds in a cascade fashion, as demonstrated by an Ac-Pro-Pro dipeptide. As a result, we demonstrate that Delta pK(a) is an experimental parameter to estimate increments in the carbonyl-carbonyl alignment, as determined by the amino acid or peptidyl context. This parameter is also important in understanding the roles of amino acids in both protein folding and translation in biological systems as well as their evolutionary appearance in the genetic code.DFG, EXC 314, Unifying Concepts in Catalysi

Bilayer thickness determines the alignment of model polyproline helices in lipid membranes

Our understanding of protein folds relies fundamentally on the set of secondary structures found in the proteomes. Yet, there also exist intriguing structures and motifs that are underrepresented in natural biopolymeric systems. One example is the polyproline II helix, which is usually considered to have a polar character and therefore does not form membrane spanning sections of membrane proteins. In our work, we have introduced specially designed polyproline II helices into the hydrophobic membrane milieu and used 19F NMR to monitor the helix alignment in oriented lipid bilayers. Our results show that these artificial hydrophobic peptides can adopt several different alignment states. If the helix is shorter than the thickness of the hydrophobic core of the membrane, it is submerged into the bilayer with its long axis parallel to the membrane plane. The polyproline helix adopts a transmembrane alignment when its length exceeds the bilayer thickness. If the peptide length roughly matches the lipid thickness, a coexistence of both states is observed. We thus show that the lipid thickness plays a determining role in the occurrence of a transmembrane polyproline II helix. We also found that the adaptation of polyproline II helices to hydrophobic mismatch is in some notable aspects different from α-helices. Finally, our results prove that the polyproline II helix is a competent structure for the construction of transmembrane peptide segments, despite the fact that no such motif has ever been reported in natural systems.DFG, 207100805, FOR 1805: Einfluss der Ribosomendynamik auf Regulation der Geschwindigkeit und Genauigkeit der TranslationTU Berlin, Open-Access-Mittel - 201

Halogenation of tyrosine perturbs large-scale protein self-organization

Protein halogenation is a common non-enzymatic post-translational modification contributing to aging, oxidative stress-related diseases and cancer. Here, we report a genetically encodable halogenation of tyrosine residues in a reconstituted prokaryotic filamentous cell-division protein (FtsZ) as a platform to elucidate the implications of halogenation that can be extrapolated to living systems of much higher complexity. We show how single halogenations can fine-tune protein structures and dynamics of FtsZ with subtle perturbations collectively amplified by the process of FtsZ self-organization. Based on experiments and theories, we have gained valuable insights into the mechanism of halogen influence. The bending of FtsZ structures occurs by affecting surface charges and internal domain distances and is reflected in the decline of GTPase activities by reducing GTP binding energy during polymerization. Our results point to a better understanding of the physiological and pathological effects of protein halogenation and may contribute to the development of potential diagnostic tools

Об одном механизме образования пространственно-неоднородных структур световых волн в оптических системах передачи информации

Spatially inhomogeneous structures of light waves are used as a mechanism of compacting information in optical and fiber-optic communication systems. In this paper, we consider a mathematical model of an optical radiation generator with a nonlinear delayed feedback loop and a stretching (compression) operator of the spatial coordinates of the light wave in a plane orthogonal to the radiation direction. It is shown that the presence of a delay in the feedback loop can lead to the generation of stable periodic spatially inhomogeneous oscillations. In the space of the main parameters of the generator, the spaces of generation of stable spatially non-uniform oscillations are constructed, the mechanism of their occurrence is studied, and approximate asymptotic formulas are constructed.Пространственно-неоднородные структуры световых волн используются как механизм уплотнения информации в системах оптической и волоконно-оптической связи. В работе рассматривается математическая модель генератора оптического излучения с контуром нелинейной запаздывающей обратной связи и оператором растяжения (сжатия) пространственных координат световой волны в плоскости, ортогональной направлению излучения. Показано, что наличие запаздывания в контуре обратной связи может привести к генерации устойчивых периодических пространственно-неоднородных колебаний. В пространстве основных параметров генератора построены области генерации устойчивых пространственно-неоднородных колебаний, изучен механизм их возникновения, построены приближенные асимптотические формулы

Conjugation of Synthetic Polyproline Moietes to Lipid II Binding Fragments of Nisin Yields Active and Stable Antimicrobials

Coupling functional moieties to lantibiotics offers exciting opportunities to produce novel derivatives with desirable properties enabling new functions and applications. Here, five different synthetic hydrophobic polyproline peptides were conjugated to either nisin AB (the first two rings of nisin) or nisin ABC (the first three rings of nisin) by using click chemistry. The antimicrobial activity of nisin ABC + O6K3 against Enterococcus faecium decreased 8-fold compared to full-length nisin, but its activity was 16-fold better than nisin ABC, suggesting that modifying nisin ABC is a promising strategy to generate semi-synthetic nisin hybrids. In addition, the resulting nisin hybrids are not prone to degradation at the C-terminus, which has been observed for nisin as it can be degraded by nisinase or other proteolytic enzymes. This methodology allows for getting more insight into the possibility of creating semi-synthetic nisin hybrids that maintain antimicrobial activity, in particular when synthetic and non-proteinaceous moieties are used. The success of this approach in creating viable nisin hybrids encourages further exploring the use of different modules, e.g., glycans, lipids, active peptide moieties, and other antimicrobial moieties

Анализ условий возникновения пространственно-неоднородных структур световых волн в оптических системах передачи информации

A model of distributed information carriers in the form of stable spatially inhomogeneous structures in optical and fiber-optic communication systems is considered. We study the conditions for the occurrence of such stable spatially inhomogeneous structures of the light wave of the generator of optical radiation. The formation of inhomogeneous structures that occur in a plane orthogonal to the direction of wave propagation is provided by a thin layer of nonlinear medium and a two-dimensional lagging feedback loop with the rotation operator of the spatial coordinates of the light wave in the emission plane of the optical generator. In the space of the main parameters of the generator (a control parameter, the angle of rotation of the spatial coordinates, the magnitude of the delay), the areas of generation of stable spatially inhomogeneous structures are constructed, the mechanisms of their occurrence are analyzed.Рассматривается модель распределенных носителей информации в виде устойчивых пространственно-неоднородных структур в системах оптической и волоконно-оптической связи. Изучаются условия возникновения таких устойчивых пространственно-неоднородных структур световой волны генератора оптического излучения. Образование неоднородных структур, которые возникают в плоскости, ортогональной направлению распространения волны, обеспечивается тонким слоем нелинейной среды и контуром двумерной запаздывающей обратной связи с оператором поворота пространственных координат световой волны в плоскости излучения оптического генератора. В пространстве основных параметров генератора (управляющий параметр, угол поворота пространственных координат, величина запаздывания) построены области генерации устойчивых пространственно-неоднородных структур, был проведен анализ механизмов их возникновения