From Synthesis of Amino Acids and Peptides to Enzymatic Catalysis: A Bottom-Up Approach in Mechanochemistry

Molecular chairs, carrying three amino acids or peptides, stack in an antiparallel fashion to give hexavalent assemblies for bottom-up construction of novel soft materials and therapeutics.

Download Full-text

Development of a method for producing new generation of protein snacks using the processes of cryo and mechanical distruction

EUREKA Life Sciences ◽

10.21303/2504-5695.2021.001877 ◽

2021 ◽

pp. 46-52

Author(s):

Viktoriya Pogarskaya ◽

Olga Yurieva ◽

Aleksey Pogarskiy ◽

Kateryna Balabai ◽

Nadiya Maksymova

Keyword(s):

Amino Acids ◽

Raw Materials ◽

Enzymatic Catalysis ◽

Bound State ◽

Biologically Active ◽

Mechanical Destruction ◽

Biological Potential ◽

Quick Freezing ◽

Complete Protein ◽

New Generation

The aim of research is to develop a method for the production of a new generation of protein snacks using a protein vegetable and milk base and vegetable fortifiers from spicy and carotene-containing vegetables using cryo and mechanical destruction processes. The method is based on the use of a deep processing method as an innovation, which consists in a complex effect on vegetable and protein raw materials of cryo and mechanical destruction processes in modern quick-freezing and low-temperature crushing equipment. The proposed method allows to get new protein snacks with a high content of protein, BAR and phytocomponents in an easily digestible form. A new generation of protein snacks has been developed to strengthen the immune system using cryogenic protein base and vegetable raw materials. Nano-additives from dried peas and specially processed soft brine cheese are used as a protein base. Pea nanoadditives obtained using non-enzymatic catalysis – mechanolysis, mechanical destruction contain 21.5 ... 23.0% of complete protein, which includes 49% of amino acids in a bound state and 51% in a free state. During the special processing of soft brine cheese with the help of mechanical destruction, 50 ... 55% of the bound amino acids of the protein are transformed into free α-amino acids in an easily digestible form. The proposed method makes it possible to more fully reveal the biological potential of vegetable and protein raw materials, to transform protein, BAS and phytocomponents in a bound form into easily digestible nanocomponents into a free easily digestible form. In addition, the processed protein base and raw materials acquire new properties - structure formation, gelation, coloring ability. The obtained protein snacks are natural, differ from the traditional ones by their high content of complete protein and the absence of synthetic impurities (preservatives, thickeners, colorants, etc.). In addition, 100 g of new products can satisfy the daily requirement for biologically active substances (β-carotene, L-ascorbic acid, phenolic compounds)

Download Full-text

Protein modeling

Physical Sciences Reviews ◽

10.1515/psr-2018-0161 ◽

2021 ◽

Vol 0 (0) ◽

Author(s):

Rodrigo S. A. de Araújo ◽

Francisco J. B. Mendonça ◽

Marcus T. Scotti ◽

Luciana Scotti

Keyword(s):

Amino Acids ◽

Genetic Information ◽

Enzymatic Catalysis ◽

Three Dimensional ◽

Cellular Function ◽

Protein Modeling ◽

Biological Role ◽

Cell Recognition ◽

Monomeric Composition

Abstract Proteins are essential and versatile polymers consisting of sequenced amino acids that often possess an organized three-dimensional arrangement, (a result of their monomeric composition), which determines their biological role in cellular function. Proteins are involved in enzymatic catalysis; they participate in genetic information decoding and transmission processes, in cell recognition, in signaling, and transport of substances, in regulation of intra and extracellular conditions, and other functions.

Download Full-text

Synthesis by enzymatic catalysis. III. Copolymerisation of amino acids and dipeptides using papain

Journal of Chemical Technology & Biotechnology ◽

10.1002/jctb.280360906 ◽

2007 ◽

Vol 36 (9) ◽

pp. 427-434 ◽

Cited By ~ 1

Author(s):

Christine Selvi ◽

Michel Baboulene ◽

Vincent Speziale ◽

Armand Lattes

Keyword(s):

Amino Acids ◽

Enzymatic Catalysis

Download Full-text

Enzyme catalysis prior to aromatic residues: reverse engineering of a dephosphoCoA kinase

10.1101/2020.11.11.377994 ◽

2020 ◽

Author(s):

Mikhail Makarov ◽

Jingwei Meng ◽

Vyacheslav Tretyachenko ◽

Pavel Srb ◽

Anna Březinová ◽

...

Keyword(s):

Amino Acids ◽

Amino Acid ◽

Genetic Code ◽

Enzyme Catalysis ◽

Enzymatic Catalysis ◽

Aromatic Amino Acids ◽

Hydrophobic Core ◽

Aquifex Aeolicus ◽

Lower Efficiency ◽

Amino Acid Alphabet

AbstractIt is well-known that the large diversity of protein functions and structures is derived from the broad spectrum of physicochemical properties of the 20 canonical amino acids. According to the generally accepted hypothesis, protein evolution was continuously associated with enrichment of this alphabet, increasing stability, specificity and spectrum of catalytic functions. Aromatic amino acids are considered the latest addition to genetic code.The main objective of this study was to test whether enzymatic catalysis can spare the aromatic amino acids (aromatics) by determining the effect of amino acid alphabet reduction on structure and function of dephospho-CoA kinase (DPCK). We designed two mutant variants of a putative DPCK from Aquifex aeolicus by substituting (i) Tyr, Phe and Trp or (ii) all aromatics (including His), i.e. ∼10% of the total sequence. Their structural characterization indicates that removal of aromatic amino acids may support rich secondary structure content although inevitably impairs a firm globular arrangement. Both variants still possess ATPase activity, although with 150-300 times lower efficiency in comparison with the wild-type phosphotransferase activity. The transfer of the phosphate group to the dephospho-CoA substrate is however heavily uncoupled and only one of the variants is still able to perform the reaction.Here we provide support to the hypothesis that proteins in the early stages of life could support at least some enzymatic activities, despite lower efficiencies resulting from the lack of a firm hydrophobic core. Based on the presented data we hypothesize that further protein scaffolding role may be provided by ligands upon binding.SignificanceAll extant proteins rely on the standard coded amino acid alphabet. However, early proteins lacked some of these amino acids that were incorporated into the genetic code only after the evolution of their respective metabolic pathways, aromatic amino acids being among the last additions. This is intriguing because of their crucial role in hydrophobic core packing, indispensable for enzyme catalysis.We designed two aromatics-less variants of a highly conserved enzyme from the CoA synthesis pathway, capable of enzyme catalysis and showing significant ordering upon substrate binding. To our knowledge, this is the first example of enzyme catalysis in complete absence of aromatic amino acids and presents a possible mechanism of how aromatics-less enzymes could potentially support an early biosphere.

Download Full-text

Homochirality as the Signature of Extra-Terrestrial Life

International Astronomical Union Colloquium ◽

10.1017/s0252921100015037 ◽

1997 ◽

Vol 161 ◽

pp. 505-510

Author(s):

Alexandra J. MacDermott ◽

Laurence D. Barron ◽

Andrè Brack ◽

Thomas Buhse ◽

John R. Cronin ◽

...

Keyword(s):

Amino Acids ◽

Protein Synthesis ◽

Optical Rotation ◽

Physical Origin ◽

Natural Choice ◽

Rosetta Mission ◽

Terrestrial Life ◽

Subsurface Layers ◽

Solar System Bodies ◽

Origin Of Homochirality

AbstractThe most characteristic hallmark of life is its homochirality: all biomolecules are usually of one hand, e.g. on Earth life uses only L-amino acids for protein synthesis and not their D mirror images. We therefore suggest that a search for extra-terrestrial life can be approached as a Search for Extra- Terrestrial Homochirality (SETH). The natural choice for a SETH instrument is optical rotation, and we describe a novel miniaturized space polarimeter, called the SETH Cigar, which could be used to detect optical rotation as the homochiral signature of life on other planets. Moving parts are avoided by replacing the normal rotating polarizer by multiple fixed polarizers at different angles as in the eye of the bee. We believe that homochirality may be found in the subsurface layers on Mars as a relic of extinct life, and on other solar system bodies as a sign of advanced pre-biotic chemistry. We discuss the chiral GC-MS planned for the Roland lander of the Rosetta mission to a comet and conclude with theories of the physical origin of homochirality.

Download Full-text

Hydrogen Cyanide Polymers from the Impact of Comet P/Shoemaker-Levy 9 on Jupiter

International Astronomical Union Colloquium ◽

10.1017/s025292110001469x ◽

1997 ◽

Vol 161 ◽

pp. 179-187

Author(s):

Clifford N. Matthews ◽

Rose A. Pesce-Rodriguez ◽

Shirley A. Liebman

Keyword(s):

Amino Acids ◽

Solar System ◽

Hydrogen Cyanide ◽

Nitrogen Heterocycles ◽

Laboratory Studies ◽

Heterogeneous Solids ◽

The Many ◽

Comet Halley ◽

The Impact ◽

By Products

AbstractHydrogen cyanide polymers – heterogeneous solids ranging in color from yellow to orange to brown to black – may be among the organic macromolecules most readily formed within the Solar System. The non-volatile black crust of comet Halley, for example, as well as the extensive orangebrown streaks in the atmosphere of Jupiter, might consist largely of such polymers synthesized from HCN formed by photolysis of methane and ammonia, the color observed depending on the concentration of HCN involved. Laboratory studies of these ubiquitous compounds point to the presence of polyamidine structures synthesized directly from hydrogen cyanide. These would be converted by water to polypeptides which can be further hydrolyzed to α-amino acids. Black polymers and multimers with conjugated ladder structures derived from HCN could also be formed and might well be the source of the many nitrogen heterocycles, adenine included, observed after pyrolysis. The dark brown color arising from the impacts of comet P/Shoemaker-Levy 9 on Jupiter might therefore be mainly caused by the presence of HCN polymers, whether originally present, deposited by the impactor or synthesized directly from HCN. Spectroscopic detection of these predicted macromolecules and their hydrolytic and pyrolytic by-products would strengthen significantly the hypothesis that cyanide polymerization is a preferred pathway for prebiotic and extraterrestrial chemistry.

Download Full-text

Methionine-Specific Staining of Collagen

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s042482010005408x ◽

1982 ◽

Vol 40 ◽

pp. 294-295

Author(s):

E.M. Kuhn ◽

K.D. Marenus ◽

M. Beer

Keyword(s):

Amino Acids ◽

Collagen Fibers ◽

Type Iii Collagen ◽

Type I ◽

Electron Microscopic ◽

Good Correspondence ◽

Specific Staining ◽

Type Iii ◽

Different Types ◽

Sulfur Containing

Fibers composed of different types of collagen cannot be differentiated by conventional electron microscopic stains. We are developing staining procedures aimed at identifying collagen fibers of different types.Pt(Gly-L-Met)Cl binds specifically to sulfur-containing amino acids. Different collagens have methionine (met) residues at somewhat different positions. A good correspondence has been reported between known met positions and Pt(GLM) bands in rat Type I SLS (collagen aggregates in which molecules lie adjacent to each other in exact register). We have confirmed this relationship in Type III collagen SLS (Fig. 1).

Download Full-text