Biochemical problems of regulation by oligopeptides

Multiple Diversity of Mitochondrial Cytochrome b Amino Acid Sequences of the Same Length in Animals

The size of natural peptide molecules (proteins) can be considered as the number of amino acid residues p (protein length). The aim of the work was to analyze the region of existence and occurrence of natural amino acid residue sequences formed as a result of matrix synthesis on the p scale. The object of the study was the Swiss-Prot database consisting of more than 5.6 × 10⁵ primary peptide structures, which were fully determined (complete sequence). Sequences containing non-standard amino acid residues, as well as identical copies of sequences, were removed from them. The remaining 463,450 different sequences with a length of 2–35,213 residues were used for further analysis. It was shown that the protein lengths of different biological domains and kingdoms are characterized by different regions of existence, and the profile shapes of the obtained curves are close to a number of known distributions. At the same time, they have sharp high peaks, indicating the existence of a large number of specific molecules with the same protein length. One of these peaks characterizes more than 1,000 different sequences of mitochondrial cytochrome b molecules at p = 379. Such examples may indicate that the most perfect protein lengths were selected in the evolutionary process to perform this function. As a result, many protein molecules with different sequences of the same length and characterized by the same functions were formed.

Effect of Inactivating Mutations on Peptide Conformational Ensembles: The Plant Polypeptide Hormone Systemin

As part of their basal immune mechanism against insect/herbivore attacks, plants have evolved systemic response mechanisms. Such a systemic wound response in tomato was found to involve an 18 amino acid polypeptide called systemin, the first polypeptide hormone to be discovered in plants. Systematic alanine scanning and deletion studies showed differential modulation in its activity, particularly a major loss of function due to alanine substitution at positions 13 and 17 and less extentive loss of function due to substitution at position 12. We have studied the conformational ensembles of wild-type systemin along with its 17 variants by carrying out a total of 5.76 μs of replica-exchange molecular dynamics simulation in an implicit solvent environment. In our simulations, wild-type systemin showed a lack of α-helical and β-sheet structures, in conformity with earlier circular dichroism and NMR data. On the other hand, two regions containing diproline segments showed a tendency to adopt polyproline II structures. Examination of conformational ensembles of the 17 variants revealed a change in the population distributions, suggesting a less flexible structure for alanine substitutions at positions 12 and 13 but not for position 17. Combined with the experimental observations that positions 1-14 of systemin are important for the formation of the peptide-receptor complex, this leads to the hypothesis that loss of conformational flexibility may play a role in the loss of activity of systemin due to the P12A and P13A substitutions, while T17A deactivation probably occurs for a different reason, most likely the loss of the threonine phosphorylation site. We also indicate possible structural reasons why the substitution of the prolines at positions 12 and 13 leads to a loss of conformational freedom in the peptide.

Synthesis and Characterization of Bradykinin Derivatives Based on a β-Cyclodextrin Core

Mono-6A-fluorenylmethyloxycarbonylamino-mono-6X-succinyl-β-cyclodextrin (1), an amino acid-based bi-functionalized derivative of β-cyclodextrin (β-CD), has been functionalized with the bioactive peptide, bradykinin and/or sulfonamides using fluorenylmethyloxycarbonyl (Fmoc) solid phase peptide synthesis (SPPS). The all-in-one molecule contains a carrier (cyclodextrin), targeting agent (bradykinin), and/or model drug (sulfonamide). Varying combinations of these bradykinin-focussed molecules have been synthesized using Fmoc SPPS on Rink amide resin. The positioning of the sulfonamide group, the bradykinin peptide and the cyclodextrin carrier are essential for biological activity. The inclusion of spacers is also important. Structure–activity studies performed on three cancer cell lines in vitro support these conclusions.

Fragmentomics of natural peptide structures

Natural fragmentation of peptide and other chemical structures is well known. They are a significant object of biochemical investigations. In this connection, the bases and determination are given for the notion of the "fragmentome" as a set of all fragments of a single substance, as well as for global fragmentome of all chemical components of living organisms. It is described how protein-peptide fragments are formed in nature, what experimental and theoretical methods are used for their investigation, as well as mathematical characteristics of fragmentomes. Individual fragmentomes of all subunits and of complete casein fragmentome are considered in detail. Structural and functional variety of its possible fragments was revealed by computer analysis. Formation in an organism of an exogenous-endogenous pool of oligopeptides and correlation of these data with concepts of structure-functional continuum of regulatory molecules is shown on an example of food protein fragments. Possible practical importance of the use of natural fragments in dietology, therapy, as well as in sanitary hygiene and cosmetics is noted.