Biochemical problems of regulation by oligopeptides

Some problems are considered which arise in biochemical studies on structure and function of natural oligopeptides consisting of 2–50 amino acid residues. The problems under consideration include the generation of oligopeptides from precursors, chemical structure, the role of functionally important radicals and spatial configuration, and structure-function relationships. Different types of regulation are shown mainly for oligopeptides involved in muscle contraction.Translated from Biokhimiya, Vol. 69, No. 11, 2004, pp. 1565–1573.Original Russian Text Copyright © 2004 by Zamyatnin.     

Fragmentomics of proteins and natural oligopeptides

The term fragmentomics is grounded and defined. Theoretical structure-function analysis of all possible fragments of a protein molecule was performed under the concept of fragmentomics to determine the regions that could be potential sources of regulatory oligopeptides. For this purpose, we used the data on the primary structure of bovine hemoglobin, the information contained in the EROP-Moscow database on the structures and functions of natural oligopeptides, and a specialized software package. This analysis revealed natural nonhemoglobin oligopeptides containing hemoglobin fragments and natural oligopeptides with the structure precisely coinciding with hemoglobin fragments. The most abundant of them are neuropeptides, antimicrobial oligopeptides, and hormones. It was demonstrated that the tetrapeptide and larger fragments of hemoglobin identified in nonhemoglobin oligopeptides and possessing a mentioned activity are present in the amino acid sequences of experimentally determined hemoglobin oligopeptides with the same function. The proposed approach allowed us to discover new potentially active sites in the hemoglobin amino acid sequence not yet studied experimentally. The possibility of natural formation of regulatory oligopeptides from hemoglobin molecules and other food proteins is discussed, as well as the generation of an exogenous oligopeptide pool in the gastrointestinal tract, and how the results match the concept of natural continuum of regulatory oligopeptides.     

An approach to the problem of the structuro-functional organization of natural peptides

Theory and computational scheme of three-dimensional structure and dynamic conformational properties of naturally occurring peptides are proposed basing on a known amino acid sequence. The diverse biological activity of a low-molecular peptide is shown to arise from a restricted number of preferable spatial structures which may occur under physiological conditions. Each particular function of an oligopeptide is connected to a definite spatial structure, belonging to the set of low-energy conformations from one biological activity of a peptide shift of the conformational equilibrium caused by a change of environmental conditions. This shift is provided for by specific intramolecular interactions, alternative in their nature, which stabilize a particular structure. An approach is suggested which enables to construct a synthetic analog with the predetermined physiologically active conformation, prior to all chemical and biological tests.     

Oligopeptides in the development of biological motivations

Data are presented, demonstrating the action of a number of oligopeptides on biological motivations of hunger, fear, self-stimulation and on alcohol addiction. In the structure of animals feeding motivation, such oligopeptides take part as beta-lipotropin and its fragments, ACTH, pentagastrin, delta-sleep inducing peptide (DSIP), substance P; in organization of defensive motivation--angiotensin II (AII), DSIP, substance P, bradykinin, beta-endorphin etc.; in organization of self-stimulation--AII, DSIP, bradykinin, ACTH, beta-endorphin etc. It is established that most of the above oligopeptides, injected to the brain lateral ventriculi, inhibit biological motivations, and only some of them have an activating action. On the basis of experiments, a hypothesis is formulated that oligopeptides act as a feedback between the genome of brain neurones and pacemaker cells of motivation centres of the hypothalamus area. Some oligopeptides elaborated by neuronal genomes under the action of dominating motivation, activate--and the other--suppress the activity of motivation hypothalamus centres.     

植物多肽类化合物研究进展

本义综述了近年来植物中的寡肽、环肽、环肽生物碱、糖肽的提取分离方法、结构签定及其生物活性等方面的研究进展。     

Study of the relationship between conformation and nature of side chains in linear oligopeptides: homologous series derived from β-branched amino acid residues

Conformational analysts of the three homologous series, from dipeptide to heptapeptide of monodisperse, N- and C-protected oligopeptides derived from the β-branched α-amino acid residues L-valine, L-isoleucine, and D-allo-isoleucine is reported. Occurrence of intermolecular β conformations in the higher oligopeptides in the solid state was established by means of infrared absorption. The extent of intramolecularly hydrogen-bonded folded structure formation was assessed as a function of chain length in solvents of low polarity at high dilution. Statistical coil and intermolecular β-conformations were shown to exist in alcohols and aqueous alcoholic mixtures. The results obtained indicate that, branching positions being equal, configuration of the asymmetric carbon atom in the lateral chain, overall bulkiness and lyophobic character of the amino acid side chains are all important factors in determining the stability of the ordered conformations of oligopeptides.     

Sequence Pattern for the Occurrence of N-Glycosylation in Proteins

To further understand the occurrence of N-glycosylation, 21 nonhomologous proteins with Asn–x–Ser/Thr sequence were investigated. The results showed that some oligopeptides with Gly residues (G–x–y or y–x–G) are adjacent to the N-glycosylated sequences. These oligopeptides are not only essential for the structure and function of the proteins, but they are also found to be often proteolytic processing sites. These properties suggest that these oligopeptides may be a sequence pattern for the occurrence of N-glycosylation. The implications of the findings for protein structure and function are discussed.     

Hemoglobin as a potential source of natural regulatory oligopeptides

Theoretical structure-function analysis of all possible hemoglobin molecule fragments was performed to determine sites that could be potential sources of regulatory oligopeptides. Known data on bovine hemoglobin primary structure and information of the EROP-Moscow database concerning structure and functions of natural oligopeptides were used along with a computer program complex. A total of 6750 natural non-hemoglobin oligopeptides with hemoglobin fragments of 2–14 amino acid residues were found. Structures of 20 of them were completely identical to hemoglobin fragments. Most of the revealed oligopeptides exhibit properties of neuropeptides, antimicrobial agents, and hormones. A number of them exhibit functions previously not known for hemoglobin fragments. The possibility of natural formation of regulatory oligopeptides from hemoglobin and other food protein molecules, generation of the exogenous oligopeptide pool, their participation in regulation processes as well as accordance of results obtained here with the oligopeptide continuum concepts are discussed.     

Synthesis, conformation, and immunoreactivity of new carrier molecules based on repeated tuftsin-like sequence

Sequential oligopeptides based on a pentapeptide (TKPKG) derived from tuftsin with different lengths were synthesized by stepwise solid phase methodology. These highly soluble oligomers were nontoxic on mouse spleen cells, and other biological data suggested that tuftsin-like properties were also presented. The (TKPKG)n (n=2,4,6,8) oligopeptides were not immunogenic; however, they increased sheep red blood cells (SRBC) antigen specific antibody response in mice, demonstrating their immunostimulatory effect. Chemotactic activity was also found on J774 monocyte cells, while MRC5 fibroblasts were chemotactically nonresponders to the tested forms of tuftsin. These oligomers showed unordered and flexible structure by CD measurements, confirmed by computer modeling studies indicating also a fairly good accessibility of the epsilon-amino group of each lysine residue. Data suggest that these new oligotuftsin derivatives can be considered as promising carriers for synthetic vaccine.     

A hierarchical approach to evaluating the significance of soil biodiversity to biogeochemical cycling

The significance of biodiversity to biogeochemical cycling is viewed most directly through the specific biogeochemical transformations that organisms perform. Although functional diversity in soils can be great, it is exceeded to a high degree by the richness of soil species. It is generally inferred from this richness that soil systems have a high level of functional redundancy. As such, indices of species richness probably contribute little to understanding the functioning of soil ecosystems. Another approach stresses the value of identifying keystone organisms, that is those that play an exceptionally important role in determining the structure and function of ecosystems. Both views tend to ignore the importance of biodiversity in maintaining the numerous and complex interactions among organisms in soils and their contributions to biogeochemical cycling. We describe some of those interactions and their importance to ecosystem function.Soil organisms alter the physical, chemical and biological properties of soils in innumerable ways. The composition and structure of biotic communities at one hierarchical level can influence the spatial heterogeneity of resource and refuge patches at other hierarchical levels. This spatial heterogeneity is supported by a number of biologically relevant spheres of influence that include the detritusphere, the drilosphere, the porosphere, the aggregatusphere and the rhizosphere. Each has fairly distinct properties that operate at different spatial scales. We discuss how these properties may function in regulating the interactions among organisms and the biogeochemical processes that they mediate. It is through the formation of a spatially and temporally heterogeneous structure that biodiversity may contribute most significantly to the functioning of soil ecosystems. Real advances in understanding the significance of biodiversity to biogeochemical cycling will come from taking a broader view of biodiversity. Such a view will necessarily encompass many levels of resolution including: 1) the importance of biodiversity to specific biogenic transformations, 2) the complexity and specificity of biotic interactions in soils that regulate biogeochemical cycling, and 3) how biodiversity may operate at different hierarchically arranged spatial and temporal scales to influence the structure and function of ecosystems.     

Tripeptidyl-peptidase II: a multi-purpose peptidase

Tripeptidyl-peptidase II is a high-molecular weight peptidase with a widespread distribution in eukaryotic cells. The enzyme sequentially removes tripeptides from a free N-terminus of longer peptides and also displays a low endopeptidase activity. A role for tripeptidyl-peptidase II in the formation of peptides for antigen presentation has recently become evident, and the enzyme also appears to be important for the degradation of some specific substrates, e.g. the neuropeptide cholecystokinin. However, it is likely that the main biological function of tripeptidyl-peptidase II is to participate in a general intracellular protein turnover. This peptidase may act on oligopeptides generated by the proteasome, or other endopeptidases, and the tripeptides formed would subsequently be good substrates for other exopeptidases. The fact that tripeptidyl-peptidase II activity is increased in sepsis-induced muscle wasting, a situation of enhanced protein turnover, corroborates this biological role.     

Optical rotatory dispersion properties of nucleic acid complexes with the oligopeptide antibiotics distamycin A and netropsin

ORD measurements of nucleic acids in the presence of the oligopeptides netropsin and distamycin A have indicated association of the antibiotics with DNA and strong conformational changes of the DNA structure with specificity to AT-rich helical regions. The RNA conformation is relatively unaffected by these antibiotics. The results are explained in terms of a perturbation of the DNA secondary structure as well as of the chromophore system of the oligopeptides.     

A tetrapeptide-based method for polyproline II-type secondary structure prediction

We describe a new method for polyproline II-type (PPII) secondary structure prediction based on tetrapeptide conformation properties using data obtained from all globular proteins in the Protein Data Bank (PDB). This is the first method for PPII prediction with a relatively high level of accuracy (approximately 60%). Our method uses only frequencies of different conformations among oligopeptides without any additional parameters. We also attempted to predict alpha-helices and beta-strands using the same approach. We find that the application of our method reveals interrelation between sequence and structure even for very short oligopeptides (tetrapeptides).     

Oligopeptidases, and the emergence of the prolyl oligopeptidase family.

Oligopeptidases are endopeptidases that are not proteinases in the strict sense, since they do not hydrolyse peptide bonds in proteins, but act only on smaller polypeptides or oligopeptides. These enzymes apparently perform important, specialized biological functions that include the modification or destruction of peptide messenger molecules. Oligopeptidases have few naturally occurring inhibitors, and their distinctive specificity prevents them from interacting with alpha 2-macroglobulin, unlike the great majority of endopeptidases. The specificity of these specialized endopeptidases doubtless depends upon the three-dimensional structure of the active site, but no crystallographic structure is yet available for an oligopeptidase. Study of the primary structure of prolyl oligopeptidase has recently shown that it is a member of a new family of serine-type peptidases most of which are exopeptidases. The alignment of the sequences leads to the identification of some catalytic triad residues that have not yet been elucidated experimentally.     

Unifying concepts of biological function from molecules to ecosystems

The concept of function arises at all levels of biological study and is often loosely and variously defined, especially within ecology. This has led to ambiguity, obscuring the common structure that unites levels of biological organisation, from molecules to ecosystems. Here we build on already successful ideas from molecular biology and complexity theory to create a precise definition of biological function which spans levels of biological organisation and can be quantified in the unifying currency of biomass, enabling comparisons of functional effectiveness (irrespective of the specific function) across the field of ecology. We give precise definitions of ecological and ecosystem function that bring clarity and precision to studies of biodiversity– ecosystem function relationships and questions of ecological redundancy. To illustrate the new concepts and their unifying power, we construct a simple community‐level model with nutrient cycling and animal‐plant mutualism, emphasising the importance of its network structure in determining overall functioning. This type of network structure is that of an autocatalytic set of functional relationships, which also appears at biochemical, cellular and organism levels of organisation, creating a nested hierarchy. This enables a common and unifying concept of function to apply from molecular interaction networks up to the global ecosystem.     

Bioinformatic discovery of novel bioactive peptides

Short synthetic oligopeptides based on regions of human proteins that encompass functional motifs are versatile reagents for understanding protein signaling and interactions. They can either mimic or inhibit the parent protein's activity and have been used in drug development. Peptide studies typically either derive peptides from a single identified protein or (at the other extreme) screen random combinatorial peptides, often without knowledge of the signaling pathways targeted. Our objective was to determine whether rational bioinformatic design of oligopeptides specifically targeted to potentially signaling-rich juxtamembrane regions could identify modulators of human platelet function. High-throughput in vitro platelet function assays of palmitylated cell-permeable oligopeptides corresponding to these regions identified many agonists and antagonists of platelet function. Many bioactive peptides were from adhesion molecules, including a specific CD226-derived inhibitor of inside-out platelet signaling. Systematic screens of this nature are highly efficient tools for discovering short signaling motifs in molecular signaling pathways.     

Binding of Ions to Oligopeptides

A model for the binding of ions to oligopeptides, in which nearest neighbor interactions are considered is developed. Equations for the titration curves are derived The apparent association constants are determined as a function of the degree of polymerization and of the interactions between nearest neighbors.     

In Situ Spatial Patterns of Soil Bacterial Populations,Mapped at Multiple Scales,in an Arable Soil

Very little is known about the spatial organization of soil microbes across scales that are relevant both to microbial function and to field-based processes. The spatial distributions of microbes and microbially mediated activity have a high intrinsic variability. This can present problems when trying to quantify the effects of disturbance, management practices, or climate change on soil microbial systems and attendant function. A spatial sampling regime was implemented in an arable field. Cores of undisturbed soil were sampled from a 3 × 3 × 0.9 m volume of soil (topsoil and subsoil) and a biological thin section, in which the in situ distribution of bacteria could be quantified, prepared from each core. Geostatistical analysis was used to quantify the nature of spatial structure from micrometers to meters and spatial point pattern analysis to test for deviations from complete spatial randomness of mapped bacteria. Spatial structure in the topsoil was only found at the microscale (micrometers), whereas evidence for nested scales of spatial structure was found in the subsoil (at the microscale, and at the centimeter to meter scale). Geostatistical ranges of spatial structure at the micro scale were greater in the topsoil and tended to decrease with depth in the subsoil. Evidence for spatial aggregation in bacteria was stronger in the topsoil and also decreased with depth in the subsoil, though extremely high degrees of aggregation were found at very short distances in the deep subsoil. The data suggest that factors that regulate the distribution of bacteria in the subsoil operate at two scales, in contrast to one scale in the topsoil, and that bacterial patches are larger and more prevalent in the topsoil.     

The place of carnosine among physiologically active peptides]

The results of analysis of EROP-Moscow data base concerning structural and functional peculiarities of endogenous regulatory oligopeptides are reviewed in relation to carnosine, the first endogenous peptide bioregulator. The dipeptide fragment ala-his is widely distributed in natural systems, in particular in various representatives of living organisms. The main structural peculiarity of carnosine is its elongated "filamentous" structure with a positively charged N-terminus and a cyclic radical characteristic of large physiologically active oligopeptides. The relatedness of carnosine to other oligopeptides also becomes apparent during the analysis of its role in various regulatory systems of the body.     

SPF: A spatial and functional data analytic approach to cell imaging data

The tumor microenvironment (TME), which characterizes the tumor and its surroundings, plays a critical role in understanding cancer development and progression. Recent advances in imaging techniques enable researchers to study spatial structure of the TME at a single-cell level. Investigating spatial patterns and interactions of cell subtypes within the TME provides useful insights into how cells with different biological purposes behave, which may consequentially impact a subject’s clinical outcomes. We utilize a class of well-known spatial summary statistics, the K-function and its variants, to explore inter-cell dependence as a function of distances between cells. Using techniques from functional data analysis, we introduce an approach to model the association between these summary spatial functions and subject-level outcomes, while controlling for other clinical scalar predictors such as age and disease stage. In particular, we leverage the additive functional Cox regression model (AFCM) to study the nonlinear impact of spatial interaction between tumor and stromal cells on overall survival in patients with non-small cell lung cancer, using multiplex immunohistochemistry (mIHC) data. The applicability of our approach is further validated using a publicly available multiplexed ion beam imaging (MIBI) triple-negative breast cancer dataset.