A way of functional classification of regulatory peptides. Parameters of divergent and convergent evolution of regulatory peptides

A mathematical method has been presented for systematization of functions of regulatory peptides (RP) and evaluation of directions of evolutionary development of RP systems. For this purpose, traditional methods of vector algebra and multi-dimensional space were used. Effects of various peptide regulators on anxiety, depression, and memory are considered by the example of the three-dimensional space. A way of the functional classification of peptides has been proposed.     

Cationic antimicrobial peptides as molecular immunity factors: multi-functionality

Cationic antimicrobial peptides (AMP) of mammals (defensins, cathelicidins, protegrins and many others) are regarded as important components of congenital immunity. AMP are multifunctional molecules, capable of killing microorganisms directly by acting as endogenic, natural antibiotics ("immediate immunity"); in addition, they may take part in congenital and adaptive immune reactions (immunoregulation) and function as signal molecules, involved into tissue reparation, inflammation (including sepsis), blood coagulation and other important processes in the body. The molecular mechanisms of the direct antimicrobial action of AMP are considered. In addition to antimicrobial and immunoregulating action, AMP have influence on immunoneuroendocrine interactions, taking part in the pathogenesis of stress reactions (corticostatic action), as well as play the role of regulatory peptides of adaptogenic action. The many-sided character of the action of AMP opens prospects to the creation of new medicinal remedies on their basis. Such requirements are met by the Russian preparation "Superlymph" (a complex of natural cytokines), containing protegrin-like AMP.     

Regulatory peptides. A functional continuum

A hypothesis postulating the regulatory peptides continuum is presented. At certain combinations, the numerous regulatory peptides (RP) make up a continuous set of bioactivity spectra, i.e., functionally continuous integrity (continuum) which provides a way for any complex influences on organism functions. Nevertheless, each RP retains its qualitative differences as compared to other RPs. Data on reciprocal influences of RP on their release into body fluids are generalized. The experimental results testify to complex chain reactions of the whole RP continuum in response to changes in any single peptide concentration.     

The threshold for radiation stochastic effects: arguments "pro" and "contra". Applied realization

This study represents the analysis of the data available in the literature and the author's findings concerning the issue of a shape of the dose stochastic effect curve in the range of low levels of radiation (LLR). The data obtained from radioepidemiological and experimental investigations are used. Also considered are the arguments "pro" and "contra" regarding approximation of these curves by means of a linear function (linear non-threshold conception) or as a quasi-plateau (threshold conception). The above analysis allows us to conclude that the threshold conception is more reliable than the non-threshold one from the standpoint of the analysis of postulate bases, theoretical paradigms, the mechanisms for radiobiological effects, epidemiological and experimental data. It is suggested that a separate radiogenic cancer risk estimation should be used in case of LLR and high level radiation instead of one overall estimation by means of the linear non-threshold model.     

Search for evolutionary ancient, relict, regulatory peptides

Among numerous regulatory peptides (RP) it is possible to presumably indicate the relict, evolutionary ancient RP. They combine three features: formation from non-specialized peptides-precursors, a comparatively high resistance to action of proteases in the organism media, and maximal simplicity of their structure. The examples of them are glyprolines—a recently identified RP family, as well as tuftsin. Several other praline-containing RP in terminal sites also seem to belong to the evolutionary ancient RP. The proposed approach to studies on the RP evolution is additional to those used traditionally in this problem.     

Subcellular dynamics of multifunctional protein regulation: mechanisms of GAPDH intracellular translocation

Multidimensional proteins such as glyceraldehyde-3-phosphate dehydrogenase (GAPDH) exhibit distinct activities unrelated to their originally identified functions. Apart from glycolysis, GAPDH participates in iron metabolism, membrane trafficking, histone biosynthesis, the maintenance of DNA integrity and receptor mediated cell signaling. Further, multifunctional proteins exhibit distinct changes in their subcellular localization reflecting their new activities. As such, GAPDH is not only a cytosolic protein but is localized in the membrane, the nucleus, polysomes, the ER and the Golgi. In addition, although the initial subcellular localizations of multifunctional proteins may be of significance, dynamic changes in intracellular distribution may occur as a consequence of those new activities. As such, regulatory mechanisms may exist through which cells control multifunctional protein expression as a function of their subcellular localization. The temporal sequence through which subcellular translocation and the acquisition of new GAPDH functions is considered as well as post-translational modification as a basis for its intracellular transport.     

Wide phylogenetic distribution of Scorpine and long-chain beta-KTx-like peptides in scorpion venoms: identification of "orphan" components

Scorpine and toxins specific for potassium channels of the family beta (beta-Ktx) are two types of structurally related scorpion venom components, characterized by an unusually long extended N-terminal segment, followed by a Cys-rich domain with some resemblance to other scorpion toxins. In this communication, we report evidence supporting the ubiquitous presence of Scorpine and beta-KTx-like polypeptides and their precursors in scorpions of the genus Tityus of the family Buthidae, but also included is the first example of such peptides in scorpions from the family Iuridae. Seven new beta-KTxs or Scorpine-like peptides and precursors are reported: five from the genus Tityus (T. costatus, T. discrepans and T. trivittatus) and two from Hadrurus gertschi. The cDNA precursors for all of these peptides were obtained by molecular cloning and their presence in the venoms were confirmed for various peptides. Analysis of the sequences revealed the existence of at least three distinct groups: (1) beta-KTx-like peptides from buthids; (2) Scorpine-like peptides from scorpionid and iurid scorpions; (3) heterogeneous peptides similar to BmTXKbeta of buthids and iurids. The biological function for most of these peptides is not well known; that is why they are here considered "orphan" peptides.     

The axial channel of the proteasome core particle is gated by the Rpt2 ATPase and controls both substrate entry and product release.

Substrates enter the proteasome core particle (CP) through a channel that opens upon association with the regulatory particle (RP). Using yeast mutants, we show that channel opening is mediated by the ATPase domain of Rpt2, one of six ATPases in the RP. To test whether degradation products exit through this channel, we analyzed their size distribution. Their median length from an open-channel CP mutant was 40% greater than that from the wild-type. Thus, channel opening may enhance the yield of peptides long enough to function in antigen presentation. These experiments demonstrate that gating of the RP channel controls both substrate entry and product release, and is specifically regulated by an ATPase in the base of the RP.     

Lysosomal carboxypeptidase A

Lysosomal carboxypeptidase A (cathepsin A) is synthetized in the form of preproenzyme, which undergoes to active enzyme as a result of post-translational modification. It splits off C-terminal amino acid residues from peptides and proteins and synergizes with other proteases in degradation of cellular proteins in lysosomes. Lysosomal carboxypeptidase A has an effect on peptide hormones and peptides of biological activity of tissues and body fluids as well. It forms complexes with some glycosidases that protects them against proteolytic degradation. Deficiency of this enzyme induces storage diseases. Lysosomal carboxypeptidase A as multifunctional enzyme plays an important regulatory role in organismal metabolism.     

Functional continuum of the regulatory peptides enhancing anxiety. Search for the optimal complexes as a basis for developing inhibitory therapeutic agents

Regulatory peptides (RP) take an active part in managing the majority of physiological processes. One of these functional applications is the monitoring of the anxiety level, of panic state. This work represents the presumptive analysis of literature data of 1960-2004 on the effects of regulatory peptides enhancing anxiety (RP-AT). This information database was used for researching the characteristics of organization and functionality of the system of anxiogenic RP. Taking into account the method of vector representation of RP effects, estimation of spectra of physiological effects that can go with each of RP-AT and their combination, was carried out. The most perspective RP complexes of anxiogenic profile for further experimental development of inhibitory therapeutic agents are proposed.     

Development and application of an expert system for analysis of the functional continuum of regulatory peptides

An expert computer system was developed to analyze the effects of regulatory peptides (RPs) and some other biologically active compounds. The database includes information on their structures and physiological and inductive effects taking into account the method of administration, doses, and types of organisms. The developed method of vector representation of RP effects and the software modules provide for the evaluation of the role of single RPs and their combinations in the regulatory system of organism. The expert system was used for solving the following tasks: (1) an analysis of the structural and functional organization of the RP continuum and a search for effective RP combinations regulating the levels of anxiety, depression, cognitive processes, etc; (2) design of a network of complicated cross inductive connections of major members of RP families; and (3) an analysis of the peculiar features of functioning of numerous internal reward factors.     

Hormones and the levels of humoral regulation]

The problems on the place of hormones secreted by "classical" endocrine glands, on their relationship with other compounds that possess physiological activity, criteria that determine the definition "hormone" are considered in this article. The conception about the levels of the humoral regulatory systems that are organized and formed during phylogenesis and ontogenesis and provide a consecutive increase in their complexity and mobility of adaptation to changes of environment and internal conditions are substantiated on the basis of numerous data. The metabolites that are products of nonspecific activity of any cell of the multicellular organism form the first and simplest level of humoral regulatory organization. The next (second) level of humoral organization is also formed by chemically simple substances. However, these substances are specialized products of the secretory activity of cells and exert potent influence on the physiological processes. Neuroamines and regulatory peptides are applied to these agents, in the first place. They arise simultaneously and jointly at the first stage of ontogenesis. The distinctive characters of the third level of the humoral regulation are increased and complication of the regulatory activity conditioned by cooperative influences of humoral agents produced by single secretory elements situated outside the classical endocrine glands. The chemically and originally different substances causing predominantly local effects are attributed to these physiologically active substances. Their participation in general adaptive reactions as well as inclusion of classical hormones into hierarchy of humoral regulation signify the formation of the forth regulatory level that provides realization of general homeostatic reactions peculiar to the whole organism.(ABSTRACT TRUNCATED AT 250 WORDS)     

Mutational analysis of the "regulatory module" of hormone-sensitive lipase

Hormone-sensitive lipase (HSL) is a rate-limiting enzyme in lipolysis that displays broad substrate specificity. HSL function is regulated by reversible phosphorylation that occurs within a 150 aa "regulatory module" of the protein. The current studies used mutational analysis to dissect the contribution of the "regulatory module" in HSL activity and substrate specificity. Deletion of the entire "regulatory module" or replacement of the "regulatory module" with the "lid" of lipoprotein lipase resulted in enzymatically inactive proteins. Deletion of sequentially longer stretches of the "regulatory module" resulted in a stepwise reduction in hydrolytic activity. Analysis of 7-19 amino acid deletional mutants that spanned the "regulatory module" showed that the N-terminal partial deletion mutants retained normal hydrolytic activity and activation by PKA. In contrast, the C-terminal partial deletion mutants displayed reduced hydrolytic activities, with preferential loss of activity against lipid-, as opposed to water-soluble, substrates. Single amino acid mutations of F650C, P651A, and F654D reduced activity against lipid-, but not water-soluble, substrates. The current results suggest that the length of the "regulatory module" and specific sequences within the C-terminal portion of the "regulatory module" of HSL (amino acids 644-683) are crucial for activity and appear to be responsible for determining lipase activity.     

Identification of functional lncRNAs in atrial fibrillation by integrative analysis of the lncRNA-mRNA network based on competing endogenous RNAs hypothesis

A mounting body of evidence has suggested that long noncoding RNAs (lncRNAs) play critical roles in human diseases by acting as competing endogenous RNAs (ceRNAs). However, the functions and ceRNA mechanisms of lncRNAs in atrial fibrillation (AF) remain to date unclear. In this study, we constructed an AF-related lncRNA-mRNA network (AFLMN) based on ceRNA theory, by integrating probe reannotation pipeline and microRNA (miRNA)-target regulatory interactions. Two lncRNAs with central topological properties in the AFLMN were first obtained. By using bidirectional hierarchical clustering, we identified two modules containing four lncRNAs, which were significantly enriched in many known pathways of AF. To elucidate the ceRNA interactions in certain disease or normal condition, the dysregulated lncRNA-mRNA crosstalks in AF were further analyzed, and six hub lncRNAs were obtained from the network. Furthermore, random walk analysis of the AFLMN suggested that lncRNA RP11-296O14.3 may function importantly in the pathological process of AF. All these eight lncRNAs that were identified from previous steps (RP11-363E7.4, GAS5, RP11-410L14.2, HAGLR, RP11-421L21.3, RP11-111K18.2, HOTAIRM1, and RP11-296O14.3) exhibited a strong diagnostic power for AF. The results of our study provide new insights into the functional roles and regulatory mechanisms of lncRNAs in AF, and facilitate the discovery of novel diagnostic biomarkers or therapeutic targets.     

Cationic Antimicrobial Peptides Derived from <Emphasis Type="Italic">Crocodylus siamensis</Emphasis> Leukocyte Extract,Revealing Anticancer Activity and Apoptotic Induction on Human Cervical Cancer Cells

Known antimicrobial peptides KT2 and RT2 as well as the novel RP9 derived from the leukocyte extract of the freshwater crocodile (Crocodylus siamensis) were used to evaluate the ability in killing human cervical cancer cells. RP9 in the extract was purified by a combination of anion exchange column and reversed-phase HPLC, and its sequence was analyzed by mass spectrometry. The novel peptide could inhibit Gram-negative Vibrio cholerae (clinical isolation) and Gram-positive Bacillus pumilus TISTR 905, and its MIC values were 61.2 µM. From scanning electron microscopy, the peptide was seen to affect bacterial surfaces directly. KT2 and RT2, which are designed antimicrobial peptides using the C. siamensis Leucrocin I template, as well as RP9 were chemically synthesized for investigation of anticancer activity. By Sulforhodamine B colorimetric assay, these antimicrobial peptides could inhibit both HeLa and CaSki cancer cell lines. The IC₅₀ values of KT2 and RT2 for HeLa and CaSki cells showed 28.7–53.4 and 17.3–30.8 µM, while those of RP9 were 126.2 and 168.3 µM, respectively. Additionally, the best candidate peptides KT2 and RT2 were used to determine the apoptotic induction on cancer cells by human apoptosis array assay. As a result, KT2 and RT2 were observed to induce apoptotic cell death in HeLa cells. Therefore, these results indicate that KT2 and RT2 with antimicrobial activity have a highly potent ability to kill human cervical cancer cells.     

Toll-like receptor homolog RP105 modulates the antigen-presenting cell function and regulates the development of collagen-induced arthritis

Introduction

RP105 is a Toll-like receptor homolog expressed on B cells, dendritic cells (DCs), and macrophages. We investigated the role of RP105 in the development of collagen-induced arthritis (CIA).

Methods

CIA was induced in RP105-deficient DBA/1 mice and the incidence and arthritis index were analyzed. The cytokine production by spleen cells was determined. The functions of the DCs and regulatory T cells (Tregs) from RP105-deficient or control mice were determined by adding these cells to the lymph node cell culture. Arthritis was also induced by incomplete Freund's adjuvant (IFA) plus collagen or by injecting anti-collagen antibody and lipopolysaccharide.

Results

RP105-deficient mice showed accelerated onset of arthritis and increased severity. Interferon-gamma (IFN-γ) and tumor necrosis factor-alpha production by spleen cells from RP105-deficient mice was increased in comparison with that from wild-type mice. The DCs from RP105-deficient mice induced more IFN-γ production, whereas Tregs from those mice showed less inhibitory effect against IFN-γ production. RP105-deficient mice also showed more severe arthritis induced by collagen with IFA.

Conclusions

These results indicate that RP105 regulates the antigen-presenting cell function and Treg development, which induced the attenuation of the cell-mediated immune responses and, as a result, suppressed the development of CIA.     

Isomerism and solution dynamics of (90)Y-labeled DTPA--biomolecule conjugates

This report describes the synthesis of two DTPA-conjugated cyclic peptides, cyclo(Arg-Gly-Asp-D-Phe-Lys)DTPA (SQ169) and [cyclo(Arg-Gly-Asp-D-Phe-Lys)](2)DTPA (SQ170), and a chromatographic study of their (90)Y complexes (RP762 and RP763, respectively). The goal is to study the solution structure and the possible isomerism of (90)Y-labeled DTPA-biomolecule conjugates at the tracer level (approximately 10(-10) M). RP762 was prepared in high radiochemical purity (RCP > 95%) by reacting 2 microg of SQ169 with 20 mCi of (90)YCl(3) (corresponding to a SQ169:Y ratio of approximately 4:1) in the 0.5 M ammonium acetate buffer (pH 8.0) at room temperature. RP763 was prepared in a similar fashion using SQ170. In both cases, the (90)Y-chelation was instantaneous. By a reversed-phase HPLC method, it was found that RP762 exists in solution as a mixture of two detectable isomers (most likely cis and trans isomers), which interconvert at room temperature. The interconversion of different isomeric forms of RP762 involves a rapid exchange of "wrapping isomers" via the "wagging" of the diethylenetriamine backbone, "shuffling" of the two NO(2) donor sets, and inversion at the ternimal amine-nitrogen atom. The inversion at a terminal nitrogen atom requires simultaneous dissociation of the NO(2) donor set. For RP763, the interconversion of different isomers is much faster than that for RP762 due to the weak bonding of two carbonyl-oxygen donors. Therefore, RP763 shows only one broad radiometric peak in its HPLC chromatogram. The rapid interconversion of different isomers is intramolecular via a partial dissociative mechanism. The results obtained in this study are consistent with the lack of kinetic inertness of (90)Y- and (111)In-labeled DTPA-biomolecule conjugates. Thus, the design of new BFCs should be focused on those which form lanthanide complexes with high thermodynamic stability and more importantly kinetic inertness.     

Mapping of radiolabeled peptides derived from proteolysis of polypeptides bound to nitrocellulose after "Western" blotting

Sections of nitrocellulose containing bound 32P-labeled polypeptides were excised from "Western" blots and exhaustively digested by trypsin in order to analyze the distribution of phosphorylation sites between the products of limited proteolysis of the multifunctional protein CAD. Using the criterion of analytical isoelectric focusing, the 32P-peptides obtained by this method were found to be similar, although not identical, to peptides obtained by a more conventional digestion of trichloroacetic acid precipitates. Digestion on Western blots is more straightforward than electrophoretic elution of individual gel slices, gives better recoveries than direct digestion of gel slices, and is particularly suitable for peptide mapping of small peptides which bind to nitrocellulose but would diffuse out of polyacrylamide gels during the commonly used fixing and staining procedures.     

"Top Down" characterization is a complementary technique to peptide sequencing for identifying protein species in complex mixtures

At present, mass spectrometry provides a rapid and sensitive means for making conclusive protein identifications from complex mixtures. Sequencing tryptic peptides derived from proteolyzed protein samples, also known as the "Bottom Up" approach, is the mass spectrometric gold standard for identifying unknowns. An alternative technology, "Top Down" characterization, is emerging as a viable option for protein identifications, which involves analyzing the intact unknowns for accurate mass and amino acid sequence tags. In this paper, both characterization methods were employed to more comprehensively differentiate two early-eluting peaks in a process-scale size-exclusion chromatography (SEC) step for a recombinant, immunoglobulin gamma-1 (IgG-1) fusion protein. The contents of each SEC peak were enzymatically digested, and the resulting peptides were mapped using reversed-phase (RP) HPLC-ion trap MS. Many low-level UV signals were observed among the fusion protein-related peptide peaks. These unknowns were collected, concentrated, and analyzed using nanoelectrospray (nanoES) collision-induced dissociation (CID) tandem (MS/MS) mass spectrometry for identification. The peptide sequencing experiments resulted in the identification of twenty host cell-related proteins. Following peptide mapping, the contents of the two SEC peaks were protein mass profiled using on-line RP HPLC coupled to a high-resolution, quadrupole time-of-flight (Qq/TOF) MS. Unknown proteins were also collected, concentrated, and dissociated using nanoES CID MS/MS. Intact protein CID experiments and accurate molecular weight information allowed for the identification of three full length host cell-derived proteins and numerous clips from these and additional proteins. The accurate molecular weight values allowed for the assignment of N- and C-terminal processing, which is difficult to conclusively access from peptide mapping data. The peptide-mapping experiments proved to be far more effective for making protein identifications from complex mixtures, whereas the protein mass profiling was useful for assessing modifications and distinguishing protein clips from full length species.