Profiling of endogenous brain peptides and small proteins: methodology, computer-assisted analysis, and application to aging and lesion models

Optimization for peptide sample preparation for urine peptidomics

Analysis of native or endogenous peptides in biofluids can provide valuable insights into disease mechanisms. Furthermore, the detected peptides may also have utility as potential biomarkers for non-invasive monitoring of human diseases. The non-invasive nature of urine collection and the abundance of peptides in the urine makes analysis by high-throughput ‘peptidomics’ methods , an attractive approach for investigating the pathogenesis of renal disease. However, urine peptidomics methodologies can be problematic with regards to difficulties associated with sample preparation. The urine matrix can provide significant background interference in making the analytical measurements that it hampers both the identification of peptides and the depth of the peptidomics read when utilizing LC-MS based peptidome analysis. We report on a novel adaptation of the standard solid phase extraction (SPE) method to a modified SPE (mSPE) approach for improved peptide yield and analysis sensitivity with LC-MS based peptidomics in terms of time, cost, clogging of the LC-MS column, peptide yield, peptide quality, and number of peptides identified by each method. Expense and time requirements were comparable for both SPE and mSPE, but more interfering contaminants from the urine matrix were evident in the SPE preparations (e.g., clogging of the LC-MS columns, yellowish background coloration of prepared samples due to retained urobilin, lower peptide yields) when compared to the mSPE method. When we compared data from technical replicates of 4 runs, the mSPE method provided significantly improved efficiencies for the preparation of samples from urine (e.g., mSPE peptide identification 82% versus 18% with SPE; p = 8.92E-05). Additionally, peptide identifications, when applying the mSPE method, highlighted the biology of differential activation of urine peptidases during acute renal transplant rejection with distinct laddering of specific peptides, which was obscured for most proteins when utilizing the conventional SPE method. In conclusion, the mSPE method was found to be superior to the conventional, standard SPE method for urine peptide sample preparation when applying LC-MS peptidomics analysis due to the optimized sample clean up that provided improved experimental inference from the confidently identified peptides.

Two-dimensional LC-MS/MS in detection of peptides in hypothalamus of the rat subjected to hypoxic stress

A capillary 2-D LC method coupled with IT MS has been used for separation and identification of peptides in rat hypothalamus. Animals of two different age groups (8 and 50 wk) were exposed to two different rates of CO(2 )in inhaled air to investigate the influence of different hypoxia/hypercapnia levels and their stress-related factor on the peptide excretion. Peptide compounds were fractionated (strong cation exchange chromatography), trapped, and separated (RP chromatography), and MS/MS mass spectra were used for identification. About 107 peptide compounds were identified and 88 of them were semiquantified. Among the characterized peptides, there were fragments from proteins such as proenkephalin A, proSAAS, prosomatostatin, prooxytocin, vasopressin, etc. Explorative principal component analysis (PCA) combined with hypothesis testing was applied to the obtained data to investigate the impact of age and hypoxic stress factors on the peptide pattern. Twenty-six peptides revealed significant differences in concentrations between the animal groups influenced by age and influx rate.

Peptidomics: a logical sequel to proteomics

Rapid progress of separation techniques as well as methods of structural analysis provided conditions in the past decade for total screening of complex biologic mixtures for any given class of biomolecules. The present review updates the reader with the modern state of peptidomics, a chapter of chemical biology that deals with structure and biologic properties of sets of peptides present in biologic tissues, cells or fluids. Scope and limitations of currently employed experimental techniques are considered and the main results are outlined. Considerable attention will be afforded to the biologic role of peptides formed in vivo by proteolysis of nonspecialized precursor proteins with other well-defined functions. In conclusion, the connection is discussed between peptidomics and the much more mature and still closely related field of proteomics.

Analysis of protein fragmentation inhibition by an MMP-inhibitor in an in vivo model of heart failure using automated chromatography

Proteomic strategies have continued to demonstrate value in studying disease by exploiting new technologies that can develop significant numbers of measurements from single samples. However, using complex samples such as tissues or blood has continued to be problematic due to the presence of major interfering substances. In this study, a process is described that uses denaturing peptide extraction from whole tissue and automated chromatography in order to allow subsequent analysis of more than 1000 tissue-derived peptides per sample. The process was employed to identify cardiac proteins that were spared degradation by administration of a heart-protecting matrix metalloproteinase (MMP) inhibitor (compound SC-621) following experimental myocardial infarction (MI). HPLC peptide fingerprints were developed from rat heart left ventricles and the resultant integrated peak data was compared across experimental animals. Surprisingly, although protein fragmentation was generally increased in MI hearts, the effect of the MMP inhibitor was only observed on a few species. The results from this study demonstrated that whole-tissue sample enrichment and peptide analysis using HPLC could be linked in order to study the effects of new compounds on a disease state. The system is flexible and amenable to improvements such as incorporating detection by mass spectrometry.

Peptidomics-based discovery of novel neuropeptides

Modern proteomic methodologies have significantly improved the possibilities of large-scale identification of proteins. However, these methodologies are limited by their inability to reliably detect endogenously expressed peptides. We describe a novel approach of combining sample preparation, comprising focused microwave irradiation and mass spectrometric peptide profiling that has enabled us to simultaneously detect more than 550 endogenous neuropeptides in 1 mg of hypothalamic extracts. Automatic switching tandem mass spectrometry and amino acid sequence determination of the peptides showed that they consist of both novel and previously described neuropeptides. The methodology includes virtual visualization of the peptides as two- and three-dimensional image maps. In addition, several novel and known post-translational modifications of the neuropeptides were identified. The peptidomic approach proved to be a powerful method for investigating endogenous peptides and their post-translational modifications in complex tissues such as the brain. It is anticipated that this approach will complement proteomic methods in the future.

Peptides comprising the bulk of rat brain extracts: isolation, amino acid sequences and biological activity

Chromatographic separation of rat brain extracts followed by automatic Edman sequencing of the major individual components resulted in identification of 61 endogenous peptides derived from known functional proteins (hemoglobin, myelin basic protein, cytochrome-c oxidase, etc.) or unknown precursors. The results are compared with the data obtained earlier for bovine brain. Although the sequences of bovine and rat hemoglobin contain about 20% of amino acid substitutions, the families of structurally related peptides are very similar in both extracts. Several other proteins also give rise to identical or closely related peptide fragments in the two mammalian species. The outlined similarity extends almost exclusively to the most abundant peptides present in the extracts. The minor components show less overlap. Four hemoglobin-derived peptides isolated from rat brain were shown to be biologically active in tumor cells. Eleven are identical to bioactive peptides from other species. Ten structurally overlap with bioactive peptides from other sources. The data obtained show similar biosynthetic pathways of pool components in different species, the resultant peptides being aimed at fulfilling related functions.

Profiling of endogenous peptides as a tool for studying development and neurological disease

The use of a method to follow changes in endogenous peptide production, as they occur in biological studies, is an excellent complement to other molecular techniques. It has the unique ability to characterize peptides that have been produced from protein precursors, and instrumentation is available that provides high resolution peptide separations that are quantitative, sensitive, and amenable to automation. All tissues express a large number of peptide species that can be visualized, or profiled, on chromatographic separations using reverse-phase high-performance liquid chromatography. This large number of peptides offers many potential molecules that can be used to identify biological mechanisms associated with experimental paradigms. Peptide analysis has been used successfully in many types of studies. In this review, we outline our experience in using peptides as biological markers and provide a description of the evolution of peptide profiling in our laboratories. Peptide expression has been used in studies ranging from how brain regions develop to identifying changes in disease processes including Alzheimer's disease and models of stroke. Some of the findings provided by these studies have been new pathways of peptide processing and the identification of accelerated proteolysis on proteins such as hemoglobin as a function of Alzheimer's disease and brain insult. Peptide profiling has also proven to be an excellent technique for studying many well-known nervous system proteins including calmodulin, PEP-19, myelin basic protein, cytoskeletal proteins, and others. It is the purpose of this review to describe our experience using the technique and to highlight improvements that have added to the power of the approach. Peptide analysis and the expansion in the instrumentation that can detect peptides will no doubt make these types of studies a powerful addition to our molecular armamentarium for conducting biological studies.

Hemoglobin as a source of endogenous bioactive peptides: the concept of tissue-specific peptide pool

Scattered literature data on biologically active hemoglobin-derived peptides are collected in the form of tables. Respective structure-functional correlations are analyzed and the general conclusion is reached that hemoglobin fragments must have a profound physiological function. Evidence is presented that generation of hemoglobin fragments starts inside the erythrocytes. At that stage alpha- and beta-globin chains of hemoglobin predominantly give rise to relatively long peptides containing ca. 30 amino acid residues. The primary proteolysis is followed by the next degradation step coupled with excretion of newly formed shorter peptides form red blood cells. Both the primary and the secondary proteolysis products are subjected to further stepwise C- and N-terminal chain shortening, giving rise to families of closely related peptides that are actually found in animal tissue extracts. The possible sites of primary proteolysis are compared with the positions of the exposed secondary structure elements within the monomeric alpha- and beta-globins as well as the tetrameric hemoglobin. Two tentative schemes are proposed for hemoglobin degradation, one of which starts at the globin loops exposed on the surface of the tetramer and the other, at monomeric globins where more sites are available for the action of proteases. The concept of a "tissue-specific peptide pool" is formulated, describing a novel system of peptidergic regulation, complementary to the conventional hormonal and neuromodulatory systems. According to that description, hemoglobin is only a single example, although an important one, of a vast number of functional proteins providing their proteolytically derived fragments for maintaining the tissue homeostasis.

GABA-induced changes of the tissue-specific peptide pool of white rat brain

Internasal administration of gamma-aminobutyric acid (GABA) induced prolonged behaviour changes and the appearance of three new compounds absent in the brain extracts of control rats. Two peptides associated with GABA administration were isolated and sequenced: Thr-Tyr-Thr-Phe, which corresponds to a gamma-immunoglobulin segment, and Val-Leu, which is present in a great number of proteins, hence its precursor could not be established. The third compound was not amenable to the Edman degradation technique. The data obtained show that the introduction of a neurotransmitter could cause specific changes in the levels of tissue-specific peptide components.

Fragments of functional proteins: role in endocrine regulation

Systematic analysis of structures, localization, formation and biological activities of endogenous peptides derived from functional proteins, such as hemoglobin, myelin basic protein, immunoglobulins, etc., allowed establishing the basic features of that group of compounds. The sets of these peptides in mammalian tissues, or "tissue-specific peptide pools" are: (i) tissue specific; (ii) stable at normal conditions; (iii) conservative in the same tissues of different mammalian species; (iv) dependent on the general state of homeostasis of tissue or the whole organism. Formation of such peptides has features of both conformation and site specificity and also involves the action of carboxy- and amino-peptidases. As a result, the families of structurally related families of peptides are generated. The fragments of functional proteins exhibit a wide range of the biological effects, characteristic both for hormones and parahormones, from hormone-releasing to growth-regulatory activity. At the same time, the molecular mechanisms of action of the majority of such peptides are unknown. On the basis of the data obtained the components of tissue-specific peptide pools are considered to form a novel regulatory system, complementary to other peptidergic systems such as hormonal, nervous, immune, etc. The biological role of the fragments of functional proteins in vivo and the patterns of interaction with other regulatory systems are suggested.

Identification of a neuronal calmodulin-binding peptide, CAP-19, containing an IQ motif

Neurons produce polypeptides which can bind the calcium-poor or pre-activated form of calmodulin. It is expected that this class of peptide will serve an important role in maintaining cellular homeostasis since it would modulate calcium-dependent target regulation and redirect intracellular signaling. The lack of conserved sequence has made the identification of these peptides difficult, consequently leading us to exploit their property of binding calcium-poor calmodulin as a means of finding new species. A new peptide termed Calmodulin-Associated Peptide-19 (CAP-19) was purified and characterized. The protein-sequence information was employed in order to recover a cDNA clone from rat which included the entire reading frame for the peptide. Like its counterparts, neuromodulin (GAP-43), neurogranin (RC3) and PEP-19, it contains an IQ motif although the remainder of the peptide is quite different. Northern blot analysis of ribonucleic acid (RNA) from animals of differing ages indicated that the message appears at birth and then persists into adulthood. Antibodies to synthetic peptide were employed for localizing CAP-19. The results indicated that the peptide was localized to neurons in several brain regions. CAP-19 is similar to other calmodulin-binding proteins in that the domain spanning the IQ motif was demonstrated to participate in binding to calmodulin. Database searching showed CAP-19 to be homologous to the silkworm protein, multiprotein bridging factor 1 (MBF1). This homology suggests a potential new role for calmodulin-associated proteins in cellular homeostasis.

A novel system of peptidergic regulation

Systematic analysis of structure and biological activity of peptide components of tissue extracts and biological fluids allows us to formulate a novel concept of a peptidergic regulatory system, complementary to the conventional regulatory systems (i.e. nervous, endocrine and paracrine systems). According to that concept, the proteolytic degradation of tissue proteins carried out by a specific and regulated system of tissue-specific enzymes and protein substrates gives rise to a large group of peptides, which we define as tissue-specific peptide pool. As a result, functional proteins provide their proteolytically derived fragments for maintaining tissue homeostasis.

Peptides from bovine brain: structure and biological role

Fractionation of bovine brain extracts followed by automatic Edman sequencing of individual components resulted in identification of 107 endogenous peptides formed from functional proteins (haemoglobin, myelin basic protein, cytochrome c oxidase, etc) or unknown precursors. Several of the newly identified brain peptides demonstrate different types of biological activity; some of the substances show considerable overlap with the known biologically active peptides. It is suggested that these peptides should participate in regulation of extracellular and intracellular biochemical processes. A concept of 'tissue-specific peptide pool' is formulated describing a novel system of peptidergic regulation, complementary to the conventional hormonal and neuromodulatory systems. According to that description functional proteins provide their proteolytically derived fragments for maintaining the tissue homeostasis by modulating the availability of peptide receptors to respective 'true' ligands.

RC3/neurogranin, a postsynaptic calpacitin for setting the response threshold to calcium influxes

In this review, we attempt to cover the descriptive, biochemical and molecular biological work that has contributed to our current knowledge about RC3/neurogranin function and its role in dendritic spine development, long-term potentiation, long-term depression, learning, and memory. Based on the data reviewed here, we propose that RC3, GAP-43, and the small cerebellum-enriched peptide, PEP-19, belong to a protein family that we have named the calpacitins. Membership in this family is based on sequence homology and, we believe, a common biochemical function. We propose a model wherein RC3 and GAP-43 regulate calmodulin availability in dendritic spines and axons, respectively, and calmodulin regulates their ability to amplify the mobilization of Ca2+ in response to metabotropic glutamate receptor stimulation. PEP-19 may serve a similar function in the cerebellum, although biochemical characterization of this molecule has lagged behind that of RC3 and GAP-43. We suggest that these molecules release CaM rapidly in response to large influxes of Ca2+ and slowly in response to small increases. This nonlinear response is analogous to the behavior of a capacitor, hence the name calpacitin. Since CaM regulates the ability of RC3 to amplify the effects of metabotropic glutamate receptor agonists, this activity must, necessarily, exhibit nonlinear kinetics as well. The capacitance of the system is regulated by phosphorylation by protein kinase C, which abrogates interactions between calmodulin and RC3 or GAP-43. We further propose that the ratio of phosphorylated to unphosphorylated RC3 determines the sliding LTP/LTD threshold in concept with Ca2+/ calmodulin-dependent kinase II. Finally, we suggest that the close association between RC3 and a subset of mitochondria serves to couple energy production with the synthetic events that accompany dendritic spine development and remodeling.

Camstatins are peptide antagonists of calmodulin based upon a conserved structural motif in PEP-19, neurogranin, and neuromodulin

Unbridled increases in intracellular ionized calcium can result in neuronal damage and death. Since many of the deleterious effects of calcium are mediated by calmodulin, we have sought to identify neuronal proteins that inhibit activation of this ubiquitous protein. PEP-19 is a 7.6-kDa neuron-specific protein, which contains a motif similar to the calmodulin binding domains of neuromodulin (GAP-43) and neurogranin (RC3). Here we show that PEP-19 binds calmodulin in an analogous calcium-independent manner with an apparent Kd near 1.2 microM. Furthermore, using the calmodulin-dependent enzyme neuronal nitric oxide synthase, we demonstrate that native PEP-19 is also an antagonist of enzyme activity. Based on the PEP-19 sequence, a series of peptide calmodulin antagonists termed camstatins were synthesized. These analogs define the minimally active domain of PEP-19 and provide a structure/activity relationship for calmodulin antagonism. There was a positive correlation between the binding affinities of the camstatins for calmodulin and their potencies as neuronal nitric oxide synthase inhibitors. Despite the similar IQ motif in PEP-19 and neuromodulin or neurogranin, PEP-19 was not a substrate for protein kinase C. The properties of PEP-19 suggest that it could fulfill a role in neuroprotection.

Neuromodulin (GAP-43) can regulate a calmodulin-dependent target in vitro

The calmodulin-binding polypeptide neuromodulin (GAP-43) was tested in vitro for its ability to modulate a typical calmodulin target, the enzyme nitric oxide synthase. The titration of enzyme with increasing neuromodulin concentrations demonstrated a concentration-dependent decrease in enzyme activity. Subsequent analysis of the ability of increased calcium concentrations to activate the enzyme was tested in the presence or absence of neuromodulin. The effect of neuromodulin on the calcium-dependent activation of the enzyme was to depress enzyme activity in the range of 0.2 to approximately 6 microM calcium. Treatment of the neuromodulin polypeptide with protein kinase C eliminated its ability to inhibit nitric oxide synthase activation. Subsequent treatment of the phosphorylated neuromodulin with calcineurin (phosphatase 2b) caused it to regain its inhibitory action on the enzyme. The results from these in vitro studies have indicated that neuromodulin has the ability to affect the activation of a calmodulin-dependent enzyme at levels of the polypeptide that exist in neurons. They also demonstrated that the regulation occurred within a physiological range of calcium concentrations. Since the inhibition of enzyme activity appeared to be occurring through the interaction of neuromodulin with calmodulin, it seems likely that neuromodulin has a general ability to impede activation of calmodulin-dependent targets.