Natural N-terminal fragments of brain abundant myristoylated protein BASP1

Molecular basis of the development of Parkinson's disease

Parkinson's disease is one of the most prevalent neurodegenerative motor disorders worldwide with postural instability, bradykinesia, resting tremor and rigidity being the most common symptoms of the disease. Despite the fact that the molecular mechanisms of Parkinson's disease pathogenesis have already been well described, there is still no coherent picture of the etiopathogenesis of this disease. According to modern concepts, neurodegeneration is induced mainly by oxidative stress, neuroinflammation, dysregulation of cerebral proteostasis, apoptotic dysregulation, and impaired autophagy. This review describes how various factors contribute to neurodegeneration in Parkinson's disease. Understanding the factors affecting fundamental cellular processes and responsible for disease progression may help develop therapeutic strategies to improve the quality of life of patients suffering from the disease. The review also discusses the role of calpains in the development of Parkinson's disease. It is known that α-synuclein is a substrate of calcium-dependent proteases of the calpain family. Truncated forms of α-synuclein are not only involved in the process of formation of the aggregates, but also increase their toxicity.

BASP1 labels neural stem cells in the neurogenic niches of mammalian brain

The mechanisms responsible for determining neural stem cell fate are numerous and complex. To begin to identify the specific components involved in these processes, we generated several mouse neural stem cell (NSC) antibodies against cultured mouse embryonic neurospheres. Our immunohistochemical data showed that the NSC-6 antibody recognized NSCs in the developing and postnatal murine brains as well as in human brain organoids. Mass spectrometry revealed the identity of the NSC-6 epitope as brain abundant, membrane-attached signal protein 1 (BASP1), a signaling protein that plays a key role in neurite outgrowth and plasticity. Western blot analysis using the NSC-6 antibody demonstrated multiple BASP1 isoforms with varying degrees of expression and correlating with distinct developmental stages. Herein, we describe the expression of BASP1 in NSCs in the developing and postnatal mammalian brains and human brain organoids, and demonstrate that the NSC-6 antibody may be a useful marker of these cells.

GAP-43 and BASP1 in Axon Regeneration: Implications for the Treatment of Neurodegenerative Diseases

Growth-associated protein-43 (GAP-43) and brain acid-soluble protein 1 (BASP1) regulate actin dynamics and presynaptic vesicle cycling at axon terminals, thereby facilitating axonal growth, regeneration, and plasticity. These functions highly depend on changes in GAP-43 and BASP1 expression levels and post-translational modifications such as phosphorylation. Interestingly, examinations of GAP-43 and BASP1 in neurodegenerative diseases reveal alterations in their expression and phosphorylation profiles. This review provides an overview of the structural properties, regulations, and functions of GAP-43 and BASP1, highlighting their involvement in neural injury response and regeneration. By discussing GAP-43 and BASP1 in the context of neurodegenerative diseases, we also explore the therapeutic potential of modulating their activities to compensate for neuron loss in neurodegenerative diseases.

NMR Spectroscopic Studies of the Conformational Ensembles of Intrinsically Disordered Proteins

Intrinsically disordered proteins (IDPs) are characterized by substantial conformational flexibility and thus not amenable to conventional structural biology techniques. Given their inherent structural flexibility NMR spectroscopy offers unique opportunities for structural and dynamic studies of IDPs. The past two decades have witnessed significant development of NMR spectroscopy that couples advances in spin physics and chemistry with a broad range of applications. This chapter will summarize key advances in NMR methodology. Despite the availability of efficient (multi-dimensional) NMR experiments for signal assignment of IDPs it is discussed that NMR of larger and more complex IDPs demands spectral simplification strategies capitalizing on specific isotope-labeling strategies. Prototypical applications of isotope labeling-strategies are described. Since IDP-ligand association and dissociation processes frequently occur on time scales that are amenable to NMR spectroscopy we describe in detail the application of CPMG relaxation dispersion techniques to studies of IDP protein binding. Finally, we demonstrate that the complementary usage of NMR and EPR data provide a more comprehensive picture about the conformational states of IDPs and can be employed to analyze the conformational ensembles of IDPs.

BASP1 and its N-end fragments (BNEMFs) dynamics in rat brain during development

Protein BASP1 was discovered in brains of mammals and birds. In presynaptic area of synapses, BASP1 is attached to plasma membrane owing to N-terminal myristoylation as well as to the positively charged "effecter domain". BASP1 interactions with other proteins as well as with lipids contribute to membrane traffic, axon outgrowth and synaptic plasticity. BASP1 is present also in other tissues, where it was found not only in cytoplasm, but also in nucleus. Nuclear BASP1 suppresses activity of transcription factor WT1 and acts as tumor suppressor. BASP1 deficiency in a cell leads to its transformation. Previously it was shown that in BASP1 samples prepared from different animals and different tissues, six BASP1 N-end myristoylated fragments (BNEMFs) are present. Together, they amount to 30 % of the whole molecules. BNEMFs presence in different species and tissues demonstrates their physiological significance. However BNEMFs remain unexplored. In this paper, the time of appearance and dynamics of both BASP1 and BNEMFs during rat development from embryo to adult animals were determined. In rat brain, the amounts of all BASP1 forms per cell systematically increase during development and remain at the highest levels in adult animals. BNEMFs appear during embryogenesis non-simultaneously and accumulate with different dynamics. These results say for formation of six BNEMFs in the course of different processes and, possibly, using different mechanisms.

Changes in the molecular phenotype of nucleus pulposus cells with intervertebral disc aging

Intervertebral disc (IVD) disorder and age-related degeneration are believed to contribute to low back pain. Cell-based therapies represent a promising strategy to treat disc degeneration; however, the cellular and molecular characteristics of disc cells during IVD maturation and aging still remain poorly defined. This study investigated novel molecular markers and their age-related changes in the rat IVD. Affymetrix cDNA microarray analysis was conducted to identify a new set of genes characterizing immature nucleus pulposus (NP) cells. Among these markers, select neuronal-related proteins (Basp1, Ncdn and Nrp-1), transcriptional factor (Brachyury T), and cell surface receptors (CD24, CD90, CD155 and CD221) were confirmed by real-time PCR and immunohistochemical (IHC) staining for differential expression between IVD tissue regions and among various ages (1, 12 and 21 months). NP cells generally possessed higher levels of mRNA or protein expression for all aforementioned markers, with the exception of CD90 in anulus fibrosus (AF) cells. In addition, CD protein (CD24 and CD90) and Brachyury (T) expression in immature disc cells were also confirmed via flow cytometry. Similar to IHC staining, results revealed a higher percentage of immature NP cells expressing CD24 and Brachyury, while higher percentage of immature AF cells was stained positively for CD90. Altogether, this study identifies that tissue-specific gene expression and age-related differential expression of the above markers do exist in immature and aged disc cells. These age-related phenotype changes provide a new insight for a molecular profile that may be used to characterize NP cells for developing cell-based regenerative therapy for IVD regeneration.

Immunoelectron microscopic study of BASP1 and MARCKS location in the early and late rat spermatids

Immunoelectron microscopy was used to locate the proteins BASP1 and MARCKS in the post-meiotic spermatids of male rat testis. It was shown that in early spermatids, BASP1 and MARCKS accumulate in chromatoid bodies, which are characteristic organelles for these cells. During spermatogenesis, while the spermatid nucleus is still active, the chromatoid body periodically moves to the cell nucleus and absorbs the precursors of definite mRNAs and small RNAs. mRNAs are preserved in the chromatoid body until the corresponding proteins are needed, but their "fresh" mRNA cannot be formed due to the nucleus inactivation. The chromatoid body (0.5-1.5μm in diameter) has a cloud-like fibrous appearance with many fairly round cavities. In the chromatoid body, BASP1 and MARCKS are distributed mainly around the cavities and at periphery. Based on the known functions of BASP1 and MARCKS in neurons, it is conceivable that these proteins participate in non-random movements of the chromatoid body to the nucleus and in Ca(2+)-calmodulin enrichment. In late spermatids, BASP1 and MARCKS are located in the outer dense fiber layer belonging to a metabolically active spermatozoon region, the tail mid-piece. In spermatozoa, as in chromatoid body, BASP1 and MARCKS may bind Ca(2+)-calmodulin and therefore contribute to the activation of calcium-dependent biochemical processes.

Tight binding of proteins to membranes from older human cells

The lens is an ideal model system for the study of macromolecular aging and its consequences for cellular function, since there is no turnover of lens fibre cells. To examine biochemical processes that take place in the lens and that may also occur in other long-lived cells, membranes were isolated from defined regions of human lenses that are synthesised at different times during life, and assayed for the presence of tightly bound cytosolic proteins using quantitative iTRAQ proteomics technology. A majority of lens beta crystallins and all gamma crystallins became increasingly membrane bound with age, however, the chaperone proteins alpha A and alpha B crystallin, as well as the thermally-stable protein, βB2 crystallin, did not. Other proteins such as brain-associated signal protein 1 and paralemmin 1 became less tightly bound in the older regions of the lens. It is evident that protein-membrane interactions change significantly with age. Selected proteins that were formerly cytosolic become increasingly tightly bound to cell membranes with age and are not removed even by treatment with 7 M urea. It is likely that such processes reflect polypeptide denaturation over time and the untoward binding of proteins to membranes may alter membrane properties and contribute to impairment of communication between older cells.

Oligomeric structure of brain abundant proteins GAP-43 and BASP1

Brain abundant proteins GAP-43 and BASP1 participate in the regulation of actin cytoskeleton dynamics in neuronal axon terminals. The proposed mechanism suggests that the proteins sequester phosphatidylinositol-4,5-diphosphate (PIP(2)) in the inner leaflet of the plasma membrane. We found that model anionic phospholipid membranes in the form of liposomes induce rapid oligomerization of GAP-43 and BASP1 proteins. Multiply charged phosphoinositides produced the most potent effect. Anionic detergent sodium dodecyl sulfate (SDS) at submicellar concentration stimulated formation of similar oligomers in solution. BASP1, but not GAP-43, also formed oligomers at sufficiently high concentration in the absence of lipids and SDS. Electron microscopy study demonstrated that the oligomers have disk-shaped or annular structure of 10-30nm in diameter. BASP1 also formed higher aggregates of linear rod-like structure, with average length of about 100nm. In outward appearance, the oligomers and linear aggregates are reminiscent of oligomers and protofibrils of amyloid proteins. Both the synthetic N-terminal peptide GAP-43(1-40) and the brain-derived fragment GAP-43-3 preserved the ability to oligomerize under the action of acidic phospholipids and SDS. On the contrary, BASP1 fragment truncated by the short N-terminal myristoylated peptide was unable to form oligomers. GAP-43 and BASP1 oligomerization can be regulated by calmodulin, which disrupts the oligomers and displaces the proteins from the membrane. We suggest that in vivo, the role of membrane-bound GAP-43 and BASP1 oligomers consists in accumulation of PIP(2) in functional clusters, which become accessible for other PIP(2)-binding proteins after dissociation of the oligomers.

BASP1 in the lens

BASP1 was detected in the embryonic and adult chicken lens, using immunological methods and by peptide sequence analysis. The protein was predominantly expressed in fiber cells and only faintly detected in annular pad cells. Localization of the protein was along the plasma membrane of fiber cells often in discrete areas. The role of BASP1 in the lens requires further study.

M-calpain-mediated cleavage of GAP-43 near Ser41 is negatively regulated by protein kinase C, calmodulin and calpain-inhibiting fragment GAP-43-3

Neuronal protein GAP-43 performs multiple functions in axon guidance, synaptic plasticity and regulation of neuronal death and survival. However, the molecular mechanisms of its action in these processes are poorly understood. We have shown that in axon terminals GAP-43 is a substrate for calcium-activated cysteine protease m-calpain, which participates in repulsion of axonal growth cones and induction of neuronal death. In pre-synaptic terminals in vivo, in synaptosomes, and in vitro, m-calpain cleaved GAP-43 in a small region near Ser41, on either side of this residue. In contrast, micro-calpain cleaved GAP-43 in vitro at several other sites, besides Ser41. Phosphorylation of Ser41 by protein kinase C or GAP-43 binding to calmodulin strongly suppressed GAP-43 proteolysis by m-calpain. A GAP-43 fragment, lacking about forty N-terminal residues (named GAP-43-3), was produced by m-calpain-mediated cleavage of GAP-43 and inhibited m-calpain, but not micro-calpain. This fragment prevented complete cleavage of intact GAP-43 by m-calpain as a negative feedback. GAP-43-3 also blocked m-calpain activity against casein, a model calpain substrate. This implies that GAP-43-3, which is present in axon terminals in high amount, can play important role in regulation of m-calpain activity in neurons. We suggest that GAP-43-3 and another (N-terminal) GAP-43 fragment produced by m-calpain participate in modulation of neuronal response to repulsive and apoptotic signals.

Identification of proteins with high affinity for refolded and native PrPC

PrPC, the cellular prion protein, is widely expressed in most tissues, including brain, muscle and the gastrointestinal tract, but its physiological role remains unclear. During propagation of transmissible spongiform encephalopathies (TSEs), prion protein is converted to the pathological isoform, PrPSc, in a process believed to be mediated by as-yet-unknown host factors. The identification of proteins associated with PrP may provide information about the biology of prions and the pathogenesis of TSEs. In the present work, we report proteins identified from brain tissue based on their ability to bind to recombinant PrP (recPrP) or form multimolecular complexes with native PrPC in the presence of cross-linkers. Immobilized his-tagged recPrP was used as an affinity matrix to isolate PrP-interacting proteins from brain homogenates of normal individuals. In parallel, PrPC-associated proteins were characterized by cross-linking and co-immunoprecipitation assays. The unknown molecules were identified by MS and the results of LC-MS/MS analysis were subsequently verified by Western blot. Both techniques resulted in identification of proteins participating in the formation of cytoskeleton and signal transduction, further supporting the hypothesis that PrP is involved in the organization and function of receptors throughout the nervous system.

Role of chirality in peptide-induced formation of cholesterol-rich domains

The chiral specificity of the interactions of peptides that induce the formation of cholesterol-rich domains has not been extensively investigated. Both the peptide and most lipids are chiral, so there is a possibility that interactions between peptide and lipid could require chiral recognition. On the other hand, in our models with small peptides, the extent of folding of the peptide to form a specific binding pocket is limited. We have determined that replacing cholesterol with its enantiomer, ent-cholesterol, alters the modulation of lipid organization by peptides. The phase-transition properties of SOPC (1-stearoyl-2-oleoylphosphatidylcholine):cholesterol [in a 6:4 ratio with 0.2 mol% PtdIns(4,5)P2] are not significantly altered when ent-cholesterol replaces cholesterol. However, in the presence of 10 mol% of a 19-amino-acid, N-terminally myristoylated fragment (myristoyl-GGKLSKKKKGYNVNDEKAK-amide) of the protein NAP-22 (neuronal axonal membrane protein), the lipid mixture containing cholesterol undergoes separation into cholesterol-rich and cholesterol-depleted domains. This does not occur when ent-cholesterol replaces cholesterol. In another example, when N-acetyl-Leu-Trp-Tyr-Ile-Lys-amide (N-acetyl-LWYIK-amide) is added to SOPC:cholesterol (7:3 ratio), there is a marked increase in the transition enthalpy of the phospholipid, indicating separation of a cholesterol-depleted domain of SOPC. This phenomenon completely disappears when ent-cholesterol replaces cholesterol. The all-D-isomer of N-acetyl-LWYIK-amide also induces the formation of cholesterol-rich domains with natural cholesterol, but does so to a lesser extent with ent-cholesterol. Thus specific peptide chirality is not required for interaction with cholesterol-containing membranes. However, a specific chirality of membrane lipids is required for peptide-induced formation of cholesterol-rich domains.

Specific Proteolysis of Neuronal Protein GAP-43 by Calpain: Characterization, Regulation, and Physiological Role

The mechanism of specific proteolysis of the neuronal protein GAP-43 in axonal terminals has been investigated. In synaptic terminals in vivo and in synaptosomes in vitro GAP-43 is cleaved only at the single peptide bond formed by Ser41; this is within the main effector domain of GAP-43. Proteolysis at this site involves the cysteine calcium-dependent neutral protease calpain. The following experimental evidences support this conclusion: 1) calcium-dependent proteolysis of GAP-43 in synaptosomes is insensitive to selective inhibitor of micro-calpain (PD151746), but it is completely blocked by micro- and m-calpain inhibitor PD150606; 2) GAP-43 proteolysis in the calcium ionophore A23187-treated synaptosomes is activated by millimolar concentration of calcium ions; 3) the pattern of fragmentation of purified GAP-43 by m-calpain (but not by micro-calpain) is identical to that observed in synaptic terminals in vivo. GAP-43 phosphorylated at Ser41 by protein kinase C (PKC) is resistant to the cleavage by calpain. In addition, calmodulin binding to GAP-43 decreases the rate of calpain-mediated GAP-43 proteolysis. Our results indicate that m-calpain-mediated GAP-43 proteolysis regulated by PKC and calmodulin is of physiological relevance, particularly in axonal growth cone guidance. We suggest that the function of the N-terminal fragment of GAP-43 (residues 1-40) formed during cleavage by m-calpain consists in activation of neuronal heterotrimeric GTP-binding protein G(o); this results in growth cone turning in response to repulsive signals.

Induction of raft-like domains by a myristoylated NAP-22 peptide and its Tyr mutant

The N-terminally myristoylated, 19-amino acid peptide, corresponding to the amino terminus of the neuronal protein NAP-22 (NAP-22 peptide) is a naturally occurring peptide that had been shown by fluorescence to cause the sequestering of a Bodipy-labeled PtdIns(4,5)P2 in a cholesterol-dependent manner. The present work, using differential scanning calorimetry (DSC), extends the observation that formation of a PtdIns(4,5)P2-rich domain is cholesterol dependent and shows that it also leads to the formation of a cholesterol-depleted domain. The PtdIns(4,5)P2 used in the present work is extracted from natural sources and does not contain any label and has the native acyl chain composition. Peptide-induced formation of a cholesterol-depleted domain is abolished when the sole aromatic amino acid, Tyr11 is replaced with a Leu. Despite this, the modified peptide can still sequester PtdIns(4,5)P2 into domains, probably because of the presence of a cluster of cationic residues in the peptide. Cholesterol and PtdIns(4,5)P2 also modulate the insertion of the peptide into the bilayer as revealed by 1H NOESY MAS/NMR. The intensity of cross peaks between the aromatic protons of the Tyr residue and the protons of the lipid indicate that in the presence of cholesterol there is a change in the nature of the interaction of the peptide with the membrane. These results have important implications for the mechanism by which NAP-22 affects actin reorganization in neurons.

Nerve Ending “Signal” Proteins GAP‐43, MARCKS, and BASP1

Mechanisms of growth cone pathfinding in the course of neuronal net formation as well as mechanisms of learning and memory have been under intense investigation for the past 20 years, but many aspects of these phenomena remain unresolved and even mysterious. "Signal" proteins accumulated mainly in the axon endings (growth cones and the presynaptic area of synapses) participate in the main brain processes. These proteins are similar in several essential structural and functional properties. The most prominent similarities are N-terminal fatty acylation and the presence of an "effector domain" (ED) that dynamically binds to the plasma membrane, to calmodulin, and to actin fibrils. Reversible phosphorylation of ED by protein kinase C modulates these interactions. However, together with similarities, there are significant differences among the proteins, such as different conditions (Ca2+ contents) for calmodulin binding and different modes of interaction with the actin cytoskeleton. In light of these facts, we consider GAP-43, MARCKS, and BASP1 both separately and in conjunction. Special attention is devoted to a discussion of apparent inconsistencies in results and opinions of different authors concerning specific questions about the structure of proteins and their interactions.

Cholesterol-dependent partitioning of PtdIns(4,5)P2 into membrane domains by the N-terminal fragment of NAP-22 (neuronal axonal myristoylated membrane protein of 22 kDa)

A myristoylated peptide corresponding to the N-terminus of NAP-22 (neuronal axonal myristoylated membrane protein of 22 kDa) causes the quenching of the fluorescence of BODIPY-TMR-labelled PtdIns(4,5) P2 in bilayers of 1-palmitoyl-2-oleoyl phosphatidylcholine containing 40 mol% cholesterol and 0.1 mol% BODIPY-PtdIns(4,5)2. Both fluorescence spectroscopy and total internal reflectance fluorescence microscopy revealed the cholesterol-dependent nature of PtdIns(4,5) P2-enriched membrane-domain formation.

Differential expression of CRABP-II in fibroblasts derived from dermis and subcutaneous fat

We have shown previously that fibroblasts derived from fat or dermal tissue differ in their functional properties, such as proliferation rate and contractile properties. To study these differences further, two-dimensional electrophoresis (2D PAGE) was performed on proteins isolated from cultured subcutaneous fat and dermal fibroblasts. The 2D gels were screened for proteins that were differentially expressed in all donors (n = 5). Five protein spots were subjected to further analysis by mass spectrometry. Two proteins could be identified: brain acid soluble protein 1 (BASP1) and cellular retinoic acid binding protein-II (CRABP-II). CRABP-II is of interest in terms of re-epithelialisation and was clearly expressed in dermal fibroblasts but not in fat fibroblasts. Real time PCR was performed to confirm the 2D data on CRABP-II. The CRABP-II mRNA level was significantly increased in dermal tissue and cultured dermal fibroblasts compared to fat tissue and cultured fat-derived fibroblasts, respectively. The mode of action of CRABP-II in skin is to mediate retinoic acid activity. Retinoic acid is known to inhibit migration and to stimulate differentiation of keratinocytes. The expression of CRABP-II by dermal fibroblasts implicates a role for these fibroblasts in wound re-epithelialisation, in contrast to subcutaneous fat-derived fibroblasts.