NMR identification of the formic acid-modified residue in Alzheimer's amyloid protein

Recombinant Spider Silk Fiber with High Dimensional Stability in Water and Its NMR Characterization

Spider dragline silk has unique characteristics of strength and extensibility, including supercontraction. When we use it as a biomaterial or material for textiles, it is important to suppress the effect of water on the fiber by as much as possible in order to maintain dimensional stability. In order to produce spider silk with a highly hydrophobic character, based on the sequence of ADF-3 silk, we produced recombinant silk (RSSP(VLI)) where all QQ sequences were replaced by VL, while single Q was replaced by I. The artificial RSSP(VLI) fiber was prepared using formic acid as the spinning solvent and methanol as the coagulant solvent. The dimensional stability and water absorption experiments of the fiber were performed for eight kinds of silk fiber. RSSP(VLI) fiber showed high dimensional stability, which is suitable for textiles. A remarkable decrease in the motion of the fiber in water was made evident by ¹³C solid-state NMR. This study using ¹³C solid-state NMR is the first trial to put spider silk to practical use and provide information regarding the molecular design of new recombinant spider silk materials with high dimensional stability in water, allowing recombinant spider silk proteins to be used in next-generation biomaterials and materials for textiles.

Presence of β-Turn Structure in Recombinant Spider Silk Dissolved in Formic Acid Revealed with NMR

Spider dragline silk is a biopolymer with excellent mechanical properties. The development of recombinant spider silk protein (RSP)-based materials with these properties is desirable. Formic acid (FA) is a spinning solvent for regenerated Bombyx mori silk fiber with excellent mechanical properties. To use FA as a spinning solvent for RSP with the sequence of major ampullate spider silk protein from Araneus diadematus, we determined the conformation of RSP in FA using solution NMR to determine the role of FA as a spinning solvent. We assigned ¹H, ¹³C, and ¹⁵N chemical shifts to 32-residue repetitive sequences, including polyAla and Gly-rich regions of RSP. Chemical shift evaluation revealed that RSP is in mainly random coil conformation with partially type II β-turn structure in the Gly-Pro-Gly-X motifs of the Gly-rich region in FA, which was confirmed by the ¹⁵N NOE data. In addition, formylation at the Ser OH groups occurred in FA. Furthermore, we evaluated the conformation of the as-cast film of RSP dissolved in FA using solid-state NMR and found that β-sheet structure was predominantly formed.

Preventing N- and O-formylation of proteins when incubated in concentrated formic acid

Concentrated formic acid is among the most effective solvents for protein solubilization. Unfortunately, this acid also presents a risk of inducing chemical modifications thereby limiting its use in proteomics. Previous reports have supported the esterification of serine and threonine residues (O-formylation) for peptides incubated in formic acid. However as shown here, exposure of histone H4 to 80% formic (1 h, 20(o) C) induces N-formylation of two independent lysine residues. Furthermore, incubating a mixture of Escherichia coli proteins in formic acid demonstrates a clear preference toward lysine modification over reactions at serine/threonine. N-formylation accounts for 84% of the 225 uniquely identified formylation sites. To prevent formylation, we provide a detailed investigation of reaction conditions (temperature, time, acid concentration) that define the parameters permitting the use of concentrated formic acid in a proteomics workflow for MS characterization. Proteins can be maintained in 80% formic acid for extended periods (24 h) without inducing modification, so long as the temperature is maintained at or below -20(o) C.

Immunohistochemical characterization of novel monoclonal antibodies against the N-terminus of amyloid β-peptide

Abstract Amyloid β-peptide (Aβ) is a key molecule in Alzheimer's disease (AD). Reliable immunohistochemical (IHC) methods to detect Aβ and Aβ-associated factors (AAF) in brain specimens are needed to determine their role in AD pathophysiology. Formic acid (FA) pre-treatment, which is generally used to enable efficient detection of Aβ with IHC, induces structural modifications within the Aβ, as well as in AAF. Consequently, interpretation of double IHC stainings becomes difficult. Therefore, serial stainings of two newly produced monoclonal antibodies (mAbs) VU-17 and IC16 and two other mAbs (6E10 and 3D6) were performed with four different pre-treatments (no pre-treatment, Tris/EDTA, citrate and FA) and additionally six IHC characteristics were scored: diffuse/compact/classic plaques, arteries with cerebral Aβ angiopathy, dyshoric angiopathy, capillaries with dyshoric angiopathy. Subsequently, these stainings were compared with IHC procedures, which are frequently used in a diagnostic setting, employing mAbs 4G8 and 6F/3D with FA pre-treatment. IHC Aβ patterns obtained with VU-17 and, IC16 and 3D6 without the use of FA pre-treatment were comparable to those obtained with 4G8 and 6F/3D upon FA pre-treatment. Omission of FA pre-treatment gives the advantage to allow double IHC stainings, detecting both Aβ and AAF that otherwise would have been structural modificated upon FA pre-treatment.

Production of disulfide-stabilized transmembrane peptide complexes for structural studies

Physical interactions among the lipid-embedded alpha-helical domains of membrane proteins play a crucial role in folding and assembly of membrane protein complexes and in dynamic processes such as transmembrane (TM) signaling and regulation of cell-surface protein levels. Understanding the structural features driving the association of particular sequences requires sophisticated biophysical and biochemical analyses of TM peptide complexes. However, the extreme hydrophobicity of TM domains makes them very difficult to manipulate using standard peptide chemistry techniques, and production of suitable study material often proves prohibitively challenging. Identifying conditions under which peptides can adopt stable helical conformations and form complexes spontaneously adds a further level of difficulty. Here we present a procedure for the production of homo- or hetero-dimeric TM peptide complexes from materials that are expressed in E. coli, thus allowing incorporation of stable isotope labels for nuclear magnetic resonance (NMR) or non-natural amino acids for other applications relatively inexpensively. The key innovation in this method is that TM complexes are produced and purified as covalently associated (disulfide-crosslinked) assemblies that can form stable, stoichiometric and homogeneous structures when reconstituted into detergent, lipid or other membrane-mimetic materials. We also present carefully optimized procedures for expression and purification that are equally applicable whether producing single TM domains or crosslinked complexes and provide advice for adapting these methods to new TM sequences.

Enhanced antigen retrieval of amyloid β immunohistochemistry: re-evaluation of amyloid β pathology in Alzheimer disease and its mouse model

Senile plaques, extracellular deposits of amyloid β peptide (Aβ), are one of the pathological hallmarks of Alzheimer disease (AD). As the standard immunohistochemical detection method for Aβ deposits, anti-Aβ immunohistochemistry combined with antigen retrieval (AR) by formic acid (FA) has been generally used. Here, we present a more efficient AR for Aβ antigen. On brain sections of AD and its mouse model, a double combination of either autoclave heating in EDTA buffer or digestion with proteinase K plus FA treatment reinforced Aβ immunoreactivity. A further triple combination of digestion with proteinase K (P), autoclave heating in EDTA buffer (A), and FA treatment (F), when employed in this order, gave a more enhanced immunoreactivity. Our PAF method prominently visualized various forms of Aβ deposits in AD that have not been clearly detected previously and revealed numerous minute-sized plaques both in AD and the mouse model. Quantification of Aβ loads showed that the AR effect by the PAF method was 1.86-fold (in the aged human brain) and 4.64-fold (in the mouse brain) higher than that by the FA method. Thus, the PAF method could have the potential to be the most sensitive tool so far to study Aβ pathology in AD and its mouse model.

Formic acid is essential for immunohistochemical detection of aggregated intraneuronal Abeta peptides in mouse models of Alzheimer's disease

The staining protocols so far applied to study intracellular Abeta accumulation in human tissue have been inconsistent with varying use of heat and formic acid (FA) for antigen retrieval. Microwave heat treatment has been reported to enhance the staining of intraneuronal Abeta as compared to no or enzymatic pretreatment. FA is widely used to increase the staining of plaque pathology in AD, yet the effect of FA on intraneuronal Abeta staining has been reported to be low and similar to the effect of heat or even to counteract the enhancing effect of heat pretreatment on intraneuronal Abeta immunohistochemical detection. To overcome these inconsistencies, there is a need for optimization of the staining protocol for intraneuronal Abeta detection and more knowledge is required concerning the effects of the different antigen retrieval methods. In the present work, we optimized the staining protocol for intraneuronal Abeta in paraffin-embedded sections in relation to heat and FA using four different mouse models known to accumulate intraneuronal Abeta peptides. It was found that FA is essential for the staining of highly aggregated intraneuronal Abeta peptides in AD transgenic mouse tissue.

Comparative analysis of an improved thioflavin-s stain, Gallyas silver stain, and immunohistochemistry for neurofibrillary tangle demonstration on the same sections

An improved thioflavin-S stain, Gallyas silver stain, and two immunostainings were quantitatively compared for demonstration of neurofibrillary tangles (NFTs) on the same sections. Sections of hippocampal formation from seven cases of Alzheimer's disease (AD) were immunofluorescently stained with a commercially available polyclonal NFT antibody or a PHF-1 monoclonal antibody, followed by an improved thioflavin-S stain, and finally by Gallyas silver staining. The thioflavin-S method was improved by using a combination quenching method that removes background autofluorescence without remarkable tissue damage and by post-treatment with concentrated phosphate buffer, which minimizes photobleaching. PHF-1 or NFT immunostaining is much less sensitive than the improved thioflavin-S staining and Gallyas silver staining, particularly in the transentorhinal region. Moreover PHF-1 immunoreactivity varied greatly among AD individuals. Thioflavin-S staining and Gallyas silver staining show almost the same sensitivity in NFT demonstration, but only the former depends on the secondary protein structure of NFTs. This study suggests that the improved thioflavin-S staining is a simple, sensitive, and consistent method for demonstration of neurofibrillary pathology.

Optimization of techniques for the maximal detection and quantification of Alzheimer's-related neuropathology with digital imaging

Prior to undertaking quantitative neuropathological studies of Alzheimer's disease, methods for detecting plaques and tangles must be optimized. While suitable antibodies have been developed with great sensitivity, specificity, and reliability, there is no standard pre-treatment protocol for key AD-related pathology. It is well known that formic acid treatment enhances the detection of beta-amyloid. But what concentration of formic acid is best; can similar methods enhance the detection of tau-related pathology? This study compared multiple antigen retrieval techniques (e.g. boiling in citrate or glycine buffer, microwaves, formic acid concentrations), to develop an optimal, standardized protocol for quantitative digital microscopy. Free-floating (40 microm) and paraffin-embedded (12 microm) sections of formalin fixed frontal cortex from mild, moderate, and severe AD cases (n = 18) were pretreated with fifteen different protocols and stained with each of the following antibodies: beta42, PHF-1, MC-1 and AT8. Random fields were digitally captured and images were thresholded to select for positively stained areas versus background (e.g. "load"). As previously reported, high concentrations of formic acid were extremely effective in enhancing the detection of beta-amyloid; as much as a 2-fold enhancement in Abeta "load" values were observed. Surprisingly, tau-related pathology detection also increased significantly following pretreatment. Depending on the antibody, between a 3-fold and 6-fold enhancement was possible relative to no pretreatment. Comparable results were found in paraffin-embedded sections. Similar enhancements in the detection of pathology were obtained following 99% formic acid exposure, microwaving in citrate buffer (pH 9.0) or exposure to 99% formic acid then boiling in citrate buffer (pH 6.0). Because the latter treatments were often harsh on the tissue and more difficult to control, we recommend a standard tissue pretreatment of 99% formic acid for seven minutes for both beta-amyloid and tau-related pathology.

A novel fluorescent method for direct visualization of neurofibrillary pathology in Alzheimer's disease

Methods currently available for detecting neurofibrillary pathology are indirect and depend on staining with exogenous chemicals or antibodies. In the present study, we report a novel method named intrinsic fluorescence induction (IFI), which allows direct visualization of neurofibrillary tangles (NFTs), neuropil threads (NTs), and neuritic plaques (NPs) in tissue sections of Alzheimer's disease (AD) brain. The IFI method is based on both induction of a red intrinsic fluorescence and quenching red background autofluorescence. The IFI procedure includes sustained hydrophobic treatment, protein secondary structure enhancement and incubation in high concentration of phosphate buffer. Following this procedure, a unique red fluorescence is generated from the structures of NFTs, NTs, and NPs in brain sections from AD patients. Sequential application of mild permanganate oxidation and 1% sodium borohydride selectively removes the red background autofluorescence, while the latter enhances the intrinsic fluorescence of neurofibrillary pathology. Comparative studies reveal that the IFI method is as sensitive as Gallyas silver staining, and more sensitive than Bielschowsky silver staining or PHF-1 immunostaining in detecting NFTs in the pre-alpha layer of entorhinal cortex and the pri-alpha layer of the entorhinal/transentorhinal cortex. Furthermore, the IFI method is sensitive in displaying plaque neurites and threads, but not NFTs in the hippocampus. This novel finding provides a direct method for detecting neurofibrillary pathology in particular regions of AD brain and a novel tool for AD research.

X-34, a fluorescent derivative of Congo red: a novel histochemical stain for Alzheimer's disease pathology

X-34, a lipophilic, highly fluorescent derivative of Congo red, was examined as a histochemical stain for pathological changes in Alzheimer's disease (AD). X-34 intensely stained neuritic and diffuse plaques, neurofibrillary tangles (NFTs), neuropil threads, and cerebrovascular amyloid. Comparison to standard methods of demonstrating AD pathology showed that X-34 correlated well with Bielschowsky and thioflavin-S staining. X-34 staining of NFTs correlated closely with anti-TAU antibody staining. A 1:1 correspondence of X-34 and anti-A beta antibody staining of plaques and cerebrovascular amyloid was observed. Both X-34 and thioflavin-S staining were eliminated by formic acid pretreatment, suggesting that beta-sheet secondary protein structure is a necessary determinant of staining. X-34 may be a general amyloid stain, like Congo red, because it also stains systemic amyloid deposits due to lambda-light chain monoclonal gammopathy. In conclusion, X-34 is a highly fluorescent marker for beta-sheet structures and intensely labels amyloid plaques, NFTs, neuropil threads, and vascular amyloid in AD brains. It can be used with both paraffin-embedded and frozen tissues as well as in combination with immunohistochemistry for double labeling. The intensity of staining and the simplicity and reproducibility of the technique suggest that it may be a useful addition to the standard techniques for evaluation of AD neuropathology. (J Histochem Cytochem 48:1223-1232, 2000)

Chemical inactivators as sterilization agents for bovine collagen materials

The use of collagen as a biomedical implant raises safety issues with regard to viruses and prions. Specific chemical agents that inactivate prion infectivity could be applied to collagen implants. The physicochemical changes and the in vitro and in vivo biocompatibility of collagen treated by formic acid (FA), trifluoroacetic acid (TFA), tetrafluorethanol (TFE), and hexafluoroisopropanol (HFIP) were investigated. In addition, the effects of these treatments on nucleic acids incorporated in collagen were analyzed. The molecules of FA and, more important, of TFA remained within collagen. FA, TFA, and HFIP treatments modify the secondary structure of collagen, as shown by Fourier transform infrared spectroscopy, while TFE does not. Differential scanning calorimetry measurements showed a decrease in the denaturation temperature compared to untreated collagen. However, resistance to collagenase was modified only after HFIP treatment. In vitro, cell growth was not impaired; in vivo, implants induced a temporary inflammatory reaction that was prolonged with TFA and HFIP treatments. TFE and FA-treated collagen were thoroughly infiltrated by fibroblasts. On the other hand, FA and TFA resulted in extensive depurination of nucleic acids while HFIP and TFE did so to a lesser degree. Among the investigated chemical scrapie inactivators, FA treatment could offer a safe and biocompatible collagen-derived material for biomedical use.

A biotechnological method provides access to aggregation competent monomeric Alzheimer's 1-42 residue amyloid peptide

Senile plaques, a neuropathological hallmark of Alzheimer's disease, consist primarily of insoluble aggregates of beta-amyloid peptide (A beta). A 42-residue peptide (A beta 1-42) appears to be the predominant form. In contrast to A beta 1-40, A beta 1-42 is characterized by its extreme tendency to aggregate into fibers or precipitate. A tailored biotechnological method prevents aggregation of A beta 1-42 monomers during its production. The method is based on a protein tail fused to the amino terminus of A beta. This tail leads to a high expression in E. coli, and a histidine affinity tag facilitates purification. Selective cleavage of the fusion tail is performed with cyanogen bromide by immobilizing the fusion protein on a reversed phase chromatography column. Cleavage then occurs only at the methionine positioned at the designed site but not at the methionine contained in the membrane anchor sequence of A beta. Furthermore, immobilization prevents aggregation of cleaved A beta. Elution from the HPLC column and all succeeding purification steps are optimized to preserve A beta 1-42 as a monomer. Solutions of monomeric A beta 1-42 spontaneously aggregate into fibers within hours. This permits the investigation of the transition of monomers into fibers and the correlation of physico-chemical properties with biological activities. Mutations of A beta 1-42 at position 35 influence the aggregation properties. Wild-type A beta 1-42 with methionine at position 35 has similar properties as A beta with a methionine sulfoxide residue. The fiber formation tendency, however, is reduced when position 35 is occupied by a glutamine, serine, leucine, or a glutamic acid residue.

Familial Alzheimer's disease cells abnormally accumulate beta-amyloid-harbouring peptides preferentially in cytosol but not in extracellular fluid

The proteolytic processing of beta-amyloid precursor protein (APP) was analyzed and compared for familial Alzheimer's disease and normal lymphoid cells, focusing on beta-amyloid-harbouring peptides and the extracellular fragments released into the medium. Tris/tricine gel electrophoresis of anti-beta A4-(8-17)-immunoprecipitated peptides and subsequent N-terminal amino acid sequencing revealed previously unidentified peptides; the 14-kDa peptide with a beta A4 N-terminus and the 12-kDa peptide with an Esch's-site N-terminus in the cytosols, and the same 12-kDa peptide predominating in the media. Moreover, some early onset familial Alzheimer's disease cells, but not normal cells, express a 4-kDa peptide with a beta-amyloid N-terminus in the cytosol. Two-dimensional gel electrophoresis of the extracellular APP peptides immunoprecipitated with anti-APP-(144-654)-peptide showed that familial Alzheimer's disease cells are deficient in processing, especially the 50-53-kDa peptides with the Kunitz-protease-inhibitor domain. This may reflect their unique expression of a serine protease identified as cleaving APP at the beta-amyloid N-terminus.