氯化钠对朊病毒结构稳定性影响的分子动力学研究

朊病毒疾病是由正常构象的PrPC转化为致病构象的PrPSc引起的一类可传染的蛋白质构象病.采用分子动力学模拟的方法研究了0～500mmol/L的NaCl溶液体系对人朊病毒构象影响并深入探讨了其分子机制.研究发现NaCl可以降低朊病毒的结构稳定性,并引起其α-螺旋含量的急剧降低.进一步的研究表明高浓度NaCl溶液体系能够显著破坏朊病毒螺旋1内部的重要盐桥Asp144-Arg148和Asp147-Arg151,同时明显降低其主要氢键Arg151 N:Asp147 O,Tyr150 N:Glu146 O,Tyr149 N:Tyr145 O和Arg148 N:Asp144 O的稳定性,并诱导朊病毒的疏水核心发生明显扩张,促使朊病毒整体稳定性的下降,这些可能是NaCl促进朊病毒构象转换的重要原因.     

Use of capillary electrophoresis and fluorescent labeled peptides to detect the abnormal prion protein in the blood of animals that are infected with a transmissible spongiform encephalopathy.

Transmissible spongiform encephalopathies in humans and in animals are fatal neuro-degenerative diseases with long incubation times. The putative cause of these diseases is a normal host protein, the prion protein, that becomes altered. This abnormal prion protein is found mostly in the brains of infected individuals in later stages of the disease, but also can be found in lymphoid and other tissues in lower amounts. In order to eradicate this disease in animals, it is important to develop a system that can concentrate the abnormal prion protein and an assay that is very sensitive. The sensitivity that can be achieved with capillary electrophoresis makes it possible to detect the abnormal protein in blood. A peptide from the carboxyl terminal region, amino acid positions 218-232, was labeled with fluorescein during the synthesis of the peptide at the amino terminus. Antibodies that have been produced to this peptide were affinity purified and used in a capillary electrophoresis immunoassay. The amount of fluorescein labeled peptide in the capillary was 50 amol. Blood was obtained from normal sheep and elk, from sheep infected with scrapie and elk infected with chronic wasting disease. Buffy coats and plasma were prepared by a conventional method. After treatment with proteinase K, which destroys the normal protein but not the altered one, the blood fractions were extracted and tested in the capillary electrophoresis immunoassay for the abnormal prion protein. The abnormal prion protein was detected in fractions from blood from infected animals but not from normal animals. This assay makes a pre-clinical assay possible for these diseases and could be adapted to test for the abnormal prion protein in process materials that are used for manufacture of pharmaceuticals and products for human consumption.     

脑神经退行性疾病中的有机化学-朊病毒(疯牛病)中的蛋白物理有机化学和自由基化学

通过关于“普里昂”蛋白病毒疾病的已有临床、医学生理、免疫和化学等方面的现象，讨论了朊病毒当中的部分蛋白氧化损伤和蛋白自由基化学本质。     

核酸适配子共轭金纳米粒子探针成像朊蛋白细胞内在化途径

将巯基修饰的核酸适配子(aptmer)偶联到金纳米粒子(AuNPs)表面,制备出朊蛋白特异性的Apt-AuNPs纳米光学探针,并成功应用到细胞表面朊蛋白的光散射成像和电子透射显微成像分析.通过对Apt-AuNPs探针进入细胞的途径及其在细胞内命运的进一步研究表明,窖蛋白介导的内吞作用可能是其进入细胞的一个重要途径.Apt-AuNPs纳米探针制备简单、成本低廉,可能被广泛应用于生物医学成像领域.     

Analysis of the performance of antibody capture methods using fluorescent peptides with capillary zone electrophoresis with laser-induced fluorescence

A method to analyze the performance of an antibody capture method using fluorescent peptides by capillary zone electrophoresis using laser-induced fluorescence (CZE-LIF) for detection has been developed. Fluorescent peptides from the prion protein were synthesized and the corresponding antibodies were produced in rabbits against these peptides. The antibodies were used to capture the fluorescent peptides. The antibodies were then bound to protein A Sepharose. After elution, the amount of fluorescent peptide that was captured vs. the total amount placed in the assay was evaluated by CZE-LIF. Of the three peptides used in this evaluation, it was found that the recovery was approximately 25-35%. When the abnormal prion protein was prepared from scrapie-infected brain samples from hamsters and a sheep using the previously described extraction method and this method, the amount of abnormal prion protein that was measured in the fluorescence immunoassay correlated with amounts estimated from Western blot. We conclude that this method can be used to detect abnormal prion protein in a tissue sample.     

Utilizing NMR and EPR spectroscopy to probe the role of copper in prion diseases

Copper is an essential nutrient for the normal development of the brain and nervous system, although the hallmark of several neurological diseases is a change in copper concentrations in the brain and central nervous system. Prion protein (PrP) is a copper‐binding, cell‐surface glycoprotein that exists in two alternatively folded conformations: a normal isoform (PrP^C) and a disease‐associated isoform (PrP^Sc). Prion diseases are a group of lethal neurodegenerative disorders that develop as a result of conformational conversion of PrP^C into PrP^Sc. The pathogenic mechanism that triggers this conformational transformation with the subsequent development of prion diseases remains unclear. It has, however, been shown repeatedly that copper plays a significant functional role in the conformational conversion of prion proteins. In this review, we focus on current research that seeks to clarify the conformational changes associated with prion diseases and the role of copper in this mechanism, with emphasis on the latest applications of NMR and EPR spectroscopy to probe the interactions of copper with prion proteins. Copyright © 2013 John Wiley & Sons, Ltd.     

Identification of the pathological prion protein allotypes in scrapie-infected heterozygous bank voles (Clethrionomys glareolus) by high-performance liquid chromatography-mass spectrometry

Cerebral formation of the pathological isoform of the prion protein (PrP) is a crucial molecular event in prion diseases. The bank vole (Clethrionomys glareolus) is a rodent species highly susceptible to natural scrapie. The PrP gene of bank vole is polymorphic (Met/Ile) at codon 109. Here we show that homozygous 109Met/Met voles have incubation times shorter than heterozygous 109Met/Ile voles after experimental challenge with three different scrapie isolates. An HPLC-MS/MS method was optimized and applied to investigate whether in heterozygous animals both PrP allotypes are able to undergo pathological conversion. The results demonstrate that both allotypes of the prion protein participate to pathological deposition.     

Solution structure of the sheep prion PrP〚142-166〛: a possible site for the conformational conversion of prion protein

In order to get deeper insight into the molecular forces responsible for prion pathogenic conversion, conformational properties of a synthetic linear peptide derived from the globular core of sheep prion protein were studied by circular dichroism (CD) and nuclear magnetic resonance (NMR) spectroscopies. The studied peptide encompassing the 〚142–166〛 (in human numbering) region of sheep prion protein, folds in physiological conditions into a β-hairpin like tertiary structure, whereas, in the non-pathogenic form of protein and in trifuoroethanol (TFE), the region is engaged in largely α-helical conformation. Such structural duality of the fragment indicates a possible transconformational site within prion protein and may explain one of the early structural causes of prion diseases.     

Discriminant analysis of prion sequences for prediction of susceptibility

Prion diseases, including ovine scrapie, bovine spongiform encephalopathy (BSE), human kuru and Creutzfeldt–Jakob disease (CJD), originate from a conformational change of the normal cellular prion protein (PrP^C) into abnormal protease-resistant prion protein (PrP^Sc). There is concern regarding these prion diseases because of the possibility of their zoonotic infections across species. Mutations and polymorphisms of prion sequences may influence prion-disease susceptibility through the modified expression and conformation of proteins. Rapid determination of susceptibility based on prion-sequence polymorphism information without complex structural and molecular biological analyses may be possible. Information regarding the effects of mutations and polymorphisms on prion-disease susceptibility was collected based on previous studies to classify the susceptibilities of sequences, whereas the BLOSUM62 scoring matrix and the position-specific scoring matrix were utilised to determine the distance of target sequences. The k-nearest neighbour analysis was validated with cross-validation methods. The results indicated that the number of polymorphisms did not influence prion-disease susceptibility, and three and four k-objects showed the best accuracy in identifying the susceptible group. Although sequences with negative polymorphisms showed relatively high accuracy for determination, polymorphisms may still not be an appropriate factor for estimating variation in susceptibility. Discriminant analysis of prion sequences with scoring matrices was attempted as a possible means of determining susceptibility to prion diseases. Further research is required to improve the utility of this method.     

朊病毒和疯牛病中蛋白自由基化学问题的探讨

２０年来,人们一直认为朊蛋白病变是导致疯牛病的原因,但对其致病机制却一直未得出公认的结论。其中的“蛋白错折叠”学说被多数人所接受,然而无法解释病中的多菌株现象,在以往的研究中,朊蛋白病变从来没有与任何化学问题有过联系。近年,我们对哺乳动物所具有的此类脑神经疾病进行分析,认为蛋白氧化损伤所形成的序列专一的长寿命朊蛋白自由基所催化下的蛋白氧化交联,可能是致病的根本原因。     

Quantifying the sequence-dependent species barrier between hamster and mouse prions

Prion diseases are transmissible neurodegenerative disorders. It is widely accepted that prions are the infectious agents responsible for disease transmission, and the sequence homology between the infectious prion and the host prion protein determines its transmission efficiency across species. However, previous studies have often reported different results regarding seeding efficiency, the efficiency of initiating amyloid propagation by adding pre-existing amyloid fibrils as seed. In the present study, we used synthetic peptides as a simple system to determine the sequence-dependent transmission barrier between hamster and mouse. We found that the heterologous seeding efficiency of hamster and mouse prion peptides was 4 times less than that of homologous seeding. Moreover, residue 139 was not the only residue in determining seeding efficiency. When the seed had Ile at this position, the homology at this position between seed and monomer determined the seeding efficiency. When the seed had Met at this position, homology at residues 109 and 112 determined the seeding efficiency.     

Single-Chain Fv Antibody Fragments Retain Binding Properties of the Monoclonal Antibody Raised Against Peptide P1 of the Human Prion Protein

Prion diseases are incurable neurodegenerative diseases that affect both humans and animals. The infectious agent is a pathogenic form of the prion protein that accumulates in brain as amyloids. Currently, there is neither cure nor reliable preclinical diagnostics on the market available. The growing number of reports shows that passive immunisation is one of the most promising strategies for prion disease therapy, where antibodies against prions may prevent and even cure the infection. Since antibodies are large molecules and, thus, might not be suitable for the therapy, different antibody fragments are a good alternative. Therefore, we have designed and prepared single-chain antibody fragments (scFvs) derived from the PrP^Sc-specific murine monoclonal antibody V5B2. Using a new expression vector pMD204, we produced scFvs in two opposing chain orientations in the periplasm of Escherichia coli. Both recombinant antibody fragments retained the specificity of the parent antibody and one of these exhibited binding properties comparable to the corresponding murine Fab fragments with the affinity in nM range. Our monovalent antibody fragments are of special interest in view of possible therapeutic reagents for prion diseases as well as for development of a new generation of diagnostics.     

Deciphering the molecular details for the binding of the prion protein to main ganglioside GM1 of neuronal membranes

The prion protein (PrP) resides in lipid rafts in?vivo, and lipids modulate misfolding of the protein to infectious isoforms. Here we demonstrate that binding of recombinant PrP to model raft membranes requires the presence of ganglioside GM1. A combination of liquid- and solid-state NMR revealed the binding sites of PrP to the saccharide head group of GM1. The binding epitope for GM1 was mapped to the folded C-terminal domain of PrP, and docking simulations identified key residues in the C-terminal region of helix C and the loop between strand S2 and helix B. Crucially, this region of PrP is linked to prion resistance in?vivo, and structural changes caused by lipid binding in this region may explain the requirement for lipids in the generation of infectious prions in?vitro.     

Prion Strains Differ in Susceptibility to Photodynamic Oxidation

Prion disorders, or transmissible spongiform encephalophaties (TSE), are fatal neurodegenerative diseases affecting mammals. Prion-infectious particles comprise of misfolded pathological prion proteins (PrP^TSE). Different TSEs are associated with distinct PrP^TSE folds called prion strains. The high resistance of prions to conventional sterilization increases the risk of prion transmission in medical, veterinary and food industry practices. Recently, we have demonstrated the ability of disulfonated hydroxyaluminum phthalocyanine to photodynamically inactivate mouse RML prions by generated singlet oxygen. Herein, we studied the efficiency of three phthalocyanine derivatives in photodynamic treatment of seven mouse adapted prion strains originating from sheep, human, and cow species. We report the different susceptibilities of the strains to photodynamic oxidative elimination of PrP^TSE epitopes: RML, A139, Fu-1 > mBSE, mvCJD > ME7, 22L. The efficiency of the phthalocyanine derivatives in the epitope elimination also differed (AlPcOH(SO₃)₂ > ZnPc(SO₃)_1-3 > SiPc(OH)₂(SO₃)_1-3) and was not correlated to the yields of generated singlet oxygen. Our data suggest that the structural properties of both the phthalocyanine and the PrP^TSE strain may affect the effectiveness of the photodynamic prion inactivation. Our finding provides a new option for the discrimination of prion strains and highlights the necessity of utilizing range of prion strains when validating the photodynamic prion decontamination procedures.     

Use of streptomycin for precipitation and detection of proteinase K resistant prion protein (PrPsc) in biological samples

The ability of streptomycin to form multimolecular aggregates with pathogenic prion proteins and their recovery by precipitation via a low-speed centrifugation step has been demonstrated; these novel properties of streptomycin make it a useful substance that increases the sensitivity of laboratory diagnostic techniques for prion infections in man and animals.     

Characterizing affinity epitopes between prion protein and β-amyloid using an epitope mapping immunoassay

Cellular prion protein, a membrane protein, is expressed in all mammals. Prion protein is also found in human blood as an anchorless protein, and this protein form is one of the many potential sources of misfolded prion protein replication during transmission. Many studies have suggested that β-amyloid_1–42 oligomer causes neurotoxicity associated with Alzheimer''s disease, which is mediated by the prion protein that acts as a receptor and regulates the hippocampal potentiation. The prevention of the binding of these proteins has been proposed as a possible preventative treatment for Alzheimer''s disease; therefore, a greater understanding of the binding hot-spots between the two molecules is necessary. In this study, the epitope mapping immunoassay was employed to characterize binding epitopes within the prion protein and complementary epitopes in β-amyloid. Residues 23–39 and 93–119 in the prion protein were involved in binding to β-amyloid_1–40 and _1–42, and monomers of this protein interacted with prion protein residues 93–113 and 123–166. Furthermore, β-amyloid antibodies against the C-terminus detected bound β-amyloid_1–42 at residues 23–40, 104–122 and 159–175. β-Amyloid epitopes necessary for the interaction with prion protein were not determined. In conclusion, charged clusters and hydrophobic regions of the prion protein were involved in binding to β-amyloid_1–40 and _1–42. The 3D structure appears to be necessary for β-amyloid to interact with prion protein. In the future, these binding sites may be utilized for 3D structure modeling, as well as for the pharmaceutical intervention of Alzheimer''s disease.     

Structural Effects of Multiple Pathogenic Mutations Suggest a Model for the Initiation of Misfolding of the Prion Protein

A molecular understanding of the prion diseases requires delineation of the origin of misfolding of the prion protein (PrP). An understanding of how different disease‐linked mutations affect the structure and dynamics of native monomeric PrP can provide a clue about how misfolding commences. In this study, hydrogen–deuterium exchange mass spectrometry was used to show that several disease‐linked mutant variants, which are thermodynamically destabilized, share a common structural perturbation in their native states: helix 1 is destabilized to an extent that correlates well with the destabilization of the native protein. The mutant variants misfold and form oligomers faster than does the wild‐type protein, at rates that increase exponentially with the extent to which helix 1 is destabilized in the native protein. It appears, therefore, that the loss of helix 1 structure marks the beginning of PrP misfolding and oligomerization.     

Fine tuning the structure of the Cu2+ complex with the prion protein chicken repeat by proline isomerization

The interaction between the single hexarepeat unit of chicken prion protein [ChPrP(54-59)] and Cu(II) was investigated by NMR, finding different coordination modes for the trans/trans and cis/trans isomers.     

Theoretical study of the prion protein based on the fragment molecular orbital method

We performed fragment molecular orbital (FMO) calculations to examine the molecular interactions between the prion protein (PrP) and GN8, which is a potential curative agent for prion diseases. This study has the following novel aspects: we introduced the counterpoise method into the FMO scheme to eliminate the basis set superposition error and examined the influence of geometrical fluctuation on the interaction energies, thereby enabling rigorous analysis of the molecular interaction between PrP and GN8. This analysis could provide information on key amino acid residues of PrP as well as key units of GN8 involved in the molecular interaction between the two molecules. The present FMO calculations were performed using an original program developed in our laboratory, called “Parallelized ab initio calculation system based on FMO (PAICS)”. © 2009 Wiley Periodicals, Inc. J Comput Chem 2009     

Mass spectrometric detection of attomole amounts of the prion protein by nanoLC/MS/MS

Sensitive quantitation of prions in biological samples is an extremely important and challenging analytical problem. Prions are the cause of several fatal neurodegenerative diseases known as transmissible spongiform encephalopathies (TSEs). At this time, there are no methods to diagnose TSEs in live animals or to assure a prion-free blood supply for humans. Prions have been shown to be present in blood by transfusion experiments, but based on the amount of infectivity found in these types of experiments, the amount of misfolded prion protein in blood is estimated to be only 30 to 625 amol/mL. More sensitive detection of prions in brain would allow earlier detection of disease and assure a safer food supply. We studied quantitation of the prion protein by use of nanoscale liquid chromatography coupled to a tandem mass spectrometer using the multiple reaction monitoring mode of operation. We developed a method based on the detection of VVEQMCTTQYQK obtained by reduction, alkylation, and digestion with trypsin of the prion protein. Detection of VVEQMCTTQYQK was more sensitive than for the derivative with phenylisothiocyanate (PITC) because of decreased ionization efficiency of the PITC-derivatized peptides. The VVEQMCTTQYQK method has a LOD of 20 to 30 amol for pure standards. Proof of principle is demonstrated by quantitation of the amount of PrP 27-30 in the brains of terminally ill Syrian hamsters.