CA2448981C - Misfolded protein sensor method - Google Patents

Abstract

A catalytic conformational sensor method for detecting abnormal proteins and proteinaceous particles. The method is based on the interaction of a peptide fragment or probe with an abnormal proteinaceous particle. The interaction catalyzes transformation of the probe to a predominately beta sheet conformation and allows the probe to bind to the abnormal proteinaceous particle. This in turn, catalyzes propagation of a signal associated with the test sample-bound probe. As a result signals can be propagated even from samples containing very low concentrations of abnormal proteinaceous particles. The peptide probes can be designed to bind to a desired peptide sequence or can even be based on dendrimer structure to control further aggregate propagation.

Description

. .

2

3 MISFOLDED PROTEIN SENSOR METHOD

4 BACKGROUND

7 1. FIELD OF THE INVENTION

9 This invention relates generally to a catalytic conformational sensor method and application of such method for detecting proteins and proteinaceous particles;
and more 11 particularly to detecting misfolded or disease-associ ated proteins and proteinaceous 12 particles.

14 2. RELATED ART
16 The present invention detects misfolded or abnormal conformations of proteins or peptides 17 such as those contributing to "folding diseases". The "folding diseases"
are characterized 18 by proteins with destabilizing conformers which tend to aggregate and eventually form 19 toxic plaques in brain and other tissue. See Bucciantini, M., et at.
(2002) Inherent Toxicity of Aggregates Implies a Common Mechanism for Protein Misfolding Diseases.
Nature 416:
21 507- 511.
22 These "folding diseases" can be hard to diagnose since the disease symptoms may be 23 latent where the aggre-1 gates are slowly building up over time and go through 2 stages of increased aggregation leading to fibril formation 3 and eventual plaque deposition leading to impairment of 4 cellular viability. Such misfolding of peptides and aggre-gate formation is believed to play a key role in Alzhei-6 mer's disease where beta-amyloid protein (or A beta, a 39-7 42 residue peptide) forms fibrillar deposits upon a con-8 former change; Huntington's disease where insoluble protein 9 aggregates are formed by expansion of poly-glutamine tracts in the N-terminus of huntingtin (Htt), an antiapoptotic 11 neuronal protein; and noninfectious cancers such as in 12 cases where tumor-associated cell surface NADH oxidase 13 (tNOX) has prion-like properties such as proteinase, abil-14 ity to form amyloid filaments and the ability to convert the normal NOX protein into tNOX. See Kelker, et al.
16 Biochemistry (2001) 40:7351-7354. for more information on 17 tNOX.
18 The present invention, however, is not limited to the 19 detection of proteins or peptides in folding-disease or infectious samples. It also includes detection of protein-21 aceous particles such as prions. Prions are small protein-22 aceous particles with no nucleic acids, thus are resistant 23 to most nucleic-acid modifying procedures and proteases.
24 The normal prion (PrP) protein is a cell-surface metallo-glyroprotein that is mostly an alpha-helix and loop struc-26 ture as shown in Fig. 8, and is usually expressed in the 27 central nevrvous and lymph systems. It's proposed function 28 is that of an antioxidant and cellular homeostasis.
29 The abnormal form of the PrP, however, is a conformer which is resistant to proteases and is predominantly beta-31 sheet in its secondary structure as shown in Fig. 9. It is 32 believed that this conformational change in secondary 1 structure is what leads to the aggregate and eventual 2 neurotoxic plaque deposition in the prion-disease process.
3 The abnormal prion are infectious particles that play 4 key roles in the transmission of several diseases such as Creutzfeldt-Jakob syndrome, chronic wasting disease (CWD), 6 nvCJD, transmissible spongiform encephalopathy (TSE), Mad 7 Cow disease (BSE) and scrapie a neurological disorder in 8 sheep and goats'.
9 Diseases caused by prions can be hard to diagnose since the disease may be latent where the infection is 11 dormant, or may even be subclinical where abnormal prion is 12 demonstrable but the disease remains an acute or chronic 13 symptomless infection. Moreover, normal homologues of a 14 prion-associated protein exist in the brains of uninfected organisms, further complicating detection.2 Prions associ-16 ate with a protein referred to as PrP 27-30, a 28 kdalton 17 hydrophobic glycoprotein, that polymerizes (aggregates) 18 into rod-like filaments, plaques of which are found in 19 infected brains. The normal protein homologue differs from prions in that it is readily degradable as opposed to 21 prions which are highly resistant to proteases. Some 22 theorists believe that prions may contain extremely small 23 amounts of highly infectious nucleic acid, undetectable by 24 conventional assay methods.3 As a result, many current techniques used to detect the presence of prion-related 26 infections rely on the gross morphology changes in the 27 brain and immunochemistry techniques that are generally 28 applied only after symptoms have already manifest them-1485. ' Clayton Thomas, Tabor's Cyclopedic Medical Dictionary (Phil., F.A.
Davis Company, 1989), at 'Ivan Roitt, et al., Immunology (Mosby-Year Book Europe Limited, 1993), at 15.1.
Benjamin Lewin, Genes IV (Oxford Univ. Press, New York, 1990), at 108.

1 selves. Many of the current detection methods rely on 2 antibody-based assays or affinity chromatography using 3 brain tissue from dead animals and in some cases capillary 4 immunoelectrophoresis using blood samples.
6 The following is an evaluation of current detection meth-7 ods.

9 o Brain Tissue Sampling. Cross-sections of brain can be used to examine and monitor gross morphology changes 11 indicative of disease states such as the appearance of 12 spongiform in the brain, in addition to immunohisto-13 chemistry techniques such as antibody-based assays or 14 affinity chromatography which can detect disease-spe-cific prion deposits. These techniques are used for a 16 conclusive bovine spongiform encephalopathy (BSE) 17 diagnosis after slaughter of animals displaying clini-18 cal symptoms. Drawbacks of tissue sampling include 19 belated detection that is possible only after symptoms appear, necessary slaughter of affected animals, and 21 results that takes days to weeks to complete.

23 o Prionic-Check also requires liquified-brain tissue for 24 use with a novel antibody under the Western Blot tech-nique. This test is as reliable as the immuno-26 chemistry technique and is more rapid, yielding re-27 suits in six to seven hours, but shares the drawbacks 28 of the six-month lag time between PrPs accumulation 29 (responsible for the gross morphology changes) in the brain and the display of clinical symptoms, along with 31 the need for slaughter of the animal to obtain a sam-32 pie.

1 o Tonsillar Biopsy Sampling. Though quite accurate, it 2 requires surgical intervention and the requisite days 3 to weeks to obtain results.

5 o Body Fluids: Blood and Cerebrospinal Sampling. As in

6 the above detection methods, results are not immediate

7

8 o Electrosprsy ionization mass spectrometry (ESI-MS),

9 nuclear magnetic resonance NMR, circular dichroism (0:) and other non-amplified structural techniques.
11 All of these techniques require a large amount of 12 infectious sample, and have the disadvantage of re-13 quiring off-site testing or a large financial invest-14 ment in equipment.
16 The following is a survey of currently approved and 17 certified European Union (EU) prion-detection tests.

19 o Prionics -in Switzerland. The test involves Western blot of monoclonal antibodies (14kBs) to detect PrP in 21 brain tissue from dead animals in seven to eight 22 hours.

24 o Enfer Scientific -in Ireland. The test involves ELISA-based testing on spinal cord tissue from dead 26 animals in under four hours.

28 o CEA -in France. The test involves a sandwich 29 immunoassay using two monoclonals on brain tissue collected after death in under twenty-four hours.

32 The EU Commission's evaluation protocol has sensitiv-33 ity, specificity and detection limits and titre. The 1 sensitivity of a test is the proportion of infected refer-2 ence animals that test positive in the assay. It previ-3 ously used 300 samples from individual animals to assess 4 this element. The specificity of a test is the proportion of uninfected reference animals that test negative in the 6 assay. Previously used 1,000 samples from individual 7 animals for this purpose. In order to test detection 8 limits, various dilutions ranging from 10 to 10-5 of posi-9 tive brain homogenate were used. A table showing an evalu-ation of EU test results is shown in Fig. 12. Even with 11 high degrees of sensitivity and specificity, however, the 12 fact remains that these tests must be performed post-mortem 13 and require working with large amounts of highly infectious 14 biohazard materials.
16 The Center for Disease Control (CDC) classifies prions 17 as Risk Group 2 agents requiring Biosafety Level 2 (BSL2) 18 containment. As a result many of the above operations are 19 carried out under BSL2 physical containment with elevated safety practices more typical of a BSL3 lab. Prions can be 21 inactivated by fresh household bleach, 1 molar NaOH, 4 22 molar guanidine reagents, or phenol followed by 4.5 hours 23 of autoclaving at 132 C. Procedures involving brain tissue 24 from human patients with neurological degenerative disor-ders pose special challenges and should be handled with the 26 same precautions as HIV+ human tissue. Thus, working with 27 large amounts of such biohazardous materials can be an 28 obstacle to quick and simple testing of mass quantities or 29 assembly-line samples as well as cumbersome even for small applications.

32 In addition to working with relatively large amounts 33 of biohazardous materials and taking several hours to weeks 1 for detection, many of the prior art methods have the added 2 difficulty that they are performed post mortem.

4 As can now be seen, the related art remains subject to significant problems, and the efforts outlined above --6 although praiseworthy -- have left room for considerable 7 refinement. The present invention introduces such refine-8 ment.

The present invention is based on the interaction 16 between low concentration levels of abnormal proteinaceous 17 particles and a peptide fragment or probe to induce trans-18 formation and propagation of the probe bound to the abnor-19 mal proteinaceous particles initially present within a test sample. Thus, in a preferred embodiment, infectious levels 21 of a test sample can be propagated even from low concentra-22 tions.

24 The present invention uses catalytic propagation to exploit conformational changes in proteins associated with 26 a particular disease process, such as transmissible spongi-27 form encephalopathy (TSE). Catalytic propagation basically 28 amplifies the number of existing protein fragments causing 29 aggregates to form. The aggregates of conformationally changed protein fragments are then easily detected using 31 common analytical techniques.
32 As a result, the present invention allows testing to 33 be done using rapid and cost-effective analytical tech-1 niques, even on, heretofore difficult to detect, small 2 sample sizes and is widely applicable to tissues and body 3 fluids other than those found in brain. Results of the 4 present invention can easily and immediately interpreted using familiar analytical instrumentation. Additionally, 6 the present invention can amplify a weak signal, thus can 7 be successfully applied to small or weak samples such as 8 those associated with body fluids; thereby opening the door 9 to analysis of tissues and fluids for the elusive diseases discussed above. Moreover, this allows the method to be 11 relatively noninvasive in that it does not need to be 12 performed post-mortem; and because it does not need to be 13 performed post-mortem it can be applied to presymptomatic-14 ally.
16 The foregoing may be a description or definition of 17 the first facet or aspect of the present invention in its 18 broadest or most general terms. Even in such general or 19 broad form, however, as can now be seen the first aspect of the invention resolves the previously outlined problems of 21 the prior art.

23 Because the present invention allows detection using 24 samples with very low levels of infectious agents and involves amplifying a peptide probe as opposed to a whole 26 potentially infectious protein, many of the previous 27 biohazard-handling concerns are reduced.

29 Now turning to another of the independent facets or aspects of the invention: in preferred embodiments of this 31 facet, the peptide probes are designed for the detection of 32 a desired sequence and so have adaptable levels of selec-33 tivity and specificity built into the method. Also, in-1 trinsic optical fluors such as pyrene can be designed into 2 the peptide probe allowing simple, single step optical 3 detection of the abnormal proteinaceous particles.

All of the foregoing operational principles and 6 advantages of the present invention will be more fully 7 appreciated upon consideration of the following detailed 8 description, with reference to the appended drawings, of 9 which:

Fig. 1 is a pictoral representation of conformers of 16 transmissible spongiform encephalopathies (TSE) and probes 17 in the form of labeled peptides and labeled dendrimers;
18 Fig. 2 is a pictoral representation of TSE protein 19 detection schema;
Fig. 3 is a graph showing the conformational changes 21 associated with a poly-L-lysine test peptide using circular 22 dichroism;
23 Fig. 4 is a graph comparing the circular dichroism 24 results of the poly-L--lysine test peptide at different temperatures and pH;
26 Fig. 5 is a table comparing the circular dichroism 27 results of the poly-L-lysine test peptide at different 28 temperatures and pH;
29 Fig. 6 is a graph of data for fluorescence resonance energy transfer (FRET) experiments for proximal and distal 31 locations in an a-helical bundle structure undergoing 32 conformational change;

FIG. 7 is a graph of the driving force necessary to overcome the energy difference between two different conformational states of a peptide that can assume a-helix and 13-sheet conformations.
FIG. 8 is a structural diagram of a normal PrPc protein, a cell-surface metallo-glycoprotein that is expressed in the central nervous and lymphatic systems, and that is characterized as having mostly an alpha-helix and loop structure;
FIG. 9 is a structural diagram of the PrPc protein that has shifted to a predominately beta structure in which it is likely to form aggregates and neurotoxic fibrils eventually leading to plaque deposition;
FIG. 10 is a pictoral representation of amplification of signal and propagation of conformational change without increased aggregation by the addition of dendrimers of the invention to a test sample;
FIG. 11 is a structural diagram of proteins used in the current prior art prion-diagnostic market; wherein FIG. lla on the left shows the PrPsens protein molecule and FIG. llb on the right shows a PrPres protein molecule;
FIG. 12 is a table evaluating the current prior art in European Union certified prion-diagnostic tests FIG. 13 is a comparison showing selected PrP
sequences among six different species, i.e., Seq. ID NO. 1 through Seq. ID NO. 6;

FIG. 14 shows peptide sequences for the synthetic peptide probes of Seq. ID NO. 7 (19-mer) and Seq. and Seq.
ID NO. 8 (14-mer) of this invention;
FIG. 15 is a graph of fluorescence detection experimental results showing the effects of peptide concentration;
FIG. 16 is a graph of fluorescence detection experimental results showing the effects of peptide concentration likely showing excimer emission at approximately 460 nanometers (nm);
FIG. 17 is a graph of fluorescence detection experimental results showing pyrene's excitation of fluorescence;
FIG. 18 is a graph of fluorescence detection experimental results showing pyrene's excitation spectra for fluorescence at 398 and approximately 460 nm;
FIG. 19 is a graph comparing the circular dichroism results of several peptides ranging in concentration from 20 to 100 milli Molar (mM) under varying buffer conditions;
FIG. 20 is a graph comparing the circular dichroism results of several peptides including the synthetic peptides of Seq. ID NO. 7 and Seq. ID NO. 8 under varying buffer conditions;
FIG. 21 shows experimental results of the conformational lability of synthetic peptides. FIG. 21a on the left shows that Seq. ID NO. 8 assumes a beta-sheet conformation while the longer analog, Seq. ID NO.7 remains coiled. FIG. 21b on the right shows that addition of Seq.
_ ID NO. 8 to Seq. ID NO. 7 initiates a phase shift to the beta-sheet form;
FIG. 22 is a conceptual illustration of a comparison of where Seq. ID NO. 7 and Seq. ID NO.8 overlap in structure;
FIG. 23 is a graph of experimental results showing that peptides can self-associate;
FIG. 24 is a graph of fluorescence data showing the efficiency of excimer formation under low concentrations;
FIG. 25 is a graph of fluorescence experimental results showing the effect of nuclei on self-association due to catalytic conformational transition;
FIG. 26 contains two graphs of fluorescence experimental results showing the interaction of Seq. ID
NO. 7 and Seq. ID NO. 8 at different ratios; wherein FIG.
26a on the left shows a 1:1 mixture and FIG. 26b on the right shows a 100:1 mixture;
FIG. 27 contains four graphs of fluorescence experimental results showing the effect of nuclei on self-association. FIGS. 27a, b, c and d show the results at 24 hours, 48 hours, 144 hours and 336 hours, respectively;
FIG. 28 is a graph of fluorescence experimental results showing the effect of nuclei on self-association due to catalytic conformational transition at 1 hour in 1 12a 3 FIG. 28a on the left and at 150 hours in FIG. 28b on the right;
4 FIG. 29 shows peptide Seq. ID No. 9, which is used to form sequences for a generalized dendrimer structure of this invention;
6 FIG. 30 shows a peptide sequence, i.e., Seq. ID No. 10, for a preferred 7 embodimentn of a specific dendrimer structure of this invention;
8 FIG. 31 is a conceptual diagram of an experimental device; and 9 FIG. 32 is a system diagram of preferred embodiments of the invention.

13 It is to be understood that the invention is not limited to the examples described 14 herein. All technical and scientific terms used herein have meanings as commonly understood by one of ordinary skill in the art unless otherwise defined.

1 The present invention detects the presence of abnormal 2 proteins and proteinaceous particles based on a method that 3 utilizes catalytic propagation. Upon interaction of a 4 sample, containing abnormal proteins or proteinaceous particles, with a peptide probe of the invention, the 6 peptide probe undergoes conformational changes resulting in 7 the formation of aggregates. The addition of the abnormal 8 proteins and proteinaceous particles catalyzes the forma-9 tion of the aggregates and causes further propagation of this conformational transition. The resulting aggregates 11 are then easily detected using common analytical instrumen-12 tation and techniques.

14 The abnormal proteins and proteinaceous particles on which the invention focuses are proteins, protein based 16 chemical structures such as prions and protein subunits 17 such as peptides that are capable of conformational changes 18 that lead to the formation of aggregates and ultimately to 19 disease states.
These proteins and proteinaceous particles form aggre-21 gates by shifting from a monomeric to a multimeric state.
22 The shift from one distinct state to the other requires a 23 driving force that is commensurate with the energetic 24 difference between the two conformational states as shown in Fig. 7.
26 A preferred example of such proteinaceous particles is 27 that of a prion protein. Prions can exist in one of two 28 distinct conformations characterized by having a secondary 29 protein structure that is either predominately alpha-heli-cal or predominately beta-sheet; where the predominately 31 beta-sheet conformation has a much higher preference to 32 exist in a multimeric state. As a result, predominately 2 beta-sheet (or beta rich) secondary structure is more typical of abnormally folded or 3 disease-causing proteinaceous particles since their preference to aggregate is likely to be 4 disruptive in an in vivo environment.
FIG. 1 shows illustrations of both the alpha-helical monomer 10 and the beta-sheet 6 dimer 12 forms of a TSE conformer (or alternative secondary structure).
Research has 7 shown that the normal wild-type (wt) form of prion protein (PrPc) prefers a monomeric 8 state, while the abnormal, disease-causing form (PrPsc) more readily takes on a multimeric 9 state. (See Fred E. Cohen, et al., Pathologic Conformations of Prion Proteins (Annu. Rev.
Biochem. 1998) 67: 793-819.) 11 This distinction between the secondary structure of the normal form of prion protein 12 and the abnormal form as well as its propensity to cause aggregation is exploited in the 13 present invention to allow detection of the abnormal form even in samples with very low 14 levels of infectious abnormal protein.
The mechanism of the invention is shown in a schematic in FIG. 2. The top row of 16 the schematic shows an example of an unknown sample of TSE protein 20 represented as 17 containing aggregated beta-sheets 12. The beta-sheets are then 18 disaggregated 22 by subjecting the sample to commonly known disaggregation methods 19 such as sonication. This is followed by the addition of labeled peptide probes 14 which are allowed to bind to the sample 20. Presence of the beta-sheet conformation in the sample 21 20 induces the peptide probes to also shift to beta-sheet formation 16.
In this manner the 22 transition to beta-sheet is propagated among the peptide probes 14 thereby causing new aggregates 18 to form. The resulting transition to a predominately beta-sheet form and amplified aggregate formation can then easily be detected using common analytical techniques such as light scattering and circular dichroism (CD); and in a particularly preferred embodiment where the peptide probe is fluorescent labeled, fluorescence detection instrumentation can also be used.
The bottom row of FIG. 2 shows an alternative example in which the unknown sample of TSE protein 20 is represented in its normal alpha-helical form 10. For consistency, the sample is subjected to the same disaggregation process described above. Upon addition of the labeled peptide probes 14, neither a transition to beta-sheet form nor binding to the unknown samples occurs.
As a result, there is no aggregate fluorescence signal in the case of a labeled peptide probe as well as no detection of aggregate formation by other analytical tools. Based on this schematic, unknown samples can be tested for the presence or absence of such abnormal protein conformations or sequences.
A preferred embodiment of the invention involves the following basic procedures. Peptide probes 14 are selected in order to be added to an unknown or test sample 20 at a later stage in the process. The peptide probes 14 are preferably proteins or peptide sequences that have secondary structures of predominately alpha-helix or random coil. In a particularly preferred embodiment, the peptide probes 14 are peptide fragments consisting of a helix-loop-helix structure as found in lysine. In another particularly preferred embodiment, the peptide probes can be made of a peptide sequence chosen from wild-type (wt) TSE, from a desired species-specific TSE peptide sequence, or even from a selectively mutated TSE sequence that has been mutated in such a manner as to render it destabilized and noninfectious. Additionally, extrinsic fluors such as pyrene can be added or designed into the peptide probe to allow detection of anticipated conformational changes using common fluorescence detection techniques.
Once a peptide probe 14 is selected, it is added to a test sample 20. Prior to the addition of the peptide probe 14, however, it is preferred to have the sample 20 subjected to disaggregation techniques commonly known in the art, such as sonication. The disaggregation step allows any potentially aggregated sample material 20 to break apart so that these disaggregated sample materials 22 are more free to recombine with the newly introduced peptide probes 14; thereby facilitating the anticipated catalytic propagation.
After the test sample 20 or disaggregated test sample 22 is allowed to interact with the peptide probes 14, the resulting mixture is then subjected to analytical methods commonly known in the art for the detection of aggregates and to fluorescence measurements in cases where fluorescent peptide probes 14 are used.
Unknown or test samples 20 containing any dominant beta-sheet formation characteristic of abnormally folded or disease-causing proteins results in an increase in beta-sheet formation and consequently aggregate formation in the final mixture containing both the test sample 20 and the peptide probes 14. Conversely, unknown or test samples 20 which lack a predominantly beta-sheet secondary 16a structure will neither catalyze a transition to beta-sheet structure 16 nor will propagate the formation of aggregates 18.

1 One of ordinary skill in the art can appreciate that 2 the 3 means by which the initial conformational change can be 4 triggered in the test samples 20 can be varied as described in the following examples. The binding of a metal ligand 6 could direct a change in the protein scaffolding and favor 7 aggregation. The expression or cleavage of different pep-8 tide sequences can promote advanced aggregation leading to 9 fibril and plaque formation. Genetic point mutations can also alter the relative energy levels required of the two 11 distinct conformations, resulting in midpoint shifts in 12 structural transitions. Furthermore, an increase in con-13 centration levels could be sufficient to favor the 14 conformational transition. Regardless of the initial trigger mechanism, however, the disease process in many of 16 the abnormal protein conformations such as in prion-related 17 diseases always involves the catalytic propagation of the 18 abnormal conformation, resulting in transformation of the 19 previously normal protein.
21 One of ordinary skill in the art can also appreciate 22 that there are many common protein aggregate detection 23 techniques many of which are based on optical measurements.
24 These optical detection techniques include, but are not limited to, light scattering, or hydrophobicity detection 26 using extrinsic fluors such as 1-anilino-8-napthalene 27 sulfonate (ANS) or Congo Red stain, fluorescence proximity 28 probes on the peptide fragments, including fluorescence 29 resonance energy transfer (FRET) & quenching of intrinsic tryptophan fluorescence through either conformational 31 change of monomer or binding at interface in alpha-beta 32 heterodimer; the N-terminal loop region is particlularly 1 interesting in this regard selective binding to target 2 protein, circular dichroism (CD) monitoring of actual 3 conformation, nuclear magnetic resonance (NMR). Other 4 detection techniques include equilibrium ultracentrifuga-tion or size-exclusion chromotography at the aggregation 6 stage as well as other structural techniques. Examples and 7 explanations of these methods can be found in Freifelder, 8 David. Physical Biochemistry: Applications to Biochemistry 9 and Molecular Biology, (W. H. Freeman Press, New York, 2nd ed. 1982). and in Copeland, Robert. Analytical Methods for 11 Proteins, (American Chemical Society Short Courses 1994).
12 both of which are wholly incorporated herein as prior art.
13 Many of these enumerated optical and structural methods are 14 rapid, cost-effective and accurate.
16 Experiments were performed using model systems to show 17 the conformational changes involved in the transition from 18 a predominately alpha-helix to a beta-rich form. The model 19 systems chosen used readily available, nonneurotoxic poly-amino acids such as polylysine and polyglutamine. The 21 polyamino acids were chosen because of their availability 22 and more importantly because they are safe to handle thus 23 eliminating the need for special handling or donning cum-24 bersome extra protective gear.
Fig. 3 shows a circular dichroism graph of experimen-26 tation with poly-L-lysine 20 micro Molar (FM) 52,000 molec-27 ular weight ODO as a peptide probe. The resulting graphs 28 show:

= Sample 24 which was maintained at pH7, 25 C result-31 ing in a minimum at approximately 205 namometers (run) 32 indicating random coil structure.

1 = Sample 26 which was maintained at pH11, 500C result-2 ing in a minimum at approximately 216 namometers (rim) 3 indicating beta-sheet structure.

= Sample 28 which was a 1:1 combination of samples 6 maintained at pH7, 25 C and at pH11, 500C resulting in 7 a minimum at approximately 216 namometers (rim) indi-8 cating beta-sheet structure.

= Sample 30 which was a 1:1 combination of samples 11 maintained at pH7, 500C and at pH11, 500C resulting in 12 a minimum at approximately 216 namometers (rim) indi-13 cating beta-sheet structure.

Fig. 4 shows an absorbance graph of experimentation 16 with poly-L-lysine 70 mircomolar (pM) 52,000 molecular 17 weight (MW) as a peptide probe. The resulting graphs show:

19 = Sample 32 which was maintained at pH 11, 25 C re-suiting in a plateau at approximately 0.12 indicating 21 predominately alpha-helical structure.

23 = Sample 34 which was maintained at pH7, 50 C result-24 ing in a a plateau at approximately 0.22 indicating random coil structure.

27 = Sample 36 which was a 10:1 combination of samples 28 maintained at pH7, 50 C and at pH11, 50 C resulting in 29 a steeper incline from approximately 0.22 to 0.33 indicating an accelerated transition from random coil 31 to beta-sheet structure.

2 = Sample 38 which was a 10:1 combination of samples maintained at 3 pH7, 25 C and at pH11, 50 C resulting in a gradual incline from 4 approximately 0.22 to 0.26 indicating a transition from random coil to beta-sheet structure.
6 FIG. 5 shows general circular dichroism results of experimentation with poly-L-lysine 7 at varying temperatures and pH indicating its potential for transitioning from random coil to 8 beta-sheet under the varying environmental conditions. The results indicate that both 9 temperature and pH play an important role in the transition.
The observations based on all of the modeling experimentation described above 11 show that the addition of a relatively small amount of beta-sheet peptide to random coil 12 sample can result in a shift towards a beta-rich conformation and such changes can be 13 accelerated depending on the temperature and pH environment of the samples.
14 FIG. 6 shows experimentation results using pyrene as a fluorescent probe in proximal and distal locations in an alpha helical bundle structure undergoing conformational 16 change. The pyrene excimer formation 15 is shown at 480 nnn 42 and the spectra for a 17 predominately alpha-helical structure 17 is contrasted 40 as well. Those skilled in the art 18 would appreciate that other fluorescent probes such as FITC can also be used.
19 A primary objective of this invention also encompasses use of the catalytic propagation of conformational change to directly correlate the measures of abnormal prion 21 pres-1 ence with levels of infectivity. For this reason we favor 2 implementation of the invention in a manner where there is 3 no increase in resulting infectious products as a result of 4 the propagation. This can be achieved by placing a "break"
in the links between the chain of infection, transmission 6 and propagation of the abnormal form. Such a "break" must 7 occur at the transitional stage between the dimer and 8 multimer forms of the aggregate. The physical formation of 9 the multimer form can be blocked by simply impeding the step which leads to its formation. This may be done, 11 preferably by using a large pendant probe or by a neutral 12 "blocker" segment, bearing in mind that probes on linkers 13 or "tethers" are more likely to encounter each other and 14 thus result in amplifying the signal.
16 In a particularly preferred embodiment of the inven-17 tion, the peptide probes 14 function in the manner de-18 scribed above. The peptide probes act as "nuclei"; wherein 19 once the peptide probe 14 binds to a test sample 20, or a sample known to have beta-rich structure 12, it is con-21 verted to a peptide probe conformer 16 which has the capac-22 ity to act as a trigger to bind to another peptide probe 14 23 and continues to induce the same conformational change.
24 Propagation of this reaction can then be controlled by the peptide sequence chosen for the peptide probe 14 and by the 26 experimental conditions. Thus, in situations where infec-27 tious levels are low and there is a need to amplify any 28 existing abnormal proteinaceous particles in an unknown 29 sample 20, it is preferred that a peptide probe 14 capable of rapid and continuous propagation of the reaction be 31 chosen with which to nucleate the unknown sample 20. On 32 the other hand, in situations where it is desired to corre-late detection of abnormally folded proteinaceous particles with levels of infectivity, it is preferred that peptide probe 14 chosen is one that is less likely to aggregate.
When more than one beta units come together, they act as nuclei to attract and stabilize other transient elements of secondary structure. See Stryer, Lubert.
Biochemsitry. W. H. Freeman Press. (3rd ed. NY 1988) p35.
In choosing the peptide probe 14 with which to nucleate this reaction there are several considerations to be made.
Associations of peptide can be controlled by the thermodynamics of the solution in which they are in and by the presence of amorphous nuclei which self-associate, crystalline nuclei which readily aggregate, specific peptide sequences which may aggregate, but may do so under low concentrations which are difficult to measure by conventional means, or larger peptide sequences modeled after known beta-sheet structures or proteins such as a beta-rich prion protein.
To demonstrate this embodiment of the invention, two peptide sequences were synthesized to be used as peptide probes 14. The peptide sequences were modeled after known prion protein (PrP) sequences shown in FIG. 13. The sequences in FIG. 13 correspond to binding regions that are very similar among the species shown. FIG. 14 shows the peptide sequences of the two synthesized peptides. The 19-mer sequence referred to as Seq. Id. No. 7 is closely modeled after residues 104 through 122 of the human sequence. The 14-mer sequence referred to as Seq. Id. No.
8 is closely modeled after residues 109 through 122 of the human PrP sequence. The synthetic peptide probes 14 were also prepared with and without pyrene butyric acid as a fluorescence marker.

1 Many experiments were performed to study the proper-2 ties of the synthetic peptides. Experiments were performed 3 using analytical techniques common in the art such as 4 absorbance, fluorescence under varying excitation and excitation of fluorescence. The peptides were studied at 6 several concentrations ranging from 1 to 100 micro Molar 7 (pM) and under varying buffer concentrations, pH, tempera-8 tures and ionic strengths.
9 Fig. 15 shows a graph of fluorescence-spectra results at different peptide concentrations. The data were col-11 lected over times ranging form one hour to one week with no 12 experimental changes observed after twenty-four hours. The 13 resulting graphs show:

= Sample 46 which was at a concentration of 5 pM with 16 a relative fluorescence peak at approximately 0.1.

18 = Sample 48 which was at a concentration of 10 pM
19 with a relative fluorescence peak at approximately 0.4.

22 = Sample .50 which was at a concentration of 150 pM
23 with a relative fluorescence peak at approximately 24 4.7.
26 Note: data were also collected for Sample 52 at a high 27 concentration of 800 pM, but is not shown in the figure.

Fig. 16 shows a graph of the fluorescence spectra for 31 samples 46 through 52 normalized to the intensity at 378 rim 32 for the initial scan. It was observed that the spectrum 1 for Sample 52 which contained the highest peptide concen-2 tration was markedly different leading to the conclusion 3 that there is excimer emission with a maximum at approxi-4 mately 460 nm.
6 Fig. 17 is a graph of experimental results showing 7 pyrene's excitation of fluorescence. The experiments were 8 performed with excitation wavelengths at 365 nm to observe 9 excimer emission at approximately 460 nm. The excitation at 348 nm, however, increases the fluorescence signal by 11 over a hundred times with no other modifications or signal 12 amplification. To confirm that the pyrene conjugate was 13 responsible for both the major 398 nm emission as well as 14 the one at approximately 460 nm, the excitation spectra for fluorescence at 398 nm and at approximately 460 nm were 16 recorded and are shown in Fig. 18. Both the excitation 17 spectra are nearly identical with a 365 nm maximum confirm-18 ing that emission at approximately 460 nm is associated 19 with the formation of excimers by two pyrene groups as in the following.

22 Pyr* + Pyr = (Pyr_pyr)*

24 where Pyr is a pyrene molecule and Pyr* is a pyrene in its excited form; the (Pyr_Pyr)* represents the formation of 26 excited dimer. More general information on excimers can be 27 found in Freifelder, David. Physical Biochemistry: Appli-28 cations to Biochemistry and Molecular Biology, (W. H.
29 Freeman Press, New York, 2nd ed. 1982), at 559.
31 Experiments were also performed to study the stability 32 of the peptides. Fig. 19 shows experimental data obtained from circular dichroism (CD) analysis of the 19-mer under different condition. The CD spectra were recorded for a number of peptide concentrations ranging from 20 to 100 mM. The results show that the 19-mer is largely coiled and exhibits high thermodynamic stability under the experimental conditions tested such as varying pH, ionic strength and temperature. As expected, the addition of organics such as acetonitrile and trifluoroethylene (TFE) encourage the formation of the secondary structure. FIG.
20 shows both the previous results and the results of a similar experiment in which the 19-mer was mixed with its shorter analog, the 14-mer. In this experiment, the 19-mer and 14-mer were combined 100:1 for one hour and assembled under dilute conditions in the micro molar range. Sample curves 60 through 64 which correspond to the mixture showed that the mixture of the oligomers significantly differed from the CD spectra of sample curves 52 through 58 which represent the 19-mer alone, indicating strong interactions between the mixed molecules. As a result, the 14-mer triggers conformational changes in a peptide probe 14 made of the 19-mer.
In a paper published by Prusiner, et al., CD data show that the Seq. Id. No. 7, 19-mer exhibits coil-like conformation, whereas the Seq. Id. No. 8, 14-mer is largely beta-sheet, as shown in FIG. 21a for a 3 mM
concentration sample from the paper. The 19-mer, however, can be transformed from its coil-like conformation to a beta-sheet conformation through interaction with a very small fraction of the 14-mer as shown in FIG. 21b which was tracked over a twenty four hour time period. See Prusiner, et al. Prion protein peptides induce alph-helix 2 to beta-sheet conformational transitions. Biochemistry. 34:4186-92 (1995).
3 FIG. 22 shows a conceptual figure of the secondary structure of the two synthetic 4 peptides (where C=coil and H=helix) based on the application of various secondary structure algorithms to the sequences of both of the synthetic peptides. The resulting 6 projection, however, does not entirely agree with the CD results. Based on the CD results, 7 the conformations of both synthetic peptides are clearly concentration dependent.
8 Moreover, while the 19-mer exhibits largely a coil conformation that is fairly stable under a 9 wide variety of the experimental conditions tested, the 14-mer exhibits a transition from coil or hairpin to beta-sheet structure depending on its concentration.
11 More experiments were performed to determine if the 19-mer could self-associate.
12 FIG. 23 shows a graph of fluorescence results showing that the 19-mer could self-associate 13 with increasing concentration as shown in Sample curve 66 and at low concentrations with 14 pH modifications to give a net neutral charge while using potassium chloride (KCI) to screen the charge as shown in Sample curve 68. The 19-mer can also self-associate at low 16 concentrations with the introduction of some type of 17 nucleating agent, as discussed earlier. Thus, the conditions for self-association can be 18 optimized to adapt to a desired type of detection.
19 The same samples; Sample curve 66 containing 0.1 M TRIS buffer at pH 6 to 9 and Sample curve 68 containing 0.1 M TRIS buffer at pH 10 to 11 in the presence of KCI at 26a 100 to 500 mM, are shown again in FIG. 24 to reflect the _ efficiency of excimer formation under low concentrations.
The ratio of the fluorescence intensities as measured at 378 nm 1 (IM) and at 460 nm (IE) was chosen to monitor the self-2 association as a function of the peptide concentration at 3 25 C. It was also shown that screening of the electro-4 static interactions (pI = 10) encouraged self-association at extremely low concentrations on the order of less than 6 10 micro Molar.
7 In order to further study the effect of nuclei on the 8 self-association of the 19-mer, more fluorescence measure-9 ments were taken of 19-mer in solution nucleating with small amounts of already self-associated 19-mer units. The 11 sample solutions range from concentrations of 200 to 800 12 micro Molar and are described in Fig. 25. The kinetics of 13 association in dilute solutions of 20 micro Molar were also 14 monitored.
Fig. 26a shows more fluorescence data of the 19-mer in 16 water 70, acetonitrile 72 and TFE 74 after twenty-four 17 hours. Fig. 26b shows the experimental results for a 100:1 18 combination of the 19-mer and 14-mer in water 76, aceto-19 nitrile 78 and TFE 80 after twenty-four hours. In both of the graphs in Fig. 26 peptide association was monitored by 21 the appearance of excimer emission at approximately 460 nm.
22 Figs. 27 a, b, c, and d show four fluorescence data 23 graphs taken at 24, 48, 144 and 336 hours, respectively.
24 The measurements were taken to determine the effect of pH, temperature, ionic strength, and organic additives on the 26 kinetics of the peptide associations studied for the 19-mer 27 model peptide. The fluorescence intensities as measured at 28 378 nm for monomeric units and 460 nm for associations were 29 used to characterize the IE/Im ratio or self-association of the peptide.
31 Additional fluorescence results are shown in Fig. 28 32 where an insoluble fraction of the peptide was extracted 2 and dissolved in organic solvent containing methanol/ethanol/dimethylformanide and then 3 analyzed. Fluorescence detection results of the "insoluble" portion show high levels of 4 peptide association wherein the 'E/'M ratio equals 2. A small aliquot of "insoluble" portion was added to nucleate 20 micro Molar 19-mer peptide solutions which were then analyzed 6 and are reported in the same graph. The results show that the presence of the nucleating 7 fraction significantly increased the efficiency of the peptide association and this can be 8 seen more dramatically in FIG. 28b at 150 hours.
9 The observations of these experiments led to some of the following conclusions.
= Fluorescence of pyrene, which is covalently attached to the peptide probe 14 11 in preferred embodiments, allows monitoring of peptide self-association in 12 this model system. It can also be used as an index of conformational change 13 and especially since at low concentrations, the peptide association is difficult 14 to measure using nonoptical techniques.
= The fluorescence data shows that self-association of the SEQ. ID. No. 7, 16 19-mer, can be promoted by adjusting ionic strength or pH.
17 = The fluorescence data also shows that the kinetics of the conformational 18 changes can be modulated by controlling solvent parameters and the 19 peptide probe sequence.

. .

2 = The kinetics of the self-assembly or association process can be controlled or 3 regulated by the addition of or by preexisting nucleating associated forms.
4 This strongly supports the conclusions that the conformational transitions of the 19-mer can be autocatalytic.
6 In a particularly preferred embodiment, the peptide probes 14 can be used to 7 detect proteinaceous particles such as in prion-like structures exhibiting coil to beta-sheet 8 transition. According to Prusiner, et al. Pr/on protein peptides induce alph-helix to 9 beta-sheet conformational transitions. Biochemistry. 34:4186-92 (1995).
As a result, synthetic peptide probes such as the SEQ. ID. No. 7, 19-mer should be conformationally 11 sensitive to the presence of prion-like substances that undergo this conformational shift.
12 Moreover, because an intrinsic optical reporter, such as pyrene can be added to the 13 peptide probe, this embodiment of the invention has the added advantage of being able to 14 detect such prion-like substances in test samples 20 such as blood, lymph, CSF and even tissues other than brain homogenate that typically contain very low levels of abnormal 16 prion substances that are otherwise too difficult to detect. The intrinsic 17 optical reporter allows optical (fluorescence) measurements to be taken of the peptide 18 probe associates that form upon interaction with nucleating samples such as an abnormal 19 prion.
In another particularly preferred embodiment of the invention, the peptide probes 21 14 are synthesized based on the structure of a dendrimer; dendrimers being synthesized _ three-dimensional highly branched macromolecules. The advantages of using a dendrimer probe 15 are multifold.
Dendrimers should increase the speed of the assay kinetics thereby relaying quicker test results. This can be especially advantageous in assembly line applications of the invention where products or specimens in mass quantities can be quickly tested for the presence of abnormal proteinaceous particles. This embodiment is also extremely beneficial in applications where quick decisions must be based on the detection results. This embodiment is also advantageous for use in these applications as well as others since the highly branched structure of the dendrimer prevents amplification of abnormal proteinaceous particles or aggregates. By preventing such amplification of the abnormal particles, it becomes very simple to correlate the detection results with the level of abnormal aggregates existing in a test sample 20. Furthermore, it is also safe to handle since the synthetic probe itself is nonneurotoxic and amplifies signal without amplification of any highly infectious particles that may be preexisting in a test sample 20. Thus, it eliminates the need for extra precautions or sterilization in many of the steps of the assay method.
A generalized dendrimer 15 structure is shown in FIG.
9 and is referred to as Seq. Id. No. 20. In a particularly preferred embodiment of the invention, a specific dendrimer structure was designed and synthesized, referred to as Seq. Id. No. 10 and is shown in FIG. 30.
In FIG. 30, the specific dendrimer structure is basically a loop-turn-loop structure as illustrated by FIG. 30a. In FIG. 30b, it is shown that the sequence is modeled after the human PrP sequence shown in FIG. 14 in residues 126 through 104 plus 109 through 126. This = structure shows the region on the right 74 as an inverted form of the PrP sequence. This was done to take advantage of the five aminoacids which naturally form a loop in order to place the hydrophobic pyrene in a corresponding hydrophobic region. Also, the valine-valine fragment has been said to be essential to beta-sheet formation, and so is retained in the sequence. In the figure, the valine, leucine, leucine, and valine residues at positions 11, 14, 20 and 23, respectively, denote possible mouse variants.
The amyloidogenic palindrome region 70 may be changed to SS or SSS/AAA. The central region 72 is a loop sequence with stearic constraints. Thus, it is possible to add tryptophan for stearic and fluorescence considerations.
Modifications of the aminoacid sequence such as one or more deletions or insertions are possible as alluded to above, provided that the dendrimer retains its branched loop-turn-loop structure as well as aminoacids essential to beta-sheet formation, and preferably contains an optical reporter.
FIG. 10 shows a schematic diagram of how the dendrimer probes 15 amplify signal and propagate conformational change without aggregation and without increasing the biohazard or infectious nature of an abnormal protein or prion test sample 12. The figure shows that once the dendrimer probes 15 come into contact with the abnormal sample 12, the dendrimer probe 15 undergoes the conformational shift to a predominately beta-sheet structure 17. The newly formed beta-rich dendrimer probe 17 nucleates other dendrimer probes 15 to make the same transition. By doing so, any optical signal associated with the dendrimer probe 15 is amplified as more probes 15 shift to the beta-rich state 17.
It is important to note that the minimal detectable concentration of pyrene only provides a number for the peptide probe 14 concentration that can be worked with;
but the detection limit of the assay is not dependent on it because it is the resultant of the fluorescent ensemble that is being observed. In other words, the real measurement of interest and the rate limiting step in the analysis is the amount of abnormal e. g. prion protein that need to be present in the sample 20 to initiate a conformer change in the peptide probe 14. Immunoassays are typically sensitive in the picomolar range. Nevertheless, once the conformer change is initiated in a single peptide probe 14, the catalytic propagation of its beta-rich structure allows detection in samples previously considered to have abnormal particles 12 at concentrations too low to detect.
Due to its ability to safely, quickly and noninvasively detect abnormal proteinaceous particles such as misfolded proteins, prions, aggregates and fibrils that may lead to toxic plaque formations, the method of this invention is widely applicable to many industries. By example, some of those industries include the diagnostics markets in animal health and human health, the food industry, pharmaceutics, especially for screening animal by-products, transplant/transfusion and vaccine supplies, research and development in such areas as chemotherapies for TSE's, as well as national security in the area of biosensors for biowarfare agents.

Accordingly, in yet another preferred embodiment of the invention, the methods discussed herein can be applied for use with a simple detection instrument such as the one shown in FIG. 31. The device shown in FIG. 31 is a simple optical device that includes a light source 80, e.g., a lamp or laser; a T-format sample cell 82; and a photomultiplier tube 84. In certain applications it may be desirable to have the method distributed as an assay that includes such a simple device.
Accordingly, the present invention is not limited to the specific embodiments illustrated herein. Those skilled in the art will recognize, or be able to ascertain that the embodiments identified herein and equivalents thereof require no more than routine experimentation, all of which are intended to be encompassed by claims.
Furthermore, it will be understood that the foregoing disclosure is intended to be merely exemplary, and not to limit the scope of the invention--which is to be determined by reference to the appended claims.

, SEQUENCE LISTING
<110> Arete Associates <120> MISFOLDED PROTEIN SENSOR METHOD
<130> 42315-0001 <140> CA 2,448,981 <141> 2002-05-30 <150> 10/494,906 <151> 2004-05-07 <150> PCT/US02/17212 <151> 2002-05-30 <150> 60/295,456 <151> 2001-05-31 <160> 10 <170> PatentIn Ver. 3.3 <210> 1 <211> 38 <212> PRT
<213> Homo sapiens <400> 1 Lys Pro Lys Thr Asn Met Lys His Met Ala Gly Ala Ala Ala Ala Gly Ala Val Val Gly Gly Leu Gly Gly Tyr Met Leu Gly Ser Ala Met Ser Arg Pro Ile Ile His Phe <210> 2 <211> 38 <212> PRT
<213> Cricetus sp.
<400> 2 Lys Pro Lys Thr Asn Met Lys His Met Ala Gly Ala Ala Ala Ala Gly Ala Val Val Gly Gly Leu Gly Gly Tyr Met Leu Gly Ser Ala Met Ser Arg Pro Met Met His Phe <210> 3 <211> 38 <212> PRT
<213> Mus sp.
Page 1 of 4 <400> 3 Lys Pro Lys Thr Asn Leu Lys His Val Ala Gly Ala Ala Ala Ala Gly Ala Val Val Gly Gly Leu Gly Gly Tyr Met Leu Gly Ser Ala Met Ser Arg Pro Met Ile His Phe <210> 4 <211> 38 <212> PRT
<213> Bos sp.
<400> 4 Lys Pro Lys Thr Asn Met Lys His Val Ala Gly Ala Ala Ala Ala Gly Ala Val Val Gly Gly Leu Gly Gly Tyr Met Leu Gly Ser Ala Met Ser Arg Pro Pro Ile His Phe <210> 5 <211> 38 <212> PRT
<213> Cervus sp.
<400> 5 Lys Pro Lys Thr Asn Met Lys His Val Ala Gly Ala Ala Ala Ala Gly Ala Val Val Gly Gly Leu Gly Gly Tyr Met Leu Gly Ser Ala Met Ser Arg Pro Leu Ile His Phe <210> 6 <211> 38 <212> PRT
<213> Odocoileus sp.
<400> 6 Lys Pro Lys Thr Asn Met Lys His Val Ala Gly Ala Ala Ala Ala Gly Ala Val Val Gly Gly Leu Gly Gly Tyr Met Leu Gly Ser Ala Met Ser Arg Pro Leu Ile His Phe Page 2 of 4 <210> 7 <211> 19 <212> PRT
<213> Artificial Sequence <220>
<223> Description of Artificial Sequence: Synthetic peptide <400> 7 Lys Pro Lys Thr Asn Met Lys His Met Ala Gly Ala Ala Ala Ala Gly Ala Val Val <210> 8 <211> 14 <212> PRT
<213> Artificial Sequence <220>
<223> Description of Artificial Sequence: Synthetic peptide <400> 8 Met Lys His Met Ala Gly Ala Ala Ala Ala Gly Ala Val Val <210> 9 <211> 19 <212> PRT
<213> Artificial Sequence <220>
<223> Description of Artificial Sequence: Synthetic peptide <400> 9 Lys Pro Lys Thr Asn Met Lys His Met Ala Gly Ala Ala Ala Ala Gly Ala Val Val <210> 10 <211> 33 <212> PRT
<213> Artificial Sequence <220>
<223> Description of Artificial Sequence: Synthetic peptide <400> 10 Val Val Ala Gly Ala Ala Ala Ala Gly Ala Val His Lys Leu Asn Thr Page 3 of 4 Lys Pro Lys Leu Lys His Val Ala Gly Ala Ala Ala Ala Gly Ala Val Val Page 4 of 4

Claims (37)

WHAT IS CLAIMED IS:

1. An in vitro method of detecting the presence of a misfolded form of a prion protein (PrP SC) or a A.beta. protein comprising a predominantly beta-sheet secondary structure in a sample, said method comprising:
(a) adding a propagation catalyst to a sample comprising body fluids, wherein the propagation catalyst is a peptide that:
(i) has a predominantly alpha-helix or random coil secondary structure that interacts with a PrP SC or a A.beta. protein, and (ii) undergoes a conformational shift that results in an increase in beta-sheet secondary structure upon contact with misfolded PrP SC or A.beta.
protein comprising a predominantly beta-sheet secondary structure or upon contact with another such propagation catalyst that has undergone such a conformational shift;
(b) allowing the catalyst and any misfolded PrP SC or A.beta. protein present in the sample to interact resulting in an increase in beta-sheet secondary structure;
and (c) detecting any increase in beta-sheet secondary structure in the mixture, the increase being due, at least in part, to an increase in beta-sheet secondary structure of the propagation catalyst, wherein any such increase indicates the presence of misfolded PrP SC
or A.beta. protein in the sample.

2. The method of claim 1, wherein the propagation catalyst is an optically labeled peptide.

3. The method of claim 2, wherein the detecting step comprises taking optical measurements.

4. The method of claim 3, wherein the propagation catalyst comprises a fluorescent label and the detecting step comprises detecting fluorescence of the propagation catalyst.

5. The method of claim 1, wherein the detecting step comprises taking structural measurements, using an analytical technique selected from light scattering and circular dichroism, or a combination thereof.

6. The method of claim 1, wherein the method further comprises, prior to the step of adding the propagation catalyst to the sample, the step of subjecting the sample to a disaggregation technique.

7. The method of claim 1, wherein the bodily fluids are obtained from a living animal.

8. The method of claim 1, wherein the body fluids comprise blood.

9. The method of claim 1, wherein the body fluids comprise cerebral spinal fluid.

10. The method of claim 1, wherein the body fluids comprise lymph.

11. The method of claim 1, wherein the PrP SC is associated with transmissible spongiform encephalopathy (TSE).

12. The method of claim 1, wherein the PrP SC is associated with Creutzfeldt-Jakob syndrome.

13. The method of claim 1, wherein the PrP SC is associated with scrapie.

14. A peptide probe for misfolded PrP SC particle or A.beta. protein, wherein said peptide:
(i) comprises an amino acid sequence of a fragment of the PrP SC particle or A.beta.
protein and exhibits a predominantly alpha-helix or random coil secondary structure, (ii) interacts with the misfolded PrP SC particle or A.beta. protein, and undergoes a conformational shift that results in an increase in beta-sheet secondary structure upon contact with misfolded PrP SC particle or A.beta. protein or upon contact with another such peptide that has undergone such a conformational shift, and (iii) is labeled at each terminus with a detectable label.

15. The peptide of claim 14, wherein the peptide has a helix-loop-helix structure.

16. A composition comprising a peptide of claim 14 and a carrier.

17. A composition comprising a peptide of claim 14 bound to a misfolded target protein.

18. The composition of claim 17, wherein the misfolded target protein is a PrP SC
particle or A.beta. protein.

19. A method for detecting the presence of a pathogenic prion protein or AP
protein in a sample comprising:
(a) contacting a sample suspected of comprising a pathogenic prion protein or A.beta. protein with a peptide according to claim 14 under conditions that allow interaction of the peptide to the pathogenic prion protein or A.beta. protein, if present;
and (b) detecting the presence the pathogenic prion protein or A.beta. protein, if any, in the sample by its interaction with the peptide.

20. The peptide of claim 14, comprising the amino acid sequence VVAGAAAAGAVHKLNTKPKLKHVAGAAAAGAVV.

21. A method for detecting the presence of a pathogenic prion protein in a sample comprising:
(a) contacting a sample suspected of comprising a pathogenic prion protein with a peptide reagent according to claim 20 under conditions that allow interaction of the peptide reagent with the pathogenic prion protein, if present; and (b) detecting the presence the pathogenic prion protein, if any, in the sample by its interaction with the peptide reagent.

22. The method of claim 2, wherein the peptide comprises an amino acid sequence comprising a first amino acid sequence corresponding to a fragment of the protein oriented in the forward direction and a second amino acid sequence corresponding to a fragment of the protein oriented in the reverse direction.

23. The method of claim 2, wherein the peptide has a helix-loop-helix structure.

24. The method of any one of claim 1 or claim 19, wherein the peptide comprises the amino acid sequence VVAGAAAAGAVHKLNTKPKLKHVAGAAAAGAVV.

25. The peptide of claim 14, wherein the detectable label is selected from the group consisting of pyrene, 1-anilino-8-napthalene sulfonate (ANS), and Congo Red.

26. The method of claim 1, wherein said method comprises detecting the presence of a misfolded form of A.beta. protein.

27. The method of claim 1, wherein said propagation catalyst is labeled at each terminus with a detectable label.

28. The method of claim 27, wherein the detectable label is pyrene.

29. The method of claim 28, wherein, when said propagation catalyst undergoes said conformational shift, interaction between the pyrene label at each terminus results in pyrene excimer formation.

30. The method of claim 29, further comprising adjusting a reaction condition to increase or decrease pyrene excimer formation.

31. The method of claim 30, wherein said reaction condition is selected from the group consisting of ionic strength of the sample, pH of the sample, concentration of the sample, temperature, and the presence or absence of nucleating agents.

32. The method of any one of claims 29 to 31, wherein the detecting step comprises detecting pyrene excimer formation.

33. The method of claim 1, wherein the detecting step comprises detecting aggregates comprising the propagation catalyst.

34. The method of claim 1, wherein the propagation catalyst is a peptide comprising an amino acid sequence of a fragment of the prion protein or A.beta. protein.

35. The peptide probe of claim 14, wherein said peptide comprises an amino acid sequence of a fragment of the A.beta. protein.

36. The composition of claim 16 or 17, wherein said peptide comprises an amino acid sequence of a fragment of the A.beta. protein.

37. The method of claim 19 or 34, wherein the peptide comprises an amino acid sequence of a fragment of the A.beta. protein.