This interesting paper implies that while amyloid fibrils appear to have a uniform structure in the plaque of a given patient with Alzheimer’s disease (AD), that structure may differ from patient to patient. This conclusion is based on data from only two people, but assuming it holds up in more cases, it could be important for our understanding of people's vulnerability (or, conversely, resistance) to developing sporadic AD. Together, this data and the recent paper by Cohen et al. showing that fibrils are important for the assembly of toxic oligomers (see ARF related news story) could mean that each individual's fibril type may have a greater or lesser capability to seed toxic oligomers, which may account for some people being more resistant to AD despite a high plaque load.
References:
Cohen SI, Linse S, Luheshi LM, Hellstrand E, White DA, Rajah L, Otzen DE, Vendruscolo M, Dobson CM, Knowles TP.
Proliferation of amyloid-β42 aggregates occurs through a secondary nucleation mechanism.
Proc Natl Acad Sci U S A. 2013 Jun 11;110(24):9758-63.
PubMed.
Tara Spires-Jones’ comment above regarding the potential importance of variation in amyloid structure from patient to patient is certainly reasonable. However, another and perhaps more likely explanation for the different results obtained by Lu et al. is that the extracts from which seed materials were derived contained factors or chemically modified proteins that altered fibril structure. For example, it is unclear what fraction of methionine residues in the seed material was oxidized. Small differences, such as methionine oxidation or other covalent modifications, may lead to profoundly different structures when such seeds are used to induce fibrillization of synthetic material.
Another concern is that Lu et al. generated the proposed three-dimensional fibril structure using relatively few geometric constraints (listed only in supplementary tables). NMR-determined protein structures are often generated with several constraints per residue. In this case, however, there were barely more than half as many constraints as residues, and most residues had no constraints at all. Models generated with so few constraints must be regarded as “underdetermined,” which implies that the final computer-generated model will be strongly influenced by the starting structure to which the constraints are applied. In this context, it seems remarkable that there is no mention of the "staggered" relationship between the two halves of the peptide described in earlier publications from this lab.
I would place greater value on the findings if the seed material was shown to be predominantly unmodified Aβ40, and if greater efforts were made to show that the final structure was independent of assumptions made about the starting structure.
1. Our structural model for Aβ40 fibrils from patient 1, described in this paper, was calculated with Xplor-NIH software using 197 NMR-based experimental structural restraints (4.925 restraints per residue on average), including torsion angle restraints derived from NMR chemical shifts; torsion angle and distance restraints derived from quantitative measurements of 13C-13C, 15N-13C, and 15N-15N dipole-dipole couplings; and semi-quantitative restraints on inter-residue distances derived from several types of two-dimensional solid-state NMR spectra. Structure calculations began with completely random structures (not from any specific assumed starting point). Symmetry restraints, which are dictated by the experimental data, were imposed during structure calculations. A very large number of structure calculations were performed over a period of many months, with various modifications of the Xplor-NIH scripts. None of these calculations produced structures that were significantly different from the structures we have deposited in the Protein Data Bank as PDB 2M4J (and also consistent with all experimental restraints). Full details of the experimental data and structure calculations are given in this paper.
2. I do not know the basis of Dr. Kennedy's comment that, "In this case, however, there were barely more than half as many constraints as residues, and most residues had no constraints at all." Perhaps he is focusing on one particular type of restraint, whereas in fact we used several types of restraints from several types of solid-state NMR (and electron microscopy) measurements.
3. The issue of "stagger" in amyloid structures is discussed in our earlier papers (Petkova et al., 2006; Paravastu et al., 2008). Stagger means that interactions between amino acid side chains of two different β-strands in an amyloid structure are displaced along the fibril axis, making these interactions intermolecular rather than intramolecular in nature. In the case of Aβ40 fibrils from patient 1, we were unable to test for stagger because this would have required additional fibril samples with different isotopic labeling, and we did not have sufficient tissue from patient 1 to prepare the requisite samples. For examples of staggering in Aβ40 fibrils, see PDB files 2LMN, 2LMO, 2LMP, and 2LMQ. (Note that the direction of stagger is very difficult or impossible to determine experimentally, which is why these PDB files include both positive and negative stagger.)
4. Earlier work by others has shown that Aβ40 and Aβ42 in brain tissue is chemically modified in various ways to various degrees. The bulk of these chemical modifications presumably occur gradually over time, after the fibrils are formed (although certain modifications of a fraction of the peptides may accelerate the initial nucleation of fibrils). Nonetheless, we have found that fibrils from brain tissue are capable of seeding unmodified Aβ40 and Aβ42 efficiently. At this point, we have no evidence that chemical modifications of Aβ40 in brain tissue affect the results in this paper, although this is an interesting suggestion. In our hands, oxidation of Met35 impedes fibril formation; peptides with oxidized Met35 are excluded from fibrils formed by unoxidized peptides.
References:
Petkova AT, Yau WM, Tycko R.
Experimental constraints on quaternary structure in Alzheimer's beta-amyloid fibrils.
Biochemistry. 2006 Jan 17;45(2):498-512.
PubMed.
Paravastu AK, Leapman RD, Yau WM, Tycko R.
Molecular structural basis for polymorphism in Alzheimer's beta-amyloid fibrils.
Proc Natl Acad Sci U S A. 2008 Nov 25;105(47):18349-54.
PubMed.
Comments
University of Edinburgh
This interesting paper implies that while amyloid fibrils appear to have a uniform structure in the plaque of a given patient with Alzheimer’s disease (AD), that structure may differ from patient to patient. This conclusion is based on data from only two people, but assuming it holds up in more cases, it could be important for our understanding of people's vulnerability (or, conversely, resistance) to developing sporadic AD. Together, this data and the recent paper by Cohen et al. showing that fibrils are important for the assembly of toxic oligomers (see ARF related news story) could mean that each individual's fibril type may have a greater or lesser capability to seed toxic oligomers, which may account for some people being more resistant to AD despite a high plaque load.
References:
Cohen SI, Linse S, Luheshi LM, Hellstrand E, White DA, Rajah L, Otzen DE, Vendruscolo M, Dobson CM, Knowles TP. Proliferation of amyloid-β42 aggregates occurs through a secondary nucleation mechanism. Proc Natl Acad Sci U S A. 2013 Jun 11;110(24):9758-63. PubMed.
Tara Spires-Jones’ comment above regarding the potential importance of variation in amyloid structure from patient to patient is certainly reasonable. However, another and perhaps more likely explanation for the different results obtained by Lu et al. is that the extracts from which seed materials were derived contained factors or chemically modified proteins that altered fibril structure. For example, it is unclear what fraction of methionine residues in the seed material was oxidized. Small differences, such as methionine oxidation or other covalent modifications, may lead to profoundly different structures when such seeds are used to induce fibrillization of synthetic material.
Another concern is that Lu et al. generated the proposed three-dimensional fibril structure using relatively few geometric constraints (listed only in supplementary tables). NMR-determined protein structures are often generated with several constraints per residue. In this case, however, there were barely more than half as many constraints as residues, and most residues had no constraints at all. Models generated with so few constraints must be regarded as “underdetermined,” which implies that the final computer-generated model will be strongly influenced by the starting structure to which the constraints are applied. In this context, it seems remarkable that there is no mention of the "staggered" relationship between the two halves of the peptide described in earlier publications from this lab.
I would place greater value on the findings if the seed material was shown to be predominantly unmodified Aβ40, and if greater efforts were made to show that the final structure was independent of assumptions made about the starting structure.
NIDDK, NIH
In response to Dr. Kennedy's comments:
1. Our structural model for Aβ40 fibrils from patient 1, described in this paper, was calculated with Xplor-NIH software using 197 NMR-based experimental structural restraints (4.925 restraints per residue on average), including torsion angle restraints derived from NMR chemical shifts; torsion angle and distance restraints derived from quantitative measurements of 13C-13C, 15N-13C, and 15N-15N dipole-dipole couplings; and semi-quantitative restraints on inter-residue distances derived from several types of two-dimensional solid-state NMR spectra. Structure calculations began with completely random structures (not from any specific assumed starting point). Symmetry restraints, which are dictated by the experimental data, were imposed during structure calculations. A very large number of structure calculations were performed over a period of many months, with various modifications of the Xplor-NIH scripts. None of these calculations produced structures that were significantly different from the structures we have deposited in the Protein Data Bank as PDB 2M4J (and also consistent with all experimental restraints). Full details of the experimental data and structure calculations are given in this paper.
2. I do not know the basis of Dr. Kennedy's comment that, "In this case, however, there were barely more than half as many constraints as residues, and most residues had no constraints at all." Perhaps he is focusing on one particular type of restraint, whereas in fact we used several types of restraints from several types of solid-state NMR (and electron microscopy) measurements.
3. The issue of "stagger" in amyloid structures is discussed in our earlier papers (Petkova et al., 2006; Paravastu et al., 2008). Stagger means that interactions between amino acid side chains of two different β-strands in an amyloid structure are displaced along the fibril axis, making these interactions intermolecular rather than intramolecular in nature. In the case of Aβ40 fibrils from patient 1, we were unable to test for stagger because this would have required additional fibril samples with different isotopic labeling, and we did not have sufficient tissue from patient 1 to prepare the requisite samples. For examples of staggering in Aβ40 fibrils, see PDB files 2LMN, 2LMO, 2LMP, and 2LMQ. (Note that the direction of stagger is very difficult or impossible to determine experimentally, which is why these PDB files include both positive and negative stagger.)
4. Earlier work by others has shown that Aβ40 and Aβ42 in brain tissue is chemically modified in various ways to various degrees. The bulk of these chemical modifications presumably occur gradually over time, after the fibrils are formed (although certain modifications of a fraction of the peptides may accelerate the initial nucleation of fibrils). Nonetheless, we have found that fibrils from brain tissue are capable of seeding unmodified Aβ40 and Aβ42 efficiently. At this point, we have no evidence that chemical modifications of Aβ40 in brain tissue affect the results in this paper, although this is an interesting suggestion. In our hands, oxidation of Met35 impedes fibril formation; peptides with oxidized Met35 are excluded from fibrils formed by unoxidized peptides.
References:
Petkova AT, Yau WM, Tycko R. Experimental constraints on quaternary structure in Alzheimer's beta-amyloid fibrils. Biochemistry. 2006 Jan 17;45(2):498-512. PubMed.
Paravastu AK, Leapman RD, Yau WM, Tycko R. Molecular structural basis for polymorphism in Alzheimer's beta-amyloid fibrils. Proc Natl Acad Sci U S A. 2008 Nov 25;105(47):18349-54. PubMed.
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