Peptides or proteins convert under some conditions from their soluble forms into highly ordered fibrillar aggregates. Such transitions can give rise to pathological conditions ranging from neurodegenerative disorders to systemic amyloidoses. In this review, we identify the diseases known to be associated with formation of fibrillar aggregates and the specific peptides and proteins involved in each case. We describe, in addition, that living organisms can take advantage of the inherent ability of proteins to form such structures to generate novel and diverse biological functions. We review recent advances toward the elucidation of the structures of amyloid fibrils and the mechanisms of their formation at a molecular level. Finally, we discuss the relative importance of the common main-chain and side-chain interactions in determining the propensities of proteins to aggregate and describe some of the evidence that the oligomeric fibril precursors are the primary origins of pathological behavior.

/pdf/protein-misfolding-functional-amyloid-and-human-disease-2w386pwb7k.pdf

Protein Misfolding, Functional Amyloid, and Human Disease

The binding of thioflavin-T to amyloid fibrils: localisation and implications.

Because understanding amyloid fibrillation in molecular detail is essential for development of strategies to control amyloid formation and overcome neurodegenerative disorders, increased understanding of present molecular probes as well as development of new probes are of utmost importance. To date, the binding modes of these molecular probes to amyloid fibrils are by no means adequately described or understood, and the large number of studies on Thioflavin T (ThT) and Congo Red (CR) binding have resulted in models that are incomplete and conflicting. Different types of binding sites are likely to be present in amyloid fibrils with differences in binding modes. ThT may bind in channels running parallel to the long axis of the fibril. In the channels, ThT may bind in either a monomeric or dimeric form of which the molecular conformation is likely to be planar. CR may bind in grooves formed along the β-sheets as a planar molecule in either a monomeric or supramolecular form.

/pdf/binding-mode-of-thioflavin-t-and-other-molecular-probes-in-2jznhxuyet.pdf

Binding mode of Thioflavin T and other molecular probes in the context of amyloid fibrils—current status

Synchrotron-based infrared and X-ray imaging shows focalized accumulation of Cu and Zn co-localized with beta-amyloid deposits in Alzheimer's disease.

Fingerprint plots of Hirshfeld surfaces were used to locate and analyze the deficiencies in various methodologies employed in the determination of the relative energies of five polymorphs of 1,8-dihydroxyanthraquinone. Nine crystallographically independent molecules were characterized by X-ray crystallography and Hirshfeld surfaces were derived from the X-ray structures. The space groups and number of independent molecules (Z′) for each of the polymorphs (1−5) is as follows: (1) P41 (or P43),Z′ = 1; (2) Pca21, Z′ = 2; (3) P1, Z′ = 4; (4) P21/n, Z′ = 1; (5) P41212 (or P43212), Z′ = 0.5. Form 1 is the most thermodynamically stable among the reproducible structures, as established by competitive solubility tests, followed by 2 and then 4. The unrestrained structures of the five polymorphs were computed using the CVFF and COMPASS force fields as well as with the density functional code, SIESTA.

Hirshfeld surfaces identify inadequacies in computations of intermolecular interactions in crystals: pentamorphic 1,8-dihydroxyanthraquinone

New advances in polarized light microscopy were used to image Congo red-stained cerebral amyloidosis in sharp relief. The rotating-polarizer method was used to separate the optical effects of transmission, linear birefringence, extinction, linear dichroism, and orientation of the electric dipole transition moments and to display them as false-color maps. These effects are typically convolved in an ordinary polarized light microscope. In this way, we show that the amyloid deposits in Alzheimer's disease plaques contain structurally disordered centers, providing clues to mechanisms of crystallization of amyloid in vivo. Comparisons are made with plaques from tissues of subjects having Down's syndrome and a prion disease. In plaques characteristic of each disease, the Congo red molecules are oriented radially. The optical orientation in amyloid deposited in blood vessels from subjects having cerebral amyloid angiopathy was 90° out of phase from that in the plaques, suggesting that the fibrils run tangentially with respect to the circumference of the blood vessels. Our result supports an early model in which Congo red molecules are aligned along the long fiber axis and is in contrast to the most recent binding models that are based on computation. This investigation illustrates that the latest methods for the optical analysis of heterogeneous substances are useful for in situ study of amyloid.

/pdf/imaging-linear-birefringence-and-dichroism-in-cerebral-892h8zcha6.pdf

Imaging linear birefringence and dichroism in cerebral amyloid pathologies

A microscope was constructed for imaging circular dichroism of heterogeneous anisotropic media. To avoid linear biases that are common with electronic circular polarization modulation, we chose a retrogressive solution: mechanical light modulation by rotating a linear polarizer with respect to a quarter wave plate continuously tuned by tilting to the operating wavelength. Our comparatively slow technique succeeds with near-perfect circular input and signal averaging using a CCD camera. We have applied the method to anomalously birefringent crystals of 1,8-dihydroxyanthraquinone that are shown to have intergrown mirror image domains, undetected by X-ray diffraction because the twinning complexity renders differences in anomalous dispersion, already small, unreliable. The origin of the anomalous birefringence and the assignment of the absolute configuration are discussed.

Circular Dichroism Imaging Microscopy: Application to Enantiomorphous Twinning in Biaxial Crystals of 1,8-Dihydroxyanthraquinone

Kinetic Stabilization of Biopolymers in Single-Crystal Hosts: Green Fluorescent Protein in α-Lactose Monohydrate

α-Lactose monohydrate single crystals as hosts for matrix isolation of guest biopolymers

Oriented gases of biopolymers in simple, single crystal hosts might be used to measure anisotropic molecular properties of analytes that could not otherwise be crystallized. Here we show two types of crystals as examples of the single crystal matrix isolation of biopolymers: green fluorescent protein in α-lactose monohydrate as a model system for studying the kinetic stabilization of biopharmaceuticals, and adenosine phosphates in potassium dihydrogen phosphate, a first step in the matrix isolation of oligonucleotides. In each case, the hosts undergo compositional zoning – both intersectoral and intrasectoral – during growth from solution. Intrasectoral zoning is evident by the selective luminescence of adjacent vicinal slopes of growth active hillocks. Nucleotides furthermore distinguish between symmetry related growth sectors enantioselectively.

https://www.cambridge.org/core/services/aop-cambridge-core/content/view/S1946427400584425

Miki Kurimoto

Papers

Imaging linear birefringence and dichroism in cerebral amyloid pathologies

Circular Dichroism Imaging Microscopy: Application to Enantiomorphous Twinning in Biaxial Crystals of 1,8-Dihydroxyanthraquinone

Kinetic Stabilization of Biopolymers in Single-Crystal Hosts: Green Fluorescent Protein in α-Lactose Monohydrate

α-Lactose monohydrate single crystals as hosts for matrix isolation of guest biopolymers

Intrasectoral zoning of proteins and nucleotides in simple crystalline hosts