Modulation of Amyloidogenic Protein Self-Assembly Using Tethered Small Molecules

Protein-protein interactions (PPIs) are involved in many of life’s essential biological functions yet are also an underlying cause of several human diseases, including amyloidosis. The modulation of PPIs presents opportunities to gain mechanistic insights into amyloid assembly, particularly through the use of methods which can trap specific intermediates for detailed study. Such information can also provide a starting point for drug discovery. Here, we demonstrate that covalently tethered small molecule fragments can be used to stabilize specific oligomers during amyloid fibril formation, facilitating the structural characterization of these assembly intermediates. We exemplify the power of covalent tethering using the naturally occurring truncated variant (ΔN6) of the human protein β2-microglobulin (β2m), which assembles into amyloid fibrils associated with dialysis-related amyloidosis. Using this approach, we have trapped tetramers formed by ΔN6 under conditions which would normally lead to fibril formation and found that the degree of tetramer stabilization depends on the site of the covalent tether and the nature of the protein-fragment interaction. The covalent protein-ligand linkage enabled structural characterization of these trapped oligomeric species using X-ray crystallography and NMR, providing insight into why tetramer stabilization inhibits amyloid assembly. Our findings highlight the power of “post-translational chemical modification" as a tool to study biological molecular mechanisms.

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Physical Determinants of Amyloid Assembly in Biofilm Formation

mBio ◽

10.1128/mbio.02279-18 ◽

2019 ◽

Vol 10 (1) ◽

Cited By ~ 15

Author(s):

Maria Andreasen ◽

Georg Meisl ◽

Jonathan D. Taylor ◽

Thomas C. T. Michaels ◽

Aviad Levin ◽

...

Keyword(s):

Extracellular Matrix ◽

Self Assembly ◽

Biofilm Formation ◽

Amyloid Fibrils ◽

Environmental Stresses ◽

Fibril Formation ◽

Functional Amyloid ◽

Content Type ◽

Wide Range ◽

Amyloid Assembly

ABSTRACTA wide range of bacterial pathogens have been shown to form biofilms, which significantly increase their resistance to environmental stresses, such as antibiotics, and are thus of central importance in the context of bacterial diseases. One of the major structural components of these bacterial biofilms are amyloid fibrils, yet the mechanism of fibril assembly and its importance for biofilm formation are currently not fully understood. By studying fibril formationin vitro, in a model system of two common but unrelated biofilm-forming proteins, FapC fromPseudomonas fluorescensand CsgA fromEscherichia coli, we found that the two proteins have a common aggregation mechanism. In both systems, fibril formation proceeds via nucleated growth of linear fibrils exhibiting similar measured rates of elongation, with negligible fibril self-replication. These similarities between two unrelated systems suggest that convergent evolution plays a key role in tuning the assembly kinetics of functional amyloid fibrils and indicates that only a narrow window of mechanisms and assembly rates allows for successful biofilm formation. Thus, the amyloid assembly reaction is likely to represent a means for controlling biofilm formation, both by the organism and by possible inhibitory drugs.IMPORTANCEBiofilms are generated by bacteria, embedded in the formed extracellular matrix. The biofilm's function is to improve the survival of a bacterial colony through, for example, increased resistance to antibiotics or other environmental stresses. Proteins secreted by the bacteria act as a major structural component of this extracellular matrix, as they self-assemble into highly stable amyloid fibrils, making the biofilm very difficult to degrade by physical and chemical means once formed. By studying the self-assembly mechanism of the fibrils from their monomeric precursors in two unrelated bacteria, our experimental and theoretical approaches shed light on the mechanism of functional amyloid assembly in the context of biofilm formation. Our results suggest that fibril formation may be a rate-limiting step in biofilm formation, which in turn has implications on the protein self-assembly reaction as a target for potential antibiotic drugs.

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Structural Characterization of Heterodinuclear ZnII-LnIII Complexes (Ln = Pr, Nd) with a Ring-Contracted H2valdien-Derived Schiff Base Ligand

Journal of Chemical Crystallography ◽

10.1007/s10870-021-00891-4 ◽

2021 ◽

Author(s):

Shabana Noor ◽

Richard Goddard ◽

Fehmeeda Khatoon ◽

Sarvendra Kumar ◽

Rüdiger W. Seidel

Keyword(s):

Molecular Structure ◽

Schiff Base ◽

Structural Characterization ◽

Schiff Base Ligand ◽

Crystal And Molecular Structure ◽

X Ray ◽

X Ray Crystallography ◽

Imidazoline Ring

AbstractSynthesis and structural characterization of two heterodinuclear ZnII-LnIII complexes with the formula [ZnLn(HL)(µ-OAc)(NO3)2(H2O)x(MeOH)1-x]NO3 · n H2O · n MeOH [Ln = Pr (1), Nd (2)] and the crystal and molecular structure of [ZnNd(HL)(µ-OAc)(NO3)2(H2O)] [ZnNd(HL)(OAc)(NO3)2(H2O)](NO3)2 · n H2O · n MeOH (3) are reported. The asymmetrical compartmental ligand (E)-2-(1-(2-((2-hydroxy-3-methoxybenzylidene)amino)-ethyl)imidazolidin-2-yl)-6-methoxyphenol (H2L) is formed from N1,N3-bis(3-methoxysalicylidene)diethylenetriamine (H2valdien) through intramolecular aminal formation, resulting in a peripheral imidazoline ring. The structures of 1–3 were revealed by X-ray crystallography. The smaller ZnII ion occupies the inner N2O2 compartment of the ligand, whereas the larger and more oxophilic LnIII ions are found in the outer O2O2’ site. Graphic Abstract Synthesis and structural characterization of two heterodinuclear ZnII-LnIII complexes (Ln = Pr, Nd) bearing an asymmetrical compartmental ligand formed in situ from N1,N3-bis(3-methoxysalicylidene)diethylenetriamine (H2valdien) through intramolecular aminal formation are reported.

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Synthesis and Structural Characterization of Three Novel Macrocyclic Coordination Complexes Formed by Self-assembly of Bridged Bi- or Tetrapyridine with Transition Metal Salts

Chinese Journal of Chemistry ◽

10.1002/cjoc.200591065 ◽

2005 ◽

Vol 23 (8) ◽

pp. 1065-1070

Author(s):

Song Li-Cheng ◽

Jin Guo-Xia ◽

Zhang Wen-Xiong ◽

Hu Qing-Mei

Keyword(s):

Transition Metal ◽

Structural Characterization ◽

Self Assembly ◽

Coordination Complexes ◽

Metal Salts ◽

Transition Metal Salts

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Synthesis and structural characterization of a magnesium phthalocyanine(3–) anion

Journal of Porphyrins and Phthalocyanines ◽

10.1142/s1088424611004440 ◽

2012 ◽

Vol 16 (01) ◽

pp. 154-162 ◽

Cited By ~ 24

Author(s):

Edwin W.Y. Wong ◽

Daniel B. Leznoff

Keyword(s):

Absorption Spectrum ◽

Solid State ◽

Single Crystal ◽

Structural Characterization ◽

Heterometallic Complex ◽

State Structure ◽

Solid State Structure ◽

X Ray ◽

X Ray Crystallography

The reduction of magnesium phthalocyanine (MgPc) with 2.2 equivalents of potassium graphite in 1,2-dimethoxyethane (DME) gives [K2(DME)4]PcMg(OH)(1) in 67% yield. Compound 1 was structurally characterized using single crystal X-ray crystallography and was found to be a monomeric, heterometallic complex consisting of a μ3-OH ligand that bridges a [MgIIPc3-]- anion to two potassium cations solvated by four DME molecules. An absorption spectrum of 1 confirms the Pc ligand is singly reduced and has a 3–charge. The solid-state structure of 1 does not indicate breaking of the aromaticity of the Pc ligand. Compound 1 is only the second Pc3- complex and the first reduced MgPc to be isolated and structurally characterized.

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Structural Characterization of a New Collagen Biomimetic Octapeptide with Nanoscale Self‐assembly Potential: Experimental and Theoretical Approaches

ChemPlusChem ◽

10.1002/cplu.202100462 ◽

2021 ◽

Author(s):

Cosmin Stefan Mocanu ◽

Brindusa Alina Petre ◽

Laura Darie Ion ◽

Gabi Drochioiu ◽

Marius Niculaua ◽

...

Keyword(s):

Structural Characterization ◽

Self Assembly ◽

Theoretical Approaches

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Examining the structure of the mature amyloid fibril

Biochemical Society Transactions ◽

10.1042/bst0300521 ◽

2002 ◽

Vol 30 (4) ◽

pp. 521-525 ◽

Cited By ~ 43

Author(s):

O. S. Makin ◽

L. C. Serpell

Keyword(s):

Self Assembly ◽

Rational Design ◽

Amyloid Fibrils ◽

Structural Information ◽

X Ray ◽

X Ray Crystallography ◽

Cryo Electron Microscopy ◽

Fibre Diffraction ◽

Complementary Techniques ◽

Mature Fibril

The pathogenesis of the group of diseases known collectively as the amyloidoses is characterized by the deposition of insoluble amyloid fibrils. These are straight, unbranching structures about 70–120 å (1 å = 0.1 nm) in diameter and of indeterminate length formed by the self-assembly of a diverse group of normally soluble proteins. Knowledge of the structure of these fibrils is necessary for the understanding of their abnormal assembly and deposition, possibly leading to the rational design of therapeutic agents for their prevention or disaggregation. Structural elucidation is impeded by fibril insolubility and inability to crystallize, thus preventing the use of X-ray crystallography and solution NMR. CD, Fourier-transform infrared spectroscopy and light scattering have been used in the study of the mechanism of fibril formation. This review concentrates on the structural information about the final, mature fibril and in particular the complementary techniques of cryo-electron microscopy, solid-state NMR and X-ray fibre diffraction.

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