The Effects of Lipids on α-Synuclein Aggregation In Vitro

Biomolecules · 2023 · 11 citations

• Chemistry
• Neuroscience
• Biology

The small neuronal protein α-synuclein (αS) is found in pre-synaptic terminals and plays a role in vesicle recycling and neurotransmission. Fibrillar aggregates of αS are the hallmark of Parkinson's disease and related neurodegenerative disorders. In both health and disease, interactions with lipids influence αS's structure and function, prompting much study of the effects of lipids on αS aggregation. A comprehensive collection (126 examples) of aggregation rate data for various αS/lipid combinations was presented, including combinations of lipid variations and mutations or post-translational modifications of αS. These data were interpreted in terms of lipid structure to identify general trends. These tabulated data serve as a resource for the community to help in the interpretation of aggregation experiments with lipids and to be potentially used as inputs for computational models of lipid effects on aggregation.

A Bond-Energy/Bond-Order and Populations Relationship

Journal of Chemical Theory and Computation · 2022 · 16 citations

• Chemistry
• Computational chemistry
• Physical chemistry

molecular energies in terms of physically insightful bond energy contributions, e.g., bond dissociation energies, resonance energies, molecular strain energies, and qualitative energetic contributions to the activation barrier in chemical reaction mechanisms. This work reports a critical benchmarking of this method as well as discussions of its strengths and weaknesses compared to hybrid DFT (i.e., B3LYP, M062X, PBE0, and APF methods), and other cost-effective approximate Hamiltonian semiempirical quantum methods (i.e., AM1, PM6, PM7, and DFTB3).

Genetic encoding of a highly photostable, long lifetime fluorescent amino acid for imaging in mammalian cells

Chemical Science · 2021 · 59 citations

• Chemistry
• Biophysics
• Biochemistry

and mammalian cells. We compare protein yields and amino acid specificity for these Acd RSs to identify an optimal construct. We also demonstrate the use of Acd in FLIM, where its long lifetime provides strong contrast compared to endogenous fluorophores and engineered fluorescent proteins, which have lifetimes less than 5 ns.

An improved fluorescent noncanonical amino acid for measuring conformational distributions using time-resolved transition metal ion FRET

eLife · 2021 · 46 citations

• Chemistry
• Biophysics
• Biochemistry

With the recent explosion in high-resolution protein structures, one of the next frontiers in biology is elucidating the mechanisms by which conformational rearrangements in proteins are regulated to meet the needs of cells under changing conditions. Rigorously measuring protein energetics and dynamics requires the development of new methods that can resolve structural heterogeneity and conformational distributions. We have previously developed steady-state transition metal ion fluorescence resonance energy transfer (tmFRET) approaches using a fluorescent noncanonical amino acid donor (Anap) and transition metal ion acceptor to probe conformational rearrangements in soluble and membrane proteins. Here, we show that the fluorescent noncanonical amino acid Acd has superior photophysical properties that extend its utility as a donor for tmFRET. Using maltose-binding protein (MBP) expressed in mammalian cells as a model system, we show that Acd is comparable to Anap in steady-state tmFRET experiments and that its long, single-exponential lifetime is better suited for probing conformational distributions using time-resolved FRET. These experiments reveal differences in heterogeneity in the apo and holo conformational states of MBP and produce accurate quantification of the distributions among apo and holo conformational states at subsaturating maltose concentrations. Our new approach using Acd for time-resolved tmFRET sets the stage for measuring the energetics of conformational rearrangements in soluble and membrane proteins in near-native conditions.

Rational design of small molecule fluorescent probes for biological applications

Organic & Biomolecular Chemistry · 2020 · 240 citations

• Chemistry
• Combinatorial chemistry
• Nanotechnology

Fluorescent small molecules are powerful tools for visualizing biological events, embodying an essential facet of chemical biology. Since the discovery of the first organic fluorophore, quinine, in 1845, both synthetic and theoretical efforts have endeavored to "modulate" fluorescent compounds. An advantage of synthetic dyes is the ability to employ modern organic chemistry strategies to tailor chemical structures and thereby rationally tune photophysical properties and functionality of the fluorophore. This review explores general factors affecting fluorophore excitation and emission spectra, molar absorption, Stokes shift, and quantum efficiency; and provides guidelines for chemist to create novel probes. Structure-property relationships concerning the substituents are discussed in detail with examples for several dye families. We also present a survey of functional probes based on PeT, FRET, and environmental or photo-sensitivity, focusing on representative recent work in each category. We believe that a full understanding of dyes with diverse chemical moieties enables the rational design of probes for the precise interrogation of biochemical and biological phenomena.

Side‐chain thioamides as fluorescence quenching probes

Biopolymers · 2020 · 11 citations

• Chemistry
• Combinatorial chemistry
• Crystallography

-thioacetyl-lysine into proteins expressed in Escherichia coli using amber codon suppression.