Nuclear magnetic resonance/single molecule fluorescence combinations to study dynamic protein systems

Current Opinion in Structural Biology, Journal Year: 2023, Volume and Issue: 82, P. 102659 - 102659

Published: July 25, 2023

Many proteins require different structural states or conformations for function, and intrinsically disordered proteins, i.e. without stable three-dimensional structure, are certainly an extreme. Single molecule fluorescence nuclear magnetic resonance (NMR) spectroscopy both exceptionally well suited to decipher describe these their interconversion. Different time scales, from picoseconds several milliseconds, can be addressed by techniques. The length scales probed the sample requirements (e.g. concentration, molecular weight, complexity) are, however, vastly different, making NMR single excellent combination integrated studies. Here, we review recently undertaken approaches combined use of study protein dynamics.

Language: Английский

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Generating Ensembles of Dynamic Misfolding Proteins

Frontiers in Neuroscience, Journal Year: 2022, Volume and Issue: 16

Published: March 31, 2022

The early stages of protein misfolding and aggregation involve disordered partially folded conformers that contain a high degree dynamic disorder. These species may undergo large-scale intra-molecular motions intrinsically (IDP) precursors, or flexible, low affinity inter-molecular binding in oligomeric assemblies. In both cases, generating atomic level visualization the interconverting captures conformations explored their physico-chemical properties remains hugely challenging. How specific sub-ensembles are on-pathway to into amyloid can be identified from aggregation-resilient counterparts within these large heterogenous pools rapidly moving molecules represents an additional complexity. Here, we describe current experimental computational approaches designed capture nature aggregation, discuss potential challenges describing because ensemble averaging restraints arise on millisecond timescale. We give perspective how machine learning methods used extract aggregation-relevant provide two examples such approach which interactions defined ensembles α-synuclein (αSyn) β

Language: Английский

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Molecular Dynamics Simulations of the Tau Amyloid Fibril Core Dimer at the Surface of a Lipid Bilayer Model: I. In Alzheimer’s Disease

The Journal of Physical Chemistry B, Journal Year: 2022, Volume and Issue: 126(26), P. 4849 - 4856

Published: June 27, 2022

A tau R3–R4 domain spanning residues 306–378 was shown to form an amyloid fibril core of a full-length in the brain patients with Alzheimer's disease. Recently, we studied dynamics monomer at surface lipid bilayer model and revealed deep insertion amino acids PHF6 motif (residues 306–311) its flanking residues. Here, explore membrane-associated conformational ensemble dimer by means atomistic molecular dynamics. Similar simulation, has propensity β-hairpin-like conformation. Unlike monomer, shows C-terminal R4 region transient adsorption motif. Taken together, these results reveal multiplicity modes into membranes depending on oligomer size.

Language: Английский

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Intrinsically disordered Pseudomonas chaperone FapA slows down the fibrillation of major biofilm‐forming functional amyloid FapC

FEBS Journal, Journal Year: 2024, Volume and Issue: 291(9), P. 1925 - 1943

Published: Feb. 13, 2024

Functional bacterial amyloids play a crucial role in the formation of biofilms, which mediate chronic infections and contribute to antimicrobial resistance. This study focuses on FapC amyloid fibrillar protein from Pseudomonas , major contributor biofilm formation. We investigate initial steps impact chaperone‐like FapA this process. Using solution nuclear magnetic resonance (NMR), we recently showed that both are intrinsically disordered proteins (IDPs). Here, secondary structure propensities (SSPs) compared alphafold (DeepMind, prediction tool/algorithm: https://alphafold.ebi.ac.uk/ ) models. further demonstrate chaperone interacts with significantly slows down fibrils. Our NMR titrations reveal ~ 18% resonances show FapA‐induced chemical shift perturbations (CSPs), has not been previously observed, largest being for A82, N201, C237, C240, A241, G245. These sites may suggest specific interaction site and/or hotspots fibrillation inhibition/control interface at repeat‐1 (R1)/loop‐2 (L2) L2/R3 transition areas C‐terminus FapC. Remarkably, 90% signals exhibit substantial CSPs upon titration FapC, S63, A69, A80, I92. A temperature‐dependent effect was observed by thioflavin T (ThT) experiments. provides detailed understanding between shedding light regulation slowing formation, important implications development therapeutic strategies targeting biofilms associated infections.

Language: Английский

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Encoding prior knowledge in ensemble refinement

The Journal of Chemical Physics, Journal Year: 2024, Volume and Issue: 160(11)

Published: March 21, 2024

The proper balancing of information from experiment and theory is a long-standing problem in the analysis noisy incomplete data. Viewed as Pareto optimization problem, improved agreement with experimental data comes at expense growing inconsistencies theoretical reference model. Here, we propose how to set exchange rate priori properly balance this trade-off. We focus on gentle ensemble refinement, where difference between potential energy surfaces refined models small thermal scale. By relating variance Kullback-Leibler divergence respective Boltzmann distributions, one can encode prior knowledge about uncertainties, i.e., force-field errors, rate. uncertainty defined space observables depends their type number thermodynamic state. highlight relation refinement free perturbation theory. A balanced encoding increases quality transparency refinement. Our findings extend non-Boltzmann becomes an information.

Language: Английский

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