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It has been recently shown that in some proteins, tertiary‐structure dynamics occur surprisingly fast, that is on the microsecond or sub‐millisecond time scales. In this State of the Art Review, we discuss how such ultrafast domain motions relate to the function of caseinolytic peptidase B (ClpB), a AAA+ disaggregation machine. ClpB is a large hexameric protein that collaborates with cellular chaperone machinery to rescue protein chains from aggregates. We used single‐molecule FRET spectroscopy to capture the dynamics of essential structural elements within this machine. It was found that the middle domain of ClpB, known to act as its activator, toggles between two states much faster than the overall activity cycle of the protein, suggesting a novel mode of continuous, tunable switching. Motions of the N‐terminal domain were observed to restrict the conformational space of the M domain in the absence of a substrate protein, thereby preventing it from tilting and spuriously activating ClpB. Finally, microsecond dynamics of pore loops responsible for substrate pulling through ClpB's central channel, together with their response to specific perturbations, point to a Brownian‐ratchet mechanism for protein translocation. Based on our findings, we propose a two‐time‐scale model for the activity of ClpB, in which fast conformational dynamics affect slower functional steps, determined by ATP hydrolysis time. Future work on this and other proteins is likely to shed further light on the role of ultrafast dynamics on protein function. [ABSTRACT FROM AUTHOR]

Enzymes play a vital role in life processes; they control chemical reactions and allow functional cycles to be synchronized. Many enzymes harness large-scale motions of their domains to achieve tremendous catalytic prowess and high selectivity for specific substrates. One outstanding example is provided by the three-domain enzyme adenylate kinase (AK), which catalyzes phosphotransfer between ATP to AMP. Here we study the phenomenon of substrate inhibition by AMP and its correlation with domain motions. Using single-molecule FRET spectroscopy, we show that AMP does not block access to the ATP binding site, neither by competitive binding to the ATP cognate site nor by directly closing the LID domain. Instead, inhibitory concentrations of AMP lead to a faster and more cooperative domain closure by ATP, leading in turn to an increased population of the closed state. The effect of AMP binding can be modulated through mutations throughout the structure of the enzyme, as shown by the screening of an extensive AK mutant library. The mutation of multiple conserved residues reduces substrate inhibition, suggesting that substrate inhibition is an evolutionary well conserved feature in AK. Combining these insights, we developed a model that explains the complex activity of AK, particularly substrate inhibition, based on the experimentally observed opening and closing rates. Notably, the model indicates that the catalytic power is affected by the microsecond balance between the open and closed states of the enzyme. Our findings highlight the crucial role of protein motions in enzymatic activity. [ABSTRACT FROM AUTHOR]

Time-resolved photoelectron imaging was used to investigate the dynamical evolution of the initially prepared S1 (ππ*) excited state of phenol (hydroxybenzene), catechol (1,2-dihydroxybenzene), resorcinol (1,3-dihydroxybenzene), and hydroquinone (1,4-dihydroxybenzene) following excitation at 267 nm. Our analysis was supported by ab initio calculations at the coupled-cluster and CASSCF levels of theory. In all cases, we observe rapid (<1 ps) intramolecular vibrational redistribution on the S1 potential surface. In catechol, the overall S1 state lifetime was observed to be 12.1 ps, which is 1-2 orders of magnitude shorter than in the other three molecules studied. This may be attributed to differences in the H atom tunnelling rate under the barrier formed by a conical intersection between the S1 state and the close lying S2 (πσ*) state, which is dissociative along the O-H stretching coordinate. Further evidence of this S1/S2 interaction is also seen in the time-dependent anisotropy of the photoelectron angular distributions we have observed. Our data analysis was assisted by a matrix inversion method for processing photoelectron images that is significantly faster than most other previously reported approaches and is extremely quick and easy to implement. [ABSTRACT FROM AUTHOR]

Background: The aggregation of the protein α-synuclein (αS) underlies a range of increasingly common neurodegenerative disorders including Parkinson's disease. One widely explored therapeutic strategy for these conditions is the use of antibodies to target aggregated αS, although a detailed molecular-level mechanism of the action of such species remains elusive. Here, we characterize αS aggregation in vitro in the presence of two αS-specific single-domain antibodies (nanobodies), NbSyn2 and NbSyn87, which bind to the highly accessible C-terminal region of αS. Results: We show that both nanobodies inhibit the formation of αS fibrils. Furthermore, using single-molecule fluorescence techniques, we demonstrate that nanobody binding promotes a rapid conformational conversion from more stable oligomers to less stable oligomers of αS, leading to a dramatic reduction in oligomer-induced cellular toxicity. Conclusions: The results indicate a novel mechanism by which diseases associated with protein aggregation can be inhibited, and suggest that NbSyn2 and NbSyn87 could have significant therapeutic potential. [ABSTRACT FROM AUTHOR]

Inelastic scattering of OH radicals from liquid surfaces has been investigated experimentally. An initially translationally and rotationally hot distribution of OH was generated by 193 nm photolysis of allyl alcohol. These radicals were scattered from an inert reference liquid, perfluorinated polyether (PFPE), and from the potentially reactive hydrocarbon liquids squalane (C30H62, 2,6,10,15,19,23-hexamethyltetracosane) and squalene (C30H50, trans-2,6,10,15,19,23-hexamethyltetracosa-2,6,10,14,18,22-hexaene). The scattered OH v = 0 products were detected by laser-induced fluorescence. Strong correlations were observed between the translational and rotational energies of the products. The high-N levels are translationally hot, consistent with a predominantly direct, impulsive scattering mechanism. Impulsive scattering also populates the lower-N levels, but a component of translationally relaxed OH, with thermal-desorption characteristics, can also be seen clearly for all three liquids. More of this translationally and rotationally relaxed OH survives from squalane than from squalene. Realistic molecular dynamics simulations confirm that double-bond sites are accessible at the squalene surface. This supports the proposition that relaxed OH may be lost on squalene via an addition mechanism. [ABSTRACT FROM AUTHOR]

The use of confocal Raman microscopy is applied to the study of whey-protein-stabilized oil-in-water emulsions. The stability of emulsions is an important parameter for many applications and is dependent on several factors including protein content and particle size. Emulsions were prepared with varying particle size ranging from 0.8 to 10.0 µm. Changes in sample volume due to laser-induced heating were monitored and correlated to protein content in samples and to particle diameters. It was found that samples with the lowest protein content and larger particle diameters experienced the largest volume changes. The newly developed approach is of a potential predictive use. Copyright © 2013 John Wiley & Sons, Ltd. [ABSTRACT FROM AUTHOR]

The protein alpha-synuclein (αS) self-assembles into toxic beta-sheet aggregates in Parkinson’s disease, while it is proposed that αS forms soluble alpha-helical multimers in healthy neurons. Here, we have made αS multimers in vitro using arachidonic acid (ARA), one of the most abundant fatty acids in the brain, and characterized them by a combination of bulk experiments and single-molecule Fӧrster resonance energy transfer (sm-FRET) measurements. The data suggest that ARA-induced oligomers are alpha-helical, resistant to fibril formation, more prone to disaggregation, enzymatic digestion and degradation by the 26S proteasome, and lead to lower neuronal damage and reduced activation of microglia compared to the oligomers formed in the absence of ARA. These multimers can be formed at physiologically-relevant concentrations, and pathological mutants of αS form less multimers than wild-type αS. Our work provides strong biophysical evidence for the formation of alpha-helical multimers of αS in the presence of a biologically relevant fatty acid, which may have a protective role with respect to the generation of beta-sheet toxic structures during αS fibrillation.