RESUMEN
Time-correlated single photon counting (TCSPC) coupled with confocal microscopy is a versatile biophysical tool that enables real-time monitoring of biomolecular dynamics across many timescales. With TCSPC, Fluorescence correlation spectroscopy (FCS) and pulsed interleaved excitation-Förster resonance energy transfer (PIE-FRET) are collected simultaneously on diffusing molecules to extract diffusion characteristics and proximity information. This article is a guide to calibrating FCS and PIE-FRET measurements with several biological samples including liposomes, streptavidin-coated quantum dots, proteins, and nucleic acids for reliable determination of diffusion coefficients and FRET efficiency. The FRET efficiency results are also compared to surface-attached single molecules using fluorescence lifetime imaging microscopy (FLIM-FRET). Combining the methods is a powerful approach to revealing mechanistic details of biological processes and pathways.
RESUMEN
DNA mismatch repair (MMR), the guardian of the genome, commences when MutS identifies a mismatch and recruits MutL to nick the error-containing strand, allowing excision and DNA resynthesis. Dominant MMR models posit that after mismatch recognition, ATP converts MutS to a hydrolysis-independent, diffusive mobile clamp that no longer recognizes the mismatch. Little is known about the postrecognition MutS mobile clamp and its interactions with MutL. Two disparate frameworks have been proposed: One in which MutS-MutL complexes remain mobile on the DNA, and one in which MutL stops MutS movement. Here we use single-molecule FRET to follow the postrecognition states of MutS and the impact of MutL on its properties. In contrast to current thinking, we find that after the initial mobile clamp formation event, MutS undergoes frequent cycles of mismatch rebinding and mobile clamp reformation without releasing DNA. Notably, ATP hydrolysis is required to alter the conformation of MutS such that it can recognize the mismatch again instead of bypassing it; thus, ATP hydrolysis licenses the MutS mobile clamp to rebind the mismatch. Moreover, interaction with MutL can both trap MutS at the mismatch en route to mobile clamp formation and stop movement of the mobile clamp on DNA. MutS's frequent rebinding of the mismatch, which increases its residence time in the vicinity of the mismatch, coupled with MutL's ability to trap MutS, should increase the probability that MutS-MutL MMR initiation complexes localize near the mismatch.
Asunto(s)
Reparación de la Incompatibilidad de ADN , ADN/metabolismo , Proteína MutS de Unión a los Apareamientos Incorrectos del ADN/metabolismo , Adenosina Trifosfatasas/metabolismo , Adenosina Trifosfato/metabolismo , Disparidad de Par Base , ADN/química , ADN/genética , Hidrólisis , Modelos Moleculares , Complejos Multiproteicos/metabolismo , Proteínas MutL/química , Proteínas MutL/metabolismo , Proteína MutS de Unión a los Apareamientos Incorrectos del ADN/química , Relación Estructura-ActividadRESUMEN
Intrinsically disordered proteins (IDPs) are often modeled using ideas from polymer physics that suggest they smoothly explore all corners of configuration space. Experimental verification of this random, dynamic behavior is difficult as random fluctuations of IDPs cannot be synchronized across an ensemble. Single molecule fluorescence (or Förster) resonance energy transfer (smFRET) is one of the few approaches that are sensitive to transient populations of sub-states within molecular ensembles. In some implementations, smFRET has sufficient time resolution to resolve transitions in IDP behaviors. Here we present experimental issues to consider when applying smFRET to study IDP configuration. We illustrate the power of applying smFRET to IDPs by discussing two cases in the literature of protein systems for which smFRET has successfully reported phosphorylation-induced modification (but not elimination) of the disordered properties that have been connected to impacts on the related biological function. The examples we discuss, PAGE4 and a disordered segment of the GluN2B subunit of the NMDA receptor, illustrate the great potential of smFRET to inform how IDP function can be regulated by controlling the detailed ensemble of disordered states within biological networks.
Asunto(s)
Transferencia Resonante de Energía de Fluorescencia , Proteínas Intrínsecamente Desordenadas/metabolismo , Imagen Individual de Molécula , Proteínas Intrínsecamente Desordenadas/química , FosforilaciónRESUMEN
MutS homologs identify base-pairing errors made in DNA during replication and initiate their repair. In the presence of adenosine triphosphate, MutS induces DNA bending upon mismatch recognition and subsequently undergoes conformational transitions that promote its interaction with MutL to signal repair. In the absence of MutL, these transitions lead to formation of a MutS mobile clamp that can move along the DNA. Previous single-molecule FRET (smFRET) studies characterized the dynamics of MutS DNA-binding domains during these transitions. Here, we use protein-DNA and DNA-DNA smFRET to monitor DNA conformational changes, and we use kinetic analyses to correlate DNA and protein conformational changes to one another and to the steps on the pathway to mobile clamp formation. The results reveal multiple sequential structural changes in both MutS and DNA, and they suggest that DNA dynamics play a critical role in the formation of the MutS mobile clamp. Taking these findings together with data from our previous studies, we propose a unified model of coordinated MutS and DNA conformational changes wherein initiation of mismatch repair is governed by a balance of DNA bending/unbending energetics and MutS conformational changes coupled to its nucleotide binding properties.
Asunto(s)
Disparidad de Par Base/genética , Reparación de la Incompatibilidad de ADN , ADN/química , Proteína MutS de Unión a los Apareamientos Incorrectos del ADN/metabolismo , Conformación de Ácido Nucleico , Emparejamiento Base/fisiología , Reparación de la Incompatibilidad de ADN/genética , Escherichia coli , Transferencia Resonante de Energía de Fluorescencia , Inestabilidad Genómica/genética , Modelos Moleculares , Proteína MutS de Unión a los Apareamientos Incorrectos del ADN/química , Proteína MutS de Unión a los Apareamientos Incorrectos del ADN/genética , Proteínas Mutantes/química , Proteínas Mutantes/metabolismo , Unión Proteica/fisiología , Conformación Proteica , Dominios Proteicos/genética , Isoformas de Proteínas/química , Isoformas de Proteínas/genética , Isoformas de Proteínas/metabolismoRESUMEN
Single molecule time-resolved fluorescence spectroscopy of CdSe/ZnS core-shell quantum dots (QDs) localized near a rough gold thin film demonstrates significant enhancement of multiphoton emission while at the same time showing a decrease in single photon emission. A rigorous analysis of time-resolved photon correlation spectroscopy and fluorescence lifetime data on single quantum dots at room temperature reveals an increase in radiative recombination rate of multiexcitons that is much higher than expected and, perhaps more significantly, is not correlated with concomitant increases in single exciton recombination rates. We believe that these results confirm a stronger coupling of multiexcitons to plasmon modes via a coupling to plasmon multipole modes.
