Domain motions in phosphoglycerate kinase: determination of interdomain distance distributions by site-specific labeling and time-resolved fluorescence energy transfer.

Haran, Gilad; Haas, Elisha; Szpikowska, B K; Mas, Maria T.

doi:10.1073/pnas.89.24.11764

Cited by 86 publications

(84 citation statements)

References 26 publications

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“…Large-scale conformational changes in proteins, although often associated with the binding of a substrate, have been suggested to be part of the intrinsic dynamics of enzymes in the unbound state (34)(35)(36). We now demonstrate how MFPT analysis can be used as a computational tool that may aid in the identification of amino acid pairs involved in such conformational changes.…”

Section: Resultsmentioning

confidence: 99%

Anomalies in the vibrational dynamics of proteins are a consequence of fractal-like structure

Reuveni

Granek

Klafter

2010

Proc. Natl. Acad. Sci. U.S.A.

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Proteins have been shown to exhibit strange/anomalous dynamics displaying non-Debye density of vibrational states, anomalous spread of vibrational energy, large conformational changes, nonexponential decay of correlations, and nonexponential unfolding times. The anomalous behavior may, in principle, stem from various factors affecting the energy landscape under which a protein vibrates. Investigating the origins of such unconventional dynamics, we focus on the structure-dynamics interplay and introduce a stochastic approach to the vibrational dynamics of proteins. We use diffusion, a method sensitive to the structural features of the protein fold and them alone, in order to probe protein structure. Conducting a large-scale study of diffusion on over 500 Protein Data Bank structures we find it to be anomalous, an indication of a fractal-like structure. Taking advantage of known and newly derived relations between vibrational dynamics and diffusion, we demonstrate the equivalence of our findings to the existence of structurally originated anomalies in the vibrational dynamics of proteins. We conclude that these anomalies are a direct result of the fractal-like structure of proteins. The duality between diffusion and vibrational dynamics allows us to make, on a single-molecule level, experimentally testable predictions. The time dependent vibrational mean square displacement of an amino acid is predicted to be subdiffusive. The thermal variance in the instantaneous distance between amino acids is shown to grow as a power law of the equilibrium distance. Mean first passage time analysis is offered as a practical tool that may aid in the identification of amino acid pairs involved in large conformational changes.protein dynamics | Gaussian network model | anomalous diffusion | intramolecular distance distributions | mean first passage time IntroductionProteins are commonly envisioned vibrating under the influence of a complicated energy landscape (1) held responsible for their intricate dynamics (1-9). Despite its overall complexity the energy landscape is approximately harmonic near its minima, a fact that does not seem to coincide with the rich dynamics mentioned above. Attacking the validity of the harmonic approximation is one way out of this puzzle. One might have suggested that the harmonic approximation is unable to capture the anomalous dynamics displayed by proteins since the latter is dominated by large excursions from the native state structure. The failure of the harmonic approximation then follows from the fact that it does not describe the energy of conformations which considerably deviate from the native state structure. In this paper we argue differently showing that the native state structure of proteins is fractal-like and hence anomalous in its basis. As a result one needs not go beyond the harmonic approximation in order to observe anomalous dynamics since anomalous structure leads to it even in the presence of the simplest interactions. Interestingly, when the structure is fractal-like, large con...

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Section: Resultsmentioning

confidence: 99%

Anomalies in the vibrational dynamics of proteins are a consequence of fractal-like structure

Reuveni

Granek

Klafter

2010

Proc. Natl. Acad. Sci. U.S.A.

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“…FRET efficiencies were transformed to ͗EED͘app by using the Fö rster equation (47), using an experimentally determined Ro of 22 Å and an orientation factor of 2/3. The donor-acceptor pair distance distribution analysis was carried out as described (47,48). The donor-only and donor-acceptor time-resolved fluorescence decays were globally fit to an analytic function described by a double-Gaussian function.…”

Section: Tcspc Data Analysismentioning

confidence: 99%

Microsecond acquisition of heterogeneous structure in the folding of a TIM barrel protein

Kondrashkina

Kayatekin

et al. 2008

Proc. Natl. Acad. Sci. U.S.A.

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The earliest kinetic folding events for (␤␣)8 barrels reflect the appearance of off-pathway intermediates. Continuous-flow microchannel mixing methods interfaced to small-angle x-ray scattering (SAXS), circular dichroism (CD), time-resolved Förster resonant energy transfer (trFRET), and time-resolved fluorescence anisotropy (trFLAN) have been used to directly monitor global and specific dimensional properties of the partially folded state in the microsecond time range for a representative (␤␣) 8 barrel protein.Within 150 s, the ␣-subunit of Trp synthase (␣TS) experiences a global collapse and the partial formation of secondary structure. The time resolution of the folding reaction was enhanced with trFRET and trFLAN to show that, within 30 s, a distinct and autonomous partially collapsed structure has already formed in the N-terminal and central regions but not in the C-terminal region. A distance distribution analysis of the trFRET data confirmed the presence of a heterogeneous ensemble that persists for several hundreds of microseconds. Ready access to locally folded, stable substructures may be a hallmark of repeat-module proteins and the source of early kinetic traps in these very common motifs. Their folding free-energy landscapes should be elaborated to capture this source of frustration.FRET ͉ microsecond mixing ͉ misfolding ͉ small-angle x-ray scattering T he funnel shape of typical protein folding-energy landscapes suggests that sequences have evolved to minimize energetic and topological frustration (1, 2). This view is supported by the twostate folding of many small proteins (3) and the significant correlation of their folding rates with native topology (4, 5). Morecomplex mechanisms, typical of larger proteins, often place intermediates on a progressive path to the native conformation. Surprisingly, a few kinetic studies (6-9) and simulations (10) have revealed that off-pathway intermediates can be populated during the refolding of single-domain globular proteins (11). Delineating the relative contributions of sequence and topology to biases in the energy landscape that lead to these kinetic traps offers potential insights into factors responsible for protein misfolding and, potentially, for numerous devastating pathologies (12).(␤/␣) 8 TIM barrels (named after triosephosphate isomerase) are one of the most common motifs in biology (13) and are of particular interest in examining the factors leading to off-pathway folding. They constitute the most common structural class of substrates of the chaperonin GroEL, which captures and sequesters partially folded proteins to facilitate their folding to the native state (14). Although the specific partially folded forms of the Escherichia coli TIM barrels responsible for binding to GroEL are not known, in vitro studies suggest two potential candidates. The folding reactions of three TIM barrels of very low sequence identity, IOLI (a protein of unknown function corresponding to the ioll gene in Bacillus subtilis), IGPS (indole-3-glycerol phosphate synthase), a...

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“…One example studied in the context of protein folding is caused by energy transfer between donors and acceptors that can be at a distribution of distances [17,18]. In this case, there is a direct relationship between the distribution of distances and the distribution of decay rates.…”

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confidence: 99%

Fluorescence lifetime distributions in membrane systems

Gratton

Parasassi

1995

J Fluoresc

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Membranes are complex biological systems that display heterogeneity at all spatial scales. At a molecular level, the heterogeneity arises from lipid and protein composition. At the cellular level, heterogeneity is due to membrane organization and large scale morphology. A quantitative evaluation of membrane heterogeneity at a microscopic level is very important for several fields of membrane studies. We have developed a method for the analysis of the decay of fluorescent membrane probes that can provide a quantity sensitive to membrane heterogeneity. This method is based on the analysis of the fluorescence decay using continuous lifetime distributions. The major challenge in the interpretation of the analysis results is in the identification, at a molecular level, of the mechanisms that influence the fluorescence decay. In this review we illustrate the principles of data analysis and we show examples of identification of the measured parameters with specific variables that affect membrane heterogeneity.

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Domain motions in phosphoglycerate kinase: determination of interdomain distance distributions by site-specific labeling and time-resolved fluorescence energy transfer.

Cited by 86 publications

References 26 publications

Anomalies in the vibrational dynamics of proteins are a consequence of fractal-like structure

Anomalies in the vibrational dynamics of proteins are a consequence of fractal-like structure

Microsecond acquisition of heterogeneous structure in the folding of a TIM barrel protein

Fluorescence lifetime distributions in membrane systems

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