The fluctuating enzyme: a single molecule approach

Edman, Lars; Földes-Papp, Zeno; Wennmalm, Stefan; Rigler, Rudolf

doi:10.1016/s0301-0104(99)00098-1

Cited by 241 publications

(245 citation statements)

References 27 publications

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“…The advantage of this assay is that extremely long trajectories can be obtained for statistical analyses because trajectory lengths are not limited by photobleaching of the fluorophore. 21,22,34 On a single-molecule basis, turnover events are intrinsically stochastic. We obtain the sequence of the time intervals between successive turnover events, the waiting times, τ, as a function of the turnover index number ( Figure 1B).…”

Section: Single-molecule Enzymatic Turnover Dynamicsmentioning

confidence: 99%

Fluctuating Enzymes: Lessons from Single-Molecule Studies

et al. 2005

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Recent single-molecule enzymology measurements with improved statistics have demonstrated that a single enzyme molecule exhibits large temporal fluctuations of the turnover rate constant at a broad range of time scales (from 1 ms to 100 s). The rate constant fluctuations, termed as dynamic disorder, are associated with fluctuations of the protein conformations observed on the same time scales. We discuss the unique information extractable from these experiments and the reconciliation of these observations with ensemble-averaged Michaelis-Menten equation. A theoretical model based on the generalized Langevin equation (GLE) treatment of Kramers' barrier crossing problem for chemical reactions accounts naturally for the observation of dynamic disorder and highly dispersed kinetics.

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Section: Single-molecule Enzymatic Turnover Dynamicsmentioning

confidence: 99%

Fluctuating Enzymes: Lessons from Single-Molecule Studies

et al. 2005

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“…The activity of horseradish peroxidase (HRP) was investigated by Rigler and collaborators using FCS on immobilized molecules. 198,199 Oxidation of the nonfluorescent dye dihydrorhodamine 6G by HRP in the presence of H 2 O 2 leads to two fluorescent Rhodamine 6G molecules per enzyme cycle, each oxidation cycle consisting in the binding of the substrate, oxidation, and product release: (23) where the asterisk indicates the only visible species (free products are released and diffuse away). For all practical purposes, the authors modeled the system as a two-state model, with one invisible species (E) and one visible one (EP), interconverting as: (24) with effective rates k 1 and k −1 .…”

Section: Quenching Due Tomentioning

confidence: 99%

Single‐Molecule Fluorescence Studies of Protein Folding and Conformational Dynamics

Michalet¹,

Weiss²,

Jaeger³

2006

ChemInform

125

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“…1) and consider a scenario in which the processes of binding, unbinding and catalysis are all stochastic [28]. This probabilistic view point, whose origins can be traced back to the work of Ninio [29], has found one of its prime applications in the analysis of single molecule experiments [23,[30][31][32], and is now well established theoretically [33][34][35]. Defining the turnover rate k turn as the reciprocal of the turnover time-the mean FPT required to complete the reaction cycle-we will be interested in the turnover-unbinding interplay.…”

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confidence: 99%

Michaelis-Menten reaction scheme as a unified approach towards the optimal restart problem

2015

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. and * T. Rotbart and S. Reuveni had equal contribution to this work.We study the effect of restart, and retry, on the mean completion time of a generic process. The need to do so arises in various branches of the sciences and we show that it can naturally be addressed by taking advantage of the classical reaction scheme of Michaelis & Menten. Stopping a process in its midst-only to start it all over again-may prolong, leave unchanged, or even shorten the time taken for its completion. Here we are interested in the optimal restart problem, i.e., in finding a restart rate which brings the mean completion time of a process to a minimum. We derive the governing equation for this problem and show that it is exactly solvable in cases of particular interest. We then continue to discover regimes at which solutions to the problem take on universal, details independent, forms which further give rise to optimal scaling laws. The formalism we develop, and the results obtained, can be utilized when optimizing stochastic search processes and randomized computer algorithms. An immediate connection with kinetic proofreading is also noted and discussed.When engaged in a specific task for a time period that extends beyond our initial expectations, we are constantly faced with two alternatives-either keep on going or stop everything and start anew. Every now and then we opt for the latter, hoping that a fresh start will break-off an unproductive course of action and expedite the completion of the task at hand. This decision could, however, turn out to be counter-productive-nipping an awaited, but unforeseen, finale in the bud. To restart, or not to restart, that is therefore the question.Not at all unique to our everyday lives, a "dilemma" similar to the one described above is relevant to virtually any physical, chemical, or biological process that can be restarted. Most notably, restart (or unbinding) is an integral part of the renown Michaelis-Menten Reaction Scheme (MMRS) illustrated in Fig. 1 [1]. Originally devised to describe enzymatic catalysis, the MMRS has attracted on-growing scientific interest for more than a century [2]. Indeed, nature is full with an astonishing variety of Michaelian processes. DNA-DNA hybridization, antigen-antibody binding, and various other molecular processes can all be described by the MMRS [3]. That and more, the simplicity and generality of the scheme have rendered it widely applicable and it is now used to describe anything from heterogeneous catalysis [4-6] to in vivo target search kinetics [7]. As a matter of fact, one can easily convince himself that any first passage time (FPT) process [8]-be it the time to target of a simple Brownian particle, or that of more sophisticated stochastic processes [9][10][11][12] and random searchers [13][14][15]-can become subject to restart [16][17][18][19][20][21][22] and is then naturally accommodated by the MMRS. Wishing to acquire a unified view on restart phenomena we identify the MMRS as an ideal object of study.Central to our understanding of the ...

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The fluctuating enzyme: a single molecule approach

Cited by 241 publications

References 27 publications

Fluctuating Enzymes: Lessons from Single-Molecule Studies

Fluctuating Enzymes: Lessons from Single-Molecule Studies

Single‐Molecule Fluorescence Studies of Protein Folding and Conformational Dynamics

Michaelis-Menten reaction scheme as a unified approach towards the optimal restart problem

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