Nonlinear response theory in chemical kinetics

Kryvohuz, Maksym; Mukamel, Shaul

doi:10.1063/1.4861588

Cited by 19 publications

(21 citation statements)

References 30 publications

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“…In this work, we apply generalized concepts of time correlation functions (TCFs) to study the ssDNA-(gp32) 2 assembly pathways (20)(21)(22)(23)(24)(25)(26)(27)(28)(29)(30). We assume that our single-molecule experiments probe the instantaneous conformational state of the system at equilibrium and that the stochastically fluctuating smFRET efficiency, E FRET , can be directly mapped onto this state.…”

Section: Significancementioning

confidence: 99%

Using microsecond single-molecule FRET to determine the assembly pathways of T4 ssDNA binding protein onto model DNA replication forks

Phelps

Israels

Jose

et al. 2017

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

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DNA replication is a core biological process that occurs in prokaryotic cells at high speeds (∼1 nucleotide residue added per millisecond) and with high fidelity (fewer than one misincorporation event per 10 nucleotide additions). The ssDNA binding protein [gene product 32 (gp32)] of the T4 bacteriophage is a central integrating component of the replication complex that must continuously bind to and unbind from transiently exposed template strands during DNA synthesis. We here report microsecond single-molecule FRET (smFRET) measurements on Cy3/Cy5-labeled primer-template (p/t) DNA constructs in the presence of gp32. These measurements probe the distance between Cy3/Cy5 fluorophores that label the ends of a short (15-nt) segment of ssDNA attached to a model p/t DNA construct and permit us to track the stochastic interconversion between various protein bound and unbound states. The length of the 15-nt ssDNA lattice is sufficient to accommodate up to two cooperatively bound gp32 proteins in either of two positions. We apply a unique multipoint time correlation function analysis to the microsecond-resolved smFRET data obtained to determine and compare the kinetics of various possible reaction pathways for the assembly of cooperatively bound gp32 protein onto ssDNA sequences located at the replication fork. The results of our analysis reveal the presence and translocation mechanisms of short-lived intermediate bound states that are likely to play a critical role in the assembly mechanisms of ssDNA binding proteins at replication forks and other ss duplex junctions.

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Section: Significancementioning

confidence: 99%

Using microsecond single-molecule FRET to determine the assembly pathways of T4 ssDNA binding protein onto model DNA replication forks

Phelps

Israels

Jose

et al. 2017

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

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“…2 of Ref. 9. As discussed in that reference, these 2D plots can suggest the order of X i , X l , and X j species in the chemical network, i.e., out of two permutations X i − X l − X j and X i − X j − X l , the one with longer correlation tail along the τ 2 axis corresponds to the correct order of species X i , X l , and X j .…”

Section: Example 3: Connectivity Of Stochastic Chemical Networkmentioning

confidence: 99%

“…We call these new quantities GRFs. 8,9 GRFs simply extend the class of correlation and response functions. For instance, in the notation of Eq.…”

Section: Generalized Response Functionsmentioning

confidence: 99%

“…In Ref. 9, we proposed to use R ++− (τ 2 , τ 1 ) to check the order of chemical species in the chemical reaction network described by macroscopic rate equations. We now consider the same example but for microscopic kinetics of the model reaction network,…”

Section: Example 3: Connectivity Of Stochastic Chemical Networkmentioning

confidence: 99%

“…That formalism a) Electronic address: mkryvohu@uci.edu was further extended to non-Hamiltonian systems, such as chemical reactions, and was used to study nonlinear kinetics and connectivity of species in chemical systems. 9 In the present paper, we introduce a generalized response theory of stochastic dynamical systems. The formalism is based on a perturbative expansion of the Fokker-Planck equation around steady state.…”

Section: Introductionmentioning

confidence: 99%

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Multidimensional characterization of stochastic dynamical systems based on multiple perturbations and measurements

Kryvohuz

Mukamel

2015

The Journal of Chemical Physics

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Generalized nonlinear response theory is presented for stochastic dynamical systems. Experiments in which multiple measurements of dynamical quantities are used along with multiple perturbations of parameters of dynamical systems are described by generalized response functions (GRFs). These constitute a new type of multidimensional measures of stochastic dynamics either in the time or the frequency domains. Closed expressions for GRFs in stochastic dynamical systems are derived and compared with numerical non-equilibrium simulations. Several types of perturbations are considered: impulsive and periodic perturbations of temperature and impulsive perturbations of coordinates. The present approach can be used to study various types of stochastic processes ranging from single-molecule conformational dynamics to chemical kinetics of finite-size reactors such as biocells. C 2015 AIP Publishing LLC. [http://dx

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Submillisecond Conformational Transitions of Short Single-Stranded DNA Lattices by Photon Correlation Single-Molecule Förster Resonance Energy Transfer

et al. 2021

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Thermally driven conformational fluctuations (or “breathing”) of DNA play important roles in the function and regulation of the “macromolecular machinery of genome expression.” Fluctuations in double-stranded (ds) DNA are involved in the transient exposure of pathways to protein binding sites within the DNA framework, leading to the binding of regulatory proteins to single-stranded (ss) DNA templates. These interactions often require that the ssDNA sequences, as well as the proteins involved, assume transient conformations critical for successful binding. Here, we use microsecond-resolved single-molecule Förster resonance energy transfer (smFRET) experiments to investigate the backbone fluctuations of short [oligo(dT) n ] templates within DNA constructs that also serve as models for ss-dsDNA junctions. Such junctions, together with the attached ssDNA sequences, are involved in interactions with the ssDNA binding (ssb) proteins that control and integrate the functions of DNA replication complexes. We analyze these data using a chemical network model based on multiorder time-correlation functions and probability distribution functions that characterize the kinetic and thermodynamic behavior of the system. We find that the oligo(dT) n tails of ss-dsDNA constructs interconvert, on submillisecond time scales, between three macrostates with distinctly different end-to-end distances. These are (i) a “compact” macrostate that represents the dominant species at equilibrium; (ii) a “partially extended” macrostate that exists as minority species; and (iii) a “highly extended” macrostate that is present in trace amounts. We propose a model for ssDNA secondary structure that advances our understanding of how spontaneously formed nucleic acid conformations may facilitate the activities of ssDNA-associating proteins.

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Nonlinear response theory in chemical kinetics

Cited by 19 publications

References 30 publications

Using microsecond single-molecule FRET to determine the assembly pathways of T4 ssDNA binding protein onto model DNA replication forks

Using microsecond single-molecule FRET to determine the assembly pathways of T4 ssDNA binding protein onto model DNA replication forks

Multidimensional characterization of stochastic dynamical systems based on multiple perturbations and measurements

Submillisecond Conformational Transitions of Short Single-Stranded DNA Lattices by Photon Correlation Single-Molecule Förster Resonance Energy Transfer

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