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Variations in kinase and effector signaling logic in a bacterial two component signaling network

Journal of Biological Chemistry 2025年第6期301卷 108534页

作者： Swingle, Danielle Epstein, Leah Aymon, Ramisha Isiorho, Eta A. Abzalimov, Rinat R. Favaro, Denize C. Gardner, Kevin H. Structural Biology Initiative CUNY Advanced Science Research Center New YorkNY United States PhD. Program in Biochemistry The Graduate Center – City University of New York New YorkNY United States Department of Chemistry and Biochemistry City College of New York New YorkNY United States PhD. Programs in Biochemistry Biology and Chemistry The Graduate Center – City University of New York New YorkNY United States

The general stress response (GSR) protects bacteria from a wide range of stressors. In Alphaproteobacteria, GSR activation is coordinated by HWE/HisKA2 family histidine kinases (HKs), which can exhibit noncanonical structure and function. For example, while most light-oxygen-voltage sensor-containing HKs are light-activated dimers, the Rubellimicrobium thermophilum RT-HK has inverted "dark on, light off" signaling logic with a tunable monomer/dimer equilibrium. Here, we further investigate these atypical behaviors of RT-HK and characterize its downstream signaling network. Using hydrogen-deuterium exchange mass spectrometry, we find that RT-HK uses a signal transduction mechanism similar to light-activated systems, despite its inverted logic. Mutagenesis reveals that RT-HK autophosphorylates in trans, with changes to the Jα helix linking sensor and kinase domains affecting autophosphorylation levels. Exploring downstream effects of RT-HK, we identified two GSR genetic regions, each encoding a copy of the central regulator PhyR. In vitro measurements of phosphotransfer from RT-HK to the two putative PhyRs revealed that RT-HK signals only to one and does so at an increased intensity in the dark, consistent with its reversed logic. X-ray crystal structures of both PhyRs revealed a substantial shift within the receiver domain of one, suggesting a basis for RT-HK specificity. We probed further down the pathway using nuclear magnetic resonance to determine that the single NepR homolog interacts with both unphosphorylated PhyRs, and this interaction is decoupled from activation in one PhyR. This work expands our understanding of HWE/HisKA2 family signal transduction, revealing marked variations from signaling mechanisms previously identified in other GSR networks. © 2025 The Authors

关键词： Signaling

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Nonadiabatic derivative couplings through multiple Franck-Condon modes dictate the energy gap law for near and short-wave infrared dye molecules

arXiv

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arXiv 2023年

作者： Ramos, Pablo Friedman, Hannah Garcia, Cesar Sletten, Ellen Caram, Justin R. Jang, Seogjoo J. 65-30 Kissena Boulevard QueensNY11367 United States Chemistry and Physics PhD programs CUNY Graduate Center United States Department of Chemistry and Biochemistry University of California Los Angeles Los AngelesCA90095 United States

Near infrared (NIR, 700 − 1, 000 nm) and short-wave infrared (SWIR, 1, 000 − 2, 000 nm) dye molecules exhibit significant nonradiative decay rates from the first singlet excited state to the ground state. While these trends can be empirically explained by a simple energy gap law, detailed mechanisms of the nearly universal behavior have remained unsettled for many cases. Theoretical and experimental results for two representative NIR/SWIR dye molecules reported here clarify an important mechanism of such nature. It is shown that the first derivative nonadiabatic coupling terms serve as major coupling pathways for nonadiabatic decay processes exhibiting the energy gap law behavior and that vibrational modes other than the highest frequency ones also make significant contributions to the rate. This assessment is corroborated by further theoretical comparison with possible alternative mechanisms of intersystem crossing to triplet states and also by comparison with experimental data for deuterated molecules. © 2023, CC BY-NC-ND.

关键词： Ground state

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Simple and general unitarity conserving numerical real time propagators of time dependent Schrödinger equation based on Magnus expansion

arXiv

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arXiv 2023年

作者： Ture, Taner M. Jang, Seogjoo J. Department of Chemistry and Biochemistry Queens College City University of New York 65-30 Kissena Boulevard QueensNY11367 United States PhD Programs in Chemistry and Physics Graduate Center of the City University of New York New York10016 United States

Magnus expansion (ME) provides a general way to expand the real time propagator of a time dependent Hamiltonian within the exponential such that the unitarity is satisfied at any order. We use this property and explicit integration of Lagrange interpolation formulas for the time dependent Hamiltonian within each time interval and derive approximations that preserve unitarity for the differential time evolution operators of general time dependent Hamiltonians. The resulting second order approximation is the same as using the average of Hamiltonians for two end points of time. We identify three fourth order approximations involving commutators of Hamiltonians at different times, and also derive a sixth order expression. Test of these approximations along with other available expressions for a two state time dependent Hamiltonian with sinusoidal time dependences provide information on relative performance of these approximations, and suggest that the derived expressions can serve as useful numerical tools for time evolution for time resolved spectroscopy, quantum control, quantum sensing, and open system quantum dynamics. © 2023, CC BY-NC-ND.

关键词： Hamiltonians

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Application of Magnus expansion for the quantum dynamics of Λ-systems under periodic driving and assessment of the rotating wave approximation

arXiv

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arXiv 2024年

作者： Ture, Taner M. Hyeon, Changbong Jang, Seogjoo J. Department of Chemistry and Biochemistry Queens College City University of New York 65-30 Kissena Boulevard QueensNY11367 United States PhD Programs in Chemistry and Physics Graduate Center of the City University of New York New York10016 United States Korea Institute for Advanced Study Hoegiro 85 Dongdaemun-gu Seoul02455 Korea Republic of

Employing a sixth order expression for the differential time evolution operator based on the Magnus expansion (ME), we conducted quantum dynamics calculations of a Λ-system driven by two sinusoidal time dependent fields. For a closed system dynamics, we confirmed the equivalence of the dynamics in the Hilbert space and the Liouville space numerically. We also conducted open system quantum dynamics calculation by generalizing the ME to the non-Hermitian dynamics in the Liouville space for the case where the effects of photonic bath are represented by Lindblad operators. In both cases, the accuracy of the rotating wave approximation (RWA) was assessed. We found significant errors of RWA during initial stages of the dynamics for representative cases where electromagnetically induced transparency or coherent population trapping can be observed. The presence of bath for open system quantum dynamics reduces the errors of RWA, but significant errors for off-diagonal elements of the density operator can still be seen. We also found that approaches to steady state limits of exact dynamics are slower than those for RWA. These results demonstrate the utility of the ME as a general and reliable tool for closed and open system quantum dynamics for time dependent Hamiltonians, and expose potential issues of drawing conclusions based solely on RWA. © 2024, CC BY-NC-ND.

关键词： Dynamics

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Fermi’s golden rule rate expression for transitions due to nonadiabatic derivative couplings in the adiabatic basis

arXiv

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arXiv 2024年

作者： Jang, Seogjoo J. Min, Byeong Ki Rhee, Young Min Department of Chemistry and Biochemistry Queens College City University of New York 65-30 Kissena Boulevard QueensNY11367 United States PhD Programs in Chemistry and Physics Graduate Center of the City University of New York New York10016 United States Department of Chemistry Korea Advanced Institute of Science and Technology Daejeon34141 Korea Republic of

Starting from a general molecular Hamiltonian expressed in the basis of adiabatic electronic and nuclear position states, where a compact and complete expression for nonadiabatic derivative coupling (NDC) Hamiltonian term is obtained, we provide a general analysis of the Fermi’s golden rule (FGR) rate expression for nonadiabatic transitions between adiabatic states. We then consider a quasi-adiabatic approximation that uses crude adiabatic states evaluated at the minimum potential energy configuration of the initial adiabatic state as the basis for the zeroth order adiabatic and NDC coupling terms of the Hamiltonian. Although application of this approximation is rather limited, it allows deriving a general FGR rate expression without further approximation and still accounts for non-Condon effect arising from momentum operators of NDC terms and its coupling with vibronic displacements. For a generic and widely used model where all nuclear degrees of freedom and environmental effects are represented as linearly coupled harmonic oscillators, we derive a closed form FGR rate expression that requires only Fourier transform. The resulting rate expression includes quadratic contributions of NDC terms and their couplings to Franck-Condon modes, which require evaluation of two additional bath spectral densities in addition to conventional one that appears in a typical FGR rate theory based on the Condon approximation. Model calculations for the case where nuclear vibrations consist of both a sharp high frequency mode and an Ohmic bath spectral density illustrate new features and implications of the rate expression. We then apply our theoretical expression to the nonradiative decay from the first excited singlet state of azulene, which illustrates the utility and implications of our theoretical results. © 2024, CC BY-NC-ND.

关键词： Hamiltonians

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General Chemical Reaction Network Theory for Olfactory Sensing Based on G-Protein-Coupled Receptors : Elucidation of Odorant Mixture Effects and Agonist-Synergist Threshold

arXiv

引用

arXiv 2023年

作者： Kim, Won Kyu Choi, Kiri Hyeon, Changbong Jang, Seogjoo J. Korea Institute for Advanced Study Hoegiro 85 Dongdaemun-gu Seoul02455 Korea Republic of Department of Chemistry and Biochemistry Queens College City University of New York 65-30 Kissena Boulevard QueensNY11367 United States PhD Programs in Chemistry and Physics Graduate Center City University of New York NY10016 United States

This work presents a general chemical reaction network theory for olfactory sensing processes that employ G-protein-coupled receptors as olfactory receptors (ORs). The theory is applicable to general mixtures of odorants and an arbitrary number of ORs. Reactions of ORs with G-proteins, both in the presence and the absence of odorants, are explicitly considered. A unique feature of the theory is the definition of an odor activity vector consisting of strengths of odorant-induced signals from ORs relative to those due to background G-protein activity in the absence of odorants. It is demonstrated that each component of the odor activity defined this way reduces to a Michaelis–Menten form capable of accounting for cooperation or competition effects between different odorants. The main features of the theory are illustrated for a two-odorant mixture. Known and potential mixture effects, such as suppression, shadowing, inhibition, and synergy are quantitatively described. Effects of relative values of rate constants, basal activity, and G-protein concentration are also demonstrated. © 2023, CC BY.

关键词： Odors

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Modified Fermi’s golden rule rate expressions

arXiv

引用

arXiv 2023年

作者： Jang, Seogjoo J. Rhee, Young Min Department of Chemistry and Biochemistry Queens College City University of New York 65-30 Kissena Boulevard QueensNY11367 United States USA & PhD Programs in Chemistry and Physics Graduate Center of the City University of New York New York10016 United States Korea Institute for Advanced Study Seoul02455 Korea Republic of Department of Chemistry Korea Advanced Institute of Science and Technology Daejeon34141 Korea Republic of

Fermi’s golden rule (FGR) serves as the basis for many expressions of spectroscopic observables and quantum transition rates. The utility of FGR has been demonstrated through decades of experimental confirmation. However, there still remain important cases where the evaluation of a FGR rate is ambiguous or ill-defined. Examples are cases where the rate has divergent terms due to the sparsity in the density of final states or time dependent fluctuations of system Hamiltonians. Strictly speaking, assumptions of FGR are no longer valid for such cases. However, it is still possible to define modified FGR rate expressions that are useful as effective rates. The resulting modified FGR rate expressions resolve a long standing ambiguity often encountered in using FGR and offer more reliable ways to model general rate processes. Simple model calculations illustrate the utility and implications of new rate expressions. Copyright © 2023, The Authors. All rights reserved.

关键词： Hamiltonians

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Fundamental trade-off between the speed of light and the Fano factor of photon current in three-level lambda systems

arXiv

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arXiv 2022年

作者： Singh, Davinder Jang, Seogjoo J. Hyeon, Changbong Korea Institute for Advanced Study Seoul02455 Korea Republic of Department of Chemistry and Biochemistry Queens College City University of New York 65-30 Kissena Boulevard QueensNY11367 United States Chemistry and Physics PhD Programs Graduate Center City University of New York 365 Fifth Avenue New YorkNY10016 United States

Electromagnetically induced slow-light medium is a promising system for quantum memory devices, but controlling its noise level remains a major challenge to overcome. This work considers the simplest model for such medium, comprised of three-level Λ-systems interacting with bosonic bath, and provides a new fundamental trade-off relation in light-matter interaction between the group velocity of light and the Fano factor of photon current due to radiative transitions. Considering the steady state limits of a newly derived Lindblad-type equation, we find that the Fano factor of the photon current maximizes to 3 at the minimal group velocity of light, which holds true universally regardless of detailed values of parameters characterizing the medium. © 2022, CC BY.

关键词： Light velocity

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A simple generalization of the energy gap law for nonradiative processes

arXiv

引用

arXiv 2021年

作者： Jang, Seogjoo J. Department of Chemistry and Biochemistry Queens College City University of New York PhD programs in Chemistry and Physics 65-30 Kissena Boulevard QueensNY11367 United States Initiative for the Theoretical Sciences Graduate Center City University of New York 365 Fifth Avenue New YorkNY10016 United States

For more than 50 years, an elegant energy gap (EG) law developed by Englman and Jortner [Mol. Phys. 18, 145 (1970)] has served as a key theory to understand and model nearly exponential dependence of nonradiative transition rates on the difference of energy between the initial and final states. This work revisits the theory, clarifies key assumptions involved in the rate expression, and provides a generalization for the cases where the effects of temperature dependence and low frequency modes cannot be ignored. For a specific example where the low frequency vibrational and/or solvation responses can be modeled as an Ohmic spectral density, a simple generalization of the EG law is provided. Test calculations demonstrate that this generalized EG law brings significant improvement over the original EG law. Both the original and generalized EG laws are also compared with stationary phase approximations developed for electron transfer theory, which suggests the possibility of a simple interpolation formula valid for any value of EG. © 2021, CC BY-NC-ND.

关键词： Energy gap

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Erratum: "Modified Fermi's golden rule rate expressions" [J. Chem. Phys. 159, 014101 (2023)]

引用

The Journal of chemical physics 2024年第1期161卷 019901页

作者： Seogjoo J Jang Young Min Rhee Department of Chemistry and Biochemistry Queens College City University of New York 65-30 Kissena Boulevard Queens New York 11367 USA and PhD Programs in Chemistry and Physics Graduate Center of the City University of New York New York 10016 USA. Department of Chemistry Korea Advanced Institute of Science and Technology Daejeon 34141 South Korea.

In our previous paper,1 there is a missing factor of 1/2 in Eq. (41). The corrected equation is as follows:CR(3)(t)≈λ32ℏωcτ04+3τ02(1+τ02)2+2(1+θ)2τ14+3τ12(1+τ12

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