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Samajdar R, Meigooni M, Yang H, Li J, Liu X, Jackson NE, Mosquera MA, Tajkhorshid E, Schroeder CM. Secondary structure determines electron transport in peptides. Proc Natl Acad Sci U S A 2024; 121:e2403324121. [PMID: 39052850 PMCID: PMC11317557 DOI: 10.1073/pnas.2403324121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2024] [Accepted: 06/14/2024] [Indexed: 07/27/2024] Open
Abstract
Proteins play a key role in biological electron transport, but the structure-function relationships governing the electronic properties of peptides are not fully understood. Despite recent progress, understanding the link between peptide conformational flexibility, hierarchical structures, and electron transport pathways has been challenging. Here, we use single-molecule experiments, molecular dynamics (MD) simulations, nonequilibrium Green's function-density functional theory (NEGF-DFT), and unsupervised machine learning to understand the role of secondary structure on electron transport in peptides. Our results reveal a two-state molecular conductance behavior for peptides across several different amino acid sequences. MD simulations and Gaussian mixture modeling are used to show that this two-state molecular conductance behavior arises due to the conformational flexibility of peptide backbones, with a high-conductance state arising due to a more defined secondary structure (beta turn or 310 helices) and a low-conductance state occurring for extended peptide structures. These results highlight the importance of helical conformations on electron transport in peptides. Conformer selection for the peptide structures is rationalized using principal component analysis of intramolecular hydrogen bonding distances along peptide backbones. Molecular conformations from MD simulations are used to model charge transport in NEGF-DFT calculations, and the results are in reasonable qualitative agreement with experiments. Projected density of states calculations and molecular orbital visualizations are further used to understand the role of amino acid side chains on transport. Overall, our results show that secondary structure plays a key role in electron transport in peptides, which provides broad avenues for understanding the electronic properties of proteins.
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Affiliation(s)
- Rajarshi Samajdar
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL61801
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL61801
| | - Moeen Meigooni
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL61801
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL61801
| | - Hao Yang
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL61801
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, IL61801
| | - Jialing Li
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL61801
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL61801
| | - Xiaolin Liu
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL61801
| | - Nicholas E. Jackson
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL61801
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL61801
| | - Martín A. Mosquera
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT59717
| | - Emad Tajkhorshid
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL61801
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL61801
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL61801
- Department of Biochemistry, University of Illinois at Urbana-Champaign, Urbana, IL61801
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL61801
| | - Charles M. Schroeder
- Department of Chemical and Biomolecular Engineering, University of Illinois at Urbana-Champaign, Urbana, IL61801
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL61801
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL61801
- Department of Materials Science and Engineering, University of Illinois at Urbana-Champaign, Urbana, IL61801
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL61801
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, IL61801
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2
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London N, Bu S, Johnson B, Ananth N. Mean-Field Ring Polymer Rates Using a Population Dividing Surface. J Phys Chem A 2024; 128:5730-5739. [PMID: 38976564 DOI: 10.1021/acs.jpca.4c00005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Mean-field ring polymer molecular dynamics offers a computationally efficient method for the simulation of reaction rates in multilevel systems. Previous work has established that, to model a nonadiabatic state-to-state reaction accurately, it is necessary to ensure reactive trajectories form kinked ring polymer configurations at the dividing surface. Building on this idea, we introduce a population difference coordinate and a reactive flux expression modified to only include contributions from kinked configurations. We test the accuracy of the resulting mean-field rate theory on a series of linear vibronic coupling model systems. We demonstrate that this new kMF-RP rate approach is efficient to implement and quantitatively accurate for models over a wide range of driving forces, coupling strengths, and temperatures.
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Affiliation(s)
- Nathan London
- Department of Chemistry, Cornell University, Ithaca, New York 14853, United States
| | - Siyu Bu
- Department of Chemistry, Cornell University, Ithaca, New York 14853, United States
| | - Britta Johnson
- Department of Chemistry, Cornell University, Ithaca, New York 14853, United States
| | - Nandini Ananth
- Department of Chemistry, Cornell University, Ithaca, New York 14853, United States
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3
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Ma C, Feng Y, Wang J, Zheng B, Wang X, Jiao N. Integrative Physiological, Transcriptome, and Proteome Analyses Provide Insights into the Photosynthetic Changes in Maize in a Maize-Peanut Intercropping System. PLANTS (BASEL, SWITZERLAND) 2023; 13:65. [PMID: 38202373 PMCID: PMC10780508 DOI: 10.3390/plants13010065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 12/08/2023] [Accepted: 12/15/2023] [Indexed: 01/12/2024]
Abstract
Intercropping is a traditional and sustainable planting method that can make rational use of natural resources such as light, temperature, fertilizer, water, and CO2. Due to its efficient resource utilization, intercropping, in particular, maize and legume intercropping, is widespread around the world. However, the molecular details of these pathways remain largely unknown. In this study, physiological, transcriptome, and proteome analyses were compared between maize monocropping and maize-peanut intercropping. The results show that an intercropping system enhanced the ability of carbon fixation and carboxylation of maize leaves. Apparent quantum yield (AQY), the light-saturated net photosynthetic rate (LSPn), the light saturation point (LSP), and the light compensation point (LCP) were increased by 11.6%, 9.4%, 8.9%, and 32.1% in the intercropping system, respectively; carboxylation efficiency (CE), the CO2 saturation point (Cisat), the Rubisco maximum carboxylation rate (Vcmax), the maximum electron transfer rate (Jmax), and the triose phosphate utilization rate (TPU) were increased by 28.5%, 7.3%, 18.7%, 29.2%, and 17.0%, respectively; meanwhile, the CO2 compensation point (Γ) decreased by 22.6%. Moreover, the transcriptome analysis confirmed the presence of 588 differentially expressed genes (DEGs), and the numbers of up-regulated and down-regulated genes were 383 and 205, respectively. The DEGs were primarily concerned with ribosomes, plant hormone signal transduction, and photosynthesis. Furthermore, 549 differentially expressed proteins (DEPs) were identified in the maize leaves in both the maize monocropping and maize-peanut intercropping systems. Bioinformatics analysis revealed that 186 DEPs were related to 37 specific KEGG pathways in each of the two treatment groups. Based on the physiological, transcriptome, and proteome analyses, it was demonstrated that the photosynthetic characteristics in maize leaves can be improved by maize-peanut intercropping. This may be related to PS I, PS II, cytochrome b6f complex, ATP synthase, and photosynthetic CO2 fixation, which is caused by the improved CO2 carboxylation efficiency. Our results provide a more in-depth understanding of the high yield and high-efficiency mechanism in maize and peanut intercropping.
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Affiliation(s)
- Chao Ma
- College of Agriculture, Henan University of Science and Technology, Luoyang 471023, China; (C.M.); (J.W.); (B.Z.); (X.W.)
| | - Yalan Feng
- College of Life Science, Wuchang University of Technology, Wuhan 430223, China;
| | - Jiangtao Wang
- College of Agriculture, Henan University of Science and Technology, Luoyang 471023, China; (C.M.); (J.W.); (B.Z.); (X.W.)
| | - Bin Zheng
- College of Agriculture, Henan University of Science and Technology, Luoyang 471023, China; (C.M.); (J.W.); (B.Z.); (X.W.)
| | - Xiaoxiao Wang
- College of Agriculture, Henan University of Science and Technology, Luoyang 471023, China; (C.M.); (J.W.); (B.Z.); (X.W.)
| | - Nianyuan Jiao
- College of Agriculture, Henan University of Science and Technology, Luoyang 471023, China; (C.M.); (J.W.); (B.Z.); (X.W.)
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Cetin E, Atilgan AR, Atilgan C. DHFR Mutants Modulate Their Synchronized Dynamics with the Substrate by Shifting Hydrogen Bond Occupancies. J Chem Inf Model 2022; 62:6715-6726. [PMID: 35984987 PMCID: PMC9795552 DOI: 10.1021/acs.jcim.2c00507] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Antibiotic resistance is a global health problem in which mutations occurring in functional proteins render drugs ineffective. The working mechanisms of the arising mutants are seldom apparent; a methodology to decipher these mechanisms systematically would render devising therapies to control the arising mutational pathways possible. Here we utilize Cα-Cβ bond vector relaxations obtained from moderate length MD trajectories to determine conduits for functionality of the resistance conferring mutants of Escherichia coli dihydrofolate reductase. We find that the whole enzyme is synchronized to the motions of the substrate, irrespective of the mutation introducing gain-of-function or loss-of function. The total coordination of the motions suggests changes in the hydrogen bond dynamics with respect to the wild type as a possible route to determine and classify the mode-of-action of individual mutants. As a result, nine trimethoprim-resistant point mutations arising frequently in evolution experiments are categorized. One group of mutants that display the largest occurrence (L28R, W30G) work directly by modifying the dihydrofolate binding region. Conversely, W30R works indirectly by the formation of the E139-R30 salt bridge which releases energy resulting from tight binding by distorting the binding cavity. A third group (D27E, F153S, I94L) arising as single, resistance invoking mutants in evolution experiment trajectories allosterically and dynamically affects a hydrogen bonding motif formed at residues 59-69-71 which in turn modifies the binding site dynamics. The final group (I5F, A26T, R98P) consists of those mutants that have properties most similar to the wild type; these only appear after one of the other mutants is fixed on the protein structure and therefore display clear epistasis. Thus, we show that the binding event is governed by the entire enzyme dynamics while the binding site residues play gating roles. The adjustments made in the total enzyme in response to point mutations are what make quantifying and pinpointing their effect a hard problem. Here, we show that hydrogen bond dynamics recorded on sub-μs time scales provide the necessary fingerprints to decipher the various mechanisms at play.
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Brkljača Z, Butumović M, Bakarić D. Water does not dance as ions sing: A new approach in elucidation of ion-invariant water fluctuations. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 271:120907. [PMID: 35144056 DOI: 10.1016/j.saa.2022.120907] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 01/07/2022] [Accepted: 01/13/2022] [Indexed: 06/14/2023]
Abstract
Aqueous solutions of salts composed from monovalent ions are explored using temperature-dependent FT-IR spectroscopy in transmission. Water combination band, being extremely sensitive to the network of hydrogen bonds due to the contribution of water librations (ρLH2O), is analyzed in uni- and multivariate fashion. Univariate analysis of the combination band maximum (νmax) reveals that perturbation of water hydrogen bond network by ions is primary driven by electrostatic interactions between water and ions. Using multivariate curve resolution with alternating least squares and evolving factor analysis this band is separated into two components that represent low- and high-density water. The observed asymmetry in their behavior is interpreted in terms of fluctuations of a hydrogen bond network of two water components. The significance of the found phenomenon is unambiguously confirmed by performing analogous analysis in the spectral range that contains partial signature of water linear bending (δHOH) and is free from ρLH2O, in which the asymmetry is absent. Additionally, we show that this phenomenon, namely ion-invariant behavior of water fluctuations, persists even in the regime of high ionic strengths. Although ions indeed participate in shaping of water hydrogen bond network, this straightforward approach shows that its temperature-dependent fluctuations are ion-independent.
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Affiliation(s)
- Zlatko Brkljača
- Division for Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia.
| | - Marija Butumović
- Division of Analytical Chemistry, Department of Chemistry, Faculty of Science, University of Zagreb, Horvatovac 102a, 10000 Zagreb, Croatia
| | - Danijela Bakarić
- Division for Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia.
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6
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Trenins G, Richardson JO. Nonadiabatic instanton rate theory beyond the golden-rule limit. J Chem Phys 2022; 156:174115. [DOI: 10.1063/5.0088518] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Fermi's golden rule describes the leading-order behaviour of the reaction rate as a function of the diabatic coupling. Its asymptotic (ℏ →0) limit is the semiclassical golden-rule instanton rate theory, which rigorously approximates nuclear quantum effects, lends itself to efficient numerical computation and gives physical insight into reaction mechanisms. However the golden rule by itself becomes insufficient as the strength of the diabatic coupling increases, so higher-order terms must be additionally considered. In this work we give a first-principles derivation of the next-order term beyond the golden rule, represented as a sum of three components. Two of them lead to new instanton pathways that extend the golden-rule case and, among other factors, account for the effects of recrossing on the full rate. The remaining component derives from the equilibrium partition function and accounts for changes in potential energy around the reactant and product wells due to diabatic coupling. The new semiclassical theory demands little computational effort beyond a golden-rule instanton calculation. It makes it possible to rigorously assess the accuracy of the golden-rule approximation and sets the stage for future work on general semiclassical nonadiabatic rate theories.
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Affiliation(s)
- George Trenins
- ETH Zurich Department of Chemistry and Applied Biosciences, Switzerland
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7
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Kontkanen OV, Biriukov D, Futera Z. Reorganization Free Energy of Copper Proteins in Solution, in Vacuum, and on Metal Surfaces. J Chem Phys 2022; 156:175101. [DOI: 10.1063/5.0085141] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Metalloproteins, known to efficiently transfer electronic charge in biological systems, recently found their utilization in nanobiotechnological devices where the protein is placed into direct contact with metal surfaces. The feasibility of oxidation/reduction of the protein redox sites is affected by the reorganization free energies, one of the key parameters determining the transfer rates. While their values have been measured and computed for proteins in their native environments, i.e., in aqueous solution, the reorganization free energies of dry proteins or proteins adsorbed to metal surfaces remain unknown. Here, we investigate the redox properties of blue copper protein azurin, a prototypical redox-active metalloprotein previously probed by various experimental techniques both in solution and on metal/vacuum interfaces. We used a hybrid QM/MM computational technique based on DFT to explore protein dynamics, flexibility, and corresponding reorganization free energies in aqueous solution, vacuum, and on vacuum gold interfaces. Somewhat surprisingly, the reorganization free energy only slightly decreases when azurin is dried because the loss of the hydration shell leads to larger flexibility of the protein near its redox site. At the vacuum gold surfaces, the energetics of the structure relaxation depends on the adsorption geometry, however, significant reduction of the reorganization free energy was not observed. These findings have important consequences for the charge transport mechanism in vacuum devices, showing that the free energy barriers for protein oxidation remain significant even under ultra-high vacuum conditions.
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Affiliation(s)
| | - Denys Biriukov
- Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences, Czech Republic
| | - Zdenek Futera
- University of South Bohemia in Ceske Budejovice Faculty of Science, Czech Republic
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8
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Fedoretz-Maxwell BP, Shin CH, MacNeil GA, Worrall LJ, Park R, Strynadka NCJ, Walsby CJ, Warren JJ. The Impact of Second Coordination Sphere Methionine-Aromatic Interactions in Copper Proteins. Inorg Chem 2022; 61:5563-5571. [DOI: 10.1021/acs.inorgchem.2c00030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Brooklyn P. Fedoretz-Maxwell
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
| | - Catherine H. Shin
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
| | - Gregory A. MacNeil
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
| | - Liam J. Worrall
- Department of Biochemistry and Molecular Biology and Centre for Blood Research, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Rachel Park
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
| | - Natalie C. J. Strynadka
- Department of Biochemistry and Molecular Biology and Centre for Blood Research, University of British Columbia, Vancouver, British Columbia V6T 1Z3, Canada
| | - Charles J. Walsby
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
| | - Jeffrey J. Warren
- Department of Chemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
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9
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Hydrogen bonding rearrangement by a mitochondrial disease mutation in cytochrome bc 1 perturbs heme b H redox potential and spin state. Proc Natl Acad Sci U S A 2021; 118:2026169118. [PMID: 34389670 PMCID: PMC8379992 DOI: 10.1073/pnas.2026169118] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
To perform their specific electron-transfer relay functions, hemes commonly adopt low spin states with fine-tuned redox potentials. Understanding molecular elements controlling these properties is crucial for the description of natural proteins and engineering redox-active systems. We describe unusual effects of mitochondrial disease-related mutation in cytochrome bc1, based on which we identify a dual role of hydrogen bonding to the propionate group of heme bH. We observe that stabilization of the hydrogen bond in mutant enhances the redox potential but destabilizes the low spin state of oxidized heme. This demonstrates a critical role of the hydrogen bonding, and heme-protein interactions in general, to secure a suitable redox potential and spin state, a notion that might be universal for other heme proteins. Hemes are common elements of biological redox cofactor chains involved in rapid electron transfer. While the redox properties of hemes and the stability of the spin state are recognized as key determinants of their function, understanding the molecular basis of control of these properties is challenging. Here, benefiting from the effects of one mitochondrial disease–related point mutation in cytochrome b, we identify a dual role of hydrogen bonding (H-bond) to the propionate group of heme bH of cytochrome bc1, a common component of energy-conserving systems. We found that replacing conserved glycine with serine in the vicinity of heme bH caused stabilization of this bond, which not only increased the redox potential of the heme but also induced structural and energetic changes in interactions between Fe ion and axial histidine ligands. The latter led to a reversible spin conversion of the oxidized Fe from 1/2 to 5/2, an effect that potentially reduces the electron transfer rate between the heme and its redox partners. We thus propose that H-bond to the propionate group and heme-protein packing contribute to the fine-tuning of the redox potential of heme and maintaining its proper spin state. A subtle balance is needed between these two contributions: While increasing the H-bond stability raises the heme potential, the extent of increase must be limited to maintain the low spin and diamagnetic form of heme. This principle might apply to other native heme proteins and can be exploited in engineering of artificial heme-containing protein maquettes.
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10
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Sang Y, Mishra S, Tassinari F, Karuppannan SK, Carmieli R, Teo RD, Migliore A, Beratan DN, Gray HB, Pecht I, Fransson J, Waldeck DH, Naaman R. Temperature Dependence of Charge and Spin Transfer in Azurin. THE JOURNAL OF PHYSICAL CHEMISTRY. C, NANOMATERIALS AND INTERFACES 2021; 125:9875-9883. [PMID: 34055128 PMCID: PMC8154855 DOI: 10.1021/acs.jpcc.1c01218] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 04/23/2021] [Indexed: 05/05/2023]
Abstract
The steady-state charge and spin transfer yields were measured for three different Ru-modified azurin derivatives in protein films on silver electrodes. While the charge-transfer yields exhibit weak temperature dependences, consistent with operation of a near activation-less mechanism, the spin selectivity of the electron transfer improves as temperature increases. This enhancement of spin selectivity with temperature is explained by a vibrationally induced spin exchange interaction between the Cu(II) and its chiral ligands. These results indicate that distinct mechanisms control charge and spin transfer within proteins. As with electron charge transfer, proteins deliver polarized electron spins with a yield that depends on the protein's structure. This finding suggests a new role for protein structure in biochemical redox processes.
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Affiliation(s)
- Yutao Sang
- Department
of Chemical and Biological Physics, Weizmann
Institute, Rehovot 76100, Israel
| | - Suryakant Mishra
- Department
of Chemical and Biological Physics, Weizmann
Institute, Rehovot 76100, Israel
| | - Francesco Tassinari
- Department
of Chemical and Biological Physics, Weizmann
Institute, Rehovot 76100, Israel
| | | | - Raanan Carmieli
- Department
of Chemical Research Support, Weizmann Institute
of Science, Rehovot 76100, Israel
| | - Ruijie D. Teo
- Department
of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Agostino Migliore
- Department
of Chemistry, Duke University, Durham, North Carolina 27708, United States
- Department
of Chemical Sciences, University of Padova, Via Marzolo 1, Padova 35122, Italy
| | - David N. Beratan
- Department
of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Harry B. Gray
- Beckman
Institute, California Institute of Technology, Pasadena, California 91125, United States
| | - Israel Pecht
- Department
of Immunology, Weizmann Institute, Rehovot 76100, Israel
| | - Jonas Fransson
- Department
of Physics and Astronomy, Uppsala University, Uppsala 752 36, Sweden
| | - David H. Waldeck
- Department
of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Ron Naaman
- Department
of Chemical and Biological Physics, Weizmann
Institute, Rehovot 76100, Israel
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11
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Chowdhury SN, Huo P. Non-adiabatic Matsubara dynamics and non-adiabatic ring-polymer molecular dynamics. J Chem Phys 2021; 154:124124. [PMID: 33810665 DOI: 10.1063/5.0042136] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
We present the non-adiabatic Matsubara dynamics, a general framework for computing the time-correlation function (TCF) of electronically non-adiabatic systems. This new formalism is derived based on the generalized Kubo-transformed TCF using the Wigner representation for both the nuclear degrees of freedom and the electronic mapping variables. By dropping the non-Matsubara nuclear normal modes in the quantum Liouvillian and explicitly integrating these modes out from the expression of the TCF, we derived the non-adiabatic Matsubara dynamics approach. Further making the approximation to drop the imaginary part of the Matsubara Liouvillian and enforce the nuclear momentum integral to be real, we arrived at the non-adiabatic ring-polymer molecular dynamics (NRPMD) approach. We have further justified the capability of NRPMD for simulating the non-equilibrium TCF. This work provides the rigorous theoretical foundation for several recently proposed state-dependent RPMD approaches and offers a general framework for developing new non-adiabatic quantum dynamics methods in the future.
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Affiliation(s)
- Sutirtha N Chowdhury
- Department of Chemistry, University of Rochester, 120 Trustee Road, Rochester, New York 14627, USA
| | - Pengfei Huo
- Department of Chemistry, University of Rochester, 120 Trustee Road, Rochester, New York 14627, USA
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12
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Chowdhury SN, Mandal A, Huo P. Ring polymer quantization of the photon field in polariton chemistry. J Chem Phys 2021; 154:044109. [PMID: 33514102 DOI: 10.1063/5.0038330] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
We use the ring polymer (RP) representation to quantize the radiation field inside an optical cavity to investigate polariton quantum dynamics. Using a charge transfer model coupled to an optical cavity, we demonstrate that the RP quantization of the photon field provides accurate rate constants of the polariton mediated electron transfer reaction compared to Fermi's golden rule. Because RP quantization uses extended phase space to describe the photon field, it significantly reduces the computational costs compared to the commonly used Fock state description of the radiation field. Compared to the other quasi-classical descriptions of the photon field, such as the classical Wigner based mean-field Ehrenfest model, the RP representation provides a much more accurate description of the polaritonic quantum dynamics because it alleviates the potential quantum distribution leakage problem associated with the photonic degrees of freedom (DOF). This work demonstrates the possibility of using the ring polymer description to treat the quantized radiation field in polariton chemistry, offering an accurate and efficient approach for future investigations in cavity quantum electrodynamics.
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Affiliation(s)
- Sutirtha N Chowdhury
- Department of Chemistry, University of Rochester, 120 Trustee Road, Rochester, New York 14627, USA
| | - Arkajit Mandal
- Department of Chemistry, University of Rochester, 120 Trustee Road, Rochester, New York 14627, USA
| | - Pengfei Huo
- Department of Chemistry, University of Rochester, 120 Trustee Road, Rochester, New York 14627, USA
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13
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Kudisch B, Oblinsky DG, Black MJ, Zieleniewska A, Emmanuel MA, Rumbles G, Hyster TK, Scholes GD. Active-Site Environmental Factors Customize the Photophysics of Photoenzymatic Old Yellow Enzymes. J Phys Chem B 2020; 124:11236-11249. [PMID: 33231450 DOI: 10.1021/acs.jpcb.0c09523] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The development of non-natural photoenzymatic systems has reinvigorated the study of photoinduced electron transfer (ET) within protein active sites, providing new and unique platforms for understanding how biological environments affect photochemical processes. In this work, we use ultrafast spectroscopy to compare the photoinduced electron transfer in known photoenzymes. 12-Oxophytodienoate reductase 1 (OPR1) is compared to Old Yellow Enzyme 1 (OYE1) and morphinone reductase (MR). The latter enzymes are structurally homologous to OPR1. We find that slight differences in the amino acid composition of the active sites of these proteins determine their distinct electron-transfer dynamics. Our work suggests that the inside of a protein active site is a complex/heterogeneous dielectric network where genetically programmed heterogeneity near the site of biological ET can significantly affect the presence and lifetime of various intermediate states. Our work motivates additional tunability of Old Yellow Enzyme active-site reorganization energy and electron-transfer energetics that could be leveraged for photoenzymatic redox approaches.
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Affiliation(s)
- Bryan Kudisch
- Department of Chemistry, Princeton University, Princeton, New Jersey 08540, United States
| | - Daniel G Oblinsky
- Department of Chemistry, Princeton University, Princeton, New Jersey 08540, United States
| | - Michael J Black
- Department of Chemistry, Princeton University, Princeton, New Jersey 08540, United States
| | - Anna Zieleniewska
- National Renewable Energy Laboratory, Golden, Colorado 80401, United States
| | - Megan A Emmanuel
- Department of Chemistry, Princeton University, Princeton, New Jersey 08540, United States
| | - Garry Rumbles
- National Renewable Energy Laboratory, Golden, Colorado 80401, United States.,Department of Chemistry and RASEI, University of Colorado Boulder, Colorado 80309, United States
| | - Todd K Hyster
- Department of Chemistry, Princeton University, Princeton, New Jersey 08540, United States
| | - Gregory D Scholes
- Department of Chemistry, Princeton University, Princeton, New Jersey 08540, United States
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14
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Lawrence JE, Manolopoulos DE. An improved path-integral method for golden-rule rates. J Chem Phys 2020; 153:154113. [PMID: 33092388 DOI: 10.1063/5.0022535] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We present a simple method for the calculation of reaction rates in the Fermi golden-rule limit, which accurately captures the effects of tunneling and zero-point energy. The method is based on a modification of the recently proposed golden-rule quantum transition state theory (GR-QTST) of Thapa, Fang, and Richardson [J. Chem. Phys. 150, 104107 (2019)]. While GR-QTST is not size consistent, leading to the possibility of unbounded errors in the rate, our modified method has no such issue and so can be reliably applied to condensed phase systems. Both methods involve path-integral sampling in a constrained ensemble; the two methods differ, however, in the choice of constraint functional. We demonstrate numerically that our modified method is as accurate as GR-QTST for the one-dimensional model considered by Thapa and co-workers. We then study a multidimensional spin-boson model, for which our method accurately predicts the true quantum rate, while GR-QTST breaks down with an increasing number of boson modes in the discretization of the spectral density. Our method is able to accurately predict reaction rates in the Marcus inverted regime without the need for the analytic continuation required by Wolynes theory.
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Affiliation(s)
- Joseph E Lawrence
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - David E Manolopoulos
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
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15
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Xiang L, Zhang P, Liu C, He X, Li HB, Li Y, Wang Z, Hihath J, Kim SH, Beratan DN, Tao N. Conductance and configuration of molecular gold-water-gold junctions under electric fields. MATTER 2020; 3:166-179. [PMID: 33103114 PMCID: PMC7584381 DOI: 10.1016/j.matt.2020.03.023] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Water molecules can mediate charge transfer in biological and chemical reactions by forming electronic coupling pathways. Understanding the mechanism requires a molecular-level electrical characterization of water. Here, we describe the measurement of single water molecular conductance at room temperature, characterize the structure of water molecules using infrared spectroscopy, and perform theoretical studies to assist in the interpretation of the experimental data. The study reveals two distinct states of water, corresponding to a parallel and perpendicular orientation of the molecules. Water molecules switch from parallel to perpendicular orientations on applying an electric field, producing switching from high to low conductance states, thus enabling the determination of single water molecular dipole moments. The work further shows that water-water interactions affect the atomic scale configuration and conductance of water molecules. These findings demonstrate the importance of the discrete nature of water molecules in electron transfer and set limits on water-mediated electron transfer rates.
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Affiliation(s)
- Limin Xiang
- Biodesign Center for Biosensors and Bioelectronics, Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA
- Lead contact
| | - Peng Zhang
- Departments of Chemistry and Physics, Duke University, Durham, North Carolina 27708, USA
| | - Chaoren Liu
- Departments of Chemistry and Physics, Duke University, Durham, North Carolina 27708, USA
| | - Xin He
- Department of Chemical Engineering and Materials Research Institute, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Haipeng B. Li
- Department of Electrical and Computing Engineering, University of California, Davis, Davis, California 95616, USA
| | - Yueqi Li
- Biodesign Center for Biosensors and Bioelectronics, Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA
| | - Zixiao Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210093, China
| | - Joshua Hihath
- Department of Electrical and Computing Engineering, University of California, Davis, Davis, California 95616, USA
| | - Seong H. Kim
- Department of Chemical Engineering and Materials Research Institute, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - David N. Beratan
- Departments of Chemistry and Physics, Duke University, Durham, North Carolina 27708, USA
- Department of Biochemistry, Duke University, Durham, North Carolina 27710, USA
| | - Nongjian Tao
- Biodesign Center for Biosensors and Bioelectronics, Biodesign Institute, Arizona State University, Tempe, Arizona 85287, USA
- School of Electrical, Computer and Energy Engineering, Arizona State University, Tempe, Arizona 85287, USA
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16
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Lawrence JE, Manolopoulos DE. A general non-adiabatic quantum instanton approximation. J Chem Phys 2020; 152:204117. [DOI: 10.1063/5.0009109] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Joseph E. Lawrence
- Department of Chemistry, University of Oxford, Physical and Theoretical Chemistry Laboratory, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - David E. Manolopoulos
- Department of Chemistry, University of Oxford, Physical and Theoretical Chemistry Laboratory, South Parks Road, Oxford OX1 3QZ, United Kingdom
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17
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Tao X, Shushkov P, Miller TF. Microcanonical rates from ring-polymer molecular dynamics: Direct-shooting, stationary-phase, and maximum-entropy approaches. J Chem Phys 2020; 152:124117. [DOI: 10.1063/1.5144307] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Affiliation(s)
- Xuecheng Tao
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Philip Shushkov
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Thomas F. Miller
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
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18
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Choudhury A, Ghosh D. Charge transfer in DHICA eumelanin-like oligomers: role of hydrogen bonds. Chem Commun (Camb) 2020; 56:10481-10484. [DOI: 10.1039/d0cc04702c] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The building blocks of eumelanin can be used as versatile material with enhanced charge transfer properties.
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Affiliation(s)
- Arpan Choudhury
- School of Chemical Science
- Indian Association for the Cultivation of Science
- Jadavpur
- India
| | - Debashree Ghosh
- School of Chemical Science
- Indian Association for the Cultivation of Science
- Jadavpur
- India
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19
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Fang W, Zarotiadis RA, Richardson JO. Revisiting nuclear tunnelling in the aqueous ferrous–ferric electron transfer. Phys Chem Chem Phys 2020; 22:10687-10698. [DOI: 10.1039/c9cp06841d] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
We find that golden-rule quantum transition-state theory predicts nearly an order of magnitude less tunnelling than some of the previous estimates. This may indicate that the spin-boson model of electron transfer is not valid in the quantum regime.
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Affiliation(s)
- Wei Fang
- Laboratory of Physical Chemistry
- ETH Zürich
- 8093 Zürich
- Switzerland
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20
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Fang W, Thapa MJ, Richardson JO. Nonadiabatic quantum transition-state theory in the golden-rule limit. II. Overcoming the pitfalls of the saddle-point and semiclassical approximations. J Chem Phys 2019; 151:214101. [DOI: 10.1063/1.5131092] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Wei Fang
- Laboratory of Physical Chemistry, ETH Zurich, 8093 Zurich, Switzerland
| | - Manish J. Thapa
- Laboratory of Physical Chemistry, ETH Zurich, 8093 Zurich, Switzerland
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21
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Pradhan B, Engelhard C, Van Mulken S, Miao X, Canters GW, Orrit M. Single electron transfer events and dynamical heterogeneity in the small protein azurin from Pseudomonas aeruginosa. Chem Sci 2019; 11:763-771. [PMID: 34123050 PMCID: PMC8146731 DOI: 10.1039/c9sc05405g] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 11/25/2019] [Indexed: 01/07/2023] Open
Abstract
Monitoring the fluorescence of single-dye-labeled azurin molecules, we observed the reaction of azurin with hexacyanoferrate under controlled redox potential yielding data on the timing of individual (forward and backward) electron transfer (ET) events. Change-point analysis of the time traces demonstrates significant fluctuations of ET rates and of mid-point potential E 0. These fluctuations are a signature of dynamical heterogeneity, here observed on a 14 kDa protein, the smallest to date. By correlating changes in forward and backward reaction rates we found that 6% of the observed change events could be explained by a change in midpoint potential, while for 25% a change of the donor-acceptor coupling could explain the data. The remaining 69% are driven by variations in complex association constants or structural changes that cause forward and back ET rates to vary independently. Thus, the observed spread in individual ET rates could be related in a unique way to variations in molecular parameters. The relevance for the understanding of metabolic processes is briefly discussed.
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Affiliation(s)
- Biswajit Pradhan
- Huygens-Kamerlingh Onnes Laboratory, Leiden University 2300 RA Leiden Netherlands
| | | | | | - Xueyan Miao
- School of Public Health, Guilin Medical University 541004 Guilin China
| | - Gerard W Canters
- Huygens-Kamerlingh Onnes Laboratory, Leiden University 2300 RA Leiden Netherlands
| | - Michel Orrit
- Huygens-Kamerlingh Onnes Laboratory, Leiden University 2300 RA Leiden Netherlands
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22
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Lawrence JE, Fletcher T, Lindoy LP, Manolopoulos DE. On the calculation of quantum mechanical electron transfer rates. J Chem Phys 2019; 151:114119. [DOI: 10.1063/1.5116800] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Joseph E. Lawrence
- Department of Chemistry, University of Oxford, Physical and Theoretical Chemistry Laboratory, South Parks Road, Oxford, OX1 3QZ, United Kingdom
| | - Theo Fletcher
- Department of Chemistry, University of Oxford, Physical and Theoretical Chemistry Laboratory, South Parks Road, Oxford, OX1 3QZ, United Kingdom
| | - Lachlan P. Lindoy
- Department of Chemistry, University of Oxford, Physical and Theoretical Chemistry Laboratory, South Parks Road, Oxford, OX1 3QZ, United Kingdom
| | - David E. Manolopoulos
- Department of Chemistry, University of Oxford, Physical and Theoretical Chemistry Laboratory, South Parks Road, Oxford, OX1 3QZ, United Kingdom
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23
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Chowdhury SN, Huo P. State dependent ring polymer molecular dynamics for investigating excited nonadiabatic dynamics. J Chem Phys 2019; 150:244102. [DOI: 10.1063/1.5096276] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Sutirtha N. Chowdhury
- Department of Chemistry, University of Rochester, 120 Trustee Road, Rochester, New York 14627, USA
| | - Pengfei Huo
- Department of Chemistry, University of Rochester, 120 Trustee Road, Rochester, New York 14627, USA
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24
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Cabral BJ. The Kohn-Sham electronic density of states of liquid HCN: Tuning a long-range corrected exchange-correlation functional for predicting electron binding energies. Chem Phys Lett 2019. [DOI: 10.1016/j.cplett.2019.03.052] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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25
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Zahler CT, Shaw BF. What Are We Missing by Not Measuring the Net Charge of Proteins? Chemistry 2019; 25:7581-7590. [PMID: 30779227 DOI: 10.1002/chem.201900178] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Indexed: 12/21/2022]
Abstract
The net electrostatic charge (Z) of a folded protein in solution represents a bird's eye view of its surface potentials-including contributions from tightly bound metal, solvent, buffer, and cosolvent ions-and remains one of its most enigmatic properties. Few tools are available to the average biochemist to rapidly and accurately measure Z at pH≠pI. Tools that have been developed more recently seem to go unnoticed. Most scientists are content with this void and estimate the net charge of a protein from its amino acid sequence, using textbook values of pKa . Thus, Z remains unmeasured for nearly all folded proteins at pH≠pI. When marveling at all that has been learned from accurately measuring the other fundamental property of a protein-its mass-one wonders: what are we missing by not measuring the net charge of folded, solvated proteins? A few big questions immediately emerge in bioinorganic chemistry. When a single electron is transferred to a metalloprotein, does the net charge of the protein change by approximately one elementary unit of charge or does charge regulation dominate, that is, do the pKa values of most ionizable residues (or just a few residues) adjust in response to (or in concert with) electron transfer? Would the free energy of charge regulation (ΔΔGz ) account for most of the outer sphere reorganization energy associated with electron transfer? Or would ΔΔGz contribute more to the redox potential? And what about metal binding itself? When an apo-metalloprotein, bearing minimal net negative charge (e.g., Z=-2.0) binds one or more metal cations, is the net charge abolished or inverted to positive? Or do metalloproteins regulate net charge when coordinating metal ions? The author's group has recently dusted off a relatively obscure tool-the "protein charge ladder"-and used it to begin to answer these basic questions.
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Affiliation(s)
- Collin T Zahler
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, 76706, USA
| | - Bryan F Shaw
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, 76706, USA
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26
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Thapa MJ, Fang W, Richardson JO. Nonadiabatic quantum transition-state theory in the golden-rule limit. I. Theory and application to model systems. J Chem Phys 2019; 150:104107. [DOI: 10.1063/1.5081108] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Manish J. Thapa
- Laboratory of Physical Chemistry, ETH Zürich, 8093 Zürich, Switzerland
| | - Wei Fang
- Laboratory of Physical Chemistry, ETH Zürich, 8093 Zürich, Switzerland
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27
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Tao X, Shushkov P, Miller TF. Simple Flux-Side Formulation of State-Resolved Thermal Reaction Rates for Ring-Polymer Surface Hopping. J Phys Chem A 2019; 123:3013-3020. [DOI: 10.1021/acs.jpca.9b00877] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Xuecheng Tao
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Philip Shushkov
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
| | - Thomas F. Miller
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, United States
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28
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Takematsu K, Pospíšil P, Pižl M, Towrie M, Heyda J, Záliš S, Kaiser JT, Winkler JR, Gray HB, Vlček A. Hole Hopping Across a Protein-Protein Interface. J Phys Chem B 2019; 123:1578-1591. [PMID: 30673250 PMCID: PMC6384139 DOI: 10.1021/acs.jpcb.8b11982] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have investigated photoinduced hole hopping in a Pseudomonas aeruginosa azurin mutant Re126WWCuI, where two adjacent tryptophan residues (W124 and W122) are inserted between the CuI center and a Re photosensitizer coordinated to a H126 imidazole (Re = ReI(H126)(CO)3(dmp)+, dmp = 4,7-dimethyl-1,10-phenanthroline). Optical excitation of this mutant in aqueous media (≤40 μM) triggers 70 ns electron transport over 23 Å, yielding a long-lived (120 μs) ReI(H126)(CO)3(dmp•-)WWCuII product. The Re126FWCuI mutant (F124, W122) is not redox-active under these conditions. Upon increasing the concentration to 0.2-2 mM, {Re126WWCuI}2 and {Re126FWCuI}2 are formed with the dmp ligand of the Re photooxidant of one molecule in close contact (3.8 Å) with the W122' indole on the neighboring chain. In addition, {Re126WWCuI}2 contains an interfacial tryptophan quadruplex of four indoles (3.3-3.7 Å apart). In both mutants, dimerization opens an intermolecular W122' → //*Re ET channel (// denotes the protein interface, *Re is the optically excited sensitizer). Excited-state relaxation and ET occur together in two steps (time constants of ∼600 ps and ∼8 ns) that lead to a charge-separated state containing a Re(H126)(CO)3(dmp•-)//(W122•+)' unit; then (CuI)' is oxidized intramolecularly (60-90 ns) by (W122•+)', forming ReI(H126)(CO)3(dmp•-)WWCuI//(CuII)'. The photocycle is closed by ∼1.6 μs ReI(H126)(CO)3(dmp•-) → //(CuII)' back ET that occurs over 12 Å, in contrast to the 23 Å, 120 μs step in Re126WWCuI. Importantly, dimerization makes Re126FWCuI photoreactive and, as in the case of {Re126WWCuI}2, channels the photoproduced "hole" to the molecule that was not initially photoexcited, thereby shortening the lifetime of ReI(H126)(CO)3(dmp•-)//CuII. Although two adjacent W124 and W122 indoles dramatically enhance CuI → *Re intramolecular multistep ET, the tryptophan quadruplex in {Re126WWCuI}2 does not accelerate intermolecular electron transport; instead, it acts as a hole storage and crossover unit between inter- and intramolecular ET pathways. Irradiation of {Re126WWCuII}2 or {Re126FWCuII}2 also triggers intermolecular W122' → //*Re ET, and the Re(H126)(CO)3(dmp•-)//(W122•+)' charge-separated state decays to the ground state by ∼50 ns ReI(H126)(CO)3(dmp•-)+ → //(W122•+)' intermolecular charge recombination. Our findings shed light on the factors that control interfacial hole/electron hopping in protein complexes and on the role of aromatic amino acids in accelerating long-range electron transport.
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Affiliation(s)
- Kana Takematsu
- Department of Chemistry, Bowdoin College, Brunswick, ME 04011, USA
| | - Petr Pospíšil
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, CZ-182 23 Prague, Czech Republic
| | - Martin Pižl
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, CZ-182 23 Prague, Czech Republic
- University of Chemistry and Technology, Prague, Technická 5, CZ-166 28 Prague, Czech Republic
| | - Michael Towrie
- Central Laser Facility, Research Complex at Harwell, Science and Technology Facilities Council, Rutherford Appleton Laboratory, Harwell Oxford, Didcot, Oxfordshire, OX11 0FA, UK
| | - Jan Heyda
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, CZ-182 23 Prague, Czech Republic
- University of Chemistry and Technology, Prague, Technická 5, CZ-166 28 Prague, Czech Republic
| | - Stanislav Záliš
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, CZ-182 23 Prague, Czech Republic
| | - Jens T. Kaiser
- Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA
| | - Jay R. Winkler
- Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA
| | - Harry B. Gray
- Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA
| | - Antonín Vlček
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejškova 3, CZ-182 23 Prague, Czech Republic
- Queen Mary University of London, School of Biological and Chemical Sciences, Mile End Road, London E1 4NS, United Kingdom
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29
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Marazzi M, Gattuso H, Fumanal M, Daniel C, Monari A. Charge-Transfer versus Charge-Separated Triplet Excited States of [Re I (dmp)(CO) 3 (His124)(Trp122)] + in Water and in Modified Pseudomonas aeruginosa Azurin Protein. Chemistry 2019; 25:2519-2526. [PMID: 30379366 DOI: 10.1002/chem.201803685] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 10/17/2018] [Indexed: 12/20/2022]
Abstract
A computational investigation of the triplet excited states of a rhenium complex electronically coupled with a tryptophan side chain and bound to an azurin protein is presented. In particular, by using high-level molecular modeling, evidence is provided for how the electronic properties of the excited-state manifolds strongly depend on coupling with the environment. Indeed, only upon explicitly taking into account the protein environment can two stable triplet states of metal-to-ligand charge transfer or charge-separated nature be recovered. In addition, it is also demonstrated how the rhenium complex plus tryptophan system in an aqueous environment experiences too much flexibility, which prevents the two chromophores from being electronically coupled. This occurrence disables the formation of a charge-separated state. The successful strategy requires a multiscale approach of combining molecular dynamics and quantum chemistry. In this context, the strategy used to parameterize the force fields for the electronic triplet states of the metal complex is also presented.
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Affiliation(s)
- Marco Marazzi
- Université de Lorraine, CNRS, LPCT UMR 7019, Boulevard des Aiguillettes, Vandoeuvre-lès-Nancy, 54000, Nancy, France.,Departamento de Química, Centro de Investigacíon en Síntesis Química (CISQ), Universidad de La Rioja, Madre de Dios, 53, 26006, Logroño, Spain
| | - Hugo Gattuso
- Université de Lorraine, CNRS, LPCT UMR 7019, Boulevard des Aiguillettes, Vandoeuvre-lès-Nancy, 54000, Nancy, France
| | - Maria Fumanal
- Laboratoire de Chimie Quantique, Institut de Chimie Strasbourg, UMR-7177, CNRS/Université de Strasbourg, 1 Rue Blaise Pascal BP 296/R8, 67008, Strasbourg, France
| | - Chantal Daniel
- Laboratoire de Chimie Quantique, Institut de Chimie Strasbourg, UMR-7177, CNRS/Université de Strasbourg, 1 Rue Blaise Pascal BP 296/R8, 67008, Strasbourg, France
| | - Antonio Monari
- Université de Lorraine, CNRS, LPCT UMR 7019, Boulevard des Aiguillettes, Vandoeuvre-lès-Nancy, 54000, Nancy, France
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30
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Skourtis SS, Beratan DN. Editorial overview: Biological pathways for electrons, protons and photo-excitations. Curr Opin Chem Biol 2018; 47:A1-A3. [PMID: 30318402 DOI: 10.1016/j.cbpa.2018.09.023] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Affiliation(s)
- Spiros S Skourtis
- Department of Physics, University of Cyprus, P.O. Box 20537, 1678 Nicosia, Cyprus.
| | - David N Beratan
- Departments of Chemistry and Physics, Duke University, Durham, NC 27708, USA; Department of Biochemistry, Duke University, Durham, NC 27710, USA.
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31
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Romero-Muñiz C, Ortega M, Vilhena JG, Díez-Pérez I, Cuevas JC, Pérez R, Zotti LA. Ab initio electronic structure calculations of entire blue copper azurins. Phys Chem Chem Phys 2018; 20:30392-30402. [DOI: 10.1039/c8cp06862c] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
We present a theoretical study of the blue-copper azurin extracted from Pseudomonas aeruginosa and several of its single amino acid mutants.
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Affiliation(s)
- Carlos Romero-Muñiz
- Departamento de Física Teórica de la Materia Condensada
- Universidad Autónoma de Madrid
- E-28049 Madrid
- Spain
| | - María Ortega
- Departamento de Física Teórica de la Materia Condensada
- Universidad Autónoma de Madrid
- E-28049 Madrid
- Spain
| | - J. G. Vilhena
- Departamento de Física Teórica de la Materia Condensada
- Universidad Autónoma de Madrid
- E-28049 Madrid
- Spain
- Department of Physics
| | - I. Díez-Pérez
- Department of Materials Science and Physical Chemistry & Institute of Theoretical and Computational Chemistry (IQTCUB)
- University of Barcelona
- Barcelona 08028
- Spain
- Department of Chemistry
| | - Juan Carlos Cuevas
- Departamento de Física Teórica de la Materia Condensada
- Universidad Autónoma de Madrid
- E-28049 Madrid
- Spain
- Condensed Matter Physics Center (IFIMAC)
| | - Rubén Pérez
- Departamento de Física Teórica de la Materia Condensada
- Universidad Autónoma de Madrid
- E-28049 Madrid
- Spain
- Condensed Matter Physics Center (IFIMAC)
| | - Linda A. Zotti
- Departamento de Física Teórica de la Materia Condensada
- Universidad Autónoma de Madrid
- E-28049 Madrid
- Spain
- Condensed Matter Physics Center (IFIMAC)
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