1
|
Migliore A, Corni S, Agostini A, Carbonera D. Unraveling the electronic origin of a special feature in the triplet-minus-singlet spectra of carotenoids in natural photosystems. Phys Chem Chem Phys 2023; 25:28998-29016. [PMID: 37859550 DOI: 10.1039/d3cp03836j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2023]
Abstract
The influence of carotenoid triplet states on the Qy electronic transitions of chlorophylls has been observed in experiments on light-harvesting complexes over the past three decades, but the interpretation of the resulting spectral feature in the triplet minus singlet (T-S) absorption spectra of photosystems is still debated, as the physical-chemical explanation of this feature has been elusive. Here, we resolve this debate, by explaining the T-S spectra of pigment complexes over the Qy-band spectral region through a comparative study of chlorophyll-carotenoid model dyads and larger pigment complexes from the main light harvesting complex of higher plants (LHCII). This goal is achieved by combining state-of-the-art time-dependent density functional theory with analysis of the relationship between electronic properties and nuclear structure, and by comparison to the experiment. We find that the special signature in the T-S spectra of both model and natural photosystems is determined by singlet-like triplet excitations that can be described as effective singlet excitations on chlorophylls influenced by a stable electronic triplet on the carotenoid. The comparison with earlier experiments on different light-harvesting complexes confirms our theoretical interpretation of the T-S spectra in the Qy spectral region. Our results indicate an important role for the chlorophyll-carotenoid electronic coupling, which is also responsible for the fast triplet-triplet energy transfer, suggesting a fast trapping of the triplet into the relaxed carotenoid structure. The gained understanding of the interplay between the electronic and nuclear structures is potentially informative for future studies of the mechanism of photoprotection by carotenoids.
Collapse
Affiliation(s)
- Agostino Migliore
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131 Padova, Italy.
| | - Stefano Corni
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131 Padova, Italy.
- CNR Institute of Nanoscience, 41125 Modena, Italy
| | - Alessandro Agostini
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131 Padova, Italy.
| | - Donatella Carbonera
- Department of Chemical Sciences, University of Padova, Via Marzolo 1, 35131 Padova, Italy.
| |
Collapse
|
2
|
Takatsuka K, Arasaki Y. Electronic-state chaos, intramolecular electronic energy redistribution, and chemical bonding in persisting multidimensional nonadiabatic systems. J Chem Phys 2023; 159:074110. [PMID: 37602802 DOI: 10.1063/5.0159178] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2023] [Accepted: 08/03/2023] [Indexed: 08/22/2023] Open
Abstract
We study the chaotic, huge fluctuation of electronic state, resultant intramolecular energy redistribution, and strong chemical bonding surviving the fluctuation with exceedingly long lifetimes of highly excited boron clusters. Those excited states constitute densely quasi-degenerate state manifolds. The huge fluctuation is induced by persisting multidimensional nonadiabatic transitions among the states in the manifold. We clarify the mechanism of their coexistence and its physical significance. In doing so, we concentrate on two theoretical aspects. One is quantum chaos and energy randomization, which are to be directly extracted from the properties of the total electronic wavefunctions. The present dynamical chaos takes place through frequent transitions from adiabatic states to others, thereby making it very rare for the system to find dissociation channels. This phenomenon leads to the concept of what we call intramolecular nonadiabatic electronic-energy redistribution, which is an electronic-state generaliztion of the notion of intramolecular vibrational energy redistribution. The other aspect is about the peculiar chemical bonding. We investigate it with the energy natural orbitals (ENOs) to see what kind of theoretical structures lie behind the huge fluctuation. The ENO energy levels representing the highly excited states under study appear to have four robust layers. We show that the energy layers responsible for chaotic dynamics and those for chemical bonding are widely separated from each other, and only when an event of what we call "inter-layer crossing" happens to burst can the destruction of these robust energy layers occur, resulting in molecular dissociation. This crossing event happens only rarely because of the large energy gaps between the ENO layers. It is shown that the layers of high energy composed of complex-valued ENOs induce the turbulent flow of electrons and electronic-energy in the cluster. In addition, the random and fast time-oscillations of those high energy ENOs serve as a random force on the nuclear dynamics, which can work to prevent a concentration of high nuclear kinetic energy in the dissociation channels.
Collapse
Affiliation(s)
- Kazuo Takatsuka
- Fukui Institute for Fundamental Chemistry, Kyoto University, 606-8103 Kyoto, Japan
| | - Yasuki Arasaki
- Fukui Institute for Fundamental Chemistry, Kyoto University, 606-8103 Kyoto, Japan
| |
Collapse
|
3
|
Yasuda S, Hayashi T, Murata T, Kinoshita M. Physical pictures of rotation mechanisms of F 1- and V 1-ATPases: Leading roles of translational, configurational entropy of water. Front Mol Biosci 2023; 10:1159603. [PMID: 37363397 PMCID: PMC10288849 DOI: 10.3389/fmolb.2023.1159603] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 05/25/2023] [Indexed: 06/28/2023] Open
Abstract
We aim to develop a theory based on a concept other than the chemo-mechanical coupling (transduction of chemical free energy of ATP to mechanical work) for an ATP-driven protein complex. Experimental results conflicting with the chemo-mechanical coupling have recently emerged. We claim that the system comprises not only the protein complex but also the aqueous solution in which the protein complex is immersed and the system performs essentially no mechanical work. We perform statistical-mechanical analyses on V1-ATPase (the A3B3DF complex) for which crystal structures in more different states are experimentally known than for F1-ATPase (the α3β3γ complex). Molecular and atomistic models are employed for water and the structure of V1-ATPase, respectively. The entropy originating from the translational displacement of water molecules in the system is treated as a pivotal factor. We find that the packing structure of the catalytic dwell state of V1-ATPase is constructed by the interplay of ATP bindings to two of the A subunits and incorporation of the DF subunit. The packing structure represents the nonuniformity with respect to the closeness of packing of the atoms in constituent proteins and protein interfaces. The physical picture of rotation mechanism of F1-ATPase recently constructed by Kinoshita is examined, and common points and differences between F1- and V1-ATPases are revealed. An ATP hydrolysis cycle comprises binding of ATP to the protein complex, hydrolysis of ATP into ADP and Pi in it, and dissociation of ADP and Pi from it. During each cycle, the chemical compounds bound to the three A or β subunits and the packing structure of the A3B3 or α3β3 complex are sequentially changed, which induces the unidirectional rotation of the central shaft for retaining the packing structure of the A3B3DF or α3β3γ complex stabilized for almost maximizing the water entropy. The torque driving the rotation is generated by water with no input of chemical free energy. The presence of ATP is indispensable as a trigger of the torque generation. The ATP hydrolysis or synthesis reaction is tightly coupled to the rotation of the central shaft in the normal or inverse direction through the water-entropy effect.
Collapse
Affiliation(s)
- Satoshi Yasuda
- Department of Chemistry, Graduate School of Science, Chiba University, Chiba, Japan
- Department of Quantum Life Science, Graduate School of Science, Chiba University, Chiba, Japan
- Membrane Protein Research and Molecular Chirality Research Centers, Chiba University, Chiba, Japan
| | - Tomohiko Hayashi
- Interdisciplinary Program of Biomedical Engineering, Assistive Technology and Art and Sports Sciences, Faculty of Engineering, Niigata University, Niigata, Japan
- Institute of Advanced Energy, Kyoto University, Kyoto, Japan
| | - Takeshi Murata
- Department of Chemistry, Graduate School of Science, Chiba University, Chiba, Japan
- Department of Quantum Life Science, Graduate School of Science, Chiba University, Chiba, Japan
- Membrane Protein Research and Molecular Chirality Research Centers, Chiba University, Chiba, Japan
| | - Masahiro Kinoshita
- Department of Chemistry, Graduate School of Science, Chiba University, Chiba, Japan
- Institute of Advanced Energy, Kyoto University, Kyoto, Japan
- Center for the Promotion of Interdisciplinary Education and Research, Kyoto University, Kyoto, Japan
| |
Collapse
|
4
|
Takatsuka K. Quantum Chaos in the Dynamics of Molecules. ENTROPY (BASEL, SWITZERLAND) 2022; 25:63. [PMID: 36673204 PMCID: PMC9857761 DOI: 10.3390/e25010063] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 12/22/2022] [Accepted: 12/22/2022] [Indexed: 06/17/2023]
Abstract
Quantum chaos is reviewed from the viewpoint of "what is molecule?", particularly placing emphasis on their dynamics. Molecules are composed of heavy nuclei and light electrons, and thereby the very basic molecular theory due to Born and Oppenheimer gives a view that quantum electronic states provide potential functions working on nuclei, which in turn are often treated classically or semiclassically. Therefore, the classic study of chaos in molecular science began with those nuclear dynamics particularly about the vibrational energy randomization within a molecule. Statistical laws in probabilities and rates of chemical reactions even for small molecules of several atoms are among the chemical phenomena requiring the notion of chaos. Particularly the dynamics behind unimolecular decomposition are referred to as Intra-molecular Vibrational energy Redistribution (IVR). Semiclassical mechanics is also one of the main research fields of quantum chaos. We herein demonstrate chaos that appears only in semiclassical and full quantum dynamics. A fundamental phenomenon possibly giving birth to quantum chaos is "bifurcation and merging" of quantum wavepackets, rather than "stretching and folding" of the baker's transformation and the horseshoe map as a geometrical foundation of classical chaos. Such wavepacket bifurcation and merging are indeed experimentally measurable as we showed before in the series of studies on real-time probing of nonadiabatic chemical reactions. After tracking these aspects of molecular chaos, we will explore quantum chaos found in nonadiabatic electron wavepacket dynamics, which emerges in the realm far beyond the Born-Oppenheimer paradigm. In this class of chaos, we propose a notion of Intra-molecular Nonadiabatic Electronic Energy Redistribution (INEER), which is a consequence of the chaotic fluxes of electrons and energy within a molecule.
Collapse
Affiliation(s)
- Kazuo Takatsuka
- Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan
| |
Collapse
|
5
|
Helmer N, Wolf S, Stock G. Energy Transport and Its Function in Heptahelical Transmembrane Proteins. J Phys Chem B 2022; 126:8735-8746. [PMID: 36261792 DOI: 10.1021/acs.jpcb.2c05892] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Photoproteins such as bacteriorhodopsin (bR) and rhodopsin (Rho) need to effectively dissipate photoinduced excess energy to prevent themselves from damage. Another well-studied seven transmembrane (TM) helices protein is the β2 adrenergic receptor (β2AR), a G protein-coupled receptor for which energy dissipation paths have been linked with allosteric communication. To study the vibrational energy transport in the active and inactive states of these proteins, a master equation approach [J. Chem. Phys.2020, 152, 045103] is employed, which uses scaling rules that allow us to calculate energy transport rates solely based on the protein structure. Despite their overall structural similarity, the three 7TM proteins reveal quite different strategies to redistribute excess energy. While bR quickly removes the energy using the TM7 helix as a "lightning rod", Rho exhibits a rather poor energy dissipation, which might eventually require the hydrolysis of the Schiff base between the protein and the retinal chromophore to prevent overheating. Heating the ligand adrenaline of β2AR, the resulting energy transport network of the protein is found to change significantly upon switching from the active state to the inactive state. While the energy flow may highlight aspects of the inter-residue couplings of β2AR, it seems not particularly suited to explain allosteric phenomena.
Collapse
Affiliation(s)
- Nadja Helmer
- Biomolecular Dynamics, Institute of Physics, University of Freiburg, 79104Freiburg, Germany
| | - Steffen Wolf
- Biomolecular Dynamics, Institute of Physics, University of Freiburg, 79104Freiburg, Germany
| | - Gerhard Stock
- Biomolecular Dynamics, Institute of Physics, University of Freiburg, 79104Freiburg, Germany
| |
Collapse
|
6
|
Li H, Wu S, Ma A. Origin of Protein Quake: Energy Waves Conducted by a Precise Mechanical Machine. J Chem Theory Comput 2022; 18:5692-5702. [PMID: 35951409 DOI: 10.1021/acs.jctc.2c00514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A long-standing challenge in protein biophysics is to understand protein quake in myoglobin─the structural dynamics responsible for redistributing the excess heme energy after photolysis. Despite extensive efforts, the molecular mechanism of this process remains elusive. Using the energy flow theory, we uncovered a fundamental new phenomenon: the heme energy is redistributed by sinusoidal waves with a ubiquitous fundamental frequency and two overtones. The energy waves emanate from the heme into the myoglobin backbone via a conduit of five consecutive dihedrals of the proximal histidine and then travel quickly along the backbone to reach sidechains across the protein. This mechanism is far more effective than the diffusion-based mechanism from previous studies because waves are systematic while diffusion is random. To propagate energy waves, coordinates must cooperate, resulting in collective modes that are singular vectors of the generalized work functional. These modes show task partitioning: a handful of high-energy modes generate large-scale breathing motion, which loosens up the protein matrix to enable hundreds of low-energy vibrational modes for energy transduction.
Collapse
Affiliation(s)
- Huiyu Li
- Richard Loan and Hill Department of Biomedical Engineering, The University of Illinois at Chicago, 851 South Morgan Street, Chicago, Illinois 60607, United States
| | - Shanshan Wu
- Richard Loan and Hill Department of Biomedical Engineering, The University of Illinois at Chicago, 851 South Morgan Street, Chicago, Illinois 60607, United States
| | - Ao Ma
- Richard Loan and Hill Department of Biomedical Engineering, The University of Illinois at Chicago, 851 South Morgan Street, Chicago, Illinois 60607, United States
| |
Collapse
|
7
|
Löffler JG, Deniz E, Feid C, Franz VG, Bredenbeck J. Versatile Vibrational Energy Sensors for Proteins. Angew Chem Int Ed Engl 2022; 61:e202200648. [PMID: 35226765 PMCID: PMC9401566 DOI: 10.1002/anie.202200648] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Indexed: 11/10/2022]
Abstract
Vibrational energy transfer (VET) is emerging as key mechanism for protein functions, possibly playing an important role for energy dissipation, allosteric regulation, and enzyme catalysis. A deep understanding of VET is required to elucidate its role in such processes. Ultrafast VIS-pump/IR-probe spectroscopy can detect pathways of VET in proteins. However, the requirement of having a VET donor and a VET sensor installed simultaneously limits the possible target proteins and sites; to increase their number we compare six IR labels regarding their utility as VET sensors. We compare these labels in terms of their FTIR, and VET signature in VET donor-sensor dipeptides in different solvents. Furthermore, we incorporated four of these labels in PDZ3 to assess their capabilities in more complex systems. Our results show that different IR labels can be used interchangeably, allowing for free choice of the right label depending on the system under investigation and the methods available.
Collapse
Affiliation(s)
- Jan G. Löffler
- Institute of BiophysicsGoethe University FrankfurtMax-von-Laue-Straße 160438Frankfurt (Main)Germany
| | - Erhan Deniz
- Institute of BiophysicsGoethe University FrankfurtMax-von-Laue-Straße 160438Frankfurt (Main)Germany
| | - Carolin Feid
- Institute of BiophysicsGoethe University FrankfurtMax-von-Laue-Straße 160438Frankfurt (Main)Germany
| | - Valentin G. Franz
- Institute of BiophysicsGoethe University FrankfurtMax-von-Laue-Straße 160438Frankfurt (Main)Germany
| | - Jens Bredenbeck
- Institute of BiophysicsGoethe University FrankfurtMax-von-Laue-Straße 160438Frankfurt (Main)Germany
| |
Collapse
|
8
|
Hacisuleyman A, Erman B. Information Flow and Allosteric Communication in Proteins. J Chem Phys 2022; 156:185101. [DOI: 10.1063/5.0088522] [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
Based on Schreiber's work on transfer entropy, a molecular theory of nonlinear information transfer in proteins is developed. The joint distribution function for residue fluctuations is expressed in terms of tensor Hermite polynomials which conveniently separate harmonic and nonlinear contributions to information transfer. The harmonic part of information transfer is expressed as the difference between time dependent and independent mutual information. Third order nonlinearities are discussed in detail. Amount and speed of information transfer between residues, important for understanding allosteric activity in proteins, are discussed. While mutual information shows the maximum amount of information that may be transferred between two residues, it does not explain the actual amount of transfer nor the transfer rate of information. For this, dynamic equations of the system are needed. The solution of the Langevin equation and molecular dynamics trajectories are used in the present work for this purpose. Allosteric communication in Human NAD-dependent isocitrate dehydrogenase is studied as an example. Calculations show that several paths contribute collectively to information transfer. Important residues on these paths are identified. Time resolved information transfer between these residues, their amplitudes and transfer rates, which are in agreement with time resolved ultraviolet resonance Raman measurements in general, are estimated. Estimated transfer rates are in the order of 1-20 megabits per second. Information transfer from third order contributions are one to two orders of magnitude smaller than the harmonic terms, showing that harmonic analysis is a good approximation to information transfer.
Collapse
Affiliation(s)
- Aysima Hacisuleyman
- Chemical and Biological Engineering, Koc University College of Engineering, Turkey
| | - Burak Erman
- College of Engineering, Koc University, Turkey
| |
Collapse
|
9
|
Yamato T, Wang T, Sugiura W, Laprévote O, Katagiri T. Computational Study on the Thermal Conductivity of a Protein. J Phys Chem B 2022; 126:3029-3036. [PMID: 35416670 DOI: 10.1021/acs.jpcb.2c00958] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Protein molecules are thermally fluctuating and tightly packed amino acid residues strongly interact with each other. Such interactions are characterized in terms of heat current at the atomic level. We calculated the thermal conductivity of a small globular protein, villin headpiece subdomain, based on the linear response theory using equilibrium molecular dynamics simulation. The value of its thermal conductivity was 0.3 ± 0.01 [W m-1 K-1], which is in good agreement with experimental and computational studies on the other proteins in the literature. Heat current along the main chain was dominated by local vibrations in the polypeptide bonds, with amide I, II, III, and A bands on the Fourier transform of the heat current autocorrelation function.
Collapse
Affiliation(s)
- Takahisa Yamato
- Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Tingting Wang
- Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Wataru Sugiura
- Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Olivier Laprévote
- Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8602, Japan
| | - Takahiro Katagiri
- Information Technology Center, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan
| |
Collapse
|
10
|
Löffler JG, Deniz E, Feid C, Franz VG, Bredenbeck J. Versatile Vibrational Energy Sensors for Proteins. Angew Chem Int Ed Engl 2022. [DOI: 10.1002/ange.202200648] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Jan G. Löffler
- Institute of Biophysics Goethe University Frankfurt Max-von-Laue-Straße 1 60438 Frankfurt (Main) Germany
| | - Erhan Deniz
- Institute of Biophysics Goethe University Frankfurt Max-von-Laue-Straße 1 60438 Frankfurt (Main) Germany
| | - Carolin Feid
- Institute of Biophysics Goethe University Frankfurt Max-von-Laue-Straße 1 60438 Frankfurt (Main) Germany
| | - Valentin G. Franz
- Institute of Biophysics Goethe University Frankfurt Max-von-Laue-Straße 1 60438 Frankfurt (Main) Germany
| | - Jens Bredenbeck
- Institute of Biophysics Goethe University Frankfurt Max-von-Laue-Straße 1 60438 Frankfurt (Main) Germany
| |
Collapse
|
11
|
Gnanasekaran R, Xu Y. Understanding the Energetic Components Influencing the Thermodynamic Quantities of Carbonic Anhydrase Protein upon Ligand Binding. ChemistrySelect 2022. [DOI: 10.1002/slct.202200024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | - Yao Xu
- Warshel Institute for Computational Biology School of Life and Health Sciences The Chinese University of Hong Kong (Shenzhen) Shenzhen 518172 P. R. China
- School of Life Science University of Science and Technology of China Hefei 230026 P. R. China
| |
Collapse
|
12
|
Wu S, Ma A. Mechanism for the rare fluctuation that powers protein conformational change. J Chem Phys 2022; 156:054119. [PMID: 35135246 PMCID: PMC8824576 DOI: 10.1063/5.0077444] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 01/17/2022] [Indexed: 11/14/2022] Open
Abstract
Most functional processes of biomolecules are rare events. Key to a rare event is the rare fluctuation that enables the energy activation process that precedes and powers crossing of the activation barrier. However, the physical nature of this rare fluctuation and how it enables energy activation and subsequently barrier crossing are unknown. We developed a novel metric, the reaction capacity pC, that rigorously defines the beginning and parameterizes the progress of energy activation. This enabled us to identify the rare fluctuation as a special phase-space condition that is necessary and sufficient for initiating systematic energy flow from the non-reaction coordinates into the reaction coordinates. The energy activation of a prototype biomolecular isomerization reaction is dominated by kinetic energy transferring into and accumulating in the reaction coordinates, administered by inertial forces alone. This mechanism for energy activation is fundamentally different from the mechanism suggested by Kramers theory.
Collapse
Affiliation(s)
- Shanshan Wu
- Richard Loan and Hill Department of Biomedical Engineering, The University of Illinois at Chicago, 851 South Morgan Street, Chicago, Illinois 60607, USA
| | - Ao Ma
- Richard Loan and Hill Department of Biomedical Engineering, The University of Illinois at Chicago, 851 South Morgan Street, Chicago, Illinois 60607, USA
| |
Collapse
|
13
|
Revuelta F, Benito RM, Borondo F. Identification of the invariant manifolds of the LiCN molecule using Lagrangian descriptors. Phys Rev E 2021; 104:044210. [PMID: 34781455 DOI: 10.1103/physreve.104.044210] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 09/28/2021] [Indexed: 11/07/2022]
Abstract
In this paper, we apply Lagrangian descriptors to study the invariant manifolds that emerge from the top of two barriers existing in the LiCN⇌LiNC isomerization reaction. We demonstrate that the integration times must be large enough compared with the characteristic stability exponents of the periodic orbit under study. The invariant manifolds manifest as singularities in the Lagrangian descriptors. Furthermore, we develop an equivalent potential energy surface with 2 degrees of freedom, which reproduces with a great accuracy previous results [F. Revuelta, R. M. Benito, and F. Borondo, Phys. Rev. E 99, 032221 (2019)2470-004510.1103/PhysRevE.99.032221]. This surface allows the use of an adiabatic approximation to develop a more simplified potential energy with solely 1 degree of freedom. The reduced dimensional model is still able to qualitatively describe the results observed with the original 2-degrees-of-freedom potential energy landscape. Likewise, it is also used to study in a more simple manner the influence on the Lagrangian descriptors of a bifurcation, where some of the previous invariant manifolds emerge, even before it takes place.
Collapse
Affiliation(s)
- F Revuelta
- Grupo de Sistemas Complejos, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Avenida Puerta de Hierro 2-4, 28040 Madrid, Spain
| | - R M Benito
- Grupo de Sistemas Complejos, Escuela Técnica Superior de Ingeniería Agronómica, Alimentaria y de Biosistemas, Universidad Politécnica de Madrid, Avenida Puerta de Hierro 2-4, 28040 Madrid, Spain
| | - F Borondo
- Instituto de Ciencias Matemáticas (ICMAT), Cantoblanco, 28049 Madrid, Spain.,Departamento de Química, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
| |
Collapse
|
14
|
Through bonds or contacts? Mapping protein vibrational energy transfer using non-canonical amino acids. Nat Commun 2021; 12:3284. [PMID: 34078890 PMCID: PMC8172543 DOI: 10.1038/s41467-021-23591-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 05/06/2021] [Indexed: 11/08/2022] Open
Abstract
Vibrational energy transfer (VET) is essential for protein function. It is responsible for efficient energy dissipation in reaction sites, and has been linked to pathways of allosteric communication. While it is understood that VET occurs via backbone as well as via non-covalent contacts, little is known about the competition of these two transport channels, which determines the VET pathways. To tackle this problem, we equipped the β-hairpin fold of a tryptophan zipper with pairs of non-canonical amino acids, one serving as a VET injector and one as a VET sensor in a femtosecond pump probe experiment. Accompanying extensive non-equilibrium molecular dynamics simulations combined with a master equation analysis unravel the VET pathways. Our joint experimental/computational endeavor reveals the efficiency of backbone vs. contact transport, showing that even if cutting short backbone stretches of only 3 to 4 amino acids in a protein, hydrogen bonds are the dominant VET pathway.
Collapse
|
15
|
Zhang X, Vázquez SA, Harvey JN. Vibrational Energy Relaxation of Deuterium Fluoride in d-Dichloromethane: Insights from Different Potentials. J Chem Theory Comput 2021; 17:1277-1289. [PMID: 33550803 DOI: 10.1021/acs.jctc.0c01059] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Vibrationally excited deuterium fluoride (DF) formed by fluorine atom reaction with a solvent was found (Science, 2015, 347, 530) to relax rapidly (less than 10 ps) in acetonitrile-d3 (CD3CN) and dichloromethane-d2 (CD2Cl2). However, insights into how CD2Cl2 facilitates this energy relaxation have so far been lacking, given the weak interaction between DF and a single CD2Cl2. In this work, we report the results of reactive simulations with a two-state reactive empirical valence bond (EVB) potential to study the energy deposited into nascent DF after transition-state passage and of nonequilibrium molecular dynamics simulations using multiple different potential energy functions to model the relaxation dynamics. For these second simulations, we used the standard Merck molecular force field (MMFF) potential, an MMFF-based covalent-ionic empirical valence bond (EVB) potential (EVBCI), a newly developed potential [referred to as MMFF(rDF)] which extends upon the MMFF potential by making the DF/CD2Cl2 interaction depend on the value of the D-F bond stretching coordinate and by taking the anisotropic charge distribution of the solvent molecules into account, the polarizable atomic multipole optimized energetics for biomolecular applications (AMOEBA) potential, and the quantum mechanics/molecular mechanics (QM/MM) potential. The relaxation is revealed to be highly sensitive to the potential used. Neither standard MMFF nor EVBCI reproduces the experimentally observed rapid relaxation dynamics, and they also fail to provide a good description of the interaction potential between DF and CD2Cl2 as calculated using CCSD(T)-F12. This is attributed to the use of a point-charge model for the solute and to failing to model the anisotropic electrostatic properties of CD2Cl2. The MMFF(rDF), AMOEBA, and QM/MM potentials all reproduce the CCSD(T)-F12 two-body DF---CD2Cl2 interaction potential rather well but only with the QM/MM approach is fast vibrational relaxation obtained (lifetimes of ∼288, ∼186, and ∼8 ps, respectively), which we attribute to differences in the solute-solvent local structure. With QM/MM, a unique "many-body" interaction pattern in which DF is in close contact with two solvent Cl atoms and more than three solvent D atoms is found, but this structure is not seen with other potentials. The QM/MM dynamics also display enhanced solute-solvent interactions with vibrationally excited DF that induce a DF band redshift and hence a resonant overlap with solvent C-D modes, which facilitate the intermolecular energy transfer. Our work also suggests that potentials used to model energy relaxation need to capture the fine structure of solute-solvent interactions and not just the two-body part.
Collapse
Affiliation(s)
- Xiaoyong Zhang
- Department of Chemistry and Division of Quantum Chemistry and Physical Chemistry, KU Leuven, Celestijnenlaan 200F, Leuven B-3001, Belgium
| | - Saulo A Vázquez
- Departamento de Química Física, Facultade de Química, Universidade de Santiago de Compostela, Santiago de Compostela 15782, Spain
| | - Jeremy N Harvey
- Department of Chemistry and Division of Quantum Chemistry and Physical Chemistry, KU Leuven, Celestijnenlaan 200F, Leuven B-3001, Belgium
| |
Collapse
|
16
|
Acceleration of catalysis in dihydrofolate reductase by transient, site-specific photothermal excitation. Proc Natl Acad Sci U S A 2021; 118:2014592118. [PMID: 33468677 DOI: 10.1073/pnas.2014592118] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We have studied the role of protein dynamics in chemical catalysis in the enzyme dihydrofolate reductase (DHFR), using a pump-probe method that employs pulsed-laser photothermal heating of a gold nanoparticle (AuNP) to directly excite a local region of the protein structure and transient absorbance to probe the effect on enzyme activity. Enzyme activity is accelerated by pulsed-laser excitation when the AuNP is attached close to a network of coupled motions in DHFR (on the FG loop, containing residues 116-132, or on a nearby alpha helix). No rate acceleration is observed when the AuNP is attached away from the network (distal mutant and His-tagged mutant) with pulsed excitation, or for any attachment site with continuous wave excitation. We interpret these results within an energy landscape model in which transient, site-specific addition of energy to the enzyme speeds up the search for reactive conformations by activating motions that facilitate this search.
Collapse
|
17
|
Marzolf DR, McKenzie AM, O’Malley MC, Ponomarenko NS, Swaim CM, Brittain TJ, Simmons NL, Pokkuluri PR, Mulfort KL, Tiede DM, Kokhan O. Mimicking Natural Photosynthesis: Designing Ultrafast Photosensitized Electron Transfer into Multiheme Cytochrome Protein Nanowires. NANOMATERIALS (BASEL, SWITZERLAND) 2020; 10:E2143. [PMID: 33126541 PMCID: PMC7693585 DOI: 10.3390/nano10112143] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 10/23/2020] [Accepted: 10/26/2020] [Indexed: 05/02/2023]
Abstract
Efficient nanomaterials for artificial photosynthesis require fast and robust unidirectional electron transfer (ET) from photosensitizers through charge-separation and accumulation units to redox-active catalytic sites. We explored the ultrafast time-scale limits of photo-induced charge transfer between a Ru(II)tris(bipyridine) derivative photosensitizer and PpcA, a 3-heme c-type cytochrome serving as a nanoscale biological wire. Four covalent attachment sites (K28C, K29C, K52C, and G53C) were engineered in PpcA enabling site-specific covalent labeling with expected donor-acceptor (DA) distances of 4-8 Å. X-ray scattering results demonstrated that mutations and chemical labeling did not disrupt the structure of the proteins. Time-resolved spectroscopy revealed three orders of magnitude difference in charge transfer rates for the systems with otherwise similar DA distances and the same number of covalent bonds separating donors and acceptors. All-atom molecular dynamics simulations provided additional insight into the structure-function requirements for ultrafast charge transfer and the requirement of van der Waals contact between aromatic atoms of photosensitizers and hemes in order to observe sub-nanosecond ET. This work demonstrates opportunities to utilize multi-heme c-cytochromes as frameworks for designing ultrafast light-driven ET into charge-accumulating biohybrid model systems, and ultimately for mimicking the photosynthetic paradigm of efficiently coupling ultrafast, light-driven electron transfer chemistry to multi-step catalysis within small, experimentally versatile photosynthetic biohybrid assemblies.
Collapse
Affiliation(s)
- Daniel R. Marzolf
- Department of Chemistry and Biochemistry, James Madison University, Harrisonburg, VA 22807, USA; (D.R.M.); (A.M.M.); (C.M.S.); (T.J.B.)
| | - Aidan M. McKenzie
- Department of Chemistry and Biochemistry, James Madison University, Harrisonburg, VA 22807, USA; (D.R.M.); (A.M.M.); (C.M.S.); (T.J.B.)
| | - Matthew C. O’Malley
- Department of Chemistry and Biochemistry, James Madison University, Harrisonburg, VA 22807, USA; (D.R.M.); (A.M.M.); (C.M.S.); (T.J.B.)
| | - Nina S. Ponomarenko
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, IL 60439, USA; (N.S.P.); (K.L.M.); (D.M.T.)
| | - Coleman M. Swaim
- Department of Chemistry and Biochemistry, James Madison University, Harrisonburg, VA 22807, USA; (D.R.M.); (A.M.M.); (C.M.S.); (T.J.B.)
| | - Tyler J. Brittain
- Department of Chemistry and Biochemistry, James Madison University, Harrisonburg, VA 22807, USA; (D.R.M.); (A.M.M.); (C.M.S.); (T.J.B.)
| | - Natalie L. Simmons
- Department of Biology, James Madison University, Harrisonburg, VA 22807, USA;
| | | | - Karen L. Mulfort
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, IL 60439, USA; (N.S.P.); (K.L.M.); (D.M.T.)
| | - David M. Tiede
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Lemont, IL 60439, USA; (N.S.P.); (K.L.M.); (D.M.T.)
| | - Oleksandr Kokhan
- Department of Chemistry and Biochemistry, James Madison University, Harrisonburg, VA 22807, USA; (D.R.M.); (A.M.M.); (C.M.S.); (T.J.B.)
| |
Collapse
|
18
|
Li H, Ma A. Kinetic energy flows in activated dynamics of biomolecules. J Chem Phys 2020; 153:094109. [DOI: 10.1063/5.0020275] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Huiyu Li
- Department of Bioengineering, The University of Illinois at Chicago, 851 South Morgan Street, Chicago, Illinois 60607, USA
| | - Ao Ma
- Department of Bioengineering, The University of Illinois at Chicago, 851 South Morgan Street, Chicago, Illinois 60607, USA
| |
Collapse
|
19
|
Valiño Borau L, Gulzar A, Stock G. Master equation model to predict energy transport pathways in proteins. J Chem Phys 2020; 152:045103. [DOI: 10.1063/1.5140070] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Affiliation(s)
- Luis Valiño Borau
- Biomolecular Dynamics, Institute of Physics, Albert Ludwigs University, 79104 Freiburg, Germany
| | - Adnan Gulzar
- Biomolecular Dynamics, Institute of Physics, Albert Ludwigs University, 79104 Freiburg, Germany
| | - Gerhard Stock
- Biomolecular Dynamics, Institute of Physics, Albert Ludwigs University, 79104 Freiburg, Germany
| |
Collapse
|
20
|
Ferrante C, Batignani G, Pontecorvo E, Montemiglio LC, Vos MH, Scopigno T. Ultrafast Dynamics and Vibrational Relaxation in Six-Coordinate Heme Proteins Revealed by Femtosecond Stimulated Raman Spectroscopy. J Am Chem Soc 2020; 142:2285-2292. [PMID: 31917551 PMCID: PMC7735705 DOI: 10.1021/jacs.9b10560] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Identifying
the structural rearrangements during photoinduced reactions is a fundamental
challenge for understanding from a microscopic perspective the dynamics
underlying the functional mechanisms of heme proteins. Here, femtosecond
stimulated Raman spectroscopy is applied to follow the ultrafast evolution
of two different proteins, each bearing a six-coordinate heme with
two amino acid axial ligands. By exploiting the sensitivity of Raman
spectra to the structural configuration, we investigate the effects
of photolysis and the binding of amino acid residues in cytochrome c and neuroglobin. By comparing the system response for
different time delays and Raman pump resonances, we show how detailed
properties of atomic motions and energy redistribution can be unveiled.
In particular, we demonstrate substantially faster energy flow from
the dissociated heme to the protein moiety in cytochrome c, which we assign to the presence of covalent heme–protein
bonds.
Collapse
Affiliation(s)
- Carino Ferrante
- Center for Life Nano Science @Sapienza , Istituto Italiano di Tecnologia , Rome I-00161 , Italy
| | | | | | | | - Marten H Vos
- LOB, Ecole Polytechnique, CNRS, INSERM , Institut Polytechnique de Paris , 91128 Palaiseau , France
| | - Tullio Scopigno
- Center for Life Nano Science @Sapienza , Istituto Italiano di Tecnologia , Rome I-00161 , Italy
| |
Collapse
|
21
|
Milosavljević AR, Jänkälä K, Ranković ML, Canon F, Bozek J, Nicolas C, Giuliani A. Oxygen K-shell spectroscopy of isolated progressively solvated peptide. Phys Chem Chem Phys 2020; 22:12909-12917. [DOI: 10.1039/d0cp00994f] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
X-ray spectroscopy of an isolated controllably hydrated peptide: core excitation of the first solvation shell enhances peptide backbone fragmentation.
Collapse
Affiliation(s)
| | - Kari Jänkälä
- Nano and Molecular Systems Research Unit
- University of Oulu
- 90014 Oulu
- Finland
| | | | - Francis Canon
- Centre des Sciences du Goût et de l’Alimentation
- CNRS
- INRAE
- Université de Bourgogne Franche-Comté
- France
| | - John Bozek
- SOLEIL, l’Orme des Merisiers
- 91192 Gif sur Yvette Cedex
- France
| | | | - Alexandre Giuliani
- SOLEIL, l’Orme des Merisiers
- 91192 Gif sur Yvette Cedex
- France
- INRAE
- UAR1008
| |
Collapse
|
22
|
Joshi J, Kalainathan S, Kanchan D, Joshi M, Parikh K. Effect of l-threonine on growth and properties of ammonium dihydrogen phosphate crystal. ARAB J CHEM 2020. [DOI: 10.1016/j.arabjc.2017.12.005] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
|
23
|
Yamato T, Laprévote O. Normal mode analysis and beyond. Biophys Physicobiol 2019; 16:322-327. [PMID: 31984187 PMCID: PMC6976091 DOI: 10.2142/biophysico.16.0_322] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 08/02/2019] [Indexed: 01/05/2023] Open
Abstract
Normal mode analysis provides a powerful tool in biophysical computations. Particularly, we shed light on its application to protein properties because they directly lead to biological functions. As a result of normal mode analysis, the protein motion is represented as a linear combination of mutually independent normal mode vectors. It has been widely accepted that the large amplitude motions throughout the entire protein molecule can be well described with a few low-frequency normal modes. Furthermore, it is possible to represent the effect of external perturbations, e.g., ligand binding, hydrostatic pressure, as the shifts of normal mode variables. Making use of this advantage, we are able to explore mechanical properties of proteins such as Young's modulus and compressibility. Within thermally fluctuating protein molecules under physiological conditions, tightly packed amino acid residues interact with each other through heat and energy exchanges. Since the structure and dynamics of protein molecules are highly anisotropic, the flow of energy and heat should also be anisotropic. Based on the harmonic approximation of the heat current operator, it is possible to analyze the communication map of a protein molecule. By using this method, the energy transfer pathways of photoactive yellow protein were calculated. It turned out that these pathways are similar to those obtained via the Green-Kubo formalism with equilibrium molecular dynamics simulations, indicating that normal mode analysis captures the intrinsic nature of the transport properties of proteins.
Collapse
Affiliation(s)
- Takahisa Yamato
- Graduate School of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan
| | - Olivier Laprévote
- Graduate School of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan
- École supérieure de biotechnologie Strasbourg, 10413 – F-67412, Illkirsh France
| |
Collapse
|
24
|
Abstract
Direct visualization of electronic and molecular events during biochemical reactions is essential to mechanistic insights. This Letter presents an in-depth analysis of the serial crystallographic data sets collected by Barends and Schlichting et al. ( Science 2015 , 350 , 445 ) that probe the ligand photodissociation in carbonmonoxy myoglobin. This analysis reveals electron density changes caused by the formation of high-spin 3d atomic orbitals of the heme iron upon photolysis and their dynamic behaviors within the first few picoseconds. The heme iron is found popping out of and recoiling back into the heme plane in succession. These findings provide long-awaited visual validations for previous works using ultrafast spectroscopy and molecular dynamics simulations. Electron density variations are also found largely in the solvent during the first period of a low-frequency oscillation. This work demonstrates the importance of the analytical methods in detecting and isolating weak, transient signals of electronic changes arising from chemical reactions.
Collapse
|
25
|
Gulzar A, Valiño Borau L, Buchenberg S, Wolf S, Stock G. Energy Transport Pathways in Proteins: A Non-equilibrium Molecular Dynamics Simulation Study. J Chem Theory Comput 2019; 15:5750-5757. [PMID: 31433644 DOI: 10.1021/acs.jctc.9b00598] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
To facilitate the observation of biomolecular energy transport in real time and with single-residue resolution, recent experiments by Baumann et al. ( Angew. Chem. Int. Ed. 2019 , 58 , 2899 , DOI: 10.1002/anie.201812995 ) have used unnatural amino acids β-(1-azulenyl)alanine (Azu) and azidohomoalanine (Aha) to site-specifically inject and probe vibrational energy in proteins. To aid the interpretation of such experiments, non-equilibrium molecular dynamics simulations of the anisotropic energy flow in proteins TrpZip2 and PDZ3 domains are presented. On this account, an efficient simulation protocol is established that accurately mimics the excitation and probing steps of Azu and Aha. The simulations quantitatively reproduce the experimentally found cooling times of the solvated proteins at room temperature and predict that the cooling slows by a factor 2 below the glass temperature of water. In PDZ3, vibrational energy is shown to travel from the initially excited peptide ligand via a complex network of inter-residue contacts and backbone transport to distal regions of the protein. The supposed connection of these energy transport pathways with pathways of allosteric communication is discussed.
Collapse
Affiliation(s)
- Adnan Gulzar
- Biomolecular Dynamics, Institute of Physics , Albert Ludwigs University , 79104 Freiburg , Germany
| | - Luis Valiño Borau
- Biomolecular Dynamics, Institute of Physics , Albert Ludwigs University , 79104 Freiburg , Germany
| | - Sebastian Buchenberg
- Biomolecular Dynamics, Institute of Physics , Albert Ludwigs University , 79104 Freiburg , Germany
| | - Steffen Wolf
- Biomolecular Dynamics, Institute of Physics , Albert Ludwigs University , 79104 Freiburg , Germany
| | - Gerhard Stock
- Biomolecular Dynamics, Institute of Physics , Albert Ludwigs University , 79104 Freiburg , Germany
| |
Collapse
|
26
|
Frankel RD. Orthogonal beam ballistic backscatter stimulated Raman microscopy. OPTICS EXPRESS 2019; 27:22770-22786. [PMID: 31510563 DOI: 10.1364/oe.27.022770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 07/11/2019] [Indexed: 06/10/2023]
Abstract
When the axial gain length of a stimulated Raman microscope is less than about 40% of the emission wavelength significant dipole-like ballistic backscatter will occur. Here we analyze a scanning microscope configured with orthogonal water dipping pump and probe objectives that satisfies this criterion. The pump beam focus may be a Gaussian spot or a droplet Bessel beam which minimizes the secondary Bessel beam lobes and provides multiple simultaneous pump focal spot regions. Radial and linearly polarized pump beams enable backscattered polarized signals along both transverse axes of the probe beam. Low level Mie backscatter is the primary photon noise source which should enable rapid sub-wavelength resolution 3-dimensional imaging of label-free Raman contrast for in-vivo pathology, as well as, imaging physiologic concentrations of Raman labelled metabolites and drugs.
Collapse
|
27
|
Jakučionis M, Chorošajev V, Abramavičius D. Vibrational damping effects on electronic energy relaxation in molecular aggregates. Chem Phys 2018. [DOI: 10.1016/j.chemphys.2018.07.018] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
28
|
Domratcheva T, Schlichting I. Spiers Memorial Lecture. Introductory lecture: the impact of structure on photoinduced processes in nucleic acids and proteins. Faraday Discuss 2018; 207:9-26. [PMID: 29583144 DOI: 10.1039/c8fd00058a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Light is an important environmental variable and most organisms have evolved means to sense, exploit or avoid it and to repair detrimental effects on their genome. In general, light absorption is the task of specific chromophores, however other biomolecules such as oligonucleotides also do so which can result in undesired outcomes such as mutations and cancer. Given the biological importance of light-induced processes and applications for imaging, optogenetics, photodynamic therapy or photovoltaics, there is a great interest in understanding the detailed molecular mechanisms of photoinduced processes in proteins and nucleic acids. The processes are typically characterized by time-resolved spectroscopic approaches or computation, inferring structural information on transient species from stable ground state structures. Recently, however, structure determination of excited states or other short-lived species has become possible with the advent of X-ray free-electron lasers. This review gives an overview of the impact of structure on the understanding of photoinduced processes in macromolecules, focusing on systems presented at this Faraday Discussion meeting.
Collapse
Affiliation(s)
- Tatiana Domratcheva
- Max Planck Institute for Medical Research, Jahnstr. 29, 69120 Heidelberg, Germany.
| | - Ilme Schlichting
- Max Planck Institute for Medical Research, Jahnstr. 29, 69120 Heidelberg, Germany.
| |
Collapse
|
29
|
Joshi JH, Joshi GM, Joshi MJ, Jethva HO, Parikh KD. Raman, photoluminescence, and a.c. electrical studies of pure and l-serine doped ammonium dihydrogen phosphate single crystals: an understanding of defect chemistry in hydrogen bonding. NEW J CHEM 2018. [DOI: 10.1039/c8nj03393e] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ammonium dihydrogen phosphate (ADP) crystals have a wide range of nonlinear optical applications.
Collapse
Affiliation(s)
- J. H. Joshi
- Department of Physics
- Saurashtra University
- Rajkot – 360 005
- India
| | - G. M. Joshi
- Polymer Nanocomposite Laboratory
- School of Advanced Sciences
- VIT University
- Vellore – 632 014
- India
| | - M. J. Joshi
- Department of Physics
- Saurashtra University
- Rajkot – 360 005
- India
| | - H. O. Jethva
- Department of Physics
- Saurashtra University
- Rajkot – 360 005
- India
| | - K. D. Parikh
- Department of Physics
- Shri M.P.Shah Arts & Science College
- Surendranagar – 363 001
- India
| |
Collapse
|
30
|
Jain A, Subotnik JE. Vibrational Energy Relaxation: A Benchmark for Mixed Quantum–Classical Methods. J Phys Chem A 2017; 122:16-27. [DOI: 10.1021/acs.jpca.7b09018] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Amber Jain
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104, United States
| | - Joseph E. Subotnik
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104, United States
| |
Collapse
|
31
|
Mizutani Y. Time-Resolved Resonance Raman Spectroscopy and Application to Studies on Ultrafast Protein Dynamics. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2017. [DOI: 10.1246/bcsj.20170218] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Yasuhisa Mizutani
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043
| |
Collapse
|
32
|
Li W, Ma A. Reaction mechanism and reaction coordinates from the viewpoint of energy flow. J Chem Phys 2017; 144:114103. [PMID: 27004858 DOI: 10.1063/1.4943581] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Reaction coordinates are of central importance for correct understanding of reaction dynamics in complex systems, but their counter-intuitive nature made it a daunting challenge to identify them. Starting from an energetic view of a reaction process as stochastic energy flows biased towards preferred channels, which we deemed the reaction coordinates, we developed a rigorous scheme for decomposing energy changes of a system, both potential and kinetic, into pairwise components. The pairwise energy flows between different coordinates provide a concrete statistical mechanical language for depicting reaction mechanisms. Application of this scheme to the C7eq → C7ax transition of the alanine dipeptide in vacuum revealed novel and intriguing mechanisms that eluded previous investigations of this well studied prototype system for biomolecular conformational dynamics. Using a cost function developed from the energy decomposition components by proper averaging over the transition path ensemble, we were able to identify signatures of the reaction coordinates of this system without requiring any input from human intuition.
Collapse
Affiliation(s)
- Wenjin Li
- Department of Bioengineering, The University of Illinois at Chicago, 851 South Morgan Street, Chicago, Illinois 60607, USA
| | - Ao Ma
- Department of Bioengineering, The University of Illinois at Chicago, 851 South Morgan Street, Chicago, Illinois 60607, USA
| |
Collapse
|
33
|
Gnanasekaran R. Probing the communication of deoxythymidine triphosphate in HIV-1 reverse transcriptase by communication maps and interaction energy studies. Phys Chem Chem Phys 2017; 19:29608-29616. [DOI: 10.1039/c7cp06386e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We calculate communication maps for HIV-1 Reverse Transcriptase (RT) to elucidate energy transfer pathways between deoxythymidine triphosphate (dTTP) and other parts of the protein.
Collapse
|
34
|
Ruggiero MT, Zeitler JA. Resolving the Origins of Crystalline Anharmonicity Using Terahertz Time-Domain Spectroscopy and ab Initio Simulations. J Phys Chem B 2016; 120:11733-11739. [PMID: 27766874 DOI: 10.1021/acs.jpcb.6b10248] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Anharmonicity has been shown to be an important piece of the fundamental framework that dictates numerous observable phenomena. In particular, anharmonicity is the driving force of vibrational relaxation processes, mechanisms that are integral to the proper function of numerous chemical processes. However, elucidating its origins has proven difficult due to experimental and theoretical challenges, specifically related to separating the anharmonic contributions from other unrelated effects. While no one technique is particularly suited for providing a complete picture of anharmonicity, by combining multiple complementary methods such a characterization can be made. In this study the role of individual atomic interactions on the anharmonic properties of crystalline purine, the building block of many DNA and RNA nucleobases, is studied by experimental terahertz time-domain spectroscopy and first-principles density functional theory (DFT) and ab initio molecular dynamics simulations (AIMD). In particular, the detailed vibrational information provided by the DFT calculations is used to interpret the atomic origins of anharmonic-related effects as determined by the AIMD calculations, which are in good agreement with the experimental data. The results highlight that anharmonicity is especially pronounced in the intermolecular interactions, particularly along the amine hydrogen bond coordinate, and yields valuable insight into what is similarly observed complex biosystems and crystalline solids.
Collapse
Affiliation(s)
- Michael T Ruggiero
- Department of Chemical Engineering and Biotechnology, University of Cambridge , Philippa Fawcett Drive, Cambridge CB3 0AS, United Kingdom
| | - J Axel Zeitler
- Department of Chemical Engineering and Biotechnology, University of Cambridge , Philippa Fawcett Drive, Cambridge CB3 0AS, United Kingdom
| |
Collapse
|
35
|
Abstract
We review studies of vibrational energy transfer in a molecular junction geometry, consisting of a molecule bridging two heat reservoirs, solids or large chemical compounds. This setup is of interest for applications in molecular electronics, thermoelectrics, and nanophononics, and for addressing basic questions in the theory of classical and quantum transport. Calculations show that system size, disorder, structure, dimensionality, internal anharmonicities, contact interaction, and quantum coherent effects are factors that combine to determine the predominant mechanism (ballistic/diffusive), effectiveness (poor/good), and functionality (linear/nonlinear) of thermal conduction at the nanoscale. We review recent experiments and relevant calculations of quantum heat transfer in molecular junctions. We recount the Landauer approach, appropriate for the study of elastic (harmonic) phononic transport, and outline techniques that incorporate molecular anharmonicities. Theoretical methods are described along with examples illustrating the challenge of reaching control over vibrational heat conduction in molecules.
Collapse
Affiliation(s)
- Dvira Segal
- Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada;,
| | | |
Collapse
|
36
|
Rodgers JM, Zhang W, Bazewicz CG, Chen J, Brewer SH, Gai F. Kinetic Isotope Effect Provides Insight into the Vibrational Relaxation Mechanism of Aromatic Molecules: Application to Cyano-phenylalanine. J Phys Chem Lett 2016; 7:1281-1287. [PMID: 26990401 PMCID: PMC4824650 DOI: 10.1021/acs.jpclett.6b00325] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Varying the reduced mass of an oscillator via isotopic substitution provides a convenient means to alter its vibrational frequency and hence has found wide applications. Herein, we show that this method can also help delineate the vibrational relaxation mechanism, using four isotopomers of the unnatural amino acid p-cyano-phenylalanine (Phe-CN) as models. In water, the nitrile stretching frequencies of these isotopomers, Phe-(12)C(14)N (1), Phe-(12)C(15)N (2), Phe-(13)C(14)N (3), and Phe-(13)C(15)N (4), are found to be equally separated by ∼27 cm(-1), whereas their vibrational lifetimes are determined to be 4.0 ± 0.2 (1), 2.2 ± 0.1 (2), 3.4 ± 0.2 (3), and 7.9 ± 0.5 ps (4), respectively. We find that an empirical relationship that considers the effective reduced mass of CN can accurately account for the observed frequency gaps, while the vibrational lifetime distribution, which suggests an intramolecular relaxation mechanism, can be rationalized by the order-specific density of states near the CN stretching frequency.
Collapse
Affiliation(s)
- Jeffrey M. Rodgers
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323
| | - Wenkai Zhang
- The Ultrafast Optical Processes Laboratory, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323
| | | | - Jianxin Chen
- The Ultrafast Optical Processes Laboratory, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323
| | - Scott H. Brewer
- Department of Chemistry, Franklin & Marshall College, Lancaster, Pennsylvania 17604-3003
| | - Feng Gai
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323
- The Ultrafast Optical Processes Laboratory, University of Pennsylvania, Philadelphia, Pennsylvania 19104-6323
| |
Collapse
|
37
|
Shenai PM, Fernandez-Alberti S, Bricker WP, Tretiak S, Zhao Y. Internal Conversion and Vibrational Energy Redistribution in Chlorophyll A. J Phys Chem B 2015; 120:49-58. [DOI: 10.1021/acs.jpcb.5b09548] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Prathamesh M. Shenai
- Division
of Materials Science, Nanyang Technological University, Singapore, Singapore 639798
| | | | - William P. Bricker
- Department
of Energy, Environmental and Chemical Engineering, Washington University, Saint Louis, Missouri 63130, United States
| | - Sergei Tretiak
- Theoretical
Division, Center for Nonlinear Studies (CNLS), and Center for Integrated
Nanotechnologies (CINT), Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Yang Zhao
- Division
of Materials Science, Nanyang Technological University, Singapore, Singapore 639798
| |
Collapse
|
38
|
Fu L, Wang Z, Batista VS, Yan ECY. New Insights from Sum Frequency Generation Vibrational Spectroscopy into the Interactions of Islet Amyloid Polypeptides with Lipid Membranes. J Diabetes Res 2015; 2016:7293063. [PMID: 26697504 PMCID: PMC4677203 DOI: 10.1155/2016/7293063] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 06/24/2015] [Indexed: 11/17/2022] Open
Abstract
Studies of amyloid polypeptides on membrane surfaces have gained increasing attention in recent years. Several studies have revealed that membranes can catalyze protein aggregation and that the early products of amyloid aggregation can disrupt membrane integrity, increasing water permeability and inducing ion cytotoxicity. Nonetheless, probing aggregation of amyloid proteins on membrane surfaces is challenging. Surface-specific methods are required to discriminate contributions of aggregates at the membrane interface from those in the bulk phase and to characterize protein secondary structures in situ and in real time without the use of perturbing spectroscopic labels. Here, we review the most recent applications of sum frequency generation (SFG) vibrational spectroscopy applied in conjunction with computational modeling techniques, a joint experimental and computational methodology that has provided valuable insights into the aggregation of islet amyloid polypeptide (IAPP) on membrane surfaces. These applications show that SFG can provide detailed information about structures, kinetics, and orientation of IAPP during interfacial aggregation, relevant to the molecular mechanisms of type II diabetes. These recent advances demonstrate the promise of SFG as a new approach for studying amyloid diseases at the molecular level and for the rational drug design targeting early aggregation products on membrane surfaces.
Collapse
Affiliation(s)
- Li Fu
- William R. Wiley Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, P.O. Box 999, Richland, WA 99352, USA
| | - Zhuguang Wang
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, CT 06520, USA
| | - Victor S. Batista
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, CT 06520, USA
| | - Elsa C. Y. Yan
- Department of Chemistry, Yale University, 225 Prospect Street, New Haven, CT 06520, USA
| |
Collapse
|
39
|
Anisotropic energy flow and allosteric ligand binding in albumin. Nat Commun 2015; 5:3100. [PMID: 24445265 DOI: 10.1038/ncomms4100] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Accepted: 12/12/2013] [Indexed: 11/08/2022] Open
Abstract
Allosteric interactions in proteins generally involve propagation of local structural changes through the protein to a remote site. Anisotropic energy transport is thought to couple the remote sites, but the nature of this process is poorly understood. Here, we report the relationship between energy flow through the structure of bovine serum albumin and allosteric interactions between remote ligand binding sites of the protein. Ultrafast infrared spectroscopy is used to probe the flow of energy through the protein backbone following excitation of a heater dye, a metalloporphyrin or malachite green, bound to different binding sites in the protein. We observe ballistic and anisotropic energy flow through the protein structure following input of thermal energy into the flexible ligand binding sites, without local heating of the rigid helix bundles that connect these sites. This efficient energy transport mechanism enables the allosteric propagation of binding energy through the connecting helix structures.
Collapse
|
40
|
Barends TRM, Foucar L, Ardevol A, Nass K, Aquila A, Botha S, Doak RB, Falahati K, Hartmann E, Hilpert M, Heinz M, Hoffmann MC, Köfinger J, Koglin JE, Kovacsova G, Liang M, Milathianaki D, Lemke HT, Reinstein J, Roome CM, Shoeman RL, Williams GJ, Burghardt I, Hummer G, Boutet S, Schlichting I. Direct observation of ultrafast collective motions in CO myoglobin upon ligand dissociation. Science 2015; 350:445-50. [PMID: 26359336 DOI: 10.1126/science.aac5492] [Citation(s) in RCA: 269] [Impact Index Per Article: 29.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2015] [Accepted: 08/26/2015] [Indexed: 11/02/2022]
Abstract
The hemoprotein myoglobin is a model system for the study of protein dynamics. We used time-resolved serial femtosecond crystallography at an x-ray free-electron laser to resolve the ultrafast structural changes in the carbonmonoxy myoglobin complex upon photolysis of the Fe-CO bond. Structural changes appear throughout the protein within 500 femtoseconds, with the C, F, and H helices moving away from the heme cofactor and the E and A helices moving toward it. These collective movements are predicted by hybrid quantum mechanics/molecular mechanics simulations. Together with the observed oscillations of residues contacting the heme, our calculations support the prediction that an immediate collective response of the protein occurs upon ligand dissociation, as a result of heme vibrational modes coupling to global modes of the protein.
Collapse
Affiliation(s)
- Thomas R M Barends
- Max-Planck-Institut für Medizinische Forschung, Jahnstraße 29, 69120 Heidelberg, Germany.
| | - Lutz Foucar
- Max-Planck-Institut für Medizinische Forschung, Jahnstraße 29, 69120 Heidelberg, Germany
| | - Albert Ardevol
- Max-Planck-Institut für Biophysik, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany
| | - Karol Nass
- Max-Planck-Institut für Medizinische Forschung, Jahnstraße 29, 69120 Heidelberg, Germany
| | - Andrew Aquila
- European XFEL GmbH, Albert-Einstein-Ring 19, 22761 Hamburg, Germany
| | - Sabine Botha
- Max-Planck-Institut für Medizinische Forschung, Jahnstraße 29, 69120 Heidelberg, Germany
| | - R Bruce Doak
- Max-Planck-Institut für Medizinische Forschung, Jahnstraße 29, 69120 Heidelberg, Germany
| | - Konstantin Falahati
- Institut für Physikalische und Theoretische Chemie, Goethe-Universität, Max-von-Laue-Straße 7, 60438 Frankfurt am Main, Germany
| | - Elisabeth Hartmann
- Max-Planck-Institut für Medizinische Forschung, Jahnstraße 29, 69120 Heidelberg, Germany
| | - Mario Hilpert
- Max-Planck-Institut für Medizinische Forschung, Jahnstraße 29, 69120 Heidelberg, Germany
| | - Marcel Heinz
- Max-Planck-Institut für Biophysik, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany. Institut für Physikalische und Theoretische Chemie, Goethe-Universität, Max-von-Laue-Straße 7, 60438 Frankfurt am Main, Germany
| | - Matthias C Hoffmann
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Jürgen Köfinger
- Max-Planck-Institut für Biophysik, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany
| | - Jason E Koglin
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Gabriela Kovacsova
- Max-Planck-Institut für Medizinische Forschung, Jahnstraße 29, 69120 Heidelberg, Germany
| | - Mengning Liang
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Despina Milathianaki
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Henrik T Lemke
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Jochen Reinstein
- Max-Planck-Institut für Medizinische Forschung, Jahnstraße 29, 69120 Heidelberg, Germany
| | - Christopher M Roome
- Max-Planck-Institut für Medizinische Forschung, Jahnstraße 29, 69120 Heidelberg, Germany
| | - Robert L Shoeman
- Max-Planck-Institut für Medizinische Forschung, Jahnstraße 29, 69120 Heidelberg, Germany
| | - Garth J Williams
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Irene Burghardt
- Institut für Physikalische und Theoretische Chemie, Goethe-Universität, Max-von-Laue-Straße 7, 60438 Frankfurt am Main, Germany
| | - Gerhard Hummer
- Max-Planck-Institut für Biophysik, Max-von-Laue-Straße 3, 60438 Frankfurt am Main, Germany
| | - Sébastien Boutet
- Linac Coherent Light Source (LCLS), SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Ilme Schlichting
- Max-Planck-Institut für Medizinische Forschung, Jahnstraße 29, 69120 Heidelberg, Germany.
| |
Collapse
|
41
|
Ishikura T, Iwata Y, Hatano T, Yamato T. Energy exchange network of inter-residue interactions within a thermally fluctuating protein molecule: A computational study. J Comput Chem 2015; 36:1709-18. [PMID: 26147235 DOI: 10.1002/jcc.23989] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2015] [Revised: 05/25/2015] [Accepted: 06/09/2015] [Indexed: 12/14/2022]
Abstract
Protein function is regulated not only by the structure but also by physical dynamics and thermal fluctuations. We have developed the computer program, CURrent calculation for proteins (CURP), for the flow analysis of physical quantities within thermally fluctuating protein media. The CURP program was used to calculate the energy flow within the third PDZ domain of the neuronal protein PSD-95, and the results were used to illustrate the energy exchange network of inter-residue interactions based on atomistic molecular dynamics simulations. The removal of the α3 helix is known to decrease ligand affinity by 21-fold without changing the overall protein structure; nevertheless, we demonstrated that the helix constitutes an essential part of the network graph.
Collapse
Affiliation(s)
- Takakazu Ishikura
- Graduate School of Science, Division of Material Science, Nagoya University, Furo-cho, Chikusa-ku Nagoya, 464-8602, Japan
| | - Yuki Iwata
- Graduate School of Science, Division of Material Science, Nagoya University, Furo-cho, Chikusa-ku Nagoya, 464-8602, Japan
| | - Tatsuro Hatano
- Graduate School of Science, Division of Material Science, Nagoya University, Furo-cho, Chikusa-ku Nagoya, 464-8602, Japan
| | - Takahisa Yamato
- Graduate School of Science, Division of Material Science, Nagoya University, Furo-cho, Chikusa-ku Nagoya, 464-8602, Japan
| |
Collapse
|
42
|
Chu GB, Shui M, Song YF, Xu T, Gu YQ, Yang YQ. Observation of Excited νs(NO2) and Relaxation Process of HNS in Solution by CARS Technique. CHINESE J CHEM PHYS 2015. [DOI: 10.1063/1674-0068/28/cjcp1409153] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
|
43
|
Leitner DM, Buchenberg S, Brettel P, Stock G. Vibrational energy flow in the villin headpiece subdomain: Master equation simulations. J Chem Phys 2015; 142:075101. [DOI: 10.1063/1.4907881] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Affiliation(s)
- David M. Leitner
- Department of Chemistry and Chemical Physics Program, University of Nevada, Reno, Nevada 89557, USA
- Freiburg Institute for Advanced Studies (FRIAS), University of Freiburg, Freiburg, Germany
| | - Sebastian Buchenberg
- Biomolecular Dynamics, Institute of Physics, University of Freiburg, Freiburg, Germany
| | - Paul Brettel
- Biomolecular Dynamics, Institute of Physics, University of Freiburg, Freiburg, Germany
| | - Gerhard Stock
- Freiburg Institute for Advanced Studies (FRIAS), University of Freiburg, Freiburg, Germany
- Biomolecular Dynamics, Institute of Physics, University of Freiburg, Freiburg, Germany
| |
Collapse
|
44
|
Qiu C, Blanchard GJ. Evidence for Preferential Solvation in the Cyclohexane/n-Butanol Binary Solvent System. J Phys Chem B 2015; 119:1986-93. [DOI: 10.1021/jp510964a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Chen Qiu
- Department of Chemistry, Michigan State University, 578 S. Shaw Lane, East Lansing, Michigan 48824, United States
| | - G. J. Blanchard
- Department of Chemistry, Michigan State University, 578 S. Shaw Lane, East Lansing, Michigan 48824, United States
| |
Collapse
|
45
|
Antoniou P, Ma Z, Zhang P, Beratan DN, Skourtis SS. Vibrational control of electron-transfer reactions: a feasibility study for the fast coherent transfer regime. Phys Chem Chem Phys 2015; 17:30854-66. [DOI: 10.1039/c5cp00610d] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Electron donors are connectedvialeft and right bridges to electron acceptors. Following electron-transfer initiation, the IR excitation of selected bridge vibrational modes can tune the directionality of electron transfer.
Collapse
Affiliation(s)
- P. Antoniou
- Department of Physics
- University of Cyprus
- Nicosia 1678
- Cyprus
| | - Z. Ma
- Department of Chemistry
- Duke University
- Durham
- 27708 USA
| | - P. Zhang
- Department of Chemistry
- Duke University
- Durham
- 27708 USA
| | - D. N. Beratan
- Department of Chemistry
- Duke University
- Durham
- 27708 USA
- Department of Physics
| | - S. S. Skourtis
- Department of Physics
- University of Cyprus
- Nicosia 1678
- Cyprus
- Freiburg institute of Advanced Studies (FRIAS)
| |
Collapse
|
46
|
Tabetah M, Matei A, Constantinescu C, Mortensen NP, Dinescu M, Schou J, Zhigilei LV. The Minimum Amount of “Matrix” Needed for Matrix-Assisted Pulsed Laser Deposition of Biomolecules. J Phys Chem B 2014; 118:13290-9. [DOI: 10.1021/jp508284n] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Marshall Tabetah
- Department
of Materials Science and Engineering, University of Virginia, 395 McCormick
Road, Charlottesville, Virginia 22904-4745, United States
| | - Andreea Matei
- DTU
Fotonik, Technical University of Denmark, DK-4000 Roskilde, Denmark
- INFLPR − National Institute for Laser, Plasma and Radiation Physics, 409 Atomistilor Boulevard, Magurele, Bucharest RO-077125, Romania
| | - Catalin Constantinescu
- DTU
Fotonik, Technical University of Denmark, DK-4000 Roskilde, Denmark
- INFLPR − National Institute for Laser, Plasma and Radiation Physics, 409 Atomistilor Boulevard, Magurele, Bucharest RO-077125, Romania
| | - Ninell P. Mortensen
- DTU
Fotonik, Technical University of Denmark, DK-4000 Roskilde, Denmark
- RTI International, 3040 Cornwallis
Road, Research Triangle Park, North Carolina 27709, United States
| | - Maria Dinescu
- INFLPR − National Institute for Laser, Plasma and Radiation Physics, 409 Atomistilor Boulevard, Magurele, Bucharest RO-077125, Romania
| | - Jørgen Schou
- DTU
Fotonik, Technical University of Denmark, DK-4000 Roskilde, Denmark
| | - Leonid V. Zhigilei
- Department
of Materials Science and Engineering, University of Virginia, 395 McCormick
Road, Charlottesville, Virginia 22904-4745, United States
| |
Collapse
|
47
|
Agbo JK, Xu Y, Zhang P, Straub JE, Leitner DM. Vibrational energy flow across heme–cytochrome c and cytochrome c–water interfaces. Theor Chem Acc 2014. [DOI: 10.1007/s00214-014-1504-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
|
48
|
Müller-Werkmeister HM, Bredenbeck J. A donor–acceptor pair for the real time study of vibrational energy transfer in proteins. Phys Chem Chem Phys 2014; 16:3261-6. [DOI: 10.1039/c3cp54760d] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
|
49
|
Matsunaga Y, Baba A, Li CB, Straub JE, Toda M, Komatsuzaki T, Berry RS. Spatio-temporal hierarchy in the dynamics of a minimalist protein model. J Chem Phys 2013; 139:215101. [DOI: 10.1063/1.4834415] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
|
50
|
Schreier WJ, Aumüller T, Haiser K, Koller FO, Löweneck M, Musiol HJ, Schrader TE, Kiefhaber T, Moroder L, Zinth W. Following the energy transfer in and out of a polyproline-peptide. Biopolymers 2013; 100:38-50. [DOI: 10.1002/bip.22171] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2012] [Revised: 10/05/2012] [Accepted: 10/09/2012] [Indexed: 01/11/2023]
|