1
|
Ren Z, Yang X. Deconvolution of dynamic heterogeneity in protein structure. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2024; 11:041302. [PMID: 39165899 PMCID: PMC11335360 DOI: 10.1063/4.0000261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Accepted: 07/30/2024] [Indexed: 08/22/2024]
Abstract
Heterogeneity is intrinsic to the dynamic process of a chemical reaction. As reactants are converted to products via intermediates, the nature and extent of heterogeneity vary temporally throughout the duration of the reaction and spatially across the molecular ensemble. The goal of many biophysical techniques, including crystallography and spectroscopy, is to establish a reaction trajectory that follows an experimentally provoked dynamic process. It is essential to properly analyze and resolve heterogeneity inevitably embedded in experimental datasets. We have developed a deconvolution technique based on singular value decomposition (SVD), which we have rigorously practiced in diverse research projects. In this review, we recapitulate the motivation and challenges in addressing the heterogeneity problem and lay out the mathematical foundation of our methodology that enables isolation of chemically sensible structural signals. We also present a few case studies to demonstrate the concept and outcome of the SVD-based deconvolution. Finally, we highlight a few recent studies with mechanistic insights made possible by heterogeneity deconvolution.
Collapse
Affiliation(s)
- Zhong Ren
- Authors to whom correspondence should be addressed: and
| | - Xiaojing Yang
- Authors to whom correspondence should be addressed: and
| |
Collapse
|
2
|
Barends TRM, Gorel A, Bhattacharyya S, Schirò G, Bacellar C, Cirelli C, Colletier JP, Foucar L, Grünbein ML, Hartmann E, Hilpert M, Holton JM, Johnson PJM, Kloos M, Knopp G, Marekha B, Nass K, Nass Kovacs G, Ozerov D, Stricker M, Weik M, Doak RB, Shoeman RL, Milne CJ, Huix-Rotllant M, Cammarata M, Schlichting I. Influence of pump laser fluence on ultrafast myoglobin structural dynamics. Nature 2024; 626:905-911. [PMID: 38355794 PMCID: PMC10881388 DOI: 10.1038/s41586-024-07032-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Accepted: 01/04/2024] [Indexed: 02/16/2024]
Abstract
High-intensity femtosecond pulses from an X-ray free-electron laser enable pump-probe experiments for the investigation of electronic and nuclear changes during light-induced reactions. On timescales ranging from femtoseconds to milliseconds and for a variety of biological systems, time-resolved serial femtosecond crystallography (TR-SFX) has provided detailed structural data for light-induced isomerization, breakage or formation of chemical bonds and electron transfer1,2. However, all ultrafast TR-SFX studies to date have employed such high pump laser energies that nominally several photons were absorbed per chromophore3-17. As multiphoton absorption may force the protein response into non-physiological pathways, it is of great concern18,19 whether this experimental approach20 allows valid conclusions to be drawn vis-à-vis biologically relevant single-photon-induced reactions18,19. Here we describe ultrafast pump-probe SFX experiments on the photodissociation of carboxymyoglobin, showing that different pump laser fluences yield markedly different results. In particular, the dynamics of structural changes and observed indicators of the mechanistically important coherent oscillations of the Fe-CO bond distance (predicted by recent quantum wavepacket dynamics21) are seen to depend strongly on pump laser energy, in line with quantum chemical analysis. Our results confirm both the feasibility and necessity of performing ultrafast TR-SFX pump-probe experiments in the linear photoexcitation regime. We consider this to be a starting point for reassessing both the design and the interpretation of ultrafast TR-SFX pump-probe experiments20 such that mechanistically relevant insight emerges.
Collapse
Affiliation(s)
| | - Alexander Gorel
- Max Planck Institute for Medical Research, Heidelberg, Germany
| | | | - Giorgio Schirò
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, Grenoble, France
| | | | | | | | - Lutz Foucar
- Max Planck Institute for Medical Research, Heidelberg, Germany
| | | | | | - Mario Hilpert
- Max Planck Institute for Medical Research, Heidelberg, Germany
| | - James M Holton
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | | | | | | | - Bogdan Marekha
- ENSL, CNRS, Laboratoire de Chimie UMR 5182, Lyon, France
| | - Karol Nass
- Paul Scherrer Institute, Villigen, Switzerland
| | | | | | | | - Martin Weik
- Institut de Biologie Structurale, Université Grenoble Alpes, CEA, CNRS, Grenoble, France
| | - R Bruce Doak
- Max Planck Institute for Medical Research, Heidelberg, Germany
| | | | | | | | | | | |
Collapse
|
3
|
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
|
4
|
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
|
5
|
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
|
6
|
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
|
7
|
He J, Zhang L, Liu L. The hydrogen-bond configuration modulates the energy transfer efficiency in helical protein nanotubes. NANOSCALE 2021; 13:991-999. [PMID: 33367447 DOI: 10.1039/d0nr06031c] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Energy transport in proteins is critical to a variety of physical, chemical, and biological processes in living organisms. While strenuous efforts have been made to study vibrational energy transport in proteins, thermal transport processes across the most fundamental building blocks of proteins, i.e. helices, are not well understood. This work studies energy transport in a group of "isomer" helices. The π-helix is shown to have the highest thermal conductivity, 110% higher than that of the α-helix and 207% higher than that of the 310-helix. The H-bond connectivity is found to govern thermal transport mechanisms including the phonon spectral energy density, dispersion, mode-specific transport, group velocity, and relaxation time. The energy transport is strongly correlated with the H-bond strength which is also modulated by the H-bond connectivity. These fundamental insights provide a novel perspective for understanding energy transfer in proteins and guiding a rational molecule-level design of novel materials with configurable H-bonds.
Collapse
Affiliation(s)
- Jinlong He
- Department of Mechanical Engineering, Temple University, Philadelphia, PA 19122, USA. and Department of Mechanical and Aerospace Engineering, Utah State University, Logan, Utah 84322, USA
| | - Lin Zhang
- Department of Engineering Mechanics, School of Civil Engineering, Shandong University, Jinan, 250061, P.R. China and Department of Mechanical Engineering and Materials Science, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Ling Liu
- Department of Mechanical Engineering, Temple University, Philadelphia, PA 19122, USA.
| |
Collapse
|
8
|
Fang C, Tang L. Mapping Structural Dynamics of Proteins with Femtosecond Stimulated Raman Spectroscopy. Annu Rev Phys Chem 2020; 71:239-265. [PMID: 32075503 DOI: 10.1146/annurev-physchem-071119-040154] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The structure-function relationships of biomolecules have captured the interest and imagination of the scientific community and general public since the field of structural biology emerged to enable the molecular understanding of life processes. Proteins that play numerous functional roles in cellular processes have remained in the forefront of research, inspiring new characterization techniques. In this review, we present key theoretical concepts and recent experimental strategies using femtosecond stimulated Raman spectroscopy (FSRS) to map the structural dynamics of proteins, highlighting the flexible chromophores on ultrafast timescales. In particular, wavelength-tunable FSRS exploits dynamic resonance conditions to track transient-species-dependent vibrational motions, enabling rational design to alter functions. Various ways of capturing excited-state chromophore structural snapshots in the time and/or frequency domains are discussed. Continuous development of experimental methodologies, synergistic correlation with theoretical modeling, and the expansion to other nonequilibrium, photoswitchable, and controllable protein systems will greatly advance the chemical, physical, and biological sciences.
Collapse
Affiliation(s)
- Chong Fang
- Department of Chemistry, Oregon State University, Corvallis, Oregon 97331, USA;
| | - Longteng Tang
- Department of Chemistry, Oregon State University, Corvallis, Oregon 97331, USA;
| |
Collapse
|
9
|
Huang BC, Yang LW. Molecular dynamics simulations and linear response theories jointly describe biphasic responses of myoglobin relaxation and reveal evolutionarily conserved frequent communicators. Biophys Physicobiol 2020; 16:473-484. [PMID: 31984199 PMCID: PMC6975898 DOI: 10.2142/biophysico.16.0_473] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 09/20/2019] [Indexed: 12/01/2022] Open
Abstract
In this study, we provide a time-dependent mechanical model, taking advantage of molecular dynamics simulations, quasiharmonic analysis of molecular dynamics trajectories, and time-dependent linear response theories to describe vibrational energy redistribution within the protein matrix. The theoretical description explained the observed biphasic responses of specific residues in myoglobin to CO-photolysis and photoexcitation on heme. The fast responses were found to be triggered by impulsive forces and propagated mainly by principal modes <40 cm−1. The predicted fast responses for individual atoms were then used to study signal propagation within the protein matrix and signals were found to propagate ~8 times faster across helices (4076 m/s) than within the helices, suggesting the importance of tertiary packing in the sensitivity of proteins to external perturbations. We further developed a method to integrate multiple intramolecular signal pathways and discover frequent “communicators”. These communicators were found to be evolutionarily conserved including those distant from the heme.
Collapse
Affiliation(s)
- Bang-Chieh Huang
- Institute of Bioinformatics and Structural Biology, National Tsing-Hua University, Hsinchu 30013, Taiwan
| | - Lee-Wei Yang
- Institute of Bioinformatics and Structural Biology, National Tsing-Hua University, Hsinchu 30013, Taiwan.,Bioinformatics Program, Taiwan International Graduate Program, Institute of Information Sciences, Academia Sinica, Taipei 11529, Taiwan.,Department of Life Science, National Tsing Hua University, Hsinchu 30013, Taiwan.,Physics Division, National Center for Theoretical Sciences, Hsinchu 30013, Taiwan
| |
Collapse
|
10
|
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
|
11
|
Krueger TD, Tang L, Zhu L, Breen IL, Wachter RM, Fang C. Dual Illumination Enhances Transformation of an Engineered Green-to-Red Photoconvertible Fluorescent Protein. Angew Chem Int Ed Engl 2020; 59:1644-1652. [PMID: 31692171 DOI: 10.1002/anie.201911379] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Indexed: 01/13/2023]
Abstract
The molecular mechanisms for the photoconversion of fluorescent proteins remain elusive owing to the challenges of monitoring chromophore structural dynamics during the light-induced processes. We implemented time-resolved electronic and stimulated Raman spectroscopies to reveal two hidden species of an engineered ancestral GFP-like protein LEA, involving semi-trapped protonated and trapped deprotonated chromophores en route to photoconversion in pH 7.9 buffer. A new dual-illumination approach was examined, using 400 and 505 nm light simultaneously to achieve faster conversion and higher color contrast. Substitution of UV irradiation with visible light benefits bioimaging, while the spectral benchmark of a trapped chromophore with characteristic ring twisting and bridge-H bending motions enables rational design of functional proteins. With the improved H-bonding network and structural motions, the photoexcited chromophore could increase the photoswitching-aided photoconversion while reducing trapped species.
Collapse
Affiliation(s)
- Taylor D Krueger
- Department of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, OR, 97331, USA
| | - Longteng Tang
- Department of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, OR, 97331, USA
| | - Liangdong Zhu
- Department of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, OR, 97331, USA
| | - Isabella L Breen
- School of Molecular Sciences, Center for Bioenergy and Photosynthesis, Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ, 85287, USA
| | - Rebekka M Wachter
- School of Molecular Sciences, Center for Bioenergy and Photosynthesis, Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ, 85287, USA
| | - Chong Fang
- Department of Chemistry, Oregon State University, 153 Gilbert Hall, Corvallis, OR, 97331, USA
| |
Collapse
|
12
|
Krueger TD, Tang L, Zhu L, Breen IL, Wachter RM, Fang C. Dual Illumination Enhances Transformation of an Engineered Green‐to‐Red Photoconvertible Fluorescent Protein. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201911379] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Taylor D. Krueger
- Department of Chemistry Oregon State University 153 Gilbert Hall Corvallis OR 97331 USA
| | - Longteng Tang
- Department of Chemistry Oregon State University 153 Gilbert Hall Corvallis OR 97331 USA
| | - Liangdong Zhu
- Department of Chemistry Oregon State University 153 Gilbert Hall Corvallis OR 97331 USA
| | - Isabella L. Breen
- School of Molecular Sciences Center for Bioenergy and Photosynthesis Biodesign Center for Applied Structural Discovery Arizona State University Tempe AZ 85287 USA
| | - Rebekka M. Wachter
- School of Molecular Sciences Center for Bioenergy and Photosynthesis Biodesign Center for Applied Structural Discovery Arizona State University Tempe AZ 85287 USA
| | - Chong Fang
- Department of Chemistry Oregon State University 153 Gilbert Hall Corvallis OR 97331 USA
| |
Collapse
|
13
|
Fang C, Tang L, Chen C. Unveiling coupled electronic and vibrational motions of chromophores in condensed phases. J Chem Phys 2019; 151:200901. [PMID: 31779327 DOI: 10.1063/1.5128388] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The quest for capturing molecular movies of functional systems has motivated scientists and engineers for decades. A fundamental understanding of electronic and nuclear motions, two principal components of the molecular Schrödinger equation, has the potential to enable the de novo rational design for targeted functionalities of molecular machines. We discuss the development and application of a relatively new structural dynamics technique, femtosecond stimulated Raman spectroscopy with broadly tunable laser pulses from the UV to near-IR region, in tracking the coupled electronic and vibrational motions of organic chromophores in solution and protein environments. Such light-sensitive moieties hold broad interest and significance in gaining fundamental knowledge about the intramolecular and intermolecular Hamiltonian and developing effective strategies to control macroscopic properties. Inspired by recent experimental and theoretical advances, we focus on the in situ characterization and spectroscopy-guided tuning of photoacidity, excited state proton transfer pathways, emission color, and internal conversion via a conical intersection.
Collapse
Affiliation(s)
- Chong Fang
- Department of Chemistry, Oregon State University, Corvallis, Oregon 97331, USA
| | - Longteng Tang
- Department of Chemistry, Oregon State University, Corvallis, Oregon 97331, USA
| | - Cheng Chen
- Department of Chemistry, Oregon State University, Corvallis, Oregon 97331, USA
| |
Collapse
|
14
|
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
|
15
|
Amadei A, Aschi M. Modelling vibrational relaxation in complex molecular systems. Phys Chem Chem Phys 2019; 21:20003-20017. [PMID: 31478042 DOI: 10.1039/c9cp03379c] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this paper we show how it is possible to treat the quantum vibrational relaxation of a chromophore, embedded in a complex atomic-molecular environment, via the explicit solution of the time-dependent Schroedinger equation once using a proper separation between quantum and semiclassical degrees of freedom. The rigorous theoretical framework derived, based on first principles and making use of well defined approximations/assumptions, is utilized to construct a general model for the kinetics of the vibrational relaxation as obtained by the direct evaluation of the density matrix for all the relevant quantum state transitions. Application to (deuterated) N-methylacetamide (the typical benchmark used as a model for the amino acids) shows that the obtained theoretical-computational approach captures the essential features of the experimental process, unveiling the basic relaxation mechanism involving several vibrational state transitions.
Collapse
Affiliation(s)
- Andrea Amadei
- Dipartimento di Scienze e Tecnologie Chimiche, Università di Roma "Tor Vergata", via della Ricerca Scientifica 1, 00133 Roma, Italy.
| | | |
Collapse
|
16
|
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
|
17
|
Ferrante C, Pontecorvo E, Cerullo G, Vos MH, Scopigno T. Direct observation of subpicosecond vibrational dynamics in photoexcited myoglobin. Nat Chem 2016; 8:1137-1143. [PMID: 27874865 DOI: 10.1038/nchem.2569] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Accepted: 06/09/2016] [Indexed: 11/10/2022]
Abstract
Determining the initial pathway for ultrafast energy redistribution within biomolecules is a challenge, and haem proteins, for which energy can be deposited locally in the haem moiety using short light pulses, are suitable model systems to address this issue. However, data acquired using existing experimental techniques that fail to combine sufficient structural sensitivity with adequate time resolution have resulted in alternative hypotheses concerning the interplay between energy flow among highly excited vibrational levels and potential concomitant electronic processes. By developing a femtosecond-stimulated Raman set-up, endowed with the necessary tunability to take advantage of different resonance conditions, here we visualize the temporal evolution of energy redistribution over different vibrational modes in myoglobin. We establish that the vibrational energy initially stored in the highly excited Franck-Condon manifold is transferred with different timescales into low- and high-frequency modes, prior to slow dissipation through the protein. These findings demonstrate that a newly proposed mechanism involving the population dynamics of specific vibrational modes settles the controversy on the existence of transient electronic intermediates.
Collapse
Affiliation(s)
- C Ferrante
- Dipartimento di Fisica, Università di Roma, La Sapienza, I-00185 Roma, Italy
| | - E Pontecorvo
- Dipartimento di Fisica, Università di Roma, La Sapienza, I-00185 Roma, Italy
| | - G Cerullo
- Istituto di Fotonica e Nanotecnologie (IFN-CNR), Dipartimento di Fisica, Politecnico di Milano, Piazza L. da Vinci 32, 20133 Milano, Italy
| | - M H Vos
- LOB, Ecole Polytechnique, CNRS, INSERM, Université Paris-Saclay, 91128 Palaiseau Cedex, France
| | - T Scopigno
- Dipartimento di Fisica, Università di Roma, La Sapienza, I-00185 Roma, Italy.,Center for Life Nano Science@Sapienza, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161 Rome, Italy
| |
Collapse
|
18
|
Pande K, Hutchison CDM, Groenhof G, Aquila A, Robinson JS, Tenboer J, Basu S, Boutet S, DePonte DP, Liang M, White TA, Zatsepin NA, Yefanov O, Morozov D, Oberthuer D, Gati C, Subramanian G, James D, Zhao Y, Koralek J, Brayshaw J, Kupitz C, Conrad C, Roy-Chowdhury S, Coe JD, Metz M, Xavier PL, Grant TD, Koglin JE, Ketawala G, Fromme R, Šrajer V, Henning R, Spence JCH, Ourmazd A, Schwander P, Weierstall U, Frank M, Fromme P, Barty A, Chapman HN, Moffat K, van Thor JJ, Schmidt M. Femtosecond structural dynamics drives the trans/cis isomerization in photoactive yellow protein. Science 2016; 352:725-9. [PMID: 27151871 DOI: 10.1126/science.aad5081] [Citation(s) in RCA: 290] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2015] [Accepted: 04/05/2016] [Indexed: 11/02/2022]
Abstract
A variety of organisms have evolved mechanisms to detect and respond to light, in which the response is mediated by protein structural changes after photon absorption. The initial step is often the photoisomerization of a conjugated chromophore. Isomerization occurs on ultrafast time scales and is substantially influenced by the chromophore environment. Here we identify structural changes associated with the earliest steps in the trans-to-cis isomerization of the chromophore in photoactive yellow protein. Femtosecond hard x-ray pulses emitted by the Linac Coherent Light Source were used to conduct time-resolved serial femtosecond crystallography on photoactive yellow protein microcrystals over a time range from 100 femtoseconds to 3 picoseconds to determine the structural dynamics of the photoisomerization reaction.
Collapse
Affiliation(s)
- Kanupriya Pande
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, USA. Center for Free Electron Laser Science, Deutsches Elektronen Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
| | | | - Gerrit Groenhof
- Nanoscience Center and Department of Chemistry, University of Jyväskylä, Post Office Box 35, 40014 Jyväskylä, Finland
| | - Andy Aquila
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Sand Hill Road, Menlo Park, CA 94025, USA
| | - Josef S Robinson
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Sand Hill Road, Menlo Park, CA 94025, USA
| | - Jason Tenboer
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, USA
| | - Shibom Basu
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287, USA
| | - Sébastien Boutet
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Sand Hill Road, Menlo Park, CA 94025, USA
| | - Daniel P DePonte
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Sand Hill Road, Menlo Park, CA 94025, USA
| | - Mengning Liang
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Sand Hill Road, Menlo Park, CA 94025, USA
| | - Thomas A White
- Center for Free Electron Laser Science, Deutsches Elektronen Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
| | - Nadia A Zatsepin
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Oleksandr Yefanov
- Center for Free Electron Laser Science, Deutsches Elektronen Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
| | - Dmitry Morozov
- Nanoscience Center and Department of Chemistry, University of Jyväskylä, Post Office Box 35, 40014 Jyväskylä, Finland
| | - Dominik Oberthuer
- Center for Free Electron Laser Science, Deutsches Elektronen Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
| | - Cornelius Gati
- Center for Free Electron Laser Science, Deutsches Elektronen Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
| | | | - Daniel James
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Yun Zhao
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Jake Koralek
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Sand Hill Road, Menlo Park, CA 94025, USA
| | - Jennifer Brayshaw
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, USA
| | - Christopher Kupitz
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, USA
| | - Chelsie Conrad
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287, USA
| | - Shatabdi Roy-Chowdhury
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287, USA
| | - Jesse D Coe
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287, USA
| | - Markus Metz
- Center for Free Electron Laser Science, Deutsches Elektronen Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
| | - Paulraj Lourdu Xavier
- Center for Free Electron Laser Science, Deutsches Elektronen Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany. IMPRS-UFAST, Max Planck Institute for Structure and Dynamics of Matter, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Thomas D Grant
- Hauptman-Woodward Institute, State University of New York at Buffalo, 700 Ellicott Street, Buffalo, NY 14203, USA
| | - Jason E Koglin
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Sand Hill Road, Menlo Park, CA 94025, USA
| | - Gihan Ketawala
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287, USA
| | - Raimund Fromme
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287, USA
| | - Vukica Šrajer
- Center for Advanced Radiation Sources, University of Chicago, Chicago, IL 60637, USA
| | - Robert Henning
- Center for Advanced Radiation Sources, University of Chicago, Chicago, IL 60637, USA
| | - John C H Spence
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Abbas Ourmazd
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, USA
| | - Peter Schwander
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, USA
| | - Uwe Weierstall
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Matthias Frank
- Lawrence Livermore National Laboratory, Livermore, CA 94550, USA
| | - Petra Fromme
- School of Molecular Sciences and Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287, USA
| | - Anton Barty
- Center for Free Electron Laser Science, Deutsches Elektronen Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany
| | - Henry N Chapman
- Center for Free Electron Laser Science, Deutsches Elektronen Synchrotron, Notkestrasse 85, 22607 Hamburg, Germany. Center for Ultrafast Imaging, University of Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany
| | - Keith Moffat
- Center for Advanced Radiation Sources, University of Chicago, Chicago, IL 60637, USA. Department of Biochemistry and Molecular Biology and Institute for Biophysical Dynamics, University of Chicago, Chicago, IL 60637, USA
| | - Jasper J van Thor
- Faculty of Natural Sciences, Department of Life Sciences, Imperial College, London SW7 2AZ, UK
| | - Marius Schmidt
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, USA
| |
Collapse
|
19
|
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
|
20
|
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]
|
21
|
Foley BM, Gorham CS, Duda JC, Cheaito R, Szwejkowski CJ, Constantin C, Kaehr B, Hopkins PE. Protein Thermal Conductivity Measured in the Solid State Reveals Anharmonic Interactions of Vibrations in a Fractal Structure. J Phys Chem Lett 2014; 5:1077-1082. [PMID: 26274452 DOI: 10.1021/jz500174x] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Energy processes and vibrations in biological macromolecules such as proteins ultimately dictate biological, chemical, and physical functions in living materials. These energetic vibrations in the ribbon-like motifs of proteins interact on self-similar structures and fractal-like objects over a range of length scales of the protein (a few angstroms to the size of the protein itself, a few nanometers). In fact, the fractal geometries of protein molecules create a complex network of vibrations; therefore, proteins represent an ideal material system to study the underlying mechanisms driving vibrational thermal transport in a dense, fractal network. However, experimental studies of thermal energy transport in proteins have been limited to dispersive protein suspensions, which limits the knowledge that can be extracted about how vibrational energy is transferred in a pure protein solid. We overcome this by synthesizing solid, water-insoluble protein films for thermal conductivity measurements via time-domain thermoreflectance. We measure the thermal conductivity of bovine serum albumin and myoglobin solid films over a range of temperatures from 77 to 296 K. These temperature trends indicate that anharmonic coupling of vibrations in the protein is contributing to thermal conductivity. This first-ever observation of anharmonic-like trends in the thermal conductivity of a fully dense protein forms the basis of validation of seminal theories of vibrational energy-transfer processes in fractal objects.
Collapse
Affiliation(s)
- Brian M Foley
- †Department of Mechanical and Aerospace Engineering, University of Virginia, 122 Engineer's Way, Charlottesville, Virginia 22904, United States
| | - Caroline S Gorham
- †Department of Mechanical and Aerospace Engineering, University of Virginia, 122 Engineer's Way, Charlottesville, Virginia 22904, United States
| | - John C Duda
- †Department of Mechanical and Aerospace Engineering, University of Virginia, 122 Engineer's Way, Charlottesville, Virginia 22904, United States
| | - Ramez Cheaito
- †Department of Mechanical and Aerospace Engineering, University of Virginia, 122 Engineer's Way, Charlottesville, Virginia 22904, United States
| | - Chester J Szwejkowski
- ‡Department of Physics and Astronomy, James Madison University, 901 Carrier Drive, Harrisonburg, Virginia 22807, United States
| | - Costel Constantin
- ‡Department of Physics and Astronomy, James Madison University, 901 Carrier Drive, Harrisonburg, Virginia 22807, United States
| | - Bryan Kaehr
- §Advanced Materials Laboratory, Sandia National Laboratories, 1001 University Dr. SE, Albuquerque, New Mexico 87106, United States
- ∥Department of Chemical and Nuclear Engineering, University of New Mexico, 209 Farris Engineering, Albuquerque, New Mexico 87106, United States
| | - Patrick E Hopkins
- †Department of Mechanical and Aerospace Engineering, University of Virginia, 122 Engineer's Way, Charlottesville, Virginia 22904, United States
| |
Collapse
|
22
|
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
|
23
|
Ren H, Jiang J, Mukamel S. Deep UV resonance Raman spectroscopy of β-sheet amyloid fibrils: a QM/MM simulation. J Phys Chem B 2011; 115:13955-62. [PMID: 22007849 PMCID: PMC3233492 DOI: 10.1021/jp207849u] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We present a combined quantum mechanics and molecular mechanics study of the deep ultraviolet ππ* resonance Raman spectra of β-sheet amyloid fibrils Aβ(34-42) and Aβ(1-40). Effects of conformational fluctuations are described using a Ramachandran angle map, thus avoiding repeated ab initio calculations. Experimentally observed effects of hydrogen-deuterium exchange are reproduced. We propose that the AmIII band redshift upon deuteration is caused by the loss of coupling between C(α)-H bending and N-D bending modes, rather than by peptide bond hydration.
Collapse
Affiliation(s)
- Hao Ren
- Department of Chemistry, University of California, Irvine, CA 92697
| | - Jun Jiang
- Department of Chemistry, University of California, Irvine, CA 92697
| | - Shaul Mukamel
- Department of Chemistry, University of California, Irvine, CA 92697
| |
Collapse
|
24
|
Soler MA, Bastida A, Farag MH, Zúñiga J, Requena A. A method for analyzing the vibrational energy flow in biomolecules in solution. J Chem Phys 2011; 135:204106. [DOI: 10.1063/1.3663707] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
25
|
Haiser K, Koller FO, Huber M, Regner N, Schrader TE, Schreier WJ, Zinth W. Nitro-Phenylalanine: A Novel Sensor for Heat Transfer in Peptides. J Phys Chem A 2011; 115:2169-75. [DOI: 10.1021/jp110597a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Karin Haiser
- BioMolekulare Optik and Center for Integrated Protein Science (Munich), Fakultät für Physik, Ludwig-Maximilians-Universität München, Oettingenstr. 67, 80538 München, Germany
| | - Florian O. Koller
- BioMolekulare Optik and Center for Integrated Protein Science (Munich), Fakultät für Physik, Ludwig-Maximilians-Universität München, Oettingenstr. 67, 80538 München, Germany
| | - Markus Huber
- BioMolekulare Optik and Center for Integrated Protein Science (Munich), Fakultät für Physik, Ludwig-Maximilians-Universität München, Oettingenstr. 67, 80538 München, Germany
| | - Nadja Regner
- BioMolekulare Optik and Center for Integrated Protein Science (Munich), Fakultät für Physik, Ludwig-Maximilians-Universität München, Oettingenstr. 67, 80538 München, Germany
| | - Tobias E. Schrader
- BioMolekulare Optik and Center for Integrated Protein Science (Munich), Fakultät für Physik, Ludwig-Maximilians-Universität München, Oettingenstr. 67, 80538 München, Germany
| | - Wolfgang J. Schreier
- BioMolekulare Optik and Center for Integrated Protein Science (Munich), Fakultät für Physik, Ludwig-Maximilians-Universität München, Oettingenstr. 67, 80538 München, Germany
| | - Wolfgang Zinth
- BioMolekulare Optik and Center for Integrated Protein Science (Munich), Fakultät für Physik, Ludwig-Maximilians-Universität München, Oettingenstr. 67, 80538 München, Germany
| |
Collapse
|
26
|
Nguyen PH, Park SM, Stock G. Nonequilibrium molecular dynamics simulation of the energy transport through a peptide helix. J Chem Phys 2010; 132:025102. [DOI: 10.1063/1.3284742] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
|
27
|
Schade M, Hamm P. Vibrational energy transport in the presence of intrasite vibrational energy redistribution. J Chem Phys 2009; 131:044511. [PMID: 19655898 DOI: 10.1063/1.3185152] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The mechanism of vibrational energy flow is studied in a regime where a diffusion equation is likely to break down, i.e., on length scales of a few chemical bonds and time scales of a few picoseconds. This situation occurs, for example, during photochemical reactions in protein environment. To that end, a toy model is introduced that on the one hand mimics the vibrational normal mode distribution of proteins, and on the other hand is small enough to numerically time propagate the system fully quantum mechanically. Comparing classical and quantum-mechanical results, the question is addressed to what extent the classical nature of the molecular dynamics simulations (which would be the only choice for the modeling of a real molecular system) affects the vibrational energy flow mechanism. Small differences are found which are due to the different ways classical and quantum mechanics distribute thermal energy over vibrational modes. In either case, a ballistic and a diffusive phase can be identified. For these small length and time scales, the latter is governed by intrasite vibrational energy redistribution, since vibrational energy does not necessarily thermalize completely within individual peptide units. Overall, the model suggests a picture that unifies many of the observations made recently in experiments.
Collapse
Affiliation(s)
- Marco Schade
- Physikalisch-Chemisches Institut, Universität Zürich, Winterthurerstr. 190, CH-8057 Zürich, Switzerland
| | | |
Collapse
|
28
|
Schade M, Moretto A, Crisma M, Toniolo C, Hamm P. Vibrational Energy Transport in Peptide Helices after Excitation of C−D Modes in Leu-d10. J Phys Chem B 2009; 113:13393-7. [DOI: 10.1021/jp906363a] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Marco Schade
- Physikalisch-Chemisches Institut, Universität Zürich, CH-8057 Zürich, Switzerland, and Institute of Biomolecular Chemistry, Padova Unit, CNR, Department of Chemistry, University of Padova, I-35131 Padova, Italy
| | - Alessandro Moretto
- Physikalisch-Chemisches Institut, Universität Zürich, CH-8057 Zürich, Switzerland, and Institute of Biomolecular Chemistry, Padova Unit, CNR, Department of Chemistry, University of Padova, I-35131 Padova, Italy
| | - Marco Crisma
- Physikalisch-Chemisches Institut, Universität Zürich, CH-8057 Zürich, Switzerland, and Institute of Biomolecular Chemistry, Padova Unit, CNR, Department of Chemistry, University of Padova, I-35131 Padova, Italy
| | - Claudio Toniolo
- Physikalisch-Chemisches Institut, Universität Zürich, CH-8057 Zürich, Switzerland, and Institute of Biomolecular Chemistry, Padova Unit, CNR, Department of Chemistry, University of Padova, I-35131 Padova, Italy
| | - Peter Hamm
- Physikalisch-Chemisches Institut, Universität Zürich, CH-8057 Zürich, Switzerland, and Institute of Biomolecular Chemistry, Padova Unit, CNR, Department of Chemistry, University of Padova, I-35131 Padova, Italy
| |
Collapse
|
29
|
Backus EHG, Nguyen PH, Botan V, Moretto A, Crisma M, Toniolo C, Zerbe O, Stock G, Hamm P. Structural Flexibility of a Helical Peptide Regulates Vibrational Energy Transport Properties. J Phys Chem B 2008; 112:15487-92. [DOI: 10.1021/jp806403p] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ellen H. G. Backus
- Chemische Institute, Universität Zürich, Winterthurerstr. 190, CH-8057 Zürich, Switzerland; Institut für Physikalische and Theoretische Chemie, J. W. Goethe Universität, Max-von-Laue-Str. 7, D-60438 Frankfurt, Germany; and Institute of Biomolecular Chemistry, Padova Unit, CNR, Department of Chemistry, University of Padova, Via Marzolo 1, I-35131 Padova, Italy
| | - Phuong H. Nguyen
- Chemische Institute, Universität Zürich, Winterthurerstr. 190, CH-8057 Zürich, Switzerland; Institut für Physikalische and Theoretische Chemie, J. W. Goethe Universität, Max-von-Laue-Str. 7, D-60438 Frankfurt, Germany; and Institute of Biomolecular Chemistry, Padova Unit, CNR, Department of Chemistry, University of Padova, Via Marzolo 1, I-35131 Padova, Italy
| | - Virgiliu Botan
- Chemische Institute, Universität Zürich, Winterthurerstr. 190, CH-8057 Zürich, Switzerland; Institut für Physikalische and Theoretische Chemie, J. W. Goethe Universität, Max-von-Laue-Str. 7, D-60438 Frankfurt, Germany; and Institute of Biomolecular Chemistry, Padova Unit, CNR, Department of Chemistry, University of Padova, Via Marzolo 1, I-35131 Padova, Italy
| | - Alessandro Moretto
- Chemische Institute, Universität Zürich, Winterthurerstr. 190, CH-8057 Zürich, Switzerland; Institut für Physikalische and Theoretische Chemie, J. W. Goethe Universität, Max-von-Laue-Str. 7, D-60438 Frankfurt, Germany; and Institute of Biomolecular Chemistry, Padova Unit, CNR, Department of Chemistry, University of Padova, Via Marzolo 1, I-35131 Padova, Italy
| | - Marco Crisma
- Chemische Institute, Universität Zürich, Winterthurerstr. 190, CH-8057 Zürich, Switzerland; Institut für Physikalische and Theoretische Chemie, J. W. Goethe Universität, Max-von-Laue-Str. 7, D-60438 Frankfurt, Germany; and Institute of Biomolecular Chemistry, Padova Unit, CNR, Department of Chemistry, University of Padova, Via Marzolo 1, I-35131 Padova, Italy
| | - Claudio Toniolo
- Chemische Institute, Universität Zürich, Winterthurerstr. 190, CH-8057 Zürich, Switzerland; Institut für Physikalische and Theoretische Chemie, J. W. Goethe Universität, Max-von-Laue-Str. 7, D-60438 Frankfurt, Germany; and Institute of Biomolecular Chemistry, Padova Unit, CNR, Department of Chemistry, University of Padova, Via Marzolo 1, I-35131 Padova, Italy
| | - Oliver Zerbe
- Chemische Institute, Universität Zürich, Winterthurerstr. 190, CH-8057 Zürich, Switzerland; Institut für Physikalische and Theoretische Chemie, J. W. Goethe Universität, Max-von-Laue-Str. 7, D-60438 Frankfurt, Germany; and Institute of Biomolecular Chemistry, Padova Unit, CNR, Department of Chemistry, University of Padova, Via Marzolo 1, I-35131 Padova, Italy
| | - Gerhard Stock
- Chemische Institute, Universität Zürich, Winterthurerstr. 190, CH-8057 Zürich, Switzerland; Institut für Physikalische and Theoretische Chemie, J. W. Goethe Universität, Max-von-Laue-Str. 7, D-60438 Frankfurt, Germany; and Institute of Biomolecular Chemistry, Padova Unit, CNR, Department of Chemistry, University of Padova, Via Marzolo 1, I-35131 Padova, Italy
| | - Peter Hamm
- Chemische Institute, Universität Zürich, Winterthurerstr. 190, CH-8057 Zürich, Switzerland; Institut für Physikalische and Theoretische Chemie, J. W. Goethe Universität, Max-von-Laue-Str. 7, D-60438 Frankfurt, Germany; and Institute of Biomolecular Chemistry, Padova Unit, CNR, Department of Chemistry, University of Padova, Via Marzolo 1, I-35131 Padova, Italy
| |
Collapse
|
30
|
Kubo M, Gruia F, Benabbas A, Barabanschikov A, Montfort WR, Maes EM, Champion PM. Low-frequency mode activity of heme: femtosecond coherence spectroscopy of iron porphine halides and nitrophorin. J Am Chem Soc 2008; 130:9800-11. [PMID: 18597456 PMCID: PMC2765994 DOI: 10.1021/ja800916d] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The low-frequency mode activity of metalloporphyrins has been studied for iron porphine-halides (Fe(P)(X), X = Cl, Br) and nitrophorin 4 (NP4) using femtosecond coherence spectroscopy (FCS) in combination with polarized resonance Raman spectroscopy and density functional theory (DFT). It is confirmed that the mode symmetry selection rules for FCS are the same as for Raman scattering and that both Franck-Condon and Jahn-Teller mode activities are observed for Fe(P)(X) under Soret resonance conditions. The DFT-calculated low-frequency (20-400 cm (-1)) modes, and their frequency shifts upon halide substitution, are in good agreement with experimental Raman and coherence data, so that mode assignments can be made. The doming mode is located at approximately 80 cm (-1) for Fe(P)(Cl) and at approximately 60 cm (-1) for Fe(P)(Br). NP4 is also studied with coherence techniques, and the NO-bound species of ferric and ferrous NP4 display a mode at approximately 30-40 cm (-1) that is associated with transient heme doming motion following NO photolysis. The coherence spectra of three ferric derivatives of NP4 with different degrees of heme ruffling distortion are also investigated. We find a mode at approximately 60 cm (-1) whose relative intensity in the coherence spectra depends quadratically on the magnitude of the ruffling distortion. To quantitatively account for this correlation, a new "distortion-induced" Raman enhancement mechanism is presented. This mechanism is unique to low-frequency "soft modes" of the molecular framework that can be distorted by environmental forces. These results demonstrate the potential of FCS as a sensitive probe of dynamic and functionally important nonplanar heme vibrational excitations that are induced by the protein environmental forces or by the chemical reactions in the aqueous phase.
Collapse
Affiliation(s)
- Minoru Kubo
- Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, Massachusetts 02115, USA
| | | | | | | | | | | | | |
Collapse
|
31
|
Abstract
Functions of biologically active molecules are frequently initiated by elementary chemical reactions such as energy and electron transfer, cis-trans isomerizations, and proton transfer. The nature of these reactions generally makes them very fast and efficient, occurring on picosecond and femtosecond timescales. Ultrafast spectroscopy has played an important role in the study of a number of biological processes and has provided unique information about several of nature's responses to light. Here I review the current understanding of light-energy collection and conversion in photosynthesis, the function of carotenoid molecules in photosynthesis, and the primary light-initiated reactions of the photoreceptors rhodopsin, bacteriorhodopsin, photoactive yellow protein, phytochrome, and a new type of blue-light receptor based on flavin chromophores.
Collapse
Affiliation(s)
- Villy Sundström
- Department of Chemical Physics, Lund University, S-221 00 Lund, Sweden.
| |
Collapse
|
32
|
Affiliation(s)
- David M. Leitner
- Department of Chemistry and Chemical Physics Program, University of Nevada, Reno, Nevada 89557;
| |
Collapse
|
33
|
Gruia F, Kubo M, Ye X, Ionascu D, Lu C, Poole RK, Yeh SR, Champion PM. Coherence spectroscopy investigations of the low-frequency vibrations of heme: effects of protein-specific perturbations. J Am Chem Soc 2008; 130:5231-44. [PMID: 18355013 DOI: 10.1021/ja7104027] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Femtosecond coherence spectroscopy is used to probe the low-frequency (20-200 cm(-1)) vibrational modes of heme proteins in solution. Horseradish peroxidase (HRP), myoglobin (Mb), and Campylobacter jejuni globin (Cgb) are compared and significant differences in the coherence spectra are revealed. It is concluded that hydrogen bonding and ligand charge do not strongly affect the low-frequency coherence spectra and that protein-specific deformations of the heme group lower its symmetry and control the relative spectral intensities. Such deformations potentially provide a means for proteins to tune heme reaction coordinates, so that they can perform a broad array of specific functions. Native HRP displays complex spectral behavior above approximately 50 cm(-1) and very weak activity below approximately 50 cm(-1). Binding of the substrate analog, benzhydroxamic acid, leads to distinct changes in the coherence and Raman spectra of HRP that are consistent with the stabilization of a heme water ligand. The CN derivatives of the three proteins are studied to make comparisons under conditions of uniform heme coordination and spin-state. MbCN is dominated by a doming mode near 40 cm(-1), while HRPCN displays a strong oscillation at higher frequency (96 cm(-1)) that can be correlated with the saddling distortion observed in the X-ray structure. In contrast, CgbCN displays low-frequency coherence spectra that contain strong modes near 30 and 80 cm(-1), probably associated with a combination of heme doming and ruffling. HRPNO displays a strong doming mode near 40 cm(-1) that is activated by photolysis. The damping of the coherent motions is significantly reduced when the heme is shielded from solvent fluctuations by the protein material and reduced still further when T approximately < 50 K, as pure dephasing processes due to the protein-solvent phonon bath are frozen out.
Collapse
Affiliation(s)
- Flaviu Gruia
- Department of Physics and Center for Interdisciplinary Research on Complex Systems, Northeastern University, Boston, Massachusetts 02115, USA
| | | | | | | | | | | | | | | |
Collapse
|
34
|
Abstract
Femtosecond stimulated Raman spectroscopy (FSRS) is a new ultrafast spectroscopic technique that provides vibrational structural information with high temporal (50-fs) and spectral (10-cm(1)) resolution. As a result of these unique capabilities, FSRS studies of chemical and biochemical reaction dynamics are expected to grow rapidly, giving previously unattainable insight into the structural dynamics of reactively evolving systems with atomic spatial and femtosecond temporal resolution. This review discusses the experimental and theoretical concepts behind FSRS, with an emphasis on the origins of its unique temporal and spectral capabilities. We illustrate these capabilities with vibrational studies of ultrafast electronic dynamics, as well as the direct structural observation of nonstationary vibrational wave-packet motion in small molecules and in complex biochemical reaction dynamics.
Collapse
Affiliation(s)
- Philipp Kukura
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
| | | | | |
Collapse
|
35
|
Browne WR, McGarvey JJ. The Raman effect and its application to electronic spectroscopies in metal-centered species: Techniques and investigations in ground and excited states. Coord Chem Rev 2007. [DOI: 10.1016/j.ccr.2006.04.019] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
|
36
|
Cerullo G, Manzoni C, Lüer L, Polli D. Time-resolved methods in biophysics. 4. Broadband pump–probe spectroscopy system with sub-20 fs temporal resolution for the study of energy transfer processes in photosynthesis. Photochem Photobiol Sci 2007; 6:135-44. [PMID: 17277836 DOI: 10.1039/b606949e] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this paper we discuss how to push the temporal resolution limits of transient absorption spectroscopy in order to detect very fast processes (energy relaxation, energy or charge transfer, vibrational coherence) taking place in molecules of biological relevance. After reviewing the main principles of femtosecond pump-probe spectroscopy, we describe an experimental setup based on two synchronized non-collinear optical parametric amplifiers (NOPAs). Each NOPA can be independently configured to generate ultra-broadband sub-10 fs visible pulses, tunable 10-15 fs visible pulses, tunable 15-40 fs near-infrared pulses (900-1500 nm). This system enables to perform pump-probe experiments over nearly two octaves of spectrum with sub-20 fs temporal resolution. We then present an application example highlighting the capability of this instrument to track excited state dynamics in biomolecules on the sub-100 fs timescale: the study of carotenoid-bacteriochlorophyll energy transfer processes in peripheral light-harvesting complexes (LH2) from purple bacteria. We show that, by comparing excited-state dynamics of the carotenoids in organic solvents and inside the LH2 complexes, it is possible to visualize in the time domain the primary events in photosynthesis.
Collapse
Affiliation(s)
- Giulio Cerullo
- National Laboratory for Ultrafast and Ultraintense Optical Science, CNR-INFM, Dipartimento di Fisica, Politecnico di Milano, Piazza L. da Vinci 32, 20133, Milano, Italy.
| | | | | | | |
Collapse
|
37
|
Cheng PY, Baskin JS, Zewail AH. Dynamics of clusters: from elementary to biological structures. Proc Natl Acad Sci U S A 2006; 103:10570-6. [PMID: 16740669 PMCID: PMC1502273 DOI: 10.1073/pnas.0507114103] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Between isolated atoms or molecules and bulk materials there lies a class of unique structures, known as clusters, that consist of a few to hundreds of atoms or molecules. Within this range of "nanophase," many physical and chemical properties of the materials evolve as a function of cluster size, and materials may exhibit novel properties due to quantum confinement effects. Understanding these phenomena is in its own rights fundamental, but clusters have the additional advantage of being controllable model systems for unraveling the complexity of condensed-phase and biological structures, not to mention their vanguard role in defining nanoscience and nanotechnology. Over the last two decades, much progress has been made, and this short overview highlights our own involvement in developing cluster dynamics, from the first experiments on elementary systems to model systems in the condensed phase, and on to biological structures.
Collapse
Affiliation(s)
| | - J. Spencer Baskin
- Laboratory for Molecular Sciences, Arthur Amos Noyes Laboratory of Chemical Physics, California Institute of Technology, Pasadena, CA 91125
| | | |
Collapse
|