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Monti M, Biancorosso L, Coccia E. Time-Resolved Circular Dichroism in Molecules: Experimental and Theoretical Advances. Molecules 2024; 29:4049. [PMID: 39274897 PMCID: PMC11396666 DOI: 10.3390/molecules29174049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2024] [Revised: 08/22/2024] [Accepted: 08/24/2024] [Indexed: 09/16/2024] Open
Abstract
Following changes in chirality can give access to relevant information on the function or reactivity of molecular systems. Time-resolved circular dichroism (TRCD) spectroscopy proves to be a valid tool to achieve this goal. Depending on the class of molecules, different temporal ranges, spanning from seconds to femtoseconds, need to be investigated to observe such chiroptical changes. Therefore, over the years, several approaches have been adopted to cover the timescale of interest, especially based on pump-probe schemes. Moreover, various theoretical approaches have been proposed to simulate and explain TRCD spectra, including linear and non-linear response methods as well as non-adiabatic molecular dynamics. In this review, an overview on both experimental and theoretical advances in the TRCD field is provided, together with selected applications. A discussion on future theoretical developments for TRCD is also given.
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Affiliation(s)
- Marta Monti
- The Abdus Salam International Centre for Theoretical Physics, Strada Costiera 11, 34151 Trieste, Italy
| | - Leonardo Biancorosso
- Dipartimento di Scienze Chimiche e Farmaceutiche, University of Trieste, Via L. Giorgieri 1, 34127 Trieste, Italy
| | - Emanuele Coccia
- Dipartimento di Scienze Chimiche e Farmaceutiche, University of Trieste, Via L. Giorgieri 1, 34127 Trieste, Italy
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Clinger JA, Chen E, Kliger DS, Phillips GN. Pump-Probe Circular Dichroism Spectroscopy of Cyanobacteriochrome TePixJ Yields: Insights into Its Photoconversion. J Phys Chem B 2021; 125:202-210. [PMID: 33355472 DOI: 10.1021/acs.jpcb.0c04822] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The bilin-containing photoreceptor TePixJ, a member of the cyanobacteriochrome (CBCR) family of phytochromes, switches between blue-light-absorbing and green-light-absorbing states in order to drive phototaxis in Thermosynechococcus elongatus. Its photoswitching process involves the formation of a thioether linkage between the C10 carbon of phycoviolobilin and the sidechain of Cys494 during the change in state from green-absorbing to blue-absorbing forms. Complex changes in the binding pocket propagate the signal to other domains for downstream signaling. Here, we report time-resolved circular dichroism experiments in addition to pump-probe absorption measurements for interpretation of the biophysical mechanism of the green-to-blue photoconversion process of this receptor.
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Affiliation(s)
- Jonathan A Clinger
- Department of Biosciences, Rice University, Houston, Texas 77005, United States
| | - Eefei Chen
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, United States
| | - David S Kliger
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, United States
| | - George N Phillips
- Department of Biosciences, Rice University, Houston, Texas 77005, United States.,Department of Chemistry, Rice University, Houston, Texas 77005, United States
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Scholz M, Morgenroth M, Cho MJ, Choi DH, Oum K, Lenzer T. Ultrafast Broadband Transient Absorption and Circular Dichroism Reveal Relaxation of a Chiral Copolymer. J Phys Chem Lett 2019; 10:5160-5166. [PMID: 31436421 DOI: 10.1021/acs.jpclett.9b02061] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
We present a study of the photoinduced dynamics of the chiral polyfluorene-phenylene copolymer PFPh in THF and in cholesteric thin films. After photoexcitation at 370 nm in THF, ultraviolet-visible-near-infrared (UV-vis-NIR) transient absorption spectra show fast subpicosecond to picosecond intrachain migration of singlet excitons, solvation dynamics, and an exciton lifetime of 410 ps. The PFPh thin film features also interchain singlet exciton migration and exhibits shorter (2.1 and 240 ps) and longer lifetime components (2800 ps, interchain recombination). Furthermore, a setup for ultrafast UV-vis broadband transient circular dichroism (TrCD) spectroscopy has been developed. Fast supramolecular relaxation processes are observed, which are linked to changes in the anisotropic polarizability and pitch length of the cholesteric film. Such combined ultrafast transient CD and absorption experiments hold promise to reveal not only details of relaxation processes in supramolecular arrangements but also structural rearrangements of chiral molecular systems featuring CD signals in the UV-vis region.
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Affiliation(s)
- Mirko Scholz
- Physical Chemistry, University of Siegen, Adolf-Reichwein-Str. 2, 57076 Siegen, Germany
| | - Marius Morgenroth
- Physical Chemistry, University of Siegen, Adolf-Reichwein-Str. 2, 57076 Siegen, Germany
| | - Min Ju Cho
- Department of Chemistry, Research Institute for Natural Sciences, Korea University, 5 Anam-dong, Sungbuk-gu, Seoul 136-701, Korea
| | - Dong Hoon Choi
- Department of Chemistry, Research Institute for Natural Sciences, Korea University, 5 Anam-dong, Sungbuk-gu, Seoul 136-701, Korea
| | - Kawon Oum
- Physical Chemistry, University of Siegen, Adolf-Reichwein-Str. 2, 57076 Siegen, Germany
| | - Thomas Lenzer
- Physical Chemistry, University of Siegen, Adolf-Reichwein-Str. 2, 57076 Siegen, Germany
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Schmid M, Martinez-Fernandez L, Markovitsi D, Santoro F, Hache F, Improta R, Changenet P. Unveiling Excited-State Chirality of Binaphthols by Femtosecond Circular Dichroism and Quantum Chemical Calculations. J Phys Chem Lett 2019; 10:4089-4094. [PMID: 31260627 DOI: 10.1021/acs.jpclett.9b00948] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Time-resolved circular dichroism (TR-CD) is a powerful tool for probing conformational dynamics of biomolecules over large time scales that are crucial for establishing their structure-function relationship. However, such experiments, notably in the femtosecond regime, remain challenging due to their extremely weak signals, prone to polarization artifacts. By using binol and two bridged derivatives (PL1 and PL2) as chiral prototypes, we present here the first comprehensive study of this type in the middle UV, combining femtosecond TR-CD and quantum mechanical calculations (TD-DFT). We show that excitation of the three compounds induces large variations of their transient CD signals, in sharp contrast to those of their achiral transient absorption. We demonstrate that these variations arise from both the alteration of the electronic distribution and the dihedral angle in the excited state. These results highlight the great sensitivity of TR-CD detection to signals hardly accessible to achiral transient absorption.
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Affiliation(s)
- Marco Schmid
- Laboratoire d'Optique et Biosciences, CNRS, INSERM , Ecole Polytechnique, Institut Polytechnique de Paris , 91128 Palaiseau Cedex, France
| | - Lara Martinez-Fernandez
- LIDYL, CEA, CNRS , Université Paris-Saclay , F-91191 Gif-sur-Yvette , France
- Departamento de Química, Facultad de Ciencias, Modúlo13 , Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC, Cantoblanco , 28049 Madrid , Spain
| | - Dimitra Markovitsi
- LIDYL, CEA, CNRS , Université Paris-Saclay , F-91191 Gif-sur-Yvette , France
| | - Fabrizio Santoro
- Consiglio Nazionale delle Ricerche , Istituto di Chimica dei Composti Organometallici, SS di Pisa, Area della Ricerca , via G. Moruzzi 1 , I-56124 Pisa , Italy
| | - François Hache
- Laboratoire d'Optique et Biosciences, CNRS, INSERM , Ecole Polytechnique, Institut Polytechnique de Paris , 91128 Palaiseau Cedex, France
| | - Roberto Improta
- LIDYL, CEA, CNRS , Université Paris-Saclay , F-91191 Gif-sur-Yvette , France
- Istituto Biostrutture e Bioimmagini , Consiglio Nazionale delle Ricerche , Via Mezzocannone 16 , I-80134 Napoli , Italy
| | - Pascale Changenet
- Laboratoire d'Optique et Biosciences, CNRS, INSERM , Ecole Polytechnique, Institut Polytechnique de Paris , 91128 Palaiseau Cedex, France
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Stadnytskyi V, Orf GS, Blankenship RE, Savikhin S. Near shot-noise limited time-resolved circular dichroism pump-probe spectrometer. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2018; 89:033104. [PMID: 29604771 DOI: 10.1063/1.5009468] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
We describe an optical near shot-noise limited time-resolved circular dichroism (TRCD) pump-probe spectrometer capable of reliably measuring circular dichroism signals in the order of μdeg with nanosecond time resolution. Such sensitivity is achieved through a modification of existing TRCD designs and introduction of a new data processing protocol that eliminates approximations that have caused substantial nonlinearities in past measurements and allows the measurement of absorption and circular dichroism transients simultaneously with a single pump pulse. The exceptional signal-to-noise ratio of the described setup makes the TRCD technique applicable to a large range of non-biological and biological systems. The spectrometer was used to record, for the first time, weak TRCD kinetics associated with the triplet state energy transfer in the photosynthetic Fenna-Matthews-Olson antenna pigment-protein complex.
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Affiliation(s)
- Valentyn Stadnytskyi
- Department of Physics and Astronomy, Purdue University, West Lafayette, Indiana 47906, USA
| | - Gregory S Orf
- Departments of Biology and Chemistry, Photosynthetic Antenna Research Center, Washington University in St. Louis, St. Louis, Missouri 63130, USA
| | - Robert E Blankenship
- Departments of Biology and Chemistry, Photosynthetic Antenna Research Center, Washington University in St. Louis, St. Louis, Missouri 63130, USA
| | - Sergei Savikhin
- Department of Physics and Astronomy, Purdue University, West Lafayette, Indiana 47906, USA
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Murdock RJ, Putnam SA, Das S, Gupta A, Chase EDZ, Seal S. High-Throughput, Protein-Targeted Biomolecular Detection Using Frequency-Domain Faraday Rotation Spectroscopy. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2017; 13:1602862. [PMID: 28090735 DOI: 10.1002/smll.201602862] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Indexed: 06/06/2023]
Abstract
A clinically relevant magneto-optical technique (fd-FRS, frequency-domain Faraday rotation spectroscopy) for characterizing proteins using antibody-functionalized magnetic nanoparticles (MNPs) is demonstrated. This technique distinguishes between the Faraday rotation of the solvent, iron oxide core, and functionalization layers of polyethylene glycol polymers (spacer) and model antibody-antigen complexes (anti-BSA/BSA, bovine serum albumin). A detection sensitivity of ≈10 pg mL-1 and broad detection range of 10 pg mL-1 ≲ cBSA ≲ 100 µg mL-1 are observed. Combining this technique with predictive analyte binding models quantifies (within an order of magnitude) the number of active binding sites on functionalized MNPs. Comparative enzyme-linked immunosorbent assay (ELISA) studies are conducted, reproducing the manufacturer advertised BSA ELISA detection limits from 1 ng mL-1 ≲ cBSA ≲ 500 ng mL-1 . In addition to the increased sensitivity, broader detection range, and similar specificity, fd-FRS can be conducted in less than ≈30 min, compared to ≈4 h with ELISA. Thus, fd-FRS is shown to be a sensitive optical technique with potential to become an efficient diagnostic in the chemical and biomolecular sciences.
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Affiliation(s)
- Richard J Murdock
- Health Sciences and Technology (HST), Institute for Medical Engineering and Science (IMES), Massachusetts Institute of Technology and Harvard University, 77 Massachusetts Avenue 76-679, Cambridge, MA, 02139, USA
| | - Shawn A Putnam
- Department of Mechanical and Aerospace Engineering, University of Central Florida, P.O. Box, 162450, ENGR 1, Rm. 213, Orlando, FL, 32816, USA
| | - Soumen Das
- Department of Materials Science and Engineering, Advanced Materials Processing and Analysis Center, (AMPAC), Nanoscience Technology Center (NSTC), University of Central Florida, P.O. Box 162455, ENGR 1, Rm. 207, Orlando, FL, 32816, USA
| | - Ankur Gupta
- Department of Materials Science and Engineering, Advanced Materials Processing and Analysis Center, (AMPAC), Nanoscience Technology Center (NSTC), University of Central Florida, P.O. Box 162455, ENGR 1, Rm. 207, Orlando, FL, 32816, USA
| | - Elyse D Z Chase
- Department of Mechanical Engineering and Applied Mechanics, University of Pennsylvania, 229, Towne Building, 220 South 33rd Street, Philadelphia, PA, 19104, USA
| | - Sudipta Seal
- Department of Materials Science and Engineering, Advanced Materials Processing and Analysis Center, (AMPAC), Nanoscience Technology Center (NSTC), University of Central Florida, P.O. Box 162455, ENGR 1, Rm. 207, Orlando, FL, 32816, USA
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Sukenik S, Pogorelov TV, Gruebele M. Can Local Probes Go Global? A Joint Experiment-Simulation Analysis of λ(6-85) Folding. J Phys Chem Lett 2016; 7:1960-1965. [PMID: 27101436 DOI: 10.1021/acs.jpclett.6b00582] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The process of protein folding is known to involve global motions in a cooperative affair; the structure of most of the protein sequences is gained or lost over a narrow range of temperature, denaturant, or pressure perturbations. At the same time, recent simulations and experiments reveal a complex structural landscape with a rich set of local motions and conformational changes. We couple experimental kinetic and thermodynamic measurements with specifically tailored analysis of simulation data to isolate local versus global folding probes. We find that local probes exhibit lower melting temperatures, smaller surface area changes, and faster kinetics compared to global ones. We also see that certain local probes of folding match the global behavior more closely than others. Our work highlights the importance of using multiple probes to fully characterize protein folding dynamics by theory and experiment.
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Affiliation(s)
- Shahar Sukenik
- Department of Chemistry, School of Chemical Sciences, and Beckman Institute for Advanced Science and Technology, #National Center for Supercomputing Applications, and ‡Department of Physics and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign , Champaign, Illinois 61801, United States
| | - Taras V Pogorelov
- Department of Chemistry, School of Chemical Sciences, and Beckman Institute for Advanced Science and Technology, #National Center for Supercomputing Applications, and ‡Department of Physics and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign , Champaign, Illinois 61801, United States
| | - Martin Gruebele
- Department of Chemistry, School of Chemical Sciences, and Beckman Institute for Advanced Science and Technology, #National Center for Supercomputing Applications, and ‡Department of Physics and Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign , Champaign, Illinois 61801, United States
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Biophysical Methods to Investigate Intrinsically Disordered Proteins: Avoiding an “Elephant and Blind Men” Situation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 870:215-60. [DOI: 10.1007/978-3-319-20164-1_7] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Chen E, Kliger DS. Deconstructing time-resolved optical rotatory dispersion kinetic measurements of cytochrome c folding: from molten globule to the native state. Methods Mol Biol 2012; 895:405-419. [PMID: 22760330 DOI: 10.1007/978-1-61779-927-3_23] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The far-UV time-resolved optical rotatory dispersion (TRORD) technique has contributed significantly to our understanding of nanosecond secondary structure kinetics in protein folding and function reactions. For reduced cytochrome c, protein folding kinetics have been probed largely from the unfolded to the native state. Here we provide details about sample preparation and the TRORD apparatus and measurements for studying folding from a partly unfolded state to the native secondary structure conformation of reduced cytochrome c.
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Affiliation(s)
- Eefei Chen
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA, USA.
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Lei H, Chen C, Xiao Y, Duan Y. The protein folding network indicates that the ultrafast folding mutant of villin headpiece subdomain has a deeper folding funnel. J Chem Phys 2011; 134:205104. [PMID: 21639484 PMCID: PMC3124538 DOI: 10.1063/1.3596272] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2011] [Accepted: 05/11/2011] [Indexed: 11/14/2022] Open
Abstract
Protein folding is a dynamic process with continuous transitions among different conformations. In this work, the dynamics in the protein folding network of villin headpiece subdomain (HP35) has been investigated based on multiple reversible folding trajectories of HP35 and its ultrafast folding mutant where sub-angstrom folding was achieved. The four folding states were clearly separated on the network, validating the classification of the states. Examination of the eight conformers with different formation of the individual helices revealed high plasticity of the three helices in all the four states. A consistent feature between the wild type and mutant protein is the dominant conformer 111 (all three helices formed) in the folded state and conformers 111 and 011 (helices II and III formed) in the major intermediate state, indicating the critical role of helices II and III in the folding mechanism. When compared to the wild type, the folding landscape of the ultrafast folding mutant exhibited a deeper folding funnel towards the folded state. The very beginning of the folding (0-10 ns) was very similar for both protein variants but it soon diverged and displayed different folding pathways. Although going through the major intermediate state is the dominant pathway for both, it was also observed that some folding went through the minor intermediate state for the mutant. The intriguing difference resulting from the mutation at two residues in helix III has been carefully analyzed and discussed in details.
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Affiliation(s)
- Hongxing Lei
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, China.
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Eom I, Ahn SH, Rhee H, Cho M. Broadband near UV to visible optical activity measurement using self-heterodyned method. OPTICS EXPRESS 2011; 19:10017-10028. [PMID: 21643260 DOI: 10.1364/oe.19.010017] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
We demonstrate that broadband electronic optical activity can be measured with supercontinuum light pulse generated by a femtosecond pump (800 nm). It is the self-heterodyned detection technique that enables us to selectively measure the real (optical rotatory dispersion, ORD) or imaginary (circular dichroism, CD) part of the chiroptical susceptibility by controlling the incident polarization state. The single-shot-based measurement that is capable of correcting power fluctuations of the continuum light is realized by using a fast CCD detector and a polarizing beam splitter. Particularly, non-differential scheme used does not rely on any polarization-switching components. We anticipate that this broadband CD/ORD spectrometry with intrinsically ultrafast time-resolution will be applied to a variety of ultrafast chiroptical dynamics studies.
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Affiliation(s)
- Intae Eom
- Korea Basic Science Institute, Seoul 136-713, South Korea
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