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Sun T, Kang L, Zhao H, Zhao Y, Gu Y. Photoacid Generators for Biomedical Applications. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2302875. [PMID: 38039443 PMCID: PMC10837391 DOI: 10.1002/advs.202302875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 10/26/2023] [Indexed: 12/03/2023]
Abstract
Photoacid generators (PAGs) are compounds capable of producing hydrogen protons (H+ ) upon irradiation, including irreversible and reversible PAGs, which have been widely studied in photoinduced polymerization and degradation for a long time. In recent years, the applications of PAGs in the biomedical field have attracted more attention due to their promising clinical value. So, an increasing number of novel PAGs have been reported. In this review, the recent progresses of PAGs for biomedical applications is systematically summarized, including tumor treatment, antibacterial treatment, regulation of protein folding and unfolding, control of drug release and so on. Furthermore, a concept of water-dependent reversible photoacid (W-RPA) and its antitumor effect are highlighted. Eventually, the challenges of PAGs for clinical applications are discussed.
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Affiliation(s)
- Tianzhen Sun
- School of Medical TechnologyBeijing Institute of TechnologyNo. 5 South Street, ZhongguancunHaidian DistrictBeijing100081China
| | - Lin Kang
- Key Laboratory of Photochemical Conversion and Optoelectronic MaterialsTechnical Institute of Physics and ChemistryChinese Academy of SciencesNo. 29 Zhongguancun East Road, Haidian DistrictBeijing100190China
- University of Chinese Academy of SciencesNo. 19A Yuquan RoadBeijing100049China
| | - Hongyou Zhao
- School of Medical TechnologyBeijing Institute of TechnologyNo. 5 South Street, ZhongguancunHaidian DistrictBeijing100081China
| | - Yuxia Zhao
- Key Laboratory of Photochemical Conversion and Optoelectronic MaterialsTechnical Institute of Physics and ChemistryChinese Academy of SciencesNo. 29 Zhongguancun East Road, Haidian DistrictBeijing100190China
- University of Chinese Academy of SciencesNo. 19A Yuquan RoadBeijing100049China
| | - Ying Gu
- Department of Laser MedicineThe First Medical CentreChinese PLA General HospitalNo. 28 Fuxing Road, Haidian DistrictBeijing100853China
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2
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Hunt NT. Biomolecular infrared spectroscopy: making time for dynamics. Chem Sci 2024; 15:414-430. [PMID: 38179520 PMCID: PMC10763549 DOI: 10.1039/d3sc05223k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 11/24/2023] [Indexed: 01/06/2024] Open
Abstract
Time resolved infrared spectroscopy of biological molecules has provided a wealth of information relating to structural dynamics, conformational changes, solvation and intermolecular interactions. Challenges still exist however arising from the wide range of timescales over which biological processes occur, stretching from picoseconds to minutes or hours. Experimental methods are often limited by vibrational lifetimes of probe groups, which are typically on the order of picoseconds, while measuring an evolving system continuously over some 18 orders of magnitude in time presents a raft of technological hurdles. In this Perspective, a series of recent advances which allow biological molecules and processes to be studied over an increasing range of timescales, while maintaining ultrafast time resolution, will be reviewed, showing that the potential for real-time observation of biomolecular function draws ever closer, while offering a new set of challenges to be overcome.
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Affiliation(s)
- Neil T Hunt
- Department of Chemistry and York Biomedical Research Institute, University of York Heslington York YO10 5DD UK
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3
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Bozovic O, Jankovic B, Hamm P. Using azobenzene photocontrol to set proteins in motion. Nat Rev Chem 2021; 6:112-124. [PMID: 37117294 DOI: 10.1038/s41570-021-00338-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/14/2021] [Indexed: 02/06/2023]
Abstract
Controlling the activity of proteins with azobenzene photoswitches is a potent tool for manipulating their biological function. With the help of light, it is possible to change binding affinities, control allostery or manipulate complex biological processes, for example. Additionally, owing to their intrinsically fast photoisomerization, azobenzene photoswitches can serve as triggers that initiate out-of-equilibrium processes. Such switching of the activity initiates a cascade of conformational events that can be accessed with time-resolved methods. In this Review, we show how the potency of azobenzene photoswitching can be combined with transient spectroscopic techniques to disclose the order of events and experimentally observe biomolecular interactions in real time. This strategy will further our understanding of how a protein can accommodate, adapt and readjust its structure to answer an incoming signal, revealing more of the dynamical character of proteins.
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4
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Eller MW, Siaw HMH, Dyer RB. Stability of HA2 Prefusion Structure and pH-Induced Conformational Changes in the HA2 Domain of H3N2 Hemagglutinin. Biochemistry 2021; 60:2623-2636. [PMID: 34435771 PMCID: PMC8485334 DOI: 10.1021/acs.biochem.1c00551] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Influenza hemagglutinin is the fusion protein that mediates fusion of the viral and host membranes through a large conformational change upon acidification in the developing endosome. The "spring-loaded" model has long been used to describe the mechanism of hemagglutinin and other type 1 viral glycoproteins. This model postulates a metastable conformation of the HA2 subunit, caged from adopting a lower-free energy conformation by the HA1 subunit. Here, using a combination of biochemical and spectroscopic methods, we study a truncated construct of HA2 (HA2*, lacking the transmembrane domain) recombinantly expressed in Escherichia coli as a model for HA2 without the influence of HA1. Our data show that HA2* folds into a conformation like that of HA2 in full length HA and forms trimers. Upon acidification, HA2* undergoes a conformational change that is consistent with the change from pre- to postfusion HA2 in HA. This conformational change is fast and occurs on a time scale that is not consistent with aggregation. These results suggest that the prefusion conformation of HA2 is stable and the change to the postfusion conformation is due to protonation of HA2 itself and not merely uncaging by HA1.
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Affiliation(s)
- Micah W Eller
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - Hew Ming Helen Siaw
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
| | - R Brian Dyer
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
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5
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Klocke JL, Kottke T. A quantum cascade laser setup for studying irreversible photoreactions in H 2O with nanosecond resolution and microlitre consumption. Phys Chem Chem Phys 2020; 22:26459-26467. [PMID: 33185227 DOI: 10.1039/d0cp03164j] [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
Time-resolved infrared spectroscopy on irreversible reactions requires in general an exchange of sample for thousands of acquisitions leading to high sample consumption. Here, we present a setup employing a modern quantum cascade laser (QCL) as a probe light source to record time-resolved difference spectra of irreversible photoreactions in H2O. The combination of the focused QCL with a pressure-tolerant flow cell and a micrometre stage orthogonal to the flow allowed us to drastically reduce the sample consumption. We investigated the irreversible photoreduction of the cofactor flavin mononucleotide (FMN) in H2O, which is a common reaction taking place in biological photoreceptors. A broad time range from 20 nanoseconds to 1 second was accessible, because the approach minimized any signal drift by the flow. Kinetics were recorded at 46 selected wavenumbers consuming 12 microlitres for a complete dataset. The tuning range of 1490-1740 cm-1 included relevant carbonyl vibrations and the region of strong water absorption at around 1650 cm-1. A continuous dataset in the spectral dimension was generated by applying a fit with a sum of Lorentzians. Subsequent global analysis allowed us to resolve reference spectra and kinetics of the photoreaction proceeding from the triplet excited state via the intermediate flavin anion radical to the product, the fully reduced state of FMN. Accordingly, the neutral radical state is not populated in the disproportionation. The approach strongly facilitates the spectroscopic access to irreversible reactions of flavin-containing photoreceptors and photoenzymes with high time resolution and small sample consumption.
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Affiliation(s)
- Jessica L Klocke
- Physical and Biophysical Chemistry, Department of Chemistry, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld, Germany.
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6
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Park J, Tabet A, Moon J, Chiang PH, Koehler F, Sahasrabudhe A, Anikeeva P. Remotely Controlled Proton Generation for Neuromodulation. NANO LETTERS 2020; 20:6535-6541. [PMID: 32786937 PMCID: PMC8558523 DOI: 10.1021/acs.nanolett.0c02281] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Understanding and modulating proton-mediated biochemical processes in living organisms have been impeded by the lack of tools to control local pH. Here, we design nanotransducers capable of converting noninvasive alternating magnetic fields (AMFs) into protons in physiological environments by combining magnetic nanoparticles (MNPs) with polymeric scaffolds. When exposed to AMFs, the heat dissipated by MNPs triggered a hydrolytic degradation of surrounding polyanhydride or polyester, releasing protons into the extracellular space. pH changes induced by these nanotransducers can be tuned by changing the polymer chemistry or AMF stimulation parameters. Remote magnetic control of local protons was shown to trigger acid-sensing ion channels and to evoke intracellular calcium influx in neurons. By offering a wireless modulation of local pH, our approach can accelerate the mechanistic investigation of the role of protons in biochemical signaling in the nervous system.
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Affiliation(s)
- Jimin Park
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge Massachusetts 02139, United States
- Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge Massachusetts 02139, United States
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Anthony Tabet
- Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge Massachusetts 02139, United States
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Junsang Moon
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge Massachusetts 02139, United States
- Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge Massachusetts 02139, United States
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Po-Han Chiang
- Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge Massachusetts 02139, United States
- Institute of Biomedical Engineering, National Chiao Tung University, Hsinchu City, Taiwan 30010, ROC
| | - Florian Koehler
- Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge Massachusetts 02139, United States
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Atharva Sahasrabudhe
- Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge Massachusetts 02139, United States
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Polina Anikeeva
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge Massachusetts 02139, United States
- Research Laboratory of Electronics, Massachusetts Institute of Technology, Cambridge Massachusetts 02139, United States
- McGovern Institute for Brain Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Department of Brain and Cognitive Sciences, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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7
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Abstract
Infrared difference spectroscopy probes vibrational changes of proteins upon their perturbation. Compared with other spectroscopic methods, it stands out by its sensitivity to the protonation state, H-bonding, and the conformation of different groups in proteins, including the peptide backbone, amino acid side chains, internal water molecules, or cofactors. In particular, the detection of protonation and H-bonding changes in a time-resolved manner, not easily obtained by other techniques, is one of the most successful applications of IR difference spectroscopy. The present review deals with the use of perturbations designed to specifically change the protein between two (or more) functionally relevant states, a strategy often referred to as reaction-induced IR difference spectroscopy. In the first half of this contribution, I review the technique of reaction-induced IR difference spectroscopy of proteins, with special emphasis given to the preparation of suitable samples and their characterization, strategies for the perturbation of proteins, and methodologies for time-resolved measurements (from nanoseconds to minutes). The second half of this contribution focuses on the spectral interpretation. It starts by reviewing how changes in H-bonding, medium polarity, and vibrational coupling affect vibrational frequencies, intensities, and bandwidths. It is followed by band assignments, a crucial aspect mostly performed with the help of isotopic labeling and site-directed mutagenesis, and complemented by integration and interpretation of the results in the context of the studied protein, an aspect increasingly supported by spectral calculations. Selected examples from the literature, predominately but not exclusively from retinal proteins, are used to illustrate the topics covered in this review.
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8
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Beuning CN, Barkley NE, Basa PN, Burdette SC, Levinger NE, Crans DC. Coordination Chemistry of a Controlled Burst of Zn 2+ in Bulk Aqueous and Nanosized Water Droplets with a Zincon Chelator. Inorg Chem 2020; 59:184-188. [DOI: 10.1021/acs.inorgchem.9b02848] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Cheryle N. Beuning
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523-1872, United States
| | - Noah E. Barkley
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523-1872, United States
| | - Prem N. Basa
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, Worcester, Massachusetts 01609, United States
| | - Shawn C. Burdette
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, Worcester, Massachusetts 01609, United States
| | - Nancy E. Levinger
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523-1872, United States
| | - Debbie C. Crans
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523-1872, United States
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9
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Wu JY, Cheng PY. Ultrafast Protonation of an Amide: Photoionization-Induced Proton Transfer in Phenol-Dimethylformamide Complex Cation. J Phys Chem A 2019; 123:10700-10713. [DOI: 10.1021/acs.jpca.9b09651] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Jun-Yi Wu
- Department of Chemistry, National Tsing Hua University, Hsinchu 30043, Taiwan, R.
O. C
| | - Po-Yuan Cheng
- Department of Chemistry, National Tsing Hua University, Hsinchu 30043, Taiwan, R.
O. C
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10
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Flanagan JC, Baiz CR. Ultrafast pH-jump two-dimensional infrared spectroscopy. OPTICS LETTERS 2019; 44:4937-4940. [PMID: 31613233 DOI: 10.1364/ol.44.004937] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 09/17/2019] [Indexed: 06/10/2023]
Abstract
We present a pH-jump two-dimensional infrared (2D IR) spectrometer to probe pH-dependent conformational changes from nanoseconds to milliseconds. The design incorporates a nanosecond 355 nm source into a pulse-shaper-based 2D IR spectrometer to trigger dissociation of a caged proton prior to probing subsequent conformational changes with femtosecond 2D IR spectroscopy. We observe a blue shift in the amide I mode (C═O stretch) of diglycine induced by protonation of the terminal amine. This method combines the bond-specific structural sensitivity of ultrafast 2D IR with triggered conformational dynamics, providing structural access to multiscale biomolecular transformations such as protein folding.
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11
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Minnes L, Greetham GM, Shaw DJ, Clark IP, Fritzsch R, Towrie M, Parker AW, Henry AJ, Taylor RJ, Hunt NT. Uncovering the Early Stages of Domain Melting in Calmodulin with Ultrafast Temperature-Jump Infrared Spectroscopy. J Phys Chem B 2019; 123:8733-8739. [PMID: 31557034 PMCID: PMC7007250 DOI: 10.1021/acs.jpcb.9b08870] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
![]()
The signaling protein
calmodulin (CaM) undergoes a well-known change
in secondary structure upon binding Ca2+, but the structural
plasticity of the Ca2+-free apo state
is linked to CaM functionality. Variable temperature studies of apo-CaM indicate two structural transitions at 46 and 58
°C that are assigned to melting of the C- and N-terminal domains,
respectively, but the molecular mechanism of domain unfolding is unknown.
We report temperature-jump time-resolved infrared (IR) spectroscopy
experiments designed to target the first steps in the C-terminal domain
melting transition of human apo-CaM. A comparison
of the nonequilibrium relaxation of apo-CaM with
the more thermodynamically stable holo-CaM, with
4 equiv of Ca2+ bound, shows that domain melting of apo-CaM begins on microsecond time scales with α-helix
destabilization. These observations enable the assignment of previously
reported dynamics of CaM on hundreds of microsecond time scales to
thermally activated melting, producing a complete mechanism for thermal
unfolding of CaM.
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Affiliation(s)
- Lucy Minnes
- Department of Physics, SUPA , University of Strathclyde , Glasgow G4 0NG , United Kingdom
| | - Gregory M Greetham
- STFC Central Laser Facility, Research Complex at Harwell , Rutherford Appleton Laboratory , Harwell Campus , Didcot OX11 0QX , United Kingdom
| | | | - Ian P Clark
- STFC Central Laser Facility, Research Complex at Harwell , Rutherford Appleton Laboratory , Harwell Campus , Didcot OX11 0QX , United Kingdom
| | - Robby Fritzsch
- Department of Physics, SUPA , University of Strathclyde , Glasgow G4 0NG , United Kingdom
| | - Michael Towrie
- STFC Central Laser Facility, Research Complex at Harwell , Rutherford Appleton Laboratory , Harwell Campus , Didcot OX11 0QX , United Kingdom
| | - Anthony W Parker
- STFC Central Laser Facility, Research Complex at Harwell , Rutherford Appleton Laboratory , Harwell Campus , Didcot OX11 0QX , United Kingdom
| | | | | | - Neil T Hunt
- Department of Chemistry and York Biomedical Research Institute , University of York , Heslington, York YO10 5DD , United Kingdom
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12
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Oppermann M, Spekowius J, Bauer B, Pfister R, Chergui M, Helbing J. Broad-Band Ultraviolet CD Spectroscopy of Ultrafast Peptide Backbone Conformational Dynamics. J Phys Chem Lett 2019; 10:2700-2705. [PMID: 31059267 DOI: 10.1021/acs.jpclett.9b01253] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The far-UV spectral window widely used for the conformational analysis of biomolecules is not easily covered with broad-band lasers. This has made it difficult to use circular dichroism (CD) spectroscopy to directly follow fast structure changes. By combining transient CD spectroscopy in the deep-UV with thioamide substitution, we demonstrate a method to overcome this difficulty. We investigated a dipeptide whose two carbonyl oxygen atoms were replaced by sulfur, red-shifting the strong lowest-lying ππ* transitions into the more accessible 250-370 nm spectral window. Coupling of the two thioamide units cannot be resolved by achiral 2D-UV spectroscopy, but it gives rise to a pronounced bisignate CD spectrum. The transient CD spectra reveal weakening of this coupling in the electronically excited state, where conformational constraints are released. Our results show that direct local probing of fast backbone conformational change via CD spectroscopy is possible in combination with site-selective thio substitution in peptides and proteins.
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Affiliation(s)
- Malte Oppermann
- Laboratory of Ultrafast Spectroscopy, ISIC and Lausanne Centre for Ultrafast Science (LACUS) , École Polytechnique Fédérale de Lausanne , CH-1015 Lausanne , Switzerland
| | - Jasmin Spekowius
- Department of Chemistry , University of Zurich , Winterthurerstrasse 190 , CH-8057 Zürich , Switzerland
| | - Benjamin Bauer
- Laboratory of Ultrafast Spectroscopy, ISIC and Lausanne Centre for Ultrafast Science (LACUS) , École Polytechnique Fédérale de Lausanne , CH-1015 Lausanne , Switzerland
| | - Rolf Pfister
- Department of Chemistry , University of Zurich , Winterthurerstrasse 190 , CH-8057 Zürich , Switzerland
| | - Majed Chergui
- Laboratory of Ultrafast Spectroscopy, ISIC and Lausanne Centre for Ultrafast Science (LACUS) , École Polytechnique Fédérale de Lausanne , CH-1015 Lausanne , Switzerland
| | - Jan Helbing
- Department of Chemistry , University of Zurich , Winterthurerstrasse 190 , CH-8057 Zürich , Switzerland
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13
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Atomistic simulations indicate the functional loop-to-coiled-coil transition in influenza hemagglutinin is not downhill. Proc Natl Acad Sci U S A 2018; 115:E7905-E7913. [PMID: 30012616 DOI: 10.1073/pnas.1805442115] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Influenza hemagglutinin (HA) mediates viral entry into host cells through a large-scale conformational rearrangement at low pH that leads to fusion of the viral and endosomal membranes. Crystallographic and biochemical data suggest that a loop-to-coiled-coil transition of the B-loop region of HA is important for driving this structural rearrangement. However, the microscopic picture for this proposed "spring-loaded" movement is missing. In this study, we focus on understanding the transition of the B loop and perform a set of all-atom molecular dynamics simulations of the full B-loop trimeric structure with the CHARMM36 force field. The free-energy profile constructed from our simulations describes a B loop that stably folds half of the postfusion coiled coil in tens of microseconds, but the full coiled coil is unfavorable. A buried hydrophilic residue, Thr59, is implicated in destabilizing the coiled coil. Interestingly, this conserved threonine is the only residue in the B loop that strictly differentiates between the group 1 and 2 HA molecules. Microsecond-scale constant temperature simulations revealed that kinetic traps in the structural switch of the B loop can be caused by nonnative, intramonomer, or intermonomer β-sheets. The addition of the A helix stabilized the postfusion state of the B loop, but introduced the possibility for further β-sheet structures. Overall, our results do not support a description of the B loop in group 2 HAs as a stiff spring, but, rather, it allows for more structural heterogeneity in the placement of the fusion peptides during the fusion process.
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14
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Stock G, Hamm P. A non-equilibrium approach to allosteric communication. Philos Trans R Soc Lond B Biol Sci 2018; 373:20170187. [PMID: 29735740 PMCID: PMC5941181 DOI: 10.1098/rstb.2017.0187] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/16/2018] [Indexed: 12/16/2022] Open
Abstract
While the theory of protein folding is well developed, including concepts such as rugged energy landscape, folding funnel, etc., the same degree of understanding has not been reached for the description of the dynamics of allosteric transitions in proteins. This is not only due to the small size of the structural change upon ligand binding to an allosteric site, but also due to challenges in designing experiments that directly observe such an allosteric transition. On the basis of recent pump-probe-type experiments (Buchli et al. 2013 Proc. Natl Acad. Sci. USA110, 11 725-11 730. (doi:10.1073/pnas.1306323110)) and non-equilibrium molecular dynamics simulations (Buchenberg et al. 2017 Proc. Natl Acad. Sci. USA114, E6804-E6811. (doi:10.1073/pnas.1707694114)) studying an photoswitchable PDZ2 domain as model for an allosteric transition, we outline in this perspective how such a description of allosteric communication might look. That is, calculating the dynamical content of both experiment and simulation (which agree remarkably well with each other), we find that allosteric communication shares some properties with downhill folding, except that it is an 'order-order' transition. Discussing the multiscale and hierarchical features of the dynamics, the validity of linear response theory as well as the meaning of 'allosteric pathways', we conclude that non-equilibrium experiments and simulations are a promising way to study dynamical aspects of allostery.This article is part of a discussion meeting issue 'Allostery and molecular machines'.
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Affiliation(s)
- Gerhard Stock
- Biomolecular Dynamics, Institute of Physics, Albert Ludwigs University, Freiburg, Germany
| | - Peter Hamm
- Department of Chemistry, University of Zurich, Zurich, Switzerland
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15
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Rimmerman D, Leshchev D, Hsu DJ, Hong J, Abraham B, Henning R, Kosheleva I, Chen LX. Probing Cytochrome c Folding Transitions upon Phototriggered Environmental Perturbations Using Time-Resolved X-ray Scattering. J Phys Chem B 2018; 122:5218-5224. [PMID: 29709179 DOI: 10.1021/acs.jpcb.8b03354] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Direct tracking of protein structural dynamics during folding-unfolding processes is important for understanding the roles of hierarchic structural factors in the formation of functional proteins. Using cytochrome c (cyt c) as a platform, we investigated its structural dynamics during folding processes triggered by local environmental changes (i.e., pH or heme iron center oxidation/spin/ligation states) with time-resolved X-ray solution scattering measurements. Starting from partially unfolded cyt c, a sudden pH drop initiated by light excitation of a photoacid caused a structural contraction in microseconds, followed by active site restructuring and unfolding in milliseconds. In contrast, the reduction of iron in the heme via photoinduced electron transfer did not affect conformational stability at short timescales (<1 ms), despite active site coordination geometry changes. These results demonstrate how different environmental perturbations can change the nature of interaction between the active site and protein conformation, even within the same metalloprotein, which will subsequently affect the folding structural dynamics.
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Affiliation(s)
- Dolev Rimmerman
- Department of Chemistry , Northwestern University , Evanston , Illinois 60208 , United States
| | - Denis Leshchev
- Department of Chemistry , Northwestern University , Evanston , Illinois 60208 , United States
| | - Darren J Hsu
- Department of Chemistry , Northwestern University , Evanston , Illinois 60208 , United States
| | - Jiyun Hong
- Department of Chemistry , Northwestern University , Evanston , Illinois 60208 , United States
| | - Baxter Abraham
- Department of Chemistry and Biochemistry , University of Delaware , Newark , Delaware 19716 , United States
| | - Robert Henning
- Center for Advanced Radiation Sources , The University of Chicago , Chicago , Illinois 60637 , United States
| | - Irina Kosheleva
- Center for Advanced Radiation Sources , The University of Chicago , Chicago , Illinois 60637 , United States
| | - Lin X Chen
- Department of Chemistry , Northwestern University , Evanston , Illinois 60208 , United States.,Chemical Sciences and Engineering Division , Argonne National Laboratory , Argonne , Illinois 60439 , United States
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16
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Jesus CSH, Cruz PF, Arnaut LG, Brito RMM, Serpa C. One Peptide Reveals the Two Faces of α-Helix Unfolding-Folding Dynamics. J Phys Chem B 2018; 122:3790-3800. [PMID: 29558133 DOI: 10.1021/acs.jpcb.8b00229] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The understanding of fast folding dynamics of single α-helices comes mostly from studies on rationally designed peptides displaying sequences with high helical propensity. The folding/unfolding dynamics and energetics of α-helix conformations in naturally occurring peptides remains largely unexplored. Here we report the study of a protein fragment analogue of the C-peptide from bovine pancreatic ribonuclease-A, RN80, a 13-amino acid residue peptide that adopts a highly populated helical conformation in aqueous solution. 1H NMR and CD structural studies of RN80 showed that α-helix formation displays a pH-dependent bell-shaped curve, with a maximum near pH 5, and a large decrease in helical content in alkaline pH. The main forces stabilizing this short α-helix were identified as a salt bridge formed between Glu-2 and Arg-10 and the cation-π interaction involving Tyr-8 and His-12. Thus, deprotonation of Glu-2 or protonation of His-12 are essential for the RN80 α-helix stability. In the present study, RN80 folding and unfolding were triggered by laser-induced pH jumps and detected by time-resolved photoacoustic calorimetry (PAC). The photoacid proton release, amino acid residue protonation, and unfolding/folding events occur at different time scales and were clearly distinguished using time-resolved PAC. The partial unfolding of the RN80 α-helix, due to protonation of Glu-2 and consequent breaking of the stabilizing salt bridge between Glu-2 and Arg-10, is characterized by a concentration-independent volume expansion in the sub-microsecond time range (0.8 mL mol-1, 369 ns). This small volume expansion reports the cost of peptide backbone rehydration upon disruption of a solvent-exposed salt bridge, as well as backbone intrinsic expansion. On the other hand, RN80 α-helix folding triggered by His-12 protonation and subsequent formation of a cation-π interaction leads to a microsecond volume contraction (-6.0 mL mol-1, ∼1.7 μs). The essential role of two discrete side chain interactions, a salt bridge, and in particular a single cation-π interaction in the folding dynamics of a naturally occurring α-helix peptide is uniquely revealed by these data.
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Affiliation(s)
- Catarina S H Jesus
- CQC, Department of Chemistry , University of Coimbra , 3004-535 Coimbra , Portugal
| | - Pedro F Cruz
- CQC, Department of Chemistry , University of Coimbra , 3004-535 Coimbra , Portugal
| | - Luis G Arnaut
- CQC, Department of Chemistry , University of Coimbra , 3004-535 Coimbra , Portugal
| | - Rui M M Brito
- CQC, Department of Chemistry , University of Coimbra , 3004-535 Coimbra , Portugal
| | - Carlos Serpa
- CQC, Department of Chemistry , University of Coimbra , 3004-535 Coimbra , Portugal
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17
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Boonstra S, Blijleven JS, Roos WH, Onck PR, van der Giessen E, van Oijen AM. Hemagglutinin-Mediated Membrane Fusion: A Biophysical Perspective. Annu Rev Biophys 2018; 47:153-173. [PMID: 29494252 DOI: 10.1146/annurev-biophys-070317-033018] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Influenza hemagglutinin (HA) is a viral membrane protein responsible for the initial steps of the entry of influenza virus into the host cell. It mediates binding of the virus particle to the host-cell membrane and catalyzes fusion of the viral membrane with that of the host. HA is therefore a major target in the development of antiviral strategies. The fusion of two membranes involves high activation barriers and proceeds through several intermediate states. Here, we provide a biophysical description of the membrane fusion process, relating its kinetic and thermodynamic properties to the large conformational changes taking place in HA and placing these in the context of multiple HA proteins working together to mediate fusion. Furthermore, we highlight the role of novel single-particle experiments and computational approaches in understanding the fusion process and their complementarity with other biophysical approaches.
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Affiliation(s)
- Sander Boonstra
- Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, The Netherlands; , , , ,
| | - Jelle S Blijleven
- Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, The Netherlands; , , , ,
| | - Wouter H Roos
- Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, The Netherlands; , , , ,
| | - Patrick R Onck
- Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, The Netherlands; , , , ,
| | - Erik van der Giessen
- Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, The Netherlands; , , , ,
| | - Antoine M van Oijen
- School of Chemistry; Faculty of Science, Medicine and Health; University of Wollongong, Wollongong, New South Wales 2522, Australia;
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18
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Schultz BJ, Mohrmann H, Lorenz-Fonfria VA, Heberle J. Protein dynamics observed by tunable mid-IR quantum cascade lasers across the time range from 10ns to 1s. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2018; 188:666-674. [PMID: 28110813 DOI: 10.1016/j.saa.2017.01.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2016] [Revised: 12/29/2016] [Accepted: 01/04/2017] [Indexed: 06/06/2023]
Abstract
We have developed a spectrometer based on tunable quantum cascade lasers (QCLs) for recording time-resolved absorption spectra of proteins in the mid-infrared range. We illustrate its performance by recording time-resolved difference spectra of bacteriorhodopsin in the carboxylic range (1800-1700cm-1) and on the CO rebinding reaction of myoglobin (1960-1840cm-1), at a spectral resolution of 1cm-1. The spectrometric setup covers the time range from 4ns to nearly a second with a response time of 10-15ns. Absorption changes as low as 1×10-4 are detected in single-shot experiments at t>1μs, and of 5×10-6 in kinetics obtained after averaging 100 shots. While previous time-resolved IR experiments have mostly been conducted on hydrated films of proteins, we demonstrate here that the brilliance of tunable quantum cascade lasers is superior to perform ns time-resolved experiments even in aqueous solution (H2O).
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Affiliation(s)
- Bernd-Joachim Schultz
- Experimental Molecular Biophysics, Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Hendrik Mohrmann
- Experimental Molecular Biophysics, Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Victor A Lorenz-Fonfria
- Experimental Molecular Biophysics, Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany; Department of Biochemistry and Molecular Biology, Universitat de València, Dr. Moliner 50, 46100 Burjassot, Spain; Interdisciplinary Research Structure for Biotechnology and Biomedicine (ERI BIOTECMED), Universitat de València, Dr. Moliner 50, 46100 Burjassot, Spain
| | - Joachim Heberle
- Experimental Molecular Biophysics, Department of Physics, Freie Universität Berlin, Arnimallee 14, 14195 Berlin, Germany.
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19
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Kraack JP. Ultrafast structural molecular dynamics investigated with 2D infrared spectroscopy methods. Top Curr Chem (Cham) 2017; 375:86. [PMID: 29071445 DOI: 10.1007/s41061-017-0172-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Accepted: 10/02/2017] [Indexed: 12/23/2022]
Abstract
Ultrafast, multi-dimensional infrared (IR) spectroscopy has been advanced in recent years to a versatile analytical tool with a broad range of applications to elucidate molecular structure on ultrafast timescales, and it can be used for samples in a many different environments. Following a short and general introduction on the benefits of 2D IR spectroscopy, the first part of this chapter contains a brief discussion on basic descriptions and conceptual considerations of 2D IR spectroscopy. Outstanding classical applications of 2D IR are used afterwards to highlight the strengths and basic applicability of the method. This includes the identification of vibrational coupling in molecules, characterization of spectral diffusion dynamics, chemical exchange of chemical bond formation and breaking, as well as dynamics of intra- and intermolecular energy transfer for molecules in bulk solution and thin films. In the second part, several important, recently developed variants and new applications of 2D IR spectroscopy are introduced. These methods focus on (i) applications to molecules under two- and three-dimensional confinement, (ii) the combination of 2D IR with electrochemistry, (iii) ultrafast 2D IR in conjunction with diffraction-limited microscopy, (iv) several variants of non-equilibrium 2D IR spectroscopy such as transient 2D IR and 3D IR, and (v) extensions of the pump and probe spectral regions for multi-dimensional vibrational spectroscopy towards mixed vibrational-electronic spectroscopies. In light of these examples, the important open scientific and conceptual questions with regard to intra- and intermolecular dynamics are highlighted. Such questions can be tackled with the existing arsenal of experimental variants of 2D IR spectroscopy to promote the understanding of fundamentally new aspects in chemistry, biology and materials science. The final part of the chapter introduces several concepts of currently performed technical developments, which aim at exploiting 2D IR spectroscopy as an analytical tool. Such developments embrace the combination of 2D IR spectroscopy and plasmonic spectroscopy for ultrasensitive analytics, merging 2D IR spectroscopy with ultra-high-resolution microscopy (nanoscopy), future variants of transient 2D IR methods, or 2D IR in conjunction with microfluidics. It is expected that these techniques will allow for groundbreaking research in many new areas of natural sciences.
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Affiliation(s)
- Jan Philip Kraack
- Department of Chemistry, University of Zürich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.
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20
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Popp A, Scheerer D, Heck B, Hauser K. Biomolecular dynamics studied with IR-spectroscopy using quantum cascade lasers combined with nanosecond perturbation techniques. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2017; 181:192-199. [PMID: 28364666 DOI: 10.1016/j.saa.2017.03.053] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 03/17/2017] [Accepted: 03/19/2017] [Indexed: 06/07/2023]
Abstract
Early events of protein folding can be studied with fast perturbation techniques triggering non-equilibrium relaxation dynamics. A nanosecond laser-excited pH-jump or temperature-jump (T-jump) was applied to initiate helix folding or unfolding of poly-l-glutamic acid (PGA). PGA is a homopolypeptide with titratable carboxyl side-chains whose protonation degree determines the PGA conformation. A pH-jump was realized by the photochemical release of protons and induces PGA folding due to protonation of the side-chains. Otherwise, the helical conformation can be unfolded by a T-jump. We operated under conditions where PGA does not aggregate and temperature and pH are the regulatory properties of its conformation. The experiments were performed in such a manner that the folding/unfolding jump proceeded to the same PGA conformation. We quantified the increase/decrease in helicity induced by the pH-/T-jump and demonstrated that the T-jump results in a relatively small change in helical content in contrast to the pH-jump. This is caused by the strong pH-dependence of the PGA conformation. The conformational changes were detected by time-resolved single wavelength IR-spectroscopy using quantum cascade lasers (QCL). We could independently observe the kinetics for α-helix folding and unfolding in PGA by using different perturbation techniques and demonstrate the high sensitivity of time-resolved IR-spectroscopy to study protein folding mechanisms.
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Affiliation(s)
- Alexander Popp
- Department of Chemistry, University of Konstanz, 78457 Konstanz, Germany
| | - David Scheerer
- Department of Chemistry, University of Konstanz, 78457 Konstanz, Germany
| | - Benjamin Heck
- Department of Chemistry, University of Konstanz, 78457 Konstanz, Germany
| | - Karin Hauser
- Department of Chemistry, University of Konstanz, 78457 Konstanz, Germany.
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21
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Jeong BS, Dyer RB. Proton Transport Mechanism of M2 Proton Channel Studied by Laser-Induced pH Jump. J Am Chem Soc 2017; 139:6621-6628. [PMID: 28467842 DOI: 10.1021/jacs.7b00617] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The M2 proton transport channel of the influenza virus A is an important model system because it conducts protons with high selectivity and unidirectionally when activated at low pH, despite the relative simplicity of its structure. Although it has been studied extensively, the molecular details of the pH-dependent gating and proton conductance mechanisms are incompletely understood. We report direct observation of the M2 proton channel activation process using a laser-induced pH jump coupled with tryptophan fluorescence as a probe. Biphasic kinetics is observed, with the fast phase corresponding to the His37 protonation, and the slow phase associated with the subsequent conformation change. Unusually fast His37 protonation was observed (2.0 × 1010 M-1 s-1), implying the existence of proton collecting antennae for expedited proton transport. The conformation change (4 × 103 s-1) was about 2 orders of magnitude slower than protonation at endosomal pH, suggesting that a transporter model is likely not feasible.
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Affiliation(s)
- Ban-Seok Jeong
- Department of Chemistry, Emory University , Atlanta, Georgia 30322, United States
| | - R Brian Dyer
- Department of Chemistry, Emory University , Atlanta, Georgia 30322, United States
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22
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Murschel F, Fortier C, Jolicoeur M, Hodges RS, De Crescenzo G. Two Complementary Approaches for the Controlled Release of Biomolecules Immobilized via Coiled-Coil Interactions: Peptide Core Mutations and Multivalent Presentation. Biomacromolecules 2017; 18:965-975. [DOI: 10.1021/acs.biomac.6b01830] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Frederic Murschel
- Department
of Chemical Engineering, Groupe de Recherche en Sciences et Technologies
Biomédicales (GRSTB), Bio-P2 Research Unit, École Polytechnique de Montréal, P.O. Box 6079, succursale Centre-Ville, Montréal, Quebec H3C 3A7, Canada
| | - Charles Fortier
- Department
of Chemical Engineering, Groupe de Recherche en Sciences et Technologies
Biomédicales (GRSTB), Bio-P2 Research Unit, École Polytechnique de Montréal, P.O. Box 6079, succursale Centre-Ville, Montréal, Quebec H3C 3A7, Canada
| | - Mario Jolicoeur
- Department
of Chemical Engineering, Groupe de Recherche en Sciences et Technologies
Biomédicales (GRSTB), Bio-P2 Research Unit, École Polytechnique de Montréal, P.O. Box 6079, succursale Centre-Ville, Montréal, Quebec H3C 3A7, Canada
| | - Robert S. Hodges
- Department
of Biochemistry and Molecular Genetics, University of Colorado, School of Medicine, Anschutz Medical Campus, Aurora, Colorado 80045, United States
| | - Gregory De Crescenzo
- Department
of Chemical Engineering, Groupe de Recherche en Sciences et Technologies
Biomédicales (GRSTB), Bio-P2 Research Unit, École Polytechnique de Montréal, P.O. Box 6079, succursale Centre-Ville, Montréal, Quebec H3C 3A7, Canada
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23
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Chaves OA, Jesus CSH, Cruz PF, Sant'Anna CMR, Brito RMM, Serpa C. Evaluation by fluorescence, STD-NMR, docking and semi-empirical calculations of the o-NBA photo-acid interaction with BSA. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2016; 169:175-181. [PMID: 27376757 DOI: 10.1016/j.saa.2016.06.028] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Revised: 06/03/2016] [Accepted: 06/17/2016] [Indexed: 06/06/2023]
Abstract
Serum albumins present reversible pH dependent conformational transitions. A sudden laser induced pH-jump is a methodology that can provide new insights on localized protein (un)folding processes that occur within the nanosecond to microsecond time scale. To generate the fast pH jump needed to fast-trigger a protein conformational event, a photo-triggered acid generator as o-nitrobenzaldehyde (o-NBA) can be conveniently used. In order to detect potential specific or nonspecific interactions between o-NBA and BSA, we have performed ligand-binding studies using fluorescence spectroscopy, saturation transfer difference (STD) NMR, molecular docking and semi-empirical calculations. Fluorescence quenching indicates the formation of a non-fluorescent complex in the ground-state between the fluorophore and the quencher, but o-NBA does not bind much effectively to the protein (Ka~4.34×10(3)M(-1)) and thus can be considered a relatively weak binder. The corresponding thermodynamic parameters: ΔG°, ΔS° and ΔH° showed that the binding process is spontaneous and entropy driven. Results of (1)H STD-NMR confirm that the photo-acid and BSA interact, and the relative intensities of the signals in the STD spectra show that all o-NBA protons are equally involved in the binding process, which should correspond to a nonspecific interaction. Molecular docking and semi-empirical calculations suggest that the o-NBA binds preferentially to the Trp-212-containing site of BSA (FA7), interacting via hydrogen bonds with Arg-217 and Tyr-149 residues.
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Affiliation(s)
- Otávio A Chaves
- Departament of Chemistry, Universidade Federal Rural do Rio de Janeiro, BR 465, km 47, 23890-000 Seropédica, RJ, Brazil; CQC, Chemistry Department, University of Coimbra, 3004-535 Coimbra, Portugal
| | - Catarina S H Jesus
- CQC, Chemistry Department, University of Coimbra, 3004-535 Coimbra, Portugal; Center for Neuroscience and Cell Biology, University of Coimbra, 3004-535 Coimbra, Portugal
| | - Pedro F Cruz
- CQC, Chemistry Department, University of Coimbra, 3004-535 Coimbra, Portugal
| | - Carlos M R Sant'Anna
- Departament of Chemistry, Universidade Federal Rural do Rio de Janeiro, BR 465, km 47, 23890-000 Seropédica, RJ, Brazil
| | - Rui M M Brito
- Departament of Chemistry, Universidade Federal Rural do Rio de Janeiro, BR 465, km 47, 23890-000 Seropédica, RJ, Brazil; CQC, Chemistry Department, University of Coimbra, 3004-535 Coimbra, Portugal
| | - Carlos Serpa
- CQC, Chemistry Department, University of Coimbra, 3004-535 Coimbra, Portugal.
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24
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Kottke T, Lórenz-Fonfría VA, Heberle J. The Grateful Infrared: Sequential Protein Structural Changes Resolved by Infrared Difference Spectroscopy. J Phys Chem B 2016; 121:335-350. [PMID: 28100053 DOI: 10.1021/acs.jpcb.6b09222] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The catalytic activity of proteins is a function of structural changes. Very often these are as minute as protonation changes, hydrogen bonding changes, and amino acid side chain reorientations. To resolve these, a methodology is afforded that not only provides the molecular sensitivity but allows for tracing the sequence of these hierarchical reactions at the same time. This feature article showcases results from time-resolved IR spectroscopy on channelrhodopsin (ChR), light-oxygen-voltage (LOV) domain protein, and cryptochrome (CRY). All three proteins are activated by blue light, but their biological role is drastically different. Channelrhodopsin is a transmembrane retinylidene protein which represents the first light-activated ion channel of its kind and which is involved in primitive vision (phototaxis) of algae. LOV and CRY are flavin-binding proteins acting as photoreceptors in a variety of signal transduction mechanisms in all kingdoms of life. Beyond their biological relevance, these proteins are employed in exciting optogenetic applications. We show here how IR difference absorption resolves crucial structural changes of the protein after photonic activation of the chromophore. Time-resolved techniques are introduced that cover the time range from nanoseconds to minutes along with some technical considerations. Finally, we provide an outlook toward novel experimental approaches that are currently developed in our laboratories or are just in our minds ("Gedankenexperimente"). We believe that some of them have the potential to provide new science.
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Affiliation(s)
- Tilman Kottke
- Department of Chemistry, Physical and Biophysical Chemistry, Bielefeld University , Universitätsstraße 25, 33615 Bielefeld, Germany
| | | | - Joachim Heberle
- Experimental Molecular Biophysics, Freie Universität Berlin , Arnimalle 14, 14195 Berlin, Germany
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25
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Shafaat OS, Winkler JR, Gray HB, Dougherty DA. Photoactivation of an Acid-Sensitive Ion Channel Associated with Vision and Pain. Chembiochem 2016; 17:1323-7. [PMID: 27123791 DOI: 10.1002/cbic.201600230] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2016] [Indexed: 01/04/2023]
Abstract
We describe the reversible photoactivation of the acid sensitive ligand-gated ion channel ASIC2a, a mammalian channel found throughout the central and peripheral nervous systems that is associated with vision and pain. We also show the activation of GLIC, an acid-sensitive prokaryotic homologue of the nicotinic acetylcholine receptor. Photoactivation was achieved by using visible light irradiation of a newly synthesized water-soluble merocyanine photoacid, 1, which was designed to remove adverse channel blocking effects of a related system. Activation of ASIC2a and GLIC occurs reversibly, in a benign manner, and only upon irradiation. Further studies using transient absorption spectroscopy showed that protonation of a colorimetric base occurred rapidly (ca. 100 μs) after excitation of 1. These results demonstrate that irradiation of 1 can induce rapid, local pH changes that can be used to investigate both biological and chemical proton transfer reactions.
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Affiliation(s)
- Oliver S Shafaat
- Beckman Institute and Division of Chemistry and Chemical Engineering, The California Institute of Technology, 1200 E. California Avenue, Pasadena, CA, 91125, USA
| | - Jay R Winkler
- Beckman Institute and Division of Chemistry and Chemical Engineering, The California Institute of Technology, 1200 E. California Avenue, Pasadena, CA, 91125, USA
| | - Harry B Gray
- Beckman Institute and Division of Chemistry and Chemical Engineering, The California Institute of Technology, 1200 E. California Avenue, Pasadena, CA, 91125, USA.
| | - Dennis A Dougherty
- Beckman Institute and Division of Chemistry and Chemical Engineering, The California Institute of Technology, 1200 E. California Avenue, Pasadena, CA, 91125, USA.
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26
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Popp A, Scheerer D, Chi H, Keiderling TA, Hauser K. Site‐Specific Dynamics of β‐Sheet Peptides with
D
Pro–Gly Turns Probed by Laser‐Excited Temperature‐Jump Infrared Spectroscopy. Chemphyschem 2016; 17:1273-80. [DOI: 10.1002/cphc.201501089] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Indexed: 11/11/2022]
Affiliation(s)
- Alexander Popp
- Department of Chemistry University of Konstanz 78457 Konstanz Germany), Fax: (+49) 7531-88-3139
| | - David Scheerer
- Department of Chemistry University of Konstanz 78457 Konstanz Germany), Fax: (+49) 7531-88-3139
| | - Heng Chi
- Department of Pharmacy and Health Management Jiangsu Food and Pharmaceutical Science College 4 E. Meicheng Rd. Huai'an Jiangsu Province 223003 P. R. China
| | - Timothy A. Keiderling
- Department of Chemistry University of Illinois at Chicago 845 W. Taylor St. Chicago Illinois 60607-7061 USA
| | - Karin Hauser
- Department of Chemistry University of Konstanz 78457 Konstanz Germany), Fax: (+49) 7531-88-3139
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27
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Haghighat S, Ostresh S, Dawlaty JM. Controlling Proton Conductivity with Light: A Scheme Based on Photoacid Doping of Materials. J Phys Chem B 2016; 120:1002-7. [DOI: 10.1021/acs.jpcb.6b00370] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Shima Haghighat
- Department
of Chemistry, University of Southern California, Los Angeles, California 90089-0482, United States
| | - Sarah Ostresh
- Department
of Chemistry, University of Southern California, Los Angeles, California 90089-0482, United States
| | - Jahan M. Dawlaty
- Department
of Chemistry, University of Southern California, Los Angeles, California 90089-0482, United States
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28
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Where the complex things are: single molecule and ensemble spectroscopic investigations of protein folding dynamics. Curr Opin Struct Biol 2015; 36:1-9. [PMID: 26687767 DOI: 10.1016/j.sbi.2015.11.006] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2015] [Accepted: 11/10/2015] [Indexed: 01/11/2023]
Abstract
Progress in our understanding of the simple folding dynamics of small proteins and the complex dynamics of large proteins is reviewed. Recent characterizations of the folding transition path of small proteins revealed a simple dynamics explainable by the native centric model. In contrast, the accumulated data showed the substates containing residual structures in the unfolded state and partially populated intermediates, causing complexity in the early folding dynamics of small proteins. The size of the unfolded proteins in the absence of denaturants is likely expanded but still controversial. The steady progress in the observation of folding of large proteins has clarified the rapid formation of long-range contacts that seem inconsistent with the native centric model, suggesting that the folding strategy of large proteins is distinct from that of small proteins.
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29
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Koziol KL, Johnson PJM, Stucki-Buchli B, Waldauer SA, Hamm P. Fast infrared spectroscopy of protein dynamics: advancing sensitivity and selectivity. Curr Opin Struct Biol 2015; 34:1-6. [PMID: 25900180 DOI: 10.1016/j.sbi.2015.03.012] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Revised: 03/27/2015] [Accepted: 03/31/2015] [Indexed: 01/08/2023]
Abstract
2D-IR spectroscopy has matured to a powerful technique to study the structure and dynamics of peptides, but its extension to larger proteins is still in its infancy, the major limitations being sensitivity and selectivity. Site-selective information requires measuring single vibrational probes at sub-millimolar concentrations where most proteins are still stable, which is a severe challenge for conventional (FT)IR spectroscopy. Besides its ultrafast time-resolution, a so far largely underappreciated potential of 2D-IR spectroscopy lies in its sensitivity gain. The present paper sets the goals and outlines strategies how to use that sensitivity gain together with properly designed vibrational labels to make IR spectroscopy a versatile tool to study a wide class of proteins.
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Affiliation(s)
- Klemens L Koziol
- Department of Chemistry, University of Zurich, Winterthurerstr. 190, CH-8057 Zürich, Switzerland
| | - Philip J M Johnson
- Department of Chemistry, University of Zurich, Winterthurerstr. 190, CH-8057 Zürich, Switzerland
| | - Brigitte Stucki-Buchli
- Department of Chemistry, University of Zurich, Winterthurerstr. 190, CH-8057 Zürich, Switzerland
| | - Steven A Waldauer
- Department of Chemistry, University of Zurich, Winterthurerstr. 190, CH-8057 Zürich, Switzerland
| | - Peter Hamm
- Department of Chemistry, University of Zurich, Winterthurerstr. 190, CH-8057 Zürich, Switzerland.
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