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Dong T, Yu P, Zhao J, Wang J. Probing the local structure and dynamics of nucleotides using vibrationally enhanced alkynyl stretching. Phys Chem Chem Phys 2022; 24:29988-29998. [PMID: 36472165 DOI: 10.1039/d2cp03920f] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Monitoring the site-specific local structure and dynamics of polynucleotides and DNA is important for understanding their biological functions. However, structurally characterizing these biomolecules with high time resolution has been known to be experimentally challenging. In this work, several 5-silylethynyl-2'-deoxynucleosides and 5-substituted phenylethynyl-2'-deoxynucleosides on the basis of deoxycytidine (dC) and deoxythymidine (dT) were synthesized, in which the alkynyl group shows intensified CC stretching vibration with infrared transition dipole moment magnitude close to that of typical CO stretching, and exhibits structural sensitivities in both vibrational frequency and spectral width. In particular, 5-trimethylsilylethynyl-2'-dC (TMSEdC, molecule 1a) was examined in detail using femtosecond nonlinear IR spectroscopy. The solvent dependent CC stretching frequency of 1a can be reasonably interpreted mainly as the hydrogen-bonding effect between the solvent and cytosine base ring structure. Transient 2D IR and pump-probe IR measurements of 1a carried out comparatively in two aprotic solvents (DMSO and THF) and one protic solvent (MeOH) further reveal solvent dependent ultrafast vibrational properties, including diagonal anharmonicity, spectral diffusion, vibrational relaxation and anisotropy dynamics. These observed sensitivities are rooted in an extended π-conjugation of the base ring structure in which the CC group is actively involved. Our results show that the intensified CC stretching vibration can potentially provide a site-specific IR probe for monitoring the equilibrium and ultrafast structural dynamics of polynucleotides.
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Affiliation(s)
- Tiantian Dong
- Beijing National Laboratory for Molecular Sciences, Molecular Reaction Dynamics Laboratory, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China. .,University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Pengyun Yu
- Beijing National Laboratory for Molecular Sciences, Molecular Reaction Dynamics Laboratory, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China. .,University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Juan Zhao
- Beijing National Laboratory for Molecular Sciences, Molecular Reaction Dynamics Laboratory, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China. .,University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Jianping Wang
- Beijing National Laboratory for Molecular Sciences, Molecular Reaction Dynamics Laboratory, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China. .,University of Chinese Academy of Sciences, Beijing 100049, P. R. China
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2
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Lee B, Papoutsis BM, Wong NY, Piacentini J, Kearney C, Huggins NA, Cruz N, Ng TT, Hao KH, Kramer JS, Fenlon EE, Nerenberg PS, Phillips-Piro CM, Brewer SH. Unraveling Complex Local Protein Environments with 4-Cyano-l-phenylalanine. J Phys Chem B 2022; 126:8957-8969. [PMID: 36317866 PMCID: PMC10234312 DOI: 10.1021/acs.jpcb.2c05954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
We present a multifaceted approach to effectively probe complex local protein environments utilizing the vibrational reporter unnatural amino acid (UAA) 4-cyano-l-phenylalanine (pCNPhe) in the model system superfolder green fluorescent protein (sfGFP). This approach combines temperature-dependent infrared (IR) spectroscopy, X-ray crystallography, and molecular dynamics (MD) simulations to provide a molecular interpretation of the local environment of the nitrile group in the protein. Specifically, a two-step enantioselective synthesis was developed that provided an 87% overall yield of pCNPhe in high purity without the need for chromatography. It was then genetically incorporated individually at three unique sites (74, 133, and 149) in sfGFP to probe these local protein environments. The incorporation of the UAA site-specifically in sfGFP utilized an engineered, orthogonal tRNA synthetase in E. coli using the Amber codon suppression protocol, and the resulting UAA-containing sfGFP constructs were then explored with this approach. This methodology was effectively utilized to further probe the local environments of two surface sites (sites 133 and 149) that we previously explored with room temperature IR spectroscopy and X-ray crystallography and a new interior site (site 74) featuring a complex local environment around the nitrile group of pCNPhe. Site 133 was found to be solvent-exposed, while site 149 was partially buried. Site 74 was found to consist of three distinct local environments around the nitrile group including nonspecific van der Waals interactions, hydrogen-bonding to a structural water, and hydrogen-bonding to a histidine side chain.
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Affiliation(s)
- ByungUk Lee
- Department of Chemistry, Franklin & Marshall College, PO Box 3003, Lancaster, PA 17604-3003
| | - Brianna M. Papoutsis
- Department of Chemistry, Franklin & Marshall College, PO Box 3003, Lancaster, PA 17604-3003
| | - Nathan Y. Wong
- Department of Chemistry, Franklin & Marshall College, PO Box 3003, Lancaster, PA 17604-3003
| | - Juliana Piacentini
- Department of Chemistry, Franklin & Marshall College, PO Box 3003, Lancaster, PA 17604-3003
| | - Caroline Kearney
- Department of Chemistry, Franklin & Marshall College, PO Box 3003, Lancaster, PA 17604-3003
| | - Nia A. Huggins
- Department of Biological Sciences, California State University, Los Angeles, 5151 State University Drive, Los Angeles, CA 90032
| | - Nicole Cruz
- Department of Biological Sciences, California State University, Los Angeles, 5151 State University Drive, Los Angeles, CA 90032
| | - Tracey T. Ng
- Department of Physics and Astronomy, California State University, Los Angeles, 5151 State University Drive, Los Angeles, CA 90032
| | - Kexin Heather Hao
- Department of Chemistry, Franklin & Marshall College, PO Box 3003, Lancaster, PA 17604-3003
| | - Jeremy S. Kramer
- Department of Chemistry, Franklin & Marshall College, PO Box 3003, Lancaster, PA 17604-3003
| | - Edward E. Fenlon
- Department of Chemistry, Franklin & Marshall College, PO Box 3003, Lancaster, PA 17604-3003
| | - Paul S. Nerenberg
- Department of Biological Sciences, California State University, Los Angeles, 5151 State University Drive, Los Angeles, CA 90032
- Department of Physics and Astronomy, California State University, Los Angeles, 5151 State University Drive, Los Angeles, CA 90032
| | | | - Scott H. Brewer
- Department of Chemistry, Franklin & Marshall College, PO Box 3003, Lancaster, PA 17604-3003
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3
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Navo CD, Oroz P, Mazo N, Blanco M, Peregrina JM, Jiménez-Osés G. Stereoselective α-Deuteration of Serine, Cysteine, Selenocysteine, and 2,3-Diaminopropanoic Acid Derivatives. Org Lett 2022; 24:6810-6815. [PMID: 36082943 DOI: 10.1021/acs.orglett.2c02715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Efficient methodologies for synthesizing enantiopure α-deuterated derivatives of serine, cysteine, selenocysteine, and 2,3-diaminopropanoic acid have been developed. H/D exchange was achieved by deprotonation of a chiral bicyclic serine equivalent followed by selective deuteration. Additionally, diastereoselective additions of thiols, selenols, and amines to a chiral bicyclic dehydroalanine in deuterated alcohols allowed site-selective deuteration at the Cα atom of cysteine, selenocysteine, and 2,3-diaminopropanoic acid derivatives. A deuterated analogue of carbocysteine, a drug for the treatment of bronchiectasis, was synthesized.
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Affiliation(s)
- Claudio D Navo
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160 Derio, Spain
| | - Paula Oroz
- Departamento de Química, Centro de Investigación en Síntesis Química, Universidad de La Rioja, 26006 Logroño, La Rioja, Spain
| | - Nuria Mazo
- Departamento de Química, Centro de Investigación en Síntesis Química, Universidad de La Rioja, 26006 Logroño, La Rioja, Spain
| | - Marina Blanco
- Departamento de Química, Centro de Investigación en Síntesis Química, Universidad de La Rioja, 26006 Logroño, La Rioja, Spain
| | - Jesús M Peregrina
- Departamento de Química, Centro de Investigación en Síntesis Química, Universidad de La Rioja, 26006 Logroño, La Rioja, Spain
| | - Gonzalo Jiménez-Osés
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160 Derio, Spain.,Ikerbasque, Basque Foundation for Science, 48013 Bilbao, Spain
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4
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Adams ZC, Olson EJ, Lopez-Silva TL, Lian Z, Kim AY, Holcomb M, Zimmermann J, Adhikary R, Dawson PE. Direct observation of peptide hydrogel self-assembly. Chem Sci 2022; 13:10020-10028. [PMID: 36128231 PMCID: PMC9430618 DOI: 10.1039/d1sc06562a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 07/14/2022] [Indexed: 11/30/2022] Open
Abstract
The characterization of self-assembling molecules presents significant experimental challenges, especially when associated with phase separation or precipitation. Transparent window infrared (IR) spectroscopy leverages site-specific probes that absorb in the “transparent window” region of the biomolecular IR spectrum. Carbon–deuterium (C–D) bonds are especially compelling transparent window probes since they are non-perturbative, can be readily introduced site selectively into peptides and proteins, and their stretch frequencies are sensitive to changes in the local molecular environment. Importantly, IR spectroscopy can be applied to a wide range of molecular samples regardless of solubility or physical state, making it an ideal technique for addressing the solubility challenges presented by self-assembling molecules. Here, we present the first continuous observation of transparent window probes following stopped-flow initiation. To demonstrate utility in a self-assembling system, we selected the MAX1 peptide hydrogel, a biocompatible material that has significant promise for use in drug delivery and medical applications. C–D labeled valine was synthetically introduced into five distinct positions of the twenty-residue MAX1 β-hairpin peptide. Consistent with current structural models, steady-state IR absorption frequencies and linewidths of C–D bonds at all labeled positions indicate that these side chains occupy a hydrophobic region of the hydrogel and that the motion of side chains located in the middle of the hairpin is more restricted than those located on the hairpin ends. Following a rapid change in ionic strength to initiate self-assembly, the peptide absorption spectra were monitored as function of time, allowing determination of site-specific time constants. We find that within the experimental resolution, MAX1 self-assembly occurs as a cooperative process. These studies suggest that stopped-flow transparent window FTIR can be extended to other time-resolved applications, such as protein folding and enzyme kinetics. To facilitate the characterization of phase-transitioning molecules, site-specific non-perturbative infrared probes are leveraged for continuous observation of the self-assembly of fibrils in a peptide hydrogel following stopped-flow initiation.![]()
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Affiliation(s)
- Zoë C. Adams
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California, 92037, USA
| | - Erika J. Olson
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California, 92037, USA
| | - Tania L. Lopez-Silva
- Chemical Biology Laboratory, National Cancer Institute, National Institutes of Health, Frederick, MD 21702, USA
| | - Zhengwen Lian
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California, 92037, USA
| | - Audrey Y. Kim
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California, 92037, USA
| | - Matthew Holcomb
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California, 92037, USA
| | - Jörg Zimmermann
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California, 92037, USA
| | - Ramkrishna Adhikary
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California, 92037, USA
| | - Philip E. Dawson
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California, 92037, USA
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5
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Abstract
Voltage gated ion channels (VGICs) shape the electrical character of cells by undergoing structural changes in response to membrane depolarization. High-resolution techniques have provided a wealth of data on individual VGIC structures, but the conformational changes of endogenous channels in live cell membranes have remained unexplored. Here, we describe methods for imaging structural changes of voltage-gated K+ channels in living cells, using peptidyl toxins labeled with fluorophores that report specific protein conformations. These Endogenous Voltage-sensor Activity Probes (EVAPs) enable study of both VGIC allostery and function in the context of endogenous live-cell membranes under different physiological states. In this chapter, we describe methods for the synthesis, imaging, and analysis of dynamic EVAPs, which can report K+ channel activity in complex tissue preparations via 2-photon excitation microscopy, and environment-sensitive EVAPs, which report voltage-dependent conformational changes at the VGIC-toxin interface. The methods here present the utility of current EVAPs and lay the groundwork for the development of other probes that act by similar mechanisms. EVAPs can be correlated with electrophysiology, offering insight into the molecular details of endogenous channel function and allostery in live cells. This enables investigation of conformational changes of channels in their native, functional states, putting structures and models into a context of live-cell membranes. The expansive array of state-dependent ligands and optical probes should enable probes more generally for investigating the molecular motions of endogenous proteins.
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Affiliation(s)
- Robert Stewart
- Department of Physiology & Membrane Biology, University of California, Davis, CA, United States
| | - Bruce E Cohen
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, United States; Division of Molecular Biophysics & Integrated Bioimaging, Lawrence Berkeley National Laboratory, Berkeley, CA, United States.
| | - Jon T Sack
- Department of Physiology & Membrane Biology, University of California, Davis, CA, United States; Department of Anesthesiology & Pain Medicine, University of California, Davis, CA, United States.
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Park JY, Kwon HJ, Mondal S, Han H, Kwak K, Cho M. Two-dimensional IR spectroscopy reveals a hidden Fermi resonance band in the azido stretch spectrum of β-azidoalanine. Phys Chem Chem Phys 2020; 22:19223-19229. [PMID: 32812969 DOI: 10.1039/d0cp02693j] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Azido stretch modes in a variety of azido-derivatized nonnatural amino acids and nucleotides have been used as a site-specific infrared (IR) probe for monitoring changes in their conformations and local electrostatic environments. The vibrational bands of azide probes are often accompanied by complex line shapes with shoulder peaks, which may arise either from incomplete background subtraction, Fermi resonance, or multiple conformers. The isotope substitution in the infrared probe has thus been introduced to remove Fermi resonances without causing a significant perturbation to the structure. Here, we synthesized and labeled the mid-N atoms of aliphatic azide derivatives with 15N to study the effects of isotope labelling on their vibrational properties. The FT-IR spectra of the aliphatic azide with asymmetric lineshape became a single symmetric band upon isotope substitution, which might be an indication of the removal of the hidden Fermi resonance from the system. We also noticed that the 2D-IR spectrum of unlabeled aliphatic azide has cross-peaks, even though it is not apparently identifiable. The 1D slice spectra obtained from the 2D-IR spectra reveal the existence of a hidden Fermi resonance peak. Furthermore, we show that this weak Fermi resonance does not produce discernible oscillatory beating patterns in the IR pump-probe spectrum, which has been used as evidence of the Fermi resonance. Therefore, we confirm that isotope labelling combined with 2D-IR spectroscopy is the most efficient and incisive way to identify the origin of small shoulder peaks in the linear and nonlinear vibrational spectra of various IR probe molecules.
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Affiliation(s)
- Jun Young Park
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Korea University, Seoul 02841, Republic of Korea. and Department of Chemistry, Korea University, Seoul 02841, Republic of Korea.
| | - Hyeok-Jun Kwon
- Department of Chemistry, Korea University, Seoul 02841, Republic of Korea.
| | - Saptarsi Mondal
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Korea University, Seoul 02841, Republic of Korea. and Department of Chemistry, Korea University, Seoul 02841, Republic of Korea.
| | - Hogyu Han
- Department of Chemistry, Korea University, Seoul 02841, Republic of Korea.
| | - Kyungwon Kwak
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Korea University, Seoul 02841, Republic of Korea. and Department of Chemistry, Korea University, Seoul 02841, Republic of Korea.
| | - Minhaeng Cho
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Korea University, Seoul 02841, Republic of Korea. and Department of Chemistry, Korea University, Seoul 02841, Republic of Korea.
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7
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Park JY, Mondal S, Kwon HJ, Sahu PK, Han H, Kwak K, Cho M. Effect of isotope substitution on the Fermi resonance and vibrational lifetime of unnatural amino acids modified with IR probe: A 2D-IR and pump-probe study of 4-azido-L-phenyl alanine. J Chem Phys 2020; 153:164309. [DOI: 10.1063/5.0025289] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Jun Young Park
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Korea University, Seoul 02841, South Korea
- Department of Chemistry, Korea University, Seoul 02841, South Korea
| | - Saptarsi Mondal
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Korea University, Seoul 02841, South Korea
- Department of Chemistry, Korea University, Seoul 02841, South Korea
| | - Hyeok-Jun Kwon
- Department of Chemistry, Korea University, Seoul 02841, South Korea
| | - Prabhat Kumar Sahu
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Korea University, Seoul 02841, South Korea
- Department of Chemistry, Korea University, Seoul 02841, South Korea
| | - Hogyu Han
- Department of Chemistry, Korea University, Seoul 02841, South Korea
| | - Kyungwon Kwak
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Korea University, Seoul 02841, South Korea
- Department of Chemistry, Korea University, Seoul 02841, South Korea
| | - Minhaeng Cho
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS), Korea University, Seoul 02841, South Korea
- Department of Chemistry, Korea University, Seoul 02841, South Korea
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Fletcher-Taylor S, Thapa P, Sepela RJ, Kaakati R, Yarov-Yarovoy V, Sack JT, Cohen BE. Distinguishing Potassium Channel Resting State Conformations in Live Cells with Environment-Sensitive Fluorescence. ACS Chem Neurosci 2020; 11:2316-2326. [PMID: 32579336 DOI: 10.1021/acschemneuro.0c00276] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Ion channels are polymorphic membrane proteins whose high-resolution structures offer images of individual conformations, giving us starting points for identifying the complex and transient allosteric changes that give rise to channel physiology. Here, we report live-cell imaging of voltage-dependent structural changes of voltage-gated Kv2.1 channels using peptidyl tarantula toxins labeled with an environment-sensitive fluorophore, whose spectral shifts enable identification of voltage-dependent conformation changes in the resting voltage sensing domain (VSD) of the channel. We synthesize a new environment-sensitive, far-red fluorophore, julolidine phenoxazone (JP) azide, and conjugate it to tarantula toxin GxTX to characterize Kv2.1 VSD allostery during membrane depolarization. JP has an inherent response to the polarity of its immediate surroundings, offering site-specific structural insight into each channel conformation. Using voltage-clamp spectroscopy to collect emission spectra as a function of membrane potential, we find that they vary with toxin labeling site, the presence of Kv2 channels, and changes in membrane potential. With a high-affinity conjugate in which the fluorophore itself interacts closely with the channel, the emission shift midpoint is 50 mV more negative than the Kv2.1 gating current midpoint. This suggests that substantial conformational changes at the toxin-channel interface are associated with early gating charge transitions and these are not concerted with VSD motions at more depolarized potentials. These fluorescent probes enable study of conformational changes that can be correlated with electrophysiology, putting channel structures and models into a context of live-cell membranes and physiological states.
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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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Luo M, Eaton CN, Hess KR, Phillips-Piro CM, Brewer SH, Fenlon EE. Paired Spectroscopic and Crystallographic Studies of Proteases. ChemistrySelect 2019; 4:9836-9843. [PMID: 34169145 PMCID: PMC8221577 DOI: 10.1002/slct.201902049] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 08/23/2019] [Indexed: 12/13/2022]
Abstract
The active sites of subtilisin and trypsin have been studied by paired IR spectroscopic and X-ray crystallographic studies. The active site serines of the proteases were reacted with 4-cyanobenzenesulfonyl fluoride (CBSF), an inhibitor that contains a nitrile vibrational reporter. The nitrile stretch vibration of the water-soluble inhibitor model, potassium 4-cyanobenzenesulfonate (KCBSO), and the inhibitor were calibrated by IR solvent studies in H2O/DMSO and the frequency-temperature line-slope (FTLS) method in H2O and THF. The inhibitor complexes were examined by FTLS and the slopes of the best fit lines for subtilisin-CBS and trypsin-CBS in aqueous buffer were both measured to be -3.5×10-2 cm-1/°C. These slopes were intermediate in value between that of KCBSO in aqueous buffer and CBSF in THF, which suggests that the active-site nitriles in both proteases are mostly solvated. The X-ray crystal structures of the subtilisin-CBS and trypsin-CBS complexes were solved at 1.27 and 1.32 Å, respectively. The inhibitor was modelled in two conformations in subtilisin-CBS and in one conformation in the trypsin-CBS. The crystallographic data support the FTLS data that the active-site nitrile groups are mostly solvated and participate in hydrogen bonds with water molecules. The combination of IR spectroscopy utilizing vibrational reporters paired with X-ray crystallography provides a powerful approach to studying protein structure.
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Affiliation(s)
- Meiqi Luo
- Department of Chemistry, Franklin & Marshall College, PO Box 3003, Lancaster, PA 17604-3003
| | - Christopher N. Eaton
- Department of Chemistry, Franklin & Marshall College, PO Box 3003, Lancaster, PA 17604-3003
| | - Kenneth R. Hess
- Department of Chemistry, Franklin & Marshall College, PO Box 3003, Lancaster, PA 17604-3003
| | | | - Scott H. Brewer
- Department of Chemistry, Franklin & Marshall College, PO Box 3003, Lancaster, PA 17604-3003
| | - Edward E. Fenlon
- Department of Chemistry, Franklin & Marshall College, PO Box 3003, Lancaster, PA 17604-3003
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11
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Wu H, Saltzberg DJ, Kratochvil HT, Jo H, Sali A, DeGrado WF. Glutamine Side Chain 13C═ 18O as a Nonperturbative IR Probe of Amyloid Fibril Hydration and Assembly. J Am Chem Soc 2019; 141:7320-7326. [PMID: 30998340 DOI: 10.1021/jacs.9b00577] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Infrared (IR) spectroscopy has provided considerable insight into the structures, dynamics, and formation mechanisms of amyloid fibrils. IR probes, such as main chain 13C═18O, have been widely employed to obtain site-specific structural information, yet only secondary structures and strand-to-strand arrangements can be probed. Very few nonperturbative IR probes are available to report on the side-chain conformation and environments, which are critical to determining sheet-to-sheet arrangements in steric zippers within amyloids. Polar residues, such as glutamine, contribute significantly to the stability of amyloids and thus are frequently found in core regions of amyloid peptides/proteins. Furthermore, polyglutamine (polyQ) repeats form toxic aggregates in several neurodegenerative diseases. Here we report the synthesis and application of a new nonperturbative IR probe-glutamine side chain 13C═18O. We use side chain 13C═18O labeling and isotope dilution to detect the presence of intermolecularly hydrogen-bonded arrays of glutamine side chains (Gln ladders) in amyloid-forming peptides. Moreover, the line width of the 13C═18O peak is highly sensitive to its local hydration environment. The IR data from side chain labeling allows us to unambiguously determine the sheet-to-sheet arrangement in a short amyloid-forming peptide, GNNQQNY, providing insight that was otherwise inaccessible through main chain labeling. With several different fibril samples, we also show the versatility of this IR probe in studying the structures and aggregation kinetics of amyloids. Finally, we demonstrate the capability of modeling amyloid structures with IR data using the integrative modeling platform (IMP) and the potential of integrating IR with other biophysical methods for more accurate structural modeling. Together, we believe that side chain 13C═18O will complement main chain isotope labeling in future IR studies of amyloids and integrative modeling using IR data will significantly expand the power of IR spectroscopy to elucidate amyloid assemblies.
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12
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Zanobini C, Bozovic O, Jankovic B, Koziol KL, Johnson PJM, Hamm P, Gulzar A, Wolf S, Stock G. Azidohomoalanine: A Minimally Invasive, Versatile, and Sensitive Infrared Label in Proteins To Study Ligand Binding. J Phys Chem B 2018; 122:10118-10125. [DOI: 10.1021/acs.jpcb.8b08368] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Claudio Zanobini
- Department of Chemistry, University of Zurich, Zurich 8057, Switzerland
| | - Olga Bozovic
- Department of Chemistry, University of Zurich, Zurich 8057, Switzerland
| | - Brankica Jankovic
- Department of Chemistry, University of Zurich, Zurich 8057, Switzerland
| | - Klemens L. Koziol
- Department of Chemistry, University of Zurich, Zurich 8057, Switzerland
| | | | - Peter Hamm
- Department of Chemistry, University of Zurich, Zurich 8057, Switzerland
| | - Adnan Gulzar
- Biomolecular Dynamics, Institute of Physics, Albert Ludwigs University, Freiburg 79104, Germany
| | - Steffen Wolf
- Biomolecular Dynamics, Institute of Physics, Albert Ludwigs University, Freiburg 79104, Germany
| | - Gerhard Stock
- Biomolecular Dynamics, Institute of Physics, Albert Ludwigs University, Freiburg 79104, Germany
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13
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Maurici N, Savidge N, Lee BU, Brewer SH, Phillips-Piro CM. Crystal structures of green fluorescent protein with the unnatural amino acid 4-nitro-L-phenylalanine. Acta Crystallogr F Struct Biol Commun 2018; 74:650-655. [PMID: 30279317 PMCID: PMC6168768 DOI: 10.1107/s2053230x1801169x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 08/17/2018] [Indexed: 11/10/2022] Open
Abstract
The X-ray crystal structures of two superfolder green fluorescent protein (sfGFP) constructs containing a genetically incorporated spectroscopic reporter unnatural amino acid, 4-nitro-L-phenylalanine (pNO2F), at two unique sites in the protein have been determined. Amber codon-suppression methodology was used to site-specifically incorporate pNO2F at a solvent-accessible (Asp133) and a partially buried (Asn149) site in sfGFP. The Asp133pNO2F sfGFP construct crystallized with two molecules per asymmetric unit in space group P3221 and the crystal structure was refined to 2.05 Å resolution. Crystals of Asn149pNO2F sfGFP contained one molecule of sfGFP per asymmetric unit in space group P4122 and the structure was refined to 1.60 Å resolution. The alignment of Asp133pNO2F or Asn149pNO2F sfGFP with wild-type sfGFP resulted in small root-mean-square deviations, illustrating that these residues do not significantly alter the protein structure and supporting the use of pNO2F as an effective spectroscopic reporter of local protein structure and dynamics.
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Affiliation(s)
- Nicole Maurici
- Department of Chemistry, Franklin and Marshall College, PO Box 3003, Lancaster, PA 17604, USA
| | - Nicole Savidge
- Department of Chemistry, Franklin and Marshall College, PO Box 3003, Lancaster, PA 17604, USA
| | - Byung Uk Lee
- Department of Chemistry, Franklin and Marshall College, PO Box 3003, Lancaster, PA 17604, USA
| | - Scott H. Brewer
- Department of Chemistry, Franklin and Marshall College, PO Box 3003, Lancaster, PA 17604, USA
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14
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Post-translational site-selective protein backbone α-deuteration. Nat Chem Biol 2018; 14:955-963. [DOI: 10.1038/s41589-018-0128-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2017] [Accepted: 07/19/2018] [Indexed: 01/29/2023]
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15
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Zhang J, Wang L, Zhang J, Zhu J, Pan X, Cui Z, Wang J, Fang W, Li Y. Identifying and Modulating Accidental Fermi Resonance: 2D IR and DFT Study of 4-Azido-l-phenylalanine. J Phys Chem B 2018; 122:8122-8133. [DOI: 10.1021/acs.jpcb.8b03887] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Jia Zhang
- Beijing National Laboratory for Condensed Matter Physics and CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, People’s Republic of China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, People’s Republic of China
| | - Li Wang
- Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, People’s Republic of China
| | - Jin Zhang
- Beijing National Laboratory for Condensed Matter Physics and CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, People’s Republic of China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, People’s Republic of China
| | - Jiangrui Zhu
- Beijing National Laboratory for Condensed Matter Physics and CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, People’s Republic of China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, People’s Republic of China
| | - Xin Pan
- Beijing National Laboratory for Condensed Matter Physics and CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, People’s Republic of China
- College of Physics and Electric Information, Anhui Normal University, Wuhu 241000, People’s Republic of China
| | - Zhifeng Cui
- College of Physics and Electric Information, Anhui Normal University, Wuhu 241000, People’s Republic of China
| | - Jiangyun Wang
- Laboratory of RNA Biology, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, People’s Republic of China
| | - Weihai Fang
- College of Chemistry, Beijing Normal University, Beijing 100875, People’s Republic of China
| | - Yunliang Li
- Beijing National Laboratory for Condensed Matter Physics and CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing 100190, People’s Republic of China
- School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, People’s Republic of China
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16
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First JT, Slocum JD, Webb LJ. Quantifying the Effects of Hydrogen Bonding on Nitrile Frequencies in GFP: Beyond Solvent Exposure. J Phys Chem B 2018; 122:6733-6743. [DOI: 10.1021/acs.jpcb.8b03907] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Jeremy T. First
- Department of Chemistry, Texas Materials Institute, and Institute for Cell and Molecular Biology, The University of Texas at Austin, 105E 24th Street, STOP A5300, Austin, Texas 78712-1224, United States
| | - Joshua D. Slocum
- Department of Chemistry, Texas Materials Institute, and Institute for Cell and Molecular Biology, The University of Texas at Austin, 105E 24th Street, STOP A5300, Austin, Texas 78712-1224, United States
| | - Lauren J. Webb
- Department of Chemistry, Texas Materials Institute, and Institute for Cell and Molecular Biology, The University of Texas at Austin, 105E 24th Street, STOP A5300, Austin, Texas 78712-1224, United States
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17
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Slocum JD, Webb LJ. Measuring Electric Fields in Biological Matter Using the Vibrational Stark Effect of Nitrile Probes. Annu Rev Phys Chem 2018; 69:253-271. [DOI: 10.1146/annurev-physchem-052516-045011] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Joshua D. Slocum
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712-1224, USA
| | - Lauren J. Webb
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712-1224, USA
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18
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Kearney C, Olenginski LT, Hirn TD, Fowler GD, Tariq D, Brewer SH, Phillips-Piro CM. Exploring local solvation environments of a heme protein using the spectroscopic reporter 4-cyano-l-phenylalanine. RSC Adv 2018; 8:13503-13512. [PMID: 29780583 PMCID: PMC5944249 DOI: 10.1039/c8ra02000k] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 03/20/2018] [Indexed: 11/21/2022] Open
Abstract
The vibrational reporter unnatural amino acid (UAA) 4-cyano-l-phenylalanine (pCNF) was genetically incorporated individually at three sites (5, 36, and 78) in the heme protein Caldanaerobacter subterraneus H-NOX to probe local hydration environments. The UAA pCNF was incorporated site-specifically using an engineered, orthogonal tRNA synthetase in E. coli. The ability of all of the pCNF-containing H-NOX proteins to form the ferrous CO, NO, or O2 ligated and unligated states was confirmed with UV-Vis spectroscopy. The solvation state at each site of the three sites of pCNF incorporation was assessed using temperature-dependent infrared spectroscopy. Specifically, the frequency-temperature line slope (FTLS) method was utilized to show that the nitrile group at site 36 was fully solvated and the nitrile group at site 78 was de-solvated (buried) in the heme pocket. The nitrile group at site 5 was found to be partially solvated suggesting that the nitrile group was involved in moderate strength hydrogen bonds. These results were confirmed by the determination of the X-ray crystal structure of the H-NOX protein construct containing pCNF at site 5.
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Affiliation(s)
- Caroline Kearney
- Department of Chemistry, Franklin & Marshall College, PO Box 3003, Lancaster, PA 17604-3003, USA. ;
| | - Lukasz T Olenginski
- Department of Chemistry, Franklin & Marshall College, PO Box 3003, Lancaster, PA 17604-3003, USA. ;
| | - Trexler D Hirn
- Department of Chemistry, Franklin & Marshall College, PO Box 3003, Lancaster, PA 17604-3003, USA. ;
| | - Gwendolyn D Fowler
- Department of Chemistry, Franklin & Marshall College, PO Box 3003, Lancaster, PA 17604-3003, USA. ;
| | - Daniyal Tariq
- Department of Chemistry, Franklin & Marshall College, PO Box 3003, Lancaster, PA 17604-3003, USA. ;
| | - Scott H Brewer
- Department of Chemistry, Franklin & Marshall College, PO Box 3003, Lancaster, PA 17604-3003, USA. ;
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19
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Kelly KL, Dalton SR, Wai RB, Ramchandani K, Xu RJ, Linse S, Londergan CH. Conformational Ensembles of Calmodulin Revealed by Nonperturbing Site-Specific Vibrational Probe Groups. J Phys Chem A 2018; 122:2947-2955. [PMID: 29400461 PMCID: PMC5867645 DOI: 10.1021/acs.jpca.8b00475] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
![]()
Seven native residues on the regulatory
protein calmodulin, including
three key methionine residues, were replaced (one by one) by the vibrational
probe amino acid cyanylated cysteine, which has a unique CN stretching
vibration that reports on its local environment. Almost no perturbation
was caused by this probe at any of the seven sites, as reported by
CD spectra of calcium-bound and apo calmodulin and
binding thermodynamics for the formation of a complex between calmodulin
and a canonical target peptide from skeletal muscle myosin light chain
kinase measured by isothermal titration. The surprising lack of perturbation
suggests that this probe group could be applied directly in many protein–protein
binding interfaces. The infrared absorption bands for the probe groups
reported many dramatic changes in the probes’ local environments
as CaM went from apo- to calcium-saturated to target
peptide-bound conditions, including large frequency shifts and a variety
of line shapes from narrow (interpreted as a rigid and invariant local
environment) to symmetric to broad and asymmetric (likely from multiple
coexisting and dynamically exchanging structures). The fast intrinsic
time scale of infrared spectroscopy means that the line shapes report
directly on site-specific details of calmodulin’s variable
structural distribution. Though quantitative interpretation of the
probe line shapes depends on a direct connection between simulated
ensembles and experimental data that does not yet exist, formation
of such a connection to data such as that reported here would provide
a new way to evaluate conformational ensembles from data that directly
contains the structural distribution. The calmodulin probe sites developed
here will also be useful in evaluating the binding mode of calmodulin
with many uncharacterized regulatory targets.
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Affiliation(s)
- Kristen L Kelly
- Department of Chemistry , Haverford College , Haverford , Pennsylvania 19041 , United States
| | - Shannon R Dalton
- Department of Chemistry , Haverford College , Haverford , Pennsylvania 19041 , United States
| | - Rebecca B Wai
- Department of Chemistry , Haverford College , Haverford , Pennsylvania 19041 , United States
| | - Kanika Ramchandani
- Department of Chemistry , Haverford College , Haverford , Pennsylvania 19041 , United States
| | - Rosalind J Xu
- Department of Chemistry , Haverford College , Haverford , Pennsylvania 19041 , United States
| | - Sara Linse
- Department of Biochemistry and Structural Biology , Lund University , 221 00 Lund , Sweden
| | - Casey H Londergan
- Department of Chemistry , Haverford College , Haverford , Pennsylvania 19041 , United States
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20
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Martin JP, Fetto NR, Tucker MJ. Comparison of biological chromophores: photophysical properties of cyanophenylalanine derivatives. Phys Chem Chem Phys 2018; 18:20750-7. [PMID: 27412819 DOI: 10.1039/c6cp04154j] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Within this work, the family of cyanophenylalanine spectroscopic reporters is extended by showing the ortho and meta derivatives have intrinsic photophysical properties that are useful for studies of protein structure and dynamics. The molar absorptivities of 2-cyanophenylalanine and 3-cyanophenylalanine are shown to be comparable to that of 4-cyanophenylalanine with similar spectral features in their absorbance and emission profiles, demonstrating that these probes can be utilized interchangeably. The fluorescence quantum yields are also on the same scale as commonly used fluorophores in peptides and proteins, tyrosine and tryptophan. These new cyano-fluorophores can be paired with either 4-cyanophenylalanine or tryptophan to capture distances in peptide structure through Förster resonance energy transfer. Additionally, the spectroscopic properties of these chromophores can report the local solvent environment via changes in fluorescence emission intensity as a result of hydrogen bonding and/or hydration. A decrease in the quantum yield is also observed in basic environments due to photoinduced electron transfer from a deprotonated amine in the free PheCN species and at the N-terminus of a short peptide, providing an avenue to detect pH in biological systems. Our results show the potential of these probes, 2-cyanophenylalanine and 3-cyanophenylalanine, to be incorporated into a single peptide chain, either individually or in tandem with 4-cyanophenylalanine, tryptophan, or tyrosine, in order to obtain information about peptide structure and dynamics.
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Affiliation(s)
- Joshua P Martin
- Department of Chemistry, University of Nevada, Reno, 89557, USA.
| | - Natalie R Fetto
- Department of Chemistry, University of Nevada, Reno, 89557, USA.
| | - Matthew J Tucker
- Department of Chemistry, University of Nevada, Reno, 89557, USA.
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21
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Stucki-Buchli B, Johnson PJM, Bozovic O, Zanobini C, Koziol KL, Hamm P, Gulzar A, Wolf S, Buchenberg S, Stock G. 2D-IR Spectroscopy of an AHA Labeled Photoswitchable PDZ2 Domain. J Phys Chem A 2017; 121:9435-9445. [DOI: 10.1021/acs.jpca.7b09675] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Brigitte Stucki-Buchli
- Department of Chemistry, University of Zurich, 8075 Zurich, Switzerland
- Biomolecular Dynamics, Institute of
Physics, Albert Ludwigs University, 79104 Freiburg, Germany
| | - Philip J. M. Johnson
- Department of Chemistry, University of Zurich, 8075 Zurich, Switzerland
- Biomolecular Dynamics, Institute of
Physics, Albert Ludwigs University, 79104 Freiburg, Germany
| | - Olga Bozovic
- Department of Chemistry, University of Zurich, 8075 Zurich, Switzerland
- Biomolecular Dynamics, Institute of
Physics, Albert Ludwigs University, 79104 Freiburg, Germany
| | - Claudio Zanobini
- Department of Chemistry, University of Zurich, 8075 Zurich, Switzerland
- Biomolecular Dynamics, Institute of
Physics, Albert Ludwigs University, 79104 Freiburg, Germany
| | - Klemens L. Koziol
- Department of Chemistry, University of Zurich, 8075 Zurich, Switzerland
- Biomolecular Dynamics, Institute of
Physics, Albert Ludwigs University, 79104 Freiburg, Germany
| | - Peter Hamm
- Department of Chemistry, University of Zurich, 8075 Zurich, Switzerland
- Biomolecular Dynamics, Institute of
Physics, Albert Ludwigs University, 79104 Freiburg, Germany
| | - Adnan Gulzar
- Department of Chemistry, University of Zurich, 8075 Zurich, Switzerland
- Biomolecular Dynamics, Institute of
Physics, Albert Ludwigs University, 79104 Freiburg, Germany
| | - Steffen Wolf
- Department of Chemistry, University of Zurich, 8075 Zurich, Switzerland
- Biomolecular Dynamics, Institute of
Physics, Albert Ludwigs University, 79104 Freiburg, Germany
| | - Sebastian Buchenberg
- Department of Chemistry, University of Zurich, 8075 Zurich, Switzerland
- Biomolecular Dynamics, Institute of
Physics, Albert Ludwigs University, 79104 Freiburg, Germany
| | - Gerhard Stock
- Department of Chemistry, University of Zurich, 8075 Zurich, Switzerland
- Biomolecular Dynamics, Institute of
Physics, Albert Ludwigs University, 79104 Freiburg, Germany
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22
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Fetto NR, Cao W, Wallace IS, Tucker MJ. Selective Excitation of Cyanophenylalanine Fluorophores for Multi-Site Binding Studies. J Phys Chem B 2017; 121:9566-9571. [PMID: 28949137 DOI: 10.1021/acs.jpcb.7b08442] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Recently, it has been shown that nitrile-derivatized phenylalanines possess distinct fluorescent properties depending on the position of the cyano-group within the aromatic ring. These fluorophores have potential as probes for studying protein dynamics due to their sensitivity to local environment. Herein, we demonstrate that 2-cyanophenylalanine (Phe2CN) and Phe4CN can independently monitor multiple sites during the Ca2+ dependent binding of a skeletal muscle myosin light chain kinase (MLCK) peptide fragment to the protein calmodulin (CaM). These cyano-probes were incorporated at two different positions along the peptide chain and monitored simultaneously via selective excitation of the two chromophores. The peptide was labeled with Phe4CN at a residue known to bind to a hydrophobic binding pocket of CaM, while Phe2CN was designed to acquire dynamics external to the binding pocket. By selectively exciting each of the chromophores, it was determined that the fluorescence emission of Phe4CN located at position 581 of MLCK was quenched in the presence of CaM, while no significant change in Phe2CN emission was observed at exposed position 594. The CaM binding affinity (Kd) of the double labeled MLCK peptide was calculated to be approximately 64 nM, which is in agreement with previous measurements. These results indicate that multiple PheCN reporters within the same peptide can simultaneously detect variations in the local environment, and that these fluorophores could be utilized to investigate a wide variety of biological problems.
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Affiliation(s)
- Natalie R Fetto
- Department of Chemistry, University of Nevada , 1664 North Virginia Street, Reno, Nevada 89557, United States
| | - Wenqiang Cao
- Department of Chemistry, University of Nevada , 1664 North Virginia Street, Reno, Nevada 89557, United States
| | - Ian S Wallace
- Department of Chemistry, University of Nevada , 1664 North Virginia Street, Reno, Nevada 89557, United States.,Department of Biochemistry and Molecular Biology, University of Nevada , 1664 North Virginia Street, Reno, Nevada 89557, United States
| | - Matthew J Tucker
- Department of Chemistry, University of Nevada , 1664 North Virginia Street, Reno, Nevada 89557, United States
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23
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Slocum JD, First JT, Webb LJ. Orthogonal Electric Field Measurements near the Green Fluorescent Protein Fluorophore through Stark Effect Spectroscopy and pKa Shifts Provide a Unique Benchmark for Electrostatics Models. J Phys Chem B 2017. [DOI: 10.1021/acs.jpcb.7b03935] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Joshua D. Slocum
- Department of Chemistry,
Center for Nano and Molecular Science and Technology, and Institute
for Cell and Molecular Biology, The University of Texas at Austin, 105
E 24th St. STOP A5300, Austin, Texas 78712-1224, United States
| | - Jeremy T. First
- Department of Chemistry,
Center for Nano and Molecular Science and Technology, and Institute
for Cell and Molecular Biology, The University of Texas at Austin, 105
E 24th St. STOP A5300, Austin, Texas 78712-1224, United States
| | - Lauren J. Webb
- Department of Chemistry,
Center for Nano and Molecular Science and Technology, and Institute
for Cell and Molecular Biology, The University of Texas at Austin, 105
E 24th St. STOP A5300, Austin, Texas 78712-1224, United States
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24
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Basom EJ, Manifold BA, Thielges MC. Conformational Heterogeneity and the Affinity of Substrate Molecular Recognition by Cytochrome P450cam. Biochemistry 2017; 56:3248-3256. [PMID: 28581729 DOI: 10.1021/acs.biochem.7b00238] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The broad and variable substrate specificity of cytochrome P450 enzymes makes them a model system for studying the determinants of protein molecular recognition. The archetypal cytochrome P450cam (P450cam) is a relatively specific P450, a feature once attributed to the high rigidity of its active site. However, increasingly studies have provided evidence of the importance of conformational changes to P450cam activity. Here we used infrared (IR) spectroscopy to investigate the molecular recognition of P450cam. Toward this goal, and to assess the influence of a hydrogen bond (H-bond) between active site residue Y96 and substrates, two variants in which Y96 is replaced by a cyanophenyl (Y96CNF) or phenyl (Y96F) group were characterized in complexes with the substrates camphor, isoborneol, and camphane. These combinations allow for a comparison of complexes in which the moieties on both the protein and substrate can serve as a H-bond donor, acceptor, or neither. The IR spectra of heme-bound CO and the site-specifically incorporated CN of Y96CNF were analyzed to characterize the number and nature of environments in each protein, both in the free and bound states. Although the IR spectra do not support the idea that protein-substrate H-bonding is central to P450cam recognition, the data altogether suggest that the differing conformational heterogeneity in the active site of the P450cam variants and changes in heterogeneity upon binding of different substrates likely contribute to their variable affinities via a conformational selection mechanism. This study further extends our understanding of the molecular recognition of archetypal P450cam and demonstrates the application of IR spectroscopy combined with selective protein modification to delineate protein-ligand interactions.
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Affiliation(s)
- Edward J Basom
- Department of Chemistry, Indiana University , 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Bryce A Manifold
- Department of Chemistry, Indiana University , 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
| | - Megan C Thielges
- Department of Chemistry, Indiana University , 800 East Kirkwood Avenue, Bloomington, Indiana 47405, United States
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25
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Adhikary R, Tan YX, Liu J, Zimmermann J, Holcomb M, Yvellez C, Dawson PE, Romesberg FE. Conformational Heterogeneity and DNA Recognition by the Morphogen Bicoid. Biochemistry 2017; 56:2787-2793. [DOI: 10.1021/acs.biochem.7b00255] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ramkrishna Adhikary
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Yun Xuan Tan
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Jian Liu
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Jörg Zimmermann
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Matthew Holcomb
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Carolyn Yvellez
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Philip E. Dawson
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Floyd E. Romesberg
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
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26
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Adhikary R, Zimmermann J, Romesberg FE. Transparent Window Vibrational Probes for the Characterization of Proteins With High Structural and Temporal Resolution. Chem Rev 2017; 117:1927-1969. [DOI: 10.1021/acs.chemrev.6b00625] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Ramkrishna Adhikary
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Jörg Zimmermann
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Floyd E. Romesberg
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
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27
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Gosavi PM, Korendovych IV. Minimalist IR and fluorescence probes of protein function. Curr Opin Chem Biol 2016; 34:103-109. [PMID: 27599185 DOI: 10.1016/j.cbpa.2016.08.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 08/16/2016] [Accepted: 08/18/2016] [Indexed: 11/19/2022]
Abstract
Spectroscopic studies of small proteins and peptides, especially those requiring fine spatial and/or temporal resolution, demand synthetic probes that confer the minimal possible steric and functional change on the native properties. Here we review the recent progress in development of minimally disruptive probes for fluorescence and infrared spectroscopies, as well as the methods to efficiently incorporate them into proteins. Advances in spectroscopy on the one hand result in high specialization of synthetic probes for a particular purpose, but on the other hand allow for the same probes be used for different techniques to gather complementary biochemical information.
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Affiliation(s)
- Pallavi M Gosavi
- Department of Chemistry, Syracuse University, Syracuse, NY 13244, United States
| | - Ivan V Korendovych
- Department of Chemistry, Syracuse University, Syracuse, NY 13244, United States.
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28
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Slocum JD, Webb LJ. Nitrile Probes of Electric Field Agree with Independently Measured Fields in Green Fluorescent Protein Even in the Presence of Hydrogen Bonding. J Am Chem Soc 2016; 138:6561-70. [DOI: 10.1021/jacs.6b02156] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Joshua D. Slocum
- Department
of Chemistry,
Center for Nano and Molecular Science and Technology, and Institute
for Cell and Molecular Biology, The University of Texas at Austin, 105
E 24th Street STOP A5300, Austin, Texas 78712-1224, United States
| | - Lauren J. Webb
- Department
of Chemistry,
Center for Nano and Molecular Science and Technology, and Institute
for Cell and Molecular Biology, The University of Texas at Austin, 105
E 24th Street STOP A5300, Austin, Texas 78712-1224, United States
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29
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Levin DE, Schmitz AJ, Hines SM, Hines KJ, Tucker MJ, Brewer SH, Fenlon EE. Synthesis and Evaluation of the Sensitivity and Vibrational Lifetimes of Thiocyanate and Selenocyanate Infrared Reporters. RSC Adv 2016; 43:36231-36237. [PMID: 27114820 DOI: 10.1039/c5ra27363c] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Two novel 2'-deoxyadenosine (dA) analogues, Si2-dA-SCN and Si2-dA-SeCN, and two novel phenylalanine (Phe) analogues, Boc-Me-PheCH2SCN and Boc-Me-PheCH2SeCN, have been synthesized and the thiocyanate (SCN) and selenocyanate (SeCN) functional groups evaluated as vibrational reporters. The syntheses of Si2-dA-SCN and Si2-dA-SeCN were accomplished in three steps in 16% and 32% overall yields, respectively, and the syntheses of Boc-Me-PheCH2SCN and Boc-Me-PheCH2SeCN were completed in four steps in 8.9% and 2.3% overall yields, respectively. The SCN and SeCN stretch vibrational modes were shown to be sensitive to the local environment by frequency shifts and full-width half-maximum (fwhm) changes in response to tetrahydrofuran (THF) and THF/water solvent mixtures. The vibrational lifetimes of the Si2-dA-SeCN (237±12 ps) and Boc-Me-PheCH2SeCN (295±31 ps) in THF solution were determined by ultrafast infrared pump-probe spectroscopy to be 1.5 to 3 times longer than those for Si2-dA-SCN (140±6 ps) and Boc-Me-PheCH2SCN (102±4 ps). The longer lifetimes for the SeCN analogues were attributed to the better insulating effects of the heavier selenium atom compared to the sulfur atom. The solvent sensitivity and longer vibrational lifetimes compared to other vibrational reporters suggest that SCN and SeCN vibrational reporters are well suited to studying several dynamic processes including protein and nucleic acid hydration and conformational changes, however stability issues may require post-synthetic modification methods to incorporate these reporters into biomacromolecules.
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Affiliation(s)
- Daniel E Levin
- Department of Chemistry, Franklin & Marshall College, Lancaster, PA 17604, USA
| | - Andrew J Schmitz
- Department of Chemistry, University of Nevada at Reno, Reno, NV 89557, USA
| | - Shawn M Hines
- Department of Chemistry, Franklin & Marshall College, Lancaster, PA 17604, USA
| | - Kevin J Hines
- Department of Chemistry, Franklin & Marshall College, Lancaster, PA 17604, USA
| | - Matthew J Tucker
- Department of Chemistry, University of Nevada at Reno, Reno, NV 89557, USA
| | - Scott H Brewer
- Department of Chemistry, Franklin & Marshall College, Lancaster, PA 17604, USA
| | - Edward E Fenlon
- Department of Chemistry, Franklin & Marshall College, Lancaster, PA 17604, USA
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30
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Dippel AB, Olenginski GM, Maurici N, Liskov MT, Brewer SH, Phillips-Piro CM. Probing the effectiveness of spectroscopic reporter unnatural amino acids: a structural study. Acta Crystallogr D Struct Biol 2016; 72:121-30. [PMID: 26894540 PMCID: PMC4756619 DOI: 10.1107/s2059798315022858] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Accepted: 11/29/2015] [Indexed: 11/10/2022] Open
Abstract
The X-ray crystal structures of superfolder green fluorescent protein (sfGFP) containing the spectroscopic reporter unnatural amino acids (UAAs) 4-cyano-L-phenylalanine (pCNF) or 4-ethynyl-L-phenylalanine (pCCF) at two unique sites in the protein have been determined. These UAAs were genetically incorporated into sfGFP in a solvent-exposed loop region and/or a partially buried site on the β-barrel of the protein. The crystal structures containing the UAAs at these two sites permit the structural implications of UAA incorporation for the native protein structure to be assessed with high resolution and permit a direct correlation between the structure and spectroscopic data to be made. The structural implications were quantified by comparing the root-mean-square deviation (r.m.s.d.) between the crystal structure of wild-type sfGFP and the protein constructs containing either pCNF or pCCF in the local environment around the UAAs and in the overall protein structure. The results suggest that the selective placement of these spectroscopic reporter UAAs permits local protein environments to be studied in a relatively nonperturbative fashion with site-specificity.
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Affiliation(s)
- Andrew B. Dippel
- Department of Chemistry, Franklin and Marshall College, PO Box 3003, Lancaster, PA 17604-3003, USA
| | - Gregory M. Olenginski
- Department of Chemistry, Franklin and Marshall College, PO Box 3003, Lancaster, PA 17604-3003, USA
| | - Nicole Maurici
- Department of Chemistry, Franklin and Marshall College, PO Box 3003, Lancaster, PA 17604-3003, USA
| | - Melanie T. Liskov
- Department of Chemistry, Franklin and Marshall College, PO Box 3003, Lancaster, PA 17604-3003, USA
| | - Scott H. Brewer
- Department of Chemistry, Franklin and Marshall College, PO Box 3003, Lancaster, PA 17604-3003, USA
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31
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Adhikary R, Zimmermann J, Dawson PE, Romesberg FE. Temperature Dependence of CN and SCN IR Absorptions Facilitates Their Interpretation and Use as Probes of Proteins. Anal Chem 2015; 87:11561-7. [DOI: 10.1021/acs.analchem.5b03437] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Ramkrishna Adhikary
- Department of Chemistry, The Scripps Research Institute, 10550 North
Torrey Pines Road, La Jolla, California 92037, United States
| | - Jörg Zimmermann
- Department of Chemistry, The Scripps Research Institute, 10550 North
Torrey Pines Road, La Jolla, California 92037, United States
| | - Philip E. Dawson
- Department of Chemistry, The Scripps Research Institute, 10550 North
Torrey Pines Road, La Jolla, California 92037, United States
| | - Floyd E. Romesberg
- Department of Chemistry, The Scripps Research Institute, 10550 North
Torrey Pines Road, La Jolla, California 92037, United States
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32
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Bobone S, De Zotti M, Bortolotti A, Biondi B, Ballano G, Palleschi A, Toniolo C, Formaggio F, Stella L. The fluorescence and infrared absorption probepara-cyanophenylalanine: Effect of labeling on the behavior of different membrane-interacting peptides. Biopolymers 2015; 104:521-32. [DOI: 10.1002/bip.22674] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Revised: 04/30/2015] [Accepted: 05/04/2015] [Indexed: 12/18/2022]
Affiliation(s)
- Sara Bobone
- Department of Chemical Sciences and Technologies; University of Rome Tor Vergata; 00133 Rome Italy
| | - Marta De Zotti
- Department of Chemistry; University of Padova; 35131 Padova Italy
| | - Annalisa Bortolotti
- Department of Chemical Sciences and Technologies; University of Rome Tor Vergata; 00133 Rome Italy
| | - Barbara Biondi
- Institute of Biomolecular Chemistry, Padova Unit, CNR; 35131 Padova Italy
| | - Gema Ballano
- Department of Chemistry; University of Padova; 35131 Padova Italy
| | - Antonio Palleschi
- Department of Chemical Sciences and Technologies; University of Rome Tor Vergata; 00133 Rome Italy
| | - Claudio Toniolo
- Department of Chemistry; University of Padova; 35131 Padova Italy
- Institute of Biomolecular Chemistry, Padova Unit, CNR; 35131 Padova Italy
| | - Fernando Formaggio
- Department of Chemistry; University of Padova; 35131 Padova Italy
- Institute of Biomolecular Chemistry, Padova Unit, CNR; 35131 Padova Italy
| | - Lorenzo Stella
- Department of Chemical Sciences and Technologies; University of Rome Tor Vergata; 00133 Rome Italy
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33
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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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34
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De Zotti M, Bobone S, Bortolotti A, Longo E, Biondi B, Peggion C, Formaggio F, Toniolo C, Dalla Bona A, Kaptein B, Stella L. 4-Cyano-α-methyl-l-phenylalanine as a Spectroscopic Marker for the Investigation of PeptaibioticMembrane Interactions. Chem Biodivers 2015; 12:513-27. [DOI: 10.1002/cbdv.201400404] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Indexed: 11/10/2022]
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35
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American Chemical Society 2015 National Award Winners. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/anie.201500775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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36
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Träger der nationalen Preise der American Chemical Society 2015. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201500775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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37
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Maj M, Ahn C, Kossowska D, Park K, Kwak K, Han H, Cho M. β-Isocyanoalanine as an IR probe: comparison of vibrational dynamics between isonitrile and nitrile-derivatized IR probes. Phys Chem Chem Phys 2015; 17:11770-8. [DOI: 10.1039/c5cp00454c] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
An infrared (IR) probe based on isonitrile (NC)-derivatized alanine 1 was synthesized and the vibrational properties of its NC stretching mode were investigated using FTIR and femtosecond IR pump–probe spectroscopy.
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Affiliation(s)
- Michał Maj
- Center for Molecular Spectroscopy and Dynamics
- Institute for Basic Science (IBS)
- Seoul 136-701, Korea
- Department of Chemistry
- Korea University
| | - Changwoo Ahn
- Department of Chemistry
- Korea University
- Seoul 136-701, Korea
| | - Dorota Kossowska
- Center for Molecular Spectroscopy and Dynamics
- Institute for Basic Science (IBS)
- Seoul 136-701, Korea
- Department of Chemistry
- Korea University
| | - Kwanghee Park
- Center for Molecular Spectroscopy and Dynamics
- Institute for Basic Science (IBS)
- Seoul 136-701, Korea
- Department of Chemistry
- Korea University
| | - Kyungwon Kwak
- Department of Chemistry
- Chung-Ang University
- Seoul 156-756, Korea
| | - Hogyu Han
- Department of Chemistry
- Korea University
- Seoul 136-701, Korea
| | - Minhaeng Cho
- Center for Molecular Spectroscopy and Dynamics
- Institute for Basic Science (IBS)
- Seoul 136-701, Korea
- Department of Chemistry
- Korea University
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38
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Tookmanian EM, Fenlon EE, Brewer SH. Synthesis and Protein Incorporation of Azido-Modified Unnatural Amino Acids. RSC Adv 2014; 5:1274-1281. [PMID: 26478813 PMCID: PMC4603873 DOI: 10.1039/c4ra14244f] [Citation(s) in RCA: 84] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Two new azidophenylalanine residues (3 and 4) have been synthesized and, in combination with 4-azido-L-phenylalanine (1) and 4-azidomethyl-L-phenylalanine (2), form a series of unnatural amino acids (UAAs) containing the azide vibrational reporter at varying distances from the aromatic ring of phenylalanine. These UAAs were designed to probe protein hydration with high spatial resolution by utilizing the large extinction coefficient and environmental sensitivity of the azide asymmetric stretch vibration. The sensitivity of the azide reporters was investigated in solvents that mimic distinct local protein environments. Three of the four azido-modified phenylalanine residues were successfully genetically incorporated into a surface site in superfolder green fluorescent protein (sfGFP) utilizing an engineered, orthogonal aminoacyl-tRNA synthetase in response to an amber codon with high efficiency and fidelity. SDS-PAGE and ESI-Q-TOF mass analysis verified the site-specific incorporation of these UAAs. The observed azide asymmetric stretch in the linear IR spectra of these UAAs incorporated into sfGFP indicated that the azide groups were hydrated in the protein.
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Affiliation(s)
- Elise M. Tookmanian
- Franklin & Marshall College, Department of Chemistry, Lancaster, PA 17604-3003 USA
| | - Edward E. Fenlon
- Franklin & Marshall College, Department of Chemistry, Lancaster, PA 17604-3003 USA
| | - Scott H. Brewer
- Franklin & Marshall College, Department of Chemistry, Lancaster, PA 17604-3003 USA
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39
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Peran I, Oudenhoven T, Woys AM, Watson M, Zhang TO, Carrico I, Zanni MT, Raleigh DP. General strategy for the bioorthogonal incorporation of strongly absorbing, solvation-sensitive infrared probes into proteins. J Phys Chem B 2014; 118:7946-53. [PMID: 24749542 PMCID: PMC4317048 DOI: 10.1021/jp5008279] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2014] [Revised: 04/19/2014] [Indexed: 11/28/2022]
Abstract
A high-sensitivity metal-carbonyl-based IR probe is described that can be incorporated into proteins or other biomolecules in very high yield via Click chemistry. A two-step strategy is demonstrated. First, a methionine auxotroph is used to incorporate the unnatural amino acid azidohomoalanine at high levels. Second, a tricarbonyl (η(5)-cyclopentadienyl) rhenium(I) probe modified with an alkynyl linkage is coupled via the Click reaction. We demonstrate these steps using the C-terminal domain of the ribosomal protein L9 as a model system. An overall incorporation level of 92% was obtained at residue 109, which is a surface-exposed residue. Incorporation of the probe into a surface site is shown not to perturb the stability or structure of the target protein. Metal carbonyls are known to be sensitive to solvation and protein electrostatics through vibrational lifetimes and frequency shifts. We report that the frequencies and lifetimes of this probe also depend on the isotopic composition of the solvent. Comparison of the lifetimes measured in H2O versus D2O provides a probe of solvent accessibility. The metal carbonyl probe reported here provides an easy and robust method to label very large proteins with an amino-acid-specific tag that is both environmentally sensitive and a very strong absorber.
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Affiliation(s)
- Ivan Peran
- Department
of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, United States
| | - Tracey Oudenhoven
- Department
of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706-1396, United States
| | - Ann Marie Woys
- Department
of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706-1396, United States
| | - Matthew
D. Watson
- Department
of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, United States
| | - Tianqi O. Zhang
- Department
of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706-1396, United States
| | - Isaac Carrico
- Department
of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, United States
| | - Martin T. Zanni
- Department
of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706-1396, United States
| | - Daniel P. Raleigh
- Department
of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, United States
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