1
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Deshmukh SH, Yadav S, Chowdhury T, Pathania A, Sapra S, Bagchi S. Probing surface interactions in CdSe quantum dots with thiocyanate ligands. NANOSCALE 2024; 16:14922-14931. [PMID: 39042097 DOI: 10.1039/d4nr01507j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/24/2024]
Abstract
Surface chemistry dictates the optoelectronic properties of semiconductor quantum dots (QDs). Tailoring these properties relies on the meticulous selection of surface ligands for efficient passivation. While long-chain organic ligands boast a well-understood passivation mechanism, the intricacies of short inorganic ionic ligands remain largely unexplored. This study sheds light on the surface-passivation mechanism of short inorganic ligands, particularly focusing on SCN- ions on CdSe QDs. Employing steady-state and time-resolved infrared spectroscopic techniques, we elucidated the surface-ligand interactions and coordination modes of SCN--capped CdSe QDs. Comparative analysis with studies on CdS QDs unveils intriguing insights into the coordination behavior and passivation efficacy of SCN- ions on Cd2+ rich QD surfaces. Our results reveal the requirement of both surface-bound (strong binding) and weakly-interacting interfacial SCN- ions for effective CdSe QD passivation. Beyond fostering a deeper understanding of surface-ligand interactions and highlighting the importance of a comprehensive exploration of ligand chemistries, this study holds implications for optimizing QD performance across diverse applications.
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Affiliation(s)
- Samadhan H Deshmukh
- Physical and Materials Chemistry Division, National Chemical Laboratory (CSIR-NCL), Dr. Homi Bhabha Road, Pune - 411008, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad - 201002, India
| | - Sushma Yadav
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Tubai Chowdhury
- Physical and Materials Chemistry Division, National Chemical Laboratory (CSIR-NCL), Dr. Homi Bhabha Road, Pune - 411008, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad - 201002, India
| | - Akhil Pathania
- Physical and Materials Chemistry Division, National Chemical Laboratory (CSIR-NCL), Dr. Homi Bhabha Road, Pune - 411008, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad - 201002, India
| | - Sameer Sapra
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Sayan Bagchi
- Physical and Materials Chemistry Division, National Chemical Laboratory (CSIR-NCL), Dr. Homi Bhabha Road, Pune - 411008, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad - 201002, India
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2
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Aydin S, Salehi SM, Töpfer K, Meuwly M. SCN as a local probe of protein structural dynamics. J Chem Phys 2024; 161:055101. [PMID: 39092954 DOI: 10.1063/5.0216657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Accepted: 07/03/2024] [Indexed: 08/04/2024] Open
Abstract
The dynamics of lysozyme is probed by attaching -SCN to all alanine residues. The one-dimensional infrared spectra exhibit frequency shifts in the position of the maximum absorption of 4 cm-1, which is consistent with experiments in different solvents and indicates moderately strong interactions of the vibrational probe with its environment. Isotopic substitution 12C → 13C leads to a redshift by -47 cm-1, which agrees quantitatively with experiments for CN-substituted copper complexes in solution. The low-frequency, far-infrared part of the protein spectra contains label-specific information in the difference spectra when compared with the wild type protein. Depending on the position of the labels, local structural changes are observed. For example, introducing the -SCN label at Ala129 leads to breaking of the α-helical structure with concomitant change in the far-infrared spectrum. Finally, changes in the local hydration of SCN-labeled alanine residues as a function of time can be related to the reorientation of the label. It is concluded that -SCN is potentially useful for probing protein dynamics, both in the high-frequency part (CN-stretch) and in the far-infrared part of the spectrum.
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Affiliation(s)
- Sena Aydin
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Seyedeh Maryam Salehi
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Kai Töpfer
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
| | - Markus Meuwly
- Department of Chemistry, University of Basel, Klingelbergstrasse 80, CH-4056 Basel, Switzerland
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, USA
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3
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Kirsh J, Weaver JB, Boxer SG, Kozuch J. Critical Evaluation of Polarizable and Nonpolarizable Force Fields for Proteins Using Experimentally Derived Nitrile Electric Fields. J Am Chem Soc 2024; 146:6983-6991. [PMID: 38415598 PMCID: PMC10941190 DOI: 10.1021/jacs.3c14775] [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] [Received: 12/28/2023] [Revised: 02/11/2024] [Accepted: 02/15/2024] [Indexed: 02/29/2024]
Abstract
Molecular dynamics (MD) simulations are frequently carried out for proteins to investigate the role of electrostatics in their biological function. The choice of force field (FF) can significantly alter the MD results, as the simulated local electrostatic interactions lack benchmarking in the absence of appropriate experimental methods. We recently reported that the transition dipole moment (TDM) of the popular nitrile vibrational probe varies linearly with the environmental electric field, overcoming well-known hydrogen bonding (H-bonding) issues for the nitrile frequency and, thus, enabling the unambiguous measurement of electric fields in proteins (J. Am. Chem. Soc. 2022, 144 (17), 7562-7567). Herein, we utilize this new strategy to enable comparisons of experimental and simulated electric fields in protein environments. Specifically, previously determined TDM electric fields exerted onto nitrile-containing o-cyanophenylalanine residues in photoactive yellow protein are compared with MD electric fields from the fixed-charge AMBER FF and the polarizable AMOEBA FF. We observe that the electric field distributions for H-bonding nitriles are substantially affected by the choice of FF. As such, AMBER underestimates electric fields for nitriles experiencing moderate field strengths; in contrast, AMOEBA robustly recapitulates the TDM electric fields. The FF dependence of the electric fields can be partly explained by the presence of additional negative charge density along the nitrile bond axis in AMOEBA, which is due to the inclusion of higher-order multipole parameters; this, in turn, begets more head-on nitrile H-bonds. We conclude by discussing the implications of the FF dependence for the simulation of nitriles and proteins in general.
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Affiliation(s)
- Jacob
M. Kirsh
- Department
of Chemistry, Stanford University, Stanford, California 94305-5012, United
States
| | - Jared Bryce Weaver
- Department
of Chemistry, Stanford University, Stanford, California 94305-5012, United
States
| | - Steven G. Boxer
- Department
of Chemistry, Stanford University, Stanford, California 94305-5012, United
States
| | - Jacek Kozuch
- Experimental
Molecular Biophysics, Department of Physics, Freie Universität Berlin, 14195 Berlin, Germany
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4
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Maia RN, Mitra S, Baiz CR. Extracting accurate infrared lineshapes from weak vibrational probes at low concentrations. MethodsX 2023; 11:102309. [PMID: 37577166 PMCID: PMC10416016 DOI: 10.1016/j.mex.2023.102309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 07/31/2023] [Indexed: 08/15/2023] Open
Abstract
Fourier-transform infrared (FTIR) spectroscopy using vibrational probes is an ideal tool to detect changes in structure and local environments within biological molecules. However, challenges arise when dealing with weak infrared probes, such as thiocyanates, due to their inherent low signal strengths and overlap with solvent bands. In this protocol we demonstrate:•A streamlined approach for the precise extraction of weak infrared absorption lineshapes from a strong solvent background.•A protocol combining a spectral filter, background modeling, and subtraction.•Our methodology successfully extracts the CN stretching mode peak from methyl thiocyanate at remarkably low concentrations (0.25 mM) in water, previously a challenge for FTIR spectroscopy.This approach offers valuable insights and tools for more accurate FTIR measurements using weak vibrational probes. This enhanced precision can potentially enable new approaches to enhance our understanding of protein structure and dynamics in solution.
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Affiliation(s)
- Raiza N.A. Maia
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712-1224, USA
| | - Sunayana Mitra
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712-1224, USA
| | - Carlos R. Baiz
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712-1224, USA
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5
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Lin YC, Ren P, Webb LJ. AMOEBA Force Field Predicts Accurate Hydrogen Bond Counts of Nitriles in SNase by Revealing Water-Protein Interaction in Vibrational Absorption Frequencies. J Phys Chem B 2023; 127:5609-5619. [PMID: 37339399 PMCID: PMC10851345 DOI: 10.1021/acs.jpcb.3c02060] [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: 06/22/2023]
Abstract
Precisely quantifying the magnitude and direction of electric fields in proteins has long been an outstanding challenge in understanding biological functions. Nitrile vibrational Stark effect probes have been shown to be minimally disruptive to the protein structure and can be better direct reporters of local electrostatic field in the native state of a protein than other measures such as pKa shifts of titratable residues. However, interpretations of the connection between measured vibrational energy and electric field rely on the accurate molecular understanding of interactions of the nitrile group and its environment, particularly from hydrogen bonding. In this work, we compared the extent of hydrogen bonding calculated in two common force fields, the fixed charge force field Amber03 and polarizable force field AMOEBA, at 10 locations of cyanocysteine (CNC) in staphylococcal nuclease (SNase) against the experimental nitrile absorption frequency in terms of full width at half-maximum (FWHM) and frequency temperature line slope (FTLS). We observed that the number of hydrogen bonds correlated well in AMOEBA trajectories with respect to both the FWHM (r = 0.88) and the FTLS (r = -0.85), whereas the correlation of Amber03 trajectories was less reliable because the Amber03 force field predicted more hydrogen bonds in some mutants. Moreover, we demonstrated that contributions from the interactions between CNC and nearby water molecules were significant in AMOEBA trajectories but were not predicted by Amber03. We conclude that although the nitrile absorption peak shape could be qualitatively predicted by the fixed charge Amber03 force field, the detailed electrostatic environment measured by the nitrile probe in terms of the extent of hydrogen bonding could only be accurately observed in the AMOEBA trajectories, where the permanent dipole, quadrupole, and dipole-induced-dipole polarizable interactions were all taken into account. The significance of this finding to the goal of accurately predicting electric fields in complex biomolecular environments is discussed.
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Affiliation(s)
- Yu-Chun Lin
- Department of Chemistry, Texas Materials Institute, and Interdisciplinary Life Sciences Program, The University of Texas at Austin, 105 E 24th St. STOP A5300, Austin, TX, 78712, USA
| | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Lauren J. Webb
- Department of Chemistry, Texas Materials Institute, and Interdisciplinary Life Sciences Program, The University of Texas at Austin, 105 E 24th St. STOP A5300, Austin, TX, 78712, USA
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6
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Shi L, Min W. Vibrational Solvatochromism Study of the C-H···O Improper Hydrogen Bond. J Phys Chem B 2023; 127:3798-3805. [PMID: 37122158 DOI: 10.1021/acs.jpcb.2c08119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
The improper C-H···O hydrogen bond is an important weak interaction, with broad implications for protein and nucleic acid structure, molecular recognition, enzyme catalysis, and drug interaction. Despite its wide identification in crystal structures, the general existence of C-H···O hydrogen bonds remains elusive especially for natural C-H groups in bulk aqueous solutions at room temperature. Vibrational spectroscopy is a promising methodology to tackle this challenge, as formation of C-H···O hydrogen bonds usually causes shifts of the C-H stretch frequency. Yet, prior observations are inconclusive, as they are all based on a simple blue-shift in aqueous solution and cannot distinguish if it is an effect caused by solvent reorganization or a specific hydrogen-bonding interaction. In this work, we used vibrational solvatochromism as a calibration of the solvent reorganization effect and identified a specific H-bonding interaction. We performed vibrational solvatochromism study of C-H(D) of multiple alcohol molecules including the CH mode of CD3CH(OH)CD3 and the CD3 modes of CD3OH, CD3CH2OH, and CD3CH(OH)CD3 in a series of solvents. We found an abnormal blue-shift of the Raman frequency of the C-H and C-D bonds at both the Cα and Cβ positions of alcohols in water, which lies in an opposite direction to the expected trend due to vibrational solvatochromism. This experimental evidence supports that the improper C-H···O hydrogen bonds might generally exist between nonpolarized C-H and water in liquid solutions at room temperature.
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Affiliation(s)
- Lixue Shi
- Department of Chemistry, Columbia University, New York, New York 10027, United States
| | - Wei Min
- Department of Chemistry, Columbia University, New York, New York 10027, United States
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7
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Ramos De Dios SM, Tiwari VK, McCune CD, Dhokale RA, Berkowitz DB. Biomacromolecule-Assisted Screening for Reaction Discovery and Catalyst Optimization. Chem Rev 2022; 122:13800-13880. [PMID: 35904776 DOI: 10.1021/acs.chemrev.2c00213] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Reaction discovery and catalyst screening lie at the heart of synthetic organic chemistry. While there are efforts at de novo catalyst design using computation/artificial intelligence, at its core, synthetic chemistry is an experimental science. This review overviews biomacromolecule-assisted screening methods and the follow-on elaboration of chemistry so discovered. All three types of biomacromolecules discussed─enzymes, antibodies, and nucleic acids─have been used as "sensors" to provide a readout on product chirality exploiting their native chirality. Enzymatic sensing methods yield both UV-spectrophotometric and visible, colorimetric readouts. Antibody sensors provide direct fluorescent readout upon analyte binding in some cases or provide for cat-ELISA (Enzyme-Linked ImmunoSorbent Assay)-type readouts. DNA biomacromolecule-assisted screening allows for templation to facilitate reaction discovery, driving bimolecular reactions into a pseudo-unimolecular format. In addition, the ability to use DNA-encoded libraries permits the barcoding of reactants. All three types of biomacromolecule-based screens afford high sensitivity and selectivity. Among the chemical transformations discovered by enzymatic screening methods are the first Ni(0)-mediated asymmetric allylic amination and a new thiocyanopalladation/carbocyclization transformation in which both C-SCN and C-C bonds are fashioned sequentially. Cat-ELISA screening has identified new classes of sydnone-alkyne cycloadditions, and DNA-encoded screening has been exploited to uncover interesting oxidative Pd-mediated amido-alkyne/alkene coupling reactions.
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Affiliation(s)
| | - Virendra K Tiwari
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
| | - Christopher D McCune
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
| | - Ranjeet A Dhokale
- Higuchi Biosciences Center, University of Kansas, Lawrence, Kansas 66047, United States
| | - David B Berkowitz
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, United States
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8
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Zhao R, Shirley JC, Lee E, Grofe A, Li H, Baiz CR, Gao J. Origin of thiocyanate spectral shifts in water and organic solvents. J Chem Phys 2022; 156:104106. [PMID: 35291777 PMCID: PMC8923707 DOI: 10.1063/5.0082969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Vibrational spectroscopy is a useful technique for probing chemical environments. The development of models that can reproduce the spectra of nitriles and azides is valuable because these probes are uniquely suited for investigating complex systems. Empirical vibrational spectroscopic maps are commonly employed to obtain the instantaneous vibrational frequencies during molecular dynamics simulations but often fail to adequately describe the behavior of these probes, especially in its transferability to a diverse range of environments. In this paper, we demonstrate several reasons for the difficulty in constructing a general-purpose vibrational map for methyl thiocyanate (MeSCN), a model for cyanylated biological probes. In particular, we found that electrostatics alone are not a sufficient metric to categorize the environments of different solvents, and the dominant features in intermolecular interactions in the energy landscape vary from solvent to solvent. Consequently, common vibrational mapping schemes do not cover all essential interaction terms adequately, especially in the treatment of van der Waals interactions. Quantum vibrational perturbation (QVP) theory, along with a combined quantum mechanical and molecular mechanical potential for solute-solvent interactions, is an alternative and efficient modeling technique, which is compared in this paper, to yield spectroscopic results in good agreement with experimental FTIR. QVP has been used to analyze the computational data, revealing the shortcomings of the vibrational maps for MeSCN in different solvents. The results indicate that insights from QVP analysis can be used to enhance the transferability of vibrational maps in future studies.
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Affiliation(s)
- Ruoqi Zhao
- Institute of Theoretical Chemistry, Jilin University, Changchun, Jilin Province 130023, China
| | - Joseph C Shirley
- Department of Chemistry, University of Texas, Austin, Texas 78712, USA
| | - Euihyun Lee
- Department of Chemistry, University of Texas, Austin, Texas 78712, USA
| | - Adam Grofe
- Institute of Theoretical Chemistry, Jilin University, Changchun, Jilin Province 130023, China
| | - Hui Li
- Institute of Theoretical Chemistry, Jilin University, Changchun, Jilin Province 130023, China
| | - Carlos R Baiz
- Department of Chemistry, University of Texas, Austin, Texas 78712, USA
| | - Jiali Gao
- Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518055, China
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9
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Chen Z, Gui Y, Cui K, Schmit JR, Yu L. Prolific Polymorph Generator ROY in Its Liquid and Glass: Two Conformational Populations Mirroring the Crystalline-State Distribution. J Phys Chem B 2021; 125:10304-10311. [PMID: 34464152 DOI: 10.1021/acs.jpcb.1c05834] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
5-Methyl-2-[(2-nitrophenyl)amino]-3-thiophenecarbonitrile, dubbed ROY for its numerous crystal polymorphs of red, orange, and yellow colors, has been studied in its liquid and glassy state by infrared spectroscopy. Two populations of conformers are observed, whose equilibrium is characterized by ΔH = 2.4 kJ/mol and ΔS = 8.0 J/K/mol. The two populations correspond to the global and local minima of the torsional energy surface and to the conformational preference of the 13 crystal polymorphs. The local minimum features a more coplanar arrangement of the two aromatic rings, greater π conjugation, and lower CN stretch frequency. In the gas phase, the lowest-energy path between the two minima has an energy barrier 3.9 kJ/mol above the global minimum, consistent with the rapid equilibration between the two populations. The relevance of our result for understanding the prolific polymorphism of ROY is discussed.
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Affiliation(s)
- Zhenxuan Chen
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Yue Gui
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
| | - Kai Cui
- Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - J R Schmit
- Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Lian Yu
- School of Pharmacy, University of Wisconsin-Madison, Madison, Wisconsin 53705, United States
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10
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Edington SC, Liu S, Baiz CR. Infrared spectroscopy probes ion binding geometries. Methods Enzymol 2021; 651:157-191. [PMID: 33888203 DOI: 10.1016/bs.mie.2020.12.028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Infrared (IR) spectroscopy is a well-established technique for probing the structure, behavior, and surroundings of molecules in their native environments. Its characteristics-most specifically high structural sensitivity, ready applicability to aqueous samples, and broad availability-make it a valuable enzymological technique, particularly for the interrogation of ion binding sites. While IR spectroscopy of the "garden variety" (steady state at room temperature with wild-type proteins) is versatile and powerful in its own right, the combination of IR spectroscopy with specialized experimental schemes for leveraging ultrafast time resolution, protein labeling, and other enhancements further extends this utility. This book chapter provides the fundamental physical background and literature context essential for harnessing IR spectroscopy in the general context of enzymology with specific focus on interrogation of ion binding. Studies of lanthanide ions binding to calmodulin are highlighted as illustrative examples of this process. Appropriate sample preparation, data collection, and spectral interpretation are discussed from a detail-oriented and practical perspective with the goal of facilitating the reader's rapid progression from reading words in a book to collecting and analyzing their own data in the lab.
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Affiliation(s)
- Sean C Edington
- Department of Chemistry, Yale University, New Haven, CT, United States
| | - Stephanie Liu
- Department of Chemistry, The University of Texas at Austin, Austin, TX, United States
| | - Carlos R Baiz
- Department of Chemistry, The University of Texas at Austin, Austin, TX, United States.
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11
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First JT, Novelli ET, Webb LJ. Beyond pKa: Experiments and Simulations of Nitrile Vibrational Probes in Staphylococcal Nuclease Show the Importance of Local Interactions. J Phys Chem B 2020; 124:3387-3399. [DOI: 10.1021/acs.jpcb.0c00747] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jeremy T. First
- Department of Chemistry, Texas Materials Institute, and Institute for Cell and Molecular Biology The University of Texas at Austin 105 East 24th Street STOP A5300, Austin, Texas 78712-1224, United States
| | - Elisa T. Novelli
- Department of Chemistry, Texas Materials Institute, and Institute for Cell and Molecular Biology The University of Texas at Austin 105 East 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 105 East 24th Street STOP A5300, Austin, Texas 78712-1224, United States
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12
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Schmidt-Engler JM, Zangl R, Guldan P, Morgner N, Bredenbeck J. Exploring the 2D-IR repertoire of the -SCN label to study site-resolved dynamics and solvation in the calcium sensor protein calmodulin. Phys Chem Chem Phys 2020; 22:5463-5475. [PMID: 32096510 DOI: 10.1039/c9cp06808b] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The calcium sensor protein calmodulin is ubiquitous among eukaryotes. It translates intracellular Ca2+ influx (by a decrease of conformational flexibility) into increased target recognition affinity. Here we demonstrate that by using the IR reporter -SCN in combination with 2D-IR spectroscopy, global structure changes and local dynamics, degree of solvent exposure and protein-ligand interaction can be characterised in great detail. The long vibrational lifetime of the -SCN label allows for centerline slope analysis of the 2D-IR line shape up to 120 ps to deduce the frequency-frequency correlation function (FFCF) of the -SCN label in various states and label positions in the protein. Based on that we show clear differences between a solvent exposed site, the environment close to the Ca2+ binding motif and three highly conserved positions for ligand binding. Furthermore, we demonstrate how these dynamics are affected by conformational change induced by the addition of Ca2+ ions and by interaction with a short helical peptide mimicking protein binding. We show that the binding mode is strongly heterogeneous among the probed key binding methionine residues. SCN's vibrational relaxation is dominated by intermolecular contributions. Changes in the vibrational lifetime upon changing between H2O and D2O buffer therefore provide a robust measure for water accessibility of the label. Characterising -SCN's extinction coefficient, vibrational lifetime in light and heavy water and its FFCF we demonstrate the vast potential it has as a label especially for nonlinear spectroscopies, such as 2D-IR spectroscopy.
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Affiliation(s)
- Julian M Schmidt-Engler
- Johann Wolfgang Goethe-University, Institute of Biophysics, Max-von-Laue-Str. 1, 60438 Frankfurt am Main, Germany.
| | - Rene Zangl
- Johann Wolfgang Goethe-University, Institute of Physical and Theoretical Chemistry, Max-von-Laue-Str. 7, 60438 Frankfurt am Main, Germany
| | - Patrick Guldan
- Johann Wolfgang Goethe-University, Institute of Biophysics, Max-von-Laue-Str. 1, 60438 Frankfurt am Main, Germany.
| | - Nina Morgner
- Johann Wolfgang Goethe-University, Institute of Physical and Theoretical Chemistry, Max-von-Laue-Str. 7, 60438 Frankfurt am Main, Germany
| | - Jens Bredenbeck
- Johann Wolfgang Goethe-University, Institute of Biophysics, Max-von-Laue-Str. 1, 60438 Frankfurt am Main, Germany.
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13
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Schmidt-Engler JM, Blankenburg L, Zangl R, Hoffmann J, Morgner N, Bredenbeck J. Local dynamics of the photo-switchable protein PYP in ground and signalling state probed by 2D-IR spectroscopy of –SCN labels. Phys Chem Chem Phys 2020; 22:22963-22972. [DOI: 10.1039/d0cp04307a] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We employ 2D-IR spectroscopy of the protein label –SCN to describe the local dynamics in the photo-switchable protein PYP in its dark state (pG) and after photoactivation, concomitant with vast structural rearrangements, in its signalling state (pB).
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Affiliation(s)
| | - Larissa Blankenburg
- Johann Wolfgang Goethe-University
- Institute of Biophysics
- 60438 Frankfurt am Main
- Germany
| | - Rene Zangl
- Johann Wolfgang Goethe-University
- Institute of Physical and Theoretical Chemistry
- Frankfurt am Main
- Germany
| | - Jan Hoffmann
- Johann Wolfgang Goethe-University
- Institute of Physical and Theoretical Chemistry
- Frankfurt am Main
- Germany
| | - Nina Morgner
- Johann Wolfgang Goethe-University
- Institute of Physical and Theoretical Chemistry
- Frankfurt am Main
- Germany
| | - Jens Bredenbeck
- Johann Wolfgang Goethe-University
- Institute of Biophysics
- 60438 Frankfurt am Main
- Germany
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14
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Bukowski GS, Horness RE, Thielges MC. Involvement of Local, Rapid Conformational Dynamics in Binding of Flexible Recognition Motifs. J Phys Chem B 2019; 123:8387-8396. [PMID: 31535866 DOI: 10.1021/acs.jpcb.9b07036] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Flexible protein sequences populate ensembles of rapidly interconverting states differentiated by small-scale fluctuations; however, elucidating whether and how the ensembles determine function experimentally is challenged by the combined high spatial and temporal resolution needed to capture the states. We used carbon-deuterium (C-D) bond vibrations incorporated as infrared probes to characterize with residue-specific detail the heterogeneity of states adopted by proline-rich (PR) sequences and assess their involvement in recognition of Src homology 3 domains. The C-D absorption envelopes provided evidence for two or three sub-populations at all proline residues. The changes in the subpopulations induced by binding generally reflected recognition by conformational selection but depended on the residue and the state of the ligand to illuminate distinct mechanisms among the PR ligands. Notably, the spectral data indicate that greater adaptability among the states is associated with reduced recognition specificity and that perturbation to the ensemble populations contributes to differences in binding entropy. Broadly, the study quantifies rapidly interconverting ensembles with residue-specific detail and implicates them in function.
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Affiliation(s)
- Gregory S Bukowski
- Department of Chemistry , Indiana University, Bloomington , Bloomington , Indiana 47405 , United States
| | - Rachel E Horness
- Department of Chemistry , Indiana University, Bloomington , Bloomington , Indiana 47405 , United States
| | - Megan C Thielges
- Department of Chemistry , Indiana University, Bloomington , Bloomington , Indiana 47405 , United States
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15
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Ramos S, Thielges MC. Site-Specific 1D and 2D IR Spectroscopy to Characterize the Conformations and Dynamics of Protein Molecular Recognition. J Phys Chem B 2019; 123:3551-3566. [PMID: 30848912 DOI: 10.1021/acs.jpcb.9b00969] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Proteins exist as ensembles of interconverting states on a complex energy landscape. A complete, molecular-level understanding of their function requires knowledge of the populated states and thus the experimental tools to characterize them. Infrared (IR) spectroscopy has an inherently fast time scale that can capture all states and their dynamics with, in principle, bond-specific spatial resolution, and 2D IR methods that provide richer information are becoming more routine. Although application of IR spectroscopy for investigation of proteins is challenged by spectral congestion, the issue can be overcome by site-specific introduction of amino acid side chains that have IR probe groups with frequency-resolved absorptions, which furthermore enables selective characterization of different locations in proteins. Here, we briefly introduce the biophysical methods and summarize the current progress toward the study of proteins. We then describe our efforts to apply site-specific 1D and 2D IR spectroscopy toward elucidation of protein conformations and dynamics to investigate their involvement in protein molecular recognition, in particular mediated by dynamic complexes: plastocyanin and its binding partner cytochrome f, cytochrome P450s and substrates or redox partners, and Src homology 3 domains and proline-rich peptide motifs. We highlight the advantages of frequency-resolved probes to characterize specific, local sites in proteins and uncover variation among different locations, as well as the advantage of the fast time scale of IR spectroscopy to detect rapidly interconverting states. In addition, we illustrate the greater insight provided by 2D methods and discuss potential routes for further advancement of the field of biomolecular 2D IR spectroscopy.
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Affiliation(s)
- Sashary Ramos
- Department of Chemistry , Indiana University , Bloomington , Indiana 47405 , United States
| | - Megan C Thielges
- Department of Chemistry , Indiana University , Bloomington , Indiana 47405 , United States
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16
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Hogle DG, Cunningham AR, Tucker MJ. Equilibrium versus Nonequilibrium Peptide Dynamics: Insights into Transient 2D IR Spectroscopy. J Phys Chem B 2018; 122:8783-8795. [PMID: 30040900 DOI: 10.1021/acs.jpcb.8b05063] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Over the past two decades, two-dimensional infrared (2D IR) spectroscopy has evolved from the theoretical underpinnings of nonlinear spectroscopy as a means of investigating detailed molecular structure on an ultrafast time scale. The combined time and spectral resolution over which spectra can be collected on complex molecular systems has led to the precise structural resolution of dynamic species that have previously been impossible to directly observe through traditional methods. The adoption of 2D IR spectroscopy for the study of protein folding and peptide interactions has provided key details of how small changes in conformations can exert major influences on the activities of these complex molecular systems. Traditional 2D IR experiments are limited to molecules under equilibrium conditions, where small motions and fluctuations of these larger molecules often still lead to functionality. Utilizing techniques that allow the rapid initiation of chemical or structural changes in conjunction with 2D IR spectroscopy, i.e., transient 2D IR, a vast dynamic range becomes available to the spectroscopist uncovering structural content far from equilibrium. Furthermore, this allows the observation of reaction pathways of these macromolecules under quasi- and nonequilibrium conditions.
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Affiliation(s)
- David G Hogle
- Department of Chemistry , University of Nevada, Reno , 1664 North Virginia Street , Reno , Nevada 89557 , United States
| | - Amy R Cunningham
- Department of Chemistry , University of Nevada, Reno , 1664 North Virginia Street , Reno , Nevada 89557 , United States
| | - Matthew J Tucker
- Department of Chemistry , University of Nevada, Reno , 1664 North Virginia Street , Reno , Nevada 89557 , United States
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17
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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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18
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Dalton SR, Vienneau AR, Burstein SR, Xu RJ, Linse S, Londergan CH. Cyanylated Cysteine Reports Site-Specific Changes at Protein-Protein-Binding Interfaces Without Perturbation. Biochemistry 2018; 57:3702-3712. [PMID: 29787228 PMCID: PMC6034165 DOI: 10.1021/acs.biochem.8b00283] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
![]()
To investigate the
cyanylated cysteine vibrational probe group’s
ability to report on binding-induced changes along a protein–protein
interface, the probe group was incorporated at several sites in a
peptide of the calmodulin (CaM)-binding domain of skeletal muscle
myosin light chain kinase. Isothermal titration calorimetry was used
to determine the binding thermodynamics between calmodulin and each
peptide. For all probe positions, the binding affinity was nearly
identical to that of the unlabeled peptide. The CN stretching infrared
band was collected for each peptide free in solution and bound to
calmodulin. Binding-induced shifts in the IR spectral frequencies
were correlated with estimated solvent accessibility based on molecular
dynamics simulations. This work generally suggests (1) that site-specific
incorporation of this vibrational probe group does not cause major
perturbations to its local structural environment and (2) that this
small probe group might be used quite broadly to map dynamic protein-binding
interfaces. However, site-specific perturbations due to artificial
labeling groups can be somewhat unpredictable and should be evaluated
on a site-by-site basis through complementary measurements. A fully
quantitative, simulation-based interpretation of the rich probe IR
spectra is still needed but appears to be possible given recent advances
in simulation techniques.
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Affiliation(s)
- Shannon R Dalton
- Department of Chemistry , Haverford College , 370 Lancaster Ave , Haverford , Pennsylvania 19041-1392 , United States
| | - Alice R Vienneau
- Department of Chemistry , Haverford College , 370 Lancaster Ave , Haverford , Pennsylvania 19041-1392 , United States
| | - Shana R Burstein
- Department of Chemistry , Haverford College , 370 Lancaster Ave , Haverford , Pennsylvania 19041-1392 , United States
| | - Rosalind J Xu
- Department of Chemistry , Haverford College , 370 Lancaster Ave , Haverford , Pennsylvania 19041-1392 , United States
| | - Sara Linse
- Department of Chemistry and Biochemistry , Lund University , Kemicentrum, Box 118 , 221 00 Lund , Sweden
| | - Casey H Londergan
- Department of Chemistry , Haverford College , 370 Lancaster Ave , Haverford , Pennsylvania 19041-1392 , United States
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19
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Xu RJ, Blasiak B, Cho M, Layfield JP, Londergan CH. A Direct, Quantitative Connection between Molecular Dynamics Simulations and Vibrational Probe Line Shapes. J Phys Chem Lett 2018; 9:2560-2567. [PMID: 29697984 DOI: 10.1021/acs.jpclett.8b00969] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
A quantitative connection between molecular dynamics simulations and vibrational spectroscopy of probe-labeled systems would enable direct translation of experimental data into structural and dynamical information. To constitute this connection, all-atom molecular dynamics (MD) simulations were performed for two SCN probe sites (solvent-exposed and buried) in a calmodulin-target peptide complex. Two frequency calculation approaches with substantial nonelectrostatic components, a quantum mechanics/molecular mechanics (QM/MM)-based technique and a solvatochromic fragment potential (SolEFP) approach, were used to simulate the infrared probe line shapes. While QM/MM results disagreed with experiment, SolEFP results matched experimental frequencies and line shapes and revealed the physical and dynamic bases for the observed spectroscopic behavior. The main determinant of the CN probe frequency is the exchange repulsion between the probe and its local structural neighbors, and there is a clear dynamic explanation for the relatively broad probe line shape observed at the "buried" probe site. This methodology should be widely applicable to vibrational probes in many environments.
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Affiliation(s)
- Rosalind J Xu
- Department of Chemistry , Haverford College , Haverford , Pennsylvania , United States
| | - Bartosz Blasiak
- Department of Physical and Quantum Chemistry, Faculty of Chemistry , Wrocław University of Science and Technology , Wybrzeże Wyspiańskiego 27 , 50-370 Wrocław , Poland
| | - Minhaeng Cho
- Center for Molecular Spectroscopy and Dynamics , Institute for Basic Science (IBS) , Seoul 02841 , Republic of Korea
- Department of Chemistry , Korea University , Seoul 02841 , Republic of Korea
| | - Joshua P Layfield
- Department of Chemistry , St. Thomas University , Minneapolis , Minnesota , United States
| | - Casey H Londergan
- Department of Chemistry , Haverford College , Haverford , Pennsylvania , United States
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20
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Malik G, Swyka RA, Tiwari VK, Fei X, Applegate GA, Berkowitz DB. A thiocyanopalladation/carbocyclization transformation identified through enzymatic screening: stereocontrolled tandem C-SCN and C-C bond formation. Chem Sci 2017; 8:8050-8060. [PMID: 29568453 PMCID: PMC5855125 DOI: 10.1039/c7sc04083k] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 09/29/2017] [Indexed: 12/31/2022] Open
Abstract
Herein we describe a formal thiocyanopalladation/carbocyclization transformation and its parametrization and optimization using a new elevated temperature plate-based version of our visual colorimetric enzymatic screening method for reaction discovery. The carbocyclization step leads to C-SCN bond formation in tandem with C-C bond construction and is highly stereoselective, showing nearly absolute 1,2-anti-stereoinduction (5 examples) for substrates bearing allylic substitution, and nearly absolute 1,3-syn-stereoinduction (16 examples) for substrates bearing propargylic substitution. Based upon these high levels of stereoinduction, the dependence of the 1,2-stereoinduction upon cyclization substrate geometry, and the generally high preference for the transoid vinyl thiocyanate alkene geometry, a mechanistic model is proposed, involving (i) Pd(ii)-enyne coordination, (ii) thiocyanopalladation, (iii) migratory insertion and (iv) β-elimination. Examples of transition metal-mediated C-SCN bond formation that proceed smoothly on unactivated substrates and allow for preservation of the SCN moiety are lacking. Yet, the thiocyanate functionality is of great value for biophysical chemistry (vibrational Stark effect) and medicinal chemistry (S,N-heterocycle construction). The title transformation accommodates C-, O-, N- and S-bridged substrates (6 examples), thereby providing the corresponding carbocyclic or heterocyclic scaffolds. The reaction is also shown to be compatible with a significant range of substituents, varying in steric and electronic demand, including a wide range of substituted aromatics, fused bicyclic and heterocyclic systems, and even biaryl systems. Combination of this new transformation with asymmetric allylation and Grubbs ring-closing metathesis provides for a streamlined enantio- and diastereoselective entry into the oxabicyclo[3.2.1]octyl core of the natural products massarilactone and annuionone A, as also evidenced by low temperature X-ray crystal structure determination. Utilizing this bicyclic scaffold, we demonstrate the versatility of the thiocyanate moiety for structural diversification post-cyclization. Thus, the bridging vinyl thiocyanate moiety is smoothly elaborated into a range of derivative functionalities utilizing transformations that cleave the S-CN bond, add the elements of RS-CN across a π-system and exploit the SCN moiety as a cycloaddition partner (7 diverse examples). Among the new functionalities thereby generated are thiotetrazole and sulfonyl tetrazole heterocycles that serve as carboxylate and phosphate surrogates, respectively, highlighting the potential of this approach for future applications in medicinal chemistry or chemical biology.
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Affiliation(s)
- G Malik
- Department of Chemistry , University of Nebraska , Lincoln , NE 68588 , USA .
| | - R A Swyka
- Department of Chemistry , University of Nebraska , Lincoln , NE 68588 , USA .
| | - V K Tiwari
- Department of Chemistry , University of Nebraska , Lincoln , NE 68588 , USA .
| | - X Fei
- Department of Chemistry , University of Nebraska , Lincoln , NE 68588 , USA .
| | - G A Applegate
- Department of Chemistry , University of Nebraska , Lincoln , NE 68588 , USA .
| | - D B Berkowitz
- Department of Chemistry , University of Nebraska , Lincoln , NE 68588 , USA .
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21
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Błasiak B, Londergan CH, Webb LJ, Cho M. Vibrational Probes: From Small Molecule Solvatochromism Theory and Experiments to Applications in Complex Systems. Acc Chem Res 2017; 50:968-976. [PMID: 28345879 DOI: 10.1021/acs.accounts.7b00002] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The vibrational frequency of a chosen normal mode is one of the most accurately measurable spectroscopic properties of molecules in condensed phases. Accordingly, infrared absorption and Raman scattering spectroscopy have provided valuable information on both distributions and ensemble-average values of molecular vibrational frequencies, and these frequencies are now routinely used to investigate structure, conformation, and even absolute configuration of chemical and biological molecules of interest. Recent advancements in coherent time-domain nonlinear vibrational spectroscopy have allowed the study of heterogeneous distributions of local structures and thermally driven ultrafast fluctuations of vibrational frequencies. To fully utilize IR probe functional groups for quantitative bioassays, a variety of biological and chemical techniques have been developed to site-specifically introduce vibrational probe groups into proteins and nucleic acids. These IR-probe-labeled biomolecules and chemically reactive systems are subject to linear and nonlinear vibrational spectroscopic investigations and provide information on the local electric field, conformational changes, site-site protein contacts, and/or function-defining features of biomolecules. A rapidly expanding library of data from such experiments requires an interpretive method with atom-level chemical accuracy. However, despite prolonged efforts to develop an all-encompassing theory for describing vibrational solvatochromism and electrochromism as well as dynamic fluctuations of instantaneous vibrational frequencies, purely empirical and highly approximate theoretical models have often been used to interpret experimental results. They are, in many cases, based on the simple assumption that the vibrational frequency of an IR reporter is solely dictated by electric potential or field distribution around the vibrational chromophore. Such simplified description of vibrational solvatochromism generally referred to as vibrational Stark effect theory has been considered to be quite appealing and, even in some cases, e.g., carbonyl stretch modes in amide, ester, ketone, and carbonate compounds or proteins, it works quantitatively well, which makes it highly useful in determining the strength of local electric field around the IR chromophore. However, noting that the vibrational frequency shift results from changes of solute-solvent intermolecular interaction potential along its normal coordinate, Pauli exclusion repulsion, polarization, charge transfer, and dispersion interactions, in addition to the electrostatic interaction between distributed charges of both vibrational chromophore and solvent molecules, are to be properly included in the theoretical description of vibrational solvatochromism. Since the electrostatic and nonelectrostatic intermolecular interaction components have distinctively different distance and orientation dependences, they affect the solvatochromic vibrational properties in a completely different manner. Over the past few years, we have developed a systematic approach to simulating vibrational solvatochromic data based on the effective fragment potential approach, one of the most accurate and rigorous theories on intermolecular interactions. We have further elucidated the interplay of local electric field with the general vibrational solvatochromism of small IR probes in either solvents or complicated biological systems, with emphasis on contributions from non-Coulombic intermolecular interactions to vibrational frequency shifts and fluctuations. With its rigorous foundation and close relation to quantitative interpretation of experimental data, this and related theoretical approaches and experiments will be of use in studying and quantifying the structure and dynamics of biomolecules with unprecedented time and spatial resolution when combined with time-resolved vibrational spectroscopy and chemically sensitive vibrational imaging techniques.
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Affiliation(s)
- Bartosz Błasiak
- Center
of Molecular Spectroscopy and Dynamics, Institute of Basic Science (IBS), 145
Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
- Department
of Chemistry, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
| | - Casey H. Londergan
- Department
of Chemistry, Haverford College, Haverford, Pennsylvania 19041-1392, 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, United States
| | - Minhaeng Cho
- Center
of Molecular Spectroscopy and Dynamics, Institute of Basic Science (IBS), 145
Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
- Department
of Chemistry, Korea University, 145 Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
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22
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Maj M, Ahn C, Błasiak B, Kwak K, Han H, Cho M. Isonitrile as an Ultrasensitive Infrared Reporter of Hydrogen-Bonding Structure and Dynamics. J Phys Chem B 2016; 120:10167-10180. [DOI: 10.1021/acs.jpcb.6b04319] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Michał Maj
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic
Science (IBS) and ‡Department of Chemistry, Korea University, Seoul 02841, Korea
| | - Changwoo Ahn
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic
Science (IBS) and ‡Department of Chemistry, Korea University, Seoul 02841, Korea
| | - Bartosz Błasiak
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic
Science (IBS) and ‡Department of Chemistry, Korea University, Seoul 02841, Korea
| | - Kyungwon Kwak
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic
Science (IBS) and ‡Department of Chemistry, Korea University, Seoul 02841, Korea
| | - Hogyu Han
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic
Science (IBS) and ‡Department of Chemistry, Korea University, Seoul 02841, Korea
| | - Minhaeng Cho
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic
Science (IBS) and ‡Department of Chemistry, Korea University, Seoul 02841, Korea
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23
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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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24
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Zhang W, Markiewicz BN, Doerksen RS, Smith AB, Gai F. C≡N stretching vibration of 5-cyanotryptophan as an infrared probe of protein local environment: what determines its frequency? Phys Chem Chem Phys 2016; 18:7027-34. [PMID: 26343769 PMCID: PMC4775302 DOI: 10.1039/c5cp04413h] [Citation(s) in RCA: 49] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Recently it has been suggested that the C≡N stretching vibration of a tryptophan analog, 5-cyanotryptophan, could be used as an infrared probe of the local environment, especially the hydration status, of tryptophan residues in proteins. However, the factors that influence the frequency of this vibrational mode are not understood. To determine these factors, herein we carried out linear and nonlinear infrared measurements on the C≡N stretching vibration of the sidechain of 5-cyanotryptophan, 3-methyl-5-cyanoindole, in a series of protic and aprotic solvents. We found that while the C≡N stretching frequencies obtained in these solvents do not correlate well with any individual Kamlet-Taft solvent parameter, i.e., π* (polarizability), β (hydrogen bond accepting ability), and α (hydrogen bond donating ability), they do however, collapse on a straight line when plotted against σ = π* + β - α. This linear relationship provides a firm indication that both specific interactions, i.e., hydrogen-bonding interactions with the C≡N (through α) and indole N-H (through β) groups, and non-specific interactions with the molecule (through π*) work together to determine the C≡N stretching frequency, thus laying a quantitative framework for applying 5-cyanotryptophan to investigate the microscopic environment of proteins in a site-specific manner. Furthermore, two-dimensional and pump-probe infrared measurements revealed that a significant portion (∼31%) of the ground state bleach signal has a decay time constant of ∼12.3 ps, due to an additional vibrational relaxation channel, making it possible to use 5-cyanotryptophan to probe dynamics occurring on a timescale on the order of tens of picoseconds.
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Affiliation(s)
- Wenkai Zhang
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA. and The Ultrafast Optical Processes Laboratory, University of Pennsylvania, Philadelphia, PA 19104, USA
| | | | - Rosalie S Doerksen
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Amos B Smith
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Feng Gai
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA. and The Ultrafast Optical Processes Laboratory, University of Pennsylvania, Philadelphia, PA 19104, USA
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25
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Gao Y, Zou Y, Ma Y, Wang D, Sun Y, Ma G. Infrared Probe Technique Reveals a Millipede-like Structure for Aβ(8-28) Amyloid Fibril. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:937-946. [PMID: 26796491 DOI: 10.1021/acs.langmuir.5b03616] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Amyloid fibrils are unique fibrous polypeptide aggregates. They have been associated with more than 20 serious human diseases including Alzheimer's disease and Parkinson's disease. Besides their pathological significance, amyloid fibrils are also gaining increasing attention as emerging nanomaterials with novel functions. Structural characterization of amyloid fibril is no doubt fundamentally important for the development of therapeutics for amyloid-related diseases and for the rational design of amyloid-based materials. In this study, we explored to use side-chain-based infrared (IR) probe to gain detailed structural insights into the amyloid fibril by a 21-residue model amyloidogenic peptide, Aβ(8-28). We first proposed an approach to incorporate thiocyanate (SCN) IR probe in a site-specific manner into amyloidogenic peptide using 1-cyano-4-dimethylaminopyridinium tetrafluoroborate as cyanylating agent. Using this approach, we obtained three Aβ(8-28) variants, labeled with SCN probe at three different positions. We then showed with thioflavin T fluorescence assay, Congo red assay, and atomic force microscopy that the three labeled Aβ(8-28) peptides can quickly form amyloid fibrils under high concentration and high salt conditions. Finally, we performed a detailed IR spectral analysis of the Aβ(8-28) fibril in both amide I and probe regions and proposed a millipede-like structure for the Aβ(8-28) fibril.
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Affiliation(s)
- Yachao Gao
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of Ministry of Education, Key Laboratory of Analytical Science and Technology of Hebei Province, College of Chemistry and Environmental Science, Hebei University , Baoding 071002, China
| | - Ye Zou
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of Ministry of Education, Key Laboratory of Analytical Science and Technology of Hebei Province, College of Chemistry and Environmental Science, Hebei University , Baoding 071002, China
| | - Yan Ma
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of Ministry of Education, Key Laboratory of Analytical Science and Technology of Hebei Province, College of Chemistry and Environmental Science, Hebei University , Baoding 071002, China
| | - Dan Wang
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of Ministry of Education, Key Laboratory of Analytical Science and Technology of Hebei Province, College of Chemistry and Environmental Science, Hebei University , Baoding 071002, China
| | - Ying Sun
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of Ministry of Education, Key Laboratory of Analytical Science and Technology of Hebei Province, College of Chemistry and Environmental Science, Hebei University , Baoding 071002, China
| | - Gang Ma
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of Ministry of Education, Key Laboratory of Analytical Science and Technology of Hebei Province, College of Chemistry and Environmental Science, Hebei University , Baoding 071002, China
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26
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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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27
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Biophysical Methods to Investigate Intrinsically Disordered Proteins: Avoiding an “Elephant and Blind Men” Situation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 870:215-60. [DOI: 10.1007/978-3-319-20164-1_7] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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28
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Synthesis and characterization of nano Ag end capped L-cysteine bridged diblock copolymer. CHINESE JOURNAL OF POLYMER SCIENCE 2015. [DOI: 10.1007/s10118-015-1688-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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29
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Abstract
Infrared spectroscopy has played an instrumental role in the study of a wide variety of biological questions. However, in many cases, it is impossible or difficult to rely on the intrinsic vibrational modes of biological molecules of interest, such as proteins, to reveal structural and environmental information in a site-specific manner. To overcome this limitation, investigators have dedicated many recent efforts to the development and application of various extrinsic vibrational probes that can be incorporated into biological molecules and used to site-specifically interrogate their structural or environmental properties. In this review, we highlight recent advancements in this rapidly growing research area.
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30
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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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31
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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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32
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Londergan CH, Baskin R, Bischak CG, Hoffman KW, Snead DM, Reynoso C. Dynamic Asymmetry and the Role of the Conserved Active-Site Thiol in Rabbit Muscle Creatine Kinase. Biochemistry 2014; 54:83-95. [DOI: 10.1021/bi5008063] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Casey H. Londergan
- Department of Chemistry, Haverford College, 370 Lancaster Avenue, Haverford, Pennsylvania 19041, United States
| | - Rachel Baskin
- Department of Chemistry, Haverford College, 370 Lancaster Avenue, Haverford, Pennsylvania 19041, United States
| | - Connor G. Bischak
- Department of Chemistry, Haverford College, 370 Lancaster Avenue, Haverford, Pennsylvania 19041, United States
| | - Kevin W. Hoffman
- Department of Chemistry, Haverford College, 370 Lancaster Avenue, Haverford, Pennsylvania 19041, United States
| | - David M. Snead
- Department of Chemistry, Haverford College, 370 Lancaster Avenue, Haverford, Pennsylvania 19041, United States
| | - Christopher Reynoso
- Department of Chemistry, Haverford College, 370 Lancaster Avenue, Haverford, Pennsylvania 19041, United States
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33
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Johnson MR, Londergan CH, Charkoudian LK. Probing the phosphopantetheine arm conformations of acyl carrier proteins using vibrational spectroscopy. J Am Chem Soc 2014; 136:11240-3. [PMID: 25080832 PMCID: PMC4140477 DOI: 10.1021/ja505442h] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Indexed: 12/23/2022]
Abstract
Acyl carrier proteins (ACPs) are universal and highly conserved domains central to both fatty acid and polyketide biosynthesis. These proteins tether reactive acyl intermediates with a swinging 4'-phosphopantetheine (Ppant) arm and interact with a suite of catalytic partners during chain transport and elongation while stabilizing the growing chain throughout the biosynthetic pathway. The flexible nature of the Ppant arm and the transient nature of ACP-enzyme interactions impose a major obstacle to obtaining structural information relevant to understanding polyketide and fatty acid biosynthesis. To overcome this challenge, we installed a thiocyanate vibrational spectroscopic probe on the terminal thiol of the ACP Ppant arm. This site-specific probe successfully reported on the local environment of the Ppant arm of two ACPs previously characterized by solution NMR, and was used to determine the solution exposure of the Ppant arm of an ACP from 6-deoxyerythronolide B synthase (DEBS). Given the sensitivity of the probe's CN stretching band to conformational distributions resolved on the picosecond time scale, this work lays a foundation for observing the dynamic action-related structural changes of ACPs using vibrational spectroscopy.
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Affiliation(s)
- Matthew
N. R. Johnson
- Department of Chemistry, Haverford College, Haverford, Pennsylvania 19041-1392, United States
| | - Casey H. Londergan
- Department of Chemistry, Haverford College, Haverford, Pennsylvania 19041-1392, United States
| | - Louise K. Charkoudian
- Department of Chemistry, Haverford College, Haverford, Pennsylvania 19041-1392, United States
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34
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Liu CT, Layfield JP, Stewart RJ, French JB, Hanoian P, Asbury JB, Hammes-Schiffer S, Benkovic SJ. Probing the electrostatics of active site microenvironments along the catalytic cycle for Escherichia coli dihydrofolate reductase. J Am Chem Soc 2014; 136:10349-60. [PMID: 24977791 PMCID: PMC4183630 DOI: 10.1021/ja5038947] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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Electrostatic interactions play an
important role in enzyme catalysis
by guiding ligand binding and facilitating chemical reactions. These
electrostatic interactions are modulated by conformational changes
occurring over the catalytic cycle. Herein, the changes in active
site electrostatic microenvironments are examined for all enzyme complexes
along the catalytic cycle of Escherichia coli dihydrofolate reductase (ecDHFR) by incorporation
of thiocyanate probes at two site-specific locations in the active
site. The electrostatics and degree of hydration of the microenvironments
surrounding the probes are investigated with spectroscopic techniques
and mixed quantum mechanical/molecular mechanical (QM/MM) calculations.
Changes in the electrostatic microenvironments along the catalytic
environment lead to different nitrile (CN) vibrational stretching
frequencies and 13C NMR chemical shifts. These environmental
changes arise from protein conformational rearrangements during catalysis.
The QM/MM calculations reproduce the experimentally measured vibrational
frequency shifts of the thiocyanate probes across the catalyzed hydride
transfer step, which spans the closed and occluded conformations of
the enzyme. Analysis of the molecular dynamics trajectories provides
insight into the conformational changes occurring between these two
states and the resulting changes in classical electrostatics and specific
hydrogen-bonding interactions. The electric fields along the CN axes
of the probes are decomposed into contributions from specific residues,
ligands, and solvent molecules that make up the microenvironments
around the probes. Moreover, calculation of the electric field along
the hydride donor–acceptor axis, along with decomposition of
this field into specific contributions, indicates that the cofactor
and substrate, as well as the enzyme, impose a substantial electric
field that facilitates hydride transfer. Overall, experimental and
theoretical data provide evidence for significant electrostatic changes
in the active site microenvironments due to conformational motion
occurring over the catalytic cycle of ecDHFR.
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Affiliation(s)
- C Tony Liu
- Department of Chemistry, Pennsylvania State University , University Park, Pennsylvania 16802, United States
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35
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Adhikary R, Zimmermann J, Dawson PE, Romesberg FE. IR Probes of Protein Microenvironments: Utility and Potential for Perturbation. Chemphyschem 2014; 15:849-53. [DOI: 10.1002/cphc.201400017] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Indexed: 11/10/2022]
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36
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Gonzalez JD, Levonyak NS, Schneider SC, Smith MJ, Cremeens ME. Using infrared spectroscopy of a nitrile labeled phenylalanine and tryptophan fluorescence to probe the α-MSH peptide’s side-chain interactions with a micelle model membrane. J Mol Struct 2014. [DOI: 10.1016/j.molstruc.2013.09.059] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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37
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van Wilderen LJGW, Kern-Michler D, Müller-Werkmeister HM, Bredenbeck J. Vibrational dynamics and solvatochromism of the label SCN in various solvents and hemoglobin by time dependent IR and 2D-IR spectroscopy. Phys Chem Chem Phys 2014; 16:19643-53. [DOI: 10.1039/c4cp01498g] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The vibrational label SCN is used to report on local structural dynamics in a protein revealing spectral diffusion on a picosecond scale. The SCN spectra are compared to the response of methylthiocyanate in solvents with different polarity and hydrogen-bonding capabilities.
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Affiliation(s)
| | - Daniela Kern-Michler
- Johann Wolfgang Goethe-University
- Institute of Biophysics
- Frankfurt am Main, Germany
| | | | - Jens Bredenbeck
- Johann Wolfgang Goethe-University
- Institute of Biophysics
- Frankfurt am Main, Germany
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38
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Kim H, Cho M. Infrared Probes for Studying the Structure and Dynamics of Biomolecules. Chem Rev 2013; 113:5817-47. [DOI: 10.1021/cr3005185] [Citation(s) in RCA: 165] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Heejae Kim
- Department of Chemistry, Korea University, Seoul 136-713, Korea
| | - Minhaeng Cho
- Department of Chemistry, Korea University, Seoul 136-713, Korea
- Multidimensional Spectroscopy Laboratory, Korea Basic Science Institute,
Seoul 136-713, Korea
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39
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Cheatum CM, Kohen A. Relationship of femtosecond-picosecond dynamics to enzyme-catalyzed H-transfer. Top Curr Chem (Cham) 2013; 337:1-39. [PMID: 23539379 PMCID: PMC4699684 DOI: 10.1007/128_2012_407] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
At physiological temperatures, enzymes exhibit a broad spectrum of conformations, which interchange via thermally activated dynamics. These conformations are sampled differently in different complexes of the protein and its ligands, and the dynamics of exchange between these conformers depends on the mass of the group that is moving and the length scale of the motion, as well as restrictions imposed by the globular fold of the enzymatic complex. Many of these motions have been examined and their role in the enzyme function illuminated, yet most experimental tools applied so far have identified dynamics at time scales of seconds to nanoseconds, which are much slower than the time scale for H-transfer between two heavy atoms. This chemical conversion and other processes involving cleavage of covalent bonds occur on picosecond to femtosecond time scales, where slower processes mask both the kinetics and dynamics. Here we present a combination of kinetic and spectroscopic methods that may enable closer examination of the relationship between enzymatic C-H → C transfer and the dynamics of the active site environment at the chemically relevant time scale. These methods include kinetic isotope effects and their temperature dependence, which are used to study the kinetic nature of the H-transfer, and 2D IR spectroscopy, which is used to study the dynamics of transition-state- and ground-state-analog complexes. The combination of these tools is likely to provide a new approach to examine the protein dynamics that directly influence the chemical conversion catalyzed by enzymes.
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40
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Pazos IM, Gai F. Solute's perspective on how trimethylamine oxide, urea, and guanidine hydrochloride affect water's hydrogen bonding ability. J Phys Chem B 2012; 116:12473-8. [PMID: 22998405 PMCID: PMC3475735 DOI: 10.1021/jp307414s] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
While the thermodynamic effects of trimethylamine oxide (TMAO), urea, and guanidine hydrochloride (GdnHCl) on protein stability are well understood, the underlying mechanisms of action are less well characterized and, in some cases, even under debate. Herein, we employ the stretching vibration of two infrared (IR) reporters, i.e., nitrile (C≡N) and carbonyl (C═O), to directly probe how these cosolvents mediate the ability of water to form hydrogen bonds with the solute of interest, e.g., a peptide. Our results show that these three agents, despite having different effects on protein stability, all act to decrease the strength of the hydrogen bonds formed between water and the infrared probe. While the behavior of TMAO appears to be consistent with its protein-protecting ability, those of urea and GdnHCl are inconsistent with their role as protein denaturants. The latter is of particular interest as it provides strong evidence indicating that although urea and GdnHCl can perturb the hydrogen-bonding property of water their protein-denaturing ability does not arise from a simple indirect mechanism.
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Affiliation(s)
- Ileana M. Pazos
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104
| | - Feng Gai
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104
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41
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Bazewicz CG, Lipkin JS, Smith EE, Liskov MT, Brewer SH. Expanding the Utility of 4-Cyano-l-Phenylalanine As a Vibrational Reporter of Protein Environments. J Phys Chem B 2012; 116:10824-31. [DOI: 10.1021/jp306886s] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Christopher G. Bazewicz
- Department of Chemistry, Franklin & Marshall College, Lancaster, Pennsylvania 17604-3003, United States
| | - Jacob S. Lipkin
- Department of Chemistry, Franklin & Marshall College, Lancaster, Pennsylvania 17604-3003, United States
| | - Emily E. Smith
- Department of Chemistry, Franklin & Marshall College, Lancaster, Pennsylvania 17604-3003, United States
| | - Melanie T. Liskov
- Department of Chemistry, Franklin & Marshall College, Lancaster, Pennsylvania 17604-3003, United States
| | - Scott H. Brewer
- Department of Chemistry, Franklin & Marshall College, Lancaster, Pennsylvania 17604-3003, United States
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42
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Schlamadinger DE, Wang Y, McCammon JA, Kim JE. Spectroscopic and computational study of melittin, cecropin A, and the hybrid peptide CM15. J Phys Chem B 2012; 116:10600-8. [PMID: 22845179 PMCID: PMC3434763 DOI: 10.1021/jp304021t] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
![]()
Antimicrobial peptides (AMPs), such as cecropin A from
silk moth,
are key components of the innate immune system. They are effective
defensive weapons against invading pathogens, yet they do not target
host eukaryotic cells. In contrast, peptide toxins, such as honeybee
melittin, are nondiscriminating and target both eukaryotic and prokaryotic
cells. An AMP-toxin hybrid peptide that is composed of cecropin A
and melittin (CM15) improves upon the antimicrobial activity of cecropin
A without displaying the nonspecific, hemolytic properties of melittin.
Here we report fluorescence and UV resonance Raman spectra of melittin,
cecropin A, and CM15 with the goal of elucidating peptide-membrane
interactions that help guide specificity. We have probed the potency
for membrane disruption, local environment and structure of the single
tryptophan residue, backbone conformation near the peptide hinge,
and amide backbone structure of the peptides in lipid environments
that mimic eukaryotic and prokaryotic membranes. These experimental
results suggest that melittin inserts deeply into the bilayer, whereas
cecropin A remains localized to the lipid headgroup region. A surprising
finding is that CM15 is a potent membrane-disruptor despite its largely
unfolded conformation. A molecular dynamics analysis complements these
data and demonstrates the ability of CM15 to associate favorably with
membranes as an unfolded peptide. This combined experimental–computational
study suggests that new models for peptide–membrane interactions
should be considered.
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Affiliation(s)
- Diana E Schlamadinger
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, United States
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43
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Wolfshorndl MP, Baskin R, Dhawan I, Londergan CH. Covalently Bound Azido Groups Are Very Specific Water Sensors, Even in Hydrogen-Bonding Environments. J Phys Chem B 2012; 116:1172-9. [DOI: 10.1021/jp209899m] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Marta P. Wolfshorndl
- Department of Chemistry, Haverford College, 370 Lancaster Avenue, Haverford, Pennsylvania 19041-1392, United States
| | - Rachel Baskin
- Department of Chemistry, Haverford College, 370 Lancaster Avenue, Haverford, Pennsylvania 19041-1392, United States
| | - Ishita Dhawan
- Department of Chemistry, Haverford College, 370 Lancaster Avenue, Haverford, Pennsylvania 19041-1392, United States
| | - Casey H. Londergan
- Department of Chemistry, Haverford College, 370 Lancaster Avenue, Haverford, Pennsylvania 19041-1392, United States
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44
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Ohta K, Tayama J, Tominaga K. Ultrafast vibrational dynamics of SCN− and N3− in polar solvents studied by nonlinear infrared spectroscopy. Phys Chem Chem Phys 2012; 14:10455-65. [DOI: 10.1039/c2cp40244k] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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45
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Yang H, Habchi J, Longhi S, Londergan CH. Monitoring structural transitions in IDPs by vibrational spectroscopy of cyanylated cysteine. Methods Mol Biol 2012; 895:245-270. [PMID: 22760324 DOI: 10.1007/978-1-61779-927-3_17] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The fast intrinsic time scale of infrared absorption and the sensitivity of molecular vibrational frequencies to their environments can be applied with site-specificity by introducing the artificial amino acid β-thiocyanatoalanine, or cyanylated cysteine, into chosen sites within intrinsically disordered proteins. This amino acid can be inserted through native chemical ligation at single cysteines introduced via site-directed mutagenesis. The CN stretching band of cyanylated cysteine is sensitive to local changes in both structural content and solvent exposure. This dual sensitivity makes cyanylated cysteine an especially useful probe of binding-induced structural transitions in IDPs. The general strategy of creating single-site cysteine mutations and chemically modifying them to create the vibrational chromophore, as well as observation, processing and analysis of the CN stretching band, is presented.
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Affiliation(s)
- Hailiu Yang
- Department of Chemistry, Haverford College, Haverford, PA, USA
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46
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Alfieri KN, Vienneau AR, Londergan CH. Using infrared spectroscopy of cyanylated cysteine to map the membrane binding structure and orientation of the hybrid antimicrobial peptide CM15. Biochemistry 2011; 50:11097-108. [PMID: 22103476 PMCID: PMC3246368 DOI: 10.1021/bi200903p] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The synthetic antimicrobial peptide CM15, a hybrid of N-terminal sequences from cecropin and melittin peptides, has been shown to be extremely potent. Its mechanism of action has been thought to involve pore formation based on prior site-directed spin labeling studies. This study examines four single-site β-thiocyanatoalanine variants of CM15 in which the artificial amino acid side chain acts as a vibrational reporter of its local environment through the frequency and line shape of the unique CN stretching band in the infrared spectrum. Circular dichroism experiments indicate that the placements of the artificial side chain have only small perturbative effects on the membrane-bound secondary structure of the CM15 peptide. All variant peptides were placed in buffer solution, in contact with dodecylphosphatidylcholine micelles, and in contact with vesicles formed from Escherichia coli polar lipid extract. At each site, the CN stretching band reports a different behavior. Time-dependent attenuated total reflectance infrared spectra were also collected for each variant as it was allowed to remodel the E. coli lipid vesicles. The results of these experiments agree with the previously proposed formation of toroidal pores, in which each peptide finds itself in an increasingly homogeneous and curved local environment without apparent peptide-peptide interactions. This work also demonstrates the excellent sensitivity of the SCN stretching vibration to small changes in the peptide-lipid interfacial structure.
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Affiliation(s)
| | - Alice R. Vienneau
- Department of Chemistry, Haverford College, Haverford, PA 19041-1392
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47
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Bazewicz CG, Lipkin JS, Lozinak KA, Watson MD, Brewer SH. Synthesis of isotopomers of N-(tert-butoxycarbonyl)-4-cyano-l-phenylalanine methyl ester: choice of cyanation solvent. Tetrahedron Lett 2011. [DOI: 10.1016/j.tetlet.2011.10.050] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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48
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Waegele MM, Culik RM, Gai F. Site-Specific Spectroscopic Reporters of the Local Electric Field, Hydration, Structure, and Dynamics of Biomolecules. J Phys Chem Lett 2011; 2:2598-2609. [PMID: 22003429 PMCID: PMC3192500 DOI: 10.1021/jz201161b] [Citation(s) in RCA: 137] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Elucidating the underlying molecular mechanisms of protein folding and function is a very exciting and active research area, but poses significant challenges. This is due in part to the fact that existing experimental techniques are incapable of capturing snapshots along the 'reaction coordinate' in question with both sufficient spatial and temporal resolutions. In this regard, recent years have seen increased interests and efforts in development and employment of site-specific probes to enhance the structural sensitivity of spectroscopic techniques in conformational and dynamical studies of biological molecules. In particular, the spectroscopic and chemical properties of nitriles, thiocyanates, and azides render these groups attractive for the interrogation of complex biochemical constructs and processes. Here, we review their signatures in vibrational, fluorescence and NMR spectra and their utility in the context of elucidating chemical structure and dynamics of protein and DNA molecules.
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Affiliation(s)
| | | | - Feng Gai
- To whom correspondence should be addressed; ; Phone: 215-573-6256; Fax: 215-573-2112
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49
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Dutta S, Rock W, Cook RJ, Kohen A, Cheatum CM. Two-dimensional infrared spectroscopy of azido-nicotinamide adenine dinucleotide in water. J Chem Phys 2011; 135:055106. [PMID: 21823737 PMCID: PMC3162616 DOI: 10.1063/1.3623418] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2011] [Accepted: 07/12/2011] [Indexed: 11/14/2022] Open
Abstract
Mid-IR active analogs of enzyme cofactors have the potential to be important spectroscopic reporters of enzyme active site dynamics. Azido-nicotinamide adenine dinucleotide (NAD(+)), which has been recently synthesized in our laboratory, is a mid-IR active analog of NAD(+), a ubiquitous redox cofactor in biology. In this study, we measure the frequency-frequency time correlation function for the antisymmetric stretching vibration of the azido group of azido-NAD(+) in water. Our results are consistent with previous studies of pseudohalides in water. We conclude that azido-NAD(+) is sensitive to local environmental fluctuations, which, in water, are dominated by hydrogen-bond dynamics of the water molecules around the probe. Our results demonstrate the potential of azido-NAD(+) as a vibrational probe and illustrate the potential of substituted NAD(+)-analogs as reporters of local structural dynamics that could be used for studies of protein dynamics in NAD-dependent enzymes.
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Affiliation(s)
- Samrat Dutta
- Department of Chemistry, University of Iowa, Iowa City, Iowa 52242, USA
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50
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Rodrigues RC, Berenguer-Murcia Á, Fernandez-Lafuente R. Coupling Chemical Modification and Immobilization to Improve the Catalytic Performance of Enzymes. Adv Synth Catal 2011. [DOI: 10.1002/adsc.201100163] [Citation(s) in RCA: 272] [Impact Index Per Article: 20.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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