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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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2
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Wang Y, Wang Z, Yang L, Zhang W, Ma G. Unravelling the non-classical nucleation mechanism of an amyloid nanosheet through atomic force microscopy and an infrared probe technique. Phys Chem Chem Phys 2024; 26:7855-7864. [PMID: 38376417 DOI: 10.1039/d3cp05345h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/21/2024]
Abstract
Understanding the amyloid nucleation mechanism is fundamentally important for the development of diagnostics and therapeutics of amyloid-related diseases and for the design and application of amyloid-based materials. To this end, we here explore the use of atomic force microscopy (AFM) and a side-chain-based infrared (IR) probe technique to investigate the amyloid nanosheet formation mechanism of an Aβ16-22 variant, KLVFXAK, where X is p-cyanophenylalanine with its side-chain cyano group being an infrared probe. Using AFM, we reveal that the formation of KLVFXAK amyloid nanosheets follows a two-step non-classical nucleation mechanism. The first step is the rapid formation of a metastable fibrillar intermediate and the second step is slow transformation to the final nanosheet. Using the side-chain-based IR probe technique, we obtain spectroscopic evidence for the proposed nucleation mechanism of the amyloid nanosheet as well as the structural details for the intermediate and amyloid nanosheet. By using the structural constraints set by the two techniques, we propose the structural models for both the fibrillar intermediate and the amyloid nanosheet. In addition, we further investigated the amyloid nanosheet formation mechanism of a similar Aβ16-22 variant, KLVFXAE, and showed the impact of mutation on the amyloid nucleation mechanism. Our work also provides a nice example of how to use the combined approach of AFM and a side-chain-based IR probe technique to unravel the complex nucleation mechanism of amyloid formation.
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Affiliation(s)
- Yao Wang
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of Ministry of Education, Key Laboratory of Analytical Science and Technology of Hebei Province, State Key Laboratory of New Pharmaceutical Preparations and Excipients, Hebei Research Center of the Basic Discipline of Synthetic Chemistry, College of Chemistry and Materials Science, Hebei University, Baoding 071002, China.
| | - Ziqi Wang
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of Ministry of Education, Key Laboratory of Analytical Science and Technology of Hebei Province, State Key Laboratory of New Pharmaceutical Preparations and Excipients, Hebei Research Center of the Basic Discipline of Synthetic Chemistry, College of Chemistry and Materials Science, Hebei University, Baoding 071002, China.
| | - Lujuan Yang
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis of Ministry of Education, Key Laboratory of Analytical Science and Technology of Hebei Province, State Key Laboratory of New Pharmaceutical Preparations and Excipients, Hebei Research Center of the Basic Discipline of Synthetic Chemistry, College of Chemistry and Materials Science, Hebei University, Baoding 071002, China.
| | - Wenkai Zhang
- Department of Physics, Applied Optics Beijing Area Major Laboratory, Center for Advanced Quantum Studies, Beijing Normal University, Beijing 100875, 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, State Key Laboratory of New Pharmaceutical Preparations and Excipients, Hebei Research Center of the Basic Discipline of Synthetic Chemistry, College of Chemistry and Materials Science, Hebei University, Baoding 071002, China.
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3
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Dong T, Yu P, Zhao J, Wang J. Probing the local structure and dynamics of nucleotides using vibrationally enhanced alkynyl stretching. Phys Chem Chem Phys 2022; 24:29988-29998. [PMID: 36472165 DOI: 10.1039/d2cp03920f] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Monitoring the site-specific local structure and dynamics of polynucleotides and DNA is important for understanding their biological functions. However, structurally characterizing these biomolecules with high time resolution has been known to be experimentally challenging. In this work, several 5-silylethynyl-2'-deoxynucleosides and 5-substituted phenylethynyl-2'-deoxynucleosides on the basis of deoxycytidine (dC) and deoxythymidine (dT) were synthesized, in which the alkynyl group shows intensified CC stretching vibration with infrared transition dipole moment magnitude close to that of typical CO stretching, and exhibits structural sensitivities in both vibrational frequency and spectral width. In particular, 5-trimethylsilylethynyl-2'-dC (TMSEdC, molecule 1a) was examined in detail using femtosecond nonlinear IR spectroscopy. The solvent dependent CC stretching frequency of 1a can be reasonably interpreted mainly as the hydrogen-bonding effect between the solvent and cytosine base ring structure. Transient 2D IR and pump-probe IR measurements of 1a carried out comparatively in two aprotic solvents (DMSO and THF) and one protic solvent (MeOH) further reveal solvent dependent ultrafast vibrational properties, including diagonal anharmonicity, spectral diffusion, vibrational relaxation and anisotropy dynamics. These observed sensitivities are rooted in an extended π-conjugation of the base ring structure in which the CC group is actively involved. Our results show that the intensified CC stretching vibration can potentially provide a site-specific IR probe for monitoring the equilibrium and ultrafast structural dynamics of polynucleotides.
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Affiliation(s)
- Tiantian Dong
- Beijing National Laboratory for Molecular Sciences, Molecular Reaction Dynamics Laboratory, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China. .,University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Pengyun Yu
- Beijing National Laboratory for Molecular Sciences, Molecular Reaction Dynamics Laboratory, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China. .,University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Juan Zhao
- Beijing National Laboratory for Molecular Sciences, Molecular Reaction Dynamics Laboratory, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China. .,University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Jianping Wang
- Beijing National Laboratory for Molecular Sciences, Molecular Reaction Dynamics Laboratory, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China. .,University of Chinese Academy of Sciences, Beijing 100049, P. R. China
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4
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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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5
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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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6
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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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7
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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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8
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Kelly KL, Dalton SR, Wai RB, Ramchandani K, Xu RJ, Linse S, Londergan CH. Conformational Ensembles of Calmodulin Revealed by Nonperturbing Site-Specific Vibrational Probe Groups. J Phys Chem A 2018; 122:2947-2955. [PMID: 29400461 PMCID: PMC5867645 DOI: 10.1021/acs.jpca.8b00475] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
![]()
Seven native residues on the regulatory
protein calmodulin, including
three key methionine residues, were replaced (one by one) by the vibrational
probe amino acid cyanylated cysteine, which has a unique CN stretching
vibration that reports on its local environment. Almost no perturbation
was caused by this probe at any of the seven sites, as reported by
CD spectra of calcium-bound and apo calmodulin and
binding thermodynamics for the formation of a complex between calmodulin
and a canonical target peptide from skeletal muscle myosin light chain
kinase measured by isothermal titration. The surprising lack of perturbation
suggests that this probe group could be applied directly in many protein–protein
binding interfaces. The infrared absorption bands for the probe groups
reported many dramatic changes in the probes’ local environments
as CaM went from apo- to calcium-saturated to target
peptide-bound conditions, including large frequency shifts and a variety
of line shapes from narrow (interpreted as a rigid and invariant local
environment) to symmetric to broad and asymmetric (likely from multiple
coexisting and dynamically exchanging structures). The fast intrinsic
time scale of infrared spectroscopy means that the line shapes report
directly on site-specific details of calmodulin’s variable
structural distribution. Though quantitative interpretation of the
probe line shapes depends on a direct connection between simulated
ensembles and experimental data that does not yet exist, formation
of such a connection to data such as that reported here would provide
a new way to evaluate conformational ensembles from data that directly
contains the structural distribution. The calmodulin probe sites developed
here will also be useful in evaluating the binding mode of calmodulin
with many uncharacterized regulatory targets.
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Affiliation(s)
- Kristen L Kelly
- Department of Chemistry , Haverford College , Haverford , Pennsylvania 19041 , United States
| | - Shannon R Dalton
- Department of Chemistry , Haverford College , Haverford , Pennsylvania 19041 , United States
| | - Rebecca B Wai
- Department of Chemistry , Haverford College , Haverford , Pennsylvania 19041 , United States
| | - Kanika Ramchandani
- Department of Chemistry , Haverford College , Haverford , Pennsylvania 19041 , United States
| | - Rosalind J Xu
- Department of Chemistry , Haverford College , Haverford , Pennsylvania 19041 , United States
| | - Sara Linse
- Department of Biochemistry and Structural Biology , Lund University , 221 00 Lund , Sweden
| | - Casey H Londergan
- Department of Chemistry , Haverford College , Haverford , Pennsylvania 19041 , United States
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9
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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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10
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Adhikary R, Zimmermann J, Romesberg FE. Transparent Window Vibrational Probes for the Characterization of Proteins With High Structural and Temporal Resolution. Chem Rev 2017; 117:1927-1969. [DOI: 10.1021/acs.chemrev.6b00625] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Ramkrishna Adhikary
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Jörg Zimmermann
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
| | - Floyd E. Romesberg
- Department of Chemistry, The Scripps Research Institute, La Jolla, California 92037, United States
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11
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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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12
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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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13
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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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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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15
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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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16
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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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17
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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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18
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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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19
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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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20
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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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21
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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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22
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Probing structural transitions in the intrinsically disordered C-terminal domain of the measles virus nucleoprotein by vibrational spectroscopy of cyanylated cysteines. Biophys J 2010; 99:1676-83. [PMID: 20816082 DOI: 10.1016/j.bpj.2010.06.060] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2010] [Revised: 06/23/2010] [Accepted: 06/28/2010] [Indexed: 11/23/2022] Open
Abstract
Four single-cysteine variants of the intrinsically disordered C-terminal domain of the measles virus nucleoprotein (N(TAIL)) were cyanylated at cysteine and their infrared spectra in the C triple bond N stretching region were recorded both in the absence and in the presence of one of the physiological partners of N(TAIL), namely the C-terminal X domain (XD) of the viral phosphoprotein. Consistent with previous studies showing that XD triggers a disorder-to-order transition within N(TAIL), the C triple bond N stretching bands of the infrared probe were found to be significantly affected by XD, with this effect being position-dependent. When the cyanylated cysteine side chain is solvent-exposed throughout the structural transition, its changing linewidth reflects a local gain of structure. When the probe becomes partially buried due to binding, its frequency reports on the mean hydrophobicity of the microenvironment surrounding the labeled side chain of the bound form. The probe moiety is small compared to other common covalently attached spectroscopic probes, thereby minimizing possible steric hindrance/perturbation at the binding interface. These results show for the first time to our knowledge the suitability of site-specific cysteine mutagenesis followed by cyanylation and infrared spectroscopy to document structural transitions occurring within intrinsically disordered regions, with regions involved in binding and folding being identifiable at the residue level.
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23
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Stafford AJ, Ensign DL, Webb LJ. Vibrational Stark Effect Spectroscopy at the Interface of Ras and Rap1A Bound to the Ras Binding Domain of RalGDS Reveals an Electrostatic Mechanism for Protein−Protein Interaction. J Phys Chem B 2010; 114:15331-44. [DOI: 10.1021/jp106974e] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Amy J. Stafford
- Department of Chemistry and Biochemistry and Institute for Cell and Molecular Biology, The University of Texas at Austin, 1 University Station, A5300, Austin, Texas 78712, United States
| | - Daniel L. Ensign
- Department of Chemistry and Biochemistry and Institute for Cell and Molecular Biology, The University of Texas at Austin, 1 University Station, A5300, Austin, Texas 78712, United States
| | - Lauren J. Webb
- Department of Chemistry and Biochemistry and Institute for Cell and Molecular Biology, The University of Texas at Austin, 1 University Station, A5300, Austin, Texas 78712, United States
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24
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Nydegger MW, Dutta S, Cheatum CM. Two-dimensional infrared study of 3-azidopyridine as a potential spectroscopic reporter of protonation state. J Chem Phys 2010; 133:134506. [DOI: 10.1063/1.3483688] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
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