51
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Lin YC, Petersson EJ, Fakhraai Z. Surface effects mediate self-assembly of amyloid-β peptides. ACS NANO 2014; 8:10178-10186. [PMID: 25229233 PMCID: PMC4212779 DOI: 10.1021/nn5031669] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2014] [Accepted: 09/17/2014] [Indexed: 05/30/2023]
Abstract
Here we present a label-free method for studying the mechanism of surface effects on amyloid aggregation. In this method, spin-coating is used to rapidly dry samples, in a homogeneous manner, after various incubation times. This technique allows the control of important parameters for self-assembly, such as the surface concentration. Atomic force microscopy is then used to obtain high-resolution images of the morphology. While imaging under dry conditions, we show that the morphologies of self-assembled aggregates of a model amyloid-β peptide, Aβ(12-28), are strongly influenced by the local surface concentration. On mica surfaces, where the peptides can freely diffuse, homogeneous, self-assembled protofibrils formed spontaneously and grew longer with longer subsequent incubation. The surface fibrillization rate was much faster than the rates of fibril formation observed in solution, with initiation occurring at much lower concentrations. These data suggest an alternative pathway for amyloid formation on surfaces where the nucleation stage is either bypassed entirely or too fast to measure. This simple preparation procedure for high-resolution atomic force microscopy imaging of amyloid oligomers and protofibrils should be applicable to any amyloidogenic protein species.
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52
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Han G, Feng N, Wang G. Fluorescence Quenching of Hen Egg Lysozyme and Bovine Serum Albumin by Azobenzene Polymer at Different pH. CHEM LETT 2014. [DOI: 10.1246/cl.140457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Guoxiang Han
- School of Materials Science and Engineering, University of Science and Technology Beijing
| | - Ning Feng
- School of Materials Science and Engineering, University of Science and Technology Beijing
| | - Guojie Wang
- School of Materials Science and Engineering, University of Science and Technology Beijing
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53
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Li HZ, Xue WJ, Wu AX. Direct synthesis of α-ketothioamides from aryl methyl ketones and amines via I2-promoted sp3 C–H functionalization. Tetrahedron 2014. [DOI: 10.1016/j.tet.2014.05.045] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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54
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Basu B, Kundu S. Unprecedented amidation of ‘transient’ aryl thioaldehydes by N,N-dimethylformamide under basic conditions. NEW J CHEM 2014. [DOI: 10.1039/c4nj00480a] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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55
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Soares JA, Kiessling LL. A symposium in honor of Peter B. Dervan, the 2014 ACS Chemical Biology Lectureship Award Winner. ACS Chem Biol 2014; 9:1221-3. [PMID: 25120068 DOI: 10.1021/cb5003703] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jitesh A Soares
- Department of Chemistry, University of Wisconsin, Madition , 433 Babcock Drive, Madison, Wisconsin 53706-1544, United States
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56
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Theoretical study (CC2, DFT and PCM) of charge transfer complexes between antithyroid thioamides and TCNE: electronic CT transitions. J Mol Model 2014; 20:2312. [DOI: 10.1007/s00894-014-2312-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Accepted: 05/19/2014] [Indexed: 10/25/2022]
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57
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Brust A, Schroeder CI, Alewood PF. High-Throughput Synthesis of Peptide α-Thioesters: A Safety Catch Linker Approach Enabling Parallel Hydrogen Fluoride Cleavage. ChemMedChem 2014; 9:1038-46. [DOI: 10.1002/cmdc.201300524] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2013] [Indexed: 11/06/2022]
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58
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Batjargal S, Huang Y, Wang YJ, Petersson EJ. Synthesis of thioester peptides for the incorporation of thioamides into proteins by native chemical ligation. J Pept Sci 2014; 20:87-91. [PMID: 24408658 PMCID: PMC4199922 DOI: 10.1002/psc.2589] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2013] [Revised: 10/21/2013] [Accepted: 10/24/2013] [Indexed: 01/24/2023]
Abstract
Thioamides can be used as photoswitches, as reporters of local environment, as inhibitors of enzymes, and as fluorescence quenchers. We have recently demonstrated the incorporation of thioamides into polypeptides and proteins using native chemical ligation (NCL). In this protocol, we describe procedures for the synthesis of a thioamide precursor and an NCL-ready thioamide-containing peptide using Dawson's N-acyl-benzimidazolinone (Nbz) process. We include a description of the synthesis by NCL of a thioamide-labeled fragment of the neuronal protein α-synuclein.
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Affiliation(s)
- Solongo Batjargal
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, USA
| | - Yun Huang
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, USA
| | - Yanxin J. Wang
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, USA
| | - E. James Petersson
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, USA
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59
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Goldberg JM, Chen X, Meinhardt N, Greenbaum DC, Petersson EJ. Thioamide-based fluorescent protease sensors. J Am Chem Soc 2014; 136:2086-93. [PMID: 24472041 PMCID: PMC3985465 DOI: 10.1021/ja412297x] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
![]()
Thioamide
quenchers can be paired with compact fluorophores to
design “turn-on” fluorescent protease substrates. We
have used this method to study a variety of serine-, cysteine-, carboxyl-,
and metallo-proteases, including trypsin, chymotrypsin, pepsin, thermolysin,
papain, and calpain. Since thioamides quench some fluorophores red-shifted
from those naturally occurring in proteins, this technique can be
used for real time monitoring of protease activity in crude preparations
of virtually any protease. We demonstrate the value of this method
in three model applications: (1) characterization of papain enzyme
kinetics using rapid-mixing experiments, (2) selective monitoring
of cleavage at a single site in a peptide with multiple proteolytic
sites, and (3) analysis of the specificity of an inhibitor of calpain
in cell lysates.
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Affiliation(s)
- Jacob M Goldberg
- Department of Chemistry, University of Pennsylvania , 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323, United States
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60
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Koniev O, Leriche G, Nothisen M, Remy JS, Strub JM, Schaeffer-Reiss C, Van Dorsselaer A, Baati R, Wagner A. Selective Irreversible Chemical Tagging of Cysteine with 3-Arylpropiolonitriles. Bioconjug Chem 2014; 25:202-6. [DOI: 10.1021/bc400469d] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
| | | | | | | | - Jean-Marc Strub
- Laboratoire
de Spectrométrie de Masse BioOrganique (UMR 7178), Institut Pluridisciplinaire Hubert Curien, University of Strasbourg, 25 rue
Becquerel, 67087 Strasbourg, France
| | - Christine Schaeffer-Reiss
- Laboratoire
de Spectrométrie de Masse BioOrganique (UMR 7178), Institut Pluridisciplinaire Hubert Curien, University of Strasbourg, 25 rue
Becquerel, 67087 Strasbourg, France
| | - Alain Van Dorsselaer
- Laboratoire
de Spectrométrie de Masse BioOrganique (UMR 7178), Institut Pluridisciplinaire Hubert Curien, University of Strasbourg, 25 rue
Becquerel, 67087 Strasbourg, France
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61
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Speight LC, Samanta M, Petersson EJ. Minimalist Approaches to Protein Labelling: Getting the Most Fluorescent Bang for Your Steric Buck. Aust J Chem 2014. [DOI: 10.1071/ch13554] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Fluorescence methods allow one to monitor protein conformational changes, protein–protein associations, and proteolysis in real time, at the single molecule level and in living cells. The information gained in such experiments is a function of the spectroscopic techniques used and the strategic placement of fluorophore labels within the protein structure. There is often a trade-off between size and utility for fluorophores, whereby large size can be disruptive to the protein’s fold or function, but valuable characteristics, such as visible wavelength absorption and emission or brightness, require sizable chromophores. Three major types of fluorophore readouts are commonly used: (1) Förster resonance energy transfer (FRET); (2) photoinduced electron transfer (PET); and (3) environmental sensitivity. This review focuses on those probes small enough to be incorporated into proteins during ribosomal translation, which allows the probes to be placed on the interiors of proteins as they are folded during synthesis. The most broadly useful method for doing so is site-specific unnatural amino acid (UAA) mutagenesis. We discuss the use of UAA probes in applications relying on FRET, PET, and environmental sensitivity. We also briefly review other methods of protein labelling and compare their relative merits to UAA mutagenesis. Finally, we discuss small probes that have thus far been used only in synthetic peptides, but which have unusual value and may be candidates for incorporation using UAA methods.
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62
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Rasale DB, Maity I, Das AK. In situ generation of redox active peptides driven by selenoester mediated native chemical ligation. Chem Commun (Camb) 2014; 50:11397-400. [DOI: 10.1039/c4cc03835e] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Redox active peptides synthesized via selenoester mediated native chemical ligation with a propensity to self-assemble in aqueous medium. A gel–sol transition of self-assembled peptide in a reducing environment makes it a versatile candidate for the development of functional biomaterials.
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Affiliation(s)
| | - Indrajit Maity
- Department of Chemistry
- Indian Institute of Technology Indore
- Indore 452017, India
| | - Apurba K. Das
- Department of Chemistry
- Indian Institute of Technology Indore
- Indore 452017, India
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63
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Mühlberg M, Siebertz KD, Schlegel B, Schmieder P, Hackenberger CPR. Controlled thioamide vs. amide formation in the thioacid–azide reaction under acidic aqueous conditions. Chem Commun (Camb) 2014; 50:4603-6. [DOI: 10.1039/c4cc00774c] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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64
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Nguyen TB, Tran MQ, Ermolenko L, Al-Mourabit A. Three-Component Reaction between Alkynes, Elemental Sulfur, and Aliphatic Amines: A General, Straightforward, and Atom Economical Approach to Thioamides. Org Lett 2013; 16:310-3. [DOI: 10.1021/ol403345e] [Citation(s) in RCA: 102] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Thanh Binh Nguyen
- Centre de Recherche de Gif-sur-Yvette,
Institut de Chimie des Substances Naturelles, CNRS, 91198 Gif-sur-Yvette Cedex, France
| | - Minh Quan Tran
- Centre de Recherche de Gif-sur-Yvette,
Institut de Chimie des Substances Naturelles, CNRS, 91198 Gif-sur-Yvette Cedex, France
| | - Ludmila Ermolenko
- Centre de Recherche de Gif-sur-Yvette,
Institut de Chimie des Substances Naturelles, CNRS, 91198 Gif-sur-Yvette Cedex, France
| | - Ali Al-Mourabit
- Centre de Recherche de Gif-sur-Yvette,
Institut de Chimie des Substances Naturelles, CNRS, 91198 Gif-sur-Yvette Cedex, France
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65
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Goldberg JM, Batjargal S, Chen BS, Petersson EJ. Thioamide quenching of fluorescent probes through photoinduced electron transfer: mechanistic studies and applications. J Am Chem Soc 2013; 135:18651-8. [PMID: 24266520 DOI: 10.1021/ja409709x] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Previously we have shown that thioamides can be incorporated into proteins as minimally perturbing fluorescence-quenching probes to study protein dynamics, folding, and aggregation. Here, we show that the spontaneity of photoinduced electron transfer between a thioamide and an excited fluorophore is governed by the redox potentials of each moiety according to a Rehm-Weller-type model. We have used this model to predict thioamide quenching of various common fluorophores, and we rigorously tested more than a dozen examples. In each case, we found excellent agreement between our theoretical predictions and experimental observations. In this way, we have been able to expand the scope of fluorophores quenched by thioamides to include dyes suitable for microscopy and single-molecule studies, including fluorescein, Alexa Fluor 488, BODIPY FL, and rhodamine 6G. We describe the photochemistry of these systems and explore applications that demonstrate the utility of thioamide quenching of fluorescein to studying protein folding and proteolysis.
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Affiliation(s)
- Jacob M Goldberg
- Department of Chemistry, University of Pennsylvania , Philadelphia, Pennsylvania 19104-6323, United States
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66
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Wissner RF, Wagner AM, Warner JB, Petersson EJ. Efficient, Traceless Semi-Synthesis of α-Synuclein Labeled with a Fluorophore/Thioamide FRET Pair. Synlett 2013; 24:2454-2458. [PMID: 26893537 PMCID: PMC4755331 DOI: 10.1055/s-0033-1339853] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
We have shown that thioamides can be incorporated into proteins through semi-synthesis and used as probes to monitor structural changes. To date, our methods have required the presence of a cysteine at the peptide ligation site, which may not be present in the native peptide sequence. Here, we present a strategy for the semi-synthesis of thioproteins using homocysteine as a ligation point with subsequent masking as methionine, making the ligation "traceless."
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Affiliation(s)
- Rebecca F. Wissner
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, USA
| | - Anne M. Wagner
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, USA
| | - John B. Warner
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, USA
| | - E. James Petersson
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104-6323, USA
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67
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TCEP-based rSDS–PAGE AND nLC–ESI-LTQ-MS/MS for oxaliplatin metalloproteomic analysis. Talanta 2013; 116:581-92. [DOI: 10.1016/j.talanta.2013.06.044] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2013] [Revised: 06/18/2013] [Accepted: 06/25/2013] [Indexed: 01/08/2023]
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68
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Patra M, Hess J, Konatschnig S, Spingler B, Gasser G. Synthesis of Ferrocenyl and Ruthenocenyl Thioamide Derivatives Using a Single-Step Three-Component Reaction. Organometallics 2013. [DOI: 10.1021/om400715m] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Malay Patra
- Institute
of Inorganic Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Jeannine Hess
- Institute
of Inorganic Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Sandro Konatschnig
- Institute
of Inorganic Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Bernhard Spingler
- Institute
of Inorganic Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - Gilles Gasser
- Institute
of Inorganic Chemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
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69
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Dunbar KL, Mitchell DA. Insights into the mechanism of peptide cyclodehydrations achieved through the chemoenzymatic generation of amide derivatives. J Am Chem Soc 2013; 135:8692-701. [PMID: 23721104 DOI: 10.1021/ja4029507] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Current strategies for generating peptides and proteins bearing amide carbonyl derivatives rely on solid-phase peptide synthesis for amide functionalization. Although such strategies have been successfully implemented, technical limitations restrict both the length and sequence of the synthetic fragments. Herein we report the repurposing of a thiazole/oxazole-modified microcin (TOMM) cyclodehydratase to site-specifically install amide backbone labels onto diverse peptide substrates, a method we refer to as azoline-mediated peptide backbone labeling (AMPL). This convenient chemoenzymatic strategy can generate both thioamides and amides with isotopically labeled oxygen atoms. Moreover, we demonstrate the first leader peptide-independent activity of a TOMM synthetase, circumventing the requirement that sequences of interest be fused to a leader peptide for modification. Through bioinformatics-guided site-directed mutagenesis, we also convert a strictly dehydrogenase-dependent TOMM azole synthetase into an azoline synthetase. This vastly expands the spectrum of substrates modifiable by AMPL by allowing any in vitro reconstituted TOMM synthetase to be employed. To demonstrate the utility of AMPL for mechanistic enzymology studies, an (18)O-labeled substrate was generated to provide direct evidence that cyclodehydrations in TOMMs occur through the phosphorylation of the carbonyl oxygen preceding the cyclized residue. Furthermore, we demonstrate that AMPL is a useful tool for establishing the location of azolines both on in vitro modified peptides and azoline-containing natural products.
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Affiliation(s)
- Kyle L Dunbar
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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70
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Newberry RW, VanVeller B, Guzei IA, Raines RT. n→π* interactions of amides and thioamides: implications for protein stability. J Am Chem Soc 2013; 135:7843-6. [PMID: 23663100 PMCID: PMC3742804 DOI: 10.1021/ja4033583] [Citation(s) in RCA: 170] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2013] [Indexed: 01/05/2023]
Abstract
Carbonyl-carbonyl interactions between adjacent backbone amides have been implicated in the conformational stability of proteins. By combining experimental and computational approaches, we show that relevant amidic carbonyl groups associate through an n→π* donor-acceptor interaction with an energy of at least 0.27 kcal/mol. The n→π* interaction between two thioamides is 3-fold stronger than between two oxoamides due to increased overlap and reduced energy difference between the donor and acceptor orbitals. This result suggests that backbone thioamide incorporation could stabilize protein structures. Finally, we demonstrate that intimate carbonyl interactions are described more completely as donor-acceptor orbital interactions rather than dipole-dipole interactions.
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Affiliation(s)
- Robert W. Newberry
- Department of Chemistry and Department of Biochemistry, University of Wisconsin—Madison, Madison, Wisconsin
53706, United States
| | - Brett VanVeller
- Department of Chemistry and Department of Biochemistry, University of Wisconsin—Madison, Madison, Wisconsin
53706, United States
| | - Ilia A. Guzei
- Department of Chemistry and Department of Biochemistry, University of Wisconsin—Madison, Madison, Wisconsin
53706, United States
| | - Ronald T. Raines
- Department of Chemistry and Department of Biochemistry, University of Wisconsin—Madison, Madison, Wisconsin
53706, United States
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71
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Mes T, Cantekin S, Balkenende DWR, Frissen MMM, Gillissen MAJ, De Waal BFM, Voets IK, Meijer EW, Palmans ARA. Thioamides: Versatile Bonds To Induce Directional and Cooperative Hydrogen Bonding in Supramolecular Polymers. Chemistry 2013; 19:8642-9. [DOI: 10.1002/chem.201204273] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2012] [Revised: 03/20/2013] [Indexed: 12/20/2022]
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72
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Wissner RF, Batjargal S, Fadzen CM, Petersson EJ. Labeling proteins with fluorophore/thioamide Förster resonant energy transfer pairs by combining unnatural amino acid mutagenesis and native chemical ligation. J Am Chem Soc 2013; 135:6529-40. [PMID: 23594264 DOI: 10.1021/ja4005943] [Citation(s) in RCA: 72] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We have recently shown that p-cyanophenylalanine (Cnf) and a thioamide can be used as a minimally perturbing Förster resonant energy transfer (FRET) pair to monitor protein conformation. We have also shown that thioamide analogues of natural amino acids can be incorporated into full-sized proteins through native chemical ligation. For intermolecular studies with Cnf/thioamide FRET pairs, Cnf can be incorporated into proteins expressed in Escherichia coli through unnatural amino acid mutagenesis using a Cnf-specific tRNA synthetase. For intramolecular studies, a Cnf-labeled protein fragment can be expressed in E. coli and then ligated to a thioamide-labeled peptide synthesized on solid phase. This combination of methods allows for rapid access to double-labeled proteins with a minimum of unnecessary chemical synthesis. We demonstrate the utility of this approach by studying the binding of peptides to the protein calmodulin and by determining the orientation of the N- and C-termini in the amyloidogenic protein α-synuclein.
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Affiliation(s)
- Rebecca F Wissner
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104-6323, USA
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73
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Laursen JS, Engel-Andreasen J, Fristrup P, Harris P, Olsen CA. Cis-trans amide bond rotamers in β-peptoids and peptoids: evaluation of stereoelectronic effects in backbone and side chains. J Am Chem Soc 2013; 135:2835-44. [PMID: 23343406 DOI: 10.1021/ja312532x] [Citation(s) in RCA: 114] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Non-natural peptide analogs have significant potential for the development of new materials and pharmacologically active ligands. One such architecture, the β-peptoids (N-alkyl-β-alanines), has found use in a variety of biologically active compounds but has been sparsely studied with respect to folding propensity. Thus, we here report an investigation of the effect of structural variations on the cis-trans amide bond rotamer equilibria in a selection of monomer model systems. In addition to various side chain effects, which correlated well with previous studies of α-peptoids, we present the synthesis and investigation of cis-trans isomerism in the first examples of peptoids and β-peptoids containing thioamide bonds as well as trifluoroacetylated peptoids and β-peptoids. These systems revealed an increase in the preference for cis-amides as compared to their parent compounds and thus provide novel strategies for affecting the folding of peptoid constructs. By using NMR spectroscopy, X-ray crystallographic analysis, and density functional theory calculations, we present evidence for the presence of thioamide-aromatic interactions through C(sp(2))-H···S(amide) hydrogen bonding, which stabilize certain peptoid conformations.
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Affiliation(s)
- Jonas S Laursen
- Department of Chemistry, Technical University of Denmark, Kemitorvet 207, DK-2800, Kongens Lyngby, Denmark
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74
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Eftekhari-Sis B, Vahdati-Khajeh S, Amini SM, Zirak M, Saraei M. Willgerodt–Kindler reaction of arylglyoxals with amines and sulfur in aqueous media: a simple and efficient synthesis of α-ketothioamides. J Sulphur Chem 2013. [DOI: 10.1080/17415993.2012.757614] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Bagher Eftekhari-Sis
- a Department of Chemistry , University of Maragheh , PO Box 55181-83111, Maragheh , Iran
| | - Saleh Vahdati-Khajeh
- a Department of Chemistry , University of Maragheh , PO Box 55181-83111, Maragheh , Iran
| | - S. Motahhareh Amini
- a Department of Chemistry , University of Maragheh , PO Box 55181-83111, Maragheh , Iran
| | - Maryam Zirak
- b Department of Chemistry , Payame Noor University , PO Box 19395-3697, Tehran , Iran
| | - Mahnaz Saraei
- b Department of Chemistry , Payame Noor University , PO Box 19395-3697, Tehran , Iran
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75
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Levine PM, Craven TW, Bonneau R, Kirshenbaum K. Chemoselective fragment condensation between peptide and peptidomimetic oligomers. Org Biomol Chem 2013; 11:4142-6. [DOI: 10.1039/c3ob40606g] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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76
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Thompson AD, Makley LN, McMenimen K, Gestwicki JE. The three cornerstones of chemical biology: innovative probes, new discoveries, and enabling tools. ACS Chem Biol 2012; 7:791-6. [PMID: 22594530 DOI: 10.1021/cb3001827] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Andrea D. Thompson
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Leah N. Makley
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
| | - Kathryn McMenimen
- Department of Chemistry, Mt. Holyoke College, South Hadley, Massachusetts 01075, United States
| | - Jason E. Gestwicki
- Life Sciences Institute, University of Michigan, Ann Arbor, Michigan 48109, United States
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77
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Culik RM, Jo H, DeGrado WF, Gai F. Using thioamides to site-specifically interrogate the dynamics of hydrogen bond formation in β-sheet folding. J Am Chem Soc 2012; 134:8026-9. [PMID: 22540162 PMCID: PMC3354031 DOI: 10.1021/ja301681v] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Thioamides are sterically almost identical to their oxoamide counterparts, but they are weaker hydrogen bond acceptors. Therefore, thioamide amino acids are excellent candidates for perturbing the energetics of backbone-backbone H-bonds in proteins and hence should be useful in elucidating protein folding mechanisms in a site-specific manner. Herein, we validate this approach by applying it to probe the dynamic role of interstrand H-bond formation in the folding kinetics of a well-studied β-hairpin, tryptophan zipper. Our results show that reducing the strength of the peptide's backbone-backbone H-bonds, except the one directly next to the β-turn, does not change the folding rate, suggesting that most native interstrand H-bonds in β-hairpins are formed only after the folding transition state.
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Affiliation(s)
- Robert M Culik
- Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
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78
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Goldberg JM, Speight LC, Fegley MW, Petersson EJ. Minimalist probes for studying protein dynamics: thioamide quenching of selectively excitable fluorescent amino acids. J Am Chem Soc 2012; 134:6088-91. [PMID: 22471784 PMCID: PMC3360930 DOI: 10.1021/ja3005094] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Fluorescent probe pairs that can be selectively excited in the presence of Trp and Tyr are of great utility in studying conformational changes in proteins. However, the size of these probe pairs can restrict their incorporation to small portions of a protein sequence where their effects on secondary and tertiary structure can be tolerated. Our findings show that a thioamide bond-a single atom substitution of the peptide backbone-can quench fluorophores that are red-shifted from intrinsic protein fluorescence, such as acridone. Using steady-state and fluorescence lifetime measurements, we further demonstrate that this quenching occurs through a dynamic electron-transfer mechanism. In a proof-of-principle experiment, we apply this technique to monitor unfolding in a model peptide system, the villin headpiece HP35 fragment. Thioamide analogues of the natural amino acids can be placed in a variety of locations in a protein sequence, allowing one to make a large number of measurements to model protein folding.
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Affiliation(s)
- Jacob M. Goldberg
- Department of Chemistry, University of Pennsylvania, 231 South 34 Street, Philadelphia, Pennsylvania 19104-6323, United States
| | - Lee C. Speight
- Department of Chemistry, University of Pennsylvania, 231 South 34 Street, Philadelphia, Pennsylvania 19104-6323, United States
| | | | - E. James Petersson
- Department of Chemistry, University of Pennsylvania, 231 South 34 Street, Philadelphia, Pennsylvania 19104-6323, United States
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79
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Monbaliu JCM, Katritzky AR. Recent trends in Cys- and Ser/Thr-based synthetic strategies for the elaboration of peptide constructs. Chem Commun (Camb) 2012; 48:11601-22. [DOI: 10.1039/c2cc34434c] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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