1
|
Xu R, Jiang Z, Yang Q, Bloino J, Biczysko M. Harmonic and anharmonic vibrational computations for biomolecular building blocks: Benchmarking DFT and basis sets by theoretical and experimental IR spectrum of glycine conformers. J Comput Chem 2024. [PMID: 38682874 DOI: 10.1002/jcc.27377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2024] [Revised: 04/01/2024] [Accepted: 04/02/2024] [Indexed: 05/01/2024]
Abstract
Advanced vibrational spectroscopic experiments have reached a level of sophistication that can only be matched by numerical simulations in order to provide an unequivocal analysis, a crucial step to understand the structure-function relationship of biomolecules. While density functional theory (DFT) has become the standard method when targeting medium-size or larger systems, the problem of its reliability and accuracy are well-known and have been abundantly documented. To establish a reliable computational protocol, especially when accuracy is critical, a tailored benchmark is usually required. This is generally done over a short list of known candidates, with the basis set often fixed a priori. In this work, we present a systematic study of the performance of DFT-based hybrid and double-hybrid functionals in the prediction of vibrational energies and infrared intensities at the harmonic level and beyond, considering anharmonic effects through vibrational perturbation theory at the second order. The study is performed for the six-lowest energy glycine conformers, utilizing available "state-of-the-art" accurate theoretical and experimental data as reference. Focusing on the most intense fundamental vibrations in the mid-infrared range of glycine conformers, the role of the basis sets is also investigated considering the balance between computational cost and accuracy. Targeting larger systems, a broad range of hybrid schemes with different computational costs is also tested.
Collapse
Affiliation(s)
- Ruiqin Xu
- Department of Physics, College of Sciences, Shanghai University, Shanghai, China
| | | | - Qin Yang
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Science, Prague, Czechia
| | - Julien Bloino
- Classe di Scienze, Scuola Normale Superiore, Pisa, Italy
| | - Malgorzata Biczysko
- Department of Physics, College of Sciences, Shanghai University, Shanghai, China
| |
Collapse
|
2
|
Le Barbu-Debus K, Pérez-Mellor A, Lepère V, Zehnacker A. How change in chirality prevents β-amyloid type interaction in a protonated cyclic dipeptide dimer. Phys Chem Chem Phys 2022; 24:19783-19791. [PMID: 35969161 DOI: 10.1039/d2cp03110h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The protonated dimers of the diketopiperazine dipeptide cyclo (LPhe-LHis) and cyclo (LPhe-DHis) are studied by laser spectroscopy combined with mass spectrometry to shed light on the influence of stereochemistry on the clustering propensity of cyclic dipeptides. The marked spectroscopic differences experimentally observed in the hydride stretch region are well accounted for by the results of DFT calculations. Both diastereomeric protonated dimers involve a strong ionic hydrogen bond from the protonated imidazole ring of one monomer to the neutral imidazole nitrogen of the other. While this strong interaction is accompanied by a single NH⋯O hydrogen bond between the amide functions of the two moieties for the protonated dimer of cyclo (LPhe-DHis), that of cyclo (LPhe-LHis) involves two NH⋯O interactions, forming the motif of an antiparallel β sheet. Therefore, a change in chirality of the residue prevents the formation of the β sheet pattern observed in the amyloid type aggregation. These results emphasize the peculiar role of the histidine residue in peptide structure and interaction.
Collapse
Affiliation(s)
- Katia Le Barbu-Debus
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Université Paris-Saclay, F-91405 Orsay, France.
| | - Ariel Pérez-Mellor
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Université Paris-Saclay, F-91405 Orsay, France.
| | - Valéria Lepère
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Université Paris-Saclay, F-91405 Orsay, France.
| | - Anne Zehnacker
- Institut des Sciences Moléculaires d'Orsay (ISMO), CNRS, Université Paris-Saclay, F-91405 Orsay, France.
| |
Collapse
|
3
|
Gloaguen E, Mons M, Schwing K, Gerhards M. Neutral Peptides in the Gas Phase: Conformation and Aggregation Issues. Chem Rev 2020; 120:12490-12562. [PMID: 33152238 DOI: 10.1021/acs.chemrev.0c00168] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Combined IR and UV laser spectroscopic techniques in molecular beams merged with theoretical approaches have proven to be an ideal tool to elucidate intrinsic structural properties on a molecular level. It offers the possibility to analyze structural changes, in a controlled molecular environment, when successively adding aggregation partners. By this, it further makes these techniques a valuable starting point for a bottom-up approach in understanding the forces shaping larger molecular systems. This bottom-up approach was successfully applied to neutral amino acids starting around the 1990s. Ever since, experimental and theoretical methods developed further, and investigations could be extended to larger peptide systems. Against this background, the review gives an introduction to secondary structures and experimental methods as well as a summary on theoretical approaches. Vibrational frequencies being characteristic probes of molecular structure and interactions are especially addressed. Archetypal biologically relevant secondary structures investigated by molecular beam spectroscopy are described, and the influences of specific peptide residues on conformational preferences as well as the competition between secondary structures are discussed. Important influences like microsolvation or aggregation behavior are presented. Beyond the linear α-peptides, the main results of structural analysis on cyclic systems as well as on β- and γ-peptides are summarized. Overall, this contribution addresses current aspects of molecular beam spectroscopy on peptides and related species and provides molecular level insights into manifold issues of chemical and biochemical relevance.
Collapse
Affiliation(s)
- Eric Gloaguen
- CEA, CNRS, Université Paris-Saclay, CEA Paris-Saclay, Bât 522, 91191 Gif-sur-Yvette, France
| | - Michel Mons
- CEA, CNRS, Université Paris-Saclay, CEA Paris-Saclay, Bât 522, 91191 Gif-sur-Yvette, France
| | - Kirsten Schwing
- TU Kaiserslautern & Research Center Optimas, Erwin-Schrödinger-Straße 52, D-67663 Kaiserslautern, Germany
| | - Markus Gerhards
- TU Kaiserslautern & Research Center Optimas, Erwin-Schrödinger-Straße 52, D-67663 Kaiserslautern, Germany
| |
Collapse
|
4
|
Blodgett KN, Jang G, Kim S, Kim MK, Choi SH, Zwier TS. Coexistence of Left- and Right-Handed 12/10-Mixed Helices in Cyclically Constrained β-Peptides and Directed Formation of Single-Handed Helices upon Site-Specific Methylation. J Phys Chem A 2020; 124:5856-5870. [PMID: 32497433 DOI: 10.1021/acs.jpca.0c03545] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
The inherent conformational preferences of the neutral β-peptide foldamer series, Ac-(ACHC)n-NHBn, n = 2-4, are studied in the gas phase using conformation-specific IR-UV double resonance methods. The cyclically constrained chiral β-amino acid cis-2-aminocyclohexane carboxylic acid (ACHC) is designed to bring both right- and left-handed helices into close energetic proximity. Comparison of the infrared spectra in the NH stretch and amide I/II regions with the predictions of DFT calculations lead to the unambiguous assignment of four out of the six observed conformations of the molecules in this series, while corroborating computational and spectral evidence, affords tentative assignments of the remaining two conformers for which IR data were not recorded. The observed structures fall into one of two conformational families: a right-handed 12/10-mixed helix or its "cap-disrupted" left-handed helical analogue, which coexist with significant populations. Site-specific and stereospecific methylation on the cyclohexane backbone at the dipeptide (n = 2) level is also tested as a means to sterically lock in a predetermined cyclohexane chair conformation. These substitutions are proven to be a means of selectively driving formation of one helical screw sense or the other. Calculated relative energies and free energies of all possible structures for the molecules provide strong supporting evidence that the rigid nature of the ACHC residue confers unusual stability to the 12/10-mixed helix conformation, regardless of local environment, temperature, or C-terminal capping unit. The simultaneous presence of both handed helices offers unique opportunities for future studies of their interconversion.
Collapse
Affiliation(s)
- Karl N Blodgett
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
| | - Geunhyuk Jang
- Department of Chemistry, Yonsei University, Seoul 03722, Korea
| | - Sojung Kim
- Department of Chemistry, Yonsei University, Seoul 03722, Korea
| | - Min Kyung Kim
- Department of Chemistry, Yonsei University, Seoul 03722, Korea
| | - Soo Hyuk Choi
- Department of Chemistry, Yonsei University, Seoul 03722, Korea
| | - Timothy S Zwier
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
| |
Collapse
|
5
|
Toward accurate prediction of amino acid derivatives structure and energetics from DFT: glycine conformers and their interconversions. J Mol Model 2020; 26:129. [DOI: 10.1007/s00894-020-4342-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 03/04/2020] [Indexed: 12/30/2022]
|
6
|
Tamura M, Sekiguchi T, Ishiuchi SI, Zehnacker-Rentien A, Fujii M. Can the Partial Peptide SIVSF of the β 2-Adrenergic Receptor Recognize Chirality of the Epinephrine Neurotransmitter? J Phys Chem Lett 2019; 10:2470-2474. [PMID: 30840461 DOI: 10.1021/acs.jpclett.9b00184] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Chirality plays an essential role in biological molecular recognition, such as neurotransmission. Here, we applied electrospray-cold ion trap spectroscopy to complexes of a partial binding motif SIVSF of a β2-adrenergic receptor pocket with L- and D-epinephrine AdH+. The ultraviolet spectrum of the SIVSF-AdH+ complex changed drastically when L-AdH+ was replaced by its enantiomer. The isomer-selected infrared spectra revealed that D-AdH+ was bound to SIVSF by its protonated amino-group or a single catechol OH and induced nonhelical secondary structures of SIVSF. This is in sharp contrast to the helical SIVSF complex with L-AdH+, which is close to the natural binding structure with two catechol OHs binding in the receptor. This shows that a short pentapeptide SIVSF can distinguish the chirality of the ligand AdH+ as well as the receptor. This stereoselectivity is suggested to arise from an additional interaction involving the hydroxyl group on the chiral carbon.
Collapse
Affiliation(s)
- Masato Tamura
- Laboratory for Chemistry and Life Science, Institute of Innovative Research , Tokyo Institute of Technology , 4259 Nagatsuta-cho, Midori-ku , Yokohama , 226-8503 , Japan
- School of Life Science and Technology , Tokyo Institute of Technology , 4259 Nagatsuta-cho, Midori-ku , Yokohama , Kanagawa 226-8501 , Japan
| | - Tsubasa Sekiguchi
- Laboratory for Chemistry and Life Science, Institute of Innovative Research , Tokyo Institute of Technology , 4259 Nagatsuta-cho, Midori-ku , Yokohama , 226-8503 , Japan
- School of Life Science and Technology , Tokyo Institute of Technology , 4259 Nagatsuta-cho, Midori-ku , Yokohama , Kanagawa 226-8501 , Japan
| | - Shun-Ichi Ishiuchi
- Laboratory for Chemistry and Life Science, Institute of Innovative Research , Tokyo Institute of Technology , 4259 Nagatsuta-cho, Midori-ku , Yokohama , 226-8503 , Japan
- School of Life Science and Technology , Tokyo Institute of Technology , 4259 Nagatsuta-cho, Midori-ku , Yokohama , Kanagawa 226-8501 , Japan
| | - Anne Zehnacker-Rentien
- Institut des Sciences Moléculaires d'Orsay (ISMO) , CNRS, Univ. Paris-Sud, Université Paris-Saclay, F-91405 Orsay , France
- Tokyo Tech World Research Hub Initiative (WRHI), Institute of Innovation Research , Tokyo Institute of Technology , 4259 Nagatsuta-cho, Midori-ku , Yokohama , Japan
| | - Masaaki Fujii
- Laboratory for Chemistry and Life Science, Institute of Innovative Research , Tokyo Institute of Technology , 4259 Nagatsuta-cho, Midori-ku , Yokohama , 226-8503 , Japan
- School of Life Science and Technology , Tokyo Institute of Technology , 4259 Nagatsuta-cho, Midori-ku , Yokohama , Kanagawa 226-8501 , Japan
- Tokyo Tech World Research Hub Initiative (WRHI), Institute of Innovation Research , Tokyo Institute of Technology , 4259 Nagatsuta-cho, Midori-ku , Yokohama , Japan
| |
Collapse
|
7
|
Fischer JL, Elvir BR, DeLucia SA, Blodgett KN, Zeller M, Kubasik MA, Zwier TS. Single-Conformation Spectroscopy of Capped Aminoisobutyric Acid Dipeptides: The Effect of C-Terminal Cap Chromophores on Conformation. J Phys Chem A 2019; 123:4178-4187. [PMID: 30973730 DOI: 10.1021/acs.jpca.9b01698] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Joshua L. Fischer
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Brayan R. Elvir
- Department of Chemistry and Biochemistry, Fairfield University, Fairfield, Connecticut 06824, United States
| | - Sally-Ann DeLucia
- Department of Chemistry and Biochemistry, Fairfield University, Fairfield, Connecticut 06824, United States
| | - Karl N. Blodgett
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Matthias Zeller
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| | - Matthew A. Kubasik
- Department of Chemistry and Biochemistry, Fairfield University, Fairfield, Connecticut 06824, United States
| | - Timothy S. Zwier
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907, United States
| |
Collapse
|
8
|
Blodgett KN, Fischer JL, Lee J, Choi SH, Zwier TS. Conformation-Specific Spectroscopy of Asparagine-Containing Peptides: Influence of Single and Adjacent Asn Residues on Inherent Conformational Preferences. J Phys Chem A 2018; 122:8762-8775. [PMID: 30343572 DOI: 10.1021/acs.jpca.8b08418] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Karl N. Blodgett
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
| | - Joshua L. Fischer
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
| | - Jaeyeon Lee
- Department of Chemistry, Yonsei University, Seoul 03722, Korea
| | - Soo Hyuk Choi
- Department of Chemistry, Yonsei University, Seoul 03722, Korea
| | - Timothy S. Zwier
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
| |
Collapse
|
9
|
Blodgett KN, Zhu X, Walsh PS, Sun D, Lee J, Choi SH, Zwier TS. Conformer-Specific and Diastereomer-Specific Spectroscopy of αβα Synthetic Foldamers: Ac–Ala−βACHC–Ala–NHBn. J Phys Chem A 2018; 122:3697-3710. [PMID: 29558801 DOI: 10.1021/acs.jpca.8b01273] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Karl N. Blodgett
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084, United States
| | - Xiao Zhu
- Research Computing, Information Technology at Purdue (ITaP), West Lafayette, Indiana 47907-2114, United States
| | - Patrick S. Walsh
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084, United States
| | - Dewei Sun
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084, United States
| | - Jaeyeon Lee
- Department of Chemistry, Yonsei University, Seoul 03722, Korea
| | - Soo Hyuk Choi
- Department of Chemistry, Yonsei University, Seoul 03722, Korea
| | - Timothy S. Zwier
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907-2084, United States
| |
Collapse
|
10
|
Habka S, Sohn WY, Vaquero-Vara V, Géléoc M, Tardivel B, Brenner V, Gloaguen E, Mons M. On the turn-inducing properties of asparagine: the structuring role of the amide side chain, from isolated model peptides to crystallized proteins. Phys Chem Chem Phys 2018; 20:3411-3423. [DOI: 10.1039/c7cp07605c] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The anchoring properties of an asparagine (Asn) residue to its local backbone environment in turn model peptides is characterized using gas phase laser spectroscopy and compared to crystallized protein structures.
Collapse
Affiliation(s)
- S. Habka
- LIDYL
- CEA
- CNRS
- Université Paris Saclay
- CEA Saclay
| | - W. Y. Sohn
- LIDYL
- CEA
- CNRS
- Université Paris Saclay
- CEA Saclay
| | | | - M. Géléoc
- LIDYL
- CEA
- CNRS
- Université Paris Saclay
- CEA Saclay
| | - B. Tardivel
- LIDYL
- CEA
- CNRS
- Université Paris Saclay
- CEA Saclay
| | - V. Brenner
- LIDYL
- CEA
- CNRS
- Université Paris Saclay
- CEA Saclay
| | - E. Gloaguen
- LIDYL
- CEA
- CNRS
- Université Paris Saclay
- CEA Saclay
| | - M. Mons
- LIDYL
- CEA
- CNRS
- Université Paris Saclay
- CEA Saclay
| |
Collapse
|
11
|
Hewett DM, Tabor DP, Fischer JL, Sibert EL, Zwier TS. Infrared-Enhanced Fluorescence-Gain Spectroscopy: Conformation-Specific Excited-State Infrared Spectra of Alkylbenzenes. J Phys Chem Lett 2017; 8:5296-5300. [PMID: 28994601 DOI: 10.1021/acs.jpclett.7b02276] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
An ultraviolet-infrared (UV-IR) double-resonance method for recording conformation-specific excited-state infrared spectra is described. The method takes advantage of an increase in fluorescence signal in phenylalkanes produced by infrared excitation of the S1 origin levels of different conformational isomers. The shorter lifetimes of these IR-excited molecules, combined with their red-shifted emission, provides a way to discriminate the fluorescence due to the infrared-excited molecules from the S1 origin fluorescence, resulting in spectra with high signal-to-noise ratios. Spectra for a series of phenylalkanes and a capped phenylalanine derivative (Ac-Phe-NHMe) demonstrate the potential of the method. The excited-state spectrum in the alkyl CH stretch region of ethylbenzene is well-fit by an anharmonic model developed for the ground electronic state, which explicitly takes into account stretch-bend Fermi resonance.
Collapse
Affiliation(s)
- Daniel M Hewett
- Department of Chemistry, Purdue University , West Lafayette, Indiana 47907, United States
| | - Daniel P Tabor
- Department of Chemistry and Chemical Biology, Harvard University , Cambridge, Massachusetts 02138, United States
| | - Joshua L Fischer
- Department of Chemistry, Purdue University , West Lafayette, Indiana 47907, United States
| | - Edwin L Sibert
- Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Timothy S Zwier
- Department of Chemistry, Purdue University , West Lafayette, Indiana 47907, United States
| |
Collapse
|
12
|
Zhang D, Blodgett KN, Zhu X, Zwier TS. Single Conformation Spectroscopy of Suberoylanilide Hydroxamic Acid: A Molecule Bites Its Tail. J Phys Chem A 2017; 121:986-997. [PMID: 28071906 DOI: 10.1021/acs.jpca.6b12464] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Suberoylanilide hydroxamic acid (SAHA) is a histone deacetylase inhibitor that causes growth arrest and differentiation of many tumor types and is an approved drug for the treatment of cancer. The chemical structure of SAHA consists of formanilide "head" and a hydroxamic acid "tail" separated by an n-hexyl chain, C6H5NH(C═O)-(CH2)6-(C═O)NHOH. The alkyl chain's preference for extended structures is in competition with tail-to-head (T-H) or head-to-tail (H-T) hydrogen bonds between the amide and hydroxamic acid groups. Laser desorption was used to bring SAHA into the gas phase and cool it in a supersonic expansion before interrogation with mass-resolved resonant two-photon ionization spectroscopy. Single conformation UV spectra in the S0-S1 region and infrared spectra in the hydride stretch and mid-IR regions were recorded using IR-UV hole-burning and resonant ion-dip infrared spectroscopy, respectively. Three conformers of SAHA were distinguished and spectroscopically characterized. Comparison of the experimental IR spectra with the predictions of density functional theory calculations (DFT, B3LYP D3BJ/6-31+G(d)) leads to assignments for the three conformers, all of which possess tightly folded alkyl chains that enable formation of a T-H (conformer A) or H-T (conformers B and C) hydrogen bonds. A modified version of the generalized Amber force field was developed to more accurately describe the hydroxamic acid OH internal rotor potential, leading to predictions for the relative energies in reasonable agreement with experiment. This force field was used to generate a disconnectivity graph for the low-energy portion of the potential energy landscape of SAHA. This disconnectivity graph contains more than one hundred minima and maps out the lowest-energy pathways between them, which could then be characterized via DFT calculations. This combination of force field and DFT calculations provides insight into the potential energy landscape and how population was funneled into the three observed conformers.
Collapse
Affiliation(s)
| | - Karl N Blodgett
- Department of Chemistry, Purdue University , West Lafayette, Indiana 47907-2084, United States
| | - Xiao Zhu
- Department of Chemistry, Purdue University , West Lafayette, Indiana 47907-2084, United States.,Rosen Center for Advanced Computing (RCAC), Purdue University , West Lafayette, Indiana 47907-2084, United States
| | - Timothy S Zwier
- Department of Chemistry, Purdue University , West Lafayette, Indiana 47907-2084, United States
| |
Collapse
|
13
|
Sohn WY, Habka S, Gloaguen E, Mons M. Unifying the microscopic picture of His-containing turns: from gas phase model peptides to crystallized proteins. Phys Chem Chem Phys 2017. [DOI: 10.1039/c7cp03058d] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The presence in crystallized proteins of a local anchoring between the side chain of a His residue, located in the central position of a γ- or β-turn, and its local main chain environment, is assessed by the comparison of protein structures with relevant isolated model peptides.
Collapse
Affiliation(s)
- Woon Yong Sohn
- LIDYL
- CEA
- CNRS
- Université Paris-Saclay
- 91191 Gif-sur-Yvette Cedex
| | - Sana Habka
- LIDYL
- CEA
- CNRS
- Université Paris-Saclay
- 91191 Gif-sur-Yvette Cedex
| | - Eric Gloaguen
- LIDYL
- CEA
- CNRS
- Université Paris-Saclay
- 91191 Gif-sur-Yvette Cedex
| | - Michel Mons
- LIDYL
- CEA
- CNRS
- Université Paris-Saclay
- 91191 Gif-sur-Yvette Cedex
| |
Collapse
|
14
|
Schwing K, Gerhards M. Investigations on isolated peptides by combined IR/UV spectroscopy in a molecular beam – structure, aggregation, solvation and molecular recognition. INT REV PHYS CHEM 2016. [DOI: 10.1080/0144235x.2016.1229331] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
|
15
|
Burke NL, DeBlase AF, Redwine JG, Hopkins JR, McLuckey SA, Zwier TS. Gas-Phase Folding of a Prototypical Protonated Pentapeptide: Spectroscopic Evidence for Formation of a Charge-Stabilized β-Hairpin. J Am Chem Soc 2016; 138:2849-57. [PMID: 26853832 DOI: 10.1021/jacs.6b00093] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Nicole L. Burke
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
| | - Andrew F. DeBlase
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
| | - James G. Redwine
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
| | - John R. Hopkins
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
| | - Scott A. McLuckey
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
| | - Timothy S. Zwier
- Department of Chemistry, Purdue University, West Lafayette, Indiana 47907-2084, United States
| |
Collapse
|
16
|
Gord JR, Hewett DM, Hernandez-Castillo AO, Blodgett KN, Rotondaro MC, Varuolo A, Kubasik MA, Zwier TS. Conformation-specific spectroscopy of capped, gas-phase Aib oligomers: tests of the Aib residue as a 310-helix former. Phys Chem Chem Phys 2016; 18:25512-25527. [PMID: 27711552 DOI: 10.1039/c6cp04909e] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Single-conformation spectroscopy is used to probe the preference for helical structural in Aib-homopeptides.
Collapse
Affiliation(s)
- Joseph R. Gord
- Department of Chemistry
- Purdue University
- West Lafayette
- USA
| | | | | | | | | | - Adalgisa Varuolo
- Department of Chemistry and Biochemistry
- Fairfield University
- Fairfield
- USA
| | - Matthew A. Kubasik
- Department of Chemistry and Biochemistry
- Fairfield University
- Fairfield
- USA
| | | |
Collapse
|
17
|
Walsh PS, Dean JC, McBurney C, Kang H, Gellman SH, Zwier TS. Conformation-specific spectroscopy of capped glutamine-containing peptides: role of a single glutamine residue on peptide backbone preferences. Phys Chem Chem Phys 2016; 18:11306-22. [PMID: 27054830 DOI: 10.1039/c6cp01062h] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The conformational preferences of a series of short, aromatic-capped, glutamine-containing peptides have been studied under jet-cooled conditions in the gas phase.
Collapse
Affiliation(s)
| | - Jacob C. Dean
- Department of Chemistry
- Purdue University
- West Lafayette
- USA
| | - Carl McBurney
- Department of Chemistry
- University of Wisconsin-Madison
- Madison
- USA
| | - Hyuk Kang
- Department of Chemistry
- Ajou University
- Republic of Korea
| | | | | |
Collapse
|
18
|
Zabuga AV, Kamrath MZ, Rizzo TR. Franck–Condon-like Progressions in Infrared Spectra of Biological Molecules. J Phys Chem A 2015; 119:10494-501. [DOI: 10.1021/acs.jpca.5b08801] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Aleksandra V. Zabuga
- Laboratoire de Chimie
Physique Moléculaire,
Ecole Polytechnique Fédérale de Lausanne, EPFL SB ISIC
LCPM, Station 6, CH-1015 Lausanne, Switzerland
| | - Michael Z. Kamrath
- Laboratoire de Chimie
Physique Moléculaire,
Ecole Polytechnique Fédérale de Lausanne, EPFL SB ISIC
LCPM, Station 6, CH-1015 Lausanne, Switzerland
| | - Thomas R. Rizzo
- Laboratoire de Chimie
Physique Moléculaire,
Ecole Polytechnique Fédérale de Lausanne, EPFL SB ISIC
LCPM, Station 6, CH-1015 Lausanne, Switzerland
| |
Collapse
|
19
|
Alauddin M, Gloaguen E, Brenner V, Tardivel B, Mons M, Zehnacker‐Rentien A, Declerck V, Aitken DJ. Intrinsic Folding Proclivities in Cyclic β‐Peptide Building Blocks: Configuration and Heteroatom Effects Analyzed by Conformer‐Selective Spectroscopy and Quantum Chemistry. Chemistry 2015; 21:16479-93. [DOI: 10.1002/chem.201501794] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Indexed: 12/13/2022]
Affiliation(s)
- Mohammad Alauddin
- CEA, Laboratoire Interactions Dynamique et Lasers (LIDyL), Bât. 522, 91191 Gif‐sur‐Yvette (France)
- CNRS, Laboratoire Francis Perrin URA 2453, 91191 Gif‐sur‐Yvette (France)
- Current address: Department of Chemistry, University of Dhaka, Dhaka‐1000 (Bangladesh)
| | - Eric Gloaguen
- CEA, Laboratoire Interactions Dynamique et Lasers (LIDyL), Bât. 522, 91191 Gif‐sur‐Yvette (France)
- CNRS, Laboratoire Francis Perrin URA 2453, 91191 Gif‐sur‐Yvette (France)
| | - Valérie Brenner
- CEA, Laboratoire Interactions Dynamique et Lasers (LIDyL), Bât. 522, 91191 Gif‐sur‐Yvette (France)
- CNRS, Laboratoire Francis Perrin URA 2453, 91191 Gif‐sur‐Yvette (France)
| | - Benjamin Tardivel
- CEA, Laboratoire Interactions Dynamique et Lasers (LIDyL), Bât. 522, 91191 Gif‐sur‐Yvette (France)
- CNRS, Laboratoire Francis Perrin URA 2453, 91191 Gif‐sur‐Yvette (France)
| | - Michel Mons
- CEA, Laboratoire Interactions Dynamique et Lasers (LIDyL), Bât. 522, 91191 Gif‐sur‐Yvette (France)
- CNRS, Laboratoire Francis Perrin URA 2453, 91191 Gif‐sur‐Yvette (France)
| | | | - Valérie Declerck
- CP3A Organic Synthesis Group, ICMMO, UMR 8182, Université Paris Sud, Bât. 420, 15 rue Georges Clemenceau, 91405 Orsay cedex (France)
| | - David J. Aitken
- CP3A Organic Synthesis Group, ICMMO, UMR 8182, Université Paris Sud, Bât. 420, 15 rue Georges Clemenceau, 91405 Orsay cedex (France)
| |
Collapse
|
20
|
Abstract
This chapter examines the structural characterisation of isolated neutral amino-acids and peptides. After a presentation of the experimental and theoretical state-of-the-art in the field, a review of the major structures and shaping interactions is presented. Special focus is made on conformationally-resolved studies which enable one to go beyond simple structural characterisation; probing flexibility and excited-state photophysics are given as examples of promising future directions.
Collapse
|
21
|
Nyakatura EK, Mortier J, Radtke VS, Wieczorek S, Rezaei Araghi R, Baldauf C, Wolber G, Koksch B. β- and γ-Amino Acids at α-Helical Interfaces: Toward the Formation of Highly Stable Foldameric Coiled Coils. ACS Med Chem Lett 2014; 5:1300-3. [PMID: 25516788 DOI: 10.1021/ml500361c] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Accepted: 10/28/2014] [Indexed: 01/10/2023] Open
Abstract
Since peptides are vital for cellular and pathogenic processes, much effort has been put into the design of unnatural oligomers that mimic natural peptide structures, also referred to as foldamers. However, to enable the specific application of foldamers, a thorough characterization of their interaction profiles in native protein environments is required. We report here the application of phage display for the identification of suitable helical environments for a sequence comprising an alternating set of β- and γ-amino acids. In vitro selected sequences show that an increase in the hydrophobic surface area at the helical interface as well as the incorporation of a polar H-bond donor functionality can significantly improve interhelical interactions involving backbone-extended amino acids. Thus, our data provide insight into the principles of the rational design of foldameric inhibitors for protein-protein interactions.
Collapse
Affiliation(s)
- Elisabeth K. Nyakatura
- Institute
of Chemistry and Biochemistry, Freie Universität Berlin, Takustraße
3, 14195 Berlin, Germany
| | - Jérémie Mortier
- Institute
of Chemistry and Biochemistry, Freie Universität Berlin, Takustraße
3, 14195 Berlin, Germany
- Institute
of Pharmacy, Freie Universität Berlin, Königin-Luisestrasse 2 +
4, 14194 Berlin, Germany
| | - Vanessa S. Radtke
- Institute
of Chemistry and Biochemistry, Freie Universität Berlin, Takustraße
3, 14195 Berlin, Germany
| | - Sebastian Wieczorek
- Institute
of Chemistry and Biochemistry, Freie Universität Berlin, Takustraße
3, 14195 Berlin, Germany
| | - Raheleh Rezaei Araghi
- Institute
of Chemistry and Biochemistry, Freie Universität Berlin, Takustraße
3, 14195 Berlin, Germany
| | - Carsten Baldauf
- Fritz Haber Institute, Faradayweg
4-6, 14195 Berlin, Germany
| | - Gerhard Wolber
- Institute
of Pharmacy, Freie Universität Berlin, Königin-Luisestrasse 2 +
4, 14194 Berlin, Germany
| | - Beate Koksch
- Institute
of Chemistry and Biochemistry, Freie Universität Berlin, Takustraße
3, 14195 Berlin, Germany
| |
Collapse
|
22
|
Sharma GVM, Thodupunuri P, Sirisha K, Basha SJ, Gurava Reddy P, Sarma AVS. Design and synthesis of peptides with hybrid helix-turn-helix (HTH) motif and their conformational study. J Org Chem 2014; 79:8614-28. [PMID: 25180942 DOI: 10.1021/jo501267k] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The present study is aimed at the design and synthesis of peptides with hybrid helix-turn-helix (HTH) motif and their conformational analysis (NMR, MD, and CD studies). The requisite peptides with heterogeneous backbones were prepared from β-, γ-, and δ-amino acids with carbohydrate side chains and α-amino acid, L-Ala. The α/β-peptides were prepared from (S)-β-Caa(l) (C-linked carbo-β-amino acid with D-lyxo furanoside side chain) and L-Ala with a 1:1 alternation. The α/β-peptides with "helix-turn" motif displayed a 11/9-helix nucleating a 13-atom H-bonding turn. The α/β-octapeptides showed the presence of HTH structures with bifurcated 11/15-H-bonded turn. Further, the α/β-hexapeptide with HT motif, independently on coupling with γ/α/γ/α- and δ/α/δ/α-tetrapeptides at the C-terminus provided access to the decapeptides with "hybrid HTH" motifs. The decapeptide ("α-β-α-β-α-β-γ-α-γ-α") showed a hybrid HTH with "11/9/11/9/11/16/9/12/10" H-bonding, while the decapeptide ("α-β-α-β-α-β-δ-α-δ-α") revealed the presence of a "11/9/11/9/11/17/9/13/11" helical pattern. The above peptides thus have shown compatibility between different types of helices and serendipitous bifurcated 11/16- and 11/17-turns. The present study thus provided the first opportunity for the design and study of "hybrid HTH" motifs with more than one kind of helical structures in them.
Collapse
Affiliation(s)
- Gangavaram V M Sharma
- Organic and Bimolecular Chemistry Division, CSIR-Indian Institute of Chemical Technology , Hyderabad 500 007, India
| | | | | | | | | | | |
Collapse
|