1
|
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: 39] [Impact Index Per Article: 9.8] [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
|
2
|
Yatsyna V, Mallat R, Gorn T, Schmitt M, Feifel R, Rijs AM, Zhaunerchyk V. Competition between folded and extended structures of alanylalanine (Ala-Ala) in a molecular beam. Phys Chem Chem Phys 2019; 21:14126-14132. [DOI: 10.1039/c9cp00140a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Structural analysis of the neutral dipeptide Ala-Ala by action spectroscopy using IRMPD-VUV spectroscopy reveals predominance of extended structure.
Collapse
Affiliation(s)
- Vasyl Yatsyna
- University of Gothenburg
- Department of Physics
- Sweden
- Radboud University
- Institute for Molecules and Materials
| | - Ranim Mallat
- University of Gothenburg
- Department of Physics
- Sweden
| | - Tim Gorn
- Heinrich-Heine-Universität
- Institut für Physikalische Chemie I
- D-40225 Düsseldorf
- Germany
| | - Michael Schmitt
- Heinrich-Heine-Universität
- Institut für Physikalische Chemie I
- D-40225 Düsseldorf
- Germany
| | | | - Anouk M. Rijs
- Radboud University
- Institute for Molecules and Materials
- FELIX Laboratory
- 6525 ED Nijmegen
- The Netherlands
| | | |
Collapse
|
3
|
Nieuwjaer N, Desfrançois C, Lecomte F, Manil B, Soorkia S, Broquier M, Grégoire G. Photodissociation Spectroscopy of Cold Protonated Synephrine: Surprising Differences between IR–UV Hole-Burning and IR Photodissociation Spectroscopy of the O–H and N–H Modes. J Phys Chem A 2018; 122:3798-3804. [DOI: 10.1021/acs.jpca.8b01422] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- N. Nieuwjaer
- Laboratoire de Physique des Lasers, CNRS, Université Paris 13, Sorbonne Paris Cité, 93430 Villetaneuse, France
| | - C. Desfrançois
- Laboratoire de Physique des Lasers, CNRS, Université Paris 13, Sorbonne Paris Cité, 93430 Villetaneuse, France
| | - F. Lecomte
- Laboratoire de Physique des Lasers, CNRS, Université Paris 13, Sorbonne Paris Cité, 93430 Villetaneuse, France
| | - B. Manil
- Laboratoire de Physique des Lasers, CNRS, Université Paris 13, Sorbonne Paris Cité, 93430 Villetaneuse, France
| | - S. Soorkia
- Institut des Sciences Moléculaires d’Orsay (ISMO), CNRS, Univ. Paris Sud, Université Paris-Saclay, F-91405 Orsay, France
- Centre Laser de l’Université Paris-Sud (CLUPS/LUMAT), Univ. Paris-Sud, CNRS, IOGS, Université Paris-Saclay, F-91405 Orsay, France
| | - M. Broquier
- Institut des Sciences Moléculaires d’Orsay (ISMO), CNRS, Univ. Paris Sud, Université Paris-Saclay, F-91405 Orsay, France
- Centre Laser de l’Université Paris-Sud (CLUPS/LUMAT), Univ. Paris-Sud, CNRS, IOGS, Université Paris-Saclay, F-91405 Orsay, France
| | - G. Grégoire
- Institut des Sciences Moléculaires d’Orsay (ISMO), CNRS, Univ. Paris Sud, Université Paris-Saclay, F-91405 Orsay, France
- Centre Laser de l’Université Paris-Sud (CLUPS/LUMAT), Univ. Paris-Sud, CNRS, IOGS, Université Paris-Saclay, F-91405 Orsay, France
| |
Collapse
|
4
|
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]
|
5
|
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
|
6
|
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
|
7
|
Ishiuchi SI, Yamada K, Oba H, Wako H, Fujii M. Gas phase ultraviolet and infrared spectroscopy on a partial peptide of β2-adrenoceptor SIVSF-NH2 by a laser desorption supersonic jet technique. Phys Chem Chem Phys 2016; 18:23277-84. [DOI: 10.1039/c6cp04196e] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Laser desorption supersonic jet laser spectroscopy has been applied to a penta-peptide, Ser-Ile-Val-Ser-Phe-NH2 (SIVSF-NH2), which is a partial sequence of a binding site in a β2-adrenaline receptor protein.
Collapse
Affiliation(s)
- Shun-ichi Ishiuchi
- Laboratory for Chemistry and Life Science
- Institute for Innovative Research
- Tokyo Institute of Technology
- Yokohama
- Japan
| | - Kohei Yamada
- Laboratory for Chemistry and Life Science
- Institute for Innovative Research
- Tokyo Institute of Technology
- Yokohama
- Japan
| | - Hikari Oba
- Laboratory for Chemistry and Life Science
- Institute for Innovative Research
- Tokyo Institute of Technology
- Yokohama
- Japan
| | - Hiromichi Wako
- Laboratory for Chemistry and Life Science
- Institute for Innovative Research
- Tokyo Institute of Technology
- Yokohama
- Japan
| | - Masaaki Fujii
- Laboratory for Chemistry and Life Science
- Institute for Innovative Research
- Tokyo Institute of Technology
- Yokohama
- Japan
| |
Collapse
|
8
|
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
|
9
|
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
|
10
|
Chaudret R, de Courcy B, Contreras-García J, Gloaguen E, Zehnacker-Rentien A, Mons M, Piquemal JP. Unraveling non-covalent interactions within flexible biomolecules: from electron density topology to gas phase spectroscopy. Phys Chem Chem Phys 2015; 16:9876-91. [PMID: 24419903 DOI: 10.1039/c3cp52774c] [Citation(s) in RCA: 131] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The NCI (Non-Covalent Interactions) method, a recently-developed theoretical strategy to visualize weak non-covalent interactions from the topological analysis of the electron density and of its reduced gradient, is applied in the present paper to document intra- and inter-molecular interactions in flexible molecules and systems of biological interest in combination with IR spectroscopy. We first describe the conditions of application of the NCI method to the specific case of intramolecular interactions. Then we apply it to a series of stable conformations of isolated molecules as an interpretative technique to decipher the different physical interactions at play in these systems. Examples are chosen among neutral molecular systems exhibiting a large diversity of interactions, for which an extensive spectroscopic characterization under gas-phase isolation conditions has been obtained using state-of-the-art conformer-specific experimental techniques. The interactions presently documented range from weak intra-molecular H-bonds in simple amino-alcohols, to more complex patterns, with interactions of various strengths in model peptides, as well as in chiral bimolecular systems, where invaluable hints for the understanding of chiral recognition are revealed. We also provide a detailed technical appendix, which discusses the choices of cut-offs as well as the applicability of the NCI analysis to specific constrained systems, where local effects require attention. Finally, the NCI technique provides IR spectroscopists with an elegant visualization of the interactions that potentially impact their vibrational probes, namely the OH and NH stretching motions. This contribution illustrates the power and the conditions of use of the NCI technique, with the aim of providing an easy tool for all chemists, experimentalists and theoreticians, for the visualization and characterization of the interactions shaping complex molecular systems.
Collapse
Affiliation(s)
- R Chaudret
- Sorbonne Universités, UPMC, Laboratoire de Chimie Théorique and CNRS, UMR 7616, 75252 Paris Cedex 05, Paris, France.
| | | | | | | | | | | | | |
Collapse
|
11
|
Heger M, Otto KE, Mata RA, Suhm MA. Bracketing subtle conformational energy differences between self-solvated and stretched trifluoropropanol. Phys Chem Chem Phys 2015; 17:9899-909. [DOI: 10.1039/c4cp05868b] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The interconversion landscape between stretched and folded trifluoropropanol conformations is characterized by Raman jet spectroscopy and theory.
Collapse
Affiliation(s)
- Matthias Heger
- Institut für Physikalische Chemie
- Universität Göttingen
- 37077 Göttingen
- Germany
| | - Katharina E. Otto
- Institut für Physikalische Chemie
- Universität Göttingen
- 37077 Göttingen
- Germany
| | - Ricardo A. Mata
- Institut für Physikalische Chemie
- Universität Göttingen
- 37077 Göttingen
- Germany
| | - Martin A. Suhm
- Institut für Physikalische Chemie
- Universität Göttingen
- 37077 Göttingen
- Germany
| |
Collapse
|
12
|
Alauddin M, Biswal HS, Gloaguen E, Mons M. Intra-residue interactions in proteins: interplay between serine or cysteine side chains and backbone conformations, revealed by laser spectroscopy of isolated model peptides. Phys Chem Chem Phys 2014; 17:2169-78. [PMID: 25482851 DOI: 10.1039/c4cp04449e] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Intra-residue interactions play an important role in proteins by influencing local folding of the backbone. Taking advantage of the capability of gas phase experiments to provide relevant information on the intrinsic H-bonding pattern of isolated peptide chains, the intra-residue interactions of serine and cysteine residues, i.e., OH/SH···OC(i) C6 and NH(i···)O/S C5 interactions in Ser/Cys residues, are probed by laser spectroscopy of isolated peptides. The strength of these local side chain-main chain interactions, elegantly documented from their IR spectral features for well-defined conformations of the main chain, demonstrates that a subtle competition exists between the two types of intra-residue bond: the C6 H-bond is the major interaction with Ser, in contrast to Cys where C5 interaction takes over. The restricted number of conformers observed in the gas phase experiment with Ser compared to Cys (where both extended and folded forms are observed) also suggests a significant mediation role of these intra-residue interactions on the competition between the several main chain folding patterns.
Collapse
Affiliation(s)
- Mohammad Alauddin
- CEA, IRAMIS, Laboratoire Interactions, Dynamique et Lasers, CEA Saclay, Bât 522, 91191 Gif-sur-Yvette, France.
| | | | | | | |
Collapse
|
13
|
Hollóczki O. Uranyl(VI) Complexes in and from Imidazolium Acetate Ionic Liquids: Carbenes versus Acetates? Inorg Chem 2013; 53:835-46. [DOI: 10.1021/ic402921b] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Oldamur Hollóczki
- Mulliken
Center for Theoretical Chemistry, University of Bonn, Beringstrasse
4 + 6, D-53115 Bonn, Germany
| |
Collapse
|
14
|
Lee JJ, Albrecht M, Rice CA, Suhm MA, Stamm A, Zimmer M, Gerhards M. Adaptive Aggregation of Peptide Model Systems. J Phys Chem A 2013; 117:7050-63. [DOI: 10.1021/jp400056n] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Juhyon J. Lee
- Institut
für Physikalische Chemie, Universität Göttingen, Tammannstraße
6, 37077 Göttingen, Germany
| | - Merwe Albrecht
- Institut
für Physikalische Chemie, Universität Göttingen, Tammannstraße
6, 37077 Göttingen, Germany
| | - Corey A. Rice
- Institut
für Physikalische Chemie, Universität Göttingen, Tammannstraße
6, 37077 Göttingen, Germany
| | - Martin A. Suhm
- Institut
für Physikalische Chemie, Universität Göttingen, Tammannstraße
6, 37077 Göttingen, Germany
| | - Anke Stamm
- Fachbereich
Chemie and Research Center OPTIMAS, Physikalische
und Theoretische Chemie, TU Kaiserslautern, Erwin-Schrödinger-Straße 52, 67663 Kaiserslautern,
Germany
| | - Manuel Zimmer
- Fachbereich
Chemie and Research Center OPTIMAS, Physikalische
und Theoretische Chemie, TU Kaiserslautern, Erwin-Schrödinger-Straße 52, 67663 Kaiserslautern,
Germany
| | - Markus Gerhards
- Fachbereich
Chemie and Research Center OPTIMAS, Physikalische
und Theoretische Chemie, TU Kaiserslautern, Erwin-Schrödinger-Straße 52, 67663 Kaiserslautern,
Germany
| |
Collapse
|
15
|
Suhm MA, Kollipost F. Femtisecond single-mole infrared spectroscopy of molecular clusters. Phys Chem Chem Phys 2013; 15:10702-21. [DOI: 10.1039/c3cp51515j] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
16
|
Jaeqx S, Du W, Meijer EJ, Oomens J, Rijs AM. Conformational Study of Z-Glu-OH and Z-Arg-OH: Dispersion Interactions versus Conventional Hydrogen Bonding. J Phys Chem A 2012; 117:1216-27. [DOI: 10.1021/jp3053339] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Weina Du
- van’t
Hoff Institute
for Molecular Sciences and Amsterdam Center for Multiscale Modeling, University of Amsterdam, Science Park 904, 1098 XH
Amsterdam, The Netherlands
| | - Evert Jan Meijer
- van’t
Hoff Institute
for Molecular Sciences and Amsterdam Center for Multiscale Modeling, University of Amsterdam, Science Park 904, 1098 XH
Amsterdam, The Netherlands
| | | | | |
Collapse
|
17
|
Atwood RE, Urban JJ. Conformations of the Glycine Tripeptide Analog Ac-Gly-Gly-NHMe: A Computational Study Including Aqueous Solvation Effects. J Phys Chem A 2012; 116:1396-408. [DOI: 10.1021/jp206152d] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Rex E. Atwood
- Chemistry Department, United States Naval Academy, 572 Holloway Road, Annapolis,
Maryland 21402, United States
| | - Joseph J. Urban
- Chemistry Department, United States Naval Academy, 572 Holloway Road, Annapolis,
Maryland 21402, United States
| |
Collapse
|
18
|
Leavitt CM, Wolk AB, Kamrath MZ, Garand E, Van Stipdonk MJ, Johnson MA. Characterizing the intramolecular H-bond and secondary structure in methylated GlyGlyH+ with H2 predissociation spectroscopy. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2011; 22:1941-1952. [PMID: 21952771 DOI: 10.1007/s13361-011-0228-3] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2011] [Revised: 08/03/2011] [Accepted: 08/03/2011] [Indexed: 05/31/2023]
Abstract
We report vibrational predissociation spectra of the four protonated dipeptides derived from glycine and sarcosine, GlyGlyH(+)•(H(2))(1,2), GlySarH(+)•(D(2))(2), SarGlyH(+)•(H(2))(2), and SarSarH(+)•(D(2))(2), generated in a cryogenic ion trap. Sharp bands were recovered by monitoring photoevaporation of the weakly bound H(2) (D(2)) molecules in a linear action regime throughout the 700-4200 cm(-1) range using a table-top laser system. The spectral patterns were analyzed in the context of the low energy structures obtained from electronic structure calculations. These results indicate that all four species are protonated on the N-terminus, and feature an intramolecular H-bond involving the amino group. The large blue-shift in the H-bonded N-H fundamental upon incorporation of a methyl group at the N-terminus indicates that this modification significantly lowers the strength of the intramolecular H-bond. Methylation at the amide nitrogen, on the other hand, induces a significant rotation (~110°) about the peptide backbone.
Collapse
Affiliation(s)
- Christopher M Leavitt
- Sterling Chemistry Laboratory, Yale University, P.O. Box 208107, New Haven, CT 06520, USA
| | | | | | | | | | | |
Collapse
|
19
|
Pandey P, Pramanik A, Chakraborty T. Probing secondary structures of end-capped tripeptide, BOC–Phe–Aib–Leu–OMe by combined study of infrared spectroscopy and quantum chemistry calculation. Chem Phys 2011. [DOI: 10.1016/j.chemphys.2011.08.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
|
20
|
Rovó P, Farkas V, Hegyi O, Szolomájer-Csikós O, Tóth GK, Perczel A. Cooperativity network of Trp-cage miniproteins: probing salt-bridges. J Pept Sci 2011; 17:610-9. [DOI: 10.1002/psc.1377] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2011] [Revised: 03/18/2011] [Accepted: 03/24/2011] [Indexed: 11/06/2022]
|
21
|
Nishizaka M, Mori T, Inoue Y. Axial chirality of donor-donor, donor-acceptor, and tethered 1,1'-binaphthyls: a theoretical revisit with dynamics trajectories. J Phys Chem A 2011; 115:5488-95. [PMID: 21557592 DOI: 10.1021/jp202776g] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The circular dichroism (CD) spectra of (R)-2,2'-dimethoxy-1,1'-binaphthyl (DD) and its untethered and tethered donor-acceptor analogues (DA and DA7-DA9) were investigated experimentally and theoretically. The experimental CD spectra of DD and DA resembled each other in several aspects, displaying a positive-positive-negative Cotton effect pattern in the (1)L(b)-(1)L(a) region and a strong negative couplet at the (1)B(b) band, but significantly differed in transition energy and rotatory strength. The couplet amplitude (A) of the main band was 1.6 times larger in DA than in DD, despite the comparable extinction coefficients and seemingly analogous conformations. An additional positive Cotton effect was observed at the CT (CT) band for donor-acceptor binaphthyl DA. Our theoretical prediction of the CD spectra of binaphthyls involves three sequential first principle quantum mechanics (QM) calculations. Thus, the geometry optimizations of a series of conformers with varying dihedral angles were performed by the dispersion-corrected DFT-D method using the B97-D functional and the TZV2P basis set. The potential curve as a function of the dihedral angle (θ) was obtained by using the SCS-MP2/TZVPP single-point energy calculations with and without application of the solvent correction. The CD spectrum of each conformer was independently calculated by the second-order approximate coupled cluster calculation (CC2 method) using the TZVPP basis sets and the resolution of the identity (RI-J) approximation. The (net) theoretical CD spectrum was obtained by averaging over all possible conformers, where the dynamics trajectories based on the relative SCS-MP2 energies were taken into account. By using 17 possible conformers at θ varying from 50 to 130° by 5° intervals, the experimental CD spectra were successfully reproduced in a quantitative manner, enabling us to characterize properly almost all of the important spectral features and chiroptical properties. The two-state model, reported previously, turned out to have led to the right answer with wrong reasons. The couplet sign and amplitude A are critical functions of θ and can be used not only for (qualitatively) determining the absolute configuration but also for quantitatively analyzing the binaphthyl conformations. The angle dependence of A was already argued in the classical coupled oscillator and exciton chirality theories to provide reasonable structure elucidations but only in a qualitative or semiquantitative manner. Our method is able to predict the A value quantitatively as a function of θ. For tethered binaphthyls DA7-DA9, particular care should be exercised in the conformational assessment based on the classical treatment because the amplitude A was shown to be significantly affected by the existence of the tether itself. In the present method, the couplet amplitude A was nicely related to the dihedral angle θ of DA and DD by the state-of-the-art ab initio calculations, enabling us to gain the quantitative information about the conformation of axially chiral binaphthyls. The Cotton effect at the CT band also serves as a complementary clue for elucidating the conformation of donor-acceptor binaphthyls.
Collapse
Affiliation(s)
- Masaki Nishizaka
- Department of Applied Chemistry, Graduate School of Engineering, Osaka University, 2-1 Yamada-oka, Suita 565-0871, Japan
| | | | | |
Collapse
|
22
|
Hua W, Xu L, Luo Y, Li S. Understanding the influence of guest-host interactions on the conformation of short peptides in a hydrophobic cavity: a computational study. Chemphyschem 2011; 12:1325-33. [PMID: 21445953 DOI: 10.1002/cphc.201001081] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2010] [Indexed: 11/10/2022]
Abstract
We performed a computational investigation to understand the conformational preferences of four short peptides in a self-assembled cage based on the experimental work by Y. Hatakeyama et al. (Angew. Chem. Int. Ed.2009, 48, 8695). For this purpose, we combined molecular dynamics simulations, Monte Carlo simulations, and quantum mechanical calculations to obtain energies and structures for several low-lying conformers of four peptides and the corresponding peptide-cage inclusion complexes. Our calculations at both B3LYP and MP2 levels show that for each peptide, the corresponding conformation within the host (as revealed by the crystal structure) does not represent the lowest-energy conformation of this peptide in vacuum. By comparing some low-lying conformers in vacuum and in the cavity (for the same peptide), we found that the cage has a significant influence on the conformational propensities of peptides. First, one carbonyl oxygen of each peptide tends to bind to one Zn(II) atom of the cage, forming a Zn-O bond. The formation of this bond leads to significant charge transfer from the cage to the peptide. Second, this Zn-O bond causes the peptide to go through some local conformational changes. For larger peptides, such as penta- and hexapeptides, our calculations also show that some of their conformers must undergo significant structural changes, due to the confinement of the host. This computational study reveals the noticeable influence of the guest-host interaction on the conformational preferences of short peptides.
Collapse
Affiliation(s)
- Weijie Hua
- School of Chemistry and Chemical Engineering, Key Laboratory of Mesoscopic Chemistry of Ministry of Education, Institute of Theoretical and Computational Chemistry, Nanjing University, Hankou Road 22, 210093 Nanjing, PR China
| | | | | | | |
Collapse
|
23
|
Plowright RJ, Gloaguen E, Mons M. Compact Folding of Isolated Four-Residue Neutral Peptide Chains: H-Bonding Patterns and Entropy Effects. Chemphyschem 2011; 12:1889-99. [DOI: 10.1002/cphc.201001023] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2010] [Indexed: 11/08/2022]
|
24
|
Biswal HS, Gloaguen E, Mons M, Bhattacharyya S, Shirhatti PR, Wategaonkar S. Structure of the Indole−Benzene Dimer Revisited. J Phys Chem A 2011; 115:9485-92. [DOI: 10.1021/jp1119684] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Himansu S. Biswal
- Laboratoire Francis Perrin, CEA/DSM/IRAMIS/SPAM—CNRS URA
2453, CEA/Saclay, 91191 Gif-sur-Yvette, France
| | - Eric Gloaguen
- Laboratoire Francis Perrin, CEA/DSM/IRAMIS/SPAM—CNRS URA
2453, CEA/Saclay, 91191 Gif-sur-Yvette, France
| | - Michel Mons
- Laboratoire Francis Perrin, CEA/DSM/IRAMIS/SPAM—CNRS URA
2453, CEA/Saclay, 91191 Gif-sur-Yvette, France
| | - Surjendu Bhattacharyya
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai
400 005, India
| | - Pranav R. Shirhatti
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai
400 005, India
| | - Sanjay Wategaonkar
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai
400 005, India
| |
Collapse
|
25
|
Gloaguen E, de Courcy B, Piquemal JP, Pilmé J, Parisel O, Pollet R, Biswal HS, Piuzzi F, Tardivel B, Broquier M, Mons M. Gas-phase folding of a two-residue model peptide chain: on the importance of an interplay between experiment and theory. J Am Chem Soc 2010; 132:11860-3. [PMID: 20687601 DOI: 10.1021/ja103996q] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
In order to assess the ability of theory to describe properly the dispersive interactions that are ubiquitous in peptide and protein systems, an isolated short peptide chain has been studied using both gas-phase laser spectroscopy and quantum chemistry. The experimentally observed coexistence of an extended form and a folded form in the supersonic expansion was found to result from comparable Gibbs free energies for the two species under the high-temperature conditions (< or = 320 K) resulting from the laser desorption technique used to vaporize the molecules. These data have been compared to results obtained using a series of quantum chemistry methods, including DFT, DFT-D, and post-Hartree-Fock methods, which give rise to a wide range of relative stabilities predicted for these two forms. The experimental observation was best reproduced by an empirically dispersion-corrected functional (B97-D) and a hybrid functional with a significant Hartree-Fock exchange term (M06-2X). In contrast, the popular post-Hartree-Fock method MP2, which is often used for benchmarking these systems, had to be discarded because of a very large basis-set superposition error. The applicability of the atomic counterpoise correction (ACP) is also discussed. This work also introduces the mandatory theoretical examination of experimental abundances. DeltaH(0 K) predictions are clearly not sufficient for discussion of folding, as the conformation inversion temperature is crucial to the conformation determination and requires taking into account thermodynamical corrections (DeltaG) in order to computationally isolate the most stable conformation.
Collapse
Affiliation(s)
- E Gloaguen
- CEA, IRAMIS, Service des Photons, Atomes et Molécules, and CNRS, Laboratoire Francis Perrin, URA 2453, 91191 Gif-sur-Yvette, France
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|