1
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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.
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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
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2
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León I, Alonso ER, Mata S, Alonso JL. A rotational study of the AlaAla dipeptide. Phys Chem Chem Phys 2020; 22:13867-13871. [PMID: 32368774 DOI: 10.1039/d0cp01043j] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Herein, we present the first rotational study of the AlaAla dipeptide, brought into the gas phase by laser ablation. Two different structures have been unveiled in the isolated environment of a supersonic expansion by Fourier transform microwave spectroscopy. These structures have been identified through their rotational and 14N quadrupole coupling constants. The flexibility of the -NH2 and -COOH ends allows the formation of strong intramolecular interactions giving rise to five- and seven-membered ring configurations.
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Affiliation(s)
- I León
- Grupo de Espectrocopía Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia, Unidad Asociada CSIC, Parque Científico UVa, Universidad de Valladolid, 47011, Valladolid, Spain.
| | - E R Alonso
- Grupo de Espectrocopía Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia, Unidad Asociada CSIC, Parque Científico UVa, Universidad de Valladolid, 47011, Valladolid, Spain. and Instituto Biofisika (UPV/EHU, CSIC), University of the Basque Country, Leioa, E-48940, Spain and Fundación Biofísica Bizkaia/Biofisika Bizkaia Fundazioa (FBB), Barrio Sarriena s/n, Leioa, E-48940, Spain
| | - S Mata
- Grupo de Espectrocopía Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia, Unidad Asociada CSIC, Parque Científico UVa, Universidad de Valladolid, 47011, Valladolid, Spain.
| | - J L Alonso
- Grupo de Espectrocopía Molecular (GEM), Edificio Quifima, Laboratorios de Espectroscopia y Bioespectroscopia, Unidad Asociada CSIC, Parque Científico UVa, Universidad de Valladolid, 47011, Valladolid, Spain.
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3
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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]
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4
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Chandramouli B, Del Galdo S, Mancini G, Tasinato N, Barone V. Tailor-made computational protocols for precise characterization of small biological building blocks using QM and MM approaches. Biopolymers 2018. [DOI: 10.1002/bip.23109] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Balasubramanian Chandramouli
- Scuola Normale Superiore, Piazza dei Cavalieri 7; Pisa 56126 Italy
- Compunet, Istituto Italiano di Tecnologia, via Morego 30; Genova Italy
| | - Sara Del Galdo
- Scuola Normale Superiore, Piazza dei Cavalieri 7; Pisa 56126 Italy
| | - Giordano Mancini
- Scuola Normale Superiore, Piazza dei Cavalieri 7; Pisa 56126 Italy
- Istituto Nazionale di Fisica Nucleare (INFN) sezione di Pisa, Largo Bruno Pontecorvo 3; Pisa 56127 Italy
| | - Nicola Tasinato
- Scuola Normale Superiore, Piazza dei Cavalieri 7; Pisa 56126 Italy
| | - Vincenzo Barone
- Scuola Normale Superiore, Piazza dei Cavalieri 7; Pisa 56126 Italy
- Istituto Nazionale di Fisica Nucleare (INFN) sezione di Pisa, Largo Bruno Pontecorvo 3; Pisa 56127 Italy
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5
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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]
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6
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Christensen A, Kubař T, Cui Q, Elstner M. Semiempirical Quantum Mechanical Methods for Noncovalent Interactions for Chemical and Biochemical Applications. Chem Rev 2016; 116:5301-37. [PMID: 27074247 PMCID: PMC4867870 DOI: 10.1021/acs.chemrev.5b00584] [Citation(s) in RCA: 243] [Impact Index Per Article: 30.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2015] [Indexed: 12/28/2022]
Abstract
Semiempirical (SE) methods can be derived from either Hartree-Fock or density functional theory by applying systematic approximations, leading to efficient computational schemes that are several orders of magnitude faster than ab initio calculations. Such numerical efficiency, in combination with modern computational facilities and linear scaling algorithms, allows application of SE methods to very large molecular systems with extensive conformational sampling. To reliably model the structure, dynamics, and reactivity of biological and other soft matter systems, however, good accuracy for the description of noncovalent interactions is required. In this review, we analyze popular SE approaches in terms of their ability to model noncovalent interactions, especially in the context of describing biomolecules, water solution, and organic materials. We discuss the most significant errors and proposed correction schemes, and we review their performance using standard test sets of molecular systems for quantum chemical methods and several recent applications. The general goal is to highlight both the value and limitations of SE methods and stimulate further developments that allow them to effectively complement ab initio methods in the analysis of complex molecular systems.
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Affiliation(s)
- Anders
S. Christensen
- Department
of Chemistry and Theoretical Chemistry Institute, University of Wisconsin—Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Tomáš Kubař
- Institute of Physical
Chemistry & Center for Functional Nanostructures and Institute of Physical
Chemistry, Karlsruhe Institute of Technology, Kaiserstrasse 12, 76131 Karlsruhe, Germany
| | - Qiang Cui
- Department
of Chemistry and Theoretical Chemistry Institute, University of Wisconsin—Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Marcus Elstner
- Institute of Physical
Chemistry & Center for Functional Nanostructures and Institute of Physical
Chemistry, Karlsruhe Institute of Technology, Kaiserstrasse 12, 76131 Karlsruhe, Germany
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7
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Stamm A, Bernhard D, Gerhards M. Structural investigations on a linear isolated depsipeptide: the importance of dispersion interactions. Phys Chem Chem Phys 2016; 18:15327-36. [DOI: 10.1039/c6cp01675h] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The first molecular beam investigations of an isolated linear depsipeptide are presented. By applying IR/UV spectroscopic methods and DFT calculations three structural arrangements are identified with the most stable structure being only stable by including dispersion interactions.
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Affiliation(s)
- A. Stamm
- TU Kaiserslautern, Fachbereich Chemie & Research Center Optimas
- D-67663 Kaiserslautern
- Germany
| | - D. Bernhard
- TU Kaiserslautern, Fachbereich Chemie & Research Center Optimas
- D-67663 Kaiserslautern
- Germany
| | - M. Gerhards
- TU Kaiserslautern, Fachbereich Chemie & Research Center Optimas
- D-67663 Kaiserslautern
- Germany
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8
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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.
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9
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Barone V, Biczysko M, Bloino J, Cimino P, Penocchio E, Puzzarini C. CC/DFT Route toward Accurate Structures and Spectroscopic Features for Observed and Elusive Conformers of Flexible Molecules: Pyruvic Acid as a Case Study. J Chem Theory Comput 2015; 11:4342-63. [PMID: 26575928 PMCID: PMC5905675 DOI: 10.1021/acs.jctc.5b00580] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The structures and relative stabilities as well as the rotational and vibrational spectra of the three low-energy conformers of pyruvic acid (PA) have been characterized using a state-of-the-art quantum-mechanical approach designed for flexible molecules. By making use of the available experimental rotational constants for several isotopologues of the most stable PA conformer, Tc-PA, the semiexperimental equilibrium structure has been derived. The latter provides a reference for the pure theoretical determination of the equilibrium geometries for all conformers, thus confirming for these structures an accuracy of 0.001 Å and 0.1 deg for bond lengths and angles, respectively. Highly accurate relative energies of all conformers (Tc-, Tt-, and Ct-PA) and of the transition states connecting them are provided along with the thermodynamic properties at low and high temperatures, thus leading to conformational enthalpies accurate to 1 kJ mol(-1). Concerning microwave spectroscopy, rotational constants accurate to about 20 MHz are provided for the Tt- and Ct-PA conformers, together with the computed centrifugal-distortion constants and dipole moments required to simulate their rotational spectra. For Ct-PA, vibrational frequencies in the mid-infrared region accurate to 10 cm(-1) are reported along with theoretical estimates for the transitions in the near-infrared range, and the corresponding infrared spectrum including fundamental transitions, overtones, and combination bands has been simulated. In addition to the new data described above, theoretical results for the Tc- and Tt-PA conformers are compared with all available experimental data to further confirm the accuracy of the hybrid coupled-cluster/density functional theory (CC/DFT) protocol applied in the present study. Finally, we discuss in detail the accuracy of computational models fully based on double-hybrid DFT functionals (mainly at the B2PLYP/aug-cc-pVTZ level) that avoid the use of very expensive CC calculations.
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Affiliation(s)
- Vincenzo Barone
- Scuola Normale Superiore,
Piazza dei Cavalieri 7, I-56126 Pisa, Italy
| | - Malgorzata Biczysko
- Consiglio Nazionale delle
Ricerche, Istituto di Chimica dei Composti
OrganoMetallici (ICCOM-CNR), UOS di Pisa, Area
della Ricerca CNR, Via G. Moruzzi 1, I-56124 Pisa,
Italy
| | - Julien Bloino
- Consiglio Nazionale delle
Ricerche, Istituto di Chimica dei Composti
OrganoMetallici (ICCOM-CNR), UOS di Pisa, Area
della Ricerca CNR, Via G. Moruzzi 1, I-56124 Pisa,
Italy
| | - Paola Cimino
- Dipartimento di Scienze
Farmaceutiche, Università degli Studi di
Salerno, via Ponte don Melillo, I-84084 Fisciano
(SA), Italy
| | | | - Cristina Puzzarini
- Dipartimento di Chimica
“Giacomo Ciamician”,
Università di Bologna, Via Selmi 2, I-40126
Bologna, Italy
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10
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Kilina S, Kilin D, Tretiak S. Light-Driven and Phonon-Assisted Dynamics in Organic and Semiconductor Nanostructures. Chem Rev 2015; 115:5929-78. [DOI: 10.1021/acs.chemrev.5b00012] [Citation(s) in RCA: 140] [Impact Index Per Article: 15.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- Svetlana Kilina
- Chemistry
and Biochemistry Department, North Dakota State University, Fargo, North Dakota 5810, United States
| | - Dmitri Kilin
- Department
of Chemistry, University of South Dakota, Vermillion, South Dakota 57069, United States
| | - Sergei Tretiak
- Theoretical
Division, Center for Nonlinear Studies (CNLS) and Center for Integrated
Nanotechnologies (CINT), Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
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11
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Yan B, Jaeqx S, van der Zande WJ, Rijs AM. A conformation-selective IR-UV study of the dipeptides Ac-Phe-Ser-NH2 and Ac-Phe-Cys-NH2: probing the SH···O and OH···O hydrogen bond interactions. Phys Chem Chem Phys 2015; 16:10770-8. [PMID: 24756311 DOI: 10.1039/c4cp00810c] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The conformational preferences of peptides are mainly controlled by the stabilizing effect of intramolecular interactions. In peptides with polar side chains, not only the backbone but also the side chain interactions determine the resulting conformations. In this paper, the conformational preferences of the capped dipeptides Ac-Phe-Ser-NH2 (FS) and Ac-Phe-Cys-NH2 (FC) are resolved under laser-desorbed jet cooling conditions using IR-UV ion dip spectroscopy and density functional theory (DFT) quantum chemistry calculations. As serine (Ser) and cysteine (Cys) only differ in an OH (Ser) or SH (Cys) moiety; this subtle alteration allows us to study the effect of the difference in hydrogen bonding for an OH and SH group in detail, and its effect on the secondary structure. IR absorption spectra are recorded in the NH stretching region (3200-3600 cm(-1)). In combination with quantum chemical calculations the spectra provide a direct view of intramolecular interactions. Here, we show that both FS as FC share a singly γ-folded backbone conformation as the most stable conformer. The hydrogen bond strength of OH···O (FS) is stronger than that of SH···O (FC), resulting in a more compact gamma turn structure. A second conformer is found for FC, showing a β turn interaction.
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Affiliation(s)
- Bin Yan
- Radboud University Nijmegen, Institute for Molecules and Materials, FELIX Facility, Toernooiveld 7, 6525 ED Nijmegen, The Netherlands.
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12
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Puzzarini C, Biczysko M. Microsolvation of 2-thiouracil: molecular structure and spectroscopic parameters of the thiouracil-water complex. J Phys Chem A 2014; 119:5386-95. [PMID: 25474644 DOI: 10.1021/jp510511d] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
State-of-the-art quantum-chemical computations have been employed to accurately determine the equilibrium structure and interaction energy of the 2-thiouracil-water complex, thus extending available reference data for biomolecule solvation patterns. The coupled-cluster level of theory in conjunction with a triple-ζ basis set has been considered together with extrapolation to the basis set limit, performed by employing second-order Møller-Plesset perturbation theory, and inclusion of core-correlation and diffuse-function corrections. On the basis of the comparison of experiment and theory for 2-thiouracil [ Puzzarini et al. Phys. Chem. Chem. Phys. 2013 , 15 , 16965 - 16975 ], structural changes due to water complexation have been pointed out. Molecular and spectroscopic properties of the 2-thiouracil-water complex have then been studied by means of the composite computational approach introduced for the molecular structure evaluation. Among the results achieved, we mention the accurate determination of the molecular dipole moment and of the spectroscopic parameters required for predicting the rotational spectrum.
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Affiliation(s)
- Cristina Puzzarini
- †Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, Via Selmi 2, I-40126 Bologna, Italy
| | - Malgorzata Biczysko
- ‡Scuola Normale Superiore, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.,§Istituto di Chimica dei Composti OrganoMetallici (ICCOM-CNR), UOS di Pisa, Area della Ricerca CNR, Consiglio Nazionale delle Ricerche, Via G. Moruzzi 1, I-56124 Pisa, Italy
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13
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Eisenberg AS, Juszczak LJ. Relating Trp-Glu dipeptide fluorescence to molecular conformation: the role of the discrete Chi 1 and Chi 2 angles. J Comput Chem 2013; 34:1549-60. [PMID: 23564660 PMCID: PMC3964880 DOI: 10.1002/jcc.23288] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2012] [Revised: 01/31/2013] [Accepted: 03/04/2013] [Indexed: 11/06/2022]
Abstract
Molecular dynamics (MD), coupled with fluorescence data for charged dipeptides of tryptophanyl glutamic acid (Trp-Glu), reveal a detailed picture of how specific conformation affects fluorescence. Fluorescence emission spectra and time-resolved emission measurements have been collected for all four charged species. MD simulations 20 to 30 ns in length have also been carried out for the Trp-Glu species, as simulation provides aqueous phase conformational data that can be correlated with the fluorescence data. The calculations show that each dipeptide species is characterized by a similar set of six, discrete Chi 1, Chi 2 dihedral angle pairs. The preferred Chi 1 angles--60°, 180°, and 300°--play the significant role in positioning the terminal amine relative to the indole ring. A Chi 1 angle of 60° results in the arching of the backbone over the indole ring and no interaction of the ring with the terminal amine. Chi 1 values of 180° and 300° result in an extension of the backbone away from the indole ring and a NH3 cation-π interaction with indole. This interaction is believed responsible for charge transfer quenching. Two fluorescence lifetimes and their corresponding amplitudes correlate with the Chi 1 angle probability distribution for all four charged Trp-Glu dipeptides. Fluorescence emission band maxima are also consistent with the proposed pattern of terminal amine cation quenching of fluorescence.
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Affiliation(s)
- Azaria Solomon Eisenberg
- Department of Chemistry, Brooklyn College of The City University of New York, 2900 Bedford Avenue, Brooklyn, New York 11210, USA
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14
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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
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15
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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
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16
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In search of OH–π interactions between 1-methylimidazole and water using a combined computational quantum chemistry and ATR-FTIR spectroscopy approach. J Mol Struct 2012. [DOI: 10.1016/j.molstruc.2012.05.028] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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17
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Schwing K, Fricke H, Bartl K, Polkowska J, Schrader T, Gerhards M. Isolated β-Turn Model Systems Investigated by Combined IR/UV Spectroscopy. Chemphyschem 2012; 13:1576-82. [DOI: 10.1002/cphc.201100805] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2011] [Revised: 02/24/2012] [Indexed: 11/08/2022]
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18
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Yu W, Wu Z, Chen H, Liu X, MacKerell AD, Lin Z. Comprehensive conformational studies of five tripeptides and a deduced method for efficient determinations of peptide structures. J Phys Chem B 2012; 116:2269-83. [PMID: 22260814 DOI: 10.1021/jp207807a] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Thorough searches on the potential energy surfaces of five tripeptides, GGG, GYG, GWG, TGG, and MGG, were performed by considering all possible combinations of the bond rotational degrees of freedom with a semiempirical and ab initio combined computational approach. Structural characteristics of the obtained stable tripeptide conformers were carefully analyzed. Conformers of the five tripeptides were found to be closely connected with conformers of their constituting dipeptides and amino acids. A method for finding all important tripeptide conformers by optimizing a small number of trial structures generated by suitable superposition of the parent amino acid and dipeptide conformers is thus proposed. Applying the method to another five tripeptides, YGG, FGG, WGG, GFA, and GGF, studied before shows that the new approach is both efficient and reliable by providing the most complete ensembles of tripeptide conformers. The method is further generalized for application to larger peptides by introducing the breeding and mutation concepts in a genetic algorithm way. The generalized method is verified to be capable of finding tetrapeptide conformers with secondary structures of strands, helices, and turns, which are highly populated in larger peptides. This show some promise for the proposed method to be applied for the structural determination of larger peptides.
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Affiliation(s)
- Wenbo Yu
- Hefei National Laboratory for Physical Sciences at Microscale, University of Science and Technology of China, 96 Jinzhai Road, Hefei, Anhui 230026, China
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19
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Antony J, Grimme S, Liakos DG, Neese F. Protein-ligand interaction energies with dispersion corrected density functional theory and high-level wave function based methods. J Phys Chem A 2011; 115:11210-20. [PMID: 21842894 DOI: 10.1021/jp203963f] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
With dispersion-corrected density functional theory (DFT-D3) intermolecular interaction energies for a diverse set of noncovalently bound protein-ligand complexes from the Protein Data Bank are calculated. The focus is on major contacts occurring between the drug molecule and the binding site. Generalized gradient approximation (GGA), meta-GGA, and hybrid functionals are used. DFT-D3 interaction energies are benchmarked against the best available wave function based results that are provided by the estimated complete basis set (CBS) limit of the local pair natural orbital coupled-electron pair approximation (LPNO-CEPA/1) and compared to MP2 and semiempirical data. The size of the complexes and their interaction energies (ΔE(PL)) varies between 50 and 300 atoms and from -1 to -65 kcal/mol, respectively. Basis set effects are considered by applying extended sets of triple- to quadruple-ζ quality. Computed total ΔE(PL) values show a good correlation with the dispersion contribution despite the fact that the protein-ligand complexes contain many hydrogen bonds. It is concluded that an adequate, for example, asymptotically correct, treatment of dispersion interactions is necessary for the realistic modeling of protein-ligand binding. Inclusion of the dispersion correction drastically reduces the dependence of the computed interaction energies on the density functional compared to uncorrected DFT results. DFT-D3 methods provide results that are consistent with LPNO-CEPA/1 and MP2, the differences of about 1-2 kcal/mol on average (<5% of ΔE(PL)) being on the order of their accuracy, while dispersion-corrected semiempirical AM1 and PM3 approaches show a deviating behavior. The DFT-D3 results are found to depend insignificantly on the choice of the short-range damping model. We propose to use DFT-D3 as an essential ingredient in a QM/MM approach for advanced virtual screening approaches of protein-ligand interactions to be combined with similarly "first-principle" accounts for the estimation of solvation and entropic effects.
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Affiliation(s)
- Jens Antony
- Organisch-Chemisches Institut, Universität Münster, Münster, Germany
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Schwing K, Reyheller C, Schaly A, Kubik S, Gerhards M. Structural Analysis of an Isolated Cyclic Tetrapeptide and its Monohydrate by Combined IR/UV Spectroscopy. Chemphyschem 2011; 12:1981-8. [DOI: 10.1002/cphc.201001055] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2010] [Revised: 04/07/2011] [Indexed: 11/10/2022]
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21
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Pomogaev V, Pomogaeva A, Avramov P, Jalkanen KJ, Kachin S. Thermo-dynamical contours of electronic-vibrational spectra simulated using the statistical quantum–mechanical methods. Theor Chem Acc 2011. [DOI: 10.1007/s00214-011-0936-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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22
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Riley KE, Hobza P. Noncovalent interactions in biochemistry. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2011. [DOI: 10.1002/wcms.8] [Citation(s) in RCA: 157] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Kevin E. Riley
- Department of Chemistry, University of Puerto Rico, Rio Piedras, Puerto Rico
| | - Pavel Hobza
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center for Biomolecules and Complex Molecular Systems, Prague, Czech Republic
- Department of Physical Chemistry, Palacky University, Olomouc, Czech Republic
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Riley KE, Pitonák M, Jurecka P, Hobza P. Stabilization and structure calculations for noncovalent interactions in extended molecular systems based on wave function and density functional theories. Chem Rev 2010; 110:5023-63. [PMID: 20486691 DOI: 10.1021/cr1000173] [Citation(s) in RCA: 562] [Impact Index Per Article: 40.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kevin E Riley
- Department of Chemistry, University of Puerto Rico, Rio Piedras, Puerto Rico 00931
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Gloaguen E, Valdes H, Pagliarulo F, Pollet R, Tardivel B, Hobza P, Piuzzi F, Mons M. Experimental and theoretical investigation of the aromatic-aromatic interaction in isolated capped dipeptides. J Phys Chem A 2010; 114:2973-82. [PMID: 19817381 DOI: 10.1021/jp904216f] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Among the forces responsible for shaping proteins, interactions between side chains of aromatic residues play an important role as they are involved in the secondary and the tertiary structures of proteins contributing to the formation of hydrophobic domains. The purpose of this paper is to document this interaction in two capped dipeptides modeling a segment of a protein chain having two consecutive Phe residues, Ac-Phe-Phe-NH(2) and Ac-Phe-D-Phe-NH(2). These two molecules have been investigated in the gas phase by IR/UV double resonance spectroscopy, and the assignment of the observed conformers has been done by comparison with quantum chemistry calculations. Both peptides are found to adopt a beta-turn type I conformation stabilized by an edge-to-face interaction between the two aromatic rings. Comparison with other dipeptides in the literature demonstrates the impact of this aromatic-aromatic interaction on the shape adopted by the peptide chain, and its role among the other shaping forces (H-bonds, NH-pi interactions) is discussed. As an illustration, the H-bond strength is found to be significantly lower in the beta-turn type I conformer, in which the two rings interact, as compared to the similar conformer where such an interaction does not exist. This structural feature due to the backbone distortion induced by the interaction between the aromatic rings makes this system a good test for evaluating the ability of computational methods to correctly account for the competition between these forces. MP2, SCS-MP2, DFT, and DFT-D methods have been assessed in this respect. Comparison between geometries, energies, and frequency calculations illustrate their respective limitations in describing conformations resulting from a subtle equilibrium between the several interactions at play.
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Affiliation(s)
- Eric Gloaguen
- Laboratoire Francis Perrin, CEA/DSM/IRAMIS/SPAM-CNRS URA 2453, CEA/Saclay, 91191 Gif-sur-Yvette, France.
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Fricke H, Schwing K, Gerlach A, Unterberg C, Gerhards M. Investigations of the water clusters of the protected amino acid Ac-Phe-OMe by applying IR/UV double resonance spectroscopy: microsolvation of the backbone. Phys Chem Chem Phys 2010; 12:3511-21. [PMID: 20336250 DOI: 10.1039/c000424c] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
In order to investigate the influence of hydration on the backbone of a peptide or protected amino acid, the successive aggregation of water to Ac-Phe-OMe is analysed by means of IR/UV double resonance spectroscopy. To achieve meaningful results the spectra have been recorded in the region of the amide A and OH stretching vibrations as well as the amide I/II modes. Comparison with ab initio and DFT calculations leads to size-selective structural assignments. Two isomers of the mono- and dihydrated clusters and one isomer of the trihydrated cluster are observed in the molecular beam leading to a formation of the first solvation shell of the backbone. In case of the trihydrated cluster the backbone geometry is remarkably changed compared to the structure of the monomer since a network of water molecules can be formed.
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Affiliation(s)
- Holger Fricke
- TU Kaiserslautern, Fachbereich Chemie and research center OPTIMAS, Erwin-Schrödinger-Strasse 52, 67663 Kaiserslautern, Germany
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26
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Albrecht M, Borba A, Le Barbu-Debus K, Dittrich B, Fausto R, Grimme S, Mahjoub A, Nedić M, Schmitt U, Schrader L, Suhm MA, Zehnacker-Rentien A, Zischang J. Chirality influence on the aggregation of methyl mandelate. NEW J CHEM 2010. [DOI: 10.1039/c0nj00142b] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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27
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Biczysko M, Panek P, Barone V. Toward spectroscopic studies of biologically relevant systems: Vibrational spectrum of adenine as a test case for performances of long-range/dispersion corrected density functionals. Chem Phys Lett 2009. [DOI: 10.1016/j.cplett.2009.05.030] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Bouteiller Y, Poully JC, Desfrançois C, Grégoire G. Evaluation of MP2, DFT, and DFT-D Methods for the Prediction of Infrared Spectra of Peptides. J Phys Chem A 2009; 113:6301-7. [DOI: 10.1021/jp901570r] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Yves Bouteiller
- Laboratoire de Physique des Lasers, CNRS, UMR 7538, Institut Galilée, Université Paris 13, 93430, Villetaneuse, France
| | - Jean Christophe Poully
- Laboratoire de Physique des Lasers, CNRS, UMR 7538, Institut Galilée, Université Paris 13, 93430, Villetaneuse, France
| | - Charles Desfrançois
- Laboratoire de Physique des Lasers, CNRS, UMR 7538, Institut Galilée, Université Paris 13, 93430, Villetaneuse, France
| | - Gilles Grégoire
- Laboratoire de Physique des Lasers, CNRS, UMR 7538, Institut Galilée, Université Paris 13, 93430, Villetaneuse, France
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Stearns JA, Seaiby C, Boyarkin OV, Rizzo TR. Spectroscopy and conformational preferences of gas-phase helices. Phys Chem Chem Phys 2009; 11:125-32. [DOI: 10.1039/b814143f] [Citation(s) in RCA: 111] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Gloaguen E, Pollet R, Piuzzi F, Tardivel B, Mons M. Gas phase folding of an (Ala)4 neutral peptide chain: spectroscopic evidence for the formation of a β-hairpin H-bonding pattern. Phys Chem Chem Phys 2009; 11:11385-8. [DOI: 10.1039/b918670k] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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31
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Shearer J. Influence of Sequential Guanidinium Methylation on the Energetics of the Guanidinium···Guanine Dimer and Guanidinium···Guanine···Cytosine Trimer: Implications for the Control of Protein···DNA Interactions by Arginine Methyltransferases. J Phys Chem B 2008; 112:16995-7002. [DOI: 10.1021/jp808288p] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Jason Shearer
- Department of Chemistry/216, University of Nevada, Reno, Nevada 89557-0216
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