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: 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.
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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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Yang B, Liu S, Lin Z. Computational study on single molecular spectroscopy of tyrosin-glycine, tryptophane-glycine and glycine-tryptophane. Sci Rep 2017; 7:15869. [PMID: 29158576 PMCID: PMC5696477 DOI: 10.1038/s41598-017-16234-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 11/09/2017] [Indexed: 12/29/2022] Open
Abstract
Quantum chemistry calculations play a fundamental role in revealing the molecular structures observed in gas-phase spectroscopic measurements. The supersonic jet cooling widely used in single molecular spectroscopy experiment is a non-equilibrium process and often causes confusion on the theoretical and experimental comparison. A computational approach is proposed here to account for the effect of the non-equilibrium cooling on the experimental spectra and applied to the cases of tyrosin-glycine (YG), tryptophane-glycine (WG) and glycine-tryptophane (GW). The low energy conformers of YG, WG and GW are obtained through thorough conformational searches. The structural features and equilibrium distributions of conformations and the energy barriers for conformer conversions are then determined. Three classes of transition energy barriers, high, medium and low, are found for the conversions among conformers with distinctly different, similar and the same structural types, respectively. The final conformation populations are determined by assuming an initial temperature of about 450 K and allowing for only the conformation conversion with a low energy barrier to occur during the rapid cooling process. The results provide a natural explanation for the numbers of YG, WG and GW conformations observed experimentally. The theoretical conformation assignments are also in good agreement with the experimental IR data.
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Affiliation(s)
- Bing Yang
- Hefei National Laboratory for Physical Sciences at Microscale & CAS Key Laboratory of Strongly-Coupled Quantum Matter Physics, Department of Physics, University of Science and Technology of China, Hefei, 230026, China
| | - Shixue Liu
- Department of Nanotechnology for Sustainable Energy, Kwansei Gakuin University, Gakuen 2-1, Sanda, Hyogo, 669-1337, Japan
| | - Zijing Lin
- Hefei National Laboratory for Physical Sciences at Microscale & CAS Key Laboratory of Strongly-Coupled Quantum Matter Physics, Department of Physics, University of Science and Technology of China, Hefei, 230026, China.
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3
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Ehrmaier J, Karsili TNV, Sobolewski AL, Domcke W. Mechanism of Photocatalytic Water Splitting with Graphitic Carbon Nitride: Photochemistry of the Heptazine-Water Complex. J Phys Chem A 2017; 121:4754-4764. [PMID: 28592110 DOI: 10.1021/acs.jpca.7b04594] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Impressive progress has recently been achieved in photocatalytic hydrogen evolution with polymeric carbon nitride materials consisting of heptazine building blocks. However, the fundamental mechanistic principles of the catalytic cycle are as yet poorly understood. Here, we provide first-principles computational evidence that water splitting with heptazine-based materials can be understood as a molecular excited-state reaction taking place in hydrogen-bonded heptazine-water complexes. The oxidation of water occurs homolytically via an electron/proton transfer from water to heptazine, resulting in ground-state heptazinyl and OH radicals. It is shown that the excess hydrogen atom of the heptazinyl radical can be photodetached by a second photon, which regenerates the heptazine molecule. Alternatively to the photodetachment reaction, two heptazinyl radicals can recombine in a dark reaction to form H2, thereby regenerating two heptazine molecules. The proposed molecular photochemical reaction scheme within hydrogen-bonded chromophore-water complexes is complementary to the traditional paradigm of photocatalytic water splitting, which assumes the separation of electrons and holes over substantial time scales and distances.
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Affiliation(s)
- Johannes Ehrmaier
- Department of Chemistry, Technical University of Munich , Garching, Germany
| | - Tolga N V Karsili
- Department of Chemistry, Technical University of Munich , Garching, Germany.,Department of Chemistry, Temple University , Philadelphia, Pennsylvania 19122, United States
| | | | - Wolfgang Domcke
- Department of Chemistry, Technical University of Munich , Garching, Germany
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4
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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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5
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Tuna D, Domcke W. Excited-state deactivation in 8-oxo-deoxyguanosine: comparison between anionic and neutral forms. Phys Chem Chem Phys 2016; 18:947-55. [DOI: 10.1039/c5cp05804j] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Ab initio explorations of excited-state potential-energy surfaces show that a radiationless deactivation mechanism via intramolecular excited-state proton transfer is available in neutral 8-oxo-deoxyguanosine, whereas it is not available in the anionic form.
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Affiliation(s)
- Deniz Tuna
- Max-Planck-Institut für Kohlenforschung
- 45470 Mülheim an der Ruhr
- Germany
| | - Wolfgang Domcke
- Department of Chemistry
- Technische Universität München
- 85747 Garching
- Germany
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6
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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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7
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Gromov EV. Unveiling the mechanism of photoinduced isomerization of the photoactive yellow protein (PYP) chromophore. J Chem Phys 2014; 141:224308. [DOI: 10.1063/1.4903174] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Affiliation(s)
- Evgeniy V. Gromov
- Theoretische Chemie, Physikalisch-Chemisches Institut, Universität Heidelberg, Heidelberg, Germany
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8
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Zabuga AV, Kamrath MZ, Boyarkin OV, Rizzo TR. Fragmentation mechanism of UV-excited peptides in the gas phase. J Chem Phys 2014; 141:154309. [DOI: 10.1063/1.4897158] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Aleksandra V. Zabuga
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
| | - Michael Z. Kamrath
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
| | - Oleg V. Boyarkin
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
| | - Thomas R. Rizzo
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, EPFL SB ISIC LCPM, Station 6, CH-1015 Lausanne, Switzerland
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9
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Tuna D, Došlić N, Mališ M, Sobolewski AL, Domcke W. Mechanisms of Photostability in Kynurenines: A Joint Electronic-Structure and Dynamics Study. J Phys Chem B 2014; 119:2112-24. [DOI: 10.1021/jp501782v] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Deniz Tuna
- Department
of Chemistry, Technische Universität München, 85747 Garching, Germany
| | - Nađa Došlić
- Division
of Physical Chemistry, Ruđer Bošković Institute, 10002 Zagreb, Croatia
| | - Momir Mališ
- Division
of Physical Chemistry, Ruđer Bošković Institute, 10002 Zagreb, Croatia
| | | | - Wolfgang Domcke
- Department
of Chemistry, Technische Universität München, 85747 Garching, Germany
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10
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Mališ M, Loquais Y, Gloaguen E, Jouvet C, Brenner V, Mons M, Ljubić I, Došlić N. Non-radiative relaxation of UV photoexcited phenylalanine residues: probing the role of conical intersections by chemical substitution. Phys Chem Chem Phys 2014; 16:2285-8. [DOI: 10.1039/c3cp53953a] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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11
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12
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Shemesh D, Lan Z, Gerber RB. Dynamics of Triplet-State Photochemistry of Pentanal: Mechanisms of Norrish I, Norrish II, and H Abstraction Reactions. J Phys Chem A 2013; 117:11711-24. [DOI: 10.1021/jp401309b] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Dorit Shemesh
- Department of Physical Chemistry
and the Fritz Haber Center for Molecular Dynamics, The Hebrew University, Jerusalem 91904, Israel
| | - Zhenggang Lan
- Key Laboratory of Biobased Materials
and the Qingdao Key Lab of Solar Energy Utilization and Energy Storage
Technology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qinqdao 266101, China
| | - R. Benny Gerber
- Department of Physical Chemistry
and the Fritz Haber Center for Molecular Dynamics, The Hebrew University, Jerusalem 91904, Israel
- Department of Chemistry, University of California—Irvine, Irvine, California
92597, United States
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13
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Wang C, Lin Z, Zhang R. Zwitterions are the most stable form for neutral arginylglycine in gas phase: Clear theoretical evidence. COMPUT THEOR CHEM 2013. [DOI: 10.1016/j.comptc.2013.01.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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14
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Guglielmi M, Doemer M, Tavernelli I, Rothlisberger U. Photodynamics of Lys+-Trp protein motifs: Hydrogen bonds ensure photostability. Faraday Discuss 2013; 163:189-203; discussion 243-75. [DOI: 10.1039/c3fd00037k] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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15
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Mališ M, Loquais Y, Gloaguen E, Biswal HS, Piuzzi F, Tardivel B, Brenner V, Broquier M, Jouvet C, Mons M, Došlić N, Ljubić I. Unraveling the Mechanisms of Nonradiative Deactivation in Model Peptides Following Photoexcitation of a Phenylalanine Residue. J Am Chem Soc 2012; 134:20340-51. [DOI: 10.1021/ja3054942] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Momir Mališ
- Division
of Physical Chemistry, Ruđer Bošković Institute, Bijenička
cesta 54, HR-10002 Zagreb, Croatia
| | - Yohan Loquais
- CEA, IRAMIS, SPAM, Lab. Francis
Perrin, URA 2453, CEA-Saclay, Bât
522, Gif-sur-Yvette, F-91191, France
- CNRS, INC & INP, Lab. Francis Perrin, URA 2453, CEA-Saclay, Bât 522, Gif-sur-Yvette, F-91191, France
| | - Eric Gloaguen
- CEA, IRAMIS, SPAM, Lab. Francis
Perrin, URA 2453, CEA-Saclay, Bât
522, Gif-sur-Yvette, F-91191, France
- CNRS, INC & INP, Lab. Francis Perrin, URA 2453, CEA-Saclay, Bât 522, Gif-sur-Yvette, F-91191, France
| | - Himansu S. Biswal
- CEA, IRAMIS, SPAM, Lab. Francis
Perrin, URA 2453, CEA-Saclay, Bât
522, Gif-sur-Yvette, F-91191, France
- CNRS, INC & INP, Lab. Francis Perrin, URA 2453, CEA-Saclay, Bât 522, Gif-sur-Yvette, F-91191, France
| | - François Piuzzi
- CEA, IRAMIS, SPAM, Lab. Francis
Perrin, URA 2453, CEA-Saclay, Bât
522, Gif-sur-Yvette, F-91191, France
- CNRS, INC & INP, Lab. Francis Perrin, URA 2453, CEA-Saclay, Bât 522, Gif-sur-Yvette, F-91191, France
| | - Benjamin Tardivel
- CEA, IRAMIS, SPAM, Lab. Francis
Perrin, URA 2453, CEA-Saclay, Bât
522, Gif-sur-Yvette, F-91191, France
- CNRS, INC & INP, Lab. Francis Perrin, URA 2453, CEA-Saclay, Bât 522, Gif-sur-Yvette, F-91191, France
| | - Valérie Brenner
- CEA, IRAMIS, SPAM, Lab. Francis
Perrin, URA 2453, CEA-Saclay, Bât
522, Gif-sur-Yvette, F-91191, France
- CNRS, INC & INP, Lab. Francis Perrin, URA 2453, CEA-Saclay, Bât 522, Gif-sur-Yvette, F-91191, France
| | - Michel Broquier
- Université Paris-Sud 11, CLUPS / CNRS, LUMAT FR 2764, Bât
106, Orsay, F-91405, France
- CNRS, Université Paris-Sud 11, ISMO, UMR 8624, Bât 210, Orsay,
F-91405, France
| | - Christophe Jouvet
- Université Paris-Sud 11, CLUPS / CNRS, LUMAT FR 2764, Bât
106, Orsay, F-91405, France
- CNRS, Université Paris-Sud 11, ISMO, UMR 8624, Bât 210, Orsay,
F-91405, France
| | - Michel Mons
- CEA, IRAMIS, SPAM, Lab. Francis
Perrin, URA 2453, CEA-Saclay, Bât
522, Gif-sur-Yvette, F-91191, France
- CNRS, INC & INP, Lab. Francis Perrin, URA 2453, CEA-Saclay, Bât 522, Gif-sur-Yvette, F-91191, France
| | - Nađa Došlić
- Division
of Physical Chemistry, Ruđer Bošković Institute, Bijenička
cesta 54, HR-10002 Zagreb, Croatia
| | - Ivan Ljubić
- Division
of Physical Chemistry, Ruđer Bošković Institute, Bijenička
cesta 54, HR-10002 Zagreb, Croatia
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16
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Egel R. Life's Order, Complexity, Organization, and Its Thermodynamic-Holistic Imperatives. Life (Basel) 2012; 2:323-63. [PMID: 25371269 PMCID: PMC4187152 DOI: 10.3390/life2040323] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2012] [Revised: 10/30/2012] [Accepted: 11/05/2012] [Indexed: 12/17/2022] Open
Abstract
In memoriam Jeffrey S. Wicken (1942-2002)-the evolutionarily minded biochemist, who in the 1970/80s strived for a synthesis of biological and physical theories to fathom the tentative origins of life. Several integrative concepts are worth remembering from Wicken's legacy. (i) Connecting life's origins and complex organization to a preexisting physical world demands a thermodynamically sound transition. (ii) Energetic 'charging' of the prebiosphere must precede the emergence of biological organization. (iii) Environmental energy gradients are exploited progressively, approaching maximum interactive structure and minimum dissipation. (iv) Dynamic self-assembly of prebiotic organic matter is driven by hydrophobic tension between water and amphiphilic building blocks, such as aggregating peptides from non-polar amino acids and base stacking in nucleic acids. (v) The dynamics of autocatalytic self-organization are facilitated by a multiplicity of weak interactions, such as hydrogen bonding, within and between macromolecular assemblies. (vi) The coevolution of (initially uncoded) proteins and nucleic acids in energy-coupled and metabolically active so-called 'microspheres' is more realistic as a kinetic transition model of primal biogenesis than 'hypercycle replication' theories for nucleic acid replicators on their own. All these considerations blend well with the current understanding that sunlight UV-induced photo-electronic excitation of colloidal metal sulfide particles appears most suitable as a prebiotic driver of organic synthesis reactions, in tight cooperation with organic, phase-separated, catalytic 'microspheres'. On the 'continuist vs. miraculist' schism described by Iris Fry for origins-of-life considerations (Table 1), Wicken was a fervent early protagonist of holistic 'continuist' views and agenda.
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Affiliation(s)
- Richard Egel
- Department of Biology, University of Copenhagen Biocenter, Ole Maaløes Vej 5, DK-2200 Copenhagen, Denmark.
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17
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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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18
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Brkljača Z, Čondić-Jurkić K, Smith AS, Smith DM. Calculation of the CD Spectrum of a Peptide from Its Conformational Phase Space: The Case of Met-enkephalin and Its Unnatural Analogue. J Chem Theory Comput 2012; 8:1694-705. [PMID: 26593663 DOI: 10.1021/ct200868y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Zlatko Brkljača
- Institute for Theoretical
Physics
and Excellence Cluster: Engineering of Advanced Materials, FA University Erlangen—Nürnberg, Nägelsbachstraße
49b, Erlangen, 91052, Germany
| | - Karmen Čondić-Jurkić
- Institute for Theoretical
Physics
and Excellence Cluster: Engineering of Advanced Materials, FA University Erlangen—Nürnberg, Nägelsbachstraße
49b, Erlangen, 91052, Germany
- Division of Organic Chemistry
and Biochemistry, Ruđer Bošković Institute, Bijenička 54, 10000, Zagreb, Croatia
| | - Ana-Sunčana Smith
- Institute for Theoretical
Physics
and Excellence Cluster: Engineering of Advanced Materials, FA University Erlangen—Nürnberg, Nägelsbachstraße
49b, Erlangen, 91052, Germany
| | - David M. Smith
- Division of Organic Chemistry
and Biochemistry, Ruđer Bošković Institute, Bijenička 54, 10000, Zagreb, Croatia
- Center for Computational Chemistry, FA University of Erlangen—Nürnberg, Nägelsbachstraße
25, Erlangen, 91052, Germany
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19
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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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20
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Egel R. Primal eukaryogenesis: on the communal nature of precellular States, ancestral to modern life. Life (Basel) 2012; 2:170-212. [PMID: 25382122 PMCID: PMC4187143 DOI: 10.3390/life2010170] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2011] [Revised: 12/29/2011] [Accepted: 01/11/2012] [Indexed: 02/08/2023] Open
Abstract
This problem-oriented, exploratory and hypothesis-driven discourse toward the unknown combines several basic tenets: (i) a photo-active metal sulfide scenario of primal biogenesis in the porespace of shallow sedimentary flats, in contrast to hot deep-sea hydrothermal vent conditions; (ii) an inherently complex communal system at the common root of present life forms; (iii) a high degree of internal compartmentalization at this communal root, progressively resembling coenocytic (syncytial) super-cells; (iv) a direct connection from such communal super-cells to proto-eukaryotic macro-cell organization; and (v) multiple rounds of micro-cellular escape with streamlined reductive evolution-leading to the major prokaryotic cell lines, as well as to megaviruses and other viral lineages. Hopefully, such nontraditional concepts and approaches will contribute to coherent and plausible views about the origins and early life on Earth. In particular, the coevolutionary emergence from a communal system at the common root can most naturally explain the vast discrepancy in subcellular organization between modern eukaryotes on the one hand and both archaea and bacteria on the other.
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Affiliation(s)
- Richard Egel
- Department of Biology, University of Copenhagen Biocenter, Ole Maaløes Vej 5, DK-2200 Copenhagen, Denmark.
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21
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Shemesh D, Domcke W. Effect of the Chirality of Residues and γ-Turns on the Electronic Excitation Spectra, Excited-State Reaction Paths and Conical Intersections of Capped Phenylalanine-Alanine Dipeptides. Chemphyschem 2011; 12:1833-40. [DOI: 10.1002/cphc.201100039] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2011] [Indexed: 11/05/2022]
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22
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Abo-Riziq A, Grace L, Crews B, Callahan MP, van Mourik T, Vries MSD. Conformational Structure of Tyrosine, Tyrosyl-glycine, and Tyrosyl-glycyl-glycine by Double Resonance Spectroscopy. J Phys Chem A 2011; 115:6077-87. [DOI: 10.1021/jp110601w] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Ali Abo-Riziq
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Louis Grace
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Bridgit Crews
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Michael P. Callahan
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Tanja van Mourik
- EaStCHEM School of Chemistry, University of St. Andrews North Haugh, St. Andrews, Fife KY16 9ST, Scotland, U.K
| | - Mattanjah S. de Vries
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
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Marazzi M, Sancho U, Castaño O, Frutos LM. First principles study of photostability within hydrogen-bonded amino acids. Phys Chem Chem Phys 2011; 13:7805-11. [PMID: 21403960 DOI: 10.1039/c0cp02554b] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The photochemistry and photophysics of a two-glycine minimal model is studied at the CASPT2//CASSCF level of theory. Different photoinduced processes are discussed, on the basis of the calculated minimum energy paths and the characterization of the electronic state crossings. Two main processes could provide UV-photostability to the hydrogen-bonded peptide system: (i) forward-backward photoinduced electron/proton transfer involving the H in the hydrogen bond, (ii) singlet-singlet energy transfer between two amino acids, providing ultrafast population of the low-energy n,π* state.
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Affiliation(s)
- Marco Marazzi
- Departamento de Química Física, Universidad de Alcalá, 28871 Alcalá de Henares (Madrid), Spain.
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Shemesh D, Sobolewski AL, Domcke W. Role of excited-state hydrogen detachment and hydrogen-transfer processes for the excited-state deactivation of an aromatic dipeptide: N-acetyl tryptophan methyl amide. Phys Chem Chem Phys 2010; 12:4899-905. [DOI: 10.1039/b927024h] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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