1
|
|
2
|
|
3
|
Koyambo-Konzapa SJ, Dhaouadi Z, Nsangou M. Hydration of l-glycylvaline and l-glycylvalylglycine zwitterions: Structural and vibrational studies using DFT method. J Mol Graph Model 2019; 88:194-202. [DOI: 10.1016/j.jmgm.2019.01.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 01/19/2019] [Accepted: 01/21/2019] [Indexed: 10/27/2022]
|
4
|
Wałęsa R, Broda MA. The influence of solvent on conformational properties of peptides with Aib residue-a DFT study. J Mol Model 2017; 23:349. [PMID: 29164349 PMCID: PMC5698364 DOI: 10.1007/s00894-017-3508-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 10/24/2017] [Indexed: 12/30/2022]
Abstract
The conformational propensities of the Aib residue on the example of two model peptides Ac-Aib-NHMe (1) and Ac-Aib-NMe2 (2), were studied by B3LYP and M06-2X functionals, in the gas phase and in the polar solvents. To verify the reliability of selected functionals, we also performed MP2 calculations for the tested molecules in vacuum. Polarizable continuum models (PCM and SMD) were used to estimate the solvent effect. Ramachandran maps were calculated to find all energy minima. Noncovalent intramolecular interactions due to hydrogen-bonds and dipole attractions between carbonyl groups are responsible for the relative stabilities of the conformers. In order to verify the theoretical results, the available conformations of similar X-ray structures from the Cambridge Crystallographic Data Center (CCDC) were analyzed. The results of the calculations show that both derivatives with the Aib residue in the gas phase prefer structures stabilized by intramolecular N-H⋯O hydrogen bonds, i.e., C5 and C7 conformations, while polar solvent promotes helical conformation with φ, ψ values equal to +/-60°, +/-40°. In addition, in the case of molecule 2, the helical conformation is the only one available in the polar environment. This result is fully consistent with the X-ray data. Graphical abstract Effect of solvent on the Ramachandran maps of the model peptides with Aib residue.
Collapse
Affiliation(s)
- Roksana Wałęsa
- Faculty of Chemistry, University of Opole, 48, Oleska St., 45-052 Opole, Poland
| | - Małgorzata A. Broda
- Faculty of Chemistry, University of Opole, 48, Oleska St., 45-052 Opole, Poland
| |
Collapse
|
5
|
Ireta J. Polyalanine α-helix microsolvation: assessing the energy of the peptide desolvation penalty with density functional theory. Theor Chem Acc 2016. [DOI: 10.1007/s00214-016-1981-y] [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]
|
6
|
Dissection of the Factors Affecting Formation of a CH∙∙∙O H-Bond. A Case Study. CRYSTALS 2015. [DOI: 10.3390/cryst5030327] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
|
7
|
Mirkin NG, Krimm S. Note: Charge transfer in a hydrated peptide group is determined mainly by its intrinsic hydrogen-bond energetics. J Chem Phys 2014; 140:046101. [DOI: 10.1063/1.4862900] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
8
|
Rabong C, Schuster C, Liptaj T, Prónayová N, Delchev VB, Jordis U, Phopase J. NXO beta structure mimicry: an ultrashort turn/hairpin mimic that folds in water. RSC Adv 2014. [DOI: 10.1039/c4ra01210k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
An NXO building block derived tetrapeptide mimic emulates a natural proline-glycine β-turn/hairpin in polar media, including water at room temperature.
Collapse
Affiliation(s)
- Constantin Rabong
- Institute of Applied Synthetic Chemistry
- Vienna University of Technology
- A-1060 Vienna, Austria
| | - Christoph Schuster
- Department of Environmental Geosciences
- University of Vienna
- A-1090 Vienna, Austria
| | - Tibor Liptaj
- Department of NMR and Mass Spectrometry
- Institute of Analytical Chemistry
- Faculty of Chemical and Food Technology
- Slovak University of Technology
- 81237 Bratislava, Slovak Republic
| | - Nadežda Prónayová
- Department of NMR and Mass Spectrometry
- Institute of Analytical Chemistry
- Faculty of Chemical and Food Technology
- Slovak University of Technology
- 81237 Bratislava, Slovak Republic
| | - Vassil B. Delchev
- Department of Physical Chemistry
- University of Plovdiv
- 4000 Plovdiv, Bulgaria
| | - Ulrich Jordis
- Institute of Applied Synthetic Chemistry
- Vienna University of Technology
- A-1060 Vienna, Austria
| | - Jaywant Phopase
- Integrative Regenerative Medicine Centre (IGEN) & Department of Physics
- Chemistry and Biology (IFM)
- 58183 Linköping, Sweden
| |
Collapse
|
9
|
Buczek A, Broda MA. DFT study of N–H···O hydrogen bond between model dehydropeptides and water molecule. Mol Phys 2013. [DOI: 10.1080/00268976.2013.847979] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
|
10
|
Siodłak D, Bujak M, Staś M. Intra- and intermolecular forces dependent main chain conformations of esters of α,β-dehydroamino acids. J Mol Struct 2013. [DOI: 10.1016/j.molstruc.2013.04.078] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
11
|
Adhikari U, Scheiner S. Preferred Configurations of Peptide–Peptide Interactions. J Phys Chem A 2013; 117:489-96. [DOI: 10.1021/jp310942u] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Upendra Adhikari
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322-0300, United
States
| | - Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322-0300, United
States
| |
Collapse
|
12
|
Yogeswari B, Kanakaraju R, Boopathi S, Kolandaivel P. Microsolvation and hydrogen bond interactions in Glycine Dipeptide: Molecular dynamics and density functional theory studies. J Mol Graph Model 2012; 35:11-20. [DOI: 10.1016/j.jmgm.2012.02.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2011] [Revised: 02/10/2012] [Accepted: 02/13/2012] [Indexed: 11/16/2022]
|
13
|
|
14
|
Scheiner S. Weak H-bonds. Comparisons of CH···O to NH···O in proteins and PH···N to direct P···N interactions. Phys Chem Chem Phys 2011; 13:13860-72. [PMID: 21573303 DOI: 10.1039/c1cp20427k] [Citation(s) in RCA: 153] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Whereas CH···O H-bonds are usually weaker than interpeptide NH···O H-bonds, this is not necessarily the case within proteins. The nominally weaker CH···O are surprisingly strong, comparable to, and in some cases stronger than, the NH···O H-bonds in the context of the forces that hold together the adjacent strands in protein β-sheets. The peptide NH is greatly weakened as proton donor in certain conformations of the protein backbone, particularly extended structures, and forms correspondingly weaker H-bonds. The PH group is a weak proton donor, but will form PH···N H-bonds. However, there is a stronger interaction in which P can engage, in which the P atom, not the H, directly approaches the N electron donor to establish a direct P···N interaction. This approach is stabilized by the same sort of electron transfer from the N lone pair to the P-H σ* antibond that characterizes the PH···N H-bond.
Collapse
Affiliation(s)
- Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT 84322-0300, USA.
| |
Collapse
|
15
|
Solimannejad M, Scheiner S. Nature of interactions in open-shell complexes pairing H2X with HXX, X=S,O. Mol Phys 2010. [DOI: 10.1080/00268970802397944] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
|
16
|
Sun CL, Wang CS. Estimation on the intramolecular hydrogen-bonding energies in proteins and peptides by the analytic potential energy function. ACTA ACUST UNITED AC 2010. [DOI: 10.1016/j.theochem.2010.06.020] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
17
|
Cooperativity of multiple H-bonds in influencing structural and spectroscopic features of the peptide unit of proteins. J Mol Struct 2010. [DOI: 10.1016/j.molstruc.2009.10.045] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
18
|
Wu H, Canfield A, Adhikari J, Huo S. Quantum mechanical studies on model alpha-pleated sheets. J Comput Chem 2010; 31:1216-23. [PMID: 19827141 DOI: 10.1002/jcc.21408] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Pauling and Corey proposed a pleated-sheet configuration, now called alpha-sheet, as one of the protein secondary structures in addition to alpha-helix and beta-sheet. Recently, it has been suggested that alpha-sheet is a common feature of amyloidogenic intermediates. We have investigated the stability of antiparallel beta-sheet and two conformations of alpha-sheet in solution phase using the density functional theoretical method. The peptides are modeled as two-strand acetyl-(Ala)(2)-N-methylamine. Using stages of geometry optimization and single point energy calculation at B3LYP/cc-pVTZ//B3LYP/6-31G* level and including zero-point energies, thermal, and entropic contribution, we have found that beta-sheet is the most stable conformation, while the alpha-sheet proposed by Pauling and Corey has 13.6 kcal/mol higher free energy than the beta-sheet. The alpha-sheet that resembles the structure observed in molecular dynamics simulations of amyloidogenic proteins at low pH becomes distorted after stages of geometry optimization in solution. Whether the alpha-sheets with longer chains would be increasingly favorable in water relative to the increase in internal energy of the chain needs further investigation. Different from the quantum mechanics results, AMBER parm94 force field gives small difference in solution phase energy between alpha-sheet and beta-sheet. The predicted amide I IR spectra of alpha-sheet shows the main band at higher frequency than beta-sheet.
Collapse
Affiliation(s)
- Hao Wu
- Gustaf H. Carlson School of Chemistry and Biochemistry, Clark University, 950 Main Street, Worcester, Massachusetts 01610, USA
| | | | | | | |
Collapse
|
19
|
Scheiner S. Identification of spectroscopic patterns of CH...O H-bonds in proteins. J Phys Chem B 2009; 113:10421-7. [PMID: 19575539 DOI: 10.1021/jp9035138] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Ab initio calculations are used to identify characteristics of vibrational and NMR spectra that signal the involvement of a protein backbone in a CH...O H-bond and that distinguish this sort of interaction from other H-bonds in which a protein might participate. Glycine and alanine dipeptides, in both their C7 and C5 minimum-energy structures, are paired with formamide in a number of different H-bonding arrangements. The CH...O H-bond is characterized by a small contraction of the C-H bond length, along with a blue shift in its stretching frequency, accompanied by an intensification of this vibrational band. In the context of NMR spectra, the bridging CH proton's chemical shift is moved downfield by 1-2 ppm. The aforementioned features are not produced by other H-bonds in which the protein backbone might participate, such as NH proton donation or accepting a proton via the peptide C=O.
Collapse
Affiliation(s)
- Steve Scheiner
- Department of Chemistry & Biochemistry, Utah State University, Logan, Utah 84322-0300, USA.
| |
Collapse
|
20
|
Keerl M, Smirnovas V, Winter R, Richtering W. Copolymer Microgels from Mono- and Disubstituted Acrylamides: Phase Behavior and Hydrogen Bonds. Macromolecules 2008. [DOI: 10.1021/ma800785w] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Martina Keerl
- Physical Chemistry, RWTH Aachen University, Landoltweg 2, D-52056 Aachen, Germany, and Department of Chemistry, Physical Chemistry I, Dortmund University of Technology, Otto-Hahn-Str. 6, D-44227 Dortmund, Germany
| | - Vytautas Smirnovas
- Physical Chemistry, RWTH Aachen University, Landoltweg 2, D-52056 Aachen, Germany, and Department of Chemistry, Physical Chemistry I, Dortmund University of Technology, Otto-Hahn-Str. 6, D-44227 Dortmund, Germany
| | - Roland Winter
- Physical Chemistry, RWTH Aachen University, Landoltweg 2, D-52056 Aachen, Germany, and Department of Chemistry, Physical Chemistry I, Dortmund University of Technology, Otto-Hahn-Str. 6, D-44227 Dortmund, Germany
| | - Walter Richtering
- Physical Chemistry, RWTH Aachen University, Landoltweg 2, D-52056 Aachen, Germany, and Department of Chemistry, Physical Chemistry I, Dortmund University of Technology, Otto-Hahn-Str. 6, D-44227 Dortmund, Germany
| |
Collapse
|
21
|
Li Q, An X, Luan F, Li W, Gong B, Cheng J. Regulating Function of Methyl Group in Strength of CH···O Hydrogen Bond: A High-Level Ab Initio Study. J Phys Chem A 2008; 112:3985-90. [DOI: 10.1021/jp800562k] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Qingzhong Li
- Science and Engineering College of Chemistry and Biology, Yantai University, Yantai 264005, China
| | - Xiulin An
- Science and Engineering College of Chemistry and Biology, Yantai University, Yantai 264005, China
| | - Feng Luan
- Science and Engineering College of Chemistry and Biology, Yantai University, Yantai 264005, China
| | - Wenzuo Li
- Science and Engineering College of Chemistry and Biology, Yantai University, Yantai 264005, China
| | - Baoan Gong
- Science and Engineering College of Chemistry and Biology, Yantai University, Yantai 264005, China
| | - Jianbo Cheng
- Science and Engineering College of Chemistry and Biology, Yantai University, Yantai 264005, China
| |
Collapse
|
22
|
Bouchoux G, Desaphy S, Bourcier S, Malosse C, Bimbong RNB. Gas-Phase Protonation Thermochemistry of Arginine. J Phys Chem B 2008; 112:3410-9. [DOI: 10.1021/jp709677c] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Guy Bouchoux
- Laboratoire des Mécanismes Réactionnels, Ecole Polytechnique, 91128 Palaiseau, France
| | - Sylvain Desaphy
- Laboratoire des Mécanismes Réactionnels, Ecole Polytechnique, 91128 Palaiseau, France
| | - Sophie Bourcier
- Laboratoire des Mécanismes Réactionnels, Ecole Polytechnique, 91128 Palaiseau, France
| | - Christian Malosse
- Laboratoire des Mécanismes Réactionnels, Ecole Polytechnique, 91128 Palaiseau, France
| | | |
Collapse
|