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Adasme-Carreño F, Ochoa-Calle A, Galván M, Ireta J. Conformational preference of dipeptide zwitterions in aqueous solvents. Phys Chem Chem Phys 2024; 26:8210-8218. [PMID: 38384231 DOI: 10.1039/d3cp05742a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2024]
Abstract
Proper description of solvent effects is challenging for theoretical methods, particularly if the solute is a zwitterion. Here, a series of theoretical procedures are used to determine the preferred solvated conformations of twelve hydrophobic dipeptides (Leu-Leu, Leu-Phe, Phe-Leu, Ile-Leu, Phe-Phe, Ala-Val, Val-Ala, Ala-Ile, Ile-Ala, Ile-Val, Val-Ile and Val-Val) in the zwitterionic state. First, the accuracy of density functional theory (DFT), combined with different implicit solvent models, for describing zwitterions in aqueous solvent is assessed by comparing the predicted against the experimental glycine tautomerization energy, i.e., the energetic difference between canonical and zwitterionic glycine in aqueous solvents. It is found that among the tested solvation schemes, the charge-asymmetric nonlocally determined local-electric solvation model (CANDLE) predicts an energetic difference in excellent agreement with the experimental value. Next, DFT-CANDLE is used to determine the most favorable solvated conformation for each of the investigated dipeptide zwitterions. The CANDLE-solvated structures are obtained by exploring the conformational space of each dipeptide zwitterion concatenating DFT calculations, in vacuum, with classical molecular dynamics simulations, in explicit solvents, and DFT calculations including explicit water molecules. It is found that the energetically most favorable conformations are similar to those of the dipeptide zwitterions in their respective crystal structures. Such structural agreement is indicative of the DFT-CANDLE accomplishment of the description of solvated zwitterions, and suggests that these biomolecules self-assemble as quasi-rigid objects.
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Affiliation(s)
- Francisco Adasme-Carreño
- Centro de Investigación de Estudios Avanzados del Maule (CIEAM), Vicerrectorá de Investigación y Postgrado Universidad Católica del Maule, Talca 3480112, Chile.
- Laboratorio de Bioinformática y Química Computacional (LBQC), Departamento de Medicina Traslacional, Facultad de Medicina, Universidad Católica del Maule, Talca 3480112, Chile
| | - Alvaro Ochoa-Calle
- Departamento de Química, División de Ciencias Básicas e Ingeniería, Universidad Autónoma Metropolitana-Iztapalapa, Ciudad de México 09340, Mexico.
| | - Marcelo Galván
- Departamento de Química, División de Ciencias Básicas e Ingeniería, Universidad Autónoma Metropolitana-Iztapalapa, Ciudad de México 09340, Mexico.
| | - Joel Ireta
- Departamento de Química, División de Ciencias Básicas e Ingeniería, Universidad Autónoma Metropolitana-Iztapalapa, Ciudad de México 09340, Mexico.
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Saffari B, Amininasab M. Crocin Inhibits the Fibrillation of Human α-synuclein and Disassembles Mature Fibrils: Experimental Findings and Mechanistic Insights from Molecular Dynamics Simulation. ACS Chem Neurosci 2021; 12:4037-4057. [PMID: 34636232 DOI: 10.1021/acschemneuro.1c00379] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The aggregation of human alpha-synuclein (hαS) is pivotally implicated in the development of most types of synucleinopathies. Molecules that can inhibit or reverse the aggregation process of amyloidogenic proteins have potential therapeutic value. The anti-aggregating activity of multiple carotenoid compounds has been reported over the past decades against a growing list of amyloidogenic polypeptides. Here, we aimed to determine whether crocin, the main carotenoid glycoside component of saffron, would inhibit hαS aggregation or could disassemble its preformed fibrils. By employing a series of biochemical and biophysical techniques, crocin was exhibited to inhibit hαS fibrillation in a dose-dependent fashion by stabilizing very early aggregation intermediates in off-pathway non-toxic conformations with little β-sheet content. We also observed that crocin at high concentrations could efficiently destabilize mature fibrils and disassemble them into seeding-incompetent intermediates by altering their β-sheet conformation and reshaping their structure. Our atomistic molecular dynamics (MD) simulations demonstrated that crocin molecules bind to both the non amyloid-β component (NAC) region and C-terminal domain of hαS. These interactions could thereby stabilize the autoinhibitory conformation of the protein and prevent it from adopting aggregation-prone structures. MD simulations further suggested that ligand molecules prefer to reside longitudinally along the fibril axis onto the edges of the inter-protofilament interface where they establish hydrogen and hydrophobic bonds with steric zipper stabilizing residues. These interactions turned out to destabilize hαS fibrils by altering the interstrand twist angles, increasing the rigidity of the fibril core, and elevating its radius of gyration. Our findings suggest the potential pharmaceutical implication of crocin in synucleinopathies.
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Affiliation(s)
- Babak Saffari
- Department of Cell and Molecular Biology, School of Biology, College of Science, University of Tehran, Tehran 14155-6455, Iran
| | - Mehriar Amininasab
- Department of Cell and Molecular Biology, School of Biology, College of Science, University of Tehran, Tehran 14155-6455, Iran
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3
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Adasme-Carreño F, Caballero J, Ireta J. PSIQUE: Protein Secondary Structure Identification on the Basis of Quaternions and Electronic Structure Calculations. J Chem Inf Model 2021; 61:1789-1800. [PMID: 33769809 DOI: 10.1021/acs.jcim.0c01343] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The secondary structure is important in protein structure analysis, classification, and modeling. We have developed a novel method for secondary structure assignment, termed PSIQUE, based on the potential energy surface (PES) of polyalanine obtained using an infinitely long chain model and density functional theory calculations. First, uniform protein segments are determined in terms of a difference of quaternions between neighboring amino acids along the protein backbone. Then, the identification of the secondary structure motifs is carried out based on the minima found in the PES. PSIQUE shows good agreement with other secondary structure assignment methods. However, it provides better discrimination of subtle secondary structures (e.g., helix types) and termini and produces more uniform segments while also accounting for local distortions. Overall, PSIQUE provides a precise and reliable assignment of secondary structures, so it should be helpful for the detailed characterization of the protein structure.
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Affiliation(s)
- Francisco Adasme-Carreño
- Departamento de Bioinformática, Centro de Bioinformática, Simulación y Modelado (CBSM), Facultad de Ingeniería, Universidad de Talca, Campus Talca, 1 Poniente No. 1141, Casilla 721, Talca 3460000, Chile
| | - Julio Caballero
- Departamento de Bioinformática, Centro de Bioinformática, Simulación y Modelado (CBSM), Facultad de Ingeniería, Universidad de Talca, Campus Talca, 1 Poniente No. 1141, Casilla 721, Talca 3460000, Chile
| | - Joel Ireta
- Departamento de Química, División de Ciencias Básicas e Ingeniería, Universidad Autónoma Metropolitana-Iztapalapa, A.P. 55-534, Ciudad de Mexico 09340, Mexico
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4
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Nochebuena J, Cuautli C, Ireta J. Origin of cooperativity in hydrogen bonding. Phys Chem Chem Phys 2017; 19:15256-15263. [DOI: 10.1039/c7cp01695f] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Hydrogen bond cooperativity results from interactions between effective point dipoles which account for many-body contributions to cooperativity.
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Affiliation(s)
- Jorge Nochebuena
- Departamento de Química
- División de Ciencias Básicas e Ingeniería
- Universidad Autónoma Metropolitana-Iztapalapa
- Ciudad de México 09340
- Mexico
| | - Cristina Cuautli
- Departamento de Química
- División de Ciencias Básicas e Ingeniería
- Universidad Autónoma Metropolitana-Iztapalapa
- Ciudad de México 09340
- Mexico
| | - Joel Ireta
- Departamento de Química
- División de Ciencias Básicas e Ingeniería
- Universidad Autónoma Metropolitana-Iztapalapa
- Ciudad de México 09340
- Mexico
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5
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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]
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6
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Nochebuena J, Ireta J. On cooperative effects and aggregation of GNNQQNY and NNQQNY peptides. J Chem Phys 2015; 143:135103. [DOI: 10.1063/1.4932083] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Affiliation(s)
- Jorge Nochebuena
- Departamento de Química, División de Ciencias Básicas e Ingeniería, Universidad Autónoma Metropolitana-Iztapalapa, A.P. 55-534, México D.F. 09340, Mexico
| | - Joel Ireta
- Departamento de Química, División de Ciencias Básicas e Ingeniería, Universidad Autónoma Metropolitana-Iztapalapa, A.P. 55-534, México D.F. 09340, Mexico
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7
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Li SS, Huang CY, Hao JJ, Wang CS. Evaluation of the binding energy for hydrogen-bonded complexes containing amides and peptides. COMPUT THEOR CHEM 2014. [DOI: 10.1016/j.comptc.2014.02.028] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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8
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Sun CL, Ding F, Ding YL, Li Y. The effect of water molecules upon the hydrogen-bonding cooperativity of three-stranded antiparallel β-sheet models. RSC Adv 2014. [DOI: 10.1039/c3ra45892j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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Li SS, Huang CY, Hao JJ, Wang CS. A polarizable dipole-dipole interaction model for evaluation of the interaction energies for NH···OC and CH···OC hydrogen-bonded complexes. J Comput Chem 2013; 35:415-26. [DOI: 10.1002/jcc.23473] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2013] [Revised: 09/30/2013] [Accepted: 10/03/2013] [Indexed: 02/02/2023]
Affiliation(s)
- Shu-Shi Li
- Department of Chemistry; Liaoning Normal University; Dalian 116029 People's Republic of China
| | - Cui-Ying Huang
- Department of Chemistry; Liaoning Normal University; Dalian 116029 People's Republic of China
| | - Jiao-Jiao Hao
- Department of Chemistry; Liaoning Normal University; Dalian 116029 People's Republic of China
| | - Chang-Sheng Wang
- Department of Chemistry; Liaoning Normal University; Dalian 116029 People's Republic of China
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Chutia S, Rossi M, Blum V. Water Adsorption at Two Unsolvated Peptides with a Protonated Lysine Residue: From Self-Solvation to Solvation. J Phys Chem B 2012; 116:14788-804. [DOI: 10.1021/jp3098268] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sucismita Chutia
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Theory
Department, D-14195 Berlin, Germany
| | - Mariana Rossi
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Theory
Department, D-14195 Berlin, Germany
| | - Volker Blum
- Fritz-Haber-Institut der Max-Planck-Gesellschaft, Theory
Department, D-14195 Berlin, Germany
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11
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Grebner C, Kästner J, Thiel W, Engels B. A New Tabu-Search-Based Algorithm for Solvation of Proteins. J Chem Theory Comput 2012; 9:814-21. [DOI: 10.1021/ct300898d] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Christoph Grebner
- Julius-Maximilians-Universität
Würzburg, Institut für Physikalische und
Theoretische Chemie, Emil-Fischer-Straße 42, D-97074 Würzburg,
Germany
| | - Johannes Kästner
- Universität
Stuttgart,
Institut für Theoretische Chemie, Pfaffenwaldring 55, D-70569
Stuttgart, Germany
| | - Walter Thiel
- Max-Planck-Institut
für
Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an
der Ruhr, Germany
| | - Bernd Engels
- Julius-Maximilians-Universität
Würzburg, Institut für Physikalische und
Theoretische Chemie, Emil-Fischer-Straße 42, D-97074 Würzburg,
Germany
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12
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Ali-Torres J, Dannenberg JJ. The folding of acetyl(Ala)28NH2 and acetyl(Ala)40NH2 extended strand peptides into antiparallel β-sheets. A density functional theory study of β-sheets with β-turns. J Phys Chem B 2012; 116:14017-22. [PMID: 23157432 DOI: 10.1021/jp3094947] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report ONIOM calculations using B3LYP/D95** and AM1 on β-sheet formation from acetyl(Ala)(N)NH(2) (N = 28 or 40). The sheets contain from one to four β-turns for N = 28 and up to six for N = 40. We have obtained four types of geometrically optimized structures. All contain only β-turns. They differ from each other in the types of β-turns formed. The unsolvated sheets containing two turns are most stable. Aqueous solvation (using the SM5.2 and CPCM methods) reduces the stabilities of the folded structures compared to the extended strands.
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Affiliation(s)
- Jorge Ali-Torres
- Department of Chemistry, City University of New York - Hunter College and the Graduate School, New York 10065, United States
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Marianski M, Dannenberg JJ. Aqueous solvation of polyalanine α-helices with specific water molecules and with the CPCM and SM5.2 aqueous continuum models using density functional theory. J Phys Chem B 2012; 116:1437-45. [PMID: 22201227 DOI: 10.1021/jp209177u] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We present density functional theory (DFT) calculations at the X3LYP/D95(d,p) level on the solvation of polyalanine α-helices in water. The study includes the effects of discrete water molecules and the CPCM and AMSOL SM5.2 solvent continuum model both separately and in combination. We find that individual water molecules cooperatively hydrogen-bond to both the C- and N-termini of the helix, which results in increases in the dipole moment of the helix/water complex to more than the vector sum of their individual dipole moments. These waters are found to be more stable than in bulk solvent. On the other hand, individual water molecules that interact with the backbone lower the dipole moment of the helix/water complex to below that of the helix itself. Small clusters of waters at the termini increase the dipole moments of the helix/water aggregates, but the effect diminishes as more waters are added. We discuss the somewhat complex behavior of the helix with the discrete waters in the continuum models.
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Affiliation(s)
- Mateusz Marianski
- Department of Chemistry, City University of New York-Hunter College and the Graduate School, 695 Park Avenue, New York, New York 10065, USA
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14
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Tachikawa H. Electron detachment dynamics of Cu−(H2O)n (n = 1–3): a direct ab initio MD study. RSC Adv 2012. [DOI: 10.1039/c2ra20907a] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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