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Boopathi S, Kolandaivel P. Molecular dynamics simulations and density functional theory studies of NALMA and NAGMA dipeptides. J Biomol Struct Dyn 2013; 31:158-73. [DOI: 10.1080/07391102.2012.698380] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Cyclo-hexa-peptides at the water/cyclohexane interface: a molecular dynamics simulation. J Mol Model 2012; 19:601-11. [DOI: 10.1007/s00894-012-1588-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Accepted: 08/28/2012] [Indexed: 10/27/2022]
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García-Fandiño R, Castedo L, Granja JR, Vázquez SA. Interaction and Dimerization Energies in Methyl-Blocked α,γ-Peptide Nanotube Segments. J Phys Chem B 2010; 114:4973-83. [DOI: 10.1021/jp910919k] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Rebeca García-Fandiño
- Departamento de Química Orgánica, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain, Departamento de Química Fundamental, Facultad de Ciencias, Universidad de A Coruña, 15071 A Coruña, Spain, and Departamento de Química Física, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Luis Castedo
- Departamento de Química Orgánica, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain, Departamento de Química Fundamental, Facultad de Ciencias, Universidad de A Coruña, 15071 A Coruña, Spain, and Departamento de Química Física, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Juan R. Granja
- Departamento de Química Orgánica, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain, Departamento de Química Fundamental, Facultad de Ciencias, Universidad de A Coruña, 15071 A Coruña, Spain, and Departamento de Química Física, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain
| | - Saulo A. Vázquez
- Departamento de Química Orgánica, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain, Departamento de Química Fundamental, Facultad de Ciencias, Universidad de A Coruña, 15071 A Coruña, Spain, and Departamento de Química Física, Universidad de Santiago de Compostela, 15782 Santiago de Compostela, Spain
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Praveena G, Kolandaivel P. Structural Properties and Anion Binding Affinity of cyclo[(1R,3S)-γ-Acc-Gly]3Hexapeptide. J Biomol Struct Dyn 2009; 27:37-48. [DOI: 10.1080/07391102.2009.10507294] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Abiram A, Kolandaivel P. Structural analysis and the effect of cyclo(His-Pro) dipeptide on neurotoxins--a dynamics and density functional theory study. J Mol Model 2009; 16:193-202. [PMID: 19554355 DOI: 10.1007/s00894-009-0531-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2009] [Accepted: 04/21/2009] [Indexed: 10/20/2022]
Abstract
The switching propensity and maximum probability of occurrence of the side chain imidazole group in the dipeptide cyclo(His-Pro) (CHP) were studied by applying molecular dynamics simulations and density functional theory. The atomistic behaviour of CHP with the neurotoxins glutamate (E) and paraquat (Pq) were also explored; E and Pq engage in hydrogen bond formation with the diketopiperazine (DKP) ring of the dipeptide, with which E shows a profound interaction, as confirmed further by NH and CO stretching vibrational frequencies. The effect of CHP was found to be greater on E than on Pq neurotoxin. A ring puckering study indicated a twist boat conformation for the six-membered DKP ring. Molecular electrostatic potential (MESP) mapping was also used to explore the hydrogen bond interactions prevailing between the neurotoxins and the DKP ring. The results of this study reveal that the DKP ring of the dipeptide CHP can be expected to play a significant role in reducing effects such as oxidative stress and cell death caused by neurotoxins.
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Interaction of metal ions with cyclo[(1R,3S)-γ-Acc-Gly]3 hexapeptide – A theoretical study. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/j.theochem.2008.12.033] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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