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Mora-Gamboa MPC, Ferrucho-Calle MC, Ardila-Leal LD, Rojas-Ojeda LM, Galindo JF, Poutou-Piñales RA, Pedroza-Rodríguez AM, Quevedo-Hidalgo BE. Statistical Improvement of rGILCC 1 and rPOXA 1B Laccases Activity Assay Conditions Supported by Molecular Dynamics. Molecules 2023; 28:7263. [PMID: 37959683 PMCID: PMC10648076 DOI: 10.3390/molecules28217263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 10/20/2023] [Accepted: 10/21/2023] [Indexed: 11/15/2023] Open
Abstract
Laccases (E.C. 1.10.3.2) are glycoproteins widely distributed in nature. Their structural conformation includes three copper sites in their catalytic center, which are responsible for facilitating substrate oxidation, leading to the generation of H2O instead of H2O2. The measurement of laccase activity (UL-1) results may vary depending on the type of laccase, buffer, redox mediators, and substrates employed. The aim was to select the best conditions for rGILCC 1 and rPOXA 1B laccases activity assay. After sequential statistical assays, the molecular dynamics proved to support this process, and we aimed to accumulate valuable insights into the potential application of these enzymes for the degradation of novel substrates with negative environmental implications. Citrate buffer treatment T2 (CB T2) (pH 3.0 ± 0.2; λ420nm, 2 mM ABTS) had the most favorable results, with 7.315 ± 0.131 UL-1 for rGILCC 1 and 5291.665 ± 45.83 UL-1 for rPOXA 1B. The use of citrate buffer increased the enzyme affinity for ABTS since lower Km values occurred for both enzymes (1.49 × 10-2 mM for rGILCC 1 and 3.72 × 10-2 mM for rPOXA 1B) compared to those obtained in acetate buffer (5.36 × 10-2 mM for rGILCC 1 and 1.72 mM for rPOXA 1B). The molecular dynamics of GILCC 1-ABTS and POXA 1B-ABTS showed stable behavior, with root mean square deviation (RMSD) values not exceeding 2.0 Å. Enzyme activities (rGILCC 1 and rPOXA 1B) and 3D model-ABTS interactions (GILCC 1-ABTS and POXA 1B-ABTS) were under the strong influence of pH, wavelength, ions, and ABTS concentration, supported by computational studies identifying the stabilizing residues and interactions. Integration of the experimental and computational approaches yielded a comprehensive understanding of enzyme-substrate interactions, offering potential applications in environmental substrate treatments.
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Affiliation(s)
- María P. C. Mora-Gamboa
- Laboratorio de Biotecnología Molecular, Grupo de Biotecnología Ambiental e Industrial (GBAI), Departamento de Microbiología, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá 110231, Colombia (M.C.F.-C.); (L.D.A.-L.)
| | - María C. Ferrucho-Calle
- Laboratorio de Biotecnología Molecular, Grupo de Biotecnología Ambiental e Industrial (GBAI), Departamento de Microbiología, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá 110231, Colombia (M.C.F.-C.); (L.D.A.-L.)
| | - Leidy D. Ardila-Leal
- Laboratorio de Biotecnología Molecular, Grupo de Biotecnología Ambiental e Industrial (GBAI), Departamento de Microbiología, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá 110231, Colombia (M.C.F.-C.); (L.D.A.-L.)
- Laboratorio de Biotecnología Vegetal, Grupo de Investigación en Asuntos Ambientales y Desarrollo Sostenible (MINDALA), Departamento de Ciencias Agrarias y del Ambiente, Universidad Francisco de Paula Santander, Ocaña 546552, Colombia
| | - Lina M. Rojas-Ojeda
- Departamento de Química, Universidad Nacional de Colombia, Bogotá 111321, Colombia
| | - Johan F. Galindo
- Departamento de Química, Universidad Nacional de Colombia, Bogotá 111321, Colombia
| | - Raúl A. Poutou-Piñales
- Laboratorio de Biotecnología Molecular, Grupo de Biotecnología Ambiental e Industrial (GBAI), Departamento de Microbiología, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá 110231, Colombia (M.C.F.-C.); (L.D.A.-L.)
| | - Aura M. Pedroza-Rodríguez
- Laboratorio de Microbiología Ambiental y Suelos, Grupo de Biotecnología Ambiental e Industrial (GBAI), Departamento de Microbiología, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá 110231, Colombia
| | - Balkys E. Quevedo-Hidalgo
- Laboratorio de Biotecnología Aplicada, Grupo de Biotecnología Ambiental e Industrial (GBAI), Departamento de Microbiología, Facultad de Ciencias, Pontificia Universidad Javeriana, Bogotá 110231, Colombia;
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Galindo JF, Freixas VM, Tretiak S, Fernandez-Alberti S. Back-and-Forth Energy Transfer during Electronic Relaxation in a Chlorin-Perylene Dyad. J Phys Chem Lett 2021; 12:10394-10401. [PMID: 34669398 DOI: 10.1021/acs.jpclett.1c03034] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Donor-acceptor dyads represent a practical approach to tuning the photophysical properties of linear conjugated polymers in materials chemistry. Depending on the absorption wavelength, the acceptor and donor roles can be interchanged, and as such, the directionality of the energy transfer can be controlled. Herein, nonadiabatic excited state molecular dynamics simulations have been performed in an arylethylene-linked perylene-chlorin dyad. After an initial photoexcitation at the Soret band of chlorin, we observe an ultrafast sequential electronic relaxation to the lowest excited state. This process is accomplished through an efficient round-trip chlorin-to-perylene-to-chlorin energy transfer. It is characterized by successive intermittent localized and delocalized vibronic dynamics. Nonradiative relaxation takes place mainly through energy transfer events with perylene acting as a "heat sink" through which the nonradiative relaxation is efficiently funneled, and the excess energy is dispersed in a larger space of vibrational degrees of freedom. Thus, our findings suggest the use of donor-acceptor dyads as a useful strategy when one needs to deactivate an electronic excitation.
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Affiliation(s)
- Johan F Galindo
- Department of Chemistry, Universidad Nacional de Colombia, Bogotá 111321, Colombia
| | - Victor M Freixas
- Departamento de Ciencia y Tecnologia, Universidad Nacional de Quilmes/CONICET, B1876BXD Bernal, Argentina
| | - 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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Ardila-Leal LD, Monterey-Gutiérrez PA, Poutou-Piñales RA, Quevedo-Hidalgo BE, Galindo JF, Pedroza-Rodríguez AM. Recombinant laccase rPOXA 1B real-time, accelerated and molecular dynamics stability study. BMC Biotechnol 2021; 21:37. [PMID: 34088291 PMCID: PMC8178886 DOI: 10.1186/s12896-021-00698-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 05/24/2021] [Indexed: 12/28/2022] Open
Abstract
Background Laccases (EC 1.10.3.2) are multi-copper oxidoreductases with great biotechnological importance due to their high oxidative potential and utility for removing synthetic dyes, oxidizing phenolic compounds, and degrading pesticides, among others. Methods A real-time stability study (RTS) was conducted for a year, by using enzyme concentrates from 3 batches (L1, L3, and L4). For which, five temperatures 243.15, 277.15, 298.15, 303.15, 308.15, and 313.15 K were assayed. Using RTS data and the Arrhenius equation, we calculated the rPOXA 1B accelerated stability (AS). Molecular dynamics (MD) computational study results were very close to those obtained experimentally at four different temperatures 241, 278, 298, and 314 K. Results In the RTS, 101.16, 115.81, 75.23, 46.09, 5.81, and 4.83% of the relative enzyme activity were recovered, at respective assayed temperatures. AS study, showed that rPOXA 1B is stable at 240.98 ± 5.38, 277.40 ± 1.32 or 297.53 ± 3.88 K; with t1/2 values of 230.8, 46.2, and 12.6 months, respectively. Kinetic and thermodynamic parameters supported the high stability of rPOXA 1B, with an Ed value of 41.40 KJ mol− 1, a low variation of KM and Vmax, at 240.98 ± 5.38, and 297.53 ± 3.88 K, and ∆G values showing deactivation reaction does not occur. The MD indicates that fluctuations in loop, coils or loops with hydrophilic or intermediate polarity amino acids as well as in some residues of POXA 1B 3D structure, increases with temperature; changing from three fluctuating residues at 278 K to six residues at 298 K, and nine residues at 314 K. Conclusions Laccase rPOXA 1B demonstrated experimentally and computationally to be a stable enzyme, with t1/2 of 230.8, 46.2 or 12.6 months, if it is preserved impure without preservatives at temperatures of 240.98 ± 5.38, 277.40 ± 1.32 or 297.53 ± 3.88 K respectively; this study could be of great utility for large scale producers. Supplementary Information The online version contains supplementary material available at 10.1186/s12896-021-00698-3.
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Affiliation(s)
- Leidy D Ardila-Leal
- Departamento de Microbiología. Facultad de Ciencias. Pontificia Universidad Javeriana (PUJ). Bogotá, Laboratorio de Biotecnología Molecular, Grupo de Biotecnología Ambiental e Industrial (GBAI), Bogotá, D.C, Colombia
| | - Pedro A Monterey-Gutiérrez
- Vicerrectoría Académica. Universidad Antonio Nariño, Programa de Maestría y Doctorado en Educación Matemática, Bogotá, D.C, Colombia
| | - Raúl A Poutou-Piñales
- Departamento de Microbiología. Facultad de Ciencias. Pontificia Universidad Javeriana (PUJ). Bogotá, Laboratorio de Biotecnología Molecular, Grupo de Biotecnología Ambiental e Industrial (GBAI), Bogotá, D.C, Colombia.
| | - Balkys E Quevedo-Hidalgo
- Departamento de Microbiología. Facultad de Ciencias. Pontificia Universidad Javeriana (PUJ), Laboratorio de Biotecnología Aplicada, Grupo de Biotecnología Ambiental e Industrial (GBAI), Bogotá, D.C, Colombia.
| | - Johan F Galindo
- Departamento de Química, Universidad Nacional de Colombia, Bogotá, D.C, Colombia.
| | - Aura M Pedroza-Rodríguez
- Departamento de Microbiología. Facultad de Ciencias. Pontificia Universidad Javeriana (PUJ). Bogotá, Laboratorio de Microbiología Ambiental y de Suelos, Grupo de Biotecnología Ambiental e Industrial (GBAI), Bogotá, D.C, Colombia
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Nelson TR, Ondarse-Alvarez D, Oldani N, Rodriguez-Hernandez B, Alfonso-Hernandez L, Galindo JF, Kleiman VD, Fernandez-Alberti S, Roitberg AE, Tretiak S. Coherent exciton-vibrational dynamics and energy transfer in conjugated organics. Nat Commun 2018; 9:2316. [PMID: 29899334 PMCID: PMC5998141 DOI: 10.1038/s41467-018-04694-8] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2018] [Accepted: 04/27/2018] [Indexed: 11/09/2022] Open
Abstract
Coherence, signifying concurrent electron-vibrational dynamics in complex natural and man-made systems, is currently a subject of intense study. Understanding this phenomenon is important when designing carrier transport in optoelectronic materials. Here, excited state dynamics simulations reveal a ubiquitous pattern in the evolution of photoexcitations for a broad range of molecular systems. Symmetries of the wavefunctions define a specific form of the non-adiabatic coupling that drives quantum transitions between excited states, leading to a collective asymmetric vibrational excitation coupled to the electronic system. This promotes periodic oscillatory evolution of the wavefunctions, preserving specific phase and amplitude relations across the ensemble of trajectories. The simple model proposed here explains the appearance of coherent exciton-vibrational dynamics due to non-adiabatic transitions, which is universal across multiple molecular systems. The observed relationships between electronic wavefunctions and the resulting functionalities allows us to understand, and potentially manipulate, excited state dynamics and energy transfer in molecular materials.
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Affiliation(s)
- Tammie R Nelson
- Theoretical Division, Center for Nonlinear studies and Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Los Alamos, NM, 81545, USA
| | | | - Nicolas Oldani
- Universidad Nacional de Quilmes/CONICET, Roque Saenz Peña 352, B1876BXD, Bernal, Argentina
| | | | | | - Johan F Galindo
- Department of Chemistry, Universidad Nacional de Colombia, Av. Cra 30 # 45-03, Bogotá, 111321, Colombia
| | - Valeria D Kleiman
- Department of Chemistry, University of Florida, Gainesville, FL, 32611, USA
| | | | - Adrian E Roitberg
- Department of Chemistry, University of Florida, Gainesville, FL, 32611, USA
| | - Sergei Tretiak
- Theoretical Division, Center for Nonlinear studies and Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Los Alamos, NM, 81545, USA.
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Pedraza-González L, Galindo JF, González R, Reyes A. Revisiting the Dielectric Constant Effect on the Nucleophile and Leaving Group of Prototypical Backside S N2 Reactions: A Reaction Force and Atomic Contribution Analysis. J Phys Chem A 2016; 120:8360-8368. [PMID: 27718576 DOI: 10.1021/acs.jpca.6b06517] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The solvent effect on the nucleophile and leaving group atoms of the prototypical F- + CH3Cl → CH3F + Cl- backside bimolecular nucleophilic substitution reaction (SN2) is analyzed employing the reaction force and the atomic contributions methods on the intrinsic reaction coordinate (IRC). Solvent effects were accounted for using the polarizable continuum solvent model. Calculations were performed employing 11 dielectric constants, ε, ranging from 1.0 to 78.5, to cover a wide spectrum of solvents. The reaction force data reveal that the solvent mainly influences the region of the IRC preceding the energy barrier, where the structural rearrangement to reach the transition state occurs. A detailed analysis of the atomic role in the reaction as a function of ε reveals that the nucleophile and the carbon atom are the ones that contribute the most to the energy barrier. In addition, we investigated the effect of the choice of nucleophile and leaving group on the ΔE0 and ΔE‡ of Y- + CH3X → YCH3 + X- (X, Y = F, Cl, Br, I) in aqueous solution. Our analysis allowed us to find relationships between the atomic contributions to the activation energy and leaving group ability and nucleophilicity.
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Affiliation(s)
- Laura Pedraza-González
- Departamento de Quı́mica, Universidad Nacional de Colombia , Av. Cra 30 # 45-03, Bogotá, Colombia
| | - Johan F Galindo
- Departamento de Quı́mica, Universidad Nacional de Colombia , Av. Cra 30 # 45-03, Bogotá, Colombia
| | - Ronald González
- Departamento de Quı́mica, Universidad Nacional de Colombia , Av. Cra 30 # 45-03, Bogotá, Colombia
| | - Andrés Reyes
- Departamento de Quı́mica, Universidad Nacional de Colombia , Av. Cra 30 # 45-03, Bogotá, Colombia
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Galindo JF, Atas E, Altan A, Kuroda DG, Fernandez-Alberti S, Tretiak S, Roitberg AE, Kleiman VD. Correction to “Dynamics of Energy Transfer in a Conjugated Dendrimer Driven by Ultrafast Localization of Excitations”. J Am Chem Soc 2015; 137:14229. [DOI: 10.1021/jacs.5b09791] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Galindo JF, Atas E, Altan A, Kuroda DG, Fernandez-Alberti S, Tretiak S, Roitberg AE, Kleiman VD. Dynamics of Energy Transfer in a Conjugated Dendrimer Driven by Ultrafast Localization of Excitations. J Am Chem Soc 2015; 137:11637-44. [DOI: 10.1021/jacs.5b04075] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Johan F. Galindo
- Department
of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Evrim Atas
- Department
of Chemistry, University of Florida, Gainesville, Florida 32611, 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
| | - Adrian E. Roitberg
- Department
of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Valeria D. Kleiman
- Department
of Chemistry, University of Florida, Gainesville, Florida 32611, United States
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Pierdominici-Sottile G, Cossio Pérez R, Galindo JF, Palma J. QM/MM molecular dynamics study of the galactopyranose → galactofuranose reaction catalysed by Trypanosoma cruzi UDP-galactopyranose mutase. PLoS One 2014; 9:e109559. [PMID: 25299056 PMCID: PMC4192007 DOI: 10.1371/journal.pone.0109559] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Accepted: 08/25/2014] [Indexed: 12/18/2022] Open
Abstract
The enzyme UDP-Galactopyranose Mutase (UGM) catalyses the conversion of galactopyranose into galactofuranose. It is known to be critical for the survival and proliferation of several pathogenic agents, both prokaryotic and eukaryotic. Among them is Trypanosoma cruzi, the parasite responsible for Chagas' disease. Since the enzyme is not present in mammals, it appears as a promising target for the design of drugs to treat this illness. A precise knowledge of the mechanism of the catalysed reaction would be crucial to assist in such design. In this article we present a detailed study of all the putative steps of the mechanism. The study is based on QM/MM free energy calculations along properly selected reaction coordinates, and on the analysis of the main structural changes and interactions taking place at every step. The results are discussed in connection with the experimental evidence and previous theoretical studies.
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Affiliation(s)
| | - Rodrigo Cossio Pérez
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Bernal, Argentina
| | - Johan F. Galindo
- Quantum and Computational Chemistry Group, Departamento de Química, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Juliana Palma
- Departamento de Ciencia y Tecnología, Universidad Nacional de Quilmes, Bernal, Argentina
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Stedwell CN, Galindo JF, Roitberg AE, Polfer NC. Structures of biomolecular ions in the gas phase probed by infrared light sources. Annu Rev Anal Chem (Palo Alto Calif) 2013; 6:267-285. [PMID: 23560933 DOI: 10.1146/annurev-anchem-062012-092700] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Infrared (IR) spectroscopy of biomolecular ions combines mass spectrometry's high sensitivity and ability to analyze complex mixtures with the enhanced structural information available from vibrational spectroscopy. IR spectroscopy is in principle well placed to distinguish isomers and allow chemical classification of unknown molecules. This review gives an outline of current instrumentation, spectroscopic approaches, and potential bottlenecks. We discuss the most promising applications in bioanalytical mass spectrometry in view of recent experimental results, as well as future applications based on bioinformatics.
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Affiliation(s)
- Corey N Stedwell
- Department of Chemistry, University of Florida, Gainesville, Florida 32611-7200, USA.
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Stedwell CN, Galindo JF, Gulyuz K, Roitberg AE, Polfer NC. Crown Complexation of Protonated Amino Acids: Influence on IRMPD Spectra. J Phys Chem A 2012; 117:1181-8. [DOI: 10.1021/jp305263b] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Corey N. Stedwell
- Department of Chemistry
and Center for Chemical Physics, University of Florida, Gainesville, P.O. Box 117200, Florida 32611-7200,
United States
| | - Johan F. Galindo
- Department of Chemistry
and Quantum Theory Project, University of Florida, Gainesville, P.O. Box 118435, Florida 32611-8435,
United States
| | - Kerim Gulyuz
- Department of Chemistry
and Center for Chemical Physics, University of Florida, Gainesville, P.O. Box 117200, Florida 32611-7200,
United States
| | - Adrian E. Roitberg
- Department of Chemistry
and Quantum Theory Project, University of Florida, Gainesville, P.O. Box 118435, Florida 32611-8435,
United States
| | - Nicolas C. Polfer
- Department of Chemistry
and Center for Chemical Physics, University of Florida, Gainesville, P.O. Box 117200, Florida 32611-7200,
United States
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Agudelo WA, Galindo JF, Patarroyo ME. Electrostatic potential as a tool to understand interactions between malaria vaccine candidate peptides and MHC II molecules. Biochem Biophys Res Commun 2011; 410:410-5. [PMID: 21672519 DOI: 10.1016/j.bbrc.2011.05.145] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2011] [Accepted: 05/31/2011] [Indexed: 01/17/2023]
Abstract
One of the most important problems in vaccine development consists in understanding receptor-ligand interactions between Class II Major Histocompatibility Complex molecules (MHC II) and antigenic peptides involved in inducing an appropriate immune response. In this study, we used X-ray crystallography structural data provided by the HLA-DRβ1*0301-CLIP peptide interaction to compare native non-immunogenic and specifically-modified immunogenic peptides derived from the malarial SALSA protein, by analyzing molecular electrostatic potential surfaces on the most important regions of the peptide binding groove (Pockets 1, 4, 6 and 9). Important differences were found on the electrostatic potential induced by these peptides, particularly in MHC II conserved residues: Qα9, Sα53, Nα62, Nα69, Yβ30, Yβ60, Wβ61, Qβ70, Kβ71 and Vβ86, the same ones involved in establishing hydrogen bonds between Class II molecule-peptide and the recognition by T cell receptor, it correlating well with the change in their immunological properties. The results clearly suggest that modifications done on the electrostatic potential of these amino acids could favor the induction of different immune responses and therefore, their identification could allow modifying peptides a priori and in silico, so as to render them into immunogenic and protection-inducers and hence suitable components of a chemically-synthesized, multi-antigenic, minimal subunit based vaccine.
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Affiliation(s)
- William A Agudelo
- Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia
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Agudelo WA, Galindo JF, Ortiz M, Villaveces JL, Daza EE, Patarroyo ME. Variations in the electrostatic landscape of class II human leukocyte antigen molecule induced by modifications in the myelin basic protein peptide: a theoretical approach. PLoS One 2009; 4:e4164. [PMID: 19132105 PMCID: PMC2613560 DOI: 10.1371/journal.pone.0004164] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2008] [Accepted: 12/03/2008] [Indexed: 12/31/2022] Open
Abstract
The receptor-ligand interactions involved in the formation of the complex between Class II Major Histocompatibility Complex molecules and antigenic peptides, which are essential for establishing an adaptive immunological response, were analyzed in the Class II Human Leukocyte Antigen (HLA) - Myelin Basic Protein (MBP) peptide complex (HLA-DRβ1*1501-MBP) using a multipolar molecular electrostatic potential approach. The Human Leukocyte Antigen - peptide complex system was divided into four pockets together with their respective peptide fragment and the corresponding occupying amino acid was replaced by each of the remaining 19 amino acids. Partial atomic charges were calculated by a quantum chemistry approach at the Hatree Fock/3-21*G level, to study the behavior of monopole, dipole and quadrupole electrostatic multipolar moments. Two types of electrostatic behavior were distinguished in the pockets' amino acids: “anchoring” located in Pocket 1 and 4, and “recognition” located in Pocket 4 and 7. According to variations in the electrostatic landscape, pockets were ordered as: Pocket 1>Pocket 9≫Pocket 4≈Pocket 7 which is in agreement with the binding ability reported for Class II Major Histocompatibility Complex pockets. In the same way, amino acids occupying the polymorphic positions β13R, β26F, β28D, β9W, β74A, β47F and β57D were shown to be key for this Receptor-Ligand interaction. The results show that the multipolar molecular electrostatic potential approach is appropriate for characterizing receptor-ligand interactions in the MHC–antigenic peptide complex, which could have potential implications for synthetic vaccine design.
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Affiliation(s)
- William A. Agudelo
- Grupo de Biomatemáticas, Fundación Instituto de Inmunología de Colombia, Bogotá, Colombia
- Grupo de Química Teórica, Universidad Nacional de Colombia, Centro de Investigaciones en Sistemas complejos CEIBA, Bogotá, Colombia
| | - Johan F. Galindo
- Grupo de Biomatemáticas, Fundación Instituto de Inmunología de Colombia, Bogotá, Colombia
- Grupo de Química Teórica, Universidad Nacional de Colombia, Centro de Investigaciones en Sistemas complejos CEIBA, Bogotá, Colombia
| | - Marysol Ortiz
- Grupo de Biomatemáticas, Fundación Instituto de Inmunología de Colombia, Bogotá, Colombia
- Grupo de Química Teórica, Universidad Nacional de Colombia, Centro de Investigaciones en Sistemas complejos CEIBA, Bogotá, Colombia
| | - José L. Villaveces
- Grupo de Química Teórica, Universidad Nacional de Colombia, Centro de Investigaciones en Sistemas complejos CEIBA, Bogotá, Colombia
- Grupo de Química Teórica, Universidad de los Andes, Centro de Investigaciones en Sistemas Complejos CEIBA, Bogotá, Colombia
| | - Edgar E. Daza
- Grupo de Química Teórica, Universidad Nacional de Colombia, Centro de Investigaciones en Sistemas complejos CEIBA, Bogotá, Colombia
| | - Manuel E. Patarroyo
- Grupo de Biomatemáticas, Fundación Instituto de Inmunología de Colombia, Bogotá, Colombia
- * E-mail:
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Galindo JF, Bermúdez CI, Daza EE. tRNA structure from a graph and quantum theoretical perspective. J Theor Biol 2006; 240:574-82. [PMID: 16337238 DOI: 10.1016/j.jtbi.2005.10.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2005] [Revised: 09/23/2005] [Accepted: 10/25/2005] [Indexed: 10/25/2022]
Abstract
One of the objectives of theoretical biochemistry is to find a suitable representation of molecules allowing us to encode what we know about their structures, interactions and reactivity. Particularly, tRNA structure is involved in some processes like aminoacylation and genetic code translation, and for this reason these molecules represent a biochemical object of the utmost importance requiring characterization. We propose here two fundamental aspects for characterizing and modeling them. The first takes into consideration the connectivity patterns, i.e. the set of linkages between atoms or molecular fragments (a key tool for this purpose is the use of graph theory), and the second one requires the knowledge of some properties related to the interactions taking place within the molecule, at least in an approximate way, and perhaps of its reactivity in certain means. We used quantum mechanics to achieve this goal; specifically, we have used partial charges as a manifestation of the reply to structural changes. These charges were appropriately modified to be used as weighted factors for elements constituting the molecular graph. This new graph-tRNA context allow us to detect some structure-function relationships.
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Affiliation(s)
- Johan F Galindo
- Grupo de Química Teórica-Universidad Nacional de Colombia, Bogotá, D.C., Colombia
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Sánchez Franco A, Lacasa millán MI, Galindo JF, Moracho JL, Martínez JL. Environmental fungus flora in quail-breeding farms. Avian Dis 1981; 25:254-9. [PMID: 7259672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
An investigation was made of the environmental fungus flora in a quail-bleeding farm during a period of 5 months (May-September 1978). A total of 5826 colonies were obtained. The genera encountered most frequently were Aspergillus (28.96%), Penicillium (21.21%), Scopulariopsis (16.84%), and Aureobasidium (13.90%). Of the Aspergillus species, A. fumigatus was isolated the most often (12.61%) of the total). The different fungal species were variously distributed according to the production zones and age of the animals in which they were found.
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