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De Sciscio M, Nardi AN, Centola F, Rossi M, Guarnera E, D’Abramo M. Molecular Modeling of the Deamidation Reaction in Solution: A Theoretical-Computational Study. J Phys Chem B 2023; 127:9550-9559. [PMID: 37903302 PMCID: PMC10641835 DOI: 10.1021/acs.jpcb.3c04662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 09/15/2023] [Accepted: 10/06/2023] [Indexed: 11/01/2023]
Abstract
In this work, a theoretical-computational method is applied to study the deamidation reaction, a critical post-translational modification in proteins, using a simple model molecule in solution. The method allows one to comprehensively address the environmental effect, thereby enabling one to accurately derive the kinetic rate constants for the three main steps of the deamidation process. The results presented, in rather good agreement with the available experimental data, underline the necessity for a rigorous treatment of environmental factors and a precise kinetic model to correctly assess the overall kinetics of the deamidation reaction.
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Affiliation(s)
- Maria
Laura De Sciscio
- Department
of Chemistry, University of Rome, Sapienza, P.le A. Moro 5, 00185 Rome, Italy
| | | | - Fabio Centola
- Global
Analytical Development, Merck Serono S.p.A., 00012 Guidonia Montecelio, Italy
| | - Mara Rossi
- Global
Analytical Development, Merck Serono S.p.A., 00012 Guidonia Montecelio, Italy
| | - Enrico Guarnera
- Global
Analytical Development, Merck Serono S.p.A., 00012 Guidonia Montecelio, Italy
- Antibody
Discovery and Protein Engineering, Merck
Healthcare KGaA, 64293 Darmstadt, Germany
| | - Marco D’Abramo
- Department
of Chemistry, University of Rome, Sapienza, P.le A. Moro 5, 00185 Rome, Italy
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Ince HH, Konuklar FAS, Ugur I, Ozcan ÖA, Sayadi M, Feig M, Aviyente V. Role of then+1 amino acid residue on the deamidation of asparagine in pentapeptides. Mol Phys 2015. [DOI: 10.1080/00268976.2015.1068394] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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de la Mora-de la Mora I, Torres-Larios A, Enríquez-Flores S, Méndez ST, Castillo-Villanueva A, Gómez-Manzo S, López-Velázquez G, Marcial-Quino J, Torres-Arroyo A, García-Torres I, Reyes-Vivas H, Oria-Hernández J. Structural effects of protein aging: terminal marking by deamidation in human triosephosphate isomerase. PLoS One 2015; 10:e0123379. [PMID: 25884638 PMCID: PMC4401446 DOI: 10.1371/journal.pone.0123379] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 02/17/2015] [Indexed: 12/04/2022] Open
Abstract
Deamidation, the loss of the ammonium group of asparagine and glutamine to form aspartic and glutamic acid, is one of the most commonly occurring post-translational modifications in proteins. Since deamidation rates are encoded in the protein structure, it has been proposed that they can serve as molecular clocks for the timing of biological processes such as protein turnover, development and aging. Despite the importance of this process, there is a lack of detailed structural information explaining the effects of deamidation on the structure of proteins. Here, we studied the effects of deamidation on human triosephosphate isomerase (HsTIM), an enzyme for which deamidation of N15 and N71 has been long recognized as the signal for terminal marking of the protein. Deamidation was mimicked by site directed mutagenesis; thus, three mutants of HsTIM (N15D, N71D and N15D/N71D) were characterized. The results show that the N71D mutant resembles, structurally and functionally, the wild type enzyme. In contrast, the N15D mutant displays all the detrimental effects related to deamidation. The N15D/N71D mutant shows only minor additional effects when compared with the N15D mutation, supporting that deamidation of N71 induces negligible effects. The crystal structures show that, in contrast to the N71D mutant, where minimal alterations are observed, the N15D mutation forms new interactions that perturb the structure of loop 1 and loop 3, both critical components of the catalytic site and the interface of HsTIM. Based on a phylogenetic analysis of TIM sequences, we propose the conservation of this mechanism for mammalian TIMs.
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Affiliation(s)
| | - Alfredo Torres-Larios
- Departamento de Bioquímica Y Biología Estructural, Instituto de Fisiología Celular, Universidad Nacional Autónoma de México, México, D.F., México
| | - Sergio Enríquez-Flores
- Laboratorio de Bioquímica-Genética, Instituto Nacional de Pediatría, Secretaría de Salud, México, D.F., México
| | - Sara-Teresa Méndez
- Laboratorio de Bioquímica-Genética, Instituto Nacional de Pediatría, Secretaría de Salud, México, D.F., México
| | - Adriana Castillo-Villanueva
- Laboratorio de Bioquímica-Genética, Instituto Nacional de Pediatría, Secretaría de Salud, México, D.F., México
| | - Saúl Gómez-Manzo
- Laboratorio de Bioquímica-Genética, Instituto Nacional de Pediatría, Secretaría de Salud, México, D.F., México
| | - Gabriel López-Velázquez
- Laboratorio de Bioquímica-Genética, Instituto Nacional de Pediatría, Secretaría de Salud, México, D.F., México
| | - Jaime Marcial-Quino
- Laboratorio de Bioquímica-Genética, Instituto Nacional de Pediatría, Secretaría de Salud, México, D.F., México
| | - Angélica Torres-Arroyo
- Laboratorio de Bioquímica-Genética, Instituto Nacional de Pediatría, Secretaría de Salud, México, D.F., México
| | - Itzhel García-Torres
- Laboratorio de Bioquímica-Genética, Instituto Nacional de Pediatría, Secretaría de Salud, México, D.F., México
| | - Horacio Reyes-Vivas
- Laboratorio de Bioquímica-Genética, Instituto Nacional de Pediatría, Secretaría de Salud, México, D.F., México
- * E-mail: (JOH); (HRV)
| | - Jesús Oria-Hernández
- Laboratorio de Bioquímica-Genética, Instituto Nacional de Pediatría, Secretaría de Salud, México, D.F., México
- * E-mail: (JOH); (HRV)
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Ugur I, Marion A, Aviyente V, Monard G. Why Does Asn71 Deamidate Faster Than Asn15 in the Enzyme Triosephosphate Isomerase? Answers from Microsecond Molecular Dynamics Simulation and QM/MM Free Energy Calculations. Biochemistry 2015; 54:1429-39. [DOI: 10.1021/bi5008047] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ilke Ugur
- Université de Lorraine, UMR 7565 SRSMC, Boulevard des Aiguillettes B.P.
70239, F-54506 Vandoeuvre-les-Nancy, France
- CNRS, UMR 7565
SRSMC, Boulevard des Aiguillettes
B.P. 70239, F-54506 Vandoeuvre-les-Nancy, France
- Department
of Chemistry, Boğaziçi University, 34342 Bebek, Istanbul, Turkey
| | - Antoine Marion
- Université de Lorraine, UMR 7565 SRSMC, Boulevard des Aiguillettes B.P.
70239, F-54506 Vandoeuvre-les-Nancy, France
- CNRS, UMR 7565
SRSMC, Boulevard des Aiguillettes
B.P. 70239, F-54506 Vandoeuvre-les-Nancy, France
| | - Viktorya Aviyente
- Department
of Chemistry, Boğaziçi University, 34342 Bebek, Istanbul, Turkey
| | - Gerald Monard
- Université de Lorraine, UMR 7565 SRSMC, Boulevard des Aiguillettes B.P.
70239, F-54506 Vandoeuvre-les-Nancy, France
- CNRS, UMR 7565
SRSMC, Boulevard des Aiguillettes
B.P. 70239, F-54506 Vandoeuvre-les-Nancy, France
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