1
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Huang XW, Li Y, Jiang LN, Zhao BK, Liu YS, Chen C, Zhao D, Zhang XL, Li ML, Jiang YY, Liu SH, Zhu L, Zhao JM. Nomogram for preoperative estimation of microvascular invasion risk in hepatocellular carcinoma. Transl Oncol 2024; 45:101986. [PMID: 38723299 PMCID: PMC11101742 DOI: 10.1016/j.tranon.2024.101986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 04/22/2024] [Accepted: 05/05/2024] [Indexed: 05/21/2024] Open
Abstract
Microvascular invasion (MVI) is an adverse prognostic indicator of tumor recurrence after surgery for hepatocellular carcinoma (HCC). Therefore, developing a nomogram for estimating the presence of MVI before liver resection is necessary. We retrospectively included 260 patients with pathologically confirmed HCC at the Fifth Medical Center of Chinese PLA General Hospital between January 2021 and April 2024. The patients were randomly divided into a training cohort (n = 182) for nomogram development, and a validation cohort (n = 78) to confirm the performance of the model (7:3 ratio). Significant clinical variables associated with MVI were then incorporated into the predictive nomogram using both univariate and multivariate logistic analyses. The predictive performance of the nomogram was assessed based on its discrimination, calibration, and clinical utility. Serum carnosine dipeptidase 1 ([CNDP1] OR 2.973; 95 % CI 1.167-7.575; p = 0.022), cirrhosis (OR 8.911; 95 % CI 1.922-41.318; p = 0.005), multiple tumors (OR 4.095; 95 % CI 1.374-12.205; p = 0.011), and tumor diameter ≥3 cm (OR 4.408; 95 % CI 1.780-10.919; p = 0.001) were independent predictors of MVI. Performance of the nomogram based on serum CNDP1, cirrhosis, number of tumors and tumor diameter was achieved with a concordance index of 0.833 (95 % CI 0.771-0.894) and 0.821 (95 % CI 0.720-0.922) in the training and validation cohorts, respectively. It fitted well in the calibration curves, and the decision curve analysis further confirmed its clinical usefulness. The nomogram, incorporating significant clinical variables and imaging features, successfully predicted the personalized risk of MVI in HCC preoperatively.
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Affiliation(s)
- Xiao-Wen Huang
- Medical School of Chinese PLA, Beijing, China; Department of Pathology and Hepatology, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Yan Li
- Department of Pathology and Hepatology, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Li-Na Jiang
- Department of Pathology and Hepatology, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Bo-Kang Zhao
- Department of Hepatology, Center of Infectious Diseases and Pathogen Biology, The First Hospital of Jilin University, Changchun, China
| | - Yi-Si Liu
- First Department of Liver Disease Center, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Chun Chen
- Senior Department of Hepatology, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Dan Zhao
- Department of Pathology and Hepatology, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Xue-Li Zhang
- Department of Pathology and Hepatology, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Mei-Ling Li
- Department of Pathology and Hepatology, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Yi-Yun Jiang
- Department of Pathology and Hepatology, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Shu-Hong Liu
- Department of Pathology and Hepatology, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Li Zhu
- Department of Pathology and Hepatology, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Jing-Min Zhao
- Medical School of Chinese PLA, Beijing, China; Department of Pathology and Hepatology, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, China.
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2
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Huang XW, Li Y, Jiang LN, Zhao BK, Liu YS, Chen C, Zhao D, Zhang XL, Li ML, Jiang YY, Liu SH, Zhu L, Zhao JM. Comprehensive pan-cancer investigation of carnosine dipeptidase 1 and its prospective prognostic significance in hepatocellular carcinoma. Open Med (Wars) 2024; 19:20240982. [PMID: 38883336 PMCID: PMC11179385 DOI: 10.1515/med-2024-0982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Revised: 05/18/2024] [Accepted: 05/21/2024] [Indexed: 06/18/2024] Open
Abstract
Carnosine dipeptidase 1 (CNDP1), an enzyme integral to the hydrolysis of dipeptides containing histidine, plays an indispensable role in myriad physiological processes, including hydrolysis of proteins, maturation of specific biochemical functionalities within proteins, tissue regeneration, and regulation of cell cycle. However, the implications of CNDP1 in oncogenesis and its prognostic value are not yet fully elucidated. Initially, we procured the GSE40367 dataset from the Gene Expression Omnibus and established a protein-protein interaction network. Thereafter, we conducted functional and pathway enrichment analyses utilizing GO, KEGG, and GSEA. Moreover, we undertook an association analysis concerning the expression of CNDP1 with immune infiltration, along with survival analysis across various cancers and specifically in hepatocellular carcinoma (HCC). Our study uncovered a total of 2,248 differentially expressed genes, with a down-regulation of CNDP1 in HCC and other cancers. Our explorations into the relationship between CNDP1 and immune infiltration disclosed a negative correlation between CNDP1 expression and the presence of immune cells in HCC. Survival analyses revealed that diminished expression of CNDP1 correlates with an adverse prognosis in HCC and several other types of cancer. These observations intimate that CNDP1 holds promise as a novel prognostic biomarker for both pan-cancer and HCC.
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Affiliation(s)
- Xiao-Wen Huang
- Medical School of Chinese PLA, Beijing, China
- Department of Pathology and Hepatology, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, 100039, China
| | - Yan Li
- Department of Pathology and Hepatology, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, 100039, China
| | - Li-Na Jiang
- Department of Pathology and Hepatology, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, 100039, China
| | - Bo-Kang Zhao
- Department of Hepatology, Center of Infectious Diseases and Pathogen Biology, The First Hospital of Jilin University, Changchun, China
| | - Yi-Si Liu
- First Department of Liver Disease Center, Beijing Youan Hospital, Capital Medical University, Beijing, China
| | - Chun Chen
- Senior Department of Hepatology, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, China
| | - Dan Zhao
- Department of Pathology and Hepatology, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, 100039, China
| | - Xue-Li Zhang
- Medical School of Chinese PLA, Beijing, China
- Department of Pathology and Hepatology, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, 100039, China
| | - Mei-Ling Li
- Department of Pathology and Hepatology, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, 100039, China
| | - Yi-Yun Jiang
- Department of Pathology and Hepatology, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, 100039, China
| | - Shu-Hong Liu
- Department of Pathology and Hepatology, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, 100039, China
| | - Li Zhu
- Department of Pathology and Hepatology, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, 100039, China
| | - Jing-Min Zhao
- Medical School of Chinese PLA, Beijing, China
- Department of Pathology and Hepatology, The Fifth Medical Center of Chinese PLA General Hospital, Beijing, 100039, China
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3
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Bowling PE, Dasgupta S, Herbert JM. Eliminating Imaginary Vibrational Frequencies in Quantum-Chemical Cluster Models of Enzymatic Active Sites. J Chem Inf Model 2024; 64:3912-3922. [PMID: 38648614 DOI: 10.1021/acs.jcim.4c00221] [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: 04/25/2024]
Abstract
In constructing finite models of enzyme active sites for quantum-chemical calculations, atoms at the periphery of the model must be constrained to prevent unphysical rearrangements during geometry relaxation. A simple fixed-atom or "coordinate-lock" approach is commonly employed but leads to undesirable artifacts in the form of small imaginary frequencies. These preclude evaluation of finite-temperature free-energy corrections, limiting thermochemical calculations to enthalpies only. Full-dimensional vibrational frequency calculations are possible by replacing the fixed-atom constraints with harmonic confining potentials. Here, we compare that approach to an alternative strategy in which fixed-atom contributions to the Hessian are simply omitted. While the latter strategy does eliminate imaginary frequencies, it tends to underestimate both the zero-point energy and the vibrational entropy while introducing artificial rigidity. Harmonic confining potentials eliminate imaginary frequencies and provide a flexible means to construct active-site models that can be used in unconstrained geometry relaxations, affording better convergence of reaction energies and barrier heights with respect to the model size, as compared to models with fixed-atom constraints.
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Affiliation(s)
- Paige E Bowling
- Biophysics Graduate Program, The Ohio State University, Columbus, Ohio 43210, United States
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Saswata Dasgupta
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
- Department of Chemistry and Biochemistry, University of California-San Diego, La Jolla, California 92093, United States
| | - John M Herbert
- Biophysics Graduate Program, The Ohio State University, Columbus, Ohio 43210, United States
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
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4
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Wappett D, Goerigk L. Benchmarking Density Functional Theory Methods for Metalloenzyme Reactions: The Introduction of the MME55 Set. J Chem Theory Comput 2023; 19:8365-8383. [PMID: 37943578 PMCID: PMC10688432 DOI: 10.1021/acs.jctc.3c00558] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 10/13/2023] [Accepted: 10/16/2023] [Indexed: 11/10/2023]
Abstract
We present a new benchmark set of metalloenzyme model reaction energies and barrier heights that we call MME55. The set contains 10 different enzymes, representing eight transition metals, both open and closed shell systems, and system sizes of up to 116 atoms. We use four DLPNO-CCSD(T)-based approaches to calculate reference values against which we then benchmark the performance of a range of density functional approximations with and without dispersion corrections. Dispersion corrections improve the results across the board, and triple-ζ basis sets provide the best balance of efficiency and accuracy. Jacob's ladder is reproduced for the whole set based on averaged mean absolute (percent) deviations, with the double hybrids SOS0-PBE0-2-D3(BJ) and revDOD-PBEP86-D4 standing out as the most accurate methods for the MME55 set. The range-separated hybrids ωB97M-V and ωB97X-V also perform well here and can be recommended as a reliable compromise between accuracy and efficiency; they have already been shown to be robust across many other types of chemical problems, as well. Despite the popularity of B3LYP in computational enzymology, it is not a strong performer on our benchmark set, and we discourage its use for enzyme energetics.
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Affiliation(s)
- Dominique
A. Wappett
- School of Chemistry, The University
of Melbourne, Melbourne, Victoria 3010, Australia
| | - Lars Goerigk
- School of Chemistry, The University
of Melbourne, Melbourne, Victoria 3010, Australia
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5
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Toviwek B, Suwanasopee T, Koonawootrittriron S, Jattawa D, Pongprayoon P. Binding Modes of Carnostatine, Homocarnosine, and Ophidine to Human Carnosinase 1. ACS OMEGA 2023; 8:42966-42975. [PMID: 38024708 PMCID: PMC10653059 DOI: 10.1021/acsomega.3c06139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 10/13/2023] [Accepted: 10/19/2023] [Indexed: 12/01/2023]
Abstract
Carnosine (CAR), anserine (ANS), homocarnosine (H-CAR), and ophidine (OPH) are histidine-containing dipeptides that show a wide range of therapeutic properties. With their potential physiological effects, these bioactive dipeptides are considered as bioactive food components. However, such dipeptides display low stability due to their rapid degradation by human serum carnosinase 1 (CN1). A dimeric CN1 hydrolyzes such histidine-containing compounds with different degrees of reactivities. A selective CN inhibitor, carnostatine (CARN), was reported to effectively inhibit CN's activity. To date, the binding mechanisms of CAR and ANS have been recently reported, while no clear information about H-CAR, OPH, and CARN binding is available. Thus, in this work, molecular dynamics simulations were employed to elucidate the binding mechanism of H-CAR, OPH, and CARN. Among all, the amine end and imidazole ring are the main players for trapping all of the ligands in a pocket. OPH shows the poorest binding affinity, while CARN displays the tightest binding. Such firm binding is due to the longer amine chain and the additional hydroxyl (-OH) group of CARN. H-CAR and CARN are analogous, but the absence of the -OH moiety in H-CAR significantly enhances its mobility, resulting in the reduction in binding affinity. For OPH which is an ANS analogue, the methylated imidazole ring destroys the OPH-CN1 interaction network at this region, consequentially leading to the poor binding ability. An insight into how CN recognizes and binds its substrates obtained here will be useful for designing an effective strategy to prolong the lifetime of CAR and its analogues after ingestion.
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Affiliation(s)
- Borvornwat Toviwek
- Department
of Chemistry, Faculty of Science, Kasetsart
University, Chatuchak, Bangkok 10900, Thailand
| | - Thanathip Suwanasopee
- Department
of Animal Science, Faculty of Agriculture, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
| | - Skorn Koonawootrittriron
- Department
of Animal Science, Faculty of Agriculture, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
| | - Danai Jattawa
- Department
of Animal Science, Faculty of Agriculture, Kasetsart University, Chatuchak, Bangkok 10900, Thailand
| | - Prapasiri Pongprayoon
- Department
of Chemistry, Faculty of Science, Kasetsart
University, Chatuchak, Bangkok 10900, Thailand
- Center
for Advanced Studies in Nanotechnology for Chemical, Food and Agricultural
Industries, KU Institute for Advanced Studies, Kasetsart University, Bangkok 10900, Thailand
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6
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Serafim LF, Jayasinghe-Arachchige VM, Wang L, Rathee P, Yang J, Moorkkannur N S, Prabhakar R. Distinct chemical factors in hydrolytic reactions catalyzed by metalloenzymes and metal complexes. Chem Commun (Camb) 2023. [PMID: 37366367 DOI: 10.1039/d3cc01380d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/28/2023]
Abstract
The selective hydrolysis of the extremely stable phosphoester, peptide and ester bonds of molecules by bio-inspired metal-based catalysts (metallohydrolases) is required in a wide range of biological, biotechnological and industrial applications. Despite the impressive advances made in the field, the ultimate goal of designing efficient enzyme mimics for these reactions is still elusive. Its realization will require a deeper understanding of the diverse chemical factors that influence the activities of both natural and synthetic catalysts. They include catalyst-substrate complexation, non-covalent interactions and the electronic nature of the metal ion, ligand environment and nucleophile. Based on our computational studies, their roles are discussed for several mono- and binuclear metallohydrolases and their synthetic analogues. Hydrolysis by natural metallohydrolases is found to be promoted by a ligand environment with low basicity, a metal bound water and a heterobinuclear metal center (in binuclear enzymes). Additionally, peptide and phosphoester hydrolysis is dominated by two competing effects, i.e. nucleophilicity and Lewis acid activation, respectively. In synthetic analogues, hydrolysis is facilitated by the inclusion of a second metal center, hydrophobic effects, a biological metal (Zn, Cu and Co) and a terminal hydroxyl nucleophile. Due to the absence of the protein environment, hydrolysis by these small molecules is exclusively influenced by nucleophile activation. The results gleaned from these studies will enhance the understanding of fundamental principles of multiple hydrolytic reactions. They will also advance the development of computational methods as a predictive tool to design more efficient catalysts for hydrolysis, Diels-Alder reaction, Michael addition, epoxide opening and aldol condensation.
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Affiliation(s)
- Leonardo F Serafim
- Department of Chemistry, University of Miami, Coral Gables, FL 33146, USA.
| | | | - Lukun Wang
- Department of Chemistry, University of Miami, Coral Gables, FL 33146, USA.
| | - Parth Rathee
- Department of Chemistry, University of Miami, Coral Gables, FL 33146, USA.
| | - Jiawen Yang
- Department of Chemistry, University of Miami, Coral Gables, FL 33146, USA.
| | | | - Rajeev Prabhakar
- Department of Chemistry, University of Miami, Coral Gables, FL 33146, USA.
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7
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Mechanism for the synthesis of medium-chain 1-alkenes from fatty acids catalyzed by binuclear iron UndA decarboxylase. J Catal 2023. [DOI: 10.1016/j.jcat.2023.02.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/05/2023]
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8
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Tancharoen C, Tovivek B, Niramitranon J, Kityakarn S, Luksirikul P, Gorinstein S, Pongprayoon P. Exploring the structural and dynamic differences between human carnosinase I (CN1) and II (CN2). Proteins 2023; 91:822-830. [PMID: 36637795 DOI: 10.1002/prot.26469] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Revised: 11/06/2022] [Accepted: 01/05/2023] [Indexed: 01/14/2023]
Abstract
Human carnosinases (CNs) are dimeric dipeptidases in the metallopeptidase M20 family. Two isoforms of carnosinases (Zn2+ -containing carnosinase 1 (CN1) found in serum and Mn2+ -carnosinase 2 (CN2) in tissue) were identified. Both CNs cleave histidine-containing (Xaa-His) dipeptides such as carnosine where CN2 was found to accept a broader spectrum of substrates. A loss of CN function, resulting in a high carnosine concentration, reduces risk for diabetes and neurological disorders. Although several studies on CN activities and its Michaelis complex were conducted, all shed the light on CN1 activity where the CN2 data is limited. Also, the molecular details on CN1 and CN2 similarity and dissimilarity in structure and function remain unclear. Thus, in this work, molecular dynamics (MD) simulations were employed to study structure and dynamics of human CN1 and CN2 in comparison. The results show that the different catalytic ability of both CNs is due to their pocket size and environment. CN2 can accept a wider range of substrate due to the wider mouth of a binding pocket. The L1 loop seems to play a role in gating activity. Comparing to CN2, CN1 provides more electronegative entrance, more wettability, and higher stability of catalytic metal ion-pair in the active site which allow more efficient water-mediated catalysis. The microscopic understanding obtained here can serve as a basis for CN inhibition strategies resulting in higher carnosine levels and consequently mitigating complications associated with diseases such as diabetes and neurological disorder.
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Affiliation(s)
| | - Borvornwat Tovivek
- Department of Chemistry, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Jitti Niramitranon
- Department of Computer Engineering, Faculty of Engineering, Kasetsart University, Bangkok, Thailand
| | - Sutasinee Kityakarn
- Department of Chemistry, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | - Patraporn Luksirikul
- Department of Chemistry, Faculty of Science, Kasetsart University, Bangkok, Thailand.,Center for Advanced Studies in Nanotechnology for Chemical, Food and Agricultural Industries, KU Institute for Advanced Studies, Kasetsart University, Bangkok, Thailand
| | - Shela Gorinstein
- Institute for Drug Research, School of Pharmacy, Faculty of Medicine, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Prapasiri Pongprayoon
- Department of Chemistry, Faculty of Science, Kasetsart University, Bangkok, Thailand.,Center for Advanced Studies in Nanotechnology for Chemical, Food and Agricultural Industries, KU Institute for Advanced Studies, Kasetsart University, Bangkok, Thailand
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9
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Toviwek B, Koonawootrittriron S, Suwanasopee T, Pongprayoon P. Molecular insights into the binding of carnosine and anserine to human serum carnosinase 1 (CN1). PEERJ PHYSICAL CHEMISTRY 2022. [DOI: 10.7717/peerj-pchem.25] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Carnosine (CAR) and anserine (ANS) are histidine-containing dipeptides that show the therapeutic properties and protective abilities against diabetes and cognitive deficit. Both dipeptides are rich in meat products and have been used as a supplement. However, in humans, both compounds have a short half-life due to the rapid degradation by dizinc carnosinase 1 (CN1) which is a hurdle for its therapeutic application. To date, a comparative study of carnosine- and anserine-CN1 complexes is limited. Thus, in this work, molecular dynamics (MD) simulations were performed to explore the binding of carnosine and anserine to CN1. CN1 comprises 2 chains (Chains A and B). Both monomers are found to work independently and alternatingly. The displacement of Zn2+ pair is found to disrupt the substrate binding. CN1 employs residues from the neighbour chain (H235, T335, and T337) to form the active site. This highlights the importance of a dimer for enzymatic activity. Anserine is more resistant to CN 1 than carnosine because of its bulky and dehydrated imidazole moiety. Although both dipeptides can direct the peptide oxygen to the active Zn2+ which can facilitate the catalytic reaction, the bulky methylated imidazole on anserine promotes various poses that can retard the hydrolytic activity in contrast to carnosine. Anserine is likely to be the temporary competitive inhibitor by retarding the carnosine catabolism.
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Affiliation(s)
- Borvornwat Toviwek
- Department of Chemistry, Faculty of Science, Kasetsart University, Bangkok, Thailand
| | | | - Thanathip Suwanasopee
- Department of Animal Science, Faculty of Agriculture, Kasetsart University, Bangkok, Thailand
| | - Prapasiri Pongprayoon
- Department of Chemistry, Faculty of Science, Kasetsart University, Bangkok, Thailand
- Center for Advanced Studies in Nanotechnology for Chemical, Food and Agricultural Industries, KU Institute for Advanced Studies, Kasetsart University, Bangkok, Thailand
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10
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Chen Y, Sun L, Ullah I, Beaudoin-Bussières G, Anand SP, Hederman AP, Tolbert WD, Sherburn R, Nguyen DN, Marchitto L, Ding S, Wu D, Luo Y, Gottumukkala S, Moran S, Kumar P, Piszczek G, Mothes W, Ackerman ME, Finzi A, Uchil PD, Gonzalez FJ, Pazgier M. Engineered ACE2-Fc counters murine lethal SARS-CoV-2 infection through direct neutralization and Fc-effector activities. SCIENCE ADVANCES 2022; 8:eabn4188. [PMID: 35857504 PMCID: PMC9278865 DOI: 10.1126/sciadv.abn4188] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 05/27/2022] [Indexed: 05/27/2023]
Abstract
Soluble angiotensin-converting enzyme 2 (ACE2) constitutes an attractive antiviral capable of targeting a wide range of coronaviruses using ACE2 as their receptor. Using structure-guided approaches, we developed a series of bivalent ACE2-Fcs harboring functionally and structurally validated mutations that enhance severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) receptor binding domain recognition by up to ~12-fold and remove angiotensin enzymatic activity. The lead variant M81 potently cross-neutralized SARS-CoV-2 variants of concern (VOCs), including Omicron, at subnanomolar half-maximal inhibitory concentration and was capable of robust Fc-effector functions, including antibody-dependent cellular cytotoxicity, phagocytosis, and complement deposition. When tested in a stringent K18-hACE2 mouse model, Fc-enhanced ACE2-Fc delayed death by 3 to 5 days or effectively resolved lethal SARS-CoV-2 infection in both prophylactic and therapeutic settings via the combined effects of neutralization and Fc-effector functions. These data add to the demonstrated utility of soluble ACE2 as a valuable SARS-CoV-2 antiviral and indicate that Fc-effector functions may constitute an important component of ACE2-Fc therapeutic activity.
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Affiliation(s)
- Yaozong Chen
- Infectious Disease Division, Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD 20814-4712, USA
| | - Lulu Sun
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Irfan Ullah
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Guillaume Beaudoin-Bussières
- Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada
| | - Sai Priya Anand
- Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada
- Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
| | | | - William D. Tolbert
- Infectious Disease Division, Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD 20814-4712, USA
| | - Rebekah Sherburn
- Infectious Disease Division, Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD 20814-4712, USA
| | - Dung N. Nguyen
- Infectious Disease Division, Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD 20814-4712, USA
| | - Lorie Marchitto
- Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada
| | - Shilei Ding
- Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada
| | - Di Wu
- Biophysics Core Facility, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Yuhong Luo
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Suneetha Gottumukkala
- Infectious Disease Division, Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD 20814-4712, USA
| | - Sean Moran
- Biomedical Instrumentation Center, Uniformed Services University of the Health Sciences, 4301 Jones Bridge Road, Bethesda, MD 20814, USA
| | - Priti Kumar
- Section of Infectious Diseases, Department of Internal Medicine, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Grzegorz Piszczek
- Biophysics Core Facility, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Walther Mothes
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06510, USA
| | | | - Andrés Finzi
- Centre de Recherche du CHUM, Montreal, QC H2X 0A9, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada
- Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
| | - Pradeep D. Uchil
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Frank J. Gonzalez
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Marzena Pazgier
- Infectious Disease Division, Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD 20814-4712, USA
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11
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Serafim LF, Jayasinghe-Arachchige VM, Wang L, Prabhakar R. Promiscuous Catalytic Activity of a Binuclear Metallohydrolase: Peptide and Phosphoester Hydrolyses. J Chem Inf Model 2022; 62:2466-2480. [PMID: 35451306 DOI: 10.1021/acs.jcim.2c00214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this study, chemical promiscuity of a binuclear metallohydrolase Streptomyces griseus aminopeptidase (SgAP) has been investigated using DFT calculations. SgAP catalyzes two diverse reactions, peptide and phosphoester hydrolyses, using its binuclear (Zn-Zn) core. On the basis of the experimental information, mechanisms of these reactions have been investigated utilizing leucine p-nitro aniline (Leu-pNA) and bis(4-nitrophenyl) phosphate (BNPP) as the substrates. The computed barriers of 16.5 and 16.8 kcal/mol for the most plausible mechanisms proposed by the DFT calculations are in good agreement with the measured values of 13.9 and 18.3 kcal/mol for the Leu-pNA and BNPP hydrolyses, respectively. The former was found to occur through the transfer of two protons, while the latter with only one proton transfer. They are in line with the experimental observations. The cleavage of the peptide bond was the rate-determining process for the Leu-pNA hydrolysis. However, the creation of the nucleophile and its attack on the electrophile phosphorus atom was the rate-determining step for the BNPP hydrolysis. These calculations showed that the chemical nature of the substrate and its binding mode influence the nucleophilicity of the metal bound hydroxyl nucleophile. Additionally, the nucleophilicity was found to be critical for the Leu-pNA hydrolysis, whereas double Lewis acid activation was needed for the BNPP hydrolysis. That could be one of the reasons why peptide hydrolysis can be catalyzed by both mononuclear and binuclear metal cofactors containing hydrolases, while phosphoester hydrolysis is almost exclusively by binuclear metallohydrolases. These results will be helpful in the development of versatile catalysts for chemically distinct hydrolytic reactions.
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Affiliation(s)
- Leonardo F Serafim
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
| | | | - Lukun Wang
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
| | - Rajeev Prabhakar
- Department of Chemistry, University of Miami, Coral Gables, Florida 33146, United States
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12
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Bím D, Navrátil M, Gutten O, Konvalinka J, Kutil Z, Culka M, Navrátil V, Alexandrova AN, Bařinka C, Rulíšek L. Predicting Effects of Site-Directed Mutagenesis on Enzyme Kinetics by QM/MM and QM Calculations: A Case of Glutamate Carboxypeptidase II. J Phys Chem B 2022; 126:132-143. [PMID: 34978450 DOI: 10.1021/acs.jpcb.1c09240] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Quantum and molecular mechanics (QM/MM) and QM-only (cluster model) modeling techniques represent the two workhorses in mechanistic understanding of enzyme catalysis. One of the stringent tests for QM/MM and/or QM approaches is to provide quantitative answers to real-world biochemical questions, such as the effect of single-point mutations on enzyme kinetics. This translates into predicting the relative activation energies to 1-2 kcal·mol-1 accuracy; such predictions can be used for the rational design of novel enzyme variants with desired/improved characteristics. Herein, we employ glutamate carboxypeptidase II (GCPII), a dizinc metallopeptidase, also known as the prostate specific membrane antigen, as a model system. The structure and activity of this major cancer antigen have been thoroughly studied, both experimentally and computationally, which makes it an ideal model system for method development. Its reaction mechanism is quite well understood: the reaction coordinate comprises a "tetrahedral intermediate" and two transition states and experimental activation Gibbs free energy of ∼17.5 kcal·mol-1 can be inferred for the known kcat ≈ 1 s-1. We correlate experimental kinetic data (including the E424H variant, newly characterized in this work) for various GCPII mutants (kcat = 8.6 × 10-5 s-1 to 2.7 s-1) with the energy profiles calculated by QM/MM and QM-only (cluster model) approaches. We show that the near-quantitative agreement between the experimental values and the calculated activation energies (ΔH⧧) can be obtained and recommend the combination of the two protocols: QM/MM optimized structures and cluster model (QM) energetics. The trend in relative activation energies is mostly independent of the QM method (DFT functional) used. Last but not least, a satisfactory correlation between experimental and theoretical data allows us to provide qualitative and fairly simple explanations of the observed kinetic effects which are thus based on a rigorous footing.
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Affiliation(s)
- Daniel Bím
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, 166 10 Praha 6, Czech Republic.,Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569, United States
| | - Michal Navrátil
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, 166 10 Praha 6, Czech Republic
| | - Ondrej Gutten
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, 166 10 Praha 6, Czech Republic
| | - Jan Konvalinka
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, 166 10 Praha 6, Czech Republic.,Department of Biochemistry, Faculty of Science, Charles University, Hlavova 2030, 2120 00 Prague, Czech Republic
| | - Zsófia Kutil
- Institute of Biotechnology of the Czech Academy of Sciences, Průmyslová 595, 252 50 Vestec, Czech Republic
| | - Martin Culka
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, 166 10 Praha 6, Czech Republic
| | - Václav Navrátil
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, 166 10 Praha 6, Czech Republic
| | - Anastassia N Alexandrova
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095-1569, United States
| | - Cyril Bařinka
- Institute of Biotechnology of the Czech Academy of Sciences, Průmyslová 595, 252 50 Vestec, Czech Republic
| | - Lubomír Rulíšek
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 2, 166 10 Praha 6, Czech Republic
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13
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Chen Y, Sun L, Ullah I, Beaudoin-Bussières G, Anand SP, Hederman AP, Tolbert WD, Sherburn R, Nguyen DN, Marchitto L, Ding S, Wu D, Luo Y, Gottumukkala S, Moran S, Kumar P, Piszczek G, Mothes W, Ackerman ME, Finzi A, Uchil PD, Gonzalez FJ, Pazgier M. Engineered ACE2-Fc counters murine lethal SARS-CoV-2 infection through direct neutralization and Fc-effector activities. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021:2021.11.24.469776. [PMID: 34845451 PMCID: PMC8629194 DOI: 10.1101/2021.11.24.469776] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Soluble Angiotensin-Converting Enzyme 2 (ACE2) constitutes an attractive antiviral capable of targeting a wide range of coronaviruses utilizing ACE2 as their receptor. Here, using structure-guided approaches, we developed divalent ACE2 molecules by grafting the extracellular ACE2-domain onto a human IgG1 or IgG3 (ACE2-Fc). These ACE2-Fcs harbor structurally validated mutations that enhance spike (S) binding and remove angiotensin enzymatic activity. The lead variant bound tightly to S, mediated in vitro neutralization of SARS-CoV-2 variants of concern (VOCs) with sub-nanomolar IC 50 and was capable of robust Fc-effector functions, including antibody-dependent-cellular cytotoxicity, phagocytosis and complement deposition. When tested in a stringent K18-hACE2 mouse model, it delayed death or effectively resolved lethal SARS-CoV-2 infection in a prophylactic or therapeutic setting utilizing the combined effect of neutralization and Fc-effector functions. These data confirm the utility of ACE2-Fcs as valuable agents in preventing and eliminating SARS-CoV-2 infection and demonstrate that ACE2-Fc therapeutic activity require Fc-effector functions.
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Affiliation(s)
- Yaozong Chen
- Infectious Disease Division, Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD 20814-4712, USA
- equal contribution
| | - Lulu Sun
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland, USA
- equal contribution
| | - Irfan Ullah
- Department of Internal Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT 06520, USA
- equal contribution
| | - Guillaume Beaudoin-Bussières
- Centre de recherche du CHUM. Montreal, QC H2X 0A9, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada
| | - Sai Priya Anand
- Centre de recherche du CHUM. Montreal, QC H2X 0A9, Canada
- Department of Microbiology and Immunology, McGill, QC, Canada
| | | | - William D. Tolbert
- Infectious Disease Division, Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD 20814-4712, USA
| | - Rebekah Sherburn
- Infectious Disease Division, Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD 20814-4712, USA
| | - Dung N. Nguyen
- Infectious Disease Division, Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD 20814-4712, USA
| | - Lorie Marchitto
- Centre de recherche du CHUM. Montreal, QC H2X 0A9, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada
| | - Shilei Ding
- Centre de recherche du CHUM. Montreal, QC H2X 0A9, Canada
| | - Di Wu
- Biophysics Core Facility, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, 20892
| | - Yuhong Luo
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - Suneetha Gottumukkala
- Infectious Disease Division, Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD 20814-4712, USA
| | - Sean Moran
- Biomedical Instrumentation Center, Uniformed Services University of the Health Sciences, 4301 Jones Bridge Road, Bethesda, MD, 20814, USA
| | - Priti Kumar
- Department of Internal Medicine, Section of Infectious Diseases, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Grzegorz Piszczek
- Biophysics Core Facility, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland, 20892
| | - Walther Mothes
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06510, USA
| | | | - Andrés Finzi
- Centre de recherche du CHUM. Montreal, QC H2X 0A9, Canada
- Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montreal, QC H2X 0A9, Canada
- Department of Microbiology and Immunology, McGill, QC, Canada
| | - Pradeep D. Uchil
- Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Frank J. Gonzalez
- Laboratory of Metabolism, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, Maryland, USA
| | - Marzena Pazgier
- Infectious Disease Division, Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, MD 20814-4712, USA
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14
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Su JX, Chen SL. A Key Piece in the Global N-Cycle: The N–N Bond Formation Presented by Heme-Dependent Hydrazine Synthase. ACS Catal 2021. [DOI: 10.1021/acscatal.1c01502] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Jing-Xuan Su
- Key Laboratory of Cluster Science of Ministry of Education, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China
| | - Shi-Lu Chen
- Key Laboratory of Cluster Science of Ministry of Education, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing 100081, China
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15
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Jiao Y, Hong J, Chen Y, Zhang Y, Guo Z, Han Z, He W. A novel binuclear Pd(ii) complex displaying synergic peptide cleavage behaviour. Dalton Trans 2020; 49:3164-3173. [PMID: 32095803 DOI: 10.1039/d0dt00130a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Mononuclear Pd(ii) complexes with two leaving groups are able to promote His-, Cys- and Met-orientated peptide hydrolysis, and exploring the peptide cleavage behavior of a novel Pd(ii) complex may provide "Omics" studies a promising artificial protease. In this study, a novel binuclear Pd(ii) complex [Pd2(μ-O-L-H)(μ-Cl)](ClO4)2 (L = 2,6-bis(N-2'-aminoethylaminomethyl)-p-cresol) was constructed to promote peptide hydrolysis. Although each Pd(ii) center has only one leaving group (Cl) in this complex, electrophoresis and LC-MS-MS determination discloses that this complex enables myoglobin cleavage on the second upstream peptide bond from His and Met. A study on peptide cleavage also confirms the His- and Met-orientated peptide hydrolysis, yet no Cys-orientated hydrolysis was observed, although the cysteine-induced peptide/complex binding is distinct. Cysteine in the peptide even prevents the complex from promoting His-orientated hydrolysis, whereas the oxidized cysteine residue recovers the His-orientated hydrolysis. This peptide cleavage behavior is quite different from the simultaneous His-, Cys-, and Met-orientated hydrolysis promoted by the mononuclear Pd(ii) complexes. A theoretical study suggests that the two Pd(ii) centers of this complex might promote His- and Met-orientated hydrolysis in a synergic manner: one Pd(ii) center binds selectively on peptides or proteins and the other coordinates with the amide bond and water favoring nucleophilic attack on the peptide bond. The thiol group of cysteine is inclined to bridge the two Pd(ii) centers to form a "closed" sulphur-bridged structure, disfavoring the Cys-orientated hydrolysis. This study not only demonstrates the peptide cleavage behavior of this binuclear Pd(ii) complex, but also provides a polynuclear strategy to regulate the peptide cleavage behavior of Pd(ii) complexes.
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Affiliation(s)
- Yang Jiao
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China.
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16
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Dasgupta S, Herbert JM. Using Atomic Confining Potentials for Geometry Optimization and Vibrational Frequency Calculations in Quantum-Chemical Models of Enzyme Active Sites. J Phys Chem B 2020; 124:1137-1147. [PMID: 31986049 DOI: 10.1021/acs.jpcb.9b11060] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Quantum-chemical studies of enzymatic reaction mechanisms sometimes use truncated active-site models as simplified alternatives to mixed quantum mechanics molecular mechanics (QM/MM) procedures. Eliminating the MM degrees of freedom reduces the complexity of the sampling problem, but the trade-off is the need to introduce geometric constraints in order to prevent structural collapse of the model system during geometry optimizations that do not contain a full protein backbone. These constraints may impair the efficiency of the optimization, and care must be taken to avoid artifacts such as imaginary vibrational frequencies. We introduce a simple alternative in which terminal atoms of the model system are placed in soft harmonic confining potentials rather than being rigidly constrained. This modification is simple to implement and straightforward to use in vibrational frequency calculations, unlike iterative constraint-satisfaction algorithms, and allows the optimization to proceed without constraint even though the practical result is to fix the anchor atoms in space. The new approach is more efficient for optimizing minima and transition states, as compared to the use of fixed-atom constraints, and also more robust against unwanted imaginary frequencies. We illustrate the method by application to several enzymatic reaction pathways where entropy makes a significant contribution to the relevant reaction barriers. The use of confining potentials correctly describes reaction paths and facilitates calculation of both vibrational zero-point and finite-temperature entropic corrections to barrier heights.
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Affiliation(s)
- Saswata Dasgupta
- Department of Chemistry and Biochemistry , The Ohio State University , Columbus , Ohio 43210 , United States
| | - John M Herbert
- Department of Chemistry and Biochemistry , The Ohio State University , Columbus , Ohio 43210 , United States
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17
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Bhat SY, Qureshi IA. Mutations of key substrate binding residues of leishmanial peptidase T alter its functional and structural dynamics. Biochim Biophys Acta Gen Subj 2020; 1864:129465. [DOI: 10.1016/j.bbagen.2019.129465] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2019] [Revised: 10/15/2019] [Accepted: 10/24/2019] [Indexed: 11/27/2022]
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18
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Yu MJ, Wu J, Chen SL. Mechanism and Inhibitor Exploration with Binuclear Mg Ketol-Acid Reductoisomerase: Targeting the Biosynthetic Pathway of Branched-Chain Amino Acids. Chembiochem 2019; 21:381-391. [PMID: 31309701 DOI: 10.1002/cbic.201900363] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Indexed: 01/01/2023]
Abstract
Binuclear Mg ketol-acid reductoisomerase (KARI), which converts (S)-2-acetolactate into (R)-2,3-dihydroxyisovalerate, is responsible for the second step of the biosynthesis of branched-chain amino acids in plants and microorganisms and thus serves as a key inhibition target potentially without effects on mammals. Here, through the use of density functional calculations and a chemical model, the KARI-catalyzed reaction has been demonstrated to include the initial deprotonation of the substrate C2 hydroxy group, bridged by the two Mg ions, alkyl migration from the C2-alkoxide carbon atom to the C3-carbonyl carbon atom, and hydride transfer from a nicotinamide adenine dinucleotide phosphate [NAD(P)H] cofactor to C2. A dead-end mechanism with a hydride transferred to the C3 carbonyl group has been ruled out. The nucleophilicity (migratory aptitude) of the migrating carbon atom and the provision of additional negative charge to the di-Mg coordination sphere have significant effects on the steps of alkyl migration and hydride transfer, respectively. Other important mechanistic characteristics are also revealed. Inspired by the mechanism, an inhibitor (2-carboxylate-lactic acid) was designed and predicted by barrier analysis to be effective in inactivating KARI, hence probably enriching the antifungal and antibacterial library. Two types of slow substrate analogues (2-trihalomethyl acetolactic acids and 2-glutaryl lactic acid) were also found.
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Affiliation(s)
- Ming-Jia Yu
- Key Laboratory of Cluster Science of the Ministry of Education, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, P. R. China
| | - Jue Wu
- Key Laboratory of Cluster Science of the Ministry of Education, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, P. R. China
| | - Shi-Lu Chen
- Key Laboratory of Cluster Science of the Ministry of Education, School of Chemistry and Chemical Engineering, Beijing Institute of Technology, Beijing, 100081, P. R. China
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19
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Sun SQ, Chen SL. How does Mo-dependent perchlorate reductase work in the decomposition of oxyanions? Dalton Trans 2019; 48:5683-5691. [DOI: 10.1039/c9dt00863b] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The mechanisms of Mo-dependent perchlorate reductase (PcrAB)-catalyzed decomposition of perchlorate, bromate, iodate, and nitrate were revealed by density functional calculations.
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Affiliation(s)
- Shuo-Qi Sun
- Key Laboratory of Cluster Science of Ministry of Education
- School of Chemistry and Chemical Engineering
- Beijing Institute of Technology
- Beijing 100081
- China
| | - Shi-Lu Chen
- Key Laboratory of Cluster Science of Ministry of Education
- School of Chemistry and Chemical Engineering
- Beijing Institute of Technology
- Beijing 100081
- China
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20
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Invergo AM, Liu S, Dicken RD, Mouat AR, Delferro M, Lohr TL, Marks TJ. How Close Is Too Close? Polymerization Behavior and Monomer-Dependent Reorganization of a Bimetallic Salphen Organotitanium Catalyst. Organometallics 2018. [DOI: 10.1021/acs.organomet.8b00220] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Anna M. Invergo
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Shaofeng Liu
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Rachel D. Dicken
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Aidan R. Mouat
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Massimiliano Delferro
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Tracy L. Lohr
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
| | - Tobin J. Marks
- Department of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208, United States
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21
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How does binuclear zinc amidohydrolase FwdA work in the initial step of methanogenesis: From formate to formyl-methanofuran. J Inorg Biochem 2018; 185:71-79. [PMID: 29778928 DOI: 10.1016/j.jinorgbio.2018.05.004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 05/05/2018] [Accepted: 05/08/2018] [Indexed: 11/22/2022]
Abstract
The initial step of methanogenesis is the fixation of CO2 to formyl-methanofuran (formyl-MFR) catalyzed by formyl-MFR dehydrogenase, which can be divided into two half reactions. Herein, the second half reaction catalyzed by FwdA (formyl-methanofuran dehydrogenase subunit A), i.e., from formate to formyl-methanofuran, has been investigated using density functional theory and a chemical model based on the X-ray crystal structure. The calculations indicate that, compared with other well-known di-zinc hydrolases, the FwdA reaction employs a reverse mechanism, including the nucleophilic attack of MFR amine on formate carbon leading to a tetrahedral gem-diolate intermediate, two steps of proton transfer from amine to formate moieties assisted by the Asp385, and the CO bond dissociation to form the formyl-MFR product. The second step of proton transfer from the amine moiety to the Asp385 is rate-limiting with an overall barrier of 21.2 kcal/mol. The two zinc ions play an important role in stabilizing the transition states and intermediates, in particular the negative charge at the formate moiety originated from the nucleophilic attack of the MFR amine. The work here appends a crucial piece in the methanogenic mechanistics and advances the understanding of the global carbon cycle.
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23
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Bozkurt E, Soares TA, Rothlisberger U. Can Biomimetic Zinc Compounds Assist a (3 + 2) Cycloaddition Reaction? A Theoretical Perspective. J Chem Theory Comput 2017; 13:6382-6390. [DOI: 10.1021/acs.jctc.7b00819] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Esra Bozkurt
- Laboratory
of Computational Chemistry and Biochemistry LCBC, ISIC, FSB BSP, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Thereza A. Soares
- Laboratory
of Computational Chemistry and Biochemistry LCBC, ISIC, FSB BSP, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
- Department
of Fundamental Chemistry, Federal University of Pernambuco, Recife 50740-560, Brazil
| | - Ursula Rothlisberger
- Laboratory
of Computational Chemistry and Biochemistry LCBC, ISIC, FSB BSP, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
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24
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Liu S, Invergo AM, McInnis JP, Mouat AR, Motta A, Lohr TL, Delferro M, Marks TJ. Distinctive Stereochemically Linked Cooperative Effects in Bimetallic Titanium Olefin Polymerization Catalysts. Organometallics 2017. [DOI: 10.1021/acs.organomet.7b00641] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Shaofeng Liu
- Department
of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
| | - Anna M. Invergo
- Department
of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
| | - Jennifer P. McInnis
- Department
of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
| | - Aidan R. Mouat
- Department
of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
| | - Alessandro Motta
- Dipartimento
di Scienze Chimiche, Università di Roma “La Sapienza” and INSTM, UdR Roma, Piazzale Aldo Moro 5, I-00185 Roma, Italy
| | - Tracy L. Lohr
- Department
of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
| | - Massimiliano Delferro
- Department
of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
| | - Tobin J. Marks
- Department
of Chemistry, Northwestern University, 2145 Sheridan Road, Evanston, Illinois 60208-3113, United States
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26
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Liu R, Qiu L, Cheng Q, Zhang H, Wang L, Song L. Evidence for Cleavage of the Metalloprotease Vsm from Vibrio splendidus Strain JZ6 by an M20 Peptidase (PepT-like Protein) at Low Temperature. Front Microbiol 2016; 7:1684. [PMID: 27826294 PMCID: PMC5078317 DOI: 10.3389/fmicb.2016.01684] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 10/07/2016] [Indexed: 11/13/2022] Open
Abstract
Metalloprotease Vsm is a major extracellular virulence factor of Vibrio splendidus. The toxicity of Vsm from V. splendidus strain JZ6 has been characterized, and production of this virulence factor proved to be temperature-regulated. The present study provides evidence that two forms (JZE1 and JZE2) of Vsm protein exist in extracellular products (ECPs) of strain JZ6, and a significant conversion of these two forms was detected by SDS-PAGE and immunoblotting analyses of samples obtained from cells grown at 4, 10, 16, 20, 24, and 28°C. Mass spectroscopy confirmed that JZE1 was composed only of the peptidase_M4 domain of Vsm, and JZE2 contained both the PepSY domain and the peptidase_M4 domain. An M20 peptidase T-like protein (PepTL) was screened from the transcriptome data of strain JZ6, which was considered as a crucial molecule to produce the active Vsm (JZE1) by cleavage of the propeptide. Similar to that of Vsm, PepTL mRNA accumulation was highest at 4°C (836.82-fold of that at 28°C), decreased with increasing of temperature and reached its lowest level at 28°C. Deletion of the gene encoding the PepTL resulted in a mutant strain that did not produce the JZE1 cleavage product. The peptidase activity of PepTL recombinant protein (rPepTL) was confirmed by cleaving the Vsm in ECPs with an in vitro degradation reaction. These results demonstrate that PepTL participates in activating Vsm in strain JZ6 by proteolytic cleavage at low temperature.
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Affiliation(s)
- Rui Liu
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences Qingdao, China
| | - Limei Qiu
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences Qingdao, China
| | - Qi Cheng
- School of Food Science and Technology, Dalian Polytechnic University Dalian, China
| | - Huan Zhang
- Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences Qingdao, China
| | - Lingling Wang
- Key Laboratory of Mariculture and Stock Enhancement in North China's Sea, Ministry of Agriculture, Dalian Ocean University Dalian, China
| | - Linsheng Song
- Key Laboratory of Mariculture and Stock Enhancement in North China's Sea, Ministry of Agriculture, Dalian Ocean University Dalian, China
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27
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What roles do the residue Asp229 and the coordination variation of calcium play of the reaction mechanism of the diisopropyl-fluorophosphatase? A DFT investigation. Theor Chem Acc 2016. [DOI: 10.1007/s00214-016-1896-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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28
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Paul TJ, Barman A, Ozbil M, Bora RP, Zhang T, Sharma G, Hoffmann Z, Prabhakar R. Mechanisms of peptide hydrolysis by aspartyl and metalloproteases. Phys Chem Chem Phys 2016; 18:24790-24801. [DOI: 10.1039/c6cp02097f] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Peptide hydrolysis has been involved in a wide range of biological, biotechnological, and industrial applications.
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Affiliation(s)
- Thomas J. Paul
- Department of Chemistry
- University of Miami
- Coral Gables
- USA
| | - Arghya Barman
- Department of Chemistry
- University of Miami
- Coral Gables
- USA
| | - Mehmet Ozbil
- Department of Chemistry
- University of Miami
- Coral Gables
- USA
| | | | - Tingting Zhang
- Department of Chemistry
- University of Miami
- Coral Gables
- USA
| | - Gaurav Sharma
- Department of Chemistry
- University of Miami
- Coral Gables
- USA
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29
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Guo N, Zhong JY, Chen SL, Liu JQ, Min Q, Shi RX. Experimental and theoretical studies of hydrolysis of nerve agent sarin by binuclear zinc biomimetic catalysts. Chem Phys 2015. [DOI: 10.1016/j.chemphys.2015.05.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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30
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Zhang HM, Chen SL. Include Dispersion in Quantum Chemical Modeling of Enzymatic Reactions: The Case of Isoaspartyl Dipeptidase. J Chem Theory Comput 2015; 11:2525-35. [DOI: 10.1021/acs.jctc.5b00246] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hai-Mei Zhang
- Key Laboratory
of Cluster
Science of Ministry of Education, Beijing Key Laboratory of Photoelectronic/Electrophotonic
Conversion Materials, School of Chemistry, Beijing Institute of Technology, Beijing 100081, China
| | - Shi-Lu Chen
- Key Laboratory
of Cluster
Science of Ministry of Education, Beijing Key Laboratory of Photoelectronic/Electrophotonic
Conversion Materials, School of Chemistry, Beijing Institute of Technology, Beijing 100081, China
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31
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Brás NF, Fernandes PA, Ramos MJ. QM/MM Study and MD Simulations on the Hypertension Regulator Angiotensin-Converting Enzyme. ACS Catal 2014. [DOI: 10.1021/cs500093h] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Natércia F. Brás
- REQUIMTE,
Departamento de
Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Pedro A. Fernandes
- REQUIMTE,
Departamento de
Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
| | - Maria J. Ramos
- REQUIMTE,
Departamento de
Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre s/n, 4169-007 Porto, Portugal
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32
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Chen SL, Liao RZ. Phosphate monoester hydrolysis by trinuclear alkaline phosphatase; DFT study of transition States and reaction mechanism. Chemphyschem 2014; 15:2321-30. [PMID: 24683174 DOI: 10.1002/cphc.201402016] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2014] [Revised: 02/25/2014] [Indexed: 12/23/2022]
Abstract
Alkaline phosphatase (AP) is a trinuclear metalloenzyme that catalyzes the hydrolysis of a broad range of phosphate monoesters to form inorganic phosphate and alcohol (or phenol). In this paper, by using density functional theory with a model based on a crystal structure, the AP-catalyzed hydrolysis of phosphate monoesters is investigated by calculating two substrates, that is, methyl and p-nitrophenyl phosphates, which represent alkyl and aryl phosphates, respectively. The calculations confirm that the AP reaction employs a "ping-pong" mechanism involving two chemical displacement steps, that is, the displacement of the substrate leaving group by a Ser102 alkoxide and the hydrolysis of the phosphoseryl intermediate by a Zn2-bound hydroxide. Both displacement steps proceed via a concerted associative pathway no matter which substrate is used. Other mechanistic aspects are also studied. Comparison of our calculations with linear free energy relationships experiments shows good agreement.
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Affiliation(s)
- Shi-Lu Chen
- Key Laboratory of Cluster Science of Ministry of Education, Beijing Key Laboratory of Photoelectronic/Electrophotonic, Conversion Materials, School of Chemistry, Beijing Institute of Technology, Beijing 100081 (China), Fax: (+86) 01-6891-1354.
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33
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Gao X, Liu Z, Cui W, Zhou L, Tian Y, Zhou Z. Enhanced thermal stability and hydrolytic ability of Bacillus subtilis aminopeptidase by removing the thermal sensitive domain in the non-catalytic region. PLoS One 2014; 9:e92357. [PMID: 24633010 PMCID: PMC3954873 DOI: 10.1371/journal.pone.0092357] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Accepted: 02/20/2014] [Indexed: 11/18/2022] Open
Abstract
Besides the catalytic ability, many enzymes contain conserved domains to perform some other physiological functions. However, sometimes these conserved domains were unnecessary or even detrimental to the catalytic process for industrial application of the enzymes. In this study, based on homology modeling and molecular dynamics simulations, we found that Bacillus subtilis aminopeptidase contained a thermal sensitive domain (protease-associated domain) in the non-catalytic region, and predicted that deletion of this flexible domain can enhance the structure stability. This prediction was then verified by the deletion of protease-associated domain from the wild-type enzyme. The thermal stability analysis showed that deletion of this domain improved the T50 (the temperature required to reduce initial activity by 50% in 30 min) of the enzyme from 71 °C to 77 °C. The melting temperature (Tm) of the enzyme also increased, which was measured by thermal denaturation experiments using circular dichroism spectroscopy. Further studies indicated that this deletion did not affect the activity and specificity of the enzyme toward aminoacyl-p-nitroanilines, but improved its hydrolytic ability toward a 12-aa-long peptide (LKRLKRFLKRLK) and soybean protein. These findings suggested the possibility of a simple technique for enzyme modification and the artificial enzyme obtained here was more suitable for the protein hydrolysis in food industry than the wild-type enzyme.
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Affiliation(s)
- Xinxing Gao
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Zhongmei Liu
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Wenjing Cui
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Li Zhou
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Yaping Tian
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
| | - Zhemin Zhou
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, Jiangsu, China
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34
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35
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Bellia F, Vecchio G, Rizzarelli E. Carnosinases, their substrates and diseases. Molecules 2014; 19:2299-329. [PMID: 24566305 PMCID: PMC6271292 DOI: 10.3390/molecules19022299] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Revised: 01/07/2014] [Accepted: 01/28/2014] [Indexed: 02/08/2023] Open
Abstract
Carnosinases are Xaa-His dipeptidases that play diverse functions throughout all kingdoms of life. Human isoforms of carnosinase (CN1 and CN2) under appropriate conditions catalyze the hydrolysis of the dipeptides carnosine (β-alanyl-l-histidine) and homocarnosine (γ-aminobutyryl-l-histidine). Alterations of serum carnosinase (CN1) activity has been associated with several pathological conditions, such as neurological disorders, chronic diseases and cancer. For this reason the use of carnosinase levels as a biomarker in cerebrospinal fluid (CSF) has been questioned. The hydrolysis of imidazole-related dipeptides in prokaryotes and eukaryotes is also catalyzed by aminoacyl-histidine dipeptidases like PepD (EC 3.4.13.3), PepV (EC 3.4.13.19) and anserinase (EC 3.4.13.5). The review deals with the structure and function of this class of enzymes in physiological and pathological conditions. The main substrates of these enzymes, i.e., carnosine, homocarnosine and anserine (β-alanyl-3-methyl-l-histidine) will also be described.
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Affiliation(s)
- Francesco Bellia
- Institute of Biostructure and Bioimaging, CNR, viale A. Doria 6, 95125 Catania, Italy.
| | - Graziella Vecchio
- Department of Chemical Sciences, University of Catania, viale A. Doria 6, 95125 Catania, Italy.
| | - Enrico Rizzarelli
- Institute of Biostructure and Bioimaging, CNR, viale A. Doria 6, 95125 Catania, Italy.
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36
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Blomberg MRA, Borowski T, Himo F, Liao RZ, Siegbahn PEM. Quantum chemical studies of mechanisms for metalloenzymes. Chem Rev 2014; 114:3601-58. [PMID: 24410477 DOI: 10.1021/cr400388t] [Citation(s) in RCA: 436] [Impact Index Per Article: 43.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Margareta R A Blomberg
- Department of Organic Chemistry, Arrhenius Laboratory, Stockholm University , SE-106 91 Stockholm, Sweden
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37
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Navrátil V, Klusák V, Rulíšek L. Theoretical Aspects of Hydrolysis of Peptide Bonds by Zinc Metalloenzymes. Chemistry 2013; 19:16634-45. [DOI: 10.1002/chem.201302663] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2013] [Revised: 08/08/2013] [Indexed: 12/11/2022]
Affiliation(s)
- Václav Navrátil
- Institute of Organic Chemistry and Biochemistry, Gilead Sciences & IOCB Research Center, Academy of Sciences of the Czech Republic, Flemingovo náměstí 2, 166 10 Praha 6 (Czech Republic)
- Charles University in Prague, Faculty of Science, Department of Biochemistry, Hlavova 2030, 128 43 Praha 2 (Czech Republic)
| | - Vojtěch Klusák
- Institute of Organic Chemistry and Biochemistry, Gilead Sciences & IOCB Research Center, Academy of Sciences of the Czech Republic, Flemingovo náměstí 2, 166 10 Praha 6 (Czech Republic)
| | - Lubomír Rulíšek
- Institute of Organic Chemistry and Biochemistry, Gilead Sciences & IOCB Research Center, Academy of Sciences of the Czech Republic, Flemingovo náměstí 2, 166 10 Praha 6 (Czech Republic)
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38
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Sun S, Li ZS, Chen SL. A dominant homolytic O-Cl bond cleavage with low-spin triplet-state Fe(IV)=O formed is revealed in the mechanism of heme-dependent chlorite dismutase. Dalton Trans 2013; 43:973-81. [PMID: 24162174 DOI: 10.1039/c3dt52171k] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Chlorite dismutase (Cld) is a heme-dependent enzyme that catalyzes the decomposition of toxic chlorite (ClO2(-)) into innocuous chloride and O2. In this paper, using the hybrid B3LYP density functional theory (DFT) method including dispersion interactions, the Cld reaction mechanism has been studied with a chemical model constructed on the X-ray crystal structure. The calculations indicate that the reaction proceeds along a stepwise pathway in the doublet state, i.e. a homolytic O-Cl bond cleavage of the substrate leading to an O-Fe(heme) species and a ClO˙ radical, followed by a rebinding O-O bond formation between them. The O-Fe(heme) species is demonstrated to be a low-spin triplet-state Fe(IV)=O diradicaloid. A low-spin singlet-state Fe(IV)=O is much less stable than the former, with an energy difference of 9.2 kcal mol(-1). The O-Cl bond cleavage is rate-limiting with a barrier of 10.6 kcal mol(-1), in good agreement with the experimental reaction rate of 2.0 × 10(5) s(-1). Furthermore, a heterolytic O-Cl bond dissociation in the initial step is shown to be unreachable, which ensures the high efficiency of the Cld enzyme by avoiding the generation of chlorate byproduct observed in the reactions of synthetic Fe porphyrins. Also, the pathways in the quartet and sextet states are unfavorable for the Cld reaction. The present results reveal a detailed mechanism III (defined in the text) including an interesting di-radical intermediate composed of a low-spin triplet-state Fe(IV)=O and a ClO˙ radical. Compared to a competitive heterolytic Cl-O cleavage in synthetic Fe porphyrins, the revelation of the domination of homolysis in Cld indicates not only the high efficiency of enzyme, but also the sensitivity of a heme and the significance of the enzymatic active-site surroundings (the His170 and Arg183 residues in the present case), which gives more insights into heme chemistry.
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Affiliation(s)
- Shuo Sun
- Key Laboratory of Cluster Science of Ministry of Education, School of Chemistry, Beijing Institute of Technology, Beijing 100081, China.
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39
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Gao X, Cui W, Ding N, Liu Z, Tian Y, Zhou Z. Structure-based approach to alter the substrate specificity of Bacillus subtilis aminopeptidase. Prion 2013; 7:328-34. [PMID: 23787698 DOI: 10.4161/pri.25147] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Aminopeptidases can selectively catalyze the cleavage of the N-terminal amino acid residues from peptides and proteins. Bacillus subtilis aminopeptidase (BSAP) is most active toward p-nitroanilides (pNAs) derivatives of Leu, Arg, and Lys. The BSAP with broad substrate specificity is expected to improve its application. Based on an analysis of the predicted structure of BSAP, four residues (Leu 370, Asn 385, Ile 387, and Val 396) located in the substrate binding region were selected for saturation mutagenesis. The hydrolytic activity toward different aminoacyl-pNAs of each mutant BSAP in the culture supernatant was measured. Although the mutations resulted in a decrease of hydrolytic activity toward Leu-pNA, N385L BSAP exhibited higher hydrolytic activities toward Lys-pNA (2.2-fold) and Ile-pNA (9.1-fold) than wild-type BSAP. Three mutant enzymes (I387A, I387C and I387S BSAPs) specially hydrolyzed Phe-pNA, which was undetectable in wild-type BSAP. Among these mutant BSAPs, N385L and I387A BSAPs were selected for further characterized and used for protein hydrolysis application. Both of N385L and I387A BSAPs showed higher hydrolysis efficiency than the wild-type BASP and a combination of the wild-type and N385L and I387A BSAPs exhibited the highest hydrolysis efficiency for protein hydrolysis. This study will greatly facilitate studies aimed on change the substrate specificity and our results obtained here should be useful for BSAP application in food industry.
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Affiliation(s)
- Xinxing Gao
- Key Laboratory of Industrial Biotechnology; Ministry of Education; School of Biotechnology, Jiangnan University; Wuxi, Jiangsu, PR China
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40
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Marino T, Russo N, Toscano M. What occurs by replacing Mn2+ with Co2+ in human arginase I: first-principles computational analysis. Inorg Chem 2012; 52:655-9. [PMID: 23273171 DOI: 10.1021/ic301703t] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The reaction mechanism of the dinuclear cobalt enzyme arginase is investigated using density functional theory. As an arginase-containing binuclear Mn(2)(2+) cluster, it catalyzes the hydrolysis of L-arginine in L-ornithine and urea. The bridging hydroxide is capable of performing nucleophilic attack on the iminium carbon ion from its bridging position, resulting in the formation of a tetrahedral intermediate, as was already obtained in a previous theoretical study on the manganese enzyme. Our theoretical investigation allows us to obtain an accurate potential energy profile and confirms that the coordination mode of the substrate to the dimetallic center is quite similar to that present in the manganese enzyme. In agreement with the experimental observations, our results show that both Mn- and Co-containing enzymes catalyze the same reaction with quite comparable energy barriers.
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Affiliation(s)
- Tiziana Marino
- Dipartimento di Chimica and Centro di Calcolo ad Alte Prestazioni per Elaborazioni Parallele e Distribuite, Universitá della Calabria, I-87030 Arcavacata di Rende (CS), Italy.
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41
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Marino T, Russo N, Toscano M. Catalytic Mechanism of the Arylsulfatase Promiscuous Enzyme fromPseudomonas Aeruginosa. Chemistry 2012; 19:2185-92. [DOI: 10.1002/chem.201201943] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Revised: 11/06/2012] [Indexed: 11/11/2022]
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42
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Theoretical study of the reaction mechanism of Mycobacterium tuberculosis type II dehydroquinate dehydratase. COMPUT THEOR CHEM 2012. [DOI: 10.1016/j.comptc.2012.10.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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43
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Theoretical investigation of astacin proteolysis. J Inorg Biochem 2012; 111:70-9. [DOI: 10.1016/j.jinorgbio.2012.02.029] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2011] [Revised: 11/06/2011] [Accepted: 02/07/2012] [Indexed: 11/19/2022]
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44
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A quantum-chemical study of the binding ability of βXaaHisGlyHis towards copper(II) ion. J Mol Model 2012; 18:1365-74. [PMID: 21761180 PMCID: PMC3313029 DOI: 10.1007/s00894-011-1162-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2011] [Accepted: 06/24/2011] [Indexed: 11/30/2022]
Abstract
The present study analyzed binding of Cu2+ to tetrapeptides in water solution at several levels of theoretical approximation. The methods used to study the energetic and structural properties of the complexes in question include semiempirical hamiltonians, density functional theory as well as ab initio approaches including electron correlation effects. In order to shed light on the character of interactions between Cu2+ and peptides, which are expected to be mainly electrostatic in nature, decomposition of interaction energy into physically meaningful components was applied.
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45
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Pan Q, Yao Y, Li ZS. New insights into the mechanism of the Schiff base formation catalyzed by type I dehydroquinate dehydratase from S. enterica. Theor Chem Acc 2012. [DOI: 10.1007/s00214-012-1204-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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46
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Yao Y, Li ZS. New insights into the mechanism of the Schiff base hydrolysis catalyzed by type I dehydroquinate dehydratase from S. enterica: a theoretical study. Org Biomol Chem 2012; 10:7037-44. [DOI: 10.1039/c2ob25605c] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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47
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Zhu X, Barman A, Ozbil M, Zhang T, Li S, Prabhakar R. Mechanism of peptide hydrolysis by co-catalytic metal centers containing leucine aminopeptidase enzyme: a DFT approach. J Biol Inorg Chem 2011; 17:209-22. [PMID: 21918843 DOI: 10.1007/s00775-011-0843-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2011] [Accepted: 08/30/2011] [Indexed: 11/28/2022]
Abstract
In this density functional theory study, reaction mechanisms of a co-catalytic binuclear metal center (Zn1-Zn2) containing enzyme leucine aminopeptidase for two different metal bridging nucleophiles (H(2)O and -OH) have been investigated. In addition, the effects of the substrate (L-leucine-p-nitroanilide → L-leucyl-p-anisidine) and metal (Zn1 → Mg and Zn2 → Co, i.e., Mg1-Zn2 and Mg1-Co2 variants) substitutions on the energetics of the mechanism have been investigated. The general acid/base mechanism utilizing a bicarbonate ion followed by this enzyme is divided into two steps: (1) the formation of the gem-diolate intermediate, and (2) the cleavage of the peptide bond. With the computed barrier of 17.8 kcal/mol, the mechanism utilizing a hydroxyl nucleophile was found to be in excellent agreement with the experimentally measured barrier of 18.7 kcal/mol. The rate-limiting step for reaction with L-leucine-p-nitroanilide is the cleavage of the peptide bond with a barrier of 17.8 kcal/mol. However, for L-leucyl-p-anisidine all steps of the mechanism were found to occur with similar barriers (18.0-19.0 kcal/mol). For the metallovariants, cleavage of the peptide bond occurs in the rate-limiting step with barriers of 17.8, 18.0, and 24.2 kcal/mol for the Zn1-Zn2, Mg1-Zn2, and Mg1-Co2 enzymes, respectively. The nature of the metal ion was found to affect only the creation of the gem-diolate intermediate, and after that all three enzymes follow essentially the same energetics. The results reported in this study have elucidated specific roles of both metal centers, the nucleophile, indirect ligands, and substrates in the catalytic functioning of this important class of binuclear metallopeptidases.
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Affiliation(s)
- Xiaoxia Zhu
- Department of Chemistry, University of Miami, 1301 Memorial Drive, Coral Gables, FL 33146, USA
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48
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DFT investigation on the reaction mechanism catalyzed by α-phosphomannomutase1 in protonated/deprotonated states. J Mol Model 2011; 17:577-85. [DOI: 10.1007/s00894-010-0743-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2009] [Accepted: 05/04/2010] [Indexed: 10/19/2022]
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49
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Amata O, Marino T, Russo N, Toscano M. Catalytic activity of a ζ-class zinc and cadmium containing carbonic anhydrase. Compared work mechanisms. Phys Chem Chem Phys 2011; 13:3468-77. [DOI: 10.1039/c0cp01053g] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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50
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Park JM, Boero M. Protonation of a hydroxide anion bridging two divalent magnesium cations in water probed by first-principles metadynamics simulation. J Phys Chem B 2010; 114:11102-9. [PMID: 20695500 DOI: 10.1021/jp102991f] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The protonation of a hydroxide anion (OH(-)) located between two magnesium cations (Mg(2+)) in aqueous solution has been investigated by first-principles metadynamics simulation. We observe that the complex Mg(2+)-OH(-)-Mg(2+) is stabilized by the coparticipation of the hydroxide anion to the first hydration shells of both the Mg(2+) cations. Contrary to the cases of OH(-) in pure water, the transfer of protons in the presence of the divalent metal ions turns out to be a slow chemical event. This can be ascribed to the decreased proton affinity of the bridging OH(-). Metadynamics simulation, used to overcome the difficulty of the long time scale required by the protonation of the bridging OH(-), has shown that the system possesses a great stability on the reactant state, characterized by a bioctahedral (6,6) solvation structure around the two Mg(2+) cations. The exploration of the free energy landscape shows that this stable bioctahedral configuration converts into a lower coordinated (5,6) structure, leading to a proton transfer from a water molecule belonging to the first solvation shell of the Mg(2+) ion having the lower coordination to the bridging OH(-); the free energy barrier for the protonation reaction is 11 kcal/mol, meaning that the bridging hydroxide is a weak base. During the proton transfer, the bridging OH(-) reverts to an H(2)O molecule, and this breaks the electrostatic coupling of the two Mg(2+) ions, which depart independently with their own hydration shells, one of which is entirely formed by water molecules. The second one carries the newly created OH(-). Our results show that the flexibility in the metal coordination plays a crucial role in both the protonation process of the bridging OH(-) and the separation of the metal cations, providing useful insight into the nature of proton transfer in binuclear divalent metal ions, with several biological implications, such as, for instance, transesterification of catalytic RNA.
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Affiliation(s)
- Jung Mee Park
- Department of Chemistry, Sungkyunkwan University, Suwon, Gyeonggi, 440-746, Korea.
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