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Relevant bibliographies by topics / Functional Modeling - Heme Enzymes

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Academic literature on the topic 'Functional Modeling - Heme Enzymes'

Author: Grafiati

Published: 7 September 2023

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Journal articles on the topic "Functional Modeling - Heme Enzymes"

1

Timmins, Amy, and Sam P. de Visser. "A Comparative Review on the Catalytic Mechanism of Nonheme Iron Hydroxylases and Halogenases." Catalysts 8, no. 8 (2018): 314. http://dx.doi.org/10.3390/catal8080314.

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Enzymatic halogenation and haloperoxidation are unusual processes in biology; however, a range of halogenases and haloperoxidases exist that are able to transfer an aliphatic or aromatic C–H bond into C–Cl/C–Br. Haloperoxidases utilize hydrogen peroxide, and in a reaction with halides (Cl−/Br−), they react to form hypohalides (OCl−/OBr−) that subsequently react with substrate by halide transfer. There are three types of haloperoxidases, namely the iron-heme, nonheme vanadium, and flavin-dependent haloperoxidases that are reviewed here. In addition, there are the nonheme iron halogenases that show structural and functional similarity to the nonheme iron hydroxylases and form an iron(IV)-oxo active species from a reaction of molecular oxygen with α-ketoglutarate on an iron(II) center. They subsequently transfer a halide (Cl−/Br−) to an aliphatic C–H bond. We review the mechanism and function of nonheme iron halogenases and hydroxylases and show recent computational modelling studies of our group on the hectochlorin biosynthesis enzyme and prolyl-4-hydroxylase as examples of nonheme iron halogenases and hydroxylases. These studies have established the catalytic mechanism of these enzymes and show the importance of substrate and oxidant positioning on the stereo-, chemo- and regioselectivity of the reaction that takes place.

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2

Robins, Tiina, Jonas Carlsson, Maria Sunnerhagen, Anna Wedell, and Bengt Persson. "Molecular Model of Human CYP21 Based on Mammalian CYP2C5: Structural Features Correlate with Clinical Severity of Mutations Causing Congenital Adrenal Hyperplasia." Molecular Endocrinology 20, no. 11 (2006): 2946–64. http://dx.doi.org/10.1210/me.2006-0172.

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Abstract Enhanced understanding of structure-function relationships of human 21-hydroxylase, CYP21, is required to better understand the molecular causes of congenital adrenal hyperplasia. To this end, a structural model of human CYP21 was calculated based on the crystal structure of rabbit CYP2C5. All but two known allelic variants of missense type, a total of 60 disease-causing mutations and six normal variants, were analyzed using this model. A structural explanation for the corresponding phenotype was found for all but two mutants for which available clinical data are also discrepant with in vitro enzyme activity. Calculations of protein stability of modeled mutants were found to correlate inversely with the corresponding clinical severity. Putative structurally important residues were identified to be involved in heme and substrate binding, redox partner interaction, and enzyme catalysis using docking calculations and analysis of structurally determined homologous cytochrome P450s (CYPs). Functional and structural consequences of seven novel mutations, V139E, C147R, R233G, T295N, L308F, R366C, and M473I, detected in Scandinavian patients with suspected congenital adrenal hyperplasia of different severity, were predicted using molecular modeling. Structural features deduced from the models are in good correlation with clinical severity of CYP21 mutants, which shows the applicability of a modeling approach in assessment of new CYP21 mutations.

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3

Krone, Nils, Yulia Grischuk, Marina Müller, et al. "Analyzing the Functional and Structural Consequences of Two Point Mutations (P94L and A368D) in the CYP11B1 Gene Causing Congenital Adrenal Hyperplasia Resulting from 11-Hydroxylase Deficiency." Journal of Clinical Endocrinology & Metabolism 91, no. 7 (2006): 2682–88. http://dx.doi.org/10.1210/jc.2006-0209.

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Abstract Context: Congenital adrenal hyperplasia is a group of autosomal recessive inherited disorders of steroidogenesis. The deficiency of steroid 11-hydroxylase (CYP11B1) resulting from mutations in the CYP11B1 gene is the second most frequent cause. Objective: We studied the functional and structural consequences of two CYP11B1 missense mutations, which were detected in a 1.8-yr-old boy with acne and precocious pseudopuberty, to prove their clinical relevance and study their impact on CYP11B1 function. Results: The in vitro expression studies in COS-7 cells revealed an almost complete absence of CYP11B1 activity for the P94L mutant to 0.05% for the conversion of 11-deoxycortisol to cortisol. The A368D mutant severely reduced the CYP11B1 enzymatic activity to 1.17%. Intracellular localization studies by immunofluorescence revealed that the mutants were correctly localized. Introducing these mutations in a three-dimensional model structure of the CYP11B1 protein provides a possible explanation for the effects measured in vitro. We hypothesize that the A368D mutation interferes with structures important for substrate specificity and heme iron binding, thus explaining its major functional impact. However, according to structural analysis, we would expect only a minor effect of the P94L mutant on 11-hydroxylase activity, which contrasts with the observed major effect of this mutation both in vitro and in vivo. Conclusion: Analyzing the in vitro enzyme function is a complementary procedure to genotyping and a valuable tool for understanding the clinical phenotype of 11-hydroxylase deficiency. This is the basis for accurate genetic counseling, prenatal diagnosis, and treatment. Moreover, the combination of in vitro enzyme function and molecular modeling provides valuable insights in cytochrome P450 structural-functional relationships, although one must be aware of the limitations of in silico-based methods.

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4

Fontecave, M., S. Ménage, and C. Duboc-Toia. "Functional models of non-heme diiron enzymes." Coordination Chemistry Reviews 178-180 (December 1998): 1555–72. http://dx.doi.org/10.1016/s0010-8545(98)00119-2.

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5

Shteinman, A. A. "Structural-functional modeling of non-heme oxygenases." Russian Chemical Bulletin 60, no. 7 (2011): 1290–300. http://dx.doi.org/10.1007/s11172-011-0197-5.

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6

Yadav, Rahul, and Emily E. Scott. "Endogenous insertion of non-native metalloporphyrins into human membrane cytochrome P450 enzymes." Journal of Biological Chemistry 293, no. 43 (2018): 16623–34. http://dx.doi.org/10.1074/jbc.ra118.005417.

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Human cytochrome P450 enzymes are membrane-bound heme-containing monooxygenases. As is the case for many heme-containing enzymes, substitution of the metal in the center of the heme can be useful for mechanistic and structural studies of P450 enzymes. For many heme proteins, the iron protoporphyrin prosthetic group can be extracted and replaced with protoporphyrin containing another metal, but human membrane P450 enzymes are not stable enough for this approach. The method reported herein was developed to endogenously produce human membrane P450 proteins with a nonnative metal in the heme. This approach involved coexpression of the P450 of interest, a heme uptake system, and a chaperone in Escherichia coli growing in iron-depleted minimal medium supplemented with the desired trans-metallated protoporphyrin. Using the steroidogenic P450 enzymes CYP17A1 and CYP21A2 and the drug-metabolizing CYP3A4, we demonstrate that this approach can be used with several human P450 enzymes and several different metals, resulting in fully folded proteins appropriate for mechanistic, functional, and structural studies including solution NMR.

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7

Nemukhin, A. V., B. L. Grigorenko, I. A. Topol, and S. K. Burt. "Modeling dioxygen binding to the non-heme iron-containing enzymes." International Journal of Quantum Chemistry 106, no. 10 (2006): 2184–90. http://dx.doi.org/10.1002/qua.20910.

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8

Boynton, Tye O., Svetlana Gerdes, Sarah H. Craven, Ellen L. Neidle, John D. Phillips, and Harry A. Dailey. "Discovery of a Gene Involved in a Third Bacterial Protoporphyrinogen Oxidase Activity through Comparative Genomic Analysis and Functional Complementation." Applied and Environmental Microbiology 77, no. 14 (2011): 4795–801. http://dx.doi.org/10.1128/aem.00171-11.

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ABSTRACTTetrapyrroles are ubiquitous molecules in nearly all living organisms. Heme, an iron-containing tetrapyrrole, is widely distributed in nature, including most characterized aerobic and facultative bacteria. A large majority of bacteria that contain heme possess the ability to synthesize it. Despite this capability and the fact that the biosynthetic pathway has been well studied, enzymes catalyzing at least three steps have remained “missing” in many bacteria. In the current work, we have employed comparative genomics via the SEED genomic platform, coupled with experimental verification utilizingAcinetobacter baylyiADP1, to identify one of the missing enzymes, a new protoporphyrinogen oxidase, the penultimate enzyme in heme biosynthesis. COG1981 was identified by genomic analysis as a candidate protein family for the missing enzyme in bacteria that lacked HemG or HemY, two known protoporphyrinogen oxidases. The predicted amino acid sequence of COG1981 is unlike those of the known enzymes HemG and HemY, but in some genomes, the gene encoding it is found neighboring other heme biosynthetic genes. When the COG1981 gene was deleted from the genome ofA. baylyi, a bacterium that lacks bothhemGandhemY, the organism became auxotrophic for heme. Cultures accumulated porphyrin intermediates, and crude cell extracts lacked protoporphyrinogen oxidase activity. The heme auxotrophy was rescued by the presence of a plasmid-borne protoporphyrinogen oxidase gene from a number of different organisms, such ashemGfromEscherichia coli,hemYfromMyxococcus xanthus, or the human gene for protoporphyrinogen oxidase.

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9

Kojima, T., T. Amano, Y. Ishii, and Y. Matsuda. "Ruthenium-pyridylamine complexes as functional models of non-heme iron enzymes." Journal of Inorganic Biochemistry 67, no. 1-4 (1997): 238. http://dx.doi.org/10.1016/s0162-0134(97)80111-0.

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10

Matsunaga, Isamu, and Yoshitsugu Shiro. "Peroxide-utilizing biocatalysts: structural and functional diversity of heme-containing enzymes." Current Opinion in Chemical Biology 8, no. 2 (2004): 127–32. http://dx.doi.org/10.1016/j.cbpa.2004.01.001.

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