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Eddehech A, Smichi N, Arhab Y, Noiriel A, Abousalham A, Gargouri Y, Zarai Z. Production, purification and functional characterization of phospholipase C from Bacillus thuringiensis with high catalytic activity. Process Biochem 2019. [DOI: 10.1016/j.procbio.2019.05.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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2
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Mirchi A, Sizochenko N, Dinadayalane T, Leszczynski J. Binding of Alkali Metal Ions with 1,3,5-Tri(phenyl)benzene and 1,3,5-Tri(naphthyl)benzene: The Effect of Phenyl and Naphthyl Ring Substitution on Cation−π Interactions Revealed by DFT Study. J Phys Chem A 2017; 121:8927-8938. [DOI: 10.1021/acs.jpca.7b08725] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Ali Mirchi
- Interdisciplinary
Center for Nanotoxicity, Department of Chemistry, Physics and Atmospheric
Sciences, Jackson State University, 1400 J. R. Lynch Street, Jackson, Mississippi 39217, United States
| | - Natalia Sizochenko
- Interdisciplinary
Center for Nanotoxicity, Department of Chemistry, Physics and Atmospheric
Sciences, Jackson State University, 1400 J. R. Lynch Street, Jackson, Mississippi 39217, United States
| | - Tandabany Dinadayalane
- Department
of Chemistry, Clark Atlanta University, 223 James P. Brawley Drive, S.W., Atlanta, Georgia 30314, United States
| | - Jerzy Leszczynski
- Interdisciplinary
Center for Nanotoxicity, Department of Chemistry, Physics and Atmospheric
Sciences, Jackson State University, 1400 J. R. Lynch Street, Jackson, Mississippi 39217, United States
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3
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Reed T, Lushington GH, Xia Y, Hirakawa H, Travis DM, Mure M, Scott EE, Limburg J. Crystal structure of histamine dehydrogenase from Nocardioides simplex. J Biol Chem 2010; 285:25782-91. [PMID: 20538584 PMCID: PMC2919140 DOI: 10.1074/jbc.m109.084301] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2009] [Revised: 05/24/2010] [Indexed: 11/06/2022] Open
Abstract
Histamine dehydrogenase (HADH) isolated from Nocardioides simplex catalyzes the oxidative deamination of histamine to imidazole acetaldehyde. HADH is highly specific for histamine, and we are interested in understanding the recognition mode of histamine in its active site. We describe the first crystal structure of a recombinant form of HADH (HADH) to 2.7-A resolution. HADH is a homodimer, where each 76-kDa subunit contains an iron-sulfur cluster ([4Fe-4S](2+)) and a 6-S-cysteinyl flavin mononucleotide (6-S-Cys-FMN) as redox cofactors. The overall structure of HADH is very similar to that of trimethylamine dehydrogenase (TMADH) from Methylotrophus methylophilus (bacterium W3A1). However, some distinct differences between the structure of HADH and TMADH have been found. Tyr(60), Trp(264), and Trp(355) provide the framework for the "aromatic bowl" that serves as a trimethylamine-binding site in TMADH is comprised of Gln(65), Trp(267), and Asp(358), respectively, in HADH. The surface Tyr(442) that is essential in transferring electrons to electron-transfer flavoprotein (ETF) in TMADH is not conserved in HADH. We use this structure to propose the binding mode for histamine in the active site of HADH through molecular modeling and to compare the interactions to those observed for other histamine-binding proteins whose structures are known.
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Affiliation(s)
| | | | - Yan Xia
- Molecular Biosciences, The University of Kansas, Lawrence, Kansas 66045
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4
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Berntzen G, Andersen JT, Ustgård K, Michaelsen TE, Mousavi SA, Qian JD, Kristiansen PE, Lauvrak V, Sandlie I. Identification of a high affinity FcgammaRIIA-binding peptide that distinguishes FcgammaRIIA from FcgammaRIIB and exploits FcgammaRIIA-mediated phagocytosis and degradation. J Biol Chem 2008; 284:1126-35. [PMID: 18957413 DOI: 10.1074/jbc.m803584200] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
FcgammaRIIA is a key activating receptor linking immune complex formation with cellular effector functions. FcgammaRIIA has 93% identity with an inhibitory receptor, FcgammaRIIB, which negatively regulates FcgammaRIIA. FcgammaRIIA is important in the therapeutic action of several monoclonal antibodies. Binding molecules that discriminate FcgammaRIIA from FcgammaRIIB may optimize receptor activity and serve as a lead for development of therapeutics with FcgammaRIIA as a key target. Here we report the use of phage display libraries to select short peptides with distinct FcgammaRIIA binding properties. An 11-mer peptide (WAWVWLTETAV) was characterized that bound FcgammaRIIA with a K(d) of 500 nm. It mediated cell internalization and degradation of a model antigen. The peptide-binding site on FcgammaRIIA was shown to involve Phe(163) and the IgG binding amino acids Trp(90) and Trp(113). It is thus overlapping but not identical to that of IgG. Neither activating receptors FcgammaRI and FcgammaRIII, nor FcgammaRIIB, all of which lack Phe(163), bound the peptide.
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Affiliation(s)
- Gøril Berntzen
- Department of Molecular Biosciences, University of Oslo, Oslo, Norway
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5
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Pashynska V, Kosevich M, Stepanian S, Adamowicz L. Noncovalent complexes of tetramethylammonium with chlorine anion and 2,5-dihydroxybenzoic acid as models of the interaction of quaternary ammonium biologically active compounds with their molecular targets: A theoretical study. ACTA ACUST UNITED AC 2007. [DOI: 10.1016/j.theochem.2007.03.019] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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6
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Benfield AP, Goodey NM, Phillips LT, Martin SF. Structural studies examining the substrate specificity profiles of PC-PLC(Bc) protein variants. Arch Biochem Biophys 2007; 460:41-7. [PMID: 17324372 PMCID: PMC1905842 DOI: 10.1016/j.abb.2007.01.023] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2006] [Revised: 01/18/2007] [Accepted: 01/23/2007] [Indexed: 10/23/2022]
Abstract
The phosphatidylcholine preferring phospholipase C from Bacillus cereus (PC-PLC(Bc)) catalyzes the hydrolysis of phospholipids in the following order of preference: phosphatidylcholine (PC)>phosphatidylethanolamine (PE)>phosphatidylserine (PS). In previous work, mutagenic, kinetic, and crystallographic experiments suggested that varying the amino acids at the 4th, 56th, and 66th positions had a significant influence upon the substrate specificity profile of PC-PLC(Bc). Here, we report the crystal structures of the native form of several PC-PLC(Bc) variants that exhibited altered substrate specificities for PC, PE, and PS at maximum resolutions of 1.90-2.05 Angstrom. Comparing the structures of these variants to the structure of the wild-type enzyme reveals only minor differences with respect to the number and location of active site water molecules and the side chain conformations of residues at the 4th and 56th positions. These results suggest that subtle changes in steric and electronic properties in the substrate binding site of PC-PLC(Bc) are responsible for the significant changes in substrate selectivity.
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Affiliation(s)
- Aaron P Benfield
- Department of Chemistry and Biochemistry, The Institute of Cellular and Molecular Biology, The University of Texas, 1 University Station - A5300, Austin, TX 78712, USA
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7
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Sakurai Y, Mizuno T, Hiroaki H, Gohda K, Oku JI, Tanaka T. High Thermal Stability Imparted by a Designed Tandem Arg-Trp Stretch in an α-Helical Coiled Coil. Angew Chem Int Ed Engl 2005; 44:6180-3. [PMID: 16124025 DOI: 10.1002/anie.200500806] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Yuuki Sakurai
- Department of Material Sciences, Graduate School of Engineering, Nagoya Institute of Technology, Gokiso-chou, Nagoya 466-8555, Japan
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8
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Sakurai Y, Mizuno T, Hiroaki H, Gohda K, Oku JI, Tanaka T. High Thermal Stability Imparted by a Designed Tandem Arg-Trp Stretch in an α-Helical Coiled Coil. Angew Chem Int Ed Engl 2005. [DOI: 10.1002/ange.200500806] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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9
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Alejandre-Durán E, Roldán-Arjona T, Ariza RR, Ruiz-Rubio M. The photolyase gene from the plant pathogen Fusarium oxysporum f. sp. lycopersici is induced by visible light and alpha-tomatine from tomato plant. Fungal Genet Biol 2004; 40:159-65. [PMID: 14516768 DOI: 10.1016/s1087-1845(03)00089-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Survival of irradiated spores from Fusarium oxysporum with ultraviolet radiation (UV) was increased following exposition to visible light, indicating that this phytopathogenic fungus has a mechanism of photoreactivation able to counteract the lethal effects of UV. A genomic sequence containing the complete photolyase gene (phr1) from F. oxysporum was isolated by heterologous hybridisation with the Neurospora crassa photolyase gene. The F. oxysporum phr1 cDNA was isolated and expressed in a photolyase deficient Escherichia coli strain. The complementation of the photoreactivation deficiency of this E. coli mutant by phr1 cDNA demonstrated that the photolyase gene from F. oxysporum encodes a functional protein. The F. oxysporum PHR1 protein has a domain characteristic of photolyases from fungi (Trichoderma harziaium, N. crassa, Magnaporthe grisea, Saccharomyces cerevisiae) to bacteria (E. coli), and clusters in the photolyases phylogenetic tree with fungal photolyases. The F. oxysporum phr1 gene was inducible by visible light. The phr1 expression was also detected in presence of alpha-tomatine, a glycoalkaloid from tomato damaging cell membranes, suggesting that phr1 is induced by this cellular stress.
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Affiliation(s)
- Encarna Alejandre-Durán
- Departamento de Genética, Facultad de Ciencias, Edificio Gregor Mendel, Campus Rabanales, Universidad de Córdoba, 14071 Córdoba, Spain
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10
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Abstract
Some molecules, particularly aromatics, have high molar extinction coefficients at wavelengths in the damaging ultraviolet radiation region of the spectrum between 200 and 400 nm. Thus, under a UV radiation flux in which these wavelengths are represented, it could be argued that a selection pressure would exist for a UV transparent biochemistry in which they were not represented. This hypothesis is explored using data made available from proteomics, focusing particularly on tryptophan, against which a selection pressure could exist on present-day Earth as a result of its absorbance shoulder at wavelengths greater than 290 nm. The abundance of tryptophan in whole proteomes is lower than expected from the degeneracy of the genetic code. A lower usage of tryptophan is found in the cytochrome c oxidase polypeptide I of UV-exposed organisms compared to nocturnal and subterranean organisms, but not in ATP synthase chain A. Examination of the amino acid composition of photolyase, an enzyme that requires exposure to light to function, shows that the tryptophan abundances exceed those of the total proteome of most organisms and the abundances expected from the degeneracy of the genetic code. This is also true for cytochrome c oxidase, another enzyme that makes extensive use of the electron transfer properties of tryptophan. We suggest that the selection pressure for the use of tryptophan caused, among other factors, by the uses of delocalised pi-electrons that this aromatic provides in active sites and binding motifs outweighs the selection pressure for UV transparency. This trade-off explains the lack of conclusive evidence for a UV transparent selection pressure. We suggest that this trade-off applies to the stacked pi-electrons of DNA. It offers a solution to the long-standing paradox of why the macromolecule responsible for the faithful replication of information has high absorbance in the damaging UV radiation region of the spectrum.
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11
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Scrutton NS, Sutcliffe MJ. Trimethylamine dehydrogenase and electron transferring flavoprotein. Subcell Biochem 2001; 35:145-81. [PMID: 11192721 DOI: 10.1007/0-306-46828-x_5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
Affiliation(s)
- N S Scrutton
- Departments of Biochemistry and Chemistry, University of Leicester LE1 7RH, UK
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Basran J, Sutcliffe MJ, Hille R, Scrutton NS. Reductive half-reaction of the H172Q mutant of trimethylamine dehydrogenase: evidence against a carbanion mechanism and assignment of kinetically influential ionizations in the enzyme-substrate complex. Biochem J 1999; 341 ( Pt 2):307-14. [PMID: 10393087 PMCID: PMC1220361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/13/2023]
Abstract
The reactions of wild-type trimethylamine dehydrogenase (TMADH) and of a His-172-->Gln (H172Q) mutant were studied by rapid-mixing stopped-flow spectroscopy over the pH range 6.0-10.5, to address the potential role of His-172 in abstracting a proton from the substrate in a 'carbanion' mechanism for C-H bond cleavage. The pH-dependence of the limiting rate for flavin reduction (klim) was studied as a function of pH for the wild-type enzyme with perdeuterated trimethylamine as substrate. The use of perdeuterated trimethylamine facilitated the unequivocal identification of two kinetically influential ionizations in the enzyme-substrate complex, with macroscopic pKa values of 6.5+/-0.2 and 8.4+/-0.1. A plot of klim/Kd revealed a bell-shaped curve and two kinetically influential ionizations with macroscopic pKa values of 9.4+/-0.1 and 10.5+/-0.1. Mutagenesis of His-172, a potential active-site base and a component of a novel Tyr-His-Asp triad in the active site of TMADH, revealed that the pKa of 8.4+/-0.1 for the wild-type enzyme-substrate complex represents ionization of the imidazolium side-chain of His-172. H172Q TMADH retains catalytic competence throughout the pH range investigated. At pH 10.5, and in contrast with the wild-type enzyme, flavin reduction in H172Q TMADH is biphasic. The fast phase is dependent on the trimethylamine concentration and exhibits a kinetic isotope effect of about 3; C-H bond cleavage is thus partially rate-limiting. In contrast, the slow phase does not show hyperbolic dependence on substrate concentration, and the observed rate shows no dependence on isotope, revealing that C-H bond cleavage is not rate-limiting. The analysis of H172Q TMADH, together with data recently acquired for the Y169F mutant of TMADH, reveals that C-H bond breakage is not initiated via abstraction of a proton from the substrate by an active-site base. The transfer of reducing equivalents to flavin via a carbanion mechanism is therefore unlikely.
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Affiliation(s)
- J Basran
- Department of Biochemistry, University of Leicester, Adrian Building, University Road, Leicester LE1 7RH, U.K
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Choi HS, Suh SB, Cho SJ, Kim KS. Ionophores and receptors using cation-pi interactions: collarenes. Proc Natl Acad Sci U S A 1998; 95:12094-9. [PMID: 9770445 PMCID: PMC22790 DOI: 10.1073/pnas.95.21.12094] [Citation(s) in RCA: 133] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Cation-pi interactions are important forces in molecular recognition by biological receptors, enzyme catalysis, and crystal engineering. We have harnessed these interactions in designing molecular systems with circular arrangement of benzene units that are capable of acting as ionophores and models for biological receptors. [n]Collarenes are promising candidates with high selectivity for a specific cation, depending on n, because of their structural rigidity and well-defined cavity size. The interaction energies of [n]collarenes with cations have been evaluated by using ab initio calculations. The selectivity of these [n]collarenes in aqueous solution was revealed by using statistical perturbation theory in conjunction with Monte Carlo and molecular dynamics simulations. It has been observed that in [n]collarenes the ratio of the interaction energies of a cation with it and the cation with the basic building unit (benzene) can be correlated to its ion selectivity. We find that collarenes are excellent and efficient ionophores that bind cations through cation-pi interactions. [6]Collarene is found to be a selective host for Li+ and Mg2+, [8]collarene for K+ and Sr2+, and [10]collarene for Cs+ and Ba2+. This finding indicates that [10]collarene and [8]collarene could be used for effective separation of highly radioactive isotopes, 137Cs and 90Sr, which are major constituents of nuclear wastes. More interestingly, collarenes of larger cavity size can be useful in capturing organic cations. [12]Collarene exhibits a pronounced affinity for tetramethylammonium cation and acetylcholine, which implies that it could serve as a model for acetylcholinestrase. Thus, collarenes can prove to be novel and effective ionophores/model-receptors capable of heralding a new direction in molecular recognition and host-guest chemistry.
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Affiliation(s)
- H S Choi
- National Creative Research Initiative Center for Superfunctional Materials and Department of Chemistry, Pohang University of Science and Technology, San 31, Hyojadong, Namgu, Pohang 790-784, Korea
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Enescu M, Gheorghe V. Molecular dynamics simulation of methylene blue–guanine complex in vacuo. ACTA ACUST UNITED AC 1998. [DOI: 10.1016/s0166-1280(97)00124-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Wolff J, Sackett DL, Knipling L. Cation selective promotion of tubulin polymerization by alkali metal chlorides. Protein Sci 1996; 5:2020-8. [PMID: 8897602 PMCID: PMC2143265 DOI: 10.1002/pro.5560051008] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
A role for charge-based interactions in protein stability at the monomer or dimer level is well known. We show here that such interactions can also be important for the higher-order structures of microtubule assembly. Alkali metal chlorides increase the rate of polymerization of pure tubulin driven by either taxol or dimethyl sulfoxide. The effect is cation selective, exhibiting a sequence Na+ > K+ > Li+ > Cs+, with optimal concentrations for Na+ at approximately 160 mM. Hofmeister anion effects are additive with these rate stimulations. Sodium is less potent than guanidinium ion stimulation reported previously, but produces a larger fraction of normal microtubules. Alkali metal cations lower the critical concentration by a factor of approximately 2, produce cold reversible polymers whose formation is sensitive to podophyllotoxin inhibition, increase the fraction of polymers present as microtubules from approximately 0.9 to 0.99, and reverse or prevent urea-induced depolymerization of microtubules. In the presence of microtubule-associated proteins, the promotion of polymerization is no longer cation selective. In the polymerization of tubulin S, in which the acidic C termini of both monomers have been cleaved, the cation enhancement is markedly decreased, although selective persists. Because the selectivity sequence is similar to that of the coil/helix transition of polyglutamic acid, we suggest that a major part, although not all, of the cation selective enhancement of polymerization results from shielding of the glutamate-rich C termini of the tubulin monomers.
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Affiliation(s)
- J Wolff
- Laboratory of Biochemical Pharmacology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
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Scrutton NS, Raine AR. Cation-pi bonding and amino-aromatic interactions in the biomolecular recognition of substituted ammonium ligands. Biochem J 1996; 319 ( Pt 1):1-8. [PMID: 8870640 PMCID: PMC1217726 DOI: 10.1042/bj3190001] [Citation(s) in RCA: 204] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Cation-pi bonds and amino-aromatic interactions are known to be important contributors to protein architecture and stability, and their role in ligand-protein interactions has also been reported. Many biologically active amines contain substituted ammonium moieties, and cation-pi bonding and amino-aromatic interactions often enable these molecules to associate with proteins. The role of organic cation-pi bonding and amino-aromatic interactions in the recognition of small-molecule amines and peptides by proteins is an important topic for those involved in structure-based drug design, and although the number of structures determined for proteins displaying these interactions is small, general features are beginning to emerge. This review explores the role of cation-pi bonding and amino-aromatic interactions in the biological molecular recognition of amine ligands. Perspectives on the design of ammonium-ligand-binding sites are also discussed.
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Affiliation(s)
- N S Scrutton
- Department of Biochemistry, University of Leicester, U.K
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Mewies M, Packman LC, Mathews FS, Scrutton NS. Flavinylation in wild-type trimethylamine dehydrogenase and differentially charged mutant enzymes: a study of the protein environment around the N1 of the flavin isoalloxazine. Biochem J 1996; 317 ( Pt 1):267-72. [PMID: 8694773 PMCID: PMC1217472 DOI: 10.1042/bj3170267] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
In wild-type trimethylamine dehydrogenase, residue Arg-222 is positioned close to the isoalloxazine N1/C2 positions of the 6S-cysteinyl FMN. The positively charged guanidino group of Arg-222 is thought to stabilize negative charge as it develops at the N1 position of the flavin during flavinylation of the enzyme. Three mutant trimethylamine dehydrogenases were constructed to alter the nature of the charge at residue 222. The amount of active flavinylated enzyme produced in Escherichia coli is reduced when Arg-222 is replaced by lysine (mutant R222K). Removal or reversal of the charge at residue 222 (mutants R222V and R222E, respectively) leads to the production of inactive enzymes that are totally devoid of flavin. A comparison of the CD spectra for the wild-type and mutant enzymes revealed no major structural change following mutagenesis. Like the wild-type protein, each mutant enzyme contained stoichiometric amounts of the 4Fe-4S cluster and ADP. Electrospray MS also indicated that the native and recombinant wild-type enzymes were isolated as a mixture of deflavo and holo enzyme, but that each of the mutant enzymes have masses expected for deflavo trimethylamine dehydrogenase. The MS data indicate that the lack of assembly of the mutant proteins with FMN is not due to detectable levels of post-translational modification of significant mass. The experiments reported here indicate that simple mutagenic changes in the FMN-binding site can reduce the proportion of flavinylated enzyme isolated from Escherichia coli and that positive charge is required at residue 222 if flavinylation is to proceed.
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Affiliation(s)
- M Mewies
- Department of Biochemistry, University of Leicester, UK
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