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Slipknotted and unknotted monovalent cation-proton antiporters evolved from a common ancestor. PLoS Comput Biol 2021; 17:e1009502. [PMID: 34648493 PMCID: PMC8562792 DOI: 10.1371/journal.pcbi.1009502] [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: 06/30/2020] [Revised: 11/02/2021] [Accepted: 09/28/2021] [Indexed: 11/20/2022] Open
Abstract
While the slipknot topology in proteins has been known for over a decade, its evolutionary origin is still a mystery. We have identified a previously overlooked slipknot motif in a family of two-domain membrane transporters. Moreover, we found that these proteins are homologous to several families of unknotted membrane proteins. This allows us to directly investigate the evolution of the slipknot motif. Based on our comprehensive analysis of 17 distantly related protein families, we have found that slipknotted and unknotted proteins share a common structural motif. Furthermore, this motif is conserved on the sequential level as well. Our results suggest that, regardless of topology, the proteins we studied evolved from a common unknotted ancestor single domain protein. Our phylogenetic analysis suggests the presence of at least seven parallel evolutionary scenarios that led to the current diversity of proteins in question. The tools we have developed in the process can now be used to investigate the evolution of other repeated-domain proteins. In proteins with the slipknot topology, the polypeptide chain forms a slipknot—a structure that is not necessarily manifest to a naked eye, but it can be detected using mathematical methods. Slipknots are conserved motifs often found at catalytic sites and are directly involved in molecular transport. Although the first proteins with slipknots were found in 2007, many questions remain unanswered, e.g. how these proteins appeared, or whether the slipknotted proteins evolved from unknotted ones or vice versa. Here we provide the first analysis of homologous slipknotted and unknotted transmembrane proteins in order to elucidate their evolutionary relationship. We show that two-domain slipknotted and unknotted membrane transporters share the same one-domain unknotted protein as an ancestor. The ancestor gene duplicated and underwent various diversification and fusion events during the evolution, which have led to the appearance of a large superfamily of secondary active transporters. The slipknot motif seems to have been created by chance after a fusion of two single domain genes. Therefore, we show here that the slipknotted transporter evolved from an unknotted one-domain protein and that there are at least seven different evolutionary scenarios that gave rise to this large superfamily of transporters.
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Adak P, Ghosh B, Bauzá A, Frontera A, Herron SR, Chattopadhyay SK. Binuclear and tetranuclear Zn(ii) complexes with thiosemicarbazones: synthesis, X-ray crystal structures, ATP-sensing, DNA-binding, phosphatase activity and theoretical calculations. RSC Adv 2020; 10:12735-12746. [PMID: 35492083 PMCID: PMC9051056 DOI: 10.1039/c9ra10549b] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Accepted: 03/13/2020] [Indexed: 11/21/2022] Open
Abstract
Two Zinc(ii) complexes [Zn4(L1)4]·2H2O (1) and [Zn2(L2)2]·2H2O (2) of pyruvaldehydethiosemicarbazone ligands are reported. The complexes were characterized by elemental analysis, IR, NMR, UV-vis spectroscopy and by single-crystal X-ray crystallography. X-ray crystal structure determinations of the complexes show that though Zn : ligand stoichiometry is 1 : 1 in both the complexes, the molecular unit is tetranuclear for 1 and binuclear for 2. Both the complexes show selective sensing of ATP at pH 7.4 (0.01 M HEPES) in CH3CN–H2O (9 : 1) medium in the presence of other anions like AcO−, NO3−, F−, Cl−, H2PO4−, HPO42− and P2O72−. The UV-titration experiments of complexes 1 and 2 with ATP results in binding constants of 2.0(±0.07) × 104 M−1 and 7.1(±0.05) × 103 M−1 respectively. The calculated detection limits of 6.7 μM and 1.7 μM for 1 and 2 respectively suggest that the complexes are sensitive detectors of ATP. High selectivity of the complexes is confirmed by the addition of ATP in presence of an excess of other anions. DFT studies confirm that the ATP complexes are more favorable than those with the other inorganic phosphate anions, in agreement with the experimental results. Phosphatase like activity of both complexes is investigated spectrophotometrically using 4-nitrophenylphosphate (NPP) as a substrate, indicating the complexes possess significant phosphate ester hydrolytic efficiency. The kinetics for the hydrolysis of the substrate NPP was studied by the initial rate method at 25 °C. Michaelis–Menten derived kinetic parameters indicate that rate of hydrolysis of the P–O bond by complex 1 is much greater than that of complex 2, the kcat values being 212(±5) and 38(±2) h−1 respectively. The DNA binding studies of the complexes were investigated using electronic absorption spectroscopy and fluorescence quenching. The absorption spectral titrations of the complexes with DNA indicate that the CT-DNA binding affinity (Kb) of complex 1 (2.10(±0.07) × 106 M−1) is slightly greater than that of 2 (1.11(±0.04) × 106 M−1). From fluorescence spectra the apparent binding constant (Kapp) values were calculated and they are found to be 5.41(±0.01) × 105 M−1 for 1 and 3.93(±0.02) × 105 M−1 for 2. The molecular dynamics simulation demonstrates that the Zn(ii) complex 1 is a good intercalator of DNA. A binuclear and a tetranuclear zinc(ii) of pyruvaldehyde thiosemicarbazone show selective sensing of ATP at pH 7.4 (0.01 M HEPES) in CH3CN–H2O (9 : 1) medium. The DNA binding and phosphatase activities of the complexes are also reported.![]()
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Affiliation(s)
- Piyali Adak
- Department of Chemistry, Indian Institute of Engineering Science and Technology Shibpur Howarh-711 103 India
| | - Bipinbihari Ghosh
- Department of Chemistry, Indian Institute of Engineering Science and Technology Shibpur Howarh-711 103 India
| | - Antonio Bauzá
- Department of Chemistry, University of the Balearic Islands Carretera de Valldemossa km 7.5 07122 Palma de Mallorca IllesBalears Spain
| | - Antonio Frontera
- Department of Chemistry, University of the Balearic Islands Carretera de Valldemossa km 7.5 07122 Palma de Mallorca IllesBalears Spain
| | - Steven R Herron
- Department of Chemistry, Utah Valley University 800W University Pkwy Orem UT 84058 USA
| | - Shyamal Kumar Chattopadhyay
- Department of Chemistry, Indian Institute of Engineering Science and Technology Shibpur Howarh-711 103 India
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Hjörleifsson JG, Ásgeirsson B. Cold-active alkaline phosphatase is irreversibly transformed into an inactive dimer by low urea concentrations. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:755-65. [DOI: 10.1016/j.bbapap.2016.03.016] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2015] [Revised: 03/08/2016] [Accepted: 03/28/2016] [Indexed: 11/25/2022]
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Brodkin HR, DeLateur NA, Somarowthu S, Mills CL, Novak WR, Beuning PJ, Ringe D, Ondrechen MJ. Prediction of distal residue participation in enzyme catalysis. Protein Sci 2015; 24:762-78. [PMID: 25627867 PMCID: PMC4420525 DOI: 10.1002/pro.2648] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2014] [Revised: 01/10/2015] [Accepted: 01/26/2015] [Indexed: 11/09/2022]
Abstract
A scoring method for the prediction of catalytically important residues in enzyme structures is presented and used to examine the participation of distal residues in enzyme catalysis. Scores are based on the Partial Order Optimum Likelihood (POOL) machine learning method, using computed electrostatic properties, surface geometric features, and information obtained from the phylogenetic tree as input features. Predictions of distal residue participation in catalysis are compared with experimental kinetics data from the literature on variants of the featured enzymes; some additional kinetics measurements are reported for variants of Pseudomonas putida nitrile hydratase (ppNH) and for Escherichia coli alkaline phosphatase (AP). The multilayer active sites of P. putida nitrile hydratase and of human phosphoglucose isomerase are predicted by the POOL log ZP scores, as is the single-layer active site of P. putida ketosteroid isomerase. The log ZP score cutoff utilized here results in over-prediction of distal residue involvement in E. coli alkaline phosphatase. While fewer experimental data points are available for P. putida mandelate racemase and for human carbonic anhydrase II, the POOL log ZP scores properly predict the previously reported participation of distal residues.
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Affiliation(s)
- Heather R Brodkin
- Department of Chemistry and Chemical Biology, Northeastern UniversityBoston, Massachusetts, 02115
- Department of Biochemistry, Rosenstiel Basic Medical Sciences Research Center, Brandeis UniversityWaltham, Massachusetts, 02454–9110
- Department of Chemistry, Rosenstiel Basic Medical Sciences Research Center, Brandeis UniversityWaltham, Massachusetts, 02454–9110
| | - Nicholas A DeLateur
- Department of Chemistry and Chemical Biology, Northeastern UniversityBoston, Massachusetts, 02115
| | - Srinivas Somarowthu
- Department of Chemistry and Chemical Biology, Northeastern UniversityBoston, Massachusetts, 02115
| | - Caitlyn L Mills
- Department of Chemistry and Chemical Biology, Northeastern UniversityBoston, Massachusetts, 02115
| | - Walter R Novak
- Department of Biochemistry, Rosenstiel Basic Medical Sciences Research Center, Brandeis UniversityWaltham, Massachusetts, 02454–9110
- Department of Chemistry, Rosenstiel Basic Medical Sciences Research Center, Brandeis UniversityWaltham, Massachusetts, 02454–9110
| | - Penny J Beuning
- Department of Chemistry and Chemical Biology, Northeastern UniversityBoston, Massachusetts, 02115
| | - Dagmar Ringe
- Department of Biochemistry, Rosenstiel Basic Medical Sciences Research Center, Brandeis UniversityWaltham, Massachusetts, 02454–9110
- Department of Chemistry, Rosenstiel Basic Medical Sciences Research Center, Brandeis UniversityWaltham, Massachusetts, 02454–9110
| | - Mary Jo Ondrechen
- Department of Chemistry and Chemical Biology, Northeastern UniversityBoston, Massachusetts, 02115
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Sunden F, Peck A, Salzman J, Ressl S, Herschlag D. Extensive site-directed mutagenesis reveals interconnected functional units in the alkaline phosphatase active site. eLife 2015; 4. [PMID: 25902402 PMCID: PMC4438272 DOI: 10.7554/elife.06181] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2014] [Accepted: 04/22/2015] [Indexed: 01/30/2023] Open
Abstract
Enzymes enable life by accelerating reaction rates to biological timescales. Conventional studies have focused on identifying the residues that have a direct involvement in an enzymatic reaction, but these so-called 'catalytic residues' are embedded in extensive interaction networks. Although fundamental to our understanding of enzyme function, evolution, and engineering, the properties of these networks have yet to be quantitatively and systematically explored. We dissected an interaction network of five residues in the active site of Escherichia coli alkaline phosphatase. Analysis of the complex catalytic interdependence of specific residues identified three energetically independent but structurally interconnected functional units with distinct modes of cooperativity. From an evolutionary perspective, this network is orders of magnitude more probable to arise than a fully cooperative network. From a functional perspective, new catalytic insights emerge. Further, such comprehensive energetic characterization will be necessary to benchmark the algorithms required to rationally engineer highly efficient enzymes.
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Affiliation(s)
- Fanny Sunden
- Department of Biochemistry, Beckman Center, Stanford University, Stanford, United States
| | - Ariana Peck
- Department of Biochemistry, Beckman Center, Stanford University, Stanford, United States
| | - Julia Salzman
- Department of Biochemistry, Beckman Center, Stanford University, Stanford, United States
| | - Susanne Ressl
- Molecular and Cellular Biochemistry Department, Indiana University Bloomington, Bloomington, United States
| | - Daniel Herschlag
- Department of Biochemistry, Beckman Center, Stanford University, Stanford, United States
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Identification of Functional Regions in the Rhodospirillum rubrum l-Asparaginase by Site-Directed Mutagenesis. Mol Biotechnol 2014; 57:251-64. [DOI: 10.1007/s12033-014-9819-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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7
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8
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Nepravishta R, Polizio F, Paci M, Melino S. A metal-binding site in the RTN1-C protein: new perspectives on the physiological role of a neuronal protein. Metallomics 2012; 4:480-7. [PMID: 22522967 DOI: 10.1039/c2mt20035j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Reticulon 1-C (RTN1-C) is an ER-associated neuronal protein characterized by horse-shoe-like topology with two transmembrane helices and the N- and C-terminal regions which are supposed in the cytosolic side of ER. The physiological role of this protein is not completely clarified, but several studies have suggested its involvement in the neuronal differentiation, membrane vesicle trafficking and induction of apoptosis. The C-terminal region of RTN1-C is characterized by the presence of a H4 histone consensus sequence that makes it able to interact with nucleic acids and HDAC enzymes both in vitro and in vivo. In the present study a potential metal ion binding motif (HxE/D) at the C-terminal of the RTN1-C has been identified and its capability to bind metals investigated by UV-vis, CD, multidimensional NMR spectroscopy and biological assays. The results suggest a possible implication of the metal ions in the mechanisms of formation of the recently observed RTNs multiprotein complexes contributing to understand the structure and function of this neuronal membrane protein, suggesting a possible effect of the metal binding property on its biological function.
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Affiliation(s)
- Ridvan Nepravishta
- Department of Sciences and Chemical Technologies, University of Rome Tor Vergata, via della Ricerca Scientifica, 00133 Rome, Italy
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9
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Bobyr E, Lassila JK, Wiersma-Koch HI, Fenn TD, Lee JJ, Nikolic-Hughes I, Hodgson KO, Rees DC, Hedman B, Herschlag D. High-resolution analysis of Zn(2+) coordination in the alkaline phosphatase superfamily by EXAFS and x-ray crystallography. J Mol Biol 2012; 415:102-17. [PMID: 22056344 PMCID: PMC3249517 DOI: 10.1016/j.jmb.2011.10.040] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2011] [Revised: 10/21/2011] [Accepted: 10/24/2011] [Indexed: 10/15/2022]
Abstract
Comparisons among evolutionarily related enzymes offer opportunities to reveal how structural differences produce different catalytic activities. Two structurally related enzymes, Escherichia coli alkaline phosphatase (AP) and Xanthomonas axonopodis nucleotide pyrophosphatase/phosphodiesterase (NPP), have nearly identical binuclear Zn(2+) catalytic centers but show tremendous differential specificity for hydrolysis of phosphate monoesters or phosphate diesters. To determine if there are differences in Zn(2+) coordination in the two enzymes that might contribute to catalytic specificity, we analyzed both x-ray absorption spectroscopic and x-ray crystallographic data. We report a 1.29-Å crystal structure of AP with bound phosphate, allowing evaluation of interactions at the AP metal site with high resolution. To make systematic comparisons between AP and NPP, we measured zinc extended x-ray absorption fine structure for AP and NPP in the free-enzyme forms, with AMP and inorganic phosphate ground-state analogs and with vanadate transition-state analogs. These studies yielded average zinc-ligand distances in AP and NPP free-enzyme forms and ground-state analog forms that were identical within error, suggesting little difference in metal ion coordination among these forms. Upon binding of vanadate to both enzymes, small increases in average metal-ligand distances were observed, consistent with an increased coordination number. Slightly longer increases were observed in NPP relative to AP, which could arise from subtle rearrangements of the active site or differences in the geometry of the bound vanadyl species. Overall, the results suggest that the binuclear Zn(2+) catalytic site remains very similar between AP and NPP during the course of a reaction cycle.
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Affiliation(s)
- Elena Bobyr
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | | | | | - Timothy D. Fenn
- Department of Molecular and Cellular Physiology, Stanford University, Stanford, CA 94305, USA
| | - Jason J. Lee
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Ivana Nikolic-Hughes
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
- Department of Chemical Engineering, Stanford University, Stanford, CA 94305, USA
| | - Keith O. Hodgson
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
- Stanford Synchrotron Radiation Lightsource, SLAC, Stanford University, Menlo Park, CA 94025, USA
| | - Douglas C. Rees
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125, USA
- Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA 91125, USA
| | - Britt Hedman
- Stanford Synchrotron Radiation Lightsource, SLAC, Stanford University, Menlo Park, CA 94025, USA
| | - Daniel Herschlag
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
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10
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Briknarová K, Thomas CJ, York J, Nunberg JH. Structure of a zinc-binding domain in the Junin virus envelope glycoprotein. J Biol Chem 2010; 286:1528-36. [PMID: 21068387 DOI: 10.1074/jbc.m110.166025] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Arenaviruses cause acute hemorrhagic fevers with high mortality. Entry of the virus into the host cell is mediated by the viral envelope glycoprotein, GPC. In contrast to other class I viral envelope glycoproteins, the mature GPC complex contains a cleaved stable signal peptide (SSP) in addition to the canonical receptor-binding (G1) and transmembrane fusion (G2) subunits. SSP is critical for intracellular transport of the GPC complex to the cell surface and for its membrane-fusion activity. Previous studies have suggested that SSP is retained in GPC through interaction with a zinc-binding domain (ZBD) in the cytoplasmic tail of G2. Here we used NMR spectroscopy to determine the structure of Junín virus (JUNV) ZBD (G2 residues 445-485) and investigate its interaction with a conserved Cys residue (Cys-57) in SSP. We show that JUNV ZBD displays a novel fold containing two zinc ions. One zinc ion is coordinated by His-447, His-449, Cys-455, and His-485. The second zinc ion is coordinated by His-459, Cys-467, and Cys-469 and readily accepts Cys-57 from SSP as the fourth ligand. Our studies describe the structural basis for retention of the unique SSP subunit and suggest a mechanism whereby SSP is positioned in the GPC complex to modulate pH-dependent membrane fusion.
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Affiliation(s)
- Klára Briknarová
- Department of Chemistry and Biochemistry, University of Montana, Missoula, Montana 59812, USA.
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Chukhrai ES, Atyaksheva LF. A physical chemistry view of the activity, stability, and adsorption properties of enzymes. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2010. [DOI: 10.1134/s0036024410050018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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12
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Chen BY, Bryant DH, Fofanov VY, Kristensen DM, Cruess AE, Kimmel M, Lichtarge O, Kavraki LE. Cavity scaling: automated refinement of cavity-aware motifs in protein function prediction. J Bioinform Comput Biol 2007; 5:353-82. [PMID: 17589966 DOI: 10.1142/s021972000700276x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2006] [Revised: 12/12/2006] [Indexed: 11/18/2022]
Abstract
Algorithms for geometric and chemical comparison of protein substructure can be useful for many applications in protein function prediction. These motif matching algorithms identify matches of geometric and chemical similarity between well-studied functional sites, motifs, and substructures of functionally uncharacterized proteins, targets. For the purpose of function prediction, the accuracy of motif matching algorithms can be evaluated with the number of statistically significant matches to functionally related proteins, true positives (TPs), and the number of statistically insignificant matches to functionally unrelated proteins, false positives (FPs). Our earlier work developed cavity-aware motifs which use motif points to represent functionally significant atoms and C-spheres to represent functionally significant volumes. We observed that cavity-aware motifs match significantly fewer FPs than matches containing only motif points. We also observed that high-impact C-spheres, which significantly contribute to the reduction of FPs, can be isolated automatically with a technique we call Cavity Scaling. This paper extends our earlier work by demonstrating that C-spheres can be used to accelerate point-based geometric and chemical comparison algorithms, maintaining accuracy while reducing runtime. We also demonstrate that the placement of C-spheres can significantly affect the number of TPs and FPs identified by a cavity-aware motif. While the optimal placement of C-spheres remains a difficult open problem, we compared two logical placement strategies to better understand C-sphere placement.
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Affiliation(s)
- Brian Y Chen
- Department of Computer Science, Rice University, Houston, TX 77005, USA
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Mitra R, Peters MW, Scott MJ. Synthesis and reactivity of a C3-symmetric trinuclear zinc(ii) hydroxide catalyst efficient at phosphate diester transesterification. Dalton Trans 2007:3924-35. [PMID: 17893790 DOI: 10.1039/b706386e] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Inspired by trinuclear Zn(II) sites in enzymatic systems, a ligand system containing three preorganized (2-pyridyl)methyl piperazine moieties anchored onto a rigid C3-symmetric triphenoxymethane platform has been developed for preorganizing three zinc ions into an environment conducive to intramolecular interaction. Zinc(II) binding by this ligand has been analyzed by means of potentiometric measurements in 50% (v/v) CH3CN-H2O solutions. Subsequently a C3-symmetric trinuclear Zn(II) hydroxide complex of the C3-symmetric ligand was synthesized and fully characterized using NMR spectroscopy and X-ray crystallography. This complex induces a 16,900-fold rate enhancement in the catalytic cyclization of the RNA model substrate, 2-hydroxypropyl-p-nitrophenyl phosphate (HPNP, pH 6.7, 25 degrees C) over the uncatalyzed reaction with multiple catalyst turnovers. The observed differences in the pH-rate profile can be attributed to the varying concentration of various trinuclear zinc species. The trinuclear Zn(II) catalyst exhibits a higher hydrolytic activity compared to its mononuclear analogue. The reactivity and structural features of this trinuclear Zn(II) complex will be discussed.
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Affiliation(s)
- Ranjan Mitra
- Department of Chemistry and Center for Catalysis, University of Florida, Gainesville, FL 32611-7200, USA
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Reddy PR, Manjula P, Mohan SK. Novel Peptide-Based Copper(II) Complexes for Total Hydrolytic Cleavage of DNA. Chem Biodivers 2005; 2:1338-50. [PMID: 17191935 DOI: 10.1002/cbdv.200590106] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Stable Cu(II) complexes with histamine- and histidine-containing dipeptides histidylserine and histidylphenylalanine have been developed. Their interaction in solution has been investigated, and the stability of their complexes was determined. The nature of binding in these complexes has been explained with the help of potentiometric pH titrations and 1H-NMR spectroscopy. The geometry of these complexes has been established by electronic spectra. The DNA-binding and -cleavage abilities of these Cu(II) complexes have been probed by the absorption, thermal denaturation, fluorescence, and electrophoresis experiments. The results suggest that these peptide-based Cu(II) complexes effectively bind and efficiently cleave DNA under mild biological conditions. Since Cu(II) complexes are known to play an important role in phosphodiester bond cleavages, these results assume importance.
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15
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Reddy PR, Mohan SK, Rao KS. Ternary Zinc(II)-Dipeptide Complexes for the Hydrolytic Cleavage of DNA at Physiological pH. Chem Biodivers 2005; 2:672-83. [PMID: 17192010 DOI: 10.1002/cbdv.200590043] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
A series of Zn(II) complexes with cysteinylglycine (CysGly) and histidylserine (HisSer), and of CysGly and histidylphenylalanine (HisPhe) were investigated. Complex stabilities were determined potentiometrically, and binding geometries were probed by means of 1H-NMR spectroscopy, using Co(II) instead of Zn(II) as a spectroscopic marker. The ternary 1:1:1 complexes [Zn(II)(CysGly)(HisSer)] and [Zn(II)(CysGly)(HisPhe)] were shown by UV experiments, fluorescence titration, and gel electrophoresis to intercalate with DNA, and to hydrolytically cleave supercoiled DNA (form-I), partly also circular (form-II) DNA, under physiological conditions (37 degrees, H2O, pH 7.5).
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Park YD, Yang Y, Chen QX, Lin HN, Liu Q, Zhou HM. Kinetics of complexing activation by the magnesium ion on green crab (Scylla serrata) alkaline phosphatase. Biochem Cell Biol 2001. [DOI: 10.1139/o01-152] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
As with mammalian enzymes, green crab (Scylla serrata) alkaline phosphatase can be activated by Mg2+through a time-dependent course. The activation is mainly a Vmaxeffect. Tsou's method was used to study the kinetic course of activation. The results show that the enzyme was activated by a complexing scheme that had not been previously identified: the enzyme first reversibly and quickly binds Mg2+and then undergoes a slow reversible course to activation, with a relatively high activation energy (78 ± 4 kJ/mol) and a slow conformational change. The activation reaction is a single molecule reaction, and the apparent activation rate constant is independent of Mg2+concentration if the concentration is sufficiently high. The microscopic rate constants of activation and the association constant were determined from the measurements. The proposed scheme may also be applied to the Mg2+activation mechanism for mammalian enzyme, to explain why the activation rate is time-dependent and not diffusion controlled. Substrate binding was also shown to affect the activation rate constant.Key words: alkaline phosphatase, green crab, kinetics, activation, magnesium ion.
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Hehir MJ, Murphy JE, Kantrowitz ER. Characterization of heterodimeric alkaline phosphatases from Escherichia coli: an investigation of intragenic complementation. J Mol Biol 2000; 304:645-56. [PMID: 11099386 DOI: 10.1006/jmbi.2000.4230] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Escherichia coli alkaline phosphatase (EC 3.1.3.1) belongs to a rare group of enzymes that exhibit intragenic complementation. When certain mutant versions of alkaline phosphatase are combined, the resulting heterodimeric enzymes exhibit a higher level of activity than would be expected based upon the relative activities of the parental enzymes. Nine previously identified alkaline phosphatase complementation mutants were re-examined in this work in order to determine a molecular explanation of intragenic complementation in this experimental system. The locations of these mutations were determined by DNA sequence analysis after PCR amplification of the phosphatase-negative phoA gene. Most of the mutations involved ligands to metal-binding sites. Each of the mutant enzymes was re-created by site-specific mutagenesis, expressed, purified, and kinetically characterized. To investigate cooperativity between the two subunits, we analyzed heterodimeric forms of some of the site-specific mutant enzymes. To enable the isolation of the heterodimeric alkaline phosphatase in pure form, the overall charge of one subunit was altered by replacing the C-terminal Lys residue with three Asp residues. This modification had no effect on the kinetic properties of the enzyme. Heterodimeric alkaline phosphatases were created using two methods: (1) in vitro formation by dissociation at acid pH followed by reassociation at slightly alkaline pH conditions in the presence of zinc and magnesium ions; and (2) in vivo expression from a plasmid carrying two different phoA genes. Increases in k(cat), as well as a large reduction in the p-nitrophenyl phosphate K(m) were observed for certain combinations of mutant enzymes. These results suggest that the structural assembly of E. coli alkaline phosphatase into the dimer induces cooperative interactions between the monomers necessary for the formation of the functional form of the holoenzyme.
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Affiliation(s)
- M J Hehir
- Department of Chemistry, Boston College, Chestnut Hill, MA 02467, USA
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Bortolato M, Besson F, Roux B. Role of metal ions on the secondary and quaternary structure of alkaline phosphatase from bovine intestinal mucosa. Proteins 1999. [DOI: 10.1002/(sici)1097-0134(19991101)37:2<310::aid-prot16>3.0.co;2-b] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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