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An array of basic residues is essential for the nucleolytic activity of the PHP domain of bacterial/archaeal PolX DNA polymerases. Sci Rep 2019; 9:9947. [PMID: 31289311 PMCID: PMC6616362 DOI: 10.1038/s41598-019-46349-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Accepted: 06/26/2019] [Indexed: 12/15/2022] Open
Abstract
Bacterial/archaeal family X DNA polymerases (PolXs) have a C-terminal PHP domain with an active site formed by nine histidines and aspartates that catalyzes 3′-5′ exonuclease, AP-endonuclease, 3′-phosphodiesterase and 3′-phosphatase activities. Multiple sequence alignments have allowed us to identify additional highly conserved residues along the PHP domain of bacterial/archaeal PolXs that form an electropositive path to the catalytic site and whose potential role in the nucleolytic activities had not been established. Here, site directed mutagenesis at the corresponding Bacillus subtilis PolX (PolXBs) residues, Arg469, Arg474, Asn498, Arg503 and Lys545, as well as to the highly conserved residue Phe440 gave rise to enzymes severely affected in all the nucleolytic activities of the enzyme while conserving a wild-type gap-filling activity, indicating a function of those residues in DNA binding at the PHP domain. Altogether, the results obtained with the mutant proteins, the spatial arrangement of those DNA binding residues, the intermolecular transference of the 3′-terminus between the PHP and polymerization active sites, and the available 3D structures of bacterial PolXs led us to propose the requirement to a great degree of a functional/structural flexibility to coordinate the synthetic and degradative activities in these enzymes.
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Ebrahimi S, Dabbagh HA, Eskandari K. Nature of intramolecular interactions of vitamin C in view of interacting quantum atoms: the role of hydrogen bond cooperativity on geometry. Phys Chem Chem Phys 2016; 18:18278-88. [PMID: 27332782 DOI: 10.1039/c6cp01678b] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The conformational analysis of six dihedral angles was calculated by second-order Moller-Plesset perturbation theory (MP2) with the correlation-consistent aug-cc-pVDZ basis set. The quantum theory of atoms in molecules (QTAIM) was applied to gain a description of the atoms and chemical bonds. A high content of hydroxyl groups in vitamin C's (VC) structure leads to a wide range of intramolecular interactions. The nature of these interactions within the selected VC conformers was studied in view of the interacting quantum atom (IQA) approach. Complete IQA analysis of the atomic and interatomic interaction energies indicated hydrogen bond formation was responsible for the stability of most of the local minima in the potential energy surface. In these conformers, the tandem participation of interactions was operating by way of two- or three-centered (bifurcated) cooperative networks. For the intramolecular hydrogen bond interplay in cooperativity, changes of the IQA atomic and interatomic interaction energies of the participant interactions were monitored during the formation of cooperative networks. The results of the intramolecular cooperativity were evaluated with changes of the delocalization index and bond distances.
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Affiliation(s)
- Saeid Ebrahimi
- Department of Chemistry, Isfahan University of Technology, Isfahan, 84156-83111, Iran.
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Hu WB, Xie CD, Hu WJ, Zhao XL, Liu YA, Huo JC, Li JS, Jiang B, Wen K. Selectivity and Cooperativity in the Binding of Multiple Guests to a Pillar[5]arene–Crown Ether Fused Tricyclic Host. J Org Chem 2015. [DOI: 10.1021/acs.joc.5b01038] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Wei-Bo Hu
- Shanghai
Advanced Research Institute, Chinese Academy of Science, Shanghai 201210, China
- University of Chinese Academy of Sciences, Beijing 100039, P. R. China
| | - Chang-Dong Xie
- School
of Materials Science and Engineering, Southwest University of Science and Technology, Mianyang 621010, Sichuan, P. R. China
| | - Wen-Jing Hu
- Shanghai
Advanced Research Institute, Chinese Academy of Science, Shanghai 201210, China
| | - Xiao-Li Zhao
- Shanghai
Key Laboratory of Green Chemistry and Chemical Processes and Department
of Chemistry, East China Normal University, Shanghai 200062, China
| | - Yahu A. Liu
- Medicinal
Chemistry, ChemBridge Research Laboratories, Inc., San Diego, California 92127, United States
| | - Ji-Chuan Huo
- School
of Materials Science and Engineering, Southwest University of Science and Technology, Mianyang 621010, Sichuan, P. R. China
| | - Jiu-Sheng Li
- Shanghai
Advanced Research Institute, Chinese Academy of Science, Shanghai 201210, China
| | - Biao Jiang
- Shanghai
Advanced Research Institute, Chinese Academy of Science, Shanghai 201210, China
| | - Ke Wen
- Shanghai
Advanced Research Institute, Chinese Academy of Science, Shanghai 201210, China
- School
of Materials Science and Engineering, Southwest University of Science and Technology, Mianyang 621010, Sichuan, P. R. China
- School of
Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
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Hu WB, Hu WJ, Liu YA, Li JS, Jiang B, Wen K. Negative Cooperativity in the Binding of Imidazolium and Viologen Ions to a Pillar[5]arene-Crown Ether Fused Host. Org Lett 2015; 17:2940-3. [DOI: 10.1021/acs.orglett.5b01209] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Wei-Bo Hu
- Shanghai
Advanced Research Institute, Chinese Academy of Science, Shanghai 201210, China
- University of Chinese Academy of Sciences, Beijing 100039, P. R. China
| | - Wen-Jing Hu
- Shanghai
Advanced Research Institute, Chinese Academy of Science, Shanghai 201210, China
| | - Yahu A. Liu
- Medicinal Chemistry,
ChemBridge Research Laboratories Inc., San Diego, California 92127, United States
| | - Jiu-Sheng Li
- Shanghai
Advanced Research Institute, Chinese Academy of Science, Shanghai 201210, China
| | - Biao Jiang
- Shanghai
Advanced Research Institute, Chinese Academy of Science, Shanghai 201210, China
| | - Ke Wen
- Shanghai
Advanced Research Institute, Chinese Academy of Science, Shanghai 201210, China
- School
of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, P. R. China
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Lee CH, Yoon H, Kim P, Cho S, Kim D, Jang WD. An indolocarbazole-bridged macrocyclic porphyrin dimer having homotropic allosterism with inhibitory control. Chem Commun (Camb) 2011; 47:4246-8. [DOI: 10.1039/c1cc00112d] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Webb JEA, Crossley MJ, Turner P, Thordarson P. Pyromellitamide Aggregates and Their Response to Anion Stimuli. J Am Chem Soc 2007; 129:7155-62. [PMID: 17497782 DOI: 10.1021/ja0713781] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The N,N',N'',N'''-1,2,4,5-tetra(ethylhexanoate) pyromellitamide is found to be capable of both intermolecular aggregation and binding to small anions. It is synthesized by aminolysis of pyromellitic anhydride with ethanolamine, followed by a reaction with hexanoyl chloride. The single-crystal X-ray structure of the pyromellitamide shows that it forms one-dimensional columnar stacks through an intermolecular hydrogen-bonding network. It also forms self-assembled gels in nonpolar solvents, presumably by a hydrogen-bonding network similar to the solid-state structure as shown by IR and XRD studies. Aggregation by intermolecular hydrogen bonding of the pyromellitamide is also observed by NMR and IR in solution. Fitting of NMR dilution data for pyromellitamide in d6-acetone to a cooperative aggregation model gave KE=232 M-1 and positive cooperativity of aggregation (rho=0.22). The pyromellitamide binds to a range of small anions with the binding strength decreasing in the order chloride>acetate>bromide>nitrate approximately iodide. The data indicate that the pyromellitamide binds two anions and that it displays negative cooperativity. The intermolecular aggregation of the pyromellitamide can also be altered using small anion stimuli; anion addition to preformed self-assembled pyromellitamide gels causes their collapse. The kinetics of anion-induced gel collapse are qualitatively correlated to the binding affinities of the same anions in solution. The cooperative anion binding properties and the sensitivity of the self-assembled gels formed by pyromellitamide toward anions could be useful in the development of sensors and switching/releasing devices.
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Affiliation(s)
- James E A Webb
- School of Chemistry, The University of Sydney NSW 2006, Australia
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Hrtska SCL, Kemp MM, Muñoz EM, Azizad O, Banerjee M, Raposo C, Kumaran J, Ghosh P, Linhardt RJ. Investigation of the mechanism of binding between internalin B and heparin using surface plasmon resonance. Biochemistry 2007; 46:2697-706. [PMID: 17305366 PMCID: PMC2034450 DOI: 10.1021/bi062021x] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Listeria monocytogenes, a food-borne pathogen that infects immunocompromised patients, enters and proliferates within mammalian cells by taking advantage of host cell machinery. While entry into macrophages and other phagocytic cells occurs constitutively, intracellular invasion of nonphagocytic cells, such as epithelial and endothelial cells, occurs through induced phagocytosis. Invasion of these nonphagocytic cell types is under the control of the secreted L. monocytogenes protein internalin B (InlB), which directly associates with and activates the receptor tyrosine kinase Met. Activation of Met by InlB has previously been shown to be potentiated by binding of glycosaminoglycans to the GW domains of this protein. We studied the interaction between heparin and full-length InlB as well as a truncated, functional form of InlB to understand the mode of interaction between these two molecules. InlB preferred long-chain (>or=dp14) heparin oligosaccharides, and the interaction with heparin fit a complicated binding model with a dissociation constant in the nanomolar range. While there are various explanations for this complicated binding model, one supported by our data involves binding and rebinding of InlB to multiple binding sites on heparin in a positive and weakly cooperative manner. This mode is consistent with enhancement of interaction of InlB with glycosaminoglycans for activation of Met.
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Affiliation(s)
- Sybil C Lang Hrtska
- Department of Chemical and Biochemical Engineering, University of Iowa, Iowa City, Iowa 52242, USA
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Thordarson P, Bijsterveld EJA, Elemans JAAW, Kasák P, Nolte RJM, Rowan AE. Highly negative homotropic allosteric binding of viologens in a double-cavity porphyrin. J Am Chem Soc 2003; 125:1186-7. [PMID: 12553818 DOI: 10.1021/ja028463n] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The synthesis of a double-cavity porphyrin with interesting allosteric binding properties toward viologens (N,N'-disubstituted 4,4'-bipyridines) is described. The porphyrin host forms very strong 1:2 complexes with viologens, displaying a negative allosteric behavior. The first viologen guest binds exceptionally tight (K > 107 M-1), and the second guest binds much more weakly (DeltaDeltaG = 9-15 kJ mol-1). The allosteric effect, one of the highest reported so far, originates in structural changes upon binding the first ligand, closely following the sequential (or induced-fit) theory of allosteric interactions by Koshland, Némethy, and Filmer (the KNF-model).
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Affiliation(s)
- Pall Thordarson
- Department of Organic Chemistry, NSRIM, University of Nijmegen, Toernooiveld 1, 6525 ED, Nijmegen, The Netherlands
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Mezo AR, Ottesen JJ, Imperiali B. Discovery and characterization of a discretely folded homotrimeric betabetaalpha peptide. J Am Chem Soc 2001; 123:1002-3. [PMID: 11456646 DOI: 10.1021/ja0038981] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- A R Mezo
- Department of Chemistry Massachusetts Institute of Technology Cambridge, Massachusetts 02139, USA
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