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Kumar A, Satpati P. Divalent-Metal-Ion Selectivity of the CRISPR-Cas System-Associated Cas1 Protein: Insights from Classical Molecular Dynamics Simulations and Electronic Structure Calculations. J Phys Chem B 2021; 125:11943-11954. [PMID: 34694813 DOI: 10.1021/acs.jpcb.1c07744] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
CRISPR-associated protein 1 (Cas1) is a universally conserved essential metalloenzyme of the clustered regularly interspaced short palindromic repeat (CRISPR) immune system of prokaryotes (bacteria, archaea) that can cut and integrate a part of viral DNA to its host genome with the help of other proteins. The integrated DNA acts as a memory of viral infection, which can be transcribed to RNA and stop future infection by recognition (based on the RNA/DNA complementarity principle) followed by protein-mediated degradation of the viral DNA. It has been proposed that the presence of a single manganese (Mn2+) ion in a conserved divalent-metal-ion binding pocket (key residues: E190, H254, D265, D268) of Cas1 is crucial for its function. Cas1-mediated DNA degradation was proposed to be hindered by metal substitution, metal chelation, or mutation of the binding pocket residues. Cas1 is active toward dsDNA degradation with both Mn2+ and Mg2+. X-ray structures of Cas1 revealed an intricate atomic interaction network of the divalent-metal-ion binding pocket and opened up the possibility of modeling related metal ions (viz., Mg2+, Ca2+) in the binding pocket of wild-type (WT) and mutated Cas1 proteins for computational analysis, which includes (1) quantitative estimation of the energetics of the divalent-metal-ion preference and (2) exploring the structural and dynamical aspects of the protein in response to divalent-metal-ion substitution or amino acid mutation. Using the X-ray structure of the Cas1 protein from Pseudomonas aeruginosa as a template (PDB 3GOD), we performed (∼2.23 μs) classical molecular dynamics (MD) simulations to compare structural and dynamical differences between Mg2+- and Ca2+-bound binding pockets of wild-type (WT) and mutant (E190A, H254A, D265A, D268A) Cas1. Furthermore, reduced binding pocket models were generated from X-ray and molecular dynamics (MD) trajectories, and the resulting structures were subjected to quantum chemical calculations. Results suggest that Cas1 prefers Mg2+ binding relative to Ca2+ and the preference is the strongest for WT and the weakest for the D268A mutant. Quantum chemical calculations indicate that Mn2+ is the most preferred relative to both Mg2+ and Ca2+ in the wild-type and mutant Cas1. Substitution of Mg2+ by Ca2+ does not alter the interaction network between Cas1 and the divalent metal ion but increases the wetness of the binding pocket by introducing a single water molecule in the first coordination shell of the latter. The strength of metal-ion preference (Mg2+ versus Ca2+) seems to be dependent on the solvent accessibility of the divalent-metal-ion binding pocket, strongest for wild-type Cas1 (in which the metal-ion binding pocket is dry, which includes two water molecules) and the weakest for the D268A mutant (in which the metal-ion binding pocket is wet, which includes four water molecules).
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Affiliation(s)
- Abhishek Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
| | - Priyadarshi Satpati
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
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2
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Naglah AM, Al-Omar MA, Almehizia AA, AlKahtani HM, Bhat MA, Al-Shakliah NS, Belgacem K, Majrashi BM, Refat MS, Adam AMA. Synthesis, thermogravimetric, and spectroscopic characterizations of three palladium metal(II) ofloxacin drug and amino acids mixed ligand complexes as advanced antimicrobial materials. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2020.129102] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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3
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Abdel‐Aal MAA, Abdel‐Aziz SA, Shaykoon MSA, Abuo‐Rahma GEA. Towards anticancer fluoroquinolones: A review article. Arch Pharm (Weinheim) 2019; 352:e1800376. [DOI: 10.1002/ardp.201800376] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Revised: 03/18/2019] [Accepted: 03/21/2019] [Indexed: 12/21/2022]
Affiliation(s)
- Mohamed A. A. Abdel‐Aal
- Department of Medicinal Chemistry, Faculty of PharmacyMinia UniversityMinia Egypt
- Department of Pharmaceutical Chemistry, Faculty of PharmacyAl‐Azhar UniversityAssiut Egypt
| | - Salah A. Abdel‐Aziz
- Department of Pharmaceutical Chemistry, Faculty of PharmacyAl‐Azhar UniversityAssiut Egypt
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4
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Puri S, Chaudhuri TK. Improvement of structural stability and functional efficiency of chaperonin GroEL mediated by mixed salt. Int J Biol Macromol 2019; 129:792-798. [PMID: 30771393 DOI: 10.1016/j.ijbiomac.2019.02.069] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Revised: 01/31/2019] [Accepted: 02/12/2019] [Indexed: 10/27/2022]
Abstract
GroEL is the most commonly used chaperonin protein for both in-vitro refolding of aggregating proteins as well as in-vivo solubilization of over-expressed aggregation-prone proteins of therapeutic and biotechnological applications. But sometimes the stress conditions like heat and a load of over-expressed/unfolded/misfolded proteins lead to a decrease in structural stability and functional efficiency of GroEL, which results in less recovery of substrate protein through the chaperone-mediated refolding process. So, to amend it, we have been able to optimize physicochemical conditions utilizing a cumulation of (NH4)2SO4/MgCl2 in the buffer. Interestingly, we found a consequential enhancement in the aggregation prevention efficiency, refolding of the denatured substrate and ATPase activity of GroEL protein. The reason for the increased refolding and aggregation prevention efficiency might be the exposure of hydrophobic sites and enhanced ATP hydrolysis rate in presence of buffer containing (NH4)2SO4/MgCl2. The present study withal shows that GroEL under optimized conditions exhibits consequential amelioration in thermal aggregation at high temperature. Hence the optimized buffer conditions are utilizable for the folding of substrate proteins under a broad temperature range.
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Affiliation(s)
- Sarita Puri
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, India
| | - Tapan K Chaudhuri
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, India.
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Mishyna M, Volokh O, Danilova Y, Gerasimova N, Pechnikova E, Sokolova OS. Effects of radiation damage in studies of protein-DNA complexes by cryo-EM. Micron 2017; 96:57-64. [PMID: 28262565 DOI: 10.1016/j.micron.2017.02.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Revised: 02/18/2017] [Accepted: 02/18/2017] [Indexed: 11/26/2022]
Abstract
Nucleic acids are responsible for the storage, transfer and realization of genetic information in the cell, which provides correct development and functioning of organisms. DNA interaction with ligands ensures the safety of this information. Over the past 10 years, advances in electron microscopy and image processing allowed to obtain the structures of key DNA-protein complexes with resolution below 4Å. However, radiation damage is a limiting factor to the potentially attainable resolution in cryo-EM. The prospect and limitations of studying protein-DNA complex interactions using cryo-electron microscopy are discussed here. We reviewed the ways to minimize radiation damage in biological specimens and the possibilities of using radiation damage (so-called 'bubblegrams') to obtain additional structural information.
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Affiliation(s)
- M Mishyna
- Lomonosov Moscow State University, 119234, Moscow, Russia.
| | - O Volokh
- Lomonosov Moscow State University, 119234, Moscow, Russia
| | - Ya Danilova
- Lomonosov Moscow State University, 119234, Moscow, Russia
| | - N Gerasimova
- Lomonosov Moscow State University, 119234, Moscow, Russia
| | - E Pechnikova
- Thermo Fisher Scientific, Materials & Structural Analysis, 5651 GG Eindhoven, Netherlands
| | - O S Sokolova
- Lomonosov Moscow State University, 119234, Moscow, Russia.
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7
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Das S, Pal U, Chandra Maiti N. Metal ions provide structural stability and compactness to tetrameric purothionin. RSC Adv 2016. [DOI: 10.1039/c6ra16576a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Metal ions impart structural stability to the purothionin tetramer.
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Affiliation(s)
- Swagata Das
- Structural Biology & Bioinformatics Division
- CSIR-Indian Institute of Chemical Biology
- Kolkata 700032
- India
| | - Uttam Pal
- Structural Biology & Bioinformatics Division
- CSIR-Indian Institute of Chemical Biology
- Kolkata 700032
- India
| | - Nakul Chandra Maiti
- Structural Biology & Bioinformatics Division
- CSIR-Indian Institute of Chemical Biology
- Kolkata 700032
- India
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Pedroza CJ, Flórez AM, Ruiz OS, Orduz S. Enzymatic hydrolysis of molecules associated with bacterial quorum sensing using an acyl homoserine lactonase from a novel Bacillus thuringiensis strain. Antonie Van Leeuwenhoek 2014; 105:253-64. [PMID: 24233057 DOI: 10.1007/s10482-013-0072-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2013] [Accepted: 10/31/2013] [Indexed: 11/26/2022]
Abstract
N-acyl homoserine lactones are key components of quorum sensing, the bacterial communication system. This communication mechanism regulates the expression of genes, including those involved in virulence and biofilm formation. This system can be interrupted by the action of enzymes that hydrolyze the signaling molecules. In this work, we studied the enzymatic properties of a recombinant AHL-lactonase from Bacillus thuringiensis strain 147-11516, using substrates with acyl chains of different length (C4-HSL, C6-HSL, C7-HSL, C8-HSL and C10-HSL), we also investigated the effect of pH (5.0–9.0), temperature (20–70 °C), concentration of monovalent, divalent and trivalent metals ions (0.2 and 2.0 mM) and EDTA. The results showed that the recombinant AHL-lactonase had biological activity in alkaline pH conditions (8.0) and high temperature (47 % of hydrolyzed substrate at 60 °C). The recombinant AHL-lactonase has activity on substrates with different acyl chain length. However, the activity of the recombinant enzyme was decreased in the two concentrations of all metal ions evaluated but was not inhibited by EDTA. The affinity of the enzyme for all substrates tested and its performance, in the evaluated conditions, suggest that the AHL-lactonase from B. thuringiensis strain 147-11516 could be used as a strategy for disruption of the Gram-negative bacteria communication system under normal and challenging conditions.
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Uivarosi V. Metal complexes of quinolone antibiotics and their applications: an update. Molecules 2013; 18:11153-97. [PMID: 24029748 PMCID: PMC6269848 DOI: 10.3390/molecules180911153] [Citation(s) in RCA: 204] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Revised: 09/02/2013] [Accepted: 09/02/2013] [Indexed: 12/29/2022] Open
Abstract
Quinolones are synthetic broad-spectrum antibiotics with good oral absorption and excellent bioavailability. Due to the chemical functions found on their nucleus (a carboxylic acid function at the 3-position, and in most cases a basic piperazinyl ring (or another N-heterocycle) at the 7-position, and a carbonyl oxygen atom at the 4-position) quinolones bind metal ions forming complexes in which they can act as bidentate, as unidentate and as bridging ligand, respectively. In the polymeric complexes in solid state, multiple modes of coordination are simultaneously possible. In strongly acidic conditions, quinolone molecules possessing a basic side nucleus are protonated and appear as cations in the ionic complexes. Interaction with metal ions has some important consequences for the solubility, pharmacokinetics and bioavailability of quinolones, and is also involved in the mechanism of action of these bactericidal agents. Many metal complexes with equal or enhanced antimicrobial activity compared to the parent quinolones were obtained. New strategies in the design of metal complexes of quinolones have led to compounds with anticancer activity. Analytical applications of complexation with metal ions were oriented toward two main directions: determination of quinolones based on complexation with metal ions or, reversely, determination of metal ions based on complexation with quinolones.
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Affiliation(s)
- Valentina Uivarosi
- Department of General and Inorganic Chemistry, Faculty of Pharmacy, Carol Davila University of Medicine and Pharmacy, 6 Traian Vuia St, Bucharest 020956, Romania.
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Sissi C, Cheng B, Lombardo V, Tse-Dinh YC, Palumbo M. Metal ion and inter-domain interactions as functional networks in E. coli topoisomerase I. Gene 2013; 524:253-60. [PMID: 23612251 DOI: 10.1016/j.gene.2013.04.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Revised: 04/08/2013] [Accepted: 04/09/2013] [Indexed: 10/26/2022]
Abstract
Escherichia coli topoisomerase I (EcTopoI) is a type IA bacterial topoisomerase which is receiving large attention due to its potential application as novel target for antibacterial therapeutics. Nevertheless, a detailed knowledge of its mechanism of action at molecular level is to some extent lacking. This is partly due to the requirement of several factors (metal ions, nucleic acid) to the proper progress of the enzyme catalytic cycle. Additionally, each of them can differently affect the protein structure. Here we assess the role of the different components (DNA, metal ions, protein domains) in a dynamic environment as in solution by monitoring the catalytic as well as the structural properties of EcTopoI. Our results clearly indicated the interaction among these components as functionally relevant and underlined their mutual involvement. Some similarities with other enzymes of the same family emerged (for example DNA prevents divalent metal ions coordination at non selective binding sites). Interestingly, same interactions (C- and N-terminal domain interaction) appear to be peculiar of this bacterial topoisomerase which suggest they could be favorably exploited to the design of selective inhibitors for this class of enzyme.
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Affiliation(s)
- Claudia Sissi
- Dept. of Pharmaceutical and Pharmacological Sciences, v. Marzolo 5, 35131 Padova, Italy.
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Bakaeean B, Kabiri M, Iranfar H, Saberi MR, Chamani J. Binding Effect of Common Ions to Human Serum Albumin in the Presence of Norfloxacin: Investigation with Spectroscopic and Zeta Potential Approaches. J SOLUTION CHEM 2012. [DOI: 10.1007/s10953-012-9895-3] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2022]
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12
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Gubaev A, Klostermeier D. Potassium ions are required for nucleotide-induced closure of gyrase N-gate. J Biol Chem 2012; 287:10916-21. [PMID: 22343632 DOI: 10.1074/jbc.m111.308247] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
DNA gyrase catalyzes ATP-dependent negative supercoiling of DNA by a strand passage mechanism that requires coordinated opening and closing of three protein interfaces, the N-, DNA-, and C-gates. ATP binding to the GyrB subunits of gyrase causes dimerization and N-gate closure. The closure of the N-gate is a key step in the gyrase catalytic cycle, as it captures the DNA segment to be transported and poises gyrase toward strand passage. We show here that K(+) ions are required for DNA supercoiling but are dispensable for ATP-independent DNA relaxation. Although DNA binding, distortion, wrapping, and DNA-induced narrowing of the N-gate occur in the absence of K(+), nucleotide-induced N-gate closure depends on their presence. Our results provide evidence that K(+) ions relay small conformational changes in the nucleotide-binding pocket to the formation of a tight dimer interface at the N-gate by connecting regions from both GyrB monomers and suggest an important role for K(+) in synchronization of N-gate closure and DNA-gate opening.
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Affiliation(s)
- Airat Gubaev
- Institute for Physical Chemistry, University of Münster, D-48149 Münster, Germany.
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14
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Akanuma S, Iwami S, Yokoi T, Nakamura N, Watanabe H, Yokobori SI, Yamagishi A. Phylogeny-Based Design of a B-Subunit of DNA Gyrase and Its ATPase Domain Using a Small Set of Homologous Amino Acid Sequences. J Mol Biol 2011; 412:212-25. [DOI: 10.1016/j.jmb.2011.07.042] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2010] [Revised: 07/19/2011] [Accepted: 07/20/2011] [Indexed: 10/17/2022]
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15
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Alt S, Mitchenall LA, Maxwell A, Heide L. Inhibition of DNA gyrase and DNA topoisomerase IV of Staphylococcus aureus and Escherichia coli by aminocoumarin antibiotics. J Antimicrob Chemother 2011; 66:2061-9. [DOI: 10.1093/jac/dkr247] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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16
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Baker NM, Weigand S, Maar-Mathias S, Mondragón A. Solution structures of DNA-bound gyrase. Nucleic Acids Res 2011; 39:755-66. [PMID: 20870749 PMCID: PMC3025574 DOI: 10.1093/nar/gkq799] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2010] [Revised: 08/20/2010] [Accepted: 08/24/2010] [Indexed: 12/02/2022] Open
Abstract
The DNA gyrase negative supercoiling mechanism involves the assembly of a large gyrase/DNA complex and conformational rearrangements coupled to ATP hydrolysis. To establish the complex arrangement that directs the reaction towards negative supercoiling, bacterial gyrase complexes bound to 137- or 217-bp DNA fragments representing the starting conformational state of the catalytic cycle were characterized by sedimentation velocity and small-angle X-ray scattering (SAXS) experiments. The experiments revealed elongated complexes with hydrodynamic radii of 70-80 Å. Molecular envelopes calculated from these SAXS data show 2-fold symmetric molecules with the C-terminal domain (CTD) of the A subunit and the ATPase domain of the B subunit at opposite ends of the complexes. The proposed gyrase model, with the DNA binding along the sides of the molecule and wrapping around the CTDs located near the exit gate of the protein, adds new information on the mechanism of DNA negative supercoiling.
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Affiliation(s)
- Nicole M. Baker
- Department of Molecular Biosciences, Northwestern University, 2205 Tech Dr, Evanston, IL 60208, USA and DND-CAT Synchrotron Research Center, APS/ANL Building 432A, 9700 S. Cass Ave., Argonne, IL 60439, USA
| | - Steven Weigand
- Department of Molecular Biosciences, Northwestern University, 2205 Tech Dr, Evanston, IL 60208, USA and DND-CAT Synchrotron Research Center, APS/ANL Building 432A, 9700 S. Cass Ave., Argonne, IL 60439, USA
| | - Sarah Maar-Mathias
- Department of Molecular Biosciences, Northwestern University, 2205 Tech Dr, Evanston, IL 60208, USA and DND-CAT Synchrotron Research Center, APS/ANL Building 432A, 9700 S. Cass Ave., Argonne, IL 60439, USA
| | - Alfonso Mondragón
- Department of Molecular Biosciences, Northwestern University, 2205 Tech Dr, Evanston, IL 60208, USA and DND-CAT Synchrotron Research Center, APS/ANL Building 432A, 9700 S. Cass Ave., Argonne, IL 60439, USA
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Joung IS, Cheatham TE. Molecular dynamics simulations of the dynamic and energetic properties of alkali and halide ions using water-model-specific ion parameters. J Phys Chem B 2009; 113:13279-90. [PMID: 19757835 PMCID: PMC2755304 DOI: 10.1021/jp902584c] [Citation(s) in RCA: 384] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The dynamic and energetic properties of the alkali and halide ions were calculated using molecular dynamics (MD) and free energy simulations with various different water and ion force fields including our recently developed water-model-specific ion parameters. The properties calculated were activity coefficients, diffusion coefficients, residence times of atomic pairs, association constants, and solubility. Through calculation of these properties, we can assess the validity and range of applicability of the simple pair potential models and better understand their limitations. Due to extreme computational demands, the activity coefficients were only calculated for a subset of the models. The results qualitatively agree with experiment. Calculated diffusion coefficients and residence times between cation-anion, water-cation, and water-anion showed differences depending on the choice of water and ion force field used. The calculated solubilities of the alkali-halide salts were generally lower than the true solubility of the salts. However, for both the TIP4P(EW) and SPC/E water-model-specific ion parameters, solubility was reasonably well-reproduced. Finally, the correlations among the various properties led to the following conclusions: (1) The reliability of the ion force fields is significantly affected by the specific choice of water model. (2) Ion-ion interactions are very important to accurately simulate the properties, especially solubility. (3) The SPC/E and TIP4P(EW) water-model-specific ion force fields are preferred for simulation in high salt environments compared to the other ion force fields.
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Affiliation(s)
- In Suk Joung
- Department of Bioengineering, College of Engineering, Department of Medicinal Chemistry, College of Pharmacy, and Department of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, University of Utah, Salt Lake City, Utah 84112, USA
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Mapping simocyclinone D8 interaction with DNA gyrase: evidence for a new binding site on GyrB. Antimicrob Agents Chemother 2009; 54:213-20. [PMID: 19858260 DOI: 10.1128/aac.00972-09] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Simocyclinone D8, a coumarin derivative isolated from Streptomyces antibioticus Tü 6040, represents an interesting new antiproliferative agent. It was originally suggested that this drug recognizes the GyrA subunit and interferes with the gyrase catalytic cycle by preventing its binding to DNA. To further characterize the mode of action of this antibiotic, we investigated its binding to the reconstituted DNA gyrase (A(2)B(2)) as well as to its GyrA and GyrB subunits and the individual domains of these proteins, by performing protein melting and proteolytic digestion studies as well as inhibition assays. Two binding sites were identified, one (anticipated) in the N-terminal domain of GyrA (GyrA59) and the other (unexpected) at the C-terminal domain of GyrB (GyrB47). Stabilization of the A subunit appears to be considerably more effective than stabilization of the B subunit. Our data suggest that these two distinct sites could cooperate in the reconstituted enzyme.
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19
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Sissi C, Palumbo M. Effects of magnesium and related divalent metal ions in topoisomerase structure and function. Nucleic Acids Res 2009; 37:702-11. [PMID: 19188255 PMCID: PMC2647314 DOI: 10.1093/nar/gkp024] [Citation(s) in RCA: 116] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The catalytic steps through which DNA topoisomerases produce their biological effects and the interference of drug molecules with the enzyme–DNA cleavage complex have been thoroughly investigated both from the biophysical and the biochemical point of view. This provides the basic structural insight on how this family of essential enzymes works in living systems and how their functions can be impaired by natural and synthetic compounds. Besides other factors, the physiological environment is known to affect substantially the biological properties of topoisomerases, a key role being played by metal ion cofactors, especially divalent ions (Mg2+), that are crucial to bestow and modulate catalytic activity by exploiting distinctive chemical features such as ionic size, hardness and characteristics of the coordination sphere including coordination number and geometry. Indeed, metal ions mediate fundamental aspects of the topoisomerase-driven transphosphorylation process by affecting the kinetics of the forward and the reverse steps and by modifying the enzyme conformation and flexibility. Of particular interest in type IA and type II enzymes are ionic interactions involving the Toprim fold, a protein domain conserved through evolution that contains a number of acidic residues essential for catalysis. A general two-metal ion mechanism is widely accepted to account for the biophysical and biochemical data thus far available.
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Affiliation(s)
- Claudia Sissi
- Department of Pharmaceutical Sciences, University of Padova, Via Marzolo 5, 35131 Padova, Italy
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Joung IS, Cheatham, TE. Determination of alkali and halide monovalent ion parameters for use in explicitly solvated biomolecular simulations. J Phys Chem B 2008; 112:9020-41. [PMID: 18593145 PMCID: PMC2652252 DOI: 10.1021/jp8001614] [Citation(s) in RCA: 2293] [Impact Index Per Article: 143.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2008] [Revised: 04/30/2008] [Indexed: 12/11/2022]
Abstract
Alkali (Li(+), Na(+), K(+), Rb(+), and Cs(+)) and halide (F(-), Cl(-), Br(-), and I(-)) ions play an important role in many biological phenomena, roles that range from stabilization of biomolecular structure, to influence on biomolecular dynamics, to key physiological influence on homeostasis and signaling. To properly model ionic interaction and stability in atomistic simulations of biomolecular structure, dynamics, folding, catalysis, and function, an accurate model or representation of the monovalent ions is critically necessary. A good model needs to simultaneously reproduce many properties of ions, including their structure, dynamics, solvation, and moreover both the interactions of these ions with each other in the crystal and in solution and the interactions of ions with other molecules. At present, the best force fields for biomolecules employ a simple additive, nonpolarizable, and pairwise potential for atomic interaction. In this work, we describe our efforts to build better models of the monovalent ions within the pairwise Coulombic and 6-12 Lennard-Jones framework, where the models are tuned to balance crystal and solution properties in Ewald simulations with specific choices of well-known water models. Although it has been clearly demonstrated that truly accurate treatments of ions will require inclusion of nonadditivity and polarizability (particularly with the anions) and ultimately even a quantum mechanical treatment, our goal was to simply push the limits of the additive treatments to see if a balanced model could be created. The applied methodology is general and can be extended to other ions and to polarizable force-field models. Our starting point centered on observations from long simulations of biomolecules in salt solution with the AMBER force fields where salt crystals formed well below their solubility limit. The likely cause of the artifact in the AMBER parameters relates to the naive mixing of the Smith and Dang chloride parameters with AMBER-adapted Aqvist cation parameters. To provide a more appropriate balance, we reoptimized the parameters of the Lennard-Jones potential for the ions and specific choices of water models. To validate and optimize the parameters, we calculated hydration free energies of the solvated ions and also lattice energies (LE) and lattice constants (LC) of alkali halide salt crystals. This is the first effort that systematically scans across the Lennard-Jones space (well depth and radius) while balancing ion properties like LE and LC across all pair combinations of the alkali ions and halide ions. The optimization across the entire monovalent series avoids systematic deviations. The ion parameters developed, optimized, and characterized were targeted for use with some of the most commonly used rigid and nonpolarizable water models, specifically TIP3P, TIP4P EW, and SPC/E. In addition to well reproducing the solution and crystal properties, the new ion parameters well reproduce binding energies of the ions to water and the radii of the first hydration shells.
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Affiliation(s)
| | - Thomas E. Cheatham,
- To whom correspondence should be addressed: Phone: (801) 587-9652. Fax: (801) 585-9119. E-mail:
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Sissi C, Chemello A, Vazquez E, Mitchenall LA, Maxwell A, Palumbo M. DNA gyrase requires DNA for effective two-site coordination of divalent metal ions: further insight into the mechanism of enzyme action. Biochemistry 2008; 47:8538-45. [PMID: 18642932 DOI: 10.1021/bi800480j] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The catalytic properties of DNA gyrase, an A 2B 2 complex, are modulated by the presence of divalent metal ions. Using circular dichroism, protein melting experiments and enzyme activity assays, we investigated the correlation between the A 2B 2 conformation, the nature of the metal ion cofactor and the enzyme activity in the presence and absence of DNA substrate. At room temperature, DNA gyrase structure is not appreciably affected by Ca (2+) or Mg (2+) but is modified by Mn (2+). In addition, metal ions strongly affect the enzyme's thermal transitions, rendering the A 2B 2 structure more flexible. Using the B subunit, we were able to identify two distinct complexes with manganese ions. The first one exhibits a 1:1 stoichiometry and is not affected by the presence of DNA. The second complex is associated with a large protein structural modification that can be remarkably modulated by addition of the DNA substrate. This behavior is conserved in the reconstituted protein. Studies with two GyrB mutants indicate that Mn (2+) interference with the TOPRIM region modulates gyrase supercoiling activity. In particular, considering the need for two divalent metal ions for an efficient catalytic cleavage of the phosphodiester bond, our data suggest that residue D500 participates in the first complexation event (DNA-independent), whereas residue D498 is involved mainly in the second process. In conclusion, a combination of the ion features (ionic size, electronegativity, coordination sphere) operating at the level of the catalytic region and of the ion-driven modifications in overall enzyme structure and flexibility contribute to the mechanism of gyrase activity. An effectual role for DNA recruiting the second catalytic metal ion is envisaged.
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Affiliation(s)
- Claudia Sissi
- Department of Pharmaceutical Sciences, University of Padova, Via Marzolo, 5, 35131 Padova, Italy
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Chen P, Jiang M, Hu T, Liu Q, Chen XS, Guo D. Biochemical characterization of exoribonuclease encoded by SARS coronavirus. BMB Rep 2008; 40:649-55. [PMID: 17927896 DOI: 10.5483/bmbrep.2007.40.5.649] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The nsp14 protein is an exoribonuclease that is encoded by severe acute respiratory syndrome coronavirus (SARS-CoV). We have cloned and expressed the nsp14 protein in Escherichia coli, and characterized the nature and the role(s) of the metal ions in the reaction chemistry. The purified recombinant nsp14 protein digested a 5'-labeled RNA molecule, but failed to digest the RNA substrate that is modified with fluorescein group at the 3'-hydroxyl group, suggesting a 3'-to-5' exoribonuclease activity. The exoribonuclease activity requires Mg2+ as a cofactor. Isothermal titration calorimetry (ITC) analysis indicated a two-metal binding mode for divalent cations by nsp14. Endogenous tryptophan fluorescence and circular dichroism (CD) spectra measurements showed that there was a structural change of nsp14 when binding with metal ions. We propose that the conformational change induced by metal ions may be a prerequisite for catalytic activity by correctly positioning the side chains of the residues located in the active site of the enzyme.
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Affiliation(s)
- Ping Chen
- State Key Laboratory of Virology and The Modern Virology Research Centre, College of Life Sciences, Wuhan University, Wuhan 430072, PR China
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