1
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Hu Y, Liu B. The Copper Efflux Regulator (CueR). Subcell Biochem 2024; 104:17-31. [PMID: 38963481 DOI: 10.1007/978-3-031-58843-3_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/05/2024]
Abstract
The copper efflux regulator (CueR) is a classical member of the MerR family of metalloregulators and is common in gram-negative bacteria. Through its C-terminal effector-binding domain, CueR senses cytoplasmic copper ions to regulate the transcription of genes contributing to copper homeostasis, an essential process for survival of all cells. In this chapter, we review the regulatory roles of CueR in the model organism Escherichia coli and the mechanisms for CueR in copper binding, DNA recognition, and interplay with RNA polymerase in regulating transcription. In light of biochemical and structural analyses, we provide molecular details for how CueR represses transcription in the absence of copper ions, how copper ions mediate CueR conformational change to form holo CueR, and how CueR bends and twists promoter DNA to activate transcription. We also characterize the functional domains and key residues involved in these processes. Since CueR is a representative member of the MerR family, elucidating its regulatory mechanisms could help to understand the CueR-like regulators in other organisms and facilitate the understanding of other metalloregulators in the same family.
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Affiliation(s)
- Yangbo Hu
- State Key Laboratory of Virology, Wuhan Institute of Virology, Center for Biosafety Mega-Science, Chinese Academy of Sciences, Wuhan, China.
| | - Bin Liu
- Section of Transcription & Gene Regulation, The Hormel Institute, University of Minnesota, Austin, MN, USA.
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2
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Sajjad H, Sajjad A, Haya RT, Khan MM, Zia M. Copper oxide nanoparticles: In vitro and in vivo toxicity, mechanisms of action and factors influencing their toxicology. Comp Biochem Physiol C Toxicol Pharmacol 2023; 271:109682. [PMID: 37328134 DOI: 10.1016/j.cbpc.2023.109682] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Revised: 05/21/2023] [Accepted: 06/11/2023] [Indexed: 06/18/2023]
Abstract
Copper oxide nanoparticles (CuO NPs) have received increasing interest due to their distinctive properties, including small particle size, high surface area, and reactivity. Due to these properties, their applications have been expanded rapidly in various areas such as biomedical properties, industrial catalysts, gas sensors, electronic materials, and environmental remediation. However, because of these widespread uses, there is now an increased risk of human exposure, which could lead to short- and long-term toxicity. This review addresses the underlying toxicity mechanisms of CuO NPs in cells which include reactive oxygen species generation, leaching of Cu ion, coordination effects, non-homeostasis effect, autophagy, and inflammation. In addition, different key factors responsible for toxicity, characterization, surface modification, dissolution, NPs dose, exposure pathways and environment are discussed to understand the toxicological impact of CuO NPs. In vitro and in vivo studies have shown that CuO NPs cause oxidative stress, cytotoxicity, genotoxicity, immunotoxicity, neurotoxicity, and inflammation in bacterial, algal, fish, rodents, and human cell lines. Therefore, to make CuO NPs a more suitable candidate for various applications, it is essential to address their potential toxic effects, and hence, more studies should be done on the long-term and chronic impacts of CuO NPs at different concentrations to assure the safe usage of CuO NPs.
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Affiliation(s)
- Humna Sajjad
- Department of Biotechnology, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Anila Sajjad
- Department of Biotechnology, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Rida Tul Haya
- Department of Biotechnology, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | | | - Muhammad Zia
- Department of Biotechnology, Quaid-i-Azam University, Islamabad 45320, Pakistan.
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3
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How Theoretical Evaluations Can Generate Guidelines for Designing/Engineering Metalloproteins with Desired Metal Affinity and Selectivity. MOLECULES (BASEL, SWITZERLAND) 2022; 28:molecules28010249. [PMID: 36615442 PMCID: PMC9822464 DOI: 10.3390/molecules28010249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 12/23/2022] [Accepted: 12/25/2022] [Indexed: 12/29/2022]
Abstract
Almost half of all known proteins contain metal co-factors. Crucial for the flawless performance of a metalloprotein is the selection with high fidelity of the cognate metal cation from the surrounding biological fluids. Therefore, elucidating the factors controlling the metal binding and selectivity in metalloproteins is of particular significance. The knowledge thus acquired not only contributes to better understanding of the intimate mechanism of these events but, also, significantly enriches the researcher's toolbox that could be used in designing/engineering novel metalloprotein structures with pre-programmed properties. A powerful tool in aid of deciphering the physical principles behind the processes of metal recognition and selectivity is theoretical modeling of metal-containing biological structures. This review summarizes recent findings in the field with an emphasis on elucidating the major factors governing these processes. The results from theoretical evaluations are discussed. It is the hope that the physical principles evaluated can serve as guidelines in designing/engineering of novel metalloproteins of interest to both science and industry.
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4
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Muhammad A, He J, Yu T, Sun C, Shi D, Jiang Y, Xianyu Y, Shao Y. Dietary exposure of copper and zinc oxides nanoparticles affect the fitness, enzyme activity, and microbial community of the model insect, silkworm Bombyx mori. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 813:152608. [PMID: 34973320 DOI: 10.1016/j.scitotenv.2021.152608] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 12/16/2021] [Accepted: 12/18/2021] [Indexed: 05/24/2023]
Abstract
Copper and Zinc oxides nanoparticles (CuO and ZnO NPs, respectively) are among the most produced and commonly used engineered nanomaterials. They can be released into the environment, thereby causing health concerns and risks to biodiversity that indicate a need to evaluate their toxicological effects in a complex situation. Here, we used the insect model organism silkworm Bombyx mori to address the concerns about the biological effects associated with dietary exposure of CuO and ZnO NPs. ICP-MS analysis revealed significant accumulation of Cu and Zn (the latter being more accumulated) in silkworms' tissues (gut, fat body, silk gland, and malpighian tubule), and some elimination through feces in the respective NPs-exposed groups. NPs-exposures led to a decrease in larval body mass, survivorship, and cocoon production, where the effects of ZnO NPs were more pronounced. We also found that NPs-exposure induced gene expression changes (Attacin, lysozyme, SOD, and Dronc) and altered the activities of antioxidant enzymes (SOD, GST, and CAT), as well as impaired nutrient metabolism (alpha-amylase). Given their antibacterial property, CuO and ZnO NPs decreased species richness and diversity of the gut bacterial community and shifted their configuration to overt microbiome i.e., decreased abundance of probiotics (e.g., Acetobacter) and increased pathobionts (e.g., Pseudomonas, Bacillus, Escherichia, Enterococcus, Ralstonia, etc.) proportions. Overall, this integrated study revealed the unintended negative effects of CuO and ZnO NPs on silkworms and highlighted the potential to inevitably affect all living things due to intensive and possible mishandling of nanomaterials.
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Affiliation(s)
- Abrar Muhammad
- Max Planck Partner Group, Institute of Sericulture and Apiculture, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Jintao He
- Max Planck Partner Group, Institute of Sericulture and Apiculture, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Ting Yu
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, China
| | - Chao Sun
- Analysis Center of Agrobiology and Environmental Sciences, Zhejiang University, Hangzhou, China
| | - Dier Shi
- Department of Chemistry, Zhejiang University, Hangzhou, China
| | - Yan Jiang
- Department of Chemistry, Zhejiang University, Hangzhou, China
| | - Yunlei Xianyu
- College of Biosystems Engineering and Food Science, Zhejiang University, Hangzhou, China
| | - Yongqi Shao
- Max Planck Partner Group, Institute of Sericulture and Apiculture, College of Animal Sciences, Zhejiang University, Hangzhou, China; Key Laboratory for Molecular Animal Nutrition, Ministry of Education, China.
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5
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Lella M, Mahalakshmi R. De novo
design of metal‐binding cleft in a
Trp‐Trp
stapled thermostable β‐hairpin peptide. Pept Sci (Hoboken) 2021. [DOI: 10.1002/pep2.24240] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Muralikrishna Lella
- Molecular Biophysics Laboratory, Department of Biological Sciences Indian Institute of Science Education and Research Bhopal India
| | - Radhakrishnan Mahalakshmi
- Molecular Biophysics Laboratory, Department of Biological Sciences Indian Institute of Science Education and Research Bhopal India
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6
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Jing Z, Rackers JA, Pratt LR, Liu C, Rempe SB, Ren P. Thermodynamics of ion binding and occupancy in potassium channels. Chem Sci 2021; 12:8920-8930. [PMID: 34257893 PMCID: PMC8246295 DOI: 10.1039/d1sc01887f] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 06/01/2021] [Indexed: 12/15/2022] Open
Abstract
Potassium channels modulate various cellular functions through efficient and selective conduction of K+ ions. The mechanism of ion conduction in potassium channels has recently emerged as a topic of debate. Crystal structures of potassium channels show four K+ ions bound to adjacent binding sites in the selectivity filter, while chemical intuition and molecular modeling suggest that the direct ion contacts are unstable. Molecular dynamics (MD) simulations have been instrumental in the study of conduction and gating mechanisms of ion channels. Based on MD simulations, two hypotheses have been proposed, in which the four-ion configuration is an artifact due to either averaged structures or low temperature in crystallographic experiments. The two hypotheses have been supported or challenged by different experiments. Here, MD simulations with polarizable force fields validated by ab initio calculations were used to investigate the ion binding thermodynamics. Contrary to previous beliefs, the four-ion configuration was predicted to be thermodynamically stable after accounting for the complex electrostatic interactions and dielectric screening. Polarization plays a critical role in the thermodynamic stabilities. As a result, the ion conduction likely operates through a simple single-vacancy and water-free mechanism. The simulations explained crystal structures, ion binding experiments and recent controversial mutagenesis experiments. This work provides a clear view of the mechanism underlying the efficient ion conduction and demonstrates the importance of polarization in ion channel simulations. Polarization shapes the energy landscape of ion conduction in potassium channels.![]()
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Affiliation(s)
- Zhifeng Jing
- Department of Biomedical Engineering, The University of Texas at Austin Austin Texas 78712 USA
| | - Joshua A Rackers
- Center for Integrated Nanotechnologies, Sandia National Laboratories Albuquerque New Mexico 87185 USA
| | - Lawrence R Pratt
- Department of Chemical and Biomolecular Engineering, Tulane University New Orleans Louisiana 70118 USA
| | - Chengwen Liu
- Department of Biomedical Engineering, The University of Texas at Austin Austin Texas 78712 USA
| | - Susan B Rempe
- Center for Integrated Nanotechnologies, Sandia National Laboratories Albuquerque New Mexico 87185 USA
| | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin Austin Texas 78712 USA
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7
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Balogh RK, Gyurcsik B, Jensen M, Thulstrup PW, Köster U, Christensen NJ, Mørch FJ, Jensen ML, Jancsó A, Hemmingsen L. Flexibility of the CueR Metal Site Probed by Instantaneous Change of Element and Oxidation State from Ag I to Cd II. Chemistry 2020; 26:7451-7457. [PMID: 32045037 PMCID: PMC7317920 DOI: 10.1002/chem.202000132] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Indexed: 02/06/2023]
Abstract
Selectivity for monovalent metal ions is an important facet of the function of the metalloregulatory protein CueR. 111Ag perturbed angular correlation of γ‐rays (PAC) spectroscopy probes the metal site structure and the relaxation accompanying the instantaneous change from AgI to CdII upon 111Ag radioactive decay. That is, a change from AgI, which activates transcription, to CdII, which does not. In the frozen state (−196 °C) two nuclear quadrupole interactions (NQIs) are observed; one (NQI1) agrees well with two coordinating thiolates and an additional longer contact to the S77 backbone carbonyl, and the other (NQI2) reflects that CdII has attracted additional ligand(s). At 1 °C only NQI2 is observed, demonstrating that relaxation to this structure occurs within ≈10 ns of the decay of 111Ag. Thus, transformation from AgI to CdII rapidly disrupts the functional linear bis(thiolato)AgI metal site structure. This inherent metal site flexibility may be central to CueR function, leading to remodelling into a non‐functional structure upon binding of non‐cognate metal ions. In a broader perspective, 111Ag PAC spectroscopy may be applied to probe the flexibility of protein metal sites.
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Affiliation(s)
- Ria K Balogh
- Department of Inorganic and Analytical Chemistry, University of Szeged, Dóm tér 7, 6720, Szeged, Hungary
| | - Béla Gyurcsik
- Department of Inorganic and Analytical Chemistry, University of Szeged, Dóm tér 7, 6720, Szeged, Hungary
| | - Mikael Jensen
- Hevesy Laboratory, DTU-Health, Technical University of Denmark, Frederiksborgvej 399, 4000, Roskilde, Denmark
| | - Peter W Thulstrup
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100, Copenhagen, Denmark
| | - Ulli Köster
- Institut Laue-Langevin, 71 avenue des Martyrs, 38042, Grenoble, France
| | - Niels Johan Christensen
- Department of Chemistry, Faculty of Science, University of Copenhagen, Thorvaldsensvej 40, 1, 871, Frederiksberg C, Denmark
| | - Frederik J Mørch
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100, Copenhagen, Denmark
| | - Marianne L Jensen
- Niels Bohr Institute, University of Copenhagen, Universitetsparken 5, 2100, Copenhagen, Denmark
| | - Attila Jancsó
- Department of Inorganic and Analytical Chemistry, University of Szeged, Dóm tér 7, 6720, Szeged, Hungary
| | - Lars Hemmingsen
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100, Copenhagen, Denmark
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8
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Song LF, Sengupta A, Merz KM. Thermodynamics of Transition Metal Ion Binding to Proteins. J Am Chem Soc 2020; 142:6365-6374. [PMID: 32141296 DOI: 10.1021/jacs.0c01329] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Modeling the thermodynamics of a transition metal (TM) ion assembly be it in proteins or in coordination complexes affords us a better understanding of the assembly and function of metalloclusters in diverse application areas including metal organic framework design, TM-based catalyst design, the trafficking of TM ions in biological systems, and drug design in metalloprotein platforms. While the structural details of TM ions bound to metalloproteins are generally well understood via experimental and computational approaches, accurate studies describing the thermodynamics of TM ion binding are rare. Herein, we demonstrate that we can obtain accurate structural and absolute binding free energies of Co2+ and Ni2+ to the enzyme glyoxalase I using an optimized 12-6-4 (m12-6-4) potential. Critically, this model simultaneously reproduces the solvation free energy of the individual TM ions and reproduces the thermodynamics of TM ion-ligand coordination as well as the thermodynamics of TM ion binding to a protein active site unlike extant models. We find the incorporation of the thermodynamics associated with protonation state changes for the TM ion (un)binding to be crucial. The high accuracy of m12-6-4 potential in this study presents an accurate route to explore more complicated processes associated with TM cluster assembly and TM ion transport.
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9
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Balogh RK, Gyurcsik B, Hunyadi‐Gulyás É, Schell J, Thulstrup PW, Hemmingsen L, Jancsó A. C-terminal Cysteines of CueR Act as Auxiliary Metal Site Ligands upon Hg II Binding-A Mechanism To Prevent Transcriptional Activation by Divalent Metal Ions? Chemistry 2019; 25:15030-15035. [PMID: 31365771 PMCID: PMC6899792 DOI: 10.1002/chem.201902940] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Indexed: 01/20/2023]
Abstract
Intracellular CuI is controlled by the transcriptional regulator CueR, which effectively discriminates between monovalent and divalent metal ions. It is intriguing that HgII does not activate transcription, as bis-thiolate metal sites exhibit high affinity for HgII . Here the binding of HgII to CueR and a truncated variant, ΔC7-CueR, without the last 7 amino acids at the C-terminus including a conserved CCHH motif is explored. ESI-MS demonstrates that up to two HgII bind to CueR, while ΔC7-CueR accommodates only one HgII . 199m Hg PAC and UV absorption spectroscopy indicate HgS2 structure at both the functional and the CCHH metal site. However, at sub-equimolar concentrations of HgII at pH 8.0, the metal binding site displays an equilibrium between HgS2 and HgS3 , involving cysteines from both sites. We hypothesize that the C-terminal CCHH motif provides auxiliary ligands that coordinate to HgII and thereby prevents activation of transcription.
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Affiliation(s)
- Ria K. Balogh
- Department of Inorganic and Analytical ChemistryUniversity of SzegedDóm tér 76720SzegedHungary
| | - Béla Gyurcsik
- Department of Inorganic and Analytical ChemistryUniversity of SzegedDóm tér 76720SzegedHungary
| | - Éva Hunyadi‐Gulyás
- Laboratory of Proteomics ResearchInstitute of Biochemistry, Biological Research Centre of the Hungarian Academy of SciencesTemesvári krt. 626726SzegedHungary
| | - Juliana Schell
- Institute for Materials Science and Center for Nanointegration Duisburg-Essen (CENIDE)University of Duisburg-Essen, 45141 Essen (Germany), European Organization for Nuclear Research (CERN)1211GenevaSwitzerland
| | - Peter W. Thulstrup
- Department of ChemistryUniversity of CopenhagenUniversitetsparken 52100CopenhagenDenmark
| | - Lars Hemmingsen
- Department of ChemistryUniversity of CopenhagenUniversitetsparken 52100CopenhagenDenmark
| | - Attila Jancsó
- Department of Inorganic and Analytical ChemistryUniversity of SzegedDóm tér 76720SzegedHungary
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10
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Qi R, Walker B, Jing Z, Yu M, Stancu G, Edupuganti R, Dalby KN, Ren P. Computational and Experimental Studies of Inhibitor Design for Aldolase A. J Phys Chem B 2019; 123:6034-6041. [PMID: 31268712 DOI: 10.1021/acs.jpcb.9b04551] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Glycolytic enzyme fructose-bisphosphate aldolase A is an emerging therapeutic target in cancer. Recently, we have solved the crystal structure of murine aldolase in complex with naphthalene-2,6-diyl bisphosphate (ND1) that served as a template of the design of bisphosphate-based inhibitors. In this work, a series of ND1 analogues containing difluoromethylene (-CF2), methylene (-CH2), or aldehyde substitutions were designed. All designed compounds were studied using molecular dynamics (MD) simulations with the AMOEBA force field. Both energetics and structural analyses have been done to understand the calculated binding free energies. The average distances between ligand and protein atoms for ND1 were very similar to those for the ND1 crystal structure, which indicates that our MD simulation is sampling the correct conformation well. CF2 insertion lowers the binding free energy by 10-15 kcal/mol, while CF2 substitution slightly increases the binding free energy, which matches the experimental measurement. In addition, we found that NDB with two CF2 insertions, the strongest binder, is entropically driven, while others including NDA with one CF2 insertion are all enthalpically driven. This work provides insights into the mechanisms underlying protein-phosphate binding and enhances the capability of applying computational and theoretical frameworks to model, predict, and design diagnostic strategies targeting cancer.
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Affiliation(s)
| | | | | | - Maiya Yu
- Department of Biochemistry and Mathematics , University of Michigan , Ann Arbor , Michigan 48109 , United States
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11
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Jing Z, Liu C, Qi R, Ren P. Many-body effect determines the selectivity for Ca 2+ and Mg 2+ in proteins. Proc Natl Acad Sci U S A 2018; 115:E7495-E7501. [PMID: 30038003 PMCID: PMC6094099 DOI: 10.1073/pnas.1805049115] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Calcium ion is a versatile messenger in many cell-signaling processes. To achieve their functions, calcium-binding proteins selectively bind Ca2+ against a background of competing ions such as Mg2+ The high specificity of calcium-binding proteins has been intriguing since Mg2+ has a higher charge density than Ca2+ and is expected to bind more tightly to the carboxylate groups in calcium-binding pockets. Here, we showed that the specificity for Ca2+ is dictated by the many-body polarization effect, which is an energetic cost arising from the dense packing of multiple residues around the metal ion. Since polarization has stronger distance dependence compared with permanent electrostatics, the cost associated with the smaller Mg2+ is much higher than that with Ca2+ and outweighs the electrostatic attraction favorable for Mg2+ With the AMOEBA (atomic multipole optimized energetics for biomolecular simulation) polarizable force field, our simulations captured the relative binding free energy between Ca2+ and Mg2+ for proteins with various types of binding pockets and explained the nonmonotonic size dependence of the binding free energy in EF-hand proteins. Without electronic polarization, the smaller ions are always favored over larger ions and the relative binding free energy is roughly proportional to the net charge of the pocket. The many-body effect depends on both the number and the arrangement of charged residues. Fine-tuning of the ion selectivity could be achieved by combining the many-body effect and geometric constraint.
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Affiliation(s)
- Zhifeng Jing
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712
| | - Chengwen Liu
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712
| | - Rui Qi
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712
| | - Pengyu Ren
- Department of Biomedical Engineering, The University of Texas at Austin, Austin, TX 78712
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12
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Qi R, Jing Z, Liu C, Piquemal JP, Dalby KN, Ren P. Elucidating the Phosphate Binding Mode of Phosphate-Binding Protein: The Critical Effect of Buffer Solution. J Phys Chem B 2018; 122:6371-6376. [PMID: 29807433 DOI: 10.1021/acs.jpcb.8b03194] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Phosphate is an essential component of cell functions, and the specific transport of phosphorus into a cell is mediated by phosphate-binding protein (PBP). The mechanism of PBP-phosphate recognition remains controversial: on the basis of similar binding affinities at acidic and basic pHs, it is believed that the hydrogen network in the binding site is flexible to adapt to different protonation states of phosphates. However, only hydrogen (1H) phosphate was observed in the sub-angstrom X-ray structures. To address this inconsistency, we performed molecular dynamics simulations using the AMOEBA polarizable force field. Structural and free energy data from simulations suggested that 1H phosphate was the preferred bound form at both pHs. The binding of dihydrogen (2H) phosphate disrupted the hydrogen-bond network in the PBP pocket, and the computed affinity was much weaker than that of 1H phosphate. Furthermore, we showed that the discrepancy in the studies described above is resolved if the interaction between phosphate and the buffer agent is taken into account. The calculated apparent binding affinities are in excellent agreement with experimental measurements. Our results suggest the high specificity of PBP for 1H phosphate and highlight the importance of the buffer solution for the binding of highly charged ligands.
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Affiliation(s)
| | | | | | - Jean-Philip Piquemal
- Sorbonne Université, CNRS, Laboratoire de Chimie Theórique , 75252 Cedex 05 Paris , France
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13
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Chen J, Yuan P, Wang L, Huang Y. Enantioselective β-Protonation of Enals via a Shuttling Strategy. J Am Chem Soc 2017; 139:7045-7051. [DOI: 10.1021/jacs.7b02889] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Jiean Chen
- Key Laboratory of Chemical
Genomics, School of Chemical Biology and Biotechnology, Shenzhen Graduate School of Peking University, Shenzhen, 518055, China
| | - Pengfei Yuan
- Key Laboratory of Chemical
Genomics, School of Chemical Biology and Biotechnology, Shenzhen Graduate School of Peking University, Shenzhen, 518055, China
| | - Leming Wang
- Key Laboratory of Chemical
Genomics, School of Chemical Biology and Biotechnology, Shenzhen Graduate School of Peking University, Shenzhen, 518055, China
| | - Yong Huang
- Key Laboratory of Chemical
Genomics, School of Chemical Biology and Biotechnology, Shenzhen Graduate School of Peking University, Shenzhen, 518055, China
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14
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Studies on hydrolysis mechanism of anticancer ruthenium drug ImH[trans-Ru(Im)2Cl4] via ABEEMσπ polarizable force field combined with QM and MD-FEP. Chem Res Chin Univ 2017. [DOI: 10.1007/s40242-017-6401-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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15
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Tuli HS, Kashyap D, Bedi SK, Kumar P, Kumar G, Sandhu SS. Molecular aspects of metal oxide nanoparticle (MO-NPs) mediated pharmacological effects. Life Sci 2015; 143:71-9. [DOI: 10.1016/j.lfs.2015.10.021] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2015] [Revised: 10/12/2015] [Accepted: 10/20/2015] [Indexed: 10/22/2022]
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16
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Szunyogh D, Szokolai H, Thulstrup PW, Larsen FH, Gyurcsik B, Christensen NJ, Stachura M, Hemmingsen L, Jancsó A. Specificity of the Metalloregulator CueR for Monovalent Metal Ions: Possible Functional Role of a Coordinated Thiol? Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201508555] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Dániel Szunyogh
- MTA‐SZTE Bioinorganic Chemistry Research Group, Dóm tér 7, 6720 Szeged (Hungary)
| | - Hajnalka Szokolai
- Department of Inorganic and Analytical Chemistry, University of Szeged, Dóm tér 7, 6720 Szeged (Hungary)
| | - Peter W. Thulstrup
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen (Denmark)
| | - Flemming H. Larsen
- Department of Food Science, University of Copenhagen, Rolighedsvej 30, 1958 Frederiksberg C (Denmark)
| | - Béla Gyurcsik
- Department of Inorganic and Analytical Chemistry, University of Szeged, Dóm tér 7, 6720 Szeged (Hungary)
| | - Niels Johan Christensen
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen (Denmark)
| | - Monika Stachura
- ISOLDE‐CERN, 1211 Geneva 23 (Switzerland)
- TRIUMF, 4004 Wesbrook Mall, Vancouver, BC V6T 2A3 (Canada)
| | - Lars Hemmingsen
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen (Denmark)
| | - Attila Jancsó
- Department of Inorganic and Analytical Chemistry, University of Szeged, Dóm tér 7, 6720 Szeged (Hungary)
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17
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Szunyogh D, Szokolai H, Thulstrup PW, Larsen FH, Gyurcsik B, Christensen NJ, Stachura M, Hemmingsen L, Jancsó A. Specificity of the Metalloregulator CueR for Monovalent Metal Ions: Possible Functional Role of a Coordinated Thiol? Angew Chem Int Ed Engl 2015; 54:15756-61. [PMID: 26563985 DOI: 10.1002/anie.201508555] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2015] [Indexed: 11/12/2022]
Abstract
Metal-ion-responsive transcriptional regulators within the MerR family effectively discriminate between mono- and divalent metal ions. Herein we address the origin of the specificity of the CueR protein for monovalent metal ions. Several spectroscopic techniques were employed to study Ag(I) , Zn(II) , and Hg(II) binding to model systems encompassing the metal-ion-binding loop of CueR from E. coli and V. cholerae. In the presence of Ag(I) , a conserved cysteine residue displays a pKa value for deprotonation of the thiol that is close to the physiological pH value. This property is only observed with the monovalent metal ion. Quantum chemically optimized structures of the CueR metal site with Cys 112 protonated demonstrate that the conserved Ser 77 backbone carbonyl oxygen atom from the other monomer of the homodimer is "pulled" towards the metal site. A common allosteric mechanism of the metalloregulatory members of the MerR family is proposed. For CueR, the mechanism relies on the protonation of Cys 112.
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Affiliation(s)
- Dániel Szunyogh
- MTA-SZTE Bioinorganic Chemistry Research Group, Dóm tér 7, 6720 Szeged (Hungary)
| | - Hajnalka Szokolai
- Department of Inorganic and Analytical Chemistry, University of Szeged, Dóm tér 7, 6720 Szeged (Hungary)
| | - Peter W Thulstrup
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen (Denmark)
| | - Flemming H Larsen
- Department of Food Science, University of Copenhagen, Rolighedsvej 30, 1958 Frederiksberg C (Denmark)
| | - Béla Gyurcsik
- Department of Inorganic and Analytical Chemistry, University of Szeged, Dóm tér 7, 6720 Szeged (Hungary)
| | - Niels Johan Christensen
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen (Denmark)
| | - Monika Stachura
- ISOLDE-CERN, 1211 Geneva 23 (Switzerland).,TRIUMF, 4004 Wesbrook Mall, Vancouver, BC V6T 2A3 (Canada)
| | - Lars Hemmingsen
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen (Denmark).
| | - Attila Jancsó
- Department of Inorganic and Analytical Chemistry, University of Szeged, Dóm tér 7, 6720 Szeged (Hungary).
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18
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Ngo V, da Silva MC, Kubillus M, Li H, Roux B, Elstner M, Cui Q, Salahub DR, Noskov SY. Quantum effects in cation interactions with first and second coordination shell ligands in metalloproteins. J Chem Theory Comput 2015; 11:4992-5001. [PMID: 26574284 PMCID: PMC4827603 DOI: 10.1021/acs.jctc.5b00524] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
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Despite
decades of investigations, the principal mechanisms responsible
for the high affinity and specificity of proteins for key physiological
cations K+, Na+, and Ca2+ remain
a hotly debated topic. At the core of the debate is an apparent need
(or lack thereof) for an accurate description of the electrostatic
response of the charge distribution in a protein to the binding of
an ion. These effects range from partial electronic polarization of
the directly ligating atoms to long-range effects related to partial
charge transfer and electronic delocalization effects. While accurate
modeling of cation recognition by metalloproteins warrants the use
of quantum-mechanics (QM) calculations, the most popular approximations
used in major biomolecular simulation packages rely on the implicit
modeling of electronic polarization effects. That is, high-level QM
computations for ion binding to proteins are desirable, but they are
often unfeasible, because of the large size of the reactive-site models
and the need to sample conformational space exhaustively at finite
temperature. Several solutions to this challenge have been proposed
in the field, ranging from the recently developed Drude polarizable
force-field for simulations of metalloproteins to approximate tight-binding
density functional theory (DFTB). To delineate the usefulness of different
approximations, we examined the accuracy of three recent and commonly
used theoretical models and numerical algorithms, namely, CHARMM C36,
the latest developed Drude polarizable force fields, and DFTB3 with
the latest 3OB parameters. We performed MD simulations for 30 cation-selective
proteins with high-resolution X-ray structures to create ensembles
of structures for analysis with different levels of theory, e.g.,
additive and polarizable force fields, DFTB3, and DFT. The results
from DFT computations were used to benchmark CHARMM C36, Drude, and
DFTB3 performance. The explicit modeling of quantum effects unveils
the key electrostatic properties of the protein sites and the importance
of specific ion-protein interactions. One of the most interesting
findings is that secondary coordination shells of proteins are noticeably
perturbed in a cation-dependent manner, showing significant delocalization
and long-range effects of charge transfer and polarization upon binding
Ca2+.
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Affiliation(s)
- Van Ngo
- Centre for Molecular Simulation and Department of Biological Sciences, University of Calgary , Calgary, Alberta, Canada T2N 1N4
| | - Mauricio C da Silva
- Centre for Molecular Simulation, Institute for Quantum Science and Technology and Department of Chemistry, University of Calgary , Calgary, Alberta, Canada T2N 1N4
| | - Maximilian Kubillus
- Institute of Physical Chemistry, Karlsruhe Institute of Technology , Kaiserstr. 12, 76021 Karlsruhe, Germany.,Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Hui Li
- Department of Biochemistry and Molecular Biology, University of Chicago , Chicago, Illinois 60637, United States
| | - Benoît Roux
- Department of Biochemistry and Molecular Biology, University of Chicago , Chicago, Illinois 60637, United States
| | - Marcus Elstner
- Institute of Physical Chemistry, Karlsruhe Institute of Technology , Kaiserstr. 12, 76021 Karlsruhe, Germany
| | - Qiang Cui
- Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Dennis R Salahub
- Centre for Molecular Simulation, Institute for Quantum Science and Technology and Department of Chemistry, University of Calgary , Calgary, Alberta, Canada T2N 1N4
| | - Sergei Yu Noskov
- Centre for Molecular Simulation and Department of Biological Sciences, University of Calgary , Calgary, Alberta, Canada T2N 1N4
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19
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A single serine residue determines selectivity to monovalent metal ions in metalloregulators of the MerR family. J Bacteriol 2015; 197:1606-13. [PMID: 25691529 DOI: 10.1128/jb.02565-14] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 02/11/2015] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED MerR metalloregulators alleviate toxicity caused by an excess of metal ions, such as copper, zinc, mercury, lead, cadmium, silver, or gold, by triggering the expression of specific efflux or detoxification systems upon metal detection. The sensor protein binds the inducer metal ion by using two conserved cysteine residues at the C-terminal metal-binding loop (MBL). Divalent metal ion sensors, such as MerR and ZntR, require a third cysteine residue, located at the beginning of the dimerization (α5) helix, for metal coordination, while monovalent metal ion sensors, such as CueR and GolS, have a serine residue at this position. This serine residue was proposed to provide hydrophobic and steric restrictions to privilege the binding of monovalent metal ions. Here we show that the presence of alanine at this position does not modify the activation pattern of monovalent metal sensors. In contrast, GolS or CueR mutant sensors with a substitution of cysteine for the serine residue respond to monovalent metal ions or Hg(II) with high sensitivities. Furthermore, in a mutant deleted of the Zn(II) exporter ZntA, they also trigger the expression of their target genes in response to either Zn(II), Cd(II), Pb(II), or Co(II). IMPORTANCE Specificity in a stressor's recognition is essential for mounting an appropriate response. MerR metalloregulators trigger the expression of specific resistance systems upon detection of heavy metal ions. Two groups of these metalloregulators can be distinguished, recognizing either +1 or +2 metal ions, depending on the presence of a conserved serine in the former or a cysteine in the latter. Here we demonstrate that the serine residue in monovalent metal ion sensors excludes divalent metal ion detection, as its replacement by cysteine renders a pan-metal ion sensor. Our results indicate that the spectrum of signals detected by these sensors is determined not only by the metal-binding ligand availability but also by the metal-binding cavity flexibility.
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20
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Gupta M, da Silva EF, Svendsen HF. Explicit Solvation Shell Model and Continuum Solvation Models for Solvation Energy and pKa Determination of Amino Acids. J Chem Theory Comput 2013; 9:5021-37. [DOI: 10.1021/ct400459y] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Mayuri Gupta
- Department
of Chemical Engineering, Norwegian University of Science and Technology, 7491 Trondheim, Norway
| | - Eirik F. da Silva
- Department
of Process Technology, SINTEF Materials and Chemistry, N-7465 Trondheim, Norway
| | - Hallvard F. Svendsen
- Department
of Chemical Engineering, Norwegian University of Science and Technology, 7491 Trondheim, Norway
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21
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Badarau A, Baslé A, Firbank SJ, Dennison C. Investigating the role of zinc and copper binding motifs of trafficking sites in the cyanobacterium Synechocystis PCC 6803. Biochemistry 2013; 52:6816-23. [PMID: 24050657 PMCID: PMC3793899 DOI: 10.1021/bi400492t] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Although zinc and copper are required by proteins with very different functions, these metals can be delivered to cellular locations by homologous metal transporters within the same organism, as demonstrated by the cyanobacterial ( Synechocystis PCC 6803) zinc exporter ZiaA and thylakoidal copper importer PacS. The N-terminal metal-binding domains of these transporters (ZiaAN and PacSN, respectively) have related ferredoxin folds also found in the metallochaperone Atx1, which delivers copper to PacS, but differ in the residues found in their M/IXCXXC metal-binding motifs. To investigate the role of the nonconserved residues in this region on metal binding, the sequence from ZiaAN has been introduced into Atx1 and PacSN, and the motifs of Atx1 and PacSN swapped. The motif sequence can tune Cu(I) affinity only approximately 3-fold. However, the introduction of the ZiaAN motif (MDCTSC) dramatically increases the Zn(II) affinity of both Atx1 and PacSN by up to 2 orders of magnitude. The Atx1 mutant with the ZiaAN motif crystallizes as a side-to-side homodimer very similar to that found for [Cu(I)2-Atx1]2 ( Badarau et al. Biochemistry 2010 , 49 , 7798 ). In a crystal structure of the PacSN mutant possessing the ZiaAN motif (PacSN(ZiaAN)), the Asp residue from the metal-binding motif coordinates Zn(II). This demonstrates that the increased Zn(II) affinity of this variant and the high Zn(II) affinity of ZiaAN are due to the ability of the carboxylate to ligate this metal ion. Comparison of the Zn(II) sites in PacSN(ZiaAN) structures provides additional insight into Zn(II) trafficking in cyanobacteria.
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Affiliation(s)
- Adriana Badarau
- Institute for Cell and Molecular Biosciences, Medical School, Newcastle University , Newcastle upon Tyne, NE2 4HH, United Kingdom
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22
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Dudev T, Lim C. Competition among metal ions for protein binding sites: determinants of metal ion selectivity in proteins. Chem Rev 2013; 114:538-56. [PMID: 24040963 DOI: 10.1021/cr4004665] [Citation(s) in RCA: 274] [Impact Index Per Article: 24.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Todor Dudev
- Institute of Biomedical Sciences, Academia Sinica , Taipei 11529, Taiwan
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23
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Hou G, Cui Q. Stabilization of different types of transition states in a single enzyme active site: QM/MM analysis of enzymes in the alkaline phosphatase superfamily. J Am Chem Soc 2013; 135:10457-69. [PMID: 23786365 PMCID: PMC3759165 DOI: 10.1021/ja403293d] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The first step for the hydrolysis of a phosphate monoester (pNPP(2-)) in enzymes of the alkaline phosphatase (AP) superfamily, R166S AP and wild-type NPP, is studied using QM/MM simulations based on an approximate density functional theory (SCC-DFTBPR) and a recently introduced QM/MM interaction Hamiltonian. The calculations suggest that similar loose transition states are involved in both enzymes, despite the fact that phosphate monoesters are the cognate substrates for AP but promiscuous substrates for NPP. The computed loose transition states are clearly different from the more synchronous ones previously calculated for diester reactions in the same AP enzymes. Therefore, our results explicitly support the proposal that AP enzymes are able to recognize and stabilize different types of transition states in a single active site. Analysis of the structural features of computed transition states indicates that the plastic nature of the bimetallic site plays a minor role in accommodating multiple types of transition states and that the high degree of solvent accessibility of the AP active site also contributes to its ability to stabilize diverse transition-state structures without the need of causing large structural distortions of the bimetallic motif. The binding mode of the leaving group in the transition state highlights that vanadate may not always be an ideal transition state analog for loose phosphoryl transfer transition states.
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Affiliation(s)
- Guanhua Hou
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706
| | - Qiang Cui
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706
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24
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Lu X, Cui Q. Charging free energy calculations using the Generalized Solvent Boundary Potential (GSBP) and periodic boundary condition: a comparative analysis using ion solvation and oxidation free energy in proteins. J Phys Chem B 2013; 117:2005-18. [PMID: 23347181 DOI: 10.1021/jp309877z] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Free energy simulations using a finite sphere boundary condition rather than a periodic boundary condition (PBC) are attractive in the study of very large biomolecular systems. To understand the quantitative impact of various approximations in such simulations, we compare charging free energies in both solution and protein systems calculated in a linear response framework with the Generalized Solvent Boundary Potential (GSBP) and PBC simulations. For simple ions in solution, we find good agreements between GSBP and PBC charging free energies, once the relevant correction terms are taken into consideration. For PBC simulations with the particle-mesh-Ewald for long-range electrostatics, the contribution (ΔG(P-M)) due to the use of a particle rather than molecule based summation scheme in real space is found to be significant, as pointed out by Hünenberger and co-workers. For GSBP, when the inner region is close to be charge neutral, the key correction is the overpolarization of water molecules at the inner/outer dielectric boundary; the magnitude of the correction (ΔG(s-pol)), however, is relatively small. For charging (oxidation) free energy in proteins, the situation is more complex, although good agreement between GSBP and PBC can still be obtained when care is exercised. The smooth dielectric boundary approximation inherent to GSBP tends to make significant errors when the inner region is featured with a high net charge. However, the error can be corrected with Poisson-Boltzmann calculations using snapshots from GSBP simulations in a straightforward and robust manner. Because of the more complex charge and solvent distributions, the magnitudes of ΔG(P-M) and ΔG(s-pol) in protein simulations appear to be different from those derived for solution simulations, leading to uncertainty in directly comparing absolute charging free energies from PBC and GSBP simulations for protein systems. The relative charging/oxidation free energies, however, are robust. With the linear response approximation, for the specific protein system (CueR) studied, the effect of freezing the protein structure in the outer region is found to be small, unless a very small (8 Å) inner region is used; even in the latter case, the result is substantially improved when the nearby metal binding loop is allowed to respond to metal oxidation. The implications of these results to the applicability of GSBP to complex biomolecules and in ab initio QM/MM simulations are discussed.
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Affiliation(s)
- Xiya Lu
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, USA
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25
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Chang YN, Zhang M, Xia L, Zhang J, Xing G. The Toxic Effects and Mechanisms of CuO and ZnO Nanoparticles. MATERIALS 2012. [PMCID: PMC5449046 DOI: 10.3390/ma5122850] [Citation(s) in RCA: 367] [Impact Index Per Article: 30.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Recent nanotechnological advances suggest that metal oxide nanoparticles (NPs) have been expected to be used in various fields, ranging from catalysis and opto-electronic materials to sensors, environmental remediation, and biomedicine. However, the growing use of NPs has led to their release into environment and the toxicity of metal oxide NPs on organisms has become a concern to both the public and scientists. Unfortunately, there are still widespread controversies and ambiguities with respect to the toxic effects and mechanisms of metal oxide NPs. Comprehensive understanding of their toxic effect is necessary to safely expand their use. In this review, we use CuO and ZnO NPs as examples to discuss how key factors such as size, surface characteristics, dissolution, and exposure routes mediate toxic effects, and we describe corresponding mechanisms, including oxidative stress, coordination effects and non-homeostasis effects.
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Affiliation(s)
- Ya-Nan Chang
- Chinese Academy of Science Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Institute of High Energy Physics, Chinese Academy of Science, Beijing 100049, China; E-Mails: (Y.-N.C.); (M.Z.)
| | - Mingyi Zhang
- Chinese Academy of Science Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Institute of High Energy Physics, Chinese Academy of Science, Beijing 100049, China; E-Mails: (Y.-N.C.); (M.Z.)
| | - Lin Xia
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China; E-Mail: (L.X.)
| | - Jun Zhang
- School of Life Science, Beijing Institute of Technology, Beijing 100081, China; E-Mail: (L.X.)
- Author to whom correspondence should be addressed; E-Mails: (G.X.); (J.Z.); Tel.: +86-10-88235738 (G.X.); +86-10-68915957-085 (J.Z.); Fax: +86-10-88236456 (G.X.)
| | - Gengmei Xing
- Chinese Academy of Science Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, Institute of High Energy Physics, Chinese Academy of Science, Beijing 100049, China; E-Mails: (Y.-N.C.); (M.Z.)
- Author to whom correspondence should be addressed; E-Mails: (G.X.); (J.Z.); Tel.: +86-10-88235738 (G.X.); +86-10-68915957-085 (J.Z.); Fax: +86-10-88236456 (G.X.)
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26
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Riccardi D, Guo HB, Parks JM, Gu B, Liang L, Smith JC. Cluster-Continuum Calculations of Hydration Free Energies of Anions and Group 12 Divalent Cations. J Chem Theory Comput 2012; 9:555-69. [DOI: 10.1021/ct300296k] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Demian Riccardi
- UT/ORNL Center for Molecular
Biophysics, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak
Ridge, Tennessee 37831-6309, United States
- Department of Biochemistry and
Cellular and Molecular Biology, University of Tennessee, Knoxville,
Tennessee 37996, United States
| | - Hao-Bo Guo
- UT/ORNL Center for Molecular
Biophysics, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak
Ridge, Tennessee 37831-6309, United States
| | - Jerry M. Parks
- UT/ORNL Center for Molecular
Biophysics, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak
Ridge, Tennessee 37831-6309, United States
| | - Baohua Gu
- Environmental Science Division,
Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United
States
| | - Liyuan Liang
- Environmental Science Division,
Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United
States
| | - Jeremy C. Smith
- UT/ORNL Center for Molecular
Biophysics, Oak Ridge National Laboratory, 1 Bethel Valley Road, Oak
Ridge, Tennessee 37831-6309, United States
- Department of Biochemistry and
Cellular and Molecular Biology, University of Tennessee, Knoxville,
Tennessee 37996, United States
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27
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Development and applications of the ABEEM fluctuating charge molecular force field in the ion-containing systems. Sci China Chem 2012. [DOI: 10.1007/s11426-012-4787-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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28
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Tamasi G, Mangani S, Cini R. Copper(I)-alkyl sulfide and -cysteine tri-nuclear clusters as models for metallo proteins: a structural density functional analysis. J Biomol Struct Dyn 2012; 30:728-51. [DOI: 10.1080/07391102.2012.689703] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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29
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Jiao D, Rempe SB. Combined Density Functional Theory (DFT) and Continuum Calculations of pKa in Carbonic Anhydrase. Biochemistry 2012; 51:5979-89. [DOI: 10.1021/bi201771q] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Dian Jiao
- Center for Biological and Materials Sciences, MS 0895, Sandia National Laboratories, Albuquerque, New Mexico
87185, United States
| | - Susan B. Rempe
- Center for Biological and Materials Sciences, MS 0895, Sandia National Laboratories, Albuquerque, New Mexico
87185, United States
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30
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Badarau A, Dennison C. Thermodynamics of copper and zinc distribution in the cyanobacterium Synechocystis PCC 6803. Proc Natl Acad Sci U S A 2011; 108:13007-12. [PMID: 21778408 PMCID: PMC3156197 DOI: 10.1073/pnas.1101448108] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Copper is supplied to plastocyanin for photosynthesis and cytochrome c oxidase for respiration in the thylakoids of Synechocystis PCC 6803 by the membrane-bound P-type ATPases CtaA and PacS, and the metallochaperone Atx1. We have determined the Cu(I) affinities of all of the soluble proteins and domains in this pathway. The Cu(I) affinities of the trafficking proteins range from 5 × 10(16) to 5 × 10(17) M(-1) at pH 7.0, consistent with values for homologues. Unusually, Atx1 binds Cu(I) significantly tighter than the metal-binding domains (MBDs) of CtaA and PacS (CtaA(N) and PacS(N)), and equilibrium copper exchange constants of approximately 0.2 are obtained for transfer to the MBDs. Dimerization of Atx1 increases the affinity for Cu(I), but the loop 5 His61 residue has little influence. The MBD of the zinc exporter ZiaA (ZiaA(N)) exhibits an almost identical Cu(I) affinity, and Cu(I) exchange with Atx1, as CtaA(N) and PacS(N), and the relative stabilities of the complexes must enable the metallochaperone to distinguish between the MBDs. The binding of potentially competing zinc to the trafficking proteins has been studied. ZiaA(N) has the highest Zn(II) affinity and thermodynamics could be important for zinc removal from the cell. Plastocyanin has a Cu(I) affinity of 2.6 × 10(17) M(-1), 15-fold tighter than that of the Cu(A) site of cytochrome c oxidase, highlighting the need for specific mechanisms to ensure copper delivery to both of these targets. The narrow range of Cu(I) affinities for the cytoplasmic copper proteins in Synechocystis will facilitate relocation when copper is limiting.
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Affiliation(s)
- Adriana Badarau
- Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Christopher Dennison
- Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
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