1
|
Yamaguchi T, Taborosi A, Sakai C, Akao K, Mori S, Kohzuma T. Systematic elucidation of the second coordination sphere effect on the structure and properties of a blue copper protein, pseudoazurin. J Inorg Biochem 2023; 246:112292. [PMID: 37354604 DOI: 10.1016/j.jinorgbio.2023.112292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 06/09/2023] [Accepted: 06/12/2023] [Indexed: 06/26/2023]
Abstract
The rational structural and computational studies of a blue copper protein, pseudoazurin (PAz), and its Met16X (X = Phe, Leu, Val, Ile) variants gave clear functional meanings of the noncovalent interaction (NCI) through the second coordination sphere. The high-resolution X-ray crystal structures of Met16X PAz demonstrated that the active site geometry is significantly affected by the substitution of Met16, which is located within the NCI distance from the His81 imidazole ring at the copper active site. The computational chemistry calculations based on the crystal structure analyses confirmed that the NCI of S-π/CH-π (wild-type), π-π (Met16Phe), double CH-π (Met16Leu), and single CH-π (Met16Val and Met16Ile). The estimated interaction energies for the NCI demonstrated that the fine-tuning of the protein stability and Cu site properties form the second coordination sphere of PAz.
Collapse
Affiliation(s)
- Takahide Yamaguchi
- Institute of Quantum Beam Science, Graduate School of Science and Engineering, Ibaraki University, Mito, Ibaraki 310-8512, Japan; Frontier Research Center for Applied Atomic Sciences, Ibaraki University, 162-1, Shirakata, Tokai, Ibaraki 319-1106, Japan
| | - Attila Taborosi
- Institute of Quantum Beam Science, Graduate School of Science and Engineering, Ibaraki University, Mito, Ibaraki 310-8512, Japan; Research Initiative for Supra-Materials, Faculty of Engineering, Shinshu University, 4-17-1, Wakasato, Nagano, Nagano 380-8553, Japan
| | - Chihiro Sakai
- Institute of Quantum Beam Science, Graduate School of Science and Engineering, Ibaraki University, Mito, Ibaraki 310-8512, Japan
| | - Kohei Akao
- Institute of Quantum Beam Science, Graduate School of Science and Engineering, Ibaraki University, Mito, Ibaraki 310-8512, Japan
| | - Seiji Mori
- Institute of Quantum Beam Science, Graduate School of Science and Engineering, Ibaraki University, Mito, Ibaraki 310-8512, Japan; Frontier Research Center for Applied Atomic Sciences, Ibaraki University, 162-1, Shirakata, Tokai, Ibaraki 319-1106, Japan
| | - Takamitsu Kohzuma
- Institute of Quantum Beam Science, Graduate School of Science and Engineering, Ibaraki University, Mito, Ibaraki 310-8512, Japan; Frontier Research Center for Applied Atomic Sciences, Ibaraki University, 162-1, Shirakata, Tokai, Ibaraki 319-1106, Japan.
| |
Collapse
|
2
|
Yamaguchi T, Akatsu M, Taborosi A, Kohzuma T. Unusual Protein Stability of the Met16Leu Pseudoazurin Variant. CHEM LETT 2020. [DOI: 10.1246/cl.200578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Takahide Yamaguchi
- Institute of Quantum Beam Science, Graduate School of Science and Engineering, Ibaraki University, Mito, Ibaraki 310-8512, Japan
- Frontier Research Center for Applied Atomic Sciences, 162-1 Shirakata, Tokai, Ibaraki 319-1106, Japan
| | - Miyu Akatsu
- Institute of Quantum Beam Science, Graduate School of Science and Engineering, Ibaraki University, Mito, Ibaraki 310-8512, Japan
| | - Attila Taborosi
- Institute of Quantum Beam Science, Graduate School of Science and Engineering, Ibaraki University, Mito, Ibaraki 310-8512, Japan
| | - Takamitsu Kohzuma
- Institute of Quantum Beam Science, Graduate School of Science and Engineering, Ibaraki University, Mito, Ibaraki 310-8512, Japan
- Frontier Research Center for Applied Atomic Sciences, 162-1 Shirakata, Tokai, Ibaraki 319-1106, Japan
| |
Collapse
|
3
|
Yamaguchi A, Edanami Y, Yamaguchi T, Shibuya Y, Fukaya N, Kohzuma T. Effect of Cavity Size of Mesoporous Silica on Type 1 Copper Site Geometry in Pseudoazurin. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2020. [DOI: 10.1246/bcsj.20190355] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Akira Yamaguchi
- Institute of Quantum Beam Science, Ibaraki University, 2-1-1 Bunkyo, Mito, Ibaraki 310-8512, Japan
| | - Yurie Edanami
- Institute of Quantum Beam Science, Ibaraki University, 2-1-1 Bunkyo, Mito, Ibaraki 310-8512, Japan
| | - Takahide Yamaguchi
- Institute of Quantum Beam Science, Ibaraki University, 2-1-1 Bunkyo, Mito, Ibaraki 310-8512, Japan
- Frontier Research Center for Applied Atomic Sciences, Ibaraki University, 162-1 Shirakata, Tokai, Ibaraki 319-1106, Japan
| | - Yuuta Shibuya
- New Industry Creation Hatchery Center, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai, Miyagi 980-8577, Japan
| | - Norihisa Fukaya
- National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba Central 5, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8565, Japan
| | - Takamitsu Kohzuma
- Institute of Quantum Beam Science, Ibaraki University, 2-1-1 Bunkyo, Mito, Ibaraki 310-8512, Japan
- Frontier Research Center for Applied Atomic Sciences, Ibaraki University, 162-1 Shirakata, Tokai, Ibaraki 319-1106, Japan
| |
Collapse
|
4
|
Yamaguchi T, Nihei Y, Sutherland DEK, Stillman MJ, Kohzuma T. Stabilization of protein structure through π-π interaction in the second coordination sphere of pseudoazurin. Protein Sci 2017; 26:1921-1931. [PMID: 28691165 DOI: 10.1002/pro.3226] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2017] [Revised: 07/01/2017] [Accepted: 07/04/2017] [Indexed: 11/11/2022]
Abstract
Noncovalent, weak interactions in the second coordination sphere of the copper active site of Pseudoazurin (PAz) from Achromobacter cycloclastes were examined using a series of Met16X variants. In this study, the differences in protein stability due to the changes in the nature of the 16th amino acid (Met, Phe, Val, Ile) were investigated by electrospray ionization mass spectrometry (ESI-MS) and far-UV circular dichroism (CD) as a result of acid denaturation. The percentage of native states (folded holo forms) of Met16Phe variants was estimated to be 75% at pH 2.9 although the wild-type (WT), Met16Val and Met16Ile PAz, became completely unfolded. The high stability under acidic conditions is correlated with the result of the active site being stabilized by the aromatic substitution of the Met16 residue. The π-π interaction in the second coordination sphere makes a significant contribution to the stability of active site and the protein matrix.
Collapse
Affiliation(s)
- Takahide Yamaguchi
- Graduate School of Science and Engineering, Institute of Quantum Beam Science, Ibaraki University, Mito, Ibaraki, 310-8512, Japan
| | - Yuko Nihei
- Graduate School of Science and Engineering, Institute of Quantum Beam Science, Ibaraki University, Mito, Ibaraki, 310-8512, Japan
| | - Duncan E K Sutherland
- Department of Biology, The University of Western Ontario, London, Ontario, Canada.,Department of Chemistry, The University of Western Ontario, London, Ontario, Canada
| | - Martin J Stillman
- Department of Biology, The University of Western Ontario, London, Ontario, Canada.,Department of Chemistry, The University of Western Ontario, London, Ontario, Canada
| | - Takamitsu Kohzuma
- Graduate School of Science and Engineering, Institute of Quantum Beam Science, Ibaraki University, Mito, Ibaraki, 310-8512, Japan
| |
Collapse
|
5
|
Arcos-López T, Qayyum M, Rivillas-Acevedo L, Miotto MC, Grande-Aztatzi R, Fernández CO, Hedman B, Hodgson KO, Vela A, Solomon EI, Quintanar L. Spectroscopic and Theoretical Study of Cu(I) Binding to His111 in the Human Prion Protein Fragment 106-115. Inorg Chem 2016; 55:2909-22. [PMID: 26930130 PMCID: PMC4804749 DOI: 10.1021/acs.inorgchem.5b02794] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Indexed: 12/19/2022]
Abstract
The ability of the cellular prion protein (PrP(C)) to bind copper in vivo points to a physiological role for PrP(C) in copper transport. Six copper binding sites have been identified in the nonstructured N-terminal region of human PrP(C). Among these sites, the His111 site is unique in that it contains a MKHM motif that would confer interesting Cu(I) and Cu(II) binding properties. We have evaluated Cu(I) coordination to the PrP(106-115) fragment of the human PrP protein, using NMR and X-ray absorption spectroscopies and electronic structure calculations. We find that Met109 and Met112 play an important role in anchoring this metal ion. Cu(I) coordination to His111 is pH-dependent: at pH >8, 2N1O1S species are formed with one Met ligand; in the range of pH 5-8, both methionine (Met) residues bind to Cu(I), forming a 1N1O2S species, where N is from His111 and O is from a backbone carbonyl or a water molecule; at pH <5, only the two Met residues remain coordinated. Thus, even upon drastic changes in the chemical environment, such as those occurring during endocytosis of PrP(C) (decreased pH and a reducing potential), the two Met residues in the MKHM motif enable PrP(C) to maintain the bound Cu(I) ions, consistent with a copper transport function for this protein. We also find that the physiologically relevant Cu(I)-1N1O2S species activates dioxygen via an inner-sphere mechanism, likely involving the formation of a copper(II) superoxide complex. In this process, the Met residues are partially oxidized to sulfoxide; this ability to scavenge superoxide may play a role in the proposed antioxidant properties of PrP(C). This study provides further insight into the Cu(I) coordination properties of His111 in human PrP(C) and the molecular mechanism of oxygen activation by this site.
Collapse
Affiliation(s)
| | - Munzarin Qayyum
- Department of Chemistry, Stanford University, Stanford, California 94395, United States
| | | | - Marco C. Miotto
- Max Planck
Laboratory for Structural Biology, Chemistry and Molecular Biophysics
of Rosario (MPLbioR, UNR-MPIbpC) and Instituto de Investigaciones
para el Descubrimiento de Fármacos de Rosario (IIDEFAR, UNR-CONICET), Universidad Nacional de Rosario, Ocampo y Esmeralda, S2002LRK Rosario, Argentina
| | | | - Claudio O. Fernández
- Max Planck
Laboratory for Structural Biology, Chemistry and Molecular Biophysics
of Rosario (MPLbioR, UNR-MPIbpC) and Instituto de Investigaciones
para el Descubrimiento de Fármacos de Rosario (IIDEFAR, UNR-CONICET), Universidad Nacional de Rosario, Ocampo y Esmeralda, S2002LRK Rosario, Argentina
| | - Britt Hedman
- Stanford Synchrotron Radiation Lightsource (SSRL), SLAC, Stanford University, Menlo Park, California 94025, United States
| | - Keith O. Hodgson
- Department of Chemistry, Stanford University, Stanford, California 94395, United States
- Stanford Synchrotron Radiation Lightsource (SSRL), SLAC, Stanford University, Menlo Park, California 94025, United States
| | - Alberto Vela
- Departamento
de Química, Cinvestav, Gustavo A. Madero, 07360 México
| | - Edward I. Solomon
- Department of Chemistry, Stanford University, Stanford, California 94395, United States
- Stanford Synchrotron Radiation Lightsource (SSRL), SLAC, Stanford University, Menlo Park, California 94025, United States
| | | |
Collapse
|
6
|
Yamaguchi T, Yano J, Yachandra VK, Nihei Y, Togashi H, Szilagyi RK, Kohzuma T. The Allosteric Regulation of Axial/Rhombic Population in a “Type 1” Copper Site: Multi-Edge X-ray Absorption Spectroscopic and Density Functional Studies of Pseudoazurin. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2015. [DOI: 10.1246/bcsj.20150225] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
| | - Junko Yano
- Physical Biosciences Division, Lawrence Berkeley National Laboratory
| | | | - Yuko Nihei
- Institute of Applied Beam Science, Ibaraki University
| | | | | | | |
Collapse
|
7
|
Clark KM, Yu Y, van der Donk WA, Blackburn N, Lu Y. Modulating the Copper-Sulfur Interaction in Type 1 Blue Copper Azurin by Replacing Cys112 with Nonproteinogenic Homocysteine. Inorg Chem Front 2014; 1:153-158. [PMID: 24707355 PMCID: PMC3972132 DOI: 10.1039/c3qi00096f] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The Cu-SCys interaction is known to play a dominant role in defining the type 1 (T1) blue copper center with respect to both its electronic structure and electron transfer function. Despite this importance, its role has yet to be probed by mutagenesis studies without dramatic change of its T1 copper character. We herein report replacement of the conserved Cys112 in azurin with the nonproteinogenic amino acid homocysteine. Based on electronic absorption, electron paramagnetic resonance, and extended x-ray absorption fine structural spectroscopic studies, this variant displays typical type 1 copper site features. Surprisingly, instead of increasing the strength of the Cu-sulfur interaction by the introduction of the extra methylene group, the Cys112Hcy azurin showed a decrease in the covalent interaction between SHcy and Cu(II) when compared with the WT SCys-Cu(II) interaction. This is likely due to geometric adjustment of the center that resulted in the copper ion moving out of the trigonal plane defined by two histidines and one Hcy and closer to Met121. These structural changes resulted in an increase of reduction potential by 35 mV, consistent with lower Cu-S covalency. These results suggest that the Cu-SCys interaction is close to being optimal in native blue copper protein. It also demonstrates the power of using nonproteinogenic amino acids in addressing important issues in bioinorganic chemistry.
Collapse
Affiliation(s)
- Kevin M Clark
- University of Illinois-Urbana, Department of Biochemistry, Urbana, IL61801; USA
| | - Yang Yu
- University of Illinois-Urbana. Center for Biophysics and Computational Biology, Urbana, IL 61801, USA
| | - Wilfred A van der Donk
- University of Illinois-Urbana, Department of Biochemistry, Urbana, IL61801; USA
- University of Illinois-Urbana. Center for Biophysics and Computational Biology, Urbana, IL 61801, USA
- University of Illinois-Urbana. Department of Chemistry, Urbana, IL 61801, USA
- Howard Hughes Medical Institute, Urbana, IL 61801, USA
| | - Ninian Blackburn
- Oregon Health & Sciences University, Institute of Environmental Health, Beaverton, OR 97006, USA
| | - Yi Lu
- University of Illinois-Urbana, Department of Biochemistry, Urbana, IL61801; USA
- University of Illinois-Urbana. Center for Biophysics and Computational Biology, Urbana, IL 61801, USA
- University of Illinois-Urbana. Department of Chemistry, Urbana, IL 61801, USA
| |
Collapse
|
8
|
Blindauer CA, Sigel A, Operschall BP, Holý A, Sigel H. Extent of Intramolecular π Stacks in Aqueous Solution in Mixed-Ligand Copper(II) Complexes Formed by Heteroaromatic Amines and 1-[2-(Phosphonomethoxy)ethyl]cytosine (PMEC), a Relative of Antivirally Active Acyclic Nucleotide Analogues (Part 72) [1, 2]. Z Anorg Allg Chem 2013. [DOI: 10.1002/zaac.201300095] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
|
9
|
Wilson TD, Yu Y, Lu Y. Understanding copper-thiolate containing electron transfer centers by incorporation of unnatural amino acids and the CuA center into the type 1 copper protein azurin. Coord Chem Rev 2013. [DOI: 10.1016/j.ccr.2012.06.015] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
|
10
|
Cambria MT, Gullotto D, Garavaglia S, Cambria A. In silico study of structural determinants modulating the redox potential ofRigidoporus lignosusand other fungal laccases. J Biomol Struct Dyn 2012; 30:89-101. [DOI: 10.1080/07391102.2012.674275] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
|
11
|
Rationally tuning the reduction potential of a single cupredoxin beyond the natural range. Nature 2009; 462:113-6. [PMID: 19890331 DOI: 10.1038/nature08551] [Citation(s) in RCA: 231] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2009] [Accepted: 09/30/2009] [Indexed: 11/08/2022]
Abstract
Redox processes are at the heart of numerous functions in chemistry and biology, from long-range electron transfer in photosynthesis and respiration to catalysis in industrial and fuel cell research. These functions are accomplished in nature by only a limited number of redox-active agents. A long-standing issue in these fields is how redox potentials are fine-tuned over a broad range with little change to the redox-active site or electron-transfer properties. Resolving this issue will not only advance our fundamental understanding of the roles of long-range, non-covalent interactions in redox processes, but also allow for design of redox-active proteins having tailor-made redox potentials for applications such as artificial photosynthetic centres or fuel cell catalysts for energy conversion. Here we show that two important secondary coordination sphere interactions, hydrophobicity and hydrogen-bonding, are capable of tuning the reduction potential of the cupredoxin azurin over a 700 mV range, surpassing the highest and lowest reduction potentials reported for any mononuclear cupredoxin, without perturbing the metal binding site beyond what is typical for the cupredoxin family of proteins. We also demonstrate that the effects of individual structural features are additive and that redox potential tuning of azurin is now predictable across the full range of cupredoxin potentials.
Collapse
|
12
|
Fernández-Botello A, Holý A, Moreno V, Operschall BP, Sigel H. Intramolecular π–π stacking interactions in aqueous solution in mixed-ligand copper(II) complexes formed by heteroaromatic amines and the nucleotide analogue 9-[2-(phosphonomethoxy)ethyl]-2-aminopurine (PME2AP), an isomer of the antivirally active 9-[2-(phosphonomethoxy)ethyl]adenine (PMEA). Inorganica Chim Acta 2009. [DOI: 10.1016/j.ica.2008.02.035] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
13
|
Yanagisawa S, Crowley PB, Firbank SJ, Lawler AT, Hunter DM, McFarlane W, Li C, Kohzuma T, Banfield MJ, Dennison C. π-Interaction Tuning of the Active Site Properties of Metalloproteins. J Am Chem Soc 2008; 130:15420-8. [DOI: 10.1021/ja8038135] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Sachiko Yanagisawa
- Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, U.K., UCD School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland, School of Natural Sciences (Chemistry), Bedson Building, Newcastle University, Newcastle upon Tyne, NE1 7RU, U.K., and Institute of Applied Beam Science, Ibaraki University, Mito, Ibaraki 310-8512, Japan
| | - Peter B. Crowley
- Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, U.K., UCD School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland, School of Natural Sciences (Chemistry), Bedson Building, Newcastle University, Newcastle upon Tyne, NE1 7RU, U.K., and Institute of Applied Beam Science, Ibaraki University, Mito, Ibaraki 310-8512, Japan
| | - Susan J. Firbank
- Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, U.K., UCD School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland, School of Natural Sciences (Chemistry), Bedson Building, Newcastle University, Newcastle upon Tyne, NE1 7RU, U.K., and Institute of Applied Beam Science, Ibaraki University, Mito, Ibaraki 310-8512, Japan
| | - Anne T. Lawler
- Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, U.K., UCD School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland, School of Natural Sciences (Chemistry), Bedson Building, Newcastle University, Newcastle upon Tyne, NE1 7RU, U.K., and Institute of Applied Beam Science, Ibaraki University, Mito, Ibaraki 310-8512, Japan
| | - David M. Hunter
- Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, U.K., UCD School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland, School of Natural Sciences (Chemistry), Bedson Building, Newcastle University, Newcastle upon Tyne, NE1 7RU, U.K., and Institute of Applied Beam Science, Ibaraki University, Mito, Ibaraki 310-8512, Japan
| | - William McFarlane
- Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, U.K., UCD School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland, School of Natural Sciences (Chemistry), Bedson Building, Newcastle University, Newcastle upon Tyne, NE1 7RU, U.K., and Institute of Applied Beam Science, Ibaraki University, Mito, Ibaraki 310-8512, Japan
| | - Chan Li
- Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, U.K., UCD School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland, School of Natural Sciences (Chemistry), Bedson Building, Newcastle University, Newcastle upon Tyne, NE1 7RU, U.K., and Institute of Applied Beam Science, Ibaraki University, Mito, Ibaraki 310-8512, Japan
| | - Takamitsu Kohzuma
- Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, U.K., UCD School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland, School of Natural Sciences (Chemistry), Bedson Building, Newcastle University, Newcastle upon Tyne, NE1 7RU, U.K., and Institute of Applied Beam Science, Ibaraki University, Mito, Ibaraki 310-8512, Japan
| | - Mark J. Banfield
- Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, U.K., UCD School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland, School of Natural Sciences (Chemistry), Bedson Building, Newcastle University, Newcastle upon Tyne, NE1 7RU, U.K., and Institute of Applied Beam Science, Ibaraki University, Mito, Ibaraki 310-8512, Japan
| | - Christopher Dennison
- Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, U.K., UCD School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland, School of Natural Sciences (Chemistry), Bedson Building, Newcastle University, Newcastle upon Tyne, NE1 7RU, U.K., and Institute of Applied Beam Science, Ibaraki University, Mito, Ibaraki 310-8512, Japan
| |
Collapse
|
14
|
Abstract
Many approaches are being used to engineer metalloproteins, with most of these informed by, and aiming to further elucidate, the basic structural requirements for biological metal centers. Cupredoxins are type 1 (T1) copper-containing electron transfer (ET) proteins with a -barrel fold that is thought to constrain metal site structure. The T1 copper ion is bound by ligands mainly originating from a single active site loop whose length and structure varies. This Highlight article will focus on protein engineering studies which have investigated the role of the metal-binding loop for active site integrity and functionality. Scaffold differences are present within the cupredoxin family and their influence has also been assessed. Given the widespread occurrence of -barrel domains in nature, and the array of metal sites in proteins composed of loop regions, the studies described on this model system have implications for a variety of metalloproteins.
Collapse
Affiliation(s)
- Christopher Dennison
- Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Newcastle upon Tyne, UK.
| |
Collapse
|
15
|
Abdelhamid RF, Obara Y, Kohzuma T. Alkaline transition of pseudoazurin Met16X mutant proteins: protein stability influenced by the substitution of Met16 in the second sphere coordination. J Inorg Biochem 2008; 102:1373-9. [PMID: 18343503 DOI: 10.1016/j.jinorgbio.2008.01.024] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2007] [Revised: 01/08/2008] [Accepted: 01/16/2008] [Indexed: 10/22/2022]
Abstract
Several blue copper proteins are known to change the active site structure at alkaline pH (alkaline transition). Spectroscopic studies of Met16Phe, Met16Tyr, Met16Trp, and Met16Val pseudoazurin variants were performed to investigate the second sphere role through alkaline transition. The visible electronic absorption and resonance Raman spectra of Met16Phe, Met16Tyr, and Met16Trp variants showed the increasing of axial component at pH approximately 11 like wild-type PAz. The visible electronic absorption and far-UV CD spectra of Met16Val demonstrated that the destabilization of the protein structure was triggered at pH>11. Resonance Raman (RR) spectra of PAz showed that the intensity-weighted averaged Cu-S(Cys) stretching frequency was shifted to higher frequency region at pH approximately 11. The higher frequency shift of Cu-S(Cys) bond is implied the stronger Cu-S(Cys) bond at alkaline transition pH approximately 11. The visible electronic absorption and far-UV CD spectra of Met16X PAz revealed that the Met16Val variant is denatured at pH>11, but Met16Phe, Met16Tyr, and Met16Trp mutant proteins are not denatured even at pH>11. These observations suggest that Met16 is important to maintain the protein structure through the possible weak interaction between methionine -SCH3 part and coordinated histidine imidazole moiety. The introduction of pi-pi interaction in the second coordination sphere may be contributed to the enhancement of protein structure stability.
Collapse
Affiliation(s)
- Rehab F Abdelhamid
- Institute of Applied Beam Science, Ibaraki University, Bunkyo 2-1-1, Mito, Ibaraki 310-8512, Japan
| | | | | |
Collapse
|
16
|
Milcic MK, Medaković VB, Sredojević DN, Juranić NO, Zarić SD. Electron delocalization mediates the metal-dependent capacity for CH/pi interactions of acetylacetonato chelates. Inorg Chem 2007; 45:4755-63. [PMID: 16749840 DOI: 10.1021/ic051926g] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
CH/pi interactions between the coordinated acetylacetonato ligand and phenyl rings were analyzed in the crystal structures from the Cambridge Structural Database and by quantum chemical calculations. The acetylacetonato ligand may engage in two types of interactions: it can be hydrogen atom donor or acceptor. The analysis of crystal structures and calculations show that interactions with the acetylacetonato ligand acting as hydrogen atom donor depend on the metal in an acetylacetonato chelate ring; the chelate rings with soft metals make stronger interactions. The same trend was not observed in the interactions where the acetylacetonato chelate ring acts as the hydrogen atom acceptor.
Collapse
Affiliation(s)
- Milos K Milcic
- Department of Chemistry, University of Belgrade, Studentski trg 16, 11000 Belgrade, Serbia and Montenegro
| | | | | | | | | |
Collapse
|
17
|
Hulsker R, Mery A, Thomassen EA, Ranieri A, Sola M, Verbeet MP, Kohzuma T, Ubbink M. Protonation of a Histidine Copper Ligand in Fern Plastocyanin. J Am Chem Soc 2007; 129:4423-9. [PMID: 17367139 DOI: 10.1021/ja0690464] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Plastocyanin is a small blue copper protein that shuttles electrons as part of the photosynthetic redox chain. Its redox behavior is changed at low pH as a result of protonation of the solvent-exposed copper-coordinating histidine. Protonation and subsequent redox inactivation could have a role in the down regulation of photosynthesis. As opposed to plastocyanin from other sources, in fern plastocyanin His90 protonation at low pH has been reported not to occur. Two possible reasons for that have been proposed: pi-pi stacking between Phe12 and His90 and lack of a hydrogen bond with the backbone oxygen of Gly36. We have produced this fern plastocyanin recombinantly and examined the properties of wild-type protein and mutants Phe12Leu, Gly36Pro, and the double mutant with NMR spectroscopy, X-ray crystallography, and cyclic voltammetry. The results demonstrate that, contrary to earlier reports, protonation of His90 in the wild-type protein does occur in solution with a pKa of 4.4 (+/-0.1). Neither the single mutants nor the double mutant exhibit a change in protonation behavior, indicating that the suggested interactions have no influence. The crystal structure at low pH of the Gly36Pro variant does not show His90 protonation, similar to what was found for the wild-type protein. The structure suggests that movement of the imidazole ring is hindered by crystal contacts. This study illustrates a significant difference between results obtained in solution by NMR and by crystallography.
Collapse
Affiliation(s)
- Rinske Hulsker
- Leiden Institute of Chemistry, Leiden University, Gorlaeus Laboratories, P.O. Box 9502, 2300 RA, Leiden, The Netherlands
| | | | | | | | | | | | | | | |
Collapse
|
18
|
Influence of metal and ligand types on stacking interactions of phenyl rings with square-planar transition metal complexes. OPEN CHEM 2007. [DOI: 10.2478/s11532-006-0068-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
AbstractIn order to find out whether metal type influences the stacking interactions of phenyl rings in square-planar complexes, geometrical parameters for Cu, Ni, Pd and Pt complexes, with and without chelate rings, were analyzed and compared. By searching the Cambridge Structural Database, 220 structures with Cu complexes, 211 with Ni complexes, 285 with Pd complexes, and 220 with Pt complexes were found. The results show that the chelate ring has a tendency to make the stacking interaction with the phenyl ring independent of metal type in the chelate ring. However, there are some differences among metals for complexes without a chelate ring. There are a number of structures containing Pd and Pt complexes, without chelate rings, that have short carbon-metal distances and parallel orientations of the phenyl ring with respect to the coordination plane. It was found that some of these complexes have a common fragment, CN, as a part of the ligands. This indicates that the CN supports stacking interactions of square planar complexes with the phenyl ring.
Collapse
|
19
|
Stirpe A, Sportelli L, Guzzi R. A comparative investigation of the thermal unfolding of pseudoazurin in the Cu(II)-holo and apo form. Biopolymers 2007; 83:487-97. [PMID: 16881076 DOI: 10.1002/bip.20579] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The contribution of the copper ion to the stability and to the unfolding pathway of pseudoazurin was investigated by a comparative analysis of the thermal unfolding of the Cu(II)-holo and apo form of the protein. The unfolding has been followed by calorimetry, fluorescence, optical density, and electron paramagnetic resonance (EPR) spectroscopy. The thermal transition of Cu(II)-holo pseudoazurin is irreversible and occurs between 60.0 and 67.3 degrees C, depending on the scan rate and technique used. The denaturation pathway of Cu(II)-holo pseudoazurin can be described by the Lumry-Eyring model: N --> U --> [corrected] F; the protein reversibly goes from the native (N) to the unfolded (U) state, and then irreversibly to the final (F) state. The simulation of the experimental calorimetric profiles, according to this model, allowed us to determine the thermodynamic and kinetic parameters of the two steps. The DeltaG value calculated for the Cu(II)-holo pseudoazurin is 39.2 kJ.mol(-1) at 25 degrees C. The sequence of events in the denaturation process of Cu(II)-holo pseudoazurin emergence starts with the disruption of the copper site and the hydrophobic core destabilization followed by the global protein unfolding. According to the EPR findings, the native type-1 copper ion shows type-2 copper features after the denaturation. The removal of the copper ion (apo form) significantly reduces the stability of the protein as evidenced by a DeltaG value of 16.5 kJ.mol(-1) at 25 degrees C. Moreover, the apo Paz unfolding occurs at 41.8 degrees C and is compatible with a two-state reversible process N --> [corrected] U.
Collapse
Affiliation(s)
- Andrea Stirpe
- Dipartimento di Fisica e Unità CNISM, Laboratorio di Biofisica Molecolare, Università della Calabria, Ponte P. Bucci - Cubo 30C, I-87036, Arcavacata di Rende (CS), Italy
| | | | | |
Collapse
|
20
|
Yajima T, Takamido R, Shimazaki Y, Odani A, Nakabayashi Y, Yamauchi O. π–π Stacking assisted binding of aromatic amino acids by copper(ii)–aromatic diimine complexes. Effects of ring substituents on ternary complex stability. Dalton Trans 2007:299-307. [PMID: 17200749 DOI: 10.1039/b612394e] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ternary Cu(ii) complexes containing an aromatic diimine (DA = di(2-pyridylmethyl)amine (dpa), 4,4'-disubstituted 2,2'-bipyridine (Y(2)bpy; Y = H (bpy), Me, Cl, N(Et)(2), CONH(2) or COOEt) or 2,2'-bipyrimidine) and an aromatic amino acid (AA = l-phenylalanine (Phe), p-substituted phenylalanine (XPhe; X = NH(2), NO(2), F, Cl or Br), l-tyrosine (Tyr), l-tryptophan (Trp) or l-alanine (Ala)) were characterized by X-ray diffraction, spectroscopic and potentiometric measurements. The structures of [Cu(dpa)(Trp)]ClO(4).2H(2)O and [Cu((CONH(2))(2)bpy)(Phe)]ClO(4).H(2)O in the solid state were revealed to have intramolecular pi-pi interactions between the Cu(ii)-coordinated aromatic ring moiety, Cu(DA) (Mpi), and the side chain aromatic ring of the AA (Lpi). The intensities of Mpi-Lpi interactions were evaluated by the stability constants of the ternary Cu(ii) complexes determined at 25 degrees C and I = 0.1 M (KNO(3)), which revealed that the stability enhancement of the Cu(DA)(AA) systems due to the interactions is in the order (CONH(2))(2)bpy < bpy < Me(2)bpy < (Et(2)N)(2)bpy with respect to DA. The results indicate that the electron density of coordinated aromatic diimines influences the intensities of the stacking interactions in the Cu(DA)(AA) systems. The Mpi-Lpi interactions are also influenced by the substituents, X, of Lpi and are in linear relationship with their Hammett sigma(p) values with the exception of X = Cl and Br.
Collapse
Affiliation(s)
- Tatsuo Yajima
- Unit of Chemistry, Faculty of Engineering, Kansai University, Suita, Osaka 564-8680, Japan
| | | | | | | | | | | |
Collapse
|
21
|
Abdelhamid RF, Obara Y, Uchida Y, Kohzuma T, Dooley DM, Brown DE, Hori H. π–π interaction between aromatic ring and copper-coordinated His81 imidazole regulates the blue copper active-site structure. J Biol Inorg Chem 2006; 12:165-73. [PMID: 17031705 DOI: 10.1007/s00775-006-0176-8] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2006] [Accepted: 09/07/2006] [Indexed: 10/24/2022]
Abstract
Noncovalent weak interactions play important roles in biological systems. In particular, such interactions in the second coordination shell of metal ions in proteins may modulate the structure and reactivity of the metal ion site in functionally significant ways. Recently, pi-pi interactions between metal ion coordinated histidine imidazoles and aromatic amino acids have been recognized as potentially important contributors to the properties of metal ion sites. In this paper we demonstrate that in pseudoazurin (a blue copper protein) the pi-pi interaction between a coordinated histidine imidazole ring and the side chains of aromatic amino acids in the second coordination sphere, significantly influences the properties of the blue copper site. Electronic absorption and electron paramagnetic resonance spectra indicate that the blue copper electronic structure is perturbed, as is the redox potential, by the introduction of a second coordination shell pi-pi interaction. We suggest that the pi-pi interaction with the metal ion coordinated histidine imidazole ring modulates the electron delocalization in the active site, and that such interactions may be functionally important in refining the reactivity of blue copper sites.
Collapse
Affiliation(s)
- Rehab F Abdelhamid
- Institute of Applied Beam Science, Ibaraki University, Mito, Ibaraki, 310-8512, Japan
| | | | | | | | | | | | | |
Collapse
|
22
|
CH/π interactions of π-system of acetylacetonato chelate ring: Comparison of CH/π interactions of Ni(II)-acetylacetonato chelate and benzene rings. Inorganica Chim Acta 2006. [DOI: 10.1016/j.ica.2006.06.022] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
|
23
|
|
24
|
Dennison C. Ligand and loop variations at type 1 copper sites: influence on structure and reactivity. Dalton Trans 2005:3436-42. [PMID: 16234922 DOI: 10.1039/b507440c] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Type 1 (T1) copper sites promote biological electron transfer and are found in the cupredoxins and a number of copper-containing enzymes including the multi-copper oxidases. A T1 copper site usually has a distorted tetrahedral geometry with strong ligands provided by the thiolate sulfur of a Cys and the imidazole nitrogens of two His residues. The active site structure is typically completed by a weak axial Met ligand (a second weak axial interaction is found in azurin resulting in a trigonal bipyramidal geometry). The axial Met is not conserved and Gln, Phe, Leu and Val are also found in this position. Three of the four ligands at a T1 copper site are situated on a single C-terminal loop whose length and structure varies. Studies are discussed which investigate both the influence of physiologically relevant axial ligand alterations, and also of mutations to the length and structure of the ligand-containing loop, on the properties of T1 copper sites.
Collapse
Affiliation(s)
- Christopher Dennison
- Institute for Cell and Molecular Biosciences, Medical School, University of Newcastle upon Tyne, Newcastle upon Tyne, UK NE2 4HH.
| |
Collapse
|
25
|
Abstract
The shortest known type 1 copper binding loop (that of amicyanin, Ami) has been introduced into three different cupredoxin beta-barrel scaffolds. All of the loop-contraction variants possess copper centers with authentic type 1 properties and are redox active. The Cu(II) and Co(II) sites experience only small structural alterations upon loop contraction with the largest changes in the azurin variant (AzAmi), which can be ascribed to the removal of a hydrogen bond to the coordinating thiolate sulfur of the Cys ligand. In all cases, loop contraction leads to an increase in the pK(a) of the His ligand found on the loop in the reduced proteins, and in the pseudoazurin (Paz) and plastocyanin (Pc) variants the values are almost identical to that of Ami ( approximately 6.7). Thus, in Paz, Pc, and Ami, the length of this loop tunes the pK(a) of the His ligand. In the AzAmi variant, the pK(a) is 5.5, which is considerably higher than the estimated value for Az (<2), and other controlling factors, along with loop length, are involved. The reduction potentials of the loop-contraction variants are all lower than those of the wild-type proteins by approximately 30-60 mV, and thus this property of a type 1 copper site is fine-tuned by the C-terminal loop. The electron self-exchange rate constant of Paz is significantly diminished by the introduction of a shorter loop. However, in PcAmi only a 2-fold decrease is observed and in AzAmi there is no effect, and thus in these two cupredoxins loop contraction does not significantly influence electron-transfer reactivity. Loop contraction provides an active site environment in all of the cupredoxins which is preferable for Cu(II), whereas previous loop elongation experiments always favored the cuprous site. Thus, the ligand-containing loop plays an important role in tuning the entatic nature of a type 1 copper center.
Collapse
Affiliation(s)
- Sachiko Yanagisawa
- School of Natural Sciences, Bedson Building, University of Newcastle upon Tyne, Newcastle upon Tyne, NE1 7RU, UK
| | | |
Collapse
|
26
|
Battistuzzi G, Borsari M, Di Rocco G, Leonardi A, Ranieri A, Sola M. Electrostatic Effects on the Thermodynamics of Protonation of Reduced Plastocyanin. Chembiochem 2005; 6:692-6. [PMID: 15750998 DOI: 10.1002/cbic.200400310] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
The L12E, L12K, Q88E, and Q88K variants of spinach plastocyanin have been electrochemically investigated. The effects of insertion of net charges near the metal site on the thermodynamics of protonation and detachment from the copper(I) ion of the His87 ligand have been evaluated. The mutation-induced changes in transition enthalpy cannot be explained by electrostatic considerations. The existence of enthalpy/entropy (H/S) compensation within the protein series indicates that solvent-reorganization effects control the differences in transition thermodynamics. Once these compensating contributions are factorized out, the resulting modest differences in transition enthalpies turn out to be those that can be expected on purely electrostatic grounds. Therefore, this work shows that the acid transition in cupredoxins involves a reorganization of the H-bonding network within the hydration sphere of the molecule in the proximity of the metal center that dominates the observed transition thermodynamics and masks the differences that are due to protein-based effects.
Collapse
Affiliation(s)
- Gianantonio Battistuzzi
- Department of Chemistry and Centro SCS, University of Modena and Reggio Emilia, Via Campi 183, 41100 Modena, Italy
| | | | | | | | | | | |
Collapse
|
27
|
Tomić Z, Novaković S, Zarić S. Intermolecular Interactions between Chelate Rings and Phenyl Rings in Square-Planar Copper(II) Complexes. Eur J Inorg Chem 2004. [DOI: 10.1002/ejic.200400086] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
|
28
|
Sułkowska A, Bojko B, Równicka J, Sułkowski W. Competition of drugs to serum albumin in combination therapy. Biopolymers 2004; 74:256-62. [PMID: 15150801 DOI: 10.1002/bip.20031] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The mechanism of cooperative binding of both cytarabine and fluorouracil, used in combination therapy, to the transporting protein [bovine serum albumin (BSA)] has been investigated. Present study shows a strategy of estimating the kind of competition between these drugs with the use of uv and NMR spectroscopy. Two mechanisms of the competition to the transporting protein are proposed. For the quantitative investigations the effect of the protein on both the line width and chemical shifts of the NMR signals of the 5-fluorouracil and cytarabine was analyzed. The pi-pi interaction between the pyrimidine ring of the drugs and the aromatic residues of the protein has been postulated. The binding site for both 5-fluorouracil and cytarabine on BSA was found to be situated in the hydrophobic IIA subdomain. The competition of these two drugs and the removal of 5-fluorouracil by cytarabine from the common binding site in serum albumin tertiary structure are observed.
Collapse
Affiliation(s)
- Anna Sułkowska
- Medical University of Silesia, Department of Physical Pharmacy, Jagiellońska 4, Sosnowiec, 41-200, Poland.
| | | | | | | |
Collapse
|
29
|
Li XZ, He JH, Liu BL, Liao DZ. π⋯π interactions between a phenyl ring and four separate unclosed π-systems in the supramolecular structure of a new macrocyclic nickel(II) complex. INORG CHEM COMMUN 2004. [DOI: 10.1016/j.inoche.2003.12.030] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
|