1
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Chen H, Su B, Zhang T, Huang A, Liu H, Yu Y, Wang J. Engineering the metal-binding loop at a type 1 copper center by circular permutation. RSC Adv 2017. [DOI: 10.1039/c7ra11512a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Circular permutation of the cupredoxin azurin creates a break on the metal binding loop, highlighting the loop's flexibility.
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Affiliation(s)
- Honghui Chen
- College of Biotechnology
- Tianjin University of Science and Technology
- Tianjin
- China
- Tianjin Institute of Industrial Biotechnology
| | - Binbin Su
- College of Biotechnology
- Tianjin University of Science and Technology
- Tianjin
- China
- Tianjin Institute of Industrial Biotechnology
| | - Tongtong Zhang
- Tianjin Institute of Industrial Biotechnology
- Chinese Academy of Sciences
- Tianjin
- China
| | - Aiping Huang
- Tianjin Institute of Industrial Biotechnology
- Chinese Academy of Sciences
- Tianjin
- China
| | - Haiping Liu
- Tianjin Institute of Industrial Biotechnology
- Chinese Academy of Sciences
- Tianjin
- China
| | - Yang Yu
- Tianjin Institute of Industrial Biotechnology
- Chinese Academy of Sciences
- Tianjin
- China
| | - Jiangyun Wang
- Laboratory of RNA Biology
- Institute of Biophysics
- Chinese Academy of Sciences
- Beijing
- China
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2
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Pérez-Henarejos SA, Alcaraz LA, Donaire A. Blue Copper Proteins: A rigid machine for efficient electron transfer, a flexible device for metal uptake. Arch Biochem Biophys 2015; 584:134-48. [DOI: 10.1016/j.abb.2015.08.020] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Revised: 08/24/2015] [Accepted: 08/28/2015] [Indexed: 10/23/2022]
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3
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Gaus M, Jin H, Demapan D, Christensen AS, Goyal P, Elstner M, Cui Q. DFTB3 Parametrization for Copper: The Importance of Orbital Angular Momentum Dependence of Hubbard Parameters. J Chem Theory Comput 2015; 11:4205-19. [PMID: 26575916 PMCID: PMC4827604 DOI: 10.1021/acs.jctc.5b00600] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We report the parametrization of a density functional tight binding method (DFTB3) for copper in a spin-polarized formulation. The parametrization is consistent with the framework of 3OB for main group elements (ONCHPS) and can be readily used for biological applications that involve copper proteins/peptides. The key to our parametrization is to introduce orbital angular momentum dependence of the Hubbard parameter and its charge derivative, thus allowing the 3d and 4s orbitals to adopt different sizes and responses to the change of charge state. The parametrization has been tested by applying to a fairly broad set of molecules of biological relevance, and the properties of interest include optimized geometries, ligand binding energies, and ligand proton affinities. Compared to the reference QM level (B3LYP/aug-cc-pVTZ, which is shown here to be similar to the B97-1 and CCSD(T) results, in terms of many properties of interest for a set of small copper containing molecules), our parametrization generally gives reliable structural properties for both Cu(I) and Cu(II) compounds, although several exceptions are also noted. For energetics, the results are more accurate for neutral ligands than for charged ligands, likely reflecting the minimal basis limitation of DFTB3; the results generally outperform NDDO based methods such as PM6 and even PBE with the 6-31+G(d,p) basis. For all ligand types, single-point B3LYP calculations at DFTB3 geometries give results very close (∼1-2 kcal/mol) to the reference B3LYP values, highlighting the consistency between DFTB3 and B3LYP structures. Possible further developments of the DFTB3 model for a better treatment of transition-metal ions are also discussed. In the current form, our first generation of DFTB3 copper model is expected to be particularly valuable as a method that drives sampling in systems that feature a dynamical copper binding site.
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Affiliation(s)
- Michael Gaus
- Department of Chemistry, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Haiyun Jin
- Department of Chemistry, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Darren Demapan
- Department of Chemistry, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Anders S Christensen
- Department of Chemistry, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Puja Goyal
- Department of Chemistry, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Marcus Elstner
- Institute of Physical Chemistry, Karlsruhe Institute of Technology , Kaiserstr. 12, 76131 Karlsruhe, Germany
| | - Qiang Cui
- Department of Chemistry, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States
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4
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McMillan AW, Lopez MS, Zhu M, Morse BC, Yeo IC, Amos J, Hull K, Romo D, Glasner ME. Role of an Active Site Loop in the Promiscuous Activities of Amycolatopsis sp. T-1-60 NSAR/OSBS. Biochemistry 2014; 53:4434-44. [DOI: 10.1021/bi500573v] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Andrew W. McMillan
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, Texas 77843-2128, United States
| | - Mariana S. Lopez
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, Texas 77843-2128, United States
| | | | - Benjamin C. Morse
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, Texas 77843-2128, United States
| | - In-Cheol Yeo
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, Texas 77843-2128, United States
| | - Jaleesia Amos
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, Texas 77843-2128, United States
| | | | | | - Margaret E. Glasner
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, Texas 77843-2128, United States
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5
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Paltrinieri L, Borsari M, Battistuzzi G, Sola M, Dennison C, de Groot BL, Corni S, Bortolotti CA. How the dynamics of the metal-binding loop region controls the acid transition in cupredoxins. Biochemistry 2013; 52:7397-404. [PMID: 24063705 DOI: 10.1021/bi400860n] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Many reduced cupredoxins undergo a pH-dependent structural rearrangement, triggered by protonation of the His ligand belonging to the C-terminal hydrophobic loop, usually termed the acid transition. At variance with several members of the cupredoxin family, the acid transition is not observed for azurin (AZ). We have addressed this issue by performing molecular dynamics simulations of AZ and four mutants, in which the C-terminal loop has been replaced with those of other cupredoxins or with polyalanine loops. All of the loop mutants undergo the acid transition in the pH range of 4.4-5.5. The main differences between AZ and its loop mutants are the average value of the active site solvent accessible surface area and the extent of its fluctuations with time, together with an altered structure of the water layer around the copper center. Using functional mode analysis, we found that these variations arise from changes in nonbonding interactions in the second coordination sphere of the copper center, resulting from the loop mutation. Our results strengthen the view that the dynamics at the site relevant for function and its surroundings are crucial for protein activity and for metal-containing electron transferases.
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Affiliation(s)
- Licia Paltrinieri
- Department of Chemical and Geological Sciences, University of Modena and Reggio Emilia , via Campi 183, 41125 Modena, Italy
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6
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Kline CD, Mayfield M, Blackburn NJ. HHM motif at the CuH-site of peptidylglycine monooxygenase is a pH-dependent conformational switch. Biochemistry 2013; 52:2586-96. [PMID: 23530865 DOI: 10.1021/bi4002248] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Peptidylglycine monooxygenase is a copper-containing enzyme that catalyzes the amidation of neuropeptides hormones, the first step of which is the conversion of a glycine-extended pro-peptide to its α-hydroxyglcine intermediate. The enzyme contains two mononuclear Cu centers termed CuM (ligated to imidazole nitrogens of H242, H244 and the thioether S of M314) and CuH (ligated to imidazole nitrogens of H107, H108, and H172) with a Cu-Cu separation of 11 Å. During catalysis, the M site binds oxygen and substrate, and the H site donates the second electron required for hydroxylation. The WT enzyme shows maximum catalytic activity at pH 5.8 and undergoes loss of activity at lower pHs due to a protonation event with a pKA of 4.6. Low pH also causes a unique structural transition in which a new S ligand coordinates to copper with an identical pKA, manifest by a large increase in Cu-S intensity in the X- ray absorption spectroscopy. In previous work (Bauman, A. T., Broers, B. A., Kline, C. D., and Blackburn, N. J. (2011) Biochemistry 50, 10819-10828), we tentatively assigned the new Cu-S interaction to binding of M109 to the H-site (part of an HHM conserved motif common to all but one member of the family). Here we follow up on these findings via studies on the catalytic activity, pH-activity profiles, and spectroscopic (electron paramagnetic resonance, XAS, and Fourier transform infrared) properties of a number of H-site variants, including H107A, H108A, H172A, and M109I. Our results establish that M109 is indeed the coordinating ligand and confirm the prediction that the low pH structural transition with associated loss of activity is abrogated when the M109 thioether is absent. The histidine mutants show more complex behavior, but the almost complete lack of activity in all three variants coupled with only minor differences in their spectroscopic properties suggests that unique structural elements at H are critical for functionality. The data suggest a more general utility for the HHM motif as a copper- and pH-dependent conformational switch.
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Affiliation(s)
- Chelsey D Kline
- Institute of Environmental, Health, Oregon Health and Sciences University, Beaverton, Oregon 97006, USA
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7
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Warren JJ, Gray HB, Winkler JR, Kozak JJ. A Euclidean Perspective on the Unfolding of Azurin: Spatial Correlations. Mol Phys 2013; 111:922-929. [PMID: 23853392 PMCID: PMC3708666 DOI: 10.1080/00268976.2012.758324] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
We investigate the stability to structural perturbation of Pseudomonas aeruginosa azurin using a previously developed geometric model. Our analysis considers Ru(2,2',6',2″-terpyridine)(1,10-phenanthroline)(His83)-labeled wild-type azurin and five variants with mutations to Cu-ligating residues. We find that in the early stages of unfolding, the β-strands exhibit the most structural stability. The conserved residues comprising the hydrophobic core are dislocated only after nearly complete unfolding of the β-barrel. Attachment of the Ru-complex at His83 does not destabilize the protein fold, despite causing some degree of structural rearrangement. Notably, replacing the Cys112 and/or Met121 Cu ligands does not affect the conformational integrity of the protein. Notably, these results are in accord with experimental evidence, as well as molecular dynamics simulations of the denaturation of azurin.
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Affiliation(s)
- Jeffrey J. Warren
- Beckman Institute, California Institute of Technology, Pasadena CA 91125
| | - Harry B. Gray
- Beckman Institute, California Institute of Technology, Pasadena CA 91125
| | - Jay R. Winkler
- Beckman Institute, California Institute of Technology, Pasadena CA 91125
| | - John J. Kozak
- DePaul University, 243 South Wabash Ave., Chicago, IL 60604-8875
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8
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Warren JJ, Lancaster KM, Richards JH, Gray HB. Inner- and outer-sphere metal coordination in blue copper proteins. J Inorg Biochem 2012; 115:119-26. [PMID: 22658756 PMCID: PMC3434318 DOI: 10.1016/j.jinorgbio.2012.05.002] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2012] [Revised: 04/30/2012] [Accepted: 05/01/2012] [Indexed: 10/28/2022]
Abstract
Blue copper proteins (BCPs) comprise classic cases of Nature's profound control over the electronic structures and chemical reactivity of transition metal ions. Early studies of BCPs focused on their inner coordination spheres, that is, residues that directly coordinate Cu. Equally important are the electronic and geometric perturbations to these ligands provided by the outer coordination sphere. In this tribute to Hans Freeman, we review investigations that have advanced the understanding of how inner-sphere and outer-sphere coordination affects biological Cu properties.
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Affiliation(s)
- Jeffrey J Warren
- Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA
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9
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Suh HS, Hung-Low F, Casadonte D, Kim HJ, Kim BS, Chang TS. Facile Synthesis of 4,7-Disubstituted Conjugation-Extended 1,10-Phenanthrolines. B KOREAN CHEM SOC 2012. [DOI: 10.5012/bkcs.2012.33.9.3133] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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10
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Monari S, Battistuzzi G, Bortolotti CA, Yanagisawa S, Sato K, Li C, Salard I, Kostrz D, Borsari M, Ranieri A, Dennison C, Sola M. Understanding the Mechanism of Short-Range Electron Transfer Using an Immobilized Cupredoxin. J Am Chem Soc 2012; 134:11848-51. [DOI: 10.1021/ja303425b] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Stefano Monari
- Department of Chemistry, University of Modena and Reggio Emilia, Via Campi 183,
41125 Modena, Italy
| | - Gianantonio Battistuzzi
- Department of Chemistry, University of Modena and Reggio Emilia, Via Campi 183,
41125 Modena, Italy
| | - Carlo A. Bortolotti
- Department of Chemistry, University of Modena and Reggio Emilia, Via Campi 183,
41125 Modena, Italy
- CNR-NANO Institute of Nanoscience, Via Campi 213/A, I-41125 Modena, Italy
| | - Sachiko Yanagisawa
- Institute for Cell and Molecular
Biosciences, Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, U.K
| | - Katsuko Sato
- Institute for Cell and Molecular
Biosciences, Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, U.K
| | - Chan Li
- Institute for Cell and Molecular
Biosciences, Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, U.K
| | - Isabelle Salard
- Institute for Cell and Molecular
Biosciences, Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, U.K
| | - Dorota Kostrz
- Institute for Cell and Molecular
Biosciences, Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, U.K
| | - Marco Borsari
- Department of Chemistry, University of Modena and Reggio Emilia, Via Campi 183,
41125 Modena, Italy
| | - Antonio Ranieri
- Department of Chemistry, University of Modena and Reggio Emilia, Via Campi 183,
41125 Modena, Italy
| | - Christopher Dennison
- Institute for Cell and Molecular
Biosciences, Medical School, Newcastle University, Newcastle upon Tyne, NE2 4HH, U.K
| | - Marco Sola
- Department of Chemistry, University of Modena and Reggio Emilia, Via Campi 183,
41125 Modena, Italy
- CNR-NANO Institute of Nanoscience, Via Campi 213/A, I-41125 Modena, Italy
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Bauman AT, Broers BA, Kline CD, Blackburn NJ. A copper-methionine interaction controls the pH-dependent activation of peptidylglycine monooxygenase. Biochemistry 2011; 50:10819-28. [PMID: 22080626 DOI: 10.1021/bi201193j] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The pH dependence of native peptidylglycine monooxygenase (PHM) and its M314H variant has been studied in detail. For wild-type (WT) PHM, the intensity of the Cu-S interaction visible in the Cu(I) extended X-ray absorption fine structure (EXAFS) data is inversely proportional to catalytic activity over the pH range of 3-8. A previous model based on more limited data was interpreted in terms of two protein conformations involving an inactive Met-on form and an active flexible Met-off form [Bauman, A. T., et al. (2006) Biochemistry 45, 11140-11150] that derived its catalytic activity from the ability to couple into vibrational modes critical for proton tunneling. The new studies comparing the WT and M314H variant have led to the evolution of this model, in which the Met-on form has been found to be derived from coordination of an additional Met residue, rather than a more rigid conformer of M314 as previously proposed. The catalytic activity of the mutant decreased by 96% because of effects on both k(cat) and K(M), but it displayed the same activity-pH profile with a maximum around pH 6. At pH 8, the reduced Cu(I) form gave spectra that could be simulated by replacement of the Cu(M) Cu-S(Met) interaction with a Cu-N/O interaction, but the data did not unambiguously assign the ligand to the imidazole side chain of H314. At pH 3.5, the EXAFS still showed the presence of a strong Cu-S interaction, establishing that the Met-on form observed at low pH in WT cannot be due to a strengthening of the Cu(M)-methionine interaction but must arise from a different Cu-S interaction. Therefore, lowering the pH causes a conformational change at one of the Cu centers that brings a new S donor residue into a favorable orientation for coordination to copper and generates an inactive form. Cys coordination is unlikely because all Cys residues in PHM are engaged in disulfide cross-links. Sequence comparison with the PHM homologues tyramine β-monooxygenase and dopamine β-monooxygenase suggests that M109 (adjacent to H site ligands H107 and H108) is the most likely candidate. A model is presented in which H108 is protonated with a pK(a) of 4.6 to generate the inactive low-pH form with Cu(H) coordinated by M109, H107, and H172.
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Affiliation(s)
- Andrew T Bauman
- Institute of Environmental Health, Oregon Health and Sciences University, Beaverton, Oregon 97006, United States
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