1
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Ghafoor MH, Song BL, Zhou L, Qiao ZY, Wang H. Self-Assembly of Peptides as an Alluring Approach toward Cancer Treatment and Imaging. ACS Biomater Sci Eng 2024; 10:2841-2862. [PMID: 38644736 DOI: 10.1021/acsbiomaterials.4c00491] [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: 04/23/2024]
Abstract
Cancer is a severe threat to humans, as it is the second leading cause of death after cardiovascular diseases and still poses the biggest challenge in the world of medicine. Due to its higher mortality rates and resistance, it requires a more focused and productive approach to provide the solution for it. Many therapies promising to deliver favorable results, such as chemotherapy and radiotherapy, have come up with more negatives than positives. Therefore, a new class of medicinal solutions and a more targeted approach is of the essence. This review highlights the alluring properties, configurations, and self-assembly of peptide molecules which benefit the traditional approach toward cancer therapy while sparing the healthy cells in the process. As targeted drug delivery systems, self-assembled peptides offer a wide spectrum of conjugation, biocompatibility, degradability-controlled responsiveness, and biomedical applications, including cancer treatment and cancer imaging.
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Affiliation(s)
- Muhammad Hamza Ghafoor
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology (NCNST), Beijing 100190, China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Ben-Li Song
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology (NCNST), Beijing 100190, China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Lei Zhou
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology (NCNST), Beijing 100190, China
| | - Zeng-Ying Qiao
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology (NCNST), Beijing 100190, China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing 100049, PR China
| | - Hao Wang
- CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology (NCNST), Beijing 100190, China
- Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing 100049, PR China
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2
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Chen X, Zhang T, Liu H, Zang J, Lv C, Du M, Zhao G. Shape-Anisotropic Assembly of Protein Nanocages with Identical Building Blocks by Designed Intermolecular π-π Interactions. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2305398. [PMID: 37870198 PMCID: PMC10724428 DOI: 10.1002/advs.202305398] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 09/12/2023] [Indexed: 10/24/2023]
Abstract
Protein lattices that shift the structure and shape anisotropy in response to environmental cues are closely coupled to potential functionality. However, to design and construct shape-anisotropic protein arrays from the same building blocks in response to different external stimuli remains challenging. Here, by a combination of the multiple, symmetric interaction sites on the outer surface of protein nanocages and the tunable features of phenylalanine-phenylalanine interactions, a protein engineering approach is reported to construct a variety of superstructures with shape anisotropy, including 3D cubic, 2D hexagonal layered, and 1D rod-like crystalline protein nanocage arrays by using one single protein building block. Notably, the assembly of these crystalline protein arrays is reversible, which can be tuned by external stimuli (pH and ionic strength). The anisotropic morphologies of the fabricated macroscopic crystals can be correlated with the Å-to-nm scale protein arrangement details by crystallographic elucidation. These results enhance the understanding of the freedom offered by an object's symmetry and inter-object π-π stacking interactions for protein building blocks to assemble into direction- and shape-anisotropic biomaterials.
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Affiliation(s)
- Xuemin Chen
- College of Food Science & Nutritional EngineeringBeijing Key Laboratory of Functional Food from Plant ResourcesChina Agricultural UniversityBeijing100083China
| | - Tuo Zhang
- College of Food Science & Nutritional EngineeringBeijing Key Laboratory of Functional Food from Plant ResourcesChina Agricultural UniversityBeijing100083China
| | - Hanxiong Liu
- School of Food Science and TechnologyNational Engineering Research Center of SeafoodDalian Polytechnic UniversityDalian116034China
| | - Jiachen Zang
- College of Food Science & Nutritional EngineeringBeijing Key Laboratory of Functional Food from Plant ResourcesChina Agricultural UniversityBeijing100083China
| | - Chenyan Lv
- College of Food Science & Nutritional EngineeringBeijing Key Laboratory of Functional Food from Plant ResourcesChina Agricultural UniversityBeijing100083China
| | - Ming Du
- School of Food Science and TechnologyNational Engineering Research Center of SeafoodDalian Polytechnic UniversityDalian116034China
| | - Guanghua Zhao
- College of Food Science & Nutritional EngineeringBeijing Key Laboratory of Functional Food from Plant ResourcesChina Agricultural UniversityBeijing100083China
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3
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Ishizuka T, Kogawa T, Ogawa C, Kotani H, Shiota Y, Yoshizawa K, Kojima T. Enhancement of Reactivity of a Ru IV-Oxo Complex in Oxygen-Atom-Transfer Catalysis by Hydrogen-Bonding with Amide Moieties in the Second Coordination Sphere. JACS AU 2023; 3:2813-2825. [PMID: 37885582 PMCID: PMC10598587 DOI: 10.1021/jacsau.3c00377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Revised: 08/25/2023] [Accepted: 08/25/2023] [Indexed: 10/28/2023]
Abstract
We have synthesized and characterized a RuII-OH2 complex (2), which has a pentadentate ligand with two pivalamide groups as bulky hydrogen-bonding (HB) moieties in the second coordination sphere (SCS). Complex 2 exhibits a coordination equilibrium through the coordination of one of the pivalamide oxygens to the Ru center in water, affording a η6-coordinated complex, 3. A detailed thermodynamic analysis of the coordination equilibrium revealed that the formation of 3 from 2 is entropy-driven owing to the dissociation of the axial aqua ligand in 2. Complex 2 was oxidized by a CeIV salt to produce the corresponding RuIII(OH) complex (5), which was characterized crystallographically. In the crystal structure of 5, hydrogen bonds are formed among the NH groups of the pivalamide moieties and the oxygen atom of the hydroxo ligand. Further 1e--oxidation of 5 yields the corresponding RuIV(O) complex, 6, which has intramolecular HB of the oxo ligand with two amide N-H protons. Additionally, the RuIII(OH) complex, 5, exhibits disproportionation to the corresponding RuIV(O) complex, 6, and a mixture of the RuII complexes, 2 and 3, in an acidic aqueous solution. We investigated the oxidation of a phenol derivative using complex 6 as the active species and clarified the switch of the reaction mechanism from hydrogen-atom transfer at pH 2.5 to electron transfer, followed by proton transfer at pH 1.0. Additionally, the intramolecular HB in 6 exerts enhancing effects on oxygen-atom transfer reactions from 6 to alkenes such as cyclohexene and its water-soluble derivative to afford the corresponding epoxides, relative to the corresponding RuIV(O) complex (6') lacking the HB moieties in the SCS.
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Affiliation(s)
- Tomoya Ishizuka
- Department
of Chemistry, Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, Ibaraki 305-8571, Japan
| | - Taichi Kogawa
- Department
of Chemistry, Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, Ibaraki 305-8571, Japan
| | - Chisato Ogawa
- Department
of Chemistry, Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, Ibaraki 305-8571, Japan
| | - Hiroaki Kotani
- Department
of Chemistry, Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, Ibaraki 305-8571, Japan
| | - Yoshihito Shiota
- Institute
for Materials Chemistry and Engineering, Kyushu University, Moto-oka, Nishi-Ku, Fukuoka 819-0395, Japan
| | - Kazunari Yoshizawa
- Institute
for Materials Chemistry and Engineering, Kyushu University, Moto-oka, Nishi-Ku, Fukuoka 819-0395, Japan
| | - Takahiko Kojima
- Department
of Chemistry, Faculty of Pure and Applied Sciences, University of Tsukuba, 1-1-1 Tennoudai, Tsukuba, Ibaraki 305-8571, Japan
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4
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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.
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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.
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5
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Martínez FA, Adler NS, Cavasotto CN, Aucar GA. Solvent effects on the NMR shieldings of stacked DNA base pairs. Phys Chem Chem Phys 2022; 24:18150-18160. [PMID: 35861154 DOI: 10.1039/d2cp00398h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Stacking effects are among the most important effects in DNA. We have recently studied their influence in fragments of DNA through the analysis of NMR magnetic shieldings, firstly in vacuo. As a continuation of this line of research we show here the influence of solvent effects on the shieldings through the application of both explicit and implicit models. We found that the explicit solvent model is more appropriate for consideration due to the results matching better in general with experiments, as well as providing clear knowledge of the electronic origin of the value of the shieldings. Our study is grounded on a recently developed theoretical model of our own, by which we are able to learn about the magnetic effects of given fragments of DNA molecules on selected base pairs. We use the shieldings of the atoms of a central base pair (guanine-cytosine) of a selected fragment of DNA molecules as descriptors of physical effects, like π-stacking and solvent effects. They can be taken separately and altogether. The effect of π-stacking is introduced through the addition of some pairs above and below of the central base pair, and now, the solvent effect is considered including a network of water molecules that consist of two solvation layers, which were fixed in the calculations performed in all fragments. We show that the solvent effects enhance the stacking effects on the magnetic shieldings of atoms that belong to the external N-H bonds. The net effect is of deshielding on both atoms. There is also a deshielding effect on the carbon atoms that belong to CO bonds, for which the oxygen atom has an explicit hydrogen bond (HB) with a solvent water molecule. Solvent effects are found to be no higher than a few percent of the total value of the shieldings (between 1% and 5%) for most atoms, although there are few for which such an effect can be higher. There is one nitrogen atom, the acceptor of the HB between guanine and cytosine, that is more highly shielded (around 15 ppm or 10%) when the explicit solvent is considered. In a similar manner, the most external nitrogen atom of cytosine and the hydrogen atom that is bonded to it are highly deshielded (around 10 ppm for nitrogen and around 3 ppm for hydrogen).
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Affiliation(s)
- Fernando A Martínez
- Institute of Modelling and Innovation on Technology (IMIT), CONICET-UNNE, Avda Libertad 5460, W3404AAS Corrientes, Argentina.,Chemistry Department, Natural and Exact Science Faculty, Northeastern University of Argentina, Avda Libertad 5460, W3404AAS Corrientes, Argentina
| | - Natalia S Adler
- Computational Drug Design and Biomedical Informatics Laboratory, Instituto de Investigaciones en Medicina Translacional (IIMT), CONICET-Universidad Austral, Pilar, Buenos Aires, Argentina.,Centro de Investigaciones en BioNanociencias (CIBION), CONICET, Buenos Aires, Argentina
| | - Claudio N Cavasotto
- Computational Drug Design and Biomedical Informatics Laboratory, Instituto de Investigaciones en Medicina Translacional (IIMT), CONICET-Universidad Austral, Pilar, Buenos Aires, Argentina.,Facultad de Ciencias Biomédicas and Facultad de Ingeniería, Universidad Austral, Pilar, Buenos Aires, Argentina.,Austral Institute for Applied Artificial Intelligence, Universidad Austral, Pilar, Buenos Aires, Argentina
| | - Gustavo A Aucar
- Institute of Modelling and Innovation on Technology (IMIT), CONICET-UNNE, Avda Libertad 5460, W3404AAS Corrientes, Argentina.,Physics Department, Natural and Exact Science Faculty, Northeastern University of Argentina, Avda Libertad 5460, W3404AAS Corrientes, Argentina.
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6
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Zhou K, Zang J, Chen H, Wang W, Wang H, Zhao G. On-Axis Alignment of Protein Nanocage Assemblies from 2D to 3D through the Aromatic Stacking Interactions of Amino Acid Residues. ACS NANO 2018; 12:11323-11332. [PMID: 30265511 DOI: 10.1021/acsnano.8b06091] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Aromatic-aromatic interactions between natural aromatic amino acids Phe, Tyr, and Trp play crucial roles in protein-protein recognition and protein folding. However, the function of such interactions in the preparation of different dimensional, ordered protein superstructures has not been recognized. Herein, by a combination of the directionality of the symmetry axes of protein building blocks and the strength of the aromatic-aromatic interactions coming from a group of aromatic amino acid residues, we built an engineering strategy to construct protein superlattices. Based on this strategy, substitution of single amino acid residue Glu162 around the C4 rotation axes near the outer surface of 24-mer ferritin nanocage with Phe, Tyr, and Trp, respectively, resulted in 2D and 3D protein superlattices where protein cages are aligned along the C4 axes, imposing a fixed disposition of neighboring ferritins. The self-assembly of these superlattices is reversible, which can be tuned by external stimuli (salt concentration or pH). Moreover, these superlattices can serve as biotemplates for the fabrication of 2D and 3D inorganic nanoparticle arrays.
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Affiliation(s)
- Kai Zhou
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering , China Agricultural University, Key Laboratory of Functional Dairy, Ministry of Education , Beijing 100083 , China
| | - Jiachen Zang
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering , China Agricultural University, Key Laboratory of Functional Dairy, Ministry of Education , Beijing 100083 , China
| | - Hai Chen
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering , China Agricultural University, Key Laboratory of Functional Dairy, Ministry of Education , Beijing 100083 , China
| | - Wenming Wang
- Key Laboratory of Chemical Biology and Molecular Engineering of Education Ministry , Institute of Molecular Science, Shanxi University , Taiyuan 030006 , China
| | - Hongfei Wang
- Key Laboratory of Chemical Biology and Molecular Engineering of Education Ministry , Institute of Molecular Science, Shanxi University , Taiyuan 030006 , China
| | - Guanghua Zhao
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Food Science & Nutritional Engineering , China Agricultural University, Key Laboratory of Functional Dairy, Ministry of Education , Beijing 100083 , China
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7
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Avelar M, Pastor N, Ramirez-Ramirez J, Ayala M. Replacement of oxidizable residues predicted by QM-MM simulation of a fungal laccase generates variants with higher operational stability. J Inorg Biochem 2018; 178:125-133. [DOI: 10.1016/j.jinorgbio.2017.10.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 10/09/2017] [Accepted: 10/10/2017] [Indexed: 11/28/2022]
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8
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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.
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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
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9
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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
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10
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Gessmann R, Papadovasilaki M, Drougkas E, Petratos K. Zinc-substituted pseudoazurin solved by S/Zn-SAD phasing. Acta Crystallogr F Struct Biol Commun 2015; 71:19-23. [PMID: 25615962 PMCID: PMC4304741 DOI: 10.1107/s2053230x14025552] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2014] [Accepted: 11/22/2014] [Indexed: 11/10/2022] Open
Abstract
The copper(II) centre of the blue copper protein pseudoazurin from Alcaligenes faecalis has been substituted by zinc(II) via denaturing the protein, chelation and removal of copper and refolding the apoprotein, followed by the addition of an aqueous solution of ZnCl2. Vapour-diffusion experiments produced colourless hexagonal crystals (space group P65), which when cryocooled had unit-cell parameters a=b=49.01, c=98.08 Å. Diffraction data collected at 100 K using a copper sealed tube were phased by the weak anomalous signal of five S atoms and one Zn atom. The structure was fitted manually and refined to 1.6 Å resolution. The zinc-substituted protein exhibits similar overall geometry to the native structure with copper. Zn2+ binds more strongly to its four ligand atoms (His40 Nδ1, Cys78 Sγ, His81 Nδ1 and Met86 Sδ) and retains the tetrahedral arrangement, although the structure is less distorted than the native copper protein.
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Affiliation(s)
- Renate Gessmann
- Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology-Hellas (FORTH), N. Plastira 100, 70 013 Heraklion, Greece
| | - Maria Papadovasilaki
- Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology-Hellas (FORTH), N. Plastira 100, 70 013 Heraklion, Greece
| | - Evangelos Drougkas
- Department of Biology, University of Crete, PO Box 2208, 71 409 Heraklion, Greece
| | - Kyriacos Petratos
- Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology-Hellas (FORTH), N. Plastira 100, 70 013 Heraklion, Greece
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11
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Gast P, Broeren FG, Sottini S, Aoki R, Takashina A, Yamaguchi T, Kohzuma T, Groenen EJ. The type 1 copper site of pseudoazurin: Axial and rhombic. J Inorg Biochem 2014; 137:57-63. [DOI: 10.1016/j.jinorgbio.2014.03.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Revised: 03/25/2014] [Accepted: 03/28/2014] [Indexed: 11/29/2022]
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12
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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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13
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Medaković VB, Bogdanović GA, Milčić MK, Janjić GV, Zarić SD. CH/π interactions in metal–porphyrin complexes with pyrrole and chelate rings as hydrogen acceptors. J Inorg Biochem 2012; 117:157-63. [DOI: 10.1016/j.jinorgbio.2012.09.002] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2012] [Revised: 09/01/2012] [Accepted: 09/01/2012] [Indexed: 10/27/2022]
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14
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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]
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15
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Dimitrijević BP, Borozan SZ, Stojanović SĐ. π–π and cation–π interactions in protein–porphyrin complex crystal structures. RSC Adv 2012. [DOI: 10.1039/c2ra21937a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
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16
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New SY, Marshall NM, Hor TSA, Xue F, Lu Y. Redox tuning of two biological copper centers through non-covalent interactions: same trend but different magnitude. Chem Commun (Camb) 2012; 48:4217-9. [DOI: 10.1039/c2cc30901g] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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17
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Salonen LM, Ellermann M, Diederich F. Aromatische Ringe in chemischer und biologischer Erkennung: Energien und Strukturen. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201007560] [Citation(s) in RCA: 245] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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18
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Salonen LM, Ellermann M, Diederich F. Aromatic rings in chemical and biological recognition: energetics and structures. Angew Chem Int Ed Engl 2011; 50:4808-42. [PMID: 21538733 DOI: 10.1002/anie.201007560] [Citation(s) in RCA: 1165] [Impact Index Per Article: 89.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2010] [Indexed: 12/12/2022]
Abstract
This review describes a multidimensional treatment of molecular recognition phenomena involving aromatic rings in chemical and biological systems. It summarizes new results reported since the appearance of an earlier review in 2003 in host-guest chemistry, biological affinity assays and biostructural analysis, data base mining in the Cambridge Structural Database (CSD) and the Protein Data Bank (PDB), and advanced computational studies. Topics addressed are arene-arene, perfluoroarene-arene, S⋅⋅⋅aromatic, cation-π, and anion-π interactions, as well as hydrogen bonding to π systems. The generated knowledge benefits, in particular, structure-based hit-to-lead development and lead optimization both in the pharmaceutical and in the crop protection industry. It equally facilitates the development of new advanced materials and supramolecular systems, and should inspire further utilization of interactions with aromatic rings to control the stereochemical outcome of synthetic transformations.
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Affiliation(s)
- Laura M Salonen
- Laboratory of Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, Hönggerberg, HCI, 8093 Zurich, Switzerland
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Galli C, Gentili P, Jolivalt C, Madzak C, Vadalà R. How is the reactivity of laccase affected by single-point mutations? Engineering laccase for improved activity towards sterically demanding substrates. Appl Microbiol Biotechnol 2011; 91:123-31. [PMID: 21468703 DOI: 10.1007/s00253-011-3240-4] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2010] [Revised: 03/07/2011] [Accepted: 03/07/2011] [Indexed: 11/28/2022]
Abstract
In spite of its broad specificity among phenols, Trametes versicolor laccase hardly succeeds in oxidizing hindered substrates. To improve the oxidation ability of this laccase towards bulky phenolic substrates, we designed a series of single-point mutants on the basis of the amino-acid layout inside the reducing substrate active site known from the crystal structure of the enzyme. Site-directed mutagenesis has addressed four phenylalanine residues in key positions 162, 265, 332, and 337 at the entrance of the binding pocket, as these residues appeared instrumental for docking of the substrate. These phenylalanines were replaced by smaller-sized but still apolar alanines. A double mutant F162A/F332A was also designed. Measurement of the oxidation efficiency towards encumbered phenols has shown that mutant F162A was more efficient than the wild-type laccase. The double mutant F162A/F332A led to 98% consumption of bisphenol A in only 5 h and was more efficient than the single mutants in the aerobic oxidation of this bulky substrate. In contrast, lack of appropriate hydrophobic interactions with the substrate possibly depresses the oxidation outcome with mutants F265A and F332A. One explanation for the lack of reactivity of mutant F337A, supported by literature reports, is that this residue is part of the second coordination shell of T1 Cu. A mutation at this position thus leads to a drastic coordination shell destabilization. Thermal stability of the mutants and their resistance in a mixed water-dioxane solvent have also been investigated.
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Affiliation(s)
- Carlo Galli
- Dipartimento di Chimica, Università La Sapienza and IMC-CNR Sezione Meccanismi di Reazione, Piazzale A. Moro 5, Rome, Italy,
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Yang CM, Zhang J. Insights into intramolecular Trp and His side-chain orientation and stereospecific π interactions surrounding metal centers: an investigation using protein metal-site mimicry in solution. Chemistry 2011; 16:10854-65. [PMID: 20669189 DOI: 10.1002/chem.200903149] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Metal-binding scaffolds incorporating a Trp/His-paired epitope are instrumental in giving novel insights into the physicochemical basis of functional and mechanistic versatility conferred by the Trp-His interplay at a metal site. Herein, by coupling biometal site mimicry and (1)H and (13)C NMR spectroscopy experiments, modular constructs EDTA-(L-Trp, L-His) (EWH; EDTA=ethylenediamino tetraacetic acid) and DTPA-(L-Trp, L-His) (DWH; DTPA=diethylenetriamino pentaacetic acid) were employed to dissect the static and transient physicochemical properties of hydrophobic/hydrophilic aromatic interactive modes surrounding biometal centers. The binding feature and identities of the stoichiometric metal-bound complexes in solution were investigated by using (1)H and (13)C NMR spectroscopy, which facilitated a cross-validation of the carboxylate, amide oxygen, and tertiary amino groups as the primary ligands and indole as the secondary ligand, with the imidazole (Im) N3 nitrogen being weakly bound to metals such as Ca(2+) owing to a multivalency effect. Surrounding the metal centers, the stereospecific orientation of aromatic rings in the diastereoisomerism is interpreted with the Ca(2+)-EWH complex. With respect to perturbed Trp side-chain rotamer heterogeneity, drastically restricted Trp side-chain flexibility and thus a dynamically constrained rotamer interconversion due to π interactions is evident from the site-selective (13)C NMR spectroscopic signal broadening of the Trp indolyl C3 atom. Furthermore, effects of Trp side-chain fluctuation on indole/Im orientation were the subject of a 2D NMR spectroscopy study by using the Ca(2+)-bound state; a C-H2(indolyl)/C-H5(Im(+)) connectivity observed in the NOESY spectra captured direct evidence that the N-H1 of the Ca(2+)-Im(+) unit interacted with the pyrrole ring of the indole unit in Ca(2+)-bound EWH but not in DWH, which is assignable to a moderately static, anomalous, T-shaped, interplanar π(+)-π stacking alignment. Nevertheless, a comparative (13)C NMR spectroscopy study of the two homologous scaffolds revealed that the overall response of the indole unit arises predominantly from global attractions between the indole ring and the entire positively charged first coordination sphere. The study thus demonstrates the coordination-sphere/geometry dependence of the Trp/His side-chain interplay, and established that π interactions allow (13)C NMR spectroscopy to offer a new window for investigating Trp rotamer heterogeneity near metal-binding centers.
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Affiliation(s)
- Chi Ming Yang
- Neurochemistry & Biophysical Organic Chemistry, College of Chemistry, Nankai University, Tianjin 300071, China.
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Ming Yang C. Biometal binding-site mimicry with modular, hetero-bifunctionally modified architecture encompassing a Trp/His motif: Insights into spatiotemporal noncovalent interactions from a comparative spectroscopic study. Dalton Trans 2011; 40:3008-27. [DOI: 10.1039/c0dt00237b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Li C, Sato K, Monari S, Salard I, Sola M, Banfield MJ, Dennison C. Metal-Binding Loop Length Is a Determinant of the pKa of a Histidine Ligand at a Type 1 Copper Site. Inorg Chem 2010; 50:482-8. [DOI: 10.1021/ic101413e] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Chan Li
- 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
| | - Stefano Monari
- Department of Chemistry, University of Modena and Reggio Emilia, Via Campi 183, 41125 Modena, Italy
| | - Isabelle Salard
- 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
| | - Mark J. Banfield
- Department of Biological Chemistry, John Innes Centre, Norwich NR4 7UH, U.K
| | - Christopher Dennison
- Institute for Cell and Molecular Biosciences, Medical School, Newcastle University, Newcastle upon Tyne NE2 4HH, U.K
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Gessmann R, Kyvelidou C, Papadovasilaki M, Petratos K. The crystal structure of cobalt-substituted pseudoazurin from Alcaligenes faecalis. Biopolymers 2010; 95:202-7. [DOI: 10.1002/bip.21553] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Farrell D, Miranda ES, Webb H, Georgi N, Crowley PB, McIntosh LP, Nielsen JE. Titration_DB: storage and analysis of NMR-monitored protein pH titration curves. Proteins 2010; 78:843-57. [PMID: 19899070 DOI: 10.1002/prot.22611] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
NMR-monitored pH titration experiments are routinely used to measure site-specific protein pKa values. Accurate experimental pKa values are essential in dissecting enzyme catalysis, in studying the pH-dependence of protein stability and ligand binding, in benchmarking pKa prediction algorithms, and ultimately in understanding electrostatic effects in proteins. However, due to the complex ways in which pH-dependent electrostatic and structural changes manifest themselves in NMR spectra, reported apparent pKa values are often dependent on the way that NMR pH-titration curves are analyzed. It is therefore important to retain the raw NMR spectroscopic data to allow for documentation and possible re-interpretation. We have constructed a database of primary NMR pH-titration data, which is accessible via a web interface. Here, we report statistics of the database contents and analyze the data with a global perspective to provide guidelines on best practice for fitting NMR titration curves. Titration_DB is available at http://enzyme.ucd.ie/Titration_DB. Proteins 2010. (c) 2009 Wiley-Liss, Inc.
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Affiliation(s)
- Damien Farrell
- School of Biomolecular and Biomedical Science, Centre for Synthesis and Chemical Biology, UCD Conway Institute, University College Dublin, Belfield, Dublin 4, Ireland
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Su P, Li H. Protonation of Type-1 Cu Bound Histidines: A Quantum Chemical Study. Inorg Chem 2009; 49:435-44. [DOI: 10.1021/ic9012735] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Peifeng Su
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588
| | - Hui Li
- Department of Chemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588
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Li YZ, Li BJ, Lu XY, Lin S, Shi ZJ. Cross Dehydrogenative Arylation (CDA) of a Benzylic CH Bond with Arenes by Iron Catalysis. Angew Chem Int Ed Engl 2009; 48:3817-20. [DOI: 10.1002/anie.200900341] [Citation(s) in RCA: 279] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Li YZ, Li BJ, Lu XY, Lin S, Shi ZJ. Cross Dehydrogenative Arylation (CDA) of a Benzylic CH Bond with Arenes by Iron Catalysis. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200900341] [Citation(s) in RCA: 105] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Active site loop dictates the thermodynamics of reduction and ligand protonation in cupredoxins. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2009; 1794:995-1000. [PMID: 19230853 DOI: 10.1016/j.bbapap.2009.02.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2008] [Revised: 01/28/2009] [Accepted: 02/03/2009] [Indexed: 11/21/2022]
Abstract
The thermodynamics of reduction and His ligand protonation have been determined for a range of loop-contraction variants of the electron transferring type 1 copper protein azurin (AZ). For AZPC, in which the native C-terminal loop containing the Cys, His and Met ligands has been replaced with the shorter sequence from plastocyanin (PC) and AZAMI, in which the even shorter amicyanin (AMI) loop has been inserted, the thermodynamics of reduction match those of the protein whose loop has been introduced which are different to the values for AZ. The enthalpic contribution to His ligand protonation, which is not observed in AZ, is similar in AZAMI and AMI. The thermodynamics of this process in AZPC are more dissimilar to those for PC. In the case of AZAMI-F, a variant possessing the (non natural) minimal loop that can bind a type 1 copper site, the reduction thermodynamics are intermediate between those of AZPC and AZAMI, whilst the thermodynamic data for His ligand protonation are very similar to those for AMI. The results for AZAMI and AZPC are primarily due to protein based enthalpic effects related to the interaction of the metal with permanent protein dipoles from the loop, and to the decreased loop length which favors His ligand protonation in the cuprous proteins. Entropic factors related to loop flexibility have little influence because of constraints imposed by metal coordination and the fact that the introduced loops pack well against the AZ scaffold. Thus, the host scaffold in general plays a minor thermodynamic role in both processes, although for AZAMI-F differences in the first and second coordination spheres influence the thermodynamics of reduction.
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Hass MAS, Vlasie MD, Ubbink M, Led JJ. Conformational exchange in pseudoazurin: different kinds of microsecond to millisecond dynamics characterized by their pH and buffer dependence using 15N NMR relaxation. Biochemistry 2009; 48:50-8. [PMID: 19072172 DOI: 10.1021/bi801858f] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The dynamics of the reduced form of the blue copper protein pseudoazurin from Alcaligenes faecalis S-6 was investigated using (15)N relaxation measurements with a focus on the dynamics of the micro- to millisecond time scale. Different types of conformational exchange processes are observed in the protein on this time scale. At low pH, the protonation of the C-terminal copper-ligated histidine, His81, is observed. A comparison of the exchange rates in the presence and absence of added buffers shows that the protonation is the rate-limiting step at low buffer concentrations. This finding agrees with previous observations for other blue copper proteins, e.g., amicyanin and plastocyanin. However, in contrast to plastocyanin but similar to amicyanin, a second conformational exchange between different conformations of the protonated copper site is observed at low pH, most likely triggered by the protonation of His81. This process has been further characterized using CPMG dispersion methods and is found to occur with a rate of a few thousands per second. Finally, micro- to millisecond motions are observed in one of the loop regions and in the alpha-helical regions. These motions are unaffected by pH and are unrelated to the conformational changes in the active site of pseudoazurin.
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Affiliation(s)
- Mathias A S Hass
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen Ø, Denmark
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Shimazaki Y, Takani M, Yamauchi O. Metal complexes of amino acids and amino acid side chain groups. Structures and properties. Dalton Trans 2009:7854-69. [PMID: 19771344 DOI: 10.1039/b905871k] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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