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Guo X, Wang R, Han B, Shao W, Chen L, Feng X. A novel EGCG-Histidine complex improves gelling and physicochemical properties of porcine myofibrillar proteins: Insight into underlying mechanisms. Food Chem 2024; 448:139070. [PMID: 38555690 DOI: 10.1016/j.foodchem.2024.139070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 02/28/2024] [Accepted: 03/16/2024] [Indexed: 04/02/2024]
Abstract
Herein, an EGCG-Histidine complex is prepared, characterized, and further used to improve gel properties of myofibrillar proteins (MP). Results of FTIR, XRD, UV-Vis spectroscopy showed that histidine is covalently bound to EGCG by Michael addition or Schiff base reaction to form EGCG-Histidine complex, and antioxidant activity of EGCG-Histidine complex is significantly increased compared to EGCG or histidine alone (P < 0.05). The addition of EGCG-Histidine complex results in cooking loss of gel decreasing from 66.7 ± 0.23 % to 40.3 ± 2.02 %, and improves rheological properties of MP, and enhances gel strength from 0.10 ± 0.01 N to 0.22 ± 0.03 N, indicating positive effect of EGCG-Histidine complex on MP gel formation, above results is supported by results of SEM, CD spectroscopy, SDS-PAGE, and tryptophan fluorescence. These results indicated that EGCG-Histidine complex can be used as a functional ingredient to improve gel quality of meat products.
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Affiliation(s)
- Xiao Guo
- College of Food Science and Engineering, Northwest A&F University, No. 22 Xinong Road, Yangling, Shaanxi 712100, China
| | - Renzheng Wang
- College of Food Science and Engineering, Northwest A&F University, No. 22 Xinong Road, Yangling, Shaanxi 712100, China
| | - Bofu Han
- College of Food Science and Engineering, Northwest A&F University, No. 22 Xinong Road, Yangling, Shaanxi 712100, China
| | - Wei Shao
- College of Food Science and Engineering, Northwest A&F University, No. 22 Xinong Road, Yangling, Shaanxi 712100, China
| | - Lin Chen
- College of Food Science and Engineering, Northwest A&F University, No. 22 Xinong Road, Yangling, Shaanxi 712100, China
| | - Xianchao Feng
- College of Food Science and Engineering, Northwest A&F University, No. 22 Xinong Road, Yangling, Shaanxi 712100, China.
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2
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Nan K, He M, Chen B, Hu B. Histidine tag modified magnetic beads for analysis of arsenic binding proteins. Anal Chim Acta 2024; 1304:342554. [PMID: 38637038 DOI: 10.1016/j.aca.2024.342554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 03/05/2024] [Accepted: 03/27/2024] [Indexed: 04/20/2024]
Abstract
BACKGROUND Many proteins with thiol groups can bind with trivalent arsenic which are termed as arsenic binding proteins, thus change their physiological functions. Therefore, it is vital to analyze the arsenic binding proteins in cells. The Pull-Down strategy based on biotinylated phenylarsenic acid (Bio-PAO(III)) probes is an effective way for analysis of arsenic binding proteins. In this strategy, streptavidin magnetic beads (SA-MBs) was applied to capture the arsenic binding proteins conjugating with Bio-PAO(III) probe. However, strong interaction between SA and biotin makes the elution of arsenic binding proteins not easy. RESULTS We developed a novel affinity separation strategy to address the challenge of eluting arsenic binding proteins, a key issue with the existing Bio-PAO(III) Pull-Down method. By employing magnetic beads modified with Nα-Bis(carboxymethyl)-l-lysine (NTA-Lys), polyhistidine-tag (His6-Tag), and SA (MB-NTA(Ni)-His6-SA), we established a more efficient purification process. This innovative approach enables selective capture of arsenic binding proteins in HepG2 cells labeled by Bio-PAO(III) probes, facilitating gentle digestion by trypsin for precise identification through capillary high performance liquid chromatography (Cap HPLC)-electrospray ionization (ESI)-tandem mass spectrometry (MS/MS). What is more, the magnetic beads can be regenerated by using imidazole as the eluent, and the obtained MB-NTA(Ni) can be reloaded with His6-SA for next use. Our method successfully identified 41 arsenic binding proteins, including those involved in cytoskeletal structure, heat shock response, transcriptional regulation, DNA damage repair, redox state regulation, mitochondrial dehydrogenase function, and protein synthesis and structure. SIGNIFICANCE This work contributes to a more comprehensive understanding of the toxic mechanisms of arsenic, potentially providing valuable insights for the prevention or treatment of arsenic-related diseases.
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Affiliation(s)
- Kai Nan
- Department of Chemistry, Wuhan University, Wuhan, 430072, PR China
| | - Man He
- Department of Chemistry, Wuhan University, Wuhan, 430072, PR China
| | - Beibei Chen
- Department of Chemistry, Wuhan University, Wuhan, 430072, PR China.
| | - Bin Hu
- Department of Chemistry, Wuhan University, Wuhan, 430072, PR China
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3
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Rossotti M, Arceri D, Mansuelle P, Bornet O, Durand A, Ouchane S, Launay H, Dorlet P. The green cupredoxin CopI is a multicopper protein able to oxidize Cu(I). J Inorg Biochem 2024; 254:112503. [PMID: 38364337 DOI: 10.1016/j.jinorgbio.2024.112503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 02/02/2024] [Accepted: 02/06/2024] [Indexed: 02/18/2024]
Abstract
Anthropogenic activities in agriculture and health use the antimicrobial properties of copper. This has led to copper accumulation in the environment and contributed to the emergence of copper resistant microorganisms. Understanding bacterial copper homeostasis diversity is therefore highly relevant since it could provide valuable targets for novel antimicrobial treatments. The periplasmic CopI protein is a monodomain cupredoxin comprising several copper binding sites and is directly involved in copper resistance in bacteria. However, its structure and mechanism of action are yet to be determined. To study the different binding sites for cupric and cuprous ions and to understand their possible interactions, we have used mutants of the putative copper binding modules of CopI and spectroscopic methods to characterize their properties. We show that CopI is able to bind a cuprous ion in its central histidine/methionine-rich region and oxidize it thanks to its cupredoxin center. The resulting cupric ion can bind to a third site at the N-terminus of the protein. Nuclear magnetic resonance spectroscopy revealed that the central histidine/methionine-rich region exhibits a dynamic behavior and interacts with the cupredoxin binding region. CopI is therefore likely to participate in copper resistance by detoxifying the cuprous ions from the periplasm.
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Affiliation(s)
- Melanie Rossotti
- CNRS, Aix Marseille Univ, BIP, Institut de Microbiologie de la Méditerranée (IMM), Marseille, France
| | - Diletta Arceri
- CNRS, Aix Marseille Univ, BIP, Institut de Microbiologie de la Méditerranée (IMM), Marseille, France
| | - Pascal Mansuelle
- CNRS, FR3479, Institut de Microbiologie de la Méditerranée (IMM), Plateforme Protéomique, Marseille Protéomique (MaP), IbiSA Labelled, Aix Marseille Univ, Marseille, France
| | - Olivier Bornet
- CNRS, Aix Marseille Univ, Institut de Microbiologie de la Méditerranée (IMM), Marseille, France
| | - Anne Durand
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Soufian Ouchane
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Hélène Launay
- CNRS, Aix Marseille Univ, BIP, Institut de Microbiologie de la Méditerranée (IMM), Marseille, France
| | - Pierre Dorlet
- CNRS, Aix Marseille Univ, BIP, Institut de Microbiologie de la Méditerranée (IMM), Marseille, France.
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4
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Le Thi HN, Le NT, Bui Thi TH, Nguyen Thi HL, Nguyen TT, Nguyen Thi Y, Ha MN, Nguyen DT. Novel melanin-derived stationary phase for immobilized metal ion affinity chromatography in recombinant His-tagged protein purification. Protein Expr Purif 2024; 217:106444. [PMID: 38365166 DOI: 10.1016/j.pep.2024.106444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 01/13/2024] [Accepted: 02/08/2024] [Indexed: 02/18/2024]
Abstract
The matrix of the stationary phase is a crucial element in affinity chromatography for protein purification. Various materials, including polymer or magnetic materials, have been employed as the matrix in the purification of His-tagged protein. Here, for the first time, we utilized a combination of melanin and alginate, both natural polymer materials, to synthesize Ni-melanin/alginate (Ni-M/A) beads for His-tagged protein purification. We investigated the binding of His-tagged Mpro on the Ni-M/A beads, referred to as Ni-M/A-Mpro, and assessed the elution efficiency of Mpro from the beads. Our examination involved FTIR, EDS, XRD, SDS-PAGE, and Western blotting methods. FTIR spectra revealed notable changes in the stretching patterns and intensities of hydroxyl, amine, carbonyl, imine and amide chemical groups, when Mpro protein was present in the Ni-M/A sample. XRD spectra demonstrated the occurrence of two Nickel peaks at 35-40 deg and 40-45 deg in Ni-M/A, but only one nickel peak at 35-40 deg in Ni-M/A-Mpro, indicating the binding of Mpro on the Nickel ions. EDS analysis reported a decrease in the concentration of Nickel on the surface of Ni-M/A from 16% to 7% when Mpro protein was loaded into the stationary phase. Importantly, our data indicated that the purity of the His-tagged protein Mpro after purification reached 97% after just one-step purification using the Ni-M/A stationary phase. Moreover, the binding capacity of Ni-M/A for Mpro was approximately 5.2 mg/g with recovery efficiency of 40%. Our results suggested Ni-M/A as a highly potential solid phase for affinity chromatography in the purification of His-tagged protein.
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Affiliation(s)
- Hong-Nhung Le Thi
- Department of Biochemistry and Molecular Biology, Faculty of Biology, VNU University of Science, Vietnam National University, 100000, Hanoi, Viet Nam
| | - Ngoc-Tram Le
- Department of Biochemistry and Molecular Biology, Faculty of Biology, VNU University of Science, Vietnam National University, 100000, Hanoi, Viet Nam
| | - Thu-Hoai Bui Thi
- Department of Biochemistry and Molecular Biology, Faculty of Biology, VNU University of Science, Vietnam National University, 100000, Hanoi, Viet Nam
| | - Hong-Loan Nguyen Thi
- Department of Biochemistry and Molecular Biology, Faculty of Biology, VNU University of Science, Vietnam National University, 100000, Hanoi, Viet Nam
| | - Thanh-Thuy Nguyen
- Department of Biochemistry and Molecular Biology, Faculty of Biology, VNU University of Science, Vietnam National University, 100000, Hanoi, Viet Nam
| | - Yen Nguyen Thi
- Department of Biochemistry and Molecular Biology, Faculty of Biology, VNU University of Science, Vietnam National University, 100000, Hanoi, Viet Nam
| | - Minh-Ngoc Ha
- VNU Key Laboratory of Advanced Materials for Green Growth, VNU University of Science, Vietnam National University, 100000, Hanoi, Viet Nam
| | - Dinh-Thang Nguyen
- Faculty of Advanced Technology and Engineering, Vietnam-Japan University, Vietnam National University, 100000, Hanoi, Viet Nam.
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5
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Kundu S, Maji MS. Solution-Phase Late-Stage Chemoselective Photocatalytic Removal of Sulfonyl and Phenacyl Groups in Peptides. Chemistry 2024; 30:e202400033. [PMID: 38345998 DOI: 10.1002/chem.202400033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2024] [Indexed: 03/07/2024]
Abstract
Herein, BPC catalyzed visible-light-triggered target-specific late-stage solution phase desulfonylation from tryptophan in oligopeptides is portrayed by overcoming the isolation issue up to octamers. This robust and mild method is highly predictable and chemoselective, tolerating myriad of functional groups in aza-heteroaromatics and peptides. Interestingly, reductive desulfonylation is also amenable to biologically significant reactive histidine and tyrosine side chains, signifying the versatility of the strategy. Additional efficacy of BPC is demonstrated by solution phase phenacyl deprotection from C-terminal in peptides. Furthermore, excellent catalyst loading of 0.5 mol% and recyclability demonstrate the practical utility and applicability of this strategy.
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Affiliation(s)
- Samrat Kundu
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur, 721302, West Bengal, India
| | - Modhu Sudan Maji
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur, 721302, West Bengal, India
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6
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Rola A, Kola A, Valensin D, Palacios O, Capdevila M, Gumienna-Kontecka E, Potocki S. Beyond copper: examining the significance of His-mutations in mycobacterial GroEL1 HRCT for Ni(II) complex stability and formation. Dalton Trans 2024; 53:6676-6689. [PMID: 38526845 DOI: 10.1039/d4dt00011k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/27/2024]
Abstract
Recently, we have studied the coordination chemistry of the Cu(II)-histidine-rich C-terminal tail (HRCT) complex of the mycobacterial GroEL1 protein. The structure of this domain differs significantly compared to the well-known methionine-glycine-rich GroEL chaperonin - it was predicted that mycobacterial GroEL1 could play a significant role in the metal homeostasis of Mycobacteria, especially copper. However, we found that this particular domain's pattern also repeats in a number of Ni(II)-binding proteins. Here, we present the studies concerning the properties of GroEL1 HRCT as a ligand for Ni(II) ions. For this purpose, we chose eight model peptides: L1 - Ac-DHDHHHGHAH, L2 - Ac-DKPAKAEDHDHHHGHAH, and 6 mutants of the latter in the pH range of 2-11. We examined the stoichiometry, stability, and spectroscopic features of copper complexes. We noticed that similar to the Cu(II)-complex, the presence of a Lys5 residue significantly increases the stability of the system. The impact of His mutations was also examined and carefully studied using NMR spectroscopy. His9 and His13 are the crucial residues for Ni(II) binding, whereas His12 has minimal relevance in complex formation.
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Affiliation(s)
- Anna Rola
- Faculty of Chemistry, University of Wroclaw, 50- 383 Wroclaw, Poland.
| | - Arian Kola
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via A. Moro 2, 53100 Siena, Italy
| | - Daniela Valensin
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via A. Moro 2, 53100 Siena, Italy
| | - Oscar Palacios
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain
| | - Merce Capdevila
- Departament de Química, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain
| | | | - Sławomir Potocki
- Faculty of Chemistry, University of Wroclaw, 50- 383 Wroclaw, Poland.
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7
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Vlachou A, Kumar VB, Tiwari OS, Rencus-Lazar S, Chen Y, Ozguney B, Gazit E, Tamamis P. Co-Assembly of Cancer Drugs with Cyclo-HH Peptides: Insights from Simulations and Experiments. ACS Appl Bio Mater 2024; 7:2309-2324. [PMID: 38478987 PMCID: PMC11022239 DOI: 10.1021/acsabm.3c01304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 02/22/2024] [Accepted: 02/25/2024] [Indexed: 04/16/2024]
Abstract
Peptide-based nanomaterials can serve as promising drug delivery agents, facilitating the release of active pharmaceutical ingredients while reducing the risk of adverse reactions. We previously demonstrated that Cyclo-Histidine-Histidine (Cyclo-HH), co-assembled with cancer drug Epirubicin, zinc, and nitrate ions, can constitute an attractive drug delivery system, combining drug self-encapsulation, enhanced fluorescence, and the ability to transport the drug into cells. Here, we investigated both computationally and experimentally whether Cyclo-HH could co-assemble, in the presence of zinc and nitrate ions, with other cancer drugs with different physicochemical properties. Our studies indicated that Methotrexate, in addition to Epirubicin and its epimer Doxorubicin, and to a lesser extent Mitomycin-C and 5-Fluorouracil, have the capacity to co-assemble with Cyclo-HH, zinc, and nitrate ions, while a significantly lower propensity was observed for Cisplatin. Epirubicin, Doxorubicin, and Methorexate showed improved drug encapsulation and drug release properties, compared to Mitomycin-C and 5-Fluorouracil. We demonstrated the biocompatibility of the co-assembled systems, as well as their ability to intracellularly release the drugs, particularly for Epirubicin, Doxorubicin, and Methorexate. Zinc and nitrate were shown to be important in the co-assembly, coordinating with drugs and/or Cyclo-HH, thereby enabling drug-peptide as well as drug-drug interactions in successfully formed nanocarriers. The insights could be used in the future design of advanced cancer therapeutic systems with improved properties.
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Affiliation(s)
- Anastasia Vlachou
- Artie
McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843-3122, United States
| | - Vijay Bhooshan Kumar
- The
Shmunis School of Biomedicine and Cancer Research, George S. Wise
Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
- Department
of Materials Science and Engineering, Iby and Aladar Fleischman Faculty
of Engineering, Tel Aviv University, Tel Aviv 6997801, Israel
- Sagol
School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Om Shanker Tiwari
- The
Shmunis School of Biomedicine and Cancer Research, George S. Wise
Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
- Department
of Materials Science and Engineering, Iby and Aladar Fleischman Faculty
of Engineering, Tel Aviv University, Tel Aviv 6997801, Israel
- Sagol
School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Sigal Rencus-Lazar
- The
Shmunis School of Biomedicine and Cancer Research, George S. Wise
Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
- Department
of Materials Science and Engineering, Iby and Aladar Fleischman Faculty
of Engineering, Tel Aviv University, Tel Aviv 6997801, Israel
- Sagol
School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Yu Chen
- The
Shmunis School of Biomedicine and Cancer Research, George S. Wise
Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
- Department
of Materials Science and Engineering, Iby and Aladar Fleischman Faculty
of Engineering, Tel Aviv University, Tel Aviv 6997801, Israel
- Sagol
School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Busra Ozguney
- Artie
McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843-3122, United States
| | - Ehud Gazit
- The
Shmunis School of Biomedicine and Cancer Research, George S. Wise
Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
- Department
of Materials Science and Engineering, Iby and Aladar Fleischman Faculty
of Engineering, Tel Aviv University, Tel Aviv 6997801, Israel
- Sagol
School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel
| | - Phanourios Tamamis
- Artie
McFerrin Department of Chemical Engineering, Texas A&M University, College Station, Texas 77843-3122, United States
- Department
of Materials Science and Engineering, Texas
A&M University, College Station, Texas 77843-3003, United States
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8
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González-Delgado JM, Thompson PM, Andrałojć W, Gdaniec Z, Ghiladi RA, Franzen S. Comparison of the Backbone Dynamics of Dehaloperoxidase-Hemoglobin Isoenzymes. J Phys Chem B 2024; 128:3383-3397. [PMID: 38563384 DOI: 10.1021/acs.jpcb.3c07176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Dehaloperoxidase (DHP) is a multifunctional hemeprotein with a functional switch generally regulated by the chemical class of the substrate. Its two isoforms, DHP-A and DHP-B, differ by only five amino acids and have an almost identical protein fold. However, the catalytic efficiency of DHP-B for oxidation by a peroxidase mechanism ranges from 2- to 6-fold greater than that of DHP-A depending on the conditions. X-ray crystallography has shown that many substrates and ligands have nearly identical binding in the two isoenzymes, suggesting that the difference in catalytic efficiency could be due to differences in the conformational dynamics. We compared the backbone dynamics of the DHP isoenzymes at pH 7 through heteronuclear relaxation dynamics at 11.75, 16.45, and 19.97 T in combination with four 300 ns MD simulations. While the overall dynamics of the isoenzymes are similar, there are specific local differences in functional regions of each protein. In DHP-A, Phe35 undergoes a slow chemical exchange between two conformational states likely coupled to a swinging motion of Tyr34. Moreover, Asn37 undergoes fast chemical exchange in DHP-A. Given that Phe35 and Asn37 are adjacent to Tyr34 and Tyr38, it is possible that their dynamics modulate the formation and migration of the active tyrosyl radicals in DHP-A at pH 7. Another significant difference is that both distal and proximal histidines have a 15-18% smaller S2 value in DHP-B, thus their greater flexibility could account for the higher catalytic activity. The distal histidine grants substrate access to the distal pocket. The greater flexibility of the proximal histidine could also accelerate H2O2 activation at the heme Fe by increased coupling of an amino acid charge relay to stabilize the ferryl Fe(IV) oxidation state in a Poulos-Kraut "push-pull"-type peroxidase mechanism.
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Affiliation(s)
| | - Peter M Thompson
- Department of Molecular and Structural Biochemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
- Molecular Education, Technology and Research Innovation Center (METRIC), North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Witold Andrałojć
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland
| | - Zofia Gdaniec
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznań, Poland
| | - Reza A Ghiladi
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Stefan Franzen
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States
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9
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Mandal S, Mallik S, Bhoumick A, Bhattacharya A, Sen P. Synthesis of Amino Acid-Based Cationic Lipids and Study of the Role of the Cationic Head Group for Enhanced Drug and Nucleic Acid Delivery. Chembiochem 2024; 25:e202300834. [PMID: 38284327 DOI: 10.1002/cbic.202300834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Revised: 01/17/2024] [Accepted: 01/26/2024] [Indexed: 01/30/2024]
Abstract
Leveraging liposomes for drug and nucleic acid delivery, though promising due to reduced toxicity and ease of preparation, faces challenges in stability and efficiency. To address this, we synthesized cationic amphiphiles from amino acids (arginine, lysine, and histidine). Histidine emerged as the superior candidate, leading to the development of three histidine-rich cationic amphiphiles for liposomes. Using the hydration method, we have prepared the liposomes and determined the optimal N/P ratios for lipoplex formation via gel electrophoresis. In vitro transfection assays compared the efficacy of our lipids to Fugene, while MTT assays gauged biocompatibility across cancer cell lines (MDA-MB 231 and MCF-7). The histidine-based lipid demonstrated marked potential in enhancing drug and nucleic acid delivery. This improvement stemmed from increased zeta potential, enhancing electrostatic interactions with nucleic acids and cellular uptake. Our findings underscore histidine's crucial role over lysine and arginine for effective delivery, revealing a significant correlation between histidine abundance and optimal performance. This study paves the way for histidine-enriched lipids as promising candidates for efficient drug and nucleic acid delivery, addressing key challenges in the field.
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Affiliation(s)
- Subhasis Mandal
- Indian Association for the Cultivation of Science, School of Biological Sciences, 2 A & 2B Raja S C Mullick Road, Kolkata, 700032
| | - Suman Mallik
- Indian Association for the Cultivation of Science, School of Biological Sciences, 2 A & 2B Raja S C Mullick Road, Kolkata, 700032
| | - Avinandan Bhoumick
- Indian Association for the Cultivation of Science, School of Biological Sciences, 2 A & 2B Raja S C Mullick Road, Kolkata, 700032
| | | | - Prosenjit Sen
- Indian Association for the Cultivation of Science, School of Biological Sciences, 2 A & 2B Raja S C Mullick Road, Kolkata, 700032
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10
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Shi Y, Sun Y, Li C, Wang S, Wang J, Shi H. Edge Substitution Effects of Histidine Tautomerization Behaviors on the Structural Properties and Aggregation Properties of Aβ(1-42) Mature Fibril. ACS Chem Neurosci 2024; 15:1055-1062. [PMID: 38379141 DOI: 10.1021/acschemneuro.4c00027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2024] Open
Abstract
Histidine behaviors play critical roles in folding and misfolding processes due to the changes in net charge and the various N/N-H orientations on imidazole rings. However, the effect of histidine tautomerization (HIE (Nε-H, ε) and HID (Nδ-H, δ) states) behaviors on the edge chain of Aβ mature fibrils remains inadequately understood, which is critical for finding a strategy to disturb fibril elongation and growth. In the current study, eight independent molecular dynamics simulations were conducted to investigate such impacts on the structural and aggregation properties. Our results from three different binding models revealed that the binding contributions of edge substitution effects are primarily located between chains 1 and 2. Histidine states significantly influence the secondary structure of each domain. Further analysis confirmed that the C1_H6//C1_E11 intrachain interaction is essential in maintaining the internal stability of chain 1, while the C1_H13//C2_H13 and C1_H14//C2_H13 interchain interactions are critical in maintaining the interchain stability of the fibril structure. Our subsequent analysis revealed that the current edge substitution leads to the loss of the C1_H13//C1_E11 intrachain and C1_H13//C2_H14 interchain interactions. The N-terminal regularity was significantly directly influenced by histidine states, particularly by the residue of C1_H13. Our study provides valuable insights into the effect of histidine behaviors on the edge chain of Aβ mature fibril, advancing our understanding of the histidine behavior hypothesis in misfolding diseases.
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Affiliation(s)
- Yaru Shi
- School of Chemistry and Chemical Engineering, Institute of Molecular Science, Shanxi University, Taiyuan 030000, China
| | - Yue Sun
- School of Chemistry and Chemical Engineering, Institute of Molecular Science, Shanxi University, Taiyuan 030000, China
| | - Changgui Li
- School of Chemistry and Chemical Engineering, Institute of Molecular Science, Shanxi University, Taiyuan 030000, China
| | - Shuo Wang
- School of Chemistry and Chemical Engineering, Institute of Molecular Science, Shanxi University, Taiyuan 030000, China
| | - Jinping Wang
- Institute of Surface Analysis and Chemical Biology, University of Jinan, Jinan 250022, Shandong, China
| | - Hu Shi
- School of Chemistry and Chemical Engineering, Institute of Molecular Science, Shanxi University, Taiyuan 030000, China
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11
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Martin WJ, McClelland LJ, Nold SM, Boshae KL, Bowler BE. Effect of proline content and histidine ligation on the dynamics of Ω-loop D and the peroxidase activity of iso-1-cytochrome c. J Inorg Biochem 2024; 252:112474. [PMID: 38176365 DOI: 10.1016/j.jinorgbio.2023.112474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 12/20/2023] [Accepted: 12/20/2023] [Indexed: 01/06/2024]
Abstract
To study how proline residues affect the dynamics of Ω-loop D (residues 70 to 85) of cytochrome c, we prepared G83P and G83A variants of yeast iso-1-cytochrome c (iso-1-Cytc) in the presence and absence of a K73H mutation. Ω-loop D is important in controlling both the electron transfer function of Cytc and the peroxidase activity of Cytc used in apoptosis because it provides the Met80 heme ligand. The G83P and G83A mutations have no effect on the global stability of iso-1-Cytc in presence or absence of the K73H mutation. However, both mutations destabilize the His73-mediated alkaline conformer relative to the native state. pH jump stopped-flow experiments show that the dynamics of the His73-mediated alkaline transition are significantly enhanced by the G83P mutation. Gated electron transfer studies show that the enhanced dynamics result from an increased rate of return to the native state, whereas the rate of loss of Met80 ligation is unchanged by the G83P mutation. Thus, the G83P substitution does not stiffen the conformation of the native state. Because bis-His heme ligation occurs when Cytc binds to cardiolipin-containing membranes, we studied the effect of His73 ligation on the peroxidase activity of Cytc, which acts as an early signal in apoptosis by causing oxygenation of cardiolipin. We find that the His73 alkaline conformer suppresses the peroxidase activity of Cytc. Thus, the bis-His ligated state of Cytc formed upon binding to cardiolipin is a negative effector for the peroxidase activity of Cytc early in apoptosis.
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Affiliation(s)
- William J Martin
- Department of Chemistry & Biochemistry, University of Montana, Missoula, MT 59812, United States
| | - Levi J McClelland
- Department of Chemistry & Biochemistry, University of Montana, Missoula, MT 59812, United States; Division of Biological Sciences, University of Montana, Missoula, MT 59812, United States; Center for Biomolecular Structure & Dynamics, University of Montana, Missoula, MT 59812, United States
| | - Shiloh M Nold
- Department of Chemistry & Biochemistry, University of Montana, Missoula, MT 59812, United States
| | - Kassandra L Boshae
- Department of Chemistry & Biochemistry, University of Montana, Missoula, MT 59812, United States
| | - Bruce E Bowler
- Department of Chemistry & Biochemistry, University of Montana, Missoula, MT 59812, United States; Center for Biomolecular Structure & Dynamics, University of Montana, Missoula, MT 59812, United States.
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12
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Hecel A, Garstka K, Kozłowski H, Rowińska-Żyrek M. -HH and -HAAAH motifs act as fishing nets for biologically relevant metal ions in metallopeptides. J Inorg Biochem 2024; 252:112456. [PMID: 38154408 DOI: 10.1016/j.jinorgbio.2023.112456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 12/08/2023] [Accepted: 12/13/2023] [Indexed: 12/30/2023]
Abstract
Histidine are one of the most common residues involved in transition metal ion binding in the active sites of metalloenzymes. In order to mimic enzymatic metal binding sites, it is crucial to understand the basic coordination modes of histidine residues, distributed at different positions in the peptide sequence. We show that: (i) the separation of two histidines has a large effect on complex stability - a sequence with adjusting histidine residues forms more stable complexes with Zn(II) than the one in which the residues are separated, while the contrary is observed for Cu(II) complexes, in which amide nitrogens participate in metal binding. No pronounced effect is observed for Ni(II) complexes, where the amides participate in binding at higher pH; (ii) non-coordinating amino acid residues (basic, acidic and aromatic ones) have a significant impact on complex stability; charged and aromatic residues may enhance Zn(II) binding, while the contrary is observed for the amide-binding Cu(II); (iii) cysteine containing sequences are much more effective Zn(II) and Ni(II) binding motifs at pH above 8, while histidine containing ligands are more suitable for effective Zn(II) and Ni(II) binding at lower pH.
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Affiliation(s)
- Aleksandra Hecel
- Faculty of Chemistry, University of Wrocław, 50-383 Wrocław, Poland.
| | - Kinga Garstka
- Faculty of Chemistry, University of Wrocław, 50-383 Wrocław, Poland
| | - Henryk Kozłowski
- Faculty of Chemistry, University of Wrocław, 50-383 Wrocław, Poland; Faculty of Health Sciences, University of Opole, 68 Katowicka St., 45-060 Opole, Poland
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13
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Rola A, Gumienna-Kontecka E, Potocki S. Exploring binding preferences: Cu(II), Ni(II), and Zn(II) complexes of mycobacterial GroEL1 His-rich and Glu/His-rich domains. Dalton Trans 2024; 53:4054-4066. [PMID: 38305693 DOI: 10.1039/d3dt03579d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2024]
Abstract
Mycobacterial histidine-rich GroEL1 protein significantly differs from the well-known methionine-glycine-rich GroEL chaperonin and most preferably participates in Cu(II) homeostasis. Some GroEL1 proteins, however, do not possess six but only three histidine residues and more acidic residues that can function as binding sites for metal ions. To evaluate the importance of this difference, we examined and compared the properties of GroEL1 His-rich or Glu/His-rich C-terminal domains as ligands for Cu(II), Ni(II), and Zn(II) ions. We studied the stoichiometry, stability, and binding sites of Cu(II)/Ni(II)/Zn(II) complexes of two model peptides: XEN = Ac-DKPEEEEDGHGHAH (M. xenopi) and ABS = Ac-DKPAEEADHGHGHHGHAH (M. abscessus) in the pH range 2-11. In the case of Cu(II), Ni(II), and Zn(II) complexes of XEN and ABS, ABS always formed more stable complexes. For XEN, there seemed to be no preference for Ni(II) or Zn(II) ions. In contrast, for ABS, Zn(II) formed a complex that was slightly more stable than the one formed by Ni(II). This may be due to the 6 His residues, which preferentially interact with Zn(II) rather than Ni(II). The study identified that an equilibrium of complexes-known as polymorphism-may occur in ABS complexes. Therefore, distinct sets of histidine residues may be involved in metal binding.
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Affiliation(s)
- Anna Rola
- Faculty of Chemistry, University of Wroclaw, 50-383 Wroclaw, Poland.
| | | | - Sławomir Potocki
- Faculty of Chemistry, University of Wroclaw, 50-383 Wroclaw, Poland.
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14
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Farahmand Kateshali A, Moghzi F, Soleimannejad J, Janczak J. Bacterial Cellulose-Based MOF Hybrid as a Sensitive Switch Off-On Luminescent Sensor for the Selective Recognition of l-Histidine. Inorg Chem 2024; 63:3560-3571. [PMID: 38330909 DOI: 10.1021/acs.inorgchem.3c04448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/10/2024]
Abstract
In this study, a stable and luminescent UiO-66-NH2 (UN) and its derivative Cu2+@UN were prepared and utilized successfully as an Off-On luminescent sensing platform for effective, selective, as well as rapid (5 min) detection of l-Histidine (l-His). The UN reveals efficient quenching in the presence of Cu2+ ions through photoinduced electron transition (PET) mechanism as a dynamic quenching process (in the range of 0.01-1 mM) forming Cu2+@UN sensing platform. However, due to the remarkable affinity between l-His and Cu2+, the luminescence of Cu2+@UN is recovered in the presence of l-His indicating Turn-On behavior via a quencher detachment mechanism (QD). A good linear relationship between the l-His concentration and luminescence intensity was observed in the range of 0.01-40 μM (R2 = 0.9978) with a detection limit of 7 nM for l-His sensing. The suggested method was successfully utilized for l-His determination in real samples with good recoveries and satisfying consequences. Moreover, the result indicates that only l-His induces a significant luminescence restoration of Cu2+@UN and that the signal is significantly greater than that of the other amino acids. Also, the portable test paper based on bacterial cellulose (BC) as the Cu2+@UNBC sensing platform was developed to conveniently evaluate the effective detection of l-His.
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Affiliation(s)
| | - Faezeh Moghzi
- School of Chemistry, College of Science, University of Tehran, P.O. Box 14155-6455 Tehran, Iran
| | - Janet Soleimannejad
- School of Chemistry, College of Science, University of Tehran, P.O. Box 14155-6455 Tehran, Iran
| | - Jan Janczak
- Institute of Low Temperature and Structure Research, Polish Academy of Science, Okólna 2, 50-950 Wroclaw, Poland
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15
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Ramek M, Sabolović J. Structure prediction of physiological bis(amino acidato)copper(II) species in aqueous solution: The copper(II) compounds with l-glutamine and l-histidine. J Inorg Biochem 2024; 251:112430. [PMID: 38006660 DOI: 10.1016/j.jinorgbio.2023.112430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 10/27/2023] [Accepted: 11/13/2023] [Indexed: 11/27/2023]
Abstract
Neutral (l-histidinato)(l-glutaminato)copper(II) [Cu(His)(Gln)] has been established as the most abundant ternary copper(II) amino acid compound of the exchangeable copper(II) pool in blood plasma. The experimental studies of Cu(His)(Gln) and bis(glutaminato)copper(II) [Cu(Gln)2] in solutions did not specify their complete geometries. To determine the geometries, this paper investigates the conformers, energy landscapes, and a structure-magnetic parameters relation of Cu(Gln)2 and Cu(His)(Gln) by the density functional theory (DFT) calculations. We assume a glycine-like coordination of Gln (other coordination patterns are dismissed because of steric reasons), and three His in-plane copper(II) binding modes. The conformational analyses are performed in the gas phase and implicitly modeled aqueous solution. The reliability of the DFT relative electronic and Gibbs free energies of the Cu(His)(Gln) conformers is confirmed by benchmarking against the corresponding energies obtained by the domain-based local pair natural orbital coupled-cluster method with singles, doubles, and perturbative triples [DLPNO-CCSD(T)]. Several cis- and trans-Cu(His)(Gln) conformers with His in the histaminate-like and glycine-like modes have low Gibbs free energies, and the greatest estimated metal-binding affinities. The DFT-calculated magnetic parameters of the low-energy conformers reproduce best the experimental electron paramagnetic resonance parameters measured in aqueous solutions for trans- and cis-Cu(Gln)2 conformers having two oxygen atoms (either from Gln or water molecules) at the apical positions, and Cu(His)(Gln) conformers having His in the histaminate-like mode with an apically placed carboxylato oxygen atom. The predicted conformational flexibility of His‑copper(II)-amino acid compounds may be connected with their physiological abundance, and the role in copper(II) exchange reactions in blood plasma.
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Affiliation(s)
- Michael Ramek
- Institute of Physical and Theoretical Chemistry, Graz University of Technology, Stremayrgasse 9, A-8010 Graz, Austria
| | - Jasmina Sabolović
- Institute for Medical Research and Occupational Health, Ksaverska cesta 2, HR-10000 Zagreb, Croatia.
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16
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Zeballos N, Comino N, Andrés-Sanz D, Santiago-Arcos J, Azkargorta M, Elortza F, Diamanti E, López-Gallego F. Region-Directed Enzyme Immobilization through Engineering Protein Surface with Histidine Clusters. ACS Appl Mater Interfaces 2024; 16:833-846. [PMID: 38135284 PMCID: PMC10788835 DOI: 10.1021/acsami.3c15993] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Revised: 11/22/2023] [Accepted: 11/22/2023] [Indexed: 12/24/2023]
Abstract
Enzyme immobilization is a key enabling technology for a myriad of industrial applications, yet immobilization science is still too empirical to reach highly active and robust heterogeneous biocatalysts through a general approach. Conventional protein immobilization methods lack control over how enzymes are oriented on solid carriers, resulting in negative conformational changes that drive enzyme deactivation. Site-selective enzyme immobilization through peptide tags and protein domains addresses the orientation issue, but this approach limits the possible orientations to the N- and C-termini of the target enzyme. In this work, we engineer the surface of two model dehydrogenases to introduce histidine clusters into flexible regions not involved in catalysis, through which immobilization is driven. By varying the position and the histidine density of the clusters, we create a small library of enzyme variants to be immobilized on different carriers functionalized with different densities of various metal chelates (Co2+, Cu2+, Ni2+, and Fe3+). We first demonstrate that His-clusters can be as efficient as the conventional His-tags in immobilizing enzymes, recovering even more activity and gaining stability against some denaturing agents. Furthermore, we find that the enzyme orientation as well as the type and density of the metal chelates affect the immobilization parameters (immobilization yield and recovered activity) and the stability of the immobilized enzymes. According to proteomic studies, His-clusters enable a different enzyme orientation as compared to His-tag. Finally, these oriented heterogeneous biocatalysts are implemented in batch reactions, demonstrating that the stability achieved by an optimized orientation translates into increased operational stability.
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Affiliation(s)
- Nicoll Zeballos
- Center
for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo Miramon 194, 20014 San Sebastián, Spain
| | - Natalia Comino
- Center
for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo Miramon 194, 20014 San Sebastián, Spain
| | - Daniel Andrés-Sanz
- Center
for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo Miramon 194, 20014 San Sebastián, Spain
| | - Javier Santiago-Arcos
- Center
for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo Miramon 194, 20014 San Sebastián, Spain
| | - Mikel Azkargorta
- Center
for Cooperative Research in Biology (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 800 Bld, 48160 Derio, Bizkaia, Spain
- Centro
de Investigación Biomédica en Red de Enfermedades Hepáticas
y Digestivas (CIBERehd), 28029 Madrid, Spain
| | - Felix Elortza
- Center
for Cooperative Research in Biology (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, 800 Bld, 48160 Derio, Bizkaia, Spain
- Centro
de Investigación Biomédica en Red de Enfermedades Hepáticas
y Digestivas (CIBERehd), 28029 Madrid, Spain
| | - Eleftheria Diamanti
- Center
for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo Miramon 194, 20014 San Sebastián, Spain
| | - Fernando López-Gallego
- Center
for Cooperative Research in Biomaterials (CIC biomaGUNE), Basque Research and Technology Alliance (BRTA), Paseo Miramon 194, 20014 San Sebastián, Spain
- Ikerbasque,
Basque Foundation for Science, 48013 Bilbao, Spain
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17
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Grigorenko BL, Khrenova MG, Jones DD, Nemukhin AV. Histidine-assisted reduction of arylnitrenes upon photo-activation of phenyl azide chromophores in GFP-like fluorescent proteins. Org Biomol Chem 2024; 22:337-347. [PMID: 38063860 DOI: 10.1039/d3ob01450a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
The photochemically active sites of the proteins sfGFP66azF and Venus66azF, members of the green fluorescent protein (GFP) family, contain a non-canonical amino acid residue p-azidophenylalanine (azF) instead of Tyr66. The light-induced decomposition of azF at these sites leads to the formation of reactive arylnitrene (nF) intermediates followed by the formation of phenylamine-containing chromophores. We report the first study of the reaction mechanism of the reduction of the arylnitrene intermediates in sfGFP66nF and Venus66nF using molecular modeling methods. The Gibbs energy profiles for the elementary steps of the chemical reaction in sfGFP66nF are computed using molecular dynamics simulations with quantum mechanics/molecular mechanics (QM/MM) potentials. Structures and energies along the reaction pathway in Venus66nF are evaluated using a QM/MM approach. According to the results of the simulations, arylnitrene reduction is coupled with oxidation of the histidine side chain on the His148 residue located near the chromophore.
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Affiliation(s)
- Bella L Grigorenko
- Chemistry Department, Lomonosov Moscow State University, Moscow, Russian Federation.
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, Russian Federation
| | - Maria G Khrenova
- Chemistry Department, Lomonosov Moscow State University, Moscow, Russian Federation.
- Bach Institute of Biochemistry, Moscow, Russian Federation
| | - D Dafydd Jones
- School of Biosciences, Molecular Biosciences Division, Cardiff University, Cardiff, UK
| | - Alexander V Nemukhin
- Chemistry Department, Lomonosov Moscow State University, Moscow, Russian Federation.
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, Russian Federation
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18
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Du P, Xu S, Wu H, Liu Y, Wang ZG. Histidine-Based Supramolecular Nanoassembly Exhibiting Dual Enzyme-Mimetic Functions: Altering the Tautomeric Preference of Histidine to Tailor Oxidative/Hydrolytic Catalysis. Nano Lett 2023; 23:11461-11468. [PMID: 38079506 DOI: 10.1021/acs.nanolett.3c02934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2023]
Abstract
Challenges persist in replicating enzyme-like active sites with functional group arrangements in supramolecular catalysis. In this study, we present a supramolecular material comprising Fmoc-modified histidine and copper. We also investigated the impact of noncanonical amino acids (δmH and εmH), isomers of histidine, on the catalytic process. The Fmoc-δmH-based nanoassembly exhibits an approximately 15-fold increase in oxidative activity and an ∼50-fold increase in hydrolytic activity compared to Fmoc-εmH (kcat/Km). This distinction arises from differences in basicity and ligation properties between the ε- and δ-nitrogen of histidine. The addition of guanosine monophosphate further enhances the oxidative activity of the histidine- and methylated histidine-based catalysts. The Fmoc-δmH/Cu2+-based nanoassembly catalyzes the oxidation/hydrolysis cascade of 2',7'-dichlorofluorescein diacetate, benefiting from the synergistic effect between the copper center and the nonligating ε-nitrogen of histidine. These findings advance the biomimetic catalyst design and provide insights into the mechanistic role of essential residues in natural systems.
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Affiliation(s)
- Peidong Du
- State Key Laboratory of Organic-Inorganic Composites, Key Lab of Biomedical Materials of Natural Macromolecules (Ministry of Education), Beijing Laboratory of Biomedical Materials, College of Materials Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Shichao Xu
- State Key Laboratory of Organic-Inorganic Composites, Key Lab of Biomedical Materials of Natural Macromolecules (Ministry of Education), Beijing Laboratory of Biomedical Materials, College of Materials Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Haifeng Wu
- State Key Laboratory of Organic-Inorganic Composites, Key Lab of Biomedical Materials of Natural Macromolecules (Ministry of Education), Beijing Laboratory of Biomedical Materials, College of Materials Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Yuanxi Liu
- State Key Laboratory of Organic-Inorganic Composites, Key Lab of Biomedical Materials of Natural Macromolecules (Ministry of Education), Beijing Laboratory of Biomedical Materials, College of Materials Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Zhen-Gang Wang
- State Key Laboratory of Organic-Inorganic Composites, Key Lab of Biomedical Materials of Natural Macromolecules (Ministry of Education), Beijing Laboratory of Biomedical Materials, College of Materials Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China
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19
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Ütkür K, Schmidt S, Mayer K, Klassen R, Brinkmann U, Schaffrath R. DPH1 Gene Mutations Identify a Candidate SAM Pocket in Radical Enzyme Dph1•Dph2 for Diphthamide Synthesis on EF2. Biomolecules 2023; 13:1655. [PMID: 38002337 PMCID: PMC10669111 DOI: 10.3390/biom13111655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Revised: 11/10/2023] [Accepted: 11/13/2023] [Indexed: 11/26/2023] Open
Abstract
In eukaryotes, the Dph1•Dph2 dimer is a non-canonical radical SAM enzyme. Using iron-sulfur (FeS) clusters, it cleaves the cosubstrate S-adenosyl-methionine (SAM) to form a 3-amino-3-carboxy-propyl (ACP) radical for the synthesis of diphthamide. The latter decorates a histidine residue on elongation factor 2 (EF2) conserved from archaea to yeast and humans and is important for accurate mRNA translation and protein synthesis. Guided by evidence from archaeal orthologues, we searched for a putative SAM-binding pocket in Dph1•Dph2 from Saccharomyces cerevisiae. We predict an SAM-binding pocket near the FeS cluster domain that is conserved across eukaryotes in Dph1 but not Dph2. Site-directed DPH1 mutagenesis and functional characterization through assay diagnostics for the loss of diphthamide reveal that the SAM pocket is essential for synthesis of the décor on EF2 in vivo. Further evidence from structural modeling suggests particularly critical residues close to the methionine moiety of SAM. Presumably, they facilitate a geometry specific for SAM cleavage and ACP radical formation that distinguishes Dph1•Dph2 from classical radical SAM enzymes, which generate canonical 5'-deoxyadenosyl (dAdo) radicals.
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Affiliation(s)
- Koray Ütkür
- Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, 34132 Kassel, Germany; (K.Ü.); (S.S.); (R.K.)
| | - Sarina Schmidt
- Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, 34132 Kassel, Germany; (K.Ü.); (S.S.); (R.K.)
| | - Klaus Mayer
- Roche Pharma Research and Early Development (pRED), Large Molecule Research, Roche Innovation Center Munich, 82377 Penzberg, Germany; (K.M.); (U.B.)
| | - Roland Klassen
- Institut für Biologie, Fachgebiet Mikrobiologie, Universität Kassel, 34132 Kassel, Germany; (K.Ü.); (S.S.); (R.K.)
| | - Ulrich Brinkmann
- Roche Pharma Research and Early Development (pRED), Large Molecule Research, Roche Innovation Center Munich, 82377 Penzberg, Germany; (K.M.); (U.B.)
| | - Raffael Schaffrath
- Roche Pharma Research and Early Development (pRED), Large Molecule Research, Roche Innovation Center Munich, 82377 Penzberg, Germany; (K.M.); (U.B.)
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20
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Al-Fakhar MSQ, Bilgin N, Moesgaard L, Witecka A, Drozak J, Kongsted J, Mecinović J. The Role of Trp79 in β-Actin on Histidine Methyltransferase SETD3 Catalysis. Chembiochem 2023; 24:e202300490. [PMID: 37581408 DOI: 10.1002/cbic.202300490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 08/15/2023] [Accepted: 08/15/2023] [Indexed: 08/16/2023]
Abstract
Nτ -methylation of His73 in actin by histidine methyltransferase SETD3 plays an important role in stabilising actin filaments in eukaryotes. Mutations in actin and overexpression of SETD3 have been related to human diseases, including cancer. Here, we investigated the importance of Trp79 in β-actin on productive human SETD3 catalysis. Substitution of Trp79 in β-actin peptides by its chemically diverse analogues reveals that the hydrophobic Trp79 binding pocket modulates the catalytic activity of SETD3, and that retaining a bulky and hydrophobic amino acid at position 79 is important for efficient His73 methylation by SETD3. Molecular dynamics simulations show that the Trp79 binding pocket of SETD3 is ideally shaped to accommodate large and hydrophobic Trp79, contributing to the favourable release of water molecules upon binding. Our results demonstrate that the distant Trp79 binding site plays an important role in efficient SETD3 catalysis, contributing to the identification of new SETD3 substrates and the development of chemical probes targeting the biomedically important SETD3.
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Affiliation(s)
- Mays S Q Al-Fakhar
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense, Denmark
| | - Nurgül Bilgin
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense, Denmark
| | - Laust Moesgaard
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense, Denmark
| | - Apolonia Witecka
- Department of Metabolic Regulation, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096, Warsaw, Poland
| | - Jakub Drozak
- Department of Metabolic Regulation, Faculty of Biology, University of Warsaw, Miecznikowa 1, 02-096, Warsaw, Poland
| | - Jacob Kongsted
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense, Denmark
| | - Jasmin Mecinović
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230, Odense, Denmark
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21
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Matsukawa R, Yamane M, Kanai M. Histidine Photooxygenation Chemistry: Mechanistic Evidence and Elucidation. CHEM REC 2023; 23:e202300198. [PMID: 37675808 DOI: 10.1002/tcr.202300198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Revised: 07/25/2023] [Indexed: 09/08/2023]
Abstract
Histidine photooxygenation has been the subject of extensive investigation for many years. The intricate nature of histidine distinguishes it from other amino acids, as its side chain readily undergoes changes in charge state and tautomerization in response to pH, and the polarity of the imidazole ring inverts upon oxidation. This complexity gives rise to a diverse range of oxidation products and mechanisms, posing challenges in their interpretation. This review aims to provide a thorough overview of the chemistry involved in histidine photooxygenation, encompassing a comprehensive analysis of resulting products, mechanisms engaged in their formation, and analytical techniques that have contributed to their identification. Additionally, it explores a wide range of applications stemming from this transformation, offering valuable insights into its practical implications in fields such as materials science, biomedical research, and drug development. By bridging the existing gap in literature, this review serves as a resource for understanding the intricacies of histidine photooxygenation and its diverse ramifications.
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Affiliation(s)
- Ryota Matsukawa
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, Japan
| | - Mina Yamane
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, Japan
| | - Motomu Kanai
- Graduate School of Pharmaceutical Sciences, The University of Tokyo, 7-3-1, Hongo, Bunkyo-ku, Tokyo, Japan
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22
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Liu J, Wu H, Liu Y, Wang ZG. Colorimetric Sensor Based on the Oxidase-Mimic Supramolecular Catalyst for Selective and Sensitive Biomolecular Detection. ACS Appl Mater Interfaces 2023; 15:48945-48951. [PMID: 37823579 DOI: 10.1021/acsami.3c09940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/13/2023]
Abstract
We have engineered a colorimetric sensor capable of selective and sensitive detection of amino acids. This sensor employs a supramolecular copper-dependent oxidase mimic as the probe, stemming from our prior research. The oxidase mimic is constructed through the self-assembly of commercially available guanosine monophosphate (GMP), Fmoc-lysine, and Cu2+. It catalyzes the formation of a red product with a maximum absorbance at 510 nm. The changes in color and absorbance are responsive to both the concentrations and types of amino acids present. This effect is most pronounced in the presence of histidine, with a detection limit (LOD) of 6.4 nM. Furthermore, the catalytic probe can distinguish histidine from histamine and imidazole propionate, as well as 1-methyl-histidine from 3-methyl-histidine, based on their distinct coordination capacities with copper. This underscores the high selectivity of the sensing platform. Both theoretical simulations and experimental results (including UV-vis spectra, fluorescence, and EPR) indicate that the amino acids may engage in copper center coordination, thereby impeding O2 access to copper─a pivotal aspect of the oxidase catalysis. This sensing platform, characteristic of its swift response, simple fabrication, and exceptional sensitivity and selectivity, can also be applied to detect other biological analytes such as nucleotides. It holds potential for use in environmental and biochemical analyses.
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Affiliation(s)
- Junhong Liu
- State Key Laboratory of Organic-Inorganic Composites, Key Lab of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology, Ministry of Education), Beijing Laboratory of Biomedical Materials, College of Materials Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Haifeng Wu
- State Key Laboratory of Organic-Inorganic Composites, Key Lab of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology, Ministry of Education), Beijing Laboratory of Biomedical Materials, College of Materials Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Yuanxi Liu
- State Key Laboratory of Organic-Inorganic Composites, Key Lab of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology, Ministry of Education), Beijing Laboratory of Biomedical Materials, College of Materials Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China
| | - Zhen-Gang Wang
- State Key Laboratory of Organic-Inorganic Composites, Key Lab of Biomedical Materials of Natural Macromolecules (Beijing University of Chemical Technology, Ministry of Education), Beijing Laboratory of Biomedical Materials, College of Materials Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, China
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23
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Salazar J, Samhan-Arias AK, Gutierrez-Merino C. Hexa-Histidine, a Peptide with Versatile Applications in the Study of Amyloid-β(1-42) Molecular Mechanisms of Action. Molecules 2023; 28:7138. [PMID: 37894616 PMCID: PMC10609148 DOI: 10.3390/molecules28207138] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 10/10/2023] [Accepted: 10/13/2023] [Indexed: 10/29/2023] Open
Abstract
Amyloid β (Aβ) oligomers are the most neurotoxic forms of Aβ, and Aβ(1-42) is the prevalent Aβ peptide found in the amyloid plaques of Alzheimer's disease patients. Aβ(25-35) is the shortest peptide that retains the toxicity of Aβ(1-42). Aβ oligomers bind to calmodulin (CaM) and calbindin-D28k with dissociation constants in the nanomolar Aβ(1-42) concentration range. Aβ and histidine-rich proteins have a high affinity for transition metal ions Cu2+, Fe3+ and Zn2+. In this work, we show that the fluorescence of Aβ(1-42) HiLyteTM-Fluor555 can be used to monitor hexa-histidine peptide (His6) interaction with Aβ(1-42). The formation of His6/Aβ(1-42) complexes is also supported by docking results yielded by the MDockPeP Server. Also, we found that micromolar concentrations of His6 block the increase in the fluorescence of Aβ(1-42) HiLyteTM-Fluor555 produced by its interaction with the proteins CaM and calbindin-D28k. In addition, we found that the His6-tag provides a high-affinity site for the binding of Aβ(1-42) and Aβ(25-35) peptides to the human recombinant cytochrome b5 reductase, and sensitizes this enzyme to inhibition by these peptides. In conclusion, our results suggest that a His6-tag could provide a valuable new tool to experimentally direct the action of neurotoxic Aβ peptides toward selected cellular targets.
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Affiliation(s)
- Jairo Salazar
- Departamento de Química, Universidad Nacional Autónoma de Nicaragua-León, León 21000, Nicaragua
| | - Alejandro K. Samhan-Arias
- Departamento de Bioquímica, Universidad Autónoma de Madrid (UAM), C\Arzobispo Morcillo 4, 28029 Madrid, Spain;
- Instituto de Investigaciones Biomédicas ‘Alberto Sols’ (CSIC-UAM), C\Arturo Duperier 4, 28029 Madrid, Spain
| | - Carlos Gutierrez-Merino
- Instituto de Biomarcadores de Patologías Moleculares, Universidad de Extremadura, 06006 Badajoz, Spain
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24
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Yu Z, Kreitler DF, Chiu YTT, Xu R, Bruchs AT, Bingman CA, Gellman SH. Harnessing Aromatic-Histidine Interactions through Synergistic Backbone Extension and Side Chain Modification. Angew Chem Int Ed Engl 2023; 62:e202308100. [PMID: 37587780 PMCID: PMC10668598 DOI: 10.1002/anie.202308100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 07/31/2023] [Accepted: 08/14/2023] [Indexed: 08/18/2023]
Abstract
Peptide engineering efforts have delivered drugs for diverse human diseases. Side chain alteration is among the most common approaches to designing new peptides for specific applications. The peptide backbone can be modified as well, but this strategy has received relatively little attention. Here we show that new and favorable contacts between a His side chain on a target protein and an aromatic side chain on a synthetic peptide ligand can be engineered by rational and coordinated side chain modification and backbone extension. Side chain modification alone was unsuccessful. Binding measurements, high-resolution structural studies and pharmacological outcomes all support the synergy between backbone and side chain modification in engineered ligands of the parathyroid hormone receptor-1, which is targeted by osteoporosis drugs. These results should motivate other structure-based designs featuring coordinated side chain modification and backbone extension to enhance the engagement of peptide ligands with target proteins.
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Affiliation(s)
- Zhen Yu
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Dale F Kreitler
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, New York, 11973, USA
| | - Yin Ting T Chiu
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Ruiwen Xu
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Austin T Bruchs
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Craig A Bingman
- Department of Biochemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Samuel H Gellman
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
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25
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Javanshad R, Taylor CJ, Delavari N, Barkman TJ, Stull F, Venter AR. Analysis of histidine-tagged recombinant proteins from nickel and copper coated surfaces by direct electrospray ionization and desorption electrospray ionization mass spectrometry. Rapid Commun Mass Spectrom 2023; 37 Suppl 1:e9516. [PMID: 37013403 DOI: 10.1002/rcm.9516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 02/28/2023] [Accepted: 03/31/2023] [Indexed: 06/19/2023]
Abstract
RATIONALE Purification of recombinant proteins is a necessary step for functional or structural studies and other applications. Immobilized metal affinity chromatography is a common recombinant protein purification method. Mass spectrometry (MS) allows for confirmation of identity of expressed proteins and unambiguous detection of enzymatic substrates and reaction products. We demonstrate the detection of enzymes purified on immobilized metal affinity surfaces by direct or ambient ionization MS, and follow their enzymatic reactions by direct electrospray ionization (ESI) or desorption electrospray ionization (DESI). METHODS A protein standard, His-Ubq, and two recombinant proteins, His-SHAN and His-CS, expressed in Escherichia coli were immobilized on two immobilized metal affinity systems, Cu-nitriloacetic acid (Cu-NTA) and Ni-NTA. The proteins were purified on surface, and released in the ESI spray solvent for direct infusion, when using the 96-well plate form factor, or analyzed directly from immobilized metal affinity-coated microscope slides by DESI-MS. Enzyme activity was followed by incubating the substrates in wells or by depositing substrate on immobilized protein on coated slides for analysis. RESULTS Small proteins (His-Ubq) and medium proteins (His-SAHN) could readily be detected from 96-well plates by direct infusion ESI, or from microscope slides by DESI-MS after purification on surface from clarified E. coli cell lysate. Protein oxidation was observed for immobilized proteins on both Cu-NTA and Ni-NTA; however, this did not hamper the enzymatic reactions of these proteins. Both the nucleosidase reaction products for His-SAHN and the methylation product of His-CS (theobromine to caffeine) were detected. CONCLUSIONS The immobilization, purification, release and detection of His-tagged recombinant proteins using immobilized metal affinity surfaces for direct infusion ESI-MS or ambient DESI-MS analyses were successfully demonstrated. Recombinant proteins were purified to allow identification directly out of clarified cell lysate. Biological activities of the recombinant proteins were preserved allowing the investigation of enzymatic activity via MS.
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Affiliation(s)
- Roshan Javanshad
- Department of Chemistry, Western Michigan University, Kalamazoo, MI, USA
| | | | - Niusha Delavari
- Department of Chemistry, Western Michigan University, Kalamazoo, MI, USA
| | - Todd J Barkman
- Department of Biological Sciences, Western Michigan University, Kalamazoo, MI, USA
| | - Frederick Stull
- Department of Chemistry, Western Michigan University, Kalamazoo, MI, USA
| | - Andre R Venter
- Department of Chemistry, Western Michigan University, Kalamazoo, MI, USA
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26
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Song J, Khare E, Rao L, Buehler MJ, Holten-Andersen N. Coordination Stoichiometry Effects on the Binding Hierarchy of Histamine and Imidazole-M 2+ Complexes. Macromol Rapid Commun 2023; 44:e2300077. [PMID: 37337912 DOI: 10.1002/marc.202300077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 06/14/2023] [Indexed: 06/21/2023]
Abstract
Histidine-M2+ coordination bonds are a recognized bond motif in biogenic materials with high hardness and extensibility, which has led to growing interest in their use in soft materials for mechanical function. However, the effect of different metal ions on the stability of the coordination complex remains poorly understood, complicating their implementation in metal-coordinated polymer materials. Herein, rheology experiments and density functional theory calculations are used to characterize the stability of coordination complexes and establish the binding hierarchy of histamine and imidazole with Ni2+ , Cu2+ , and Zn2+ . It is found that the binding hierarchy is driven by the specific affinity of the metal ions to different coordination states, which can be macroscopically tuned by changing the metal-to-ligand stoichiometry of the metal-coordinated network. These findings facilitate the rational selection of metal ions for optimizing the mechanical properties of metal-coordinated materials.
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Affiliation(s)
- Jake Song
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Eesha Khare
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
- Laboratory for Atomistic and Molecular Mechanics (LAMM), Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Li Rao
- Department of Chemistry, Central China Normal University, Wuhan, 430079, P. R. China
| | - Markus J Buehler
- Laboratory for Atomistic and Molecular Mechanics (LAMM), Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
- Center for Computational Science and Engineering, Schwarzman College of Computing, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
| | - Niels Holten-Andersen
- Department of Materials Science and Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA
- Department of Bioengineering and Department of Materials Science and Engineering, Lehigh University, 27 Memorial Dr W, Bethlehem, PA, 18015, USA
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27
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Zhang Y, Ballesteros ME, Schöneich C. Photo-induced site-specific oxidative fragmentation of IgG1 mediated by iron(III)-containing histidine buffer: Mechanistic studies and excipient effects. Eur J Pharm Biopharm 2023; 190:121-130. [PMID: 37482364 DOI: 10.1016/j.ejpb.2023.07.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 07/14/2023] [Accepted: 07/21/2023] [Indexed: 07/25/2023]
Abstract
Fragmentation may compromise the clinical efficacy and safety profile of monoclonal antibodies (mAbs). We recently reported that Fe(III)-containing histidine (His) buffer mediates site-specific mAb fragmentation within the Fc domain when exposed to visible light (Y. Zhang and C. Schöneich, Mol. Pharm. 2023, 20, 650-662). Here, we show that this fragmentation proceeds even more efficiently under near-UV light. Several formulation strategies were applied in an attempt to reduce the photo-induced fragmentation. In solution formulations, the fragmentation can be mitigated by reducing the concentration of His buffer, adding Fe(III)-chelating agents, and replacing His with other amino acids. Fragmentation can be almost completely inhibited by formulating the protein in the lyophilized state. Mechanistically, His plays a critical role in the fragmentation process, likely due to its affinity for Fe(II), driving a photo-redox reaction towards product formation.
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Affiliation(s)
- Yilue Zhang
- Department of Pharmaceutical Chemistry, University of Kansas, 2093 Constant Avenue, Lawrence, KS 66047, USA
| | | | - Christian Schöneich
- Department of Pharmaceutical Chemistry, University of Kansas, 2093 Constant Avenue, Lawrence, KS 66047, USA.
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28
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Van der Stede T, Spaas J, de Jager S, De Brandt J, Hansen C, Stautemas J, Vercammen B, De Baere S, Croubels S, Van Assche CH, Pastor BC, Vandenbosch M, Van Thienen R, Verboven K, Hansen D, Bové T, Lapauw B, Van Praet C, Decaestecker K, Vanaudenaerde B, Eijnde BO, Gliemann L, Hellsten Y, Derave W. Extensive profiling of histidine-containing dipeptides reveals species- and tissue-specific distribution and metabolism in mice, rats, and humans. Acta Physiol (Oxf) 2023; 239:e14020. [PMID: 37485756 DOI: 10.1111/apha.14020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 06/26/2023] [Accepted: 07/13/2023] [Indexed: 07/25/2023]
Abstract
AIM Histidine-containing dipeptides (HCDs) are pleiotropic homeostatic molecules with potent antioxidative and carbonyl quenching properties linked to various inflammatory, metabolic, and neurological diseases, as well as exercise performance. However, the distribution and metabolism of HCDs across tissues and species are still unclear. METHODS Using a sensitive UHPLC-MS/MS approach and an optimized quantification method, we performed a systematic and extensive profiling of HCDs in the mouse, rat, and human body (in n = 26, n = 25, and n = 19 tissues, respectively). RESULTS Our data show that tissue HCD levels are uniquely produced by carnosine synthase (CARNS1), an enzyme that was preferentially expressed by fast-twitch skeletal muscle fibres and brain oligodendrocytes. Cardiac HCD levels are remarkably low compared to other excitable tissues. Carnosine is unstable in human plasma, but is preferentially transported within red blood cells in humans but not rodents. The low abundant carnosine analogue N-acetylcarnosine is the most stable plasma HCD, and is enriched in human skeletal muscles. Here, N-acetylcarnosine is continuously secreted into the circulation, which is further induced by acute exercise in a myokine-like fashion. CONCLUSION Collectively, we provide a novel basis to unravel tissue-specific, paracrine, and endocrine roles of HCDs in human health and disease.
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Affiliation(s)
- Thibaux Van der Stede
- Department of Movement and Sports Sciences, Ghent University, Ghent, Belgium
- Department of Nutrition, Exercise and Sports, Copenhagen University, Copenhagen, Denmark
| | - Jan Spaas
- Department of Movement and Sports Sciences, Ghent University, Ghent, Belgium
- University MS Center (UMSC) Hasselt, Pelt, Belgium
- BIOMED Biomedical Research Institute, Hasselt University, Diepenbeek, Belgium
| | - Sarah de Jager
- Department of Movement and Sports Sciences, Ghent University, Ghent, Belgium
| | - Jana De Brandt
- BIOMED Biomedical Research Institute, Hasselt University, Diepenbeek, Belgium
- REVAL Rehabilitation Research Center, Hasselt University, Hasselt, Belgium
| | - Camilla Hansen
- Department of Nutrition, Exercise and Sports, Copenhagen University, Copenhagen, Denmark
| | - Jan Stautemas
- Department of Movement and Sports Sciences, Ghent University, Ghent, Belgium
| | - Bjarne Vercammen
- Department of Movement and Sports Sciences, Ghent University, Ghent, Belgium
| | - Siegrid De Baere
- Department of Pathobiology, Pharmacology and Zoological Medicine, Ghent University, Ghent, Belgium
| | - Siska Croubels
- Department of Pathobiology, Pharmacology and Zoological Medicine, Ghent University, Ghent, Belgium
| | - Charles-Henri Van Assche
- The Maastricht MultiModal Molecular Imaging (M4I) institute, Maastricht University, Maastricht, The Netherlands
| | - Berta Cillero Pastor
- The Maastricht MultiModal Molecular Imaging (M4I) institute, Maastricht University, Maastricht, The Netherlands
| | - Michiel Vandenbosch
- The Maastricht MultiModal Molecular Imaging (M4I) institute, Maastricht University, Maastricht, The Netherlands
| | - Ruud Van Thienen
- Department of Movement and Sports Sciences, Ghent University, Ghent, Belgium
| | - Kenneth Verboven
- BIOMED Biomedical Research Institute, Hasselt University, Diepenbeek, Belgium
- REVAL Rehabilitation Research Center, Hasselt University, Hasselt, Belgium
| | - Dominique Hansen
- BIOMED Biomedical Research Institute, Hasselt University, Diepenbeek, Belgium
- REVAL Rehabilitation Research Center, Hasselt University, Hasselt, Belgium
- Heart Center Hasselt, Jessa Hospital Hasselt, Hasselt, Belgium
| | - Thierry Bové
- Department of Cardiac Surgery, Ghent University Hospital, Ghent, Belgium
| | - Bruno Lapauw
- Department of Endocrinology, Ghent University Hospital, Ghent, Belgium
| | - Charles Van Praet
- Department of Urology, Ghent University Hospital, Ghent, Belgium
- Department of Human Structure and Repair, Ghent University, Ghent, Belgium
| | - Karel Decaestecker
- Department of Urology, Ghent University Hospital, Ghent, Belgium
- Department of Human Structure and Repair, Ghent University, Ghent, Belgium
| | - Bart Vanaudenaerde
- Department of Chronic Diseases and Metabolism, KU Leuven, Leuven, Belgium
| | - Bert O Eijnde
- University MS Center (UMSC) Hasselt, Pelt, Belgium
- SMRC Sports Medical Research Center, BIOMED Biomedical Research Institute, Hasselt University, Diepenbeek, Belgium
- Division of Sport Science, Stellenbosch University, Stellenbosch, South Africa
| | - Lasse Gliemann
- Department of Nutrition, Exercise and Sports, Copenhagen University, Copenhagen, Denmark
| | - Ylva Hellsten
- Department of Nutrition, Exercise and Sports, Copenhagen University, Copenhagen, Denmark
| | - Wim Derave
- Department of Movement and Sports Sciences, Ghent University, Ghent, Belgium
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29
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Brotherton EE, Josland D, György C, Johnson EC, Chan DHH, Smallridge MJ, Armes SP. Histidine-Functionalized Diblock Copolymer Nanoparticles Exhibit Enhanced Adsorption onto Planar Stainless Steel. Macromol Rapid Commun 2023; 44:e2200903. [PMID: 36534428 DOI: 10.1002/marc.202200903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 12/12/2022] [Indexed: 12/23/2022]
Abstract
RAFT aqueous emulsion polymerization of isopropylideneglycerol monomethacrylate (IPGMA) is used to prepare a series of PGEO5MA46 -PIPGMAy nanoparticles, where PGEO5MA is a hydrophilic methacrylic steric stabilizer block bearing pendent cis-diol groups. TEM studies confirm a spherical morphology while dynamic light scattering (DLS) analysis indicated that the z-average particle diameter can be adjusted by varying the target degree of polymerization for the core-forming PIPGMA block. Periodate oxidation is used to convert the cis-diol groups on PGEO5MA46 -PIPGMA500 and PGEO5MA46 -PIPGMA1000 nanoparticles into the analogous aldehyde-functionalized nanoparticles, which are then reacted with histidine via reductive amination. In each case, the extent of functionalization is more than 99% as determined by 1 H NMR spectroscopy. Aqueous electrophoresis studies indicate that such derivatization converts initially neutral nanoparticles into zwitterionic nanoparticles with an isoelectric point at pH 7. DLS studies confirm that such histidine-derivatized nanoparticles remain colloidally stable over a wide pH range. A quartz crystal microbalance is employed at 25°C to assess the adsorption of both the cis-diol- and histidine-functionalized nanoparticles onto planar stainless steel at pH 6. The histidine-bearing nanoparticles adsorb much more strongly than their cis-diol counterparts. For the highest adsorbed amount of 70.5 mg m-2 , SEM indicates a fractional surface coverage of 0.23 for the adsorbed nanoparticles.
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Affiliation(s)
- Emma E Brotherton
- Dainton Building, Department of Chemistry, The University of Sheffield, Brook Hill, Sheffield, South Yorkshire, S3 7HF, UK
| | - Daniel Josland
- Dainton Building, Department of Chemistry, The University of Sheffield, Brook Hill, Sheffield, South Yorkshire, S3 7HF, UK
| | - Csilla György
- Dainton Building, Department of Chemistry, The University of Sheffield, Brook Hill, Sheffield, South Yorkshire, S3 7HF, UK
| | - Edwin C Johnson
- Dainton Building, Department of Chemistry, The University of Sheffield, Brook Hill, Sheffield, South Yorkshire, S3 7HF, UK
| | - Derek H H Chan
- Dainton Building, Department of Chemistry, The University of Sheffield, Brook Hill, Sheffield, South Yorkshire, S3 7HF, UK
| | - Mark J Smallridge
- GEO Specialty Chemicals, Hythe, Southampton, Hampshire, SO45 3ZG, UK
| | - Steven P Armes
- Dainton Building, Department of Chemistry, The University of Sheffield, Brook Hill, Sheffield, South Yorkshire, S3 7HF, UK
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30
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Rodnin MV, Vasques-Montes V, Kyrychenko A, Oliveira NFB, Kashipathy MM, Battaile KP, Douglas J, Lovell S, Machuqueiro M, Ladokhin AS. Histidine Protonation and Conformational Switching in Diphtheria Toxin Translocation Domain. Toxins (Basel) 2023; 15:410. [PMID: 37505680 PMCID: PMC10467104 DOI: 10.3390/toxins15070410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Revised: 06/06/2023] [Accepted: 06/21/2023] [Indexed: 07/29/2023] Open
Abstract
Protonation of key histidine residues has been long implicated in the acid-mediated cellular action of the diphtheria toxin translocation (T-) domain, responsible for the delivery of the catalytic domain into the cell. Here, we use a combination of computational (constant-pH Molecular Dynamics simulations) and experimental (NMR, circular dichroism, and fluorescence spectroscopy along with the X-ray crystallography) approaches to characterize the initial stages of conformational change happening in solution in the wild-type T-domain and in the H223Q/H257Q double mutant. This replacement suppresses the acid-induced transition, resulting in the retention of a more stable protein structure in solutions at pH 5.5 and, consequently, in reduced membrane-disrupting activity. Here, for the first time, we report the pKa values of the histidine residues of the T-domain, measured by NMR-monitored pH titrations. Most peaks in the histidine side chain spectral region are titrated with pKas ranging from 6.2 to 6.8. However, the two most up-field peaks display little change down to pH 6, which is a limiting pH for this protein in solution at concentrations required for NMR. These peaks are absent in the double mutant, suggesting they belong to H223 and H257. The constant-pH simulations indicate that for the T-domain in solution, the pKa values for histidine residues range from 3.0 to 6.5, with those most difficult to protonate being H251 and H257. Taken together, our experimental and computational data demonstrate that previously suggested cooperative protonation of all six histidines in the T-domain does not occur.
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Affiliation(s)
- Mykola V. Rodnin
- Department of Biochemistry and Molecular Biology, University of Kansas School of Medicine, Kansas City, KS 66160, USA (A.K.)
| | - Victor Vasques-Montes
- Department of Biochemistry and Molecular Biology, University of Kansas School of Medicine, Kansas City, KS 66160, USA (A.K.)
| | - Alexander Kyrychenko
- Department of Biochemistry and Molecular Biology, University of Kansas School of Medicine, Kansas City, KS 66160, USA (A.K.)
- Institute of Chemistry and School of Chemistry, V. N. Karazin Kharkiv National University, 61022 Kharkiv, Ukraine
| | - Nuno F. B. Oliveira
- Institute of Biosystems and Integrative Sciences, University of Lisbon, 1749-016 Lisbon, Portugal (M.M.)
| | - Maithri M. Kashipathy
- Protein Structure and X-ray Crystallography Laboratory, University of Kansas, Lawrence, KS 66047, USA (S.L.)
| | | | - Justin Douglas
- COBRE Bio-NMR Laboratory, University of Kansas, Lawrence, KS 66045, USA;
| | - Scott Lovell
- Protein Structure and X-ray Crystallography Laboratory, University of Kansas, Lawrence, KS 66047, USA (S.L.)
| | - Miguel Machuqueiro
- Institute of Biosystems and Integrative Sciences, University of Lisbon, 1749-016 Lisbon, Portugal (M.M.)
| | - Alexey S. Ladokhin
- Department of Biochemistry and Molecular Biology, University of Kansas School of Medicine, Kansas City, KS 66160, USA (A.K.)
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31
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Salimi A, Chatterjee S, Lee JY. Exposure to the electric field: A potential way to block the aggregation of histidine tautomeric isomers of β-amyloid. Int J Biol Macromol 2023; 232:123385. [PMID: 36693605 DOI: 10.1016/j.ijbiomac.2023.123385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 01/17/2023] [Accepted: 01/18/2023] [Indexed: 01/22/2023]
Abstract
Controlling protein misfolding and accumulation in neurodegeneration is a challenge in chemical neuroscience. The application of appropriate electric fields (EFs) can be a potential noninvasive therapy to treat neuro disorders. The effect of EFs of varying intensities and directions on the conformational dynamics of β-Amyloid40 (Aβ40) under histidine tautomerism has been investigated for the first time. Our findings suggest that peptides tend to align their dipole moments with the orientation of EF. Irrespective of the EF direction, the dipole moment magnitude is affected by the EF strength. With the conformational changes, the EF strength equal to 0.5 V/nm destroyed the β-sheet content of the δδδ isomer as a potentially toxic agent. The content of the alpha-helical structure which can be transformed into the β-sheet is reduced. The strength of the EF showed a significant influence on the reduction of the number of intra-protein hydrogen bonds especially when EF is equal to 0.5 V/nm which could facilitate destabilization of the structure of the peptides. Current findings provide quantitative insights into the tautomerization-mediated Aβ40 dynamic and conformational changes induced by the external EFs in aqueous solutions, which may provide beneficial information for use as a therapeutic technique.
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Affiliation(s)
- Abbas Salimi
- Department of Chemistry, Sungkyunkwan University, Suwon 16419, Republic of Korea.
| | - Sompriya Chatterjee
- Department of Chemistry, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Jin Yong Lee
- Department of Chemistry, Sungkyunkwan University, Suwon 16419, Republic of Korea.
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32
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Sani MA, Le Brun AP, Rajput S, Attard T, Separovic F. The membrane activity of the antimicrobial peptide caerin 1.1 is pH dependent. Biophys J 2023; 122:1058-1067. [PMID: 36680343 PMCID: PMC10111263 DOI: 10.1016/j.bpj.2023.01.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 12/09/2022] [Accepted: 01/18/2023] [Indexed: 01/22/2023] Open
Abstract
Antimicrobial peptides are an important class of membrane-active peptides that can provide alternatives or complements to classic antibiotics. Among the many classes of AMPs, the histidine-rich family is of particular interest since they may induce pH-sensitive interactions with cell membranes. The AMP caerin 1.1 (Cae-1), from Australian tree frogs, has three histidine residues, and thus we studied the pH dependence of its interactions with model cell membranes. Using NMR spectroscopy and molecular dynamics simulations, we showed that Cae-1 induced greater perturbation of the lipid dynamics and water penetrations within the membrane interior in an acidic environment compared with physiological conditions. Using 31P solid-state NMR, the packing, chemical environment, and dynamics of the lipid headgroup were monitored. 2H solid-state NMR showed that Cae-1 ordered the acyl chains of the hydrophobic core of the bilayer. These results supported the molecular dynamics data, which showed that Cae-1 was mainly inserted within the lipid bilayer for both neutral and negatively charged membranes, with the charged residues pulling the water and phosphate groups inward. This could be an early step in the mechanism of membrane disruption by histidine-rich antimicrobial peptides and indicated that Cae-1 acts via a transmembrane mechanism in bilayers of neutral and anionic phospholipid membranes, especially in acidic conditions.
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Affiliation(s)
- Marc-Antoine Sani
- Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia.
| | - Anton P Le Brun
- Australian Centre for Neutron Scattering, Australian Nuclear Science and Technology Organisation, Kirrawee, New South Wales, Australia
| | - Sunnia Rajput
- Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia
| | - Troy Attard
- Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia
| | - Frances Separovic
- Bio21 Institute, University of Melbourne, Melbourne, Victoria, Australia; School of Chemistry, University of Melbourne, Melbourne, Victoria, Australia.
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33
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Zheng X, Sutton AT, Yang RS, Miller DV, Pagels B, Rustandi RR, Welch J, Payne A, Haverick M. Extensive Characterization of Polysorbate 80 Oxidative Degradation Under Stainless Steel Conditions. J Pharm Sci 2023; 112:779-789. [PMID: 36252652 DOI: 10.1016/j.xphs.2022.10.012] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 10/07/2022] [Accepted: 10/09/2022] [Indexed: 11/06/2022]
Abstract
Polysorbate-80 (PS-80) is a common surfactant used in biologics formulations. However, the tendency of oxidation to PS-80 when exposed to stainless steel surfaces brings various challenges during manufacturing processes, such as inconsistent shelf-life of PS-80 solutions, which can further impact the biologics and vaccines production. In this work, the root causes of PS-80 oxidation when in contact with stainless steel conditions were thoroughly investigated through the use of various complementary analytical techniques including U/HPLC-CAD, LC-MS, ICP-MS, peroxide assay, and EPR spectroscopy. The analytical tool kit used in this work successfully revealed a PS-80 degradation mechanism from the perspective of PS-80 content, PS-80 profile, iron content, peroxide production, and radical species. The combined datasets reveal that PS-80 oxidative degradation occurs in the presence of histidine and iron in addition to being combined with the hydroperoxides in PS-80 material. The oxidative pathway and potential degradants were identified by LC-MS. The PS-80 profile based on the U/HPLC-CAD assay provided an effective way to identify early-signs of PS-80 degradation. The results from a peroxide assay observed increased hydroperoxide along with PS-80 degradation. EPR spectra confirmed the presence of histidine-related radicals during PS-80 oxidation identifying how histidine is involved in the oxidation. All assays and findings introduced in this work will provide insight into how PS-80 oxidative degradation can be avoided, controlled, or detected. It will also provide valuable evaluations on techniques that can be used to identify PS-80 degradation related events that occur during the manufacturing process.
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Affiliation(s)
- Xiwei Zheng
- Analytical Research Development, Merck & Co., Inc., Rahway, NJ, USA.
| | - Adam T Sutton
- Analytical Research Development, Merck & Co., Inc., Rahway, NJ, USA
| | - Rong-Sheng Yang
- Analytical Research Development, Merck & Co., Inc., Rahway, NJ, USA
| | | | - Becca Pagels
- Manufacturing Division, Merck & Co., Inc., Rahway, NJ, USA
| | | | - Jonathan Welch
- Analytical Research Development, Merck & Co., Inc., Rahway, NJ, USA
| | - Anne Payne
- Analytical Research Development, Merck & Co., Inc., Rahway, NJ, USA
| | - Mark Haverick
- Analytical Research Development, Merck & Co., Inc., Rahway, NJ, USA.
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Tiwari OS, Aizen R, Meli M, Colombo G, Shimon LJW, Tal N, Gazit E. Entropically-Driven Co-assembly of l-Histidine and l-Phenylalanine to Form Supramolecular Materials. ACS Nano 2023; 17:3506-3517. [PMID: 36745579 DOI: 10.1021/acsnano.2c09872] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Molecular self- and co-assembly allow the formation of diverse and well-defined supramolecular structures with notable physical properties. Among the associating molecules, amino acids are especially attractive due to their inherent biocompatibility and simplicity. The biologically active enantiomer of l-histidine (l-His) plays structural and functional roles in proteins but does not self-assemble to form discrete nanostructures. In order to expand the structural space to include l-His-containing materials, we explored the co-assembly of l-His with all aromatic amino acids, including phenylalanine (Phe), tyrosine (Tyr), and tryptophan (Trp), all in both enantiomeric forms. In contrast to pristine l-His, the combination of this building block with all aromatic amino acids resulted in distinct morphologies including fibers, rods, and flake-like structures. Electrospray ionization mass spectrometry (ESI-MS) indicated the formation of supramolecular co-assemblies in all six combinations, but time-of-flight secondary-ion mass spectrometry (ToF-SIMS) indicated the best seamless co-assembly occurs between l-His and l-Phe while in the other cases, different degrees of phase separation could be observed. Indeed, isothermal titration calorimetry (ITC) suggested the highest affinity between l-His and l-Phe where the formation of co-assembled structures was driven by entropy. In accordance, among all the combinations, the co-assembly of l-His and l-Phe produced single crystals. The structure revealed the formation of a 3D network with nanocavities stabilized by hydrogen bonding between -N (l-His) and -NH (l-Phe). Taken together, using the co-assembly approach we expanded the field of amino acid nanomaterials and showed the ability to obtain discrete supramolecular nanostructures containing l-His based on its specific interactions with l-Phe.
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Affiliation(s)
- Om Shanker Tiwari
- The Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Tel Aviv 6997801, Israel
| | - Ruth Aizen
- The Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Tel Aviv 6997801, Israel
| | | | - Giorgio Colombo
- Department of Chemistry, University of Pavia, via Taramelli 12, 27100 Pavia, Italy
| | - Linda J W Shimon
- Department of Chemical Research Support, Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Noam Tal
- School of Chemistry, Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Ramat Aviv, Tel Aviv 6997801, Israel
| | - Ehud Gazit
- The Shmunis School of Biomedicine and Cancer Research, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Ramat Aviv, Tel Aviv 6997801, Israel
- Department of Materials Science and Engineering, The Iby and Aladar Fleischman Faculty of Engineering, Tel Aviv University, Ramat Aviv, Tel Aviv 6997801, Israel
- Sagol School of Neuroscience, Tel Aviv University, Ramat Aviv, Tel Aviv 6997801, Israel
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Mamardashvili G, Kaigorodova E, Lebedev I, Mamardashvili N. Molecular Recognition of Imidazole-Based Drug Molecules by Cobalt(III)- and Zinc(II)-Coproporphyrins in Aqueous Media. Molecules 2023; 28:molecules28030964. [PMID: 36770632 PMCID: PMC9920418 DOI: 10.3390/molecules28030964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 01/13/2023] [Accepted: 01/15/2023] [Indexed: 01/21/2023] Open
Abstract
The methods of 1H NMR, spectrophotometric titration, mass spectrometry and elemental analysis are applied to determine the selective binding ability of Co(III)- and Zn(II)-coproporphyrins I towards a series of imidazole-based drug molecules with a wide spectrum of pharmacological activity (metronidazole, histamine, histidine, tinidazole, mercazolil, and pilocarpine) in phosphate buffer (pH 7.4) simulating the blood plasma environment. It is shown that in aqueous buffer media, Co(III)-coproporphyrin I, unlike Zn(II)-coproporphyrin I, binds two imidazole derivatives, and the stability of mono-axial Co-coproporphyrin imidazole complexes is two to three orders of magnitude higher than that of similar complexes of Zn-coproporphyrin I. The studied porphyrinates are found to have the highest binding ability to histamine and histidine due to the formation of two additional hydrogen bonds between the carboxyl groups of the porphyrinate side chains and the binding sites of the ligands in the case of histidine and a hydrogen bond between the amino group of the ligand and the carbonyl oxygen atom of the carboxyl group of the porphyrinate in the case of histamine. The structures of the resulting complexes are optimized by DFT quantum chemical calculations. The results of these studies may be of use in the design of biosensors, including those for the detection, control and verification of various veterinary drug residues in human food samples.
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36
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Jiang Y, Huang Z, Tian J, Dong X, Yu XQ, Yu S. A chiral BINOL-based supramolecular gel enabling sensitive enantioselective and chemoselective collapse toward histidine. Soft Matter 2023; 19:430-435. [PMID: 36541446 DOI: 10.1039/d2sm01424f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
A chiral small molecule gelator (R)-H3L based on 1,1'-bi-2,2'-naphthol (BINOL)-phosphoric acid was designed and prepared, which spontaneously forms a stable water-induced gel. The gelation mechanism was revealed by single crystal X-ray diffraction analysis and a number of spectroscopic methods. Addition of Cu2+ improved the gelation ability, and the resultant metal organic gel realized visual enantioselective and chemoselective recognition toward L-histidine from enantiomers of 19 amino acids via gel collapse. The gel showed a highly sensitive response to L-histidine, and as low as 0.01 equiv. of L-histidine relative to the critical gelation concentration of (R)-H3L-Cu caused the gel to collapse. This strategy of regulating the assembly behavior through the interaction of amino acids and metal ions not only provides a simple and direct way to distinguish enantiomers, but also provides insight into how metal ions regulate the organization of biological supramolecular systems.
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Affiliation(s)
- Yixuan Jiang
- Key Laboratory of Green Chemistry and Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu 610064, China.
| | - Zeng Huang
- Institute of Nuclear Physics and Chemistry, China Academy of Engineering Physics, Mianyang 621900, China
| | - Jun Tian
- Key Laboratory of Green Chemistry and Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu 610064, China.
| | - Xin Dong
- Key Laboratory of Green Chemistry and Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu 610064, China.
| | - Xiao-Qi Yu
- Key Laboratory of Green Chemistry and Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu 610064, China.
- Asymmetric Synthesis and Chiral Technology Key Laboratory of Sichuan Province, Department of Chemistry, Xihua University, Chengdu 610039, P. R. China
| | - Shanshan Yu
- Key Laboratory of Green Chemistry and Technology, Ministry of Education, College of Chemistry, Sichuan University, Chengdu 610064, China.
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37
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Sheveleva NN, Tarasenko II, Vovk MA, Mikhailova ME, Neelov IM, Markelov DA. NMR Studies of Two Lysine Based Dendrimers with Insertion of Similar Histidine-Arginine and Arginine-Histidine Spacers Having Different Properties for Application in Drug Delivery. Int J Mol Sci 2023; 24:ijms24020949. [PMID: 36674466 PMCID: PMC9866564 DOI: 10.3390/ijms24020949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 12/14/2022] [Accepted: 12/20/2022] [Indexed: 01/06/2023] Open
Abstract
In this paper we study two lysine-based peptide dendrimers with Lys-His-Arg and Lys-Arg-His repeating units and terminal lysine groups. Combination of His and Arg properties in a dendrimer could be important for biomedical applications, especially for prevention of dendrimer aggregation and for penetration of dendrimers through various cell membranes. We describe the synthesis of these dendrimers and the confirmation of their structure using 1D and 2D Nuclear Magnetic Resonance (NMR) spectroscopy. NMR spectroscopy and relaxation are used to study the structural and dynamic properties of these macromolecules and to compare them with properties of previously studied dendrimers with Lys-2Arg and Lys-2His repeating units. Our results demonstrate that both Lys-His-Arg and Lys-Arg-His dendrimers have pH sensitive conformation and dynamics. However, properties of Lys-His-Arg at normal pH are more similar to those of the more hydrophobic Lys-2His dendrimer, which has tendency towards aggregation, while the Lys-Arg-His dendrimer is more hydrophilic. Thus, the conformation with the same amino acid composition of Lys-His-Arg is more pH sensitive than Lys-Arg-His, while the presence of Arg groups undoubtedly increases its hydrophilicity compared to Lys-2His. Hence, the Lys-His-Arg dendrimer could be a more suitable (in comparison with Lys-2His and Lys-Arg-His) candidate as a pH sensitive nanocontainer for drug delivery.
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Affiliation(s)
- Nadezhda N. Sheveleva
- Saint Petersburg State University, 7/9 Universitetskaya Nab, 199034 Saint Petersburg, Russia
| | - Irina I. Tarasenko
- Institute of Macromolecular Compounds, Russian Academy of Sciences, Bolshoi Prospect 31, V.O., 199004 Saint Petersburg, Russia
| | - Mikhail A. Vovk
- Saint Petersburg State University, 7/9 Universitetskaya Nab, 199034 Saint Petersburg, Russia
| | - Mariya E. Mikhailova
- Saint Petersburg State University, 7/9 Universitetskaya Nab, 199034 Saint Petersburg, Russia
| | - Igor M. Neelov
- School of Computer Technologies and Control, Saint Petersburg National Research University of Information Technologies, Mechanics and Optics (ITMO University), Kronverkskiy Pr. 49, 197101 Saint Petersburg, Russia
| | - Denis A. Markelov
- Saint Petersburg State University, 7/9 Universitetskaya Nab, 199034 Saint Petersburg, Russia
- Correspondence:
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38
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Zhao YY, Deng H, Rahman A, Xu XL, Qian P, Guo H. Computational Study of Methionine Methylation Process Catalyzed by SETD3. Interdiscip Sci 2022; 14:929-936. [PMID: 35419695 DOI: 10.1007/s12539-022-00516-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/17/2022] [Accepted: 03/22/2022] [Indexed: 06/14/2023]
Abstract
The SETD3 enzyme has been identified as the methyltransferase for the His73 methylation in β-actin, and such methylation plays an important role in regulating the actin's biochemical properties and fine-tuning the protein's cellular roles. Further studies have demonstrated that SETD3 may be able to methylase some other residues, including lysine and methionine, that substitute His73 in the β-actin peptide. The activity of SETD3 on the Met73 peptide is low without turnover. Interestingly, it has been shown that the N255V and N255A mutations of SETD3 can increase the activity by about 3-fold for the methionine methylation, while such mutations lead to a significant reduction of kcat for the His73 methylation. The detailed mechanism that leads to such increase of the activity for the Met73 methylation as a result of the mutations has not been understood. In this work, QM/MM molecular dynamics (MD) and potential of mean force (PMF) free energy simulations are undertaken for investigating structural, dynamic, and energetic properties involving the complex of SETD3 and Met73 peptide and to study the SETD3-catalyzed methionine methylation and the effects of the N255V mutation. It is demonstrated that the free energy barrier in the case of the methionine methylation in SETD3 is about 10 kcal/mol higher than that for the histidine methylation. Moreover, the free energy barrier for the methionine methylation in the N255V mutant is about 1 kcal/mol lower than that in the wild-type enzyme. These results agree with previous experimental observation. The origin of the free-energy barrier changes as a result of the H to M substitution on the β-actin peptide and the N255V mutation of SETD3 is discussed based on the data obtained from the simulations.
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Affiliation(s)
- Yuan-Yuan Zhao
- Chemistry and Material Science Faculty, Shandong Agricultural University, Taian, 271018, People's Republic of China
| | - Hao Deng
- Chemistry and Material Science Faculty, Shandong Agricultural University, Taian, 271018, People's Republic of China
| | - Adua Rahman
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, 37996, USA
| | - Xiao-Long Xu
- Chemistry and Material Science Faculty, Shandong Agricultural University, Taian, 271018, People's Republic of China
| | - Ping Qian
- Chemistry and Material Science Faculty, Shandong Agricultural University, Taian, 271018, People's Republic of China.
- Key Laboratory of Agricultural Film Application of Ministry of Agriculture and Rural Affairs, Taian, 271018, People's Republic of China.
| | - Hong Guo
- Department of Biochemistry and Cellular and Molecular Biology, University of Tennessee, Knoxville, TN, 37996, USA.
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39
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Jayawardena BM, Peacey L, Gamsjaeger R, Jones CE. Essential Role of Histidine for Rapid Copper(II)-Mediated Disassembly of Neurokinin B Amyloid. Biomolecules 2022; 12:biom12111585. [PMID: 36358935 PMCID: PMC9687585 DOI: 10.3390/biom12111585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 10/21/2022] [Accepted: 10/25/2022] [Indexed: 12/02/2022] Open
Abstract
Neurokinin B is a tachykinin peptide involved in a diverse range of neuronal functions. It rapidly forms an amyloid, which is considered physiologically important for efficient packing into dense core secretory vesicles within hypothalamic neurons. Disassembly of the amyloid is thought to require the presence of copper ions, which interact with histidine at the third position in the peptide sequence. However, it is unclear how the histidine is involved in the amyloid structure and why copper coordination can trigger disassembly. In this work, we demonstrate that histidine contributes to the amyloid structure via π-stacking interactions with nearby phenylalanine residues. The ability of neurokinin B to form an amyloid is dependent on any aromatic residue at the third position in the sequence; however, only the presence of histidine leads to both amyloid formation and rapid copper-induced disassembly.
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Zdaniauskienė A, Talaikis M, Charkova T, Sadzevičienė R, Labanauskas L, Niaura G. Electrochemical Shell-Isolated Nanoparticle-Enhanced Raman Spectroscopy of Imidazole Ring Functionalized Monolayer on Smooth Gold Electrode. Molecules 2022; 27:molecules27196531. [PMID: 36235068 PMCID: PMC9573715 DOI: 10.3390/molecules27196531] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 09/20/2022] [Accepted: 09/23/2022] [Indexed: 11/16/2022]
Abstract
The imidazole ring (Im) of histidine side chains plays a unique role in the function of proteins through covalent bonding with metal ions and hydrogen bonding interactions with adjusted biomolecules and water. At biological interfaces, these interactions are modified because of the presence of an electric field. Self-assembled monolayers (SAMs) with the functional Im group mimic the histidine side chain at electrified interfaces. In this study, we applied in-situ shell-isolated nanoparticle-enhanced Raman spectroscopy (SHINERS) to probe the structure and hydrogen bonding of Im-functionalized SAM on smooth Au at the electrochemical interface. The self-assembly of molecules on the Au induced the proton shift from N1 atom (Tautomer-I), which is the dominant form of Im in the bulk sample, to N3 atom (Tautomer-II). The impact of electrode potential on the hydrogen bonding interaction strength of the Im ring was identified by SHINERS. Temperature-Raman measurements and density functional theory (DFT) analysis revealed the spectral marker for Im ring packing (mode near 1496-1480 cm-1) that allowed us to associate the confined and strongly hydrogen bonded interfacial Im groups with electrode polarization at -0.8 V. Reflection adsorption IR (RAIR) spectra of SAMs with and without Im revealed that the bulky ring prevented the formation of a strongly hydrogen bonded amide group network.
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Affiliation(s)
- Agnė Zdaniauskienė
- Center for Physical Sciences and Technology (FTMC), Department of Organic Chemistry, Sauletekio Ave. 3, LT-10257 Vilnius, Lithuania
| | - Martynas Talaikis
- Life Sciences Center, Institute of Biochemistry, Department of Bioelectrochemistry and Biospectroscopy, Vilnius University, Sauletekio Ave. 7, LT-10257 Vilnius, Lithuania
- Correspondence: (M.T.); (G.N.)
| | - Tatjana Charkova
- Center for Physical Sciences and Technology (FTMC), Department of Organic Chemistry, Sauletekio Ave. 3, LT-10257 Vilnius, Lithuania
| | - Rita Sadzevičienė
- Center for Physical Sciences and Technology (FTMC), Department of Organic Chemistry, Sauletekio Ave. 3, LT-10257 Vilnius, Lithuania
| | - Linas Labanauskas
- Center for Physical Sciences and Technology (FTMC), Department of Organic Chemistry, Sauletekio Ave. 3, LT-10257 Vilnius, Lithuania
| | - Gediminas Niaura
- Center for Physical Sciences and Technology (FTMC), Department of Organic Chemistry, Sauletekio Ave. 3, LT-10257 Vilnius, Lithuania
- Life Sciences Center, Institute of Biochemistry, Department of Bioelectrochemistry and Biospectroscopy, Vilnius University, Sauletekio Ave. 7, LT-10257 Vilnius, Lithuania
- Correspondence: (M.T.); (G.N.)
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Osei-Owusu J, Kots E, Ruan Z, Mihaljević L, Chen KH, Tamhaney A, Ye X, Lü W, Weinstein H, Qiu Z. Molecular determinants of pH sensing in the proton-activated chloride channel. Proc Natl Acad Sci U S A 2022; 119:e2200727119. [PMID: 35878032 PMCID: PMC9351481 DOI: 10.1073/pnas.2200727119] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 05/31/2022] [Indexed: 01/27/2023] Open
Abstract
In response to acidic pH, the widely expressed proton-activated chloride (PAC) channel opens and conducts anions across cellular membranes. By doing so, PAC plays an important role in both cellular physiology (endosome acidification) and diseases associated with tissue acidosis (acid-induced cell death). Despite the available structural information, how proton binding in the extracellular domain (ECD) leads to PAC channel opening remains largely unknown. Here, through comprehensive mutagenesis and electrophysiological studies, we identified several critical titratable residues, including two histidine residues (H130 and H131) and an aspartic acid residue (D269) at the distal end of the ECD, together with the previously characterized H98 at the transmembrane domain-ECD interface, as potential pH sensors for human PAC. Mutations of these residues resulted in significant changes in pH sensitivity. Some combined mutants also exhibited large basal PAC channel activities at neutral pH. By combining molecular dynamics simulations with structural and functional analysis, we further found that the β12 strand at the intersubunit interface and the associated "joint region" connecting the upper and lower ECDs allosterically regulate the proton-dependent PAC activation. Our studies suggest a distinct pH-sensing and gating mechanism of this new family of ion channels sensitive to acidic environment.
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Affiliation(s)
- James Osei-Owusu
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Ekaterina Kots
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065
| | - Zheng Ruan
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI 49503
| | - Ljubica Mihaljević
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Kevin Hong Chen
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Ami Tamhaney
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205
| | - Xinyu Ye
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI 49503
| | - Wei Lü
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI 49503
| | - Harel Weinstein
- Department of Physiology and Biophysics, Weill Cornell Medicine, New York, NY 10065
| | - Zhaozhu Qiu
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205
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42
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Raval P, Trébosc J, Pawlak T, Nishiyama Y, Brown SP, Manjunatha Reddy GN. Combining heteronuclear correlation NMR with spin-diffusion to detect relayed Cl-H-H and N-H-H proximities in molecular solids. Solid State Nucl Magn Reson 2022; 120:101808. [PMID: 35780556 DOI: 10.1016/j.ssnmr.2022.101808] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 06/11/2022] [Accepted: 06/12/2022] [Indexed: 06/15/2023]
Abstract
Analysis of short-to-intermediate range intermolecular interactions offers a great way of characterizing the solid-state organization of small molecules and materials. This can be achieved by two-dimensional (2D) homo- and heteronuclear correlation NMR spectroscopy, for example, by carrying out experiments at high magnetic fields in conjunction with fast magic-angle spinning (MAS) techniques. But, detecting 2D peaks for heteronuclear dipolar coupled spin pairs separated by greater than 3 Å is not always straightforward, particularly when low-gamma quadrupolar nuclei are involved. Here, we present a 2D correlation NMR experiment that combines the advantages of heteronuclear-multiple quantum coherence (HMQC) and proton-based spin-diffusion (SD) pulse sequences using radio-frequency-driven-recouping (RFDR) to probe inter and intramolecular 1H-X (X = 14N, 35Cl) interactions. This experiment can be used to acquire 2D 1H{X}-HMQC filtered 1H-1H correlation as well as 2D 1H-X HMQC spectra. Powder forms of dopamine·HCl and l-histidine·HCl·H2O are characterized at high fields (21.1 T and 18.8 T) with fast MAS (60 kHz) using the 2D HMQC-SD-RFDR approach. Solid-state NMR results are complemented with NMR crystallography analyses using the gauge-including projector augmented wave (GIPAW) approach. For histidine·HCl·H2O, 2D peaks associated with 14N-1H-1H and 35Cl-1H-1H distances of up to 4.4 and 3.9 Å have been detected. This is further corroborated by the observation of 2D peaks corresponding to 14N-1H-1H and 35Cl-1H-1H distances of up to 4.2 and 3.7 Å in dopamine·HCl, indicating the suitability of the HMQC-SD-RFDR experiments for detecting medium-range proximities in molecular solids.
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Affiliation(s)
- Parth Raval
- University of Lille, CNRS, Centrale Lille Institut, Univ. Artois, UMR 8181-UCCS- Unité de Catalyse et Chimie du Solide, F, 59000, Lille, France
| | - Julien Trébosc
- Univ. Lille, CNRS, INRAE, Centrale Lille, Univ. Artois, FR 2638 - IMEC - Institut Michel-Eugène Chevreul, F, 59000, Lille, France
| | - Tomasz Pawlak
- Centre of Molecular and Macromolecular Studies, Polish Academy of Sciences, Sienkiewicza 112, 90-363, Lodz, Poland
| | - Yusuke Nishiyama
- RIKEN-JEOL Collaboration Centre, RIKEN, Yokohama Campus, Yokohama, Kanagawa, 230-0045, Japan; JEOL RESONANCE Inc., Akishima, Tokyo, 196-8558, Japan
| | - Steven P Brown
- Department of Physics, University of Warwick, Coventry, CV4 7AL, UK.
| | - G N Manjunatha Reddy
- University of Lille, CNRS, Centrale Lille Institut, Univ. Artois, UMR 8181-UCCS- Unité de Catalyse et Chimie du Solide, F, 59000, Lille, France.
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Krošl I, Košćak M, Ribičić K, Žinić B, Majhen D, Božinović K, Piantanida I. Impact of the Histidine-Triazole and Tryptophan-Pyrene Exchange in the WHW Peptide: Cu(II) Binding, DNA/RNA Interactions and Bioactivity. Int J Mol Sci 2022; 23:ijms23137006. [PMID: 35806009 PMCID: PMC9266797 DOI: 10.3390/ijms23137006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Revised: 06/20/2022] [Accepted: 06/21/2022] [Indexed: 12/10/2022] Open
Abstract
In three novel peptidoids based on the tryptophan—histidine—tryptophan (WHW) peptide, the central histidine was replaced by Ala-(triazole), and two derivatives also had one tryptophan replaced with pyrene-alkyls of different lengths and flexibility. Pyrene analogues show strong fluorescence at 480–500 nm, attributed to intramolecular exciplex formation with tryptophan. All three peptidoids bind Cu2+ cation in water with strong affinity, with Trp- Ala-(triazole)-Trp binding comparably to the parent WHW, and the pyrene analogues even stronger, demonstrating that replacement of histidine with triazole in peptides does not hamper Cu2+ coordination. The studied peptidoids strongly bind to ds-DNA and ds-RNA, whereby their complexes with Cu2+ exhibit distinctively different interactions in comparison to metal-free analogues, particularly in the stabilization of ds-DNA against thermal denaturation. The pyrene peptidoids efficiently enter living cells with no apparent cytotoxic effect, whereby their red-shifted emission compared to the parent pyrene allows intracellular confocal microscopy imaging, showing accumulation in cytoplasmic organelles. However, irradiation with 350 nm light resulted in evident antiproliferative effect on cells treated with micromolar concentrations of the pyrene analogues, presumably attributed to pyrene-induced production of singlet oxygen and consecutive cellular damage.
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Affiliation(s)
- Ivona Krošl
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (I.K.); (M.K.); (K.R.); (B.Ž.)
| | - Marta Košćak
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (I.K.); (M.K.); (K.R.); (B.Ž.)
| | - Karla Ribičić
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (I.K.); (M.K.); (K.R.); (B.Ž.)
| | - Biserka Žinić
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (I.K.); (M.K.); (K.R.); (B.Ž.)
| | - Dragomira Majhen
- Division of Molecular Biology, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (D.M.); (K.B.)
| | - Ksenija Božinović
- Division of Molecular Biology, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (D.M.); (K.B.)
| | - Ivo Piantanida
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (I.K.); (M.K.); (K.R.); (B.Ž.)
- Correspondence: ; Tel.: +385-1-4571-326
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Zlibut E, May JC, McLean JA. Enantiomer Differentiation of Amino Acid Stereoisomers by Structural Mass Spectrometry Using Noncovalent Trinuclear Copper Complexes. J Am Soc Mass Spectrom 2022; 33:996-1002. [PMID: 35580025 DOI: 10.1021/jasms.2c00059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Previous work has demonstrated that copper complexation strategies can be used with tandem MS (MS/MS) and, more recently, ion mobility-mass spectrometry (IM-MS) to differentiate chiral isomers based upon enantiomeric-specific binding. In this study, we investigate the separation of chiral amino acids (AAs) forming trinuclear complexes that can be directly resolved by IM-MS analyses. Twenty standard AAs of both d- and l-chirality were investigated. Specific AAs including d/l-histidine, d/l-proline, d/l-glutamine, d/l-tyrosine, and d/l-tryptophan were evaluated as "chiral selectors" that, when combined with copper, were found to promote selective complexation with specific AA enantiomers. Significant enantiomer differentiation was observed in the IM spectra for hydrophobic AAs acids with peak-to-peak resolutions ranging from 0.63 to 1.15. Among the chiral selectors investigated, histidine provided the best enantioselectivity, followed by tryptophan, suggesting the aromatic structure plays an important role in forming chiral-specific ion complexes. Unlike MS/MS methods where chiral selectors with l-stereochemistry enhance the differentiation, the chirality of the selector was found to have no significant effect on observed IM separation with both d- and l-selectors providing similar resolutions but with inverted IM arrival time ordering. To investigate the structural differences between resolvable chiral complexes, a combination of MS/MS, collision cross-section (CCS) measurements, and molecular mechanics techniques was used. Candidate trinuclear structures of the stoichiometry [(Cu2+)3(d/lIle)3(lHis)2 - 5H]+ were constructed with guidance from empirical MS/MS results. Of the 48 theoretical structures generated, one enantiomeric cluster pair yielded close correlation (<1%) with experimental CCS measurements, suggesting the most enantioselective ion complexes observed in this work are bridged by three coppers.
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Affiliation(s)
- Emanuel Zlibut
- Center for Innovative Technology, Department of Chemistry, Institute of Chemical Biology, Institute for Integrative Biosystems Research and Education, Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37235 United States
| | - Jody C May
- Center for Innovative Technology, Department of Chemistry, Institute of Chemical Biology, Institute for Integrative Biosystems Research and Education, Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37235 United States
| | - John A McLean
- Center for Innovative Technology, Department of Chemistry, Institute of Chemical Biology, Institute for Integrative Biosystems Research and Education, Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37235 United States
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Carnahan SL, Chen Y, Wishart JF, Lubach JW, Rossini AJ. Magic angle spinning dynamic nuclear polarization solid-state NMR spectroscopy of γ-irradiated molecular organic solids. Solid State Nucl Magn Reson 2022; 119:101785. [PMID: 35405629 DOI: 10.1016/j.ssnmr.2022.101785] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2021] [Revised: 02/22/2022] [Accepted: 03/04/2022] [Indexed: 06/14/2023]
Abstract
In the past 15 years, magic angle spinning (MAS) dynamic nuclear polarization (DNP) has emerged as a method to increase the sensitivity of high-resolution solid-state NMR spectroscopy experiments. Recently, γ-irradiation has been used to generate significant concentrations of homogeneously distributed free radicals in a variety of solids, including quartz, glucose, and cellulose. Both γ-irradiated quartz and glucose previously showed significant MAS DNP enhancements. Here, γ-irradiation is applied to twelve small organic molecules to test the applicability of γ-irradiation as a general method of creating stable free radicals for MAS DNP experiments on organic solids and pharmaceuticals. Radical concentrations in the range of 0.25 mM-10 mM were observed in irradiated glucose, histidine, malic acid, and malonic acid, and significant 1H DNP enhancements of 32, 130, 19, and 11 were obtained, respectively, as measured by 1H→13C CPMAS experiments. However, concentrations of free radicals below 0.05 mM were generally observed in organic molecules containing aromatic rings, preventing sizeable DNP enhancements. DNP sensitivity gains for several of the irradiated compounds exceed that which can be obtained with the relayed DNP approach that uses exogeneous polarizing agent solutions and impregnation procedures. In several cases, significant 1H DNP enhancements were realized at room temperature. This study demonstrates that in many cases γ-irradiation is a viable alternative to addition of stable exogenous radicals for DNP experiments on organic solids.
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Affiliation(s)
- Scott L Carnahan
- US DOE Ames Laboratory, Ames, IA, 50011, USA; Iowa State University, Department of Chemistry, Ames, IA, 50011, USA
| | - Yunhua Chen
- US DOE Ames Laboratory, Ames, IA, 50011, USA; Iowa State University, Department of Chemistry, Ames, IA, 50011, USA
| | - James F Wishart
- Brookhaven National Laboratory, Chemistry Division, Upton, NY, 11973, United States
| | - Joseph W Lubach
- Genentech Inc., South San Francisco, CA, 94080, United States
| | - Aaron J Rossini
- US DOE Ames Laboratory, Ames, IA, 50011, USA; Iowa State University, Department of Chemistry, Ames, IA, 50011, USA.
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Regazzoni L, Fumagalli L, Artasensi A, Gervasoni S, Gilardoni E, Mazzolari A, Aldini G, Vistoli G. Cyclo(His-Pro) Exerts Protective Carbonyl Quenching Effects through Its Open Histidine Containing Dipeptides. Nutrients 2022; 14:1775. [PMID: 35565743 PMCID: PMC9103439 DOI: 10.3390/nu14091775] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Revised: 04/11/2022] [Accepted: 04/19/2022] [Indexed: 12/12/2022] Open
Abstract
Cyclo(His-Pro) (CHP) is a cyclic dipeptide which is endowed with favorable pharmacokinetic properties combined with a variety of biological activities. CHP is found in a number of protein-rich foods and dietary supplements. While being stable at physiological pH, CHP can open yielding two symmetric dipeptides (His-Pro, Pro-His), the formation of which might be particularly relevant from dietary CHP due to the gastric acidic environment. The antioxidant and protective CHP properties were repeatedly reported although the non-enzymatic mechanisms were scantly investigated. The CHP detoxifying activity towards α,β unsaturated carbonyls was never investigated in detail, although its open dipeptides might be effective as already observed for histidine containing dipeptides. Hence, this study investigated the scavenging properties of TRH, CHP and its open derivatives towards 4-hydroxy-2-nonenal. The obtained results revealed that Pro-His possesses a marked activity and is more reactive than l-carnosine. As investigated by DFT calculations, the enhanced reactivity can be ascribed to the greater electrophilicity of the involved iminium intermediate. These findings emphasize that the primary amine (as seen in l-carnosine) can be replaced by secondary amines with beneficial effects on the quenching mechanisms. Serum stability of the tested peptides was also evaluated, showing that Pro-His is characterized by a greater stability than l-carnosine. Docking simulations suggested that its hydrolysis can be catalyzed by serum carnosinase. Altogether, the reported results evidence that the antioxidant CHP properties can be also due to the detoxifying activity of its open dipeptides, which might be thus responsible for the beneficial effects induced by CHP containing food.
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Affiliation(s)
- Luca Regazzoni
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, I-20133 Milano, Italy; (L.R.); (L.F.); (A.A.); (S.G.); (E.G.); (A.M.); (G.A.)
| | - Laura Fumagalli
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, I-20133 Milano, Italy; (L.R.); (L.F.); (A.A.); (S.G.); (E.G.); (A.M.); (G.A.)
| | - Angelica Artasensi
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, I-20133 Milano, Italy; (L.R.); (L.F.); (A.A.); (S.G.); (E.G.); (A.M.); (G.A.)
| | - Silvia Gervasoni
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, I-20133 Milano, Italy; (L.R.); (L.F.); (A.A.); (S.G.); (E.G.); (A.M.); (G.A.)
- Department of Physics, Università di Cagliari, Citt. Universitaria, I-09042 Monserrato, Italy
| | - Ettore Gilardoni
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, I-20133 Milano, Italy; (L.R.); (L.F.); (A.A.); (S.G.); (E.G.); (A.M.); (G.A.)
| | - Angelica Mazzolari
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, I-20133 Milano, Italy; (L.R.); (L.F.); (A.A.); (S.G.); (E.G.); (A.M.); (G.A.)
| | - Giancarlo Aldini
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, I-20133 Milano, Italy; (L.R.); (L.F.); (A.A.); (S.G.); (E.G.); (A.M.); (G.A.)
| | - Giulio Vistoli
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Milano, I-20133 Milano, Italy; (L.R.); (L.F.); (A.A.); (S.G.); (E.G.); (A.M.); (G.A.)
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47
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Song Y, Zhan J, Li M, Zhao H, Shi G, Wu M, Fang H. Enhancement of the Water Affinity of Histidine by Zinc and Copper Ions. Int J Mol Sci 2022; 23:ijms23073957. [PMID: 35409317 PMCID: PMC8999569 DOI: 10.3390/ijms23073957] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Revised: 03/27/2022] [Accepted: 03/30/2022] [Indexed: 02/04/2023] Open
Abstract
Histidine (His) is widely involved in the structure and function of biomolecules. Transition-metal ions, such as Zn2+ and Cu2+, widely exist in biological environments, and they are crucial to many life-sustaining physiological processes. Herein, by employing density function calculations, we theoretically show that the water affinity of His can be enhanced by the strong cation–π interaction between His and Zn2+ and Cu2+. Further, the solubility of His is experimentally demonstrated to be greatly enhanced in ZnCl2 and CuCl2 solutions. The existence of cation–π interaction is demonstrated by fluorescence, ultraviolet (UV) spectroscopy and nuclear magnetic resonance (NMR) experiments. These findings are of great importance for the bioavailability of aromatic drugs and provide new insight for understanding the physiological functions of transition metal ions.
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Affiliation(s)
- Yongshun Song
- School of Physics, East China University of Science and Technology, Shanghai 200237, China;
| | - Jing Zhan
- Shanghai Applied Radiation Institute, Shanghai University, Shanghai 200444, China; (J.Z.); (M.L.); (G.S.)
| | - Minyue Li
- Shanghai Applied Radiation Institute, Shanghai University, Shanghai 200444, China; (J.Z.); (M.L.); (G.S.)
| | - Hongwei Zhao
- Zhangjiang Laboratory, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China;
- Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Guosheng Shi
- Shanghai Applied Radiation Institute, Shanghai University, Shanghai 200444, China; (J.Z.); (M.L.); (G.S.)
| | - Minghong Wu
- Shanghai Applied Radiation Institute, Shanghai University, Shanghai 200444, China; (J.Z.); (M.L.); (G.S.)
- Correspondence: (M.W.); (H.F.)
| | - Haiping Fang
- School of Physics, East China University of Science and Technology, Shanghai 200237, China;
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325000, China
- Correspondence: (M.W.); (H.F.)
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Shi H, Ali Khan I, Zhang R, Zou Y, Xu W, Wang D. Evaluation of ultrasound-assisted L-histidine marination on beef M. semitendinosus: Insight into meat quality and actomyosin properties. Ultrason Sonochem 2022; 85:105987. [PMID: 35339000 PMCID: PMC8956927 DOI: 10.1016/j.ultsonch.2022.105987] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 03/15/2022] [Accepted: 03/21/2022] [Indexed: 05/02/2023]
Abstract
This paper aimed to evaluate the effects of ultrasound-assisted L-histidine marination (UMH) on meat quality and actomyosin properties of beef M. semitendinosus. Our results found that UMH treatment effectively avoided excessive liquid withdrawal, and disrupted myofibril integrity by modifying the water distribution and weakening connection of actin-myosin with increased muscle pH. The ultrasound-treated sample provided more opportunity for the filtration of L-histidine to intervene the isoelectric point and conformation of muscle protein. The activated caspase-3 and changes of ATPase activity in UMH-treated meat accelerated the postmortem ageing, and L-histidine might competitively inhibit the actin-myosin binding by the imidazole group. UMH decreased the surface hydrophobicity by shielding hydrophobic area and unfolding the actomyosin structure. In addition, the increased actomyosin solubility with smaller particle size enhanced the SH content for better cross-linking of myosin tail, and formation of heat-set gelling protein structure. Therefore, UMH treatment manifested the potential to improve beef quality.
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Affiliation(s)
- Haibo Shi
- Institute of Agricultural Products Processing, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, PR China; Key Lab of Food Quality and Safety of Jiangsu Province-State Key Laboratory Breeding Base, 210014, PR China; School of Food Science and Engineering, South China University of Technology, Guangzhou, 510641, PR China
| | - Iftikhar Ali Khan
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, PR China
| | - Ruyi Zhang
- School of Food Science and Engineering, South China University of Technology, Guangzhou, 510641, PR China
| | - Ye Zou
- Institute of Agricultural Products Processing, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, PR China; Key Lab of Food Quality and Safety of Jiangsu Province-State Key Laboratory Breeding Base, 210014, PR China.
| | - Weimin Xu
- Institute of Agricultural Products Processing, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, PR China; Key Lab of Food Quality and Safety of Jiangsu Province-State Key Laboratory Breeding Base, 210014, PR China
| | - Daoying Wang
- Institute of Agricultural Products Processing, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, PR China; Key Lab of Food Quality and Safety of Jiangsu Province-State Key Laboratory Breeding Base, 210014, PR China.
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Magrì A, Tabbì G, Naletova I, Attanasio F, Arena G, Rizzarelli E. A Deeper Insight in Metal Binding to the hCtr1 N-terminus Fragment: Affinity, Speciation and Binding Mode of Binuclear Cu 2+ and Mononuclear Ag + Complex Species. Int J Mol Sci 2022; 23:ijms23062929. [PMID: 35328348 PMCID: PMC8953729 DOI: 10.3390/ijms23062929] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 03/02/2022] [Accepted: 03/05/2022] [Indexed: 01/27/2023] Open
Abstract
Ctr1 regulates copper uptake and its intracellular distribution. The first 14 amino acid sequence of the Ctr1 ectodomain Ctr1(1-14) encompasses the characteristic Amino Terminal Cu2+ and Ni2+ binding motif (ATCUN) as well as the bis-His binding motif (His5 and His6). We report a combined thermodynamic and spectroscopic (UV-vis, CD, EPR) study dealing with the formation of Cu2+ homobinuclear complexes with Ctr1(1-14), the percentage of which is not negligible even in the presence of a small Cu2+ excess and clearly prevails at a M/L ratio of 1.9. Ascorbate fails to reduce Cu2+ when bound to the ATCUN motif, while it reduces Cu2+ when bound to the His5-His6 motif involved in the formation of binuclear species. The histidine diade characterizes the second binding site and is thought to be responsible for ascorbate oxidation. Binding constants and speciation of Ag+ complexes with Ctr1(1-14), which are assumed to mimic Cu+ interaction with N-terminus of Ctr1(1-14), were also determined. A preliminary immunoblot assay evidences that the anti-Ctr1 extracellular antibody recognizes Ctr1(1-14) in a different way from the longer Ctr1(1-25) that encompasses a second His and Met rich domain.
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Affiliation(s)
- Antonio Magrì
- Institute of Crystallography, National Council of Research, CNR, S.S. Catania, Via P. Gaifami 18, 95126 Catania, Italy; (A.M.); (G.T.); (I.N.)
| | - Giovanni Tabbì
- Institute of Crystallography, National Council of Research, CNR, S.S. Catania, Via P. Gaifami 18, 95126 Catania, Italy; (A.M.); (G.T.); (I.N.)
| | - Irina Naletova
- Institute of Crystallography, National Council of Research, CNR, S.S. Catania, Via P. Gaifami 18, 95126 Catania, Italy; (A.M.); (G.T.); (I.N.)
- Consorzio Interuniversitario per la Ricerca dei Metalli nei Sistemi Biologici, Via Ulpiani 27, 70126 Bari, Italy
| | - Francesco Attanasio
- Institute of Crystallography, National Council of Research, CNR, S.S. Catania, Via P. Gaifami 18, 95126 Catania, Italy; (A.M.); (G.T.); (I.N.)
- Correspondence: (F.A.); (E.R.); Tel.: +39-095-7385070 (E.R.)
| | - Giuseppe Arena
- Department of Chemical Sciences, University of Catania, Viale A. Doria 6, 95125 Catania, Italy;
| | - Enrico Rizzarelli
- Institute of Crystallography, National Council of Research, CNR, S.S. Catania, Via P. Gaifami 18, 95126 Catania, Italy; (A.M.); (G.T.); (I.N.)
- Consorzio Interuniversitario per la Ricerca dei Metalli nei Sistemi Biologici, Via Ulpiani 27, 70126 Bari, Italy
- Department of Chemical Sciences, University of Catania, Viale A. Doria 6, 95125 Catania, Italy;
- Correspondence: (F.A.); (E.R.); Tel.: +39-095-7385070 (E.R.)
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50
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Wang Y, Xu B, Ma S, Wang H, Shang L, Zhu C, Ye S. Discovery of SARS-CoV-2 3CL Pro Peptidomimetic Inhibitors through the Catalytic Dyad Histidine-Specific Protein-Ligand Interactions. Int J Mol Sci 2022; 23:ijms23042392. [PMID: 35216507 PMCID: PMC8878928 DOI: 10.3390/ijms23042392] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 02/16/2022] [Accepted: 02/19/2022] [Indexed: 12/22/2022] Open
Abstract
As the etiological agent for the coronavirus disease 2019, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) challenges the ongoing efforts of vaccine development and drug design. Due to the accumulating cases of breakthrough infections, there are urgent needs for broad-spectrum antiviral medicines. Here, we designed and examined five new tetrapeptidomimetic anti-SARS-CoV-2 inhibitors targeting the 3C-Like protease (3CLPro), which is highly conserved among coronaviruses and essential for viral replications. We significantly improved the efficacy of a ketoamide lead compound based on high-resolution co-crystal structures, all-atom simulations, and binding energy calculations. The inhibitors successfully engaged the catalytic dyad histidine residue (H41) of 3CLPro as designed, and they exhibited nanomolar inhibitory capacity as well as mitigated the viral loads of SARS-CoV-2 in cellular assays. As a widely applicable design principle, our results revealed that the potencies of 3CLPro-specific drug candidates were determined by the interplay between 3CLPro H41 residue and the peptidomimetic inhibitors.
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Affiliation(s)
- Yaxin Wang
- Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin 300072, China; (Y.W.); (B.X.); (S.M.)
| | - Binghong Xu
- Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin 300072, China; (Y.W.); (B.X.); (S.M.)
| | - Sen Ma
- Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin 300072, China; (Y.W.); (B.X.); (S.M.)
| | - Hao Wang
- KLMDASR of Tianjin and Drug Discovery Center for Infectious Disease, State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Tianjin 300353, China; (H.W.); (L.S.)
| | - Luqing Shang
- KLMDASR of Tianjin and Drug Discovery Center for Infectious Disease, State Key Laboratory of Medicinal Chemical Biology, College of Pharmacy, Nankai University, Tianjin 300353, China; (H.W.); (L.S.)
| | - Cheng Zhu
- Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin 300072, China; (Y.W.); (B.X.); (S.M.)
- Correspondence: (C.Z.); (S.Y.)
| | - Sheng Ye
- Tianjin Key Laboratory of Function and Application of Biological Macromolecular Structures, School of Life Sciences, Tianjin University, Tianjin 300072, China; (Y.W.); (B.X.); (S.M.)
- Correspondence: (C.Z.); (S.Y.)
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