1
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Lei H, Xiong W, Li M, Qi Q, Liu X, Wang S, Tian T, Zhou X. Enhanced control of RNA modification and CRISPR-Cas activity through redox-triggered disulfide cleavage. Bioorg Med Chem 2024; 112:117878. [PMID: 39167979 DOI: 10.1016/j.bmc.2024.117878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Revised: 08/07/2024] [Accepted: 08/13/2024] [Indexed: 08/23/2024]
Abstract
Chemical RNA modification has emerged as a flexible approach for post-synthetic modifications in chemical biology research. Guide RNA (gRNA) plays a crucial role in the clustered regularly interspaced short palindromic repeats and associated protein system (CRISPR-Cas). Several toolkits have been developed to regulate gene expression and editing through modifications of gRNA. However, conditional regulation strategies to control gene editing in cells as required are still lacking. In this context, we introduce a strategy employing a cyclic disulfide-substituted acylating agent to randomly acylate the 2'-OH group on the gRNA strand. The CRISPR-Cas systems demonstrate off-on transformation activity driven by redox-triggered disulfide cleavage and undergo intramolecular cyclization, which releases the functionalized gRNA. Dithiothreitol (DTT) exhibits superior reductive capabilities in cleaving disulfides compared to glutathione (GSH), requiring fewer reductants. This acylation method with cyclic disulfides enables conditional control of CRISPR-Cas9, CRISPR-Cas13a, RNA hybridization, and aptamer folding. Our strategy facilitates precise in vivo control of gene editing, making it particularly valuable for targeted applications.
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Affiliation(s)
- Huajun Lei
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, The Institute of Molecular Medicine, Wuhan University People's Hospital, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan 430072, Hubei, China
| | - Wei Xiong
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, The Institute of Molecular Medicine, Wuhan University People's Hospital, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan 430072, Hubei, China
| | - Ming Li
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, The Institute of Molecular Medicine, Wuhan University People's Hospital, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan 430072, Hubei, China
| | - Qianqian Qi
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, The Institute of Molecular Medicine, Wuhan University People's Hospital, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan 430072, Hubei, China
| | - Xingyu Liu
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, The Institute of Molecular Medicine, Wuhan University People's Hospital, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan 430072, Hubei, China
| | - Shaoru Wang
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, The Institute of Molecular Medicine, Wuhan University People's Hospital, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan 430072, Hubei, China
| | - Tian Tian
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, The Institute of Molecular Medicine, Wuhan University People's Hospital, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan 430072, Hubei, China.
| | - Xiang Zhou
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, The Institute of Molecular Medicine, Wuhan University People's Hospital, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University, Wuhan 430072, Hubei, China
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2
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Yang X, Su XC, Xuan W. Genetically Encoded Photocaged Proteinogenic and Non-Proteinogenic Amino Acids. Chembiochem 2024; 25:e202400393. [PMID: 38831474 DOI: 10.1002/cbic.202400393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 05/31/2024] [Accepted: 06/03/2024] [Indexed: 06/05/2024]
Abstract
Photocaged amino acids could be genetically encoded into proteins via genetic code expansion (GCE) and constitute unique tools for innovative protein engineering. There are a number of photocaged proteinogenic amino acids that allow strategic conversion of proteins into their photocaged variants, thus enabling spatiotemporal and non-invasive regulation of protein functions using light. Meanwhile, there are a hand of photocaged non-proteinogenic amino acids that address the challenges in directly encoding certain non-canonical amino acids (ncAAs) that structurally resemble proteinogenic ones or possess highly reactive functional groups. Herein, we would like to summarize the efforts in encoding photocaged proteinogenic and non-proteinogenic amino acids, hoping to draw more attention to this fruitful and exciting scientific campaign.
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Affiliation(s)
- Xiaochen Yang
- Frontier Science Center for Synthetic Biology (Ministry of Education), School of Life Sciences, Faculty of Medicine, Tianjin University, Tianjin, 300072, China
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Xun-Cheng Su
- State Key Laboratory and Institute of Elemento-Organic Chemistry, College of Chemistry, Nankai University, Tianjin, 300071, China
| | - Weimin Xuan
- Frontier Science Center for Synthetic Biology (Ministry of Education), School of Life Sciences, Faculty of Medicine, Tianjin University, Tianjin, 300072, China
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3
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Ma YH, Wang C, Yang J, Li B, Han X, Lu X. Disulfide-Driven Charge and Hydrophobicity Rearrangement of Remodeled Membrane Proteins toward Amyloid-Type Aggregation. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:16145-16150. [PMID: 39054779 DOI: 10.1021/acs.langmuir.4c01201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/27/2024]
Abstract
As a common pathological hallmark, protein aggregation into amyloids is a highly complicated phenomenon, attracting extensive research interest for elucidating its structural details and formation mechanisms. Membrane deposition and disulfide-driven protein misfolding play critical roles in amyloid-type aggregation, yet the underlying molecular process remains unclear. Here, we employed sum frequency generation (SFG) vibrational spectroscopy to comprehensively investigate the remodeling process of lysozyme, as the model protein, into amyloid-type aggregates at the cell membrane interface. It was discovered that disulfide reduction concurrently induced the transition of membrane-bound lysozyme from predominantly α-helical to antiparallel β-sheet structures, under a mode switch of membrane interaction from electrostatic to hydrophobic, and subsequent oligomeric aggregation. These findings shed light on the systematic understanding of dynamic molecular mechanisms underlying membrane-interactive amyloid oligomer formation.
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Affiliation(s)
- Yong-Hao Ma
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Chu Wang
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Jingjing Yang
- Department of Biochemistry and Molecular Biology, School of Medicine & Holistic Integrative Medicine, Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization, Nanjing University of Chinese Medicine, Nanjing 210023, China
| | - Bolin Li
- Anhui Key Laboratory of Condensed Matter Physics at Extreme Conditions, High Magnetic Field Laboratory, HFIPS, Chinese Academy of Sciences, Hefei 230031, China
| | - Xiaofeng Han
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Xiaolin Lu
- State Key Laboratory of Digital Medical Engineering, School of Biological Science and Medical Engineering, Southeast University, Nanjing 210096, China
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4
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Zhang W, Zhang J, Hu F, Wang W, Du Z, Ke Y, Ma Q, Mou X, Lu J, Yang Z. Active Dual-Protein Coating Assisted by Stepwise Protein-Protein Interactions Assembly Reduces Thrombosis and Infection. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2310259. [PMID: 38424734 PMCID: PMC11077678 DOI: 10.1002/advs.202310259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 02/04/2024] [Indexed: 03/02/2024]
Abstract
Universal protein coatings have recently gained wide interest in medical applications due to their biocompatibility and ease of fabrication. However, the challenge persists in protein activity preservation, significantly complicating the functional design of these coatings. Herein, an active dual-protein surface engineering strategy assisted by a facile stepwise protein-protein interactions assembly (SPPIA) method for catheters to reduce clot formation and infection is proposed. This strategy is realized first by the partial oxidation of bovine serum albumin (BSA) and lysozyme (LZM) for creating stable nucleation platforms via hydrophobic interaction, followed by the assembly of nonoxidized BSA (pI, the isoelectric point, ≈4.7) and LZM (pI ≈11) through electrostatic interaction owing to their opposite charge under neutral conditions. The SPPIA method effectively preserves the conformation and functionality of both BSA and LZM, thus endowing the resultant coating with potent antithrombotic and bactericidal properties. Furthermore, the stable nucleation platform ensures the adhesion and durability of the coating, resisting thrombosis and bacterial proliferation even after 15 days of PBS immersion. Overall, the SPPIA approach not only provides a new strategy for the fabrication of active protein coatings but also shows promise for the surface engineering technology of catheters.
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Affiliation(s)
- Wentai Zhang
- Dongguan Key Laboratory of Smart Biomaterials and Regenerative MedicineThe Tenth Affiliated HospitalSouthern Medical UniversityDongguanGuangdong523000China
| | - Jiangling Zhang
- School of Materials Science and EngineeringKey Lab of Advanced Technology for Materials of Education MinistrySouthwest Jiaotong UniversityChengdu610031China
| | - Fangkun Hu
- School of Materials Science and EngineeringKey Lab of Advanced Technology for Materials of Education MinistrySouthwest Jiaotong UniversityChengdu610031China
| | - Wenxuan Wang
- School of Materials Science and EngineeringKey Lab of Advanced Technology for Materials of Education MinistrySouthwest Jiaotong UniversityChengdu610031China
| | - Zeyu Du
- Dongguan Key Laboratory of Smart Biomaterials and Regenerative MedicineThe Tenth Affiliated HospitalSouthern Medical UniversityDongguanGuangdong523000China
- School of Materials Science and EngineeringKey Lab of Advanced Technology for Materials of Education MinistrySouthwest Jiaotong UniversityChengdu610031China
| | - You Ke
- Dongguan Key Laboratory of Smart Biomaterials and Regenerative MedicineThe Tenth Affiliated HospitalSouthern Medical UniversityDongguanGuangdong523000China
- School of Materials Science and EngineeringKey Lab of Advanced Technology for Materials of Education MinistrySouthwest Jiaotong UniversityChengdu610031China
| | - Qing Ma
- Dongguan Key Laboratory of Smart Biomaterials and Regenerative MedicineThe Tenth Affiliated HospitalSouthern Medical UniversityDongguanGuangdong523000China
- School of Materials Science and EngineeringKey Lab of Advanced Technology for Materials of Education MinistrySouthwest Jiaotong UniversityChengdu610031China
| | - Xiaohui Mou
- Dongguan Key Laboratory of Smart Biomaterials and Regenerative MedicineThe Tenth Affiliated HospitalSouthern Medical UniversityDongguanGuangdong523000China
- School of Materials Science and EngineeringKey Lab of Advanced Technology for Materials of Education MinistrySouthwest Jiaotong UniversityChengdu610031China
| | - Jing Lu
- Department of AnesthesiologySichuan Provincial People's HospitalUniversity of Electronic Science and Technology of ChinaChengduSichuan610072China
| | - Zhilu Yang
- Dongguan Key Laboratory of Smart Biomaterials and Regenerative MedicineThe Tenth Affiliated HospitalSouthern Medical UniversityDongguanGuangdong523000China
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Zhang Q, Fan S, Tang M, Wang C, Li X, Jin Y, Yang Z. Computation-Guided Rational Design of Cysteine-Less Protein Variants in Engineered hCGL. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:9937-9946. [PMID: 38651303 DOI: 10.1021/acs.jafc.3c06821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
The engineered human cystathionine-γ-lyase (hCGL) resulting in enhanced activity toward both cysteine and cystine unveils a potential robust antitumor activity. However, the presence of cysteine residues has the potential to induce oligomerization or incorrect disulfide bonding, which may decrease the bioavailability of biopharmaceuticals. Through a meticulous design process targeting the cysteine residues within engineered hCGL, a set of potential beneficial mutants were obtained by virtual screening employing Rosetta and ABACUS. Experimental measurements have revealed that most of the mutants showed increased activity toward both substrates l-Cys and CSSC. Furthermore, mutants C109V and C229D demonstrated Tm value increases of 8.2 and 1.8 °C, respectively. After an 80 min incubation at 60 °C, mutant C229D still maintained high residual activity. Unexpectedly, mutant C109V, displaying activity approximately 2-fold higher than the activity of wild type (WT) for both substrates, showed disappointing instability in plasma, which suggests that computational design still requires further consideration. Analysis of their structure and molecular dynamics (MD) simulation revealed the impact of hydrophobic interaction, hydrogen bonds, and near-attack conformation (NAC) stability on activity and stability. This study acquired information about mutants that exhibit enhanced activity or thermal resistance and serve as valuable guidance for subsequent specific cysteine modifications.
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Affiliation(s)
- Qian Zhang
- NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Shuai Fan
- NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Mengjia Tang
- School of Pharmacy, North China University of Science and Technology, Tangshan 063210, Hebei, China
| | - Chenyu Wang
- School of Pharmacy, North China University of Science and Technology, Tangshan 063210, Hebei, China
| | - Xiaoxiao Li
- School of Pharmacy, North China University of Science and Technology, Tangshan 063210, Hebei, China
| | - Yuanyuan Jin
- NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
| | - Zhaoyong Yang
- NHC Key Laboratory of Biotechnology of Antibiotics, Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100050, China
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6
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Lv W, Xu Y, Yang T, Wang L, Huang J, Huang H, Feng G. Unveiling the underappreciated: The bonding features of C-H⋯S-S interactions observed from rotational spectroscopy. J Chem Phys 2024; 160:134302. [PMID: 38557843 DOI: 10.1063/5.0200788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 03/18/2024] [Indexed: 04/04/2024] Open
Abstract
The C-H⋯S-S interactions are fundamentally important to understand the stability of biomacromolecules and their binding with small molecules, but they are still underappreciated. Herein, we characterized the C-H⋯S-S interactions in model molecular complexes. The rotational spectra of the complexes of diethyl disulfide with CH2CH2 and CH2CHF were measured and analyzed. All the detected structures are mainly stabilized by a C-H⋯S-S hydrogen bond, providing stabilization energies of 2.3-7.2 kJ mol-1. Incidental C-H⋯π or C-H⋯F interactions enhance the stabilization of the complexes. London dispersion, which accounts for 54%-68% of the total attractions, is the main driving force of stabilization. The provided bonding features of C-H⋯S-S are crucial for understanding the stabilizing role of this type of interaction in diverse processes such as supramolecular recognition, protein stability, and enzyme activity.
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Affiliation(s)
- Wenqi Lv
- School of Chemistry and Chemical Engineering, Chongqing University, Chongqing 401331, China
| | - Yugao Xu
- School of Chemistry and Chemical Engineering, Chongqing University, Chongqing 401331, China
| | - Tingting Yang
- School of Chemistry and Chemical Engineering, Chongqing University, Chongqing 401331, China
| | - Liuting Wang
- School of Chemistry and Chemical Engineering, Chongqing University, Chongqing 401331, China
| | - Jinxi Huang
- School of Chemistry and Chemical Engineering, Chongqing University, Chongqing 401331, China
| | - Haiying Huang
- School of Chemistry and Chemical Engineering, Chongqing University, Chongqing 401331, China
| | - Gang Feng
- School of Chemistry and Chemical Engineering, Chongqing University, Chongqing 401331, China
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7
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Noel JK, Haglund E. Topological Reaction Coordinate Captures the Folding Transition State Ensemble in a Pierced Lasso Protein. J Phys Chem B 2024; 128:117-124. [PMID: 38118146 DOI: 10.1021/acs.jpcb.3c06678] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2023]
Abstract
Proteins with a pierced lasso topology (PLT) have a covalent loop created by a disulfide bond, and the backbone circles back to thread the loop. This threaded topology has unique features compared to knotted topologies; notably, the topology is controlled by the chemical environment and the covalent loop remains intact even when denatured. In this work, we use the hormone leptin as our model PLT system and study its folding using molecular dynamics simulations that employ a structure-based (Go̅-like) model. We find that the reduced protein has a two-state folding mechanism with a transition state ensemble (TSE) that can be characterized by the reaction coordinate Q, the fraction of native contacts formed. In contrast, the oxidized protein, which must thread part of the polypeptide chain through a covalent loop, has a folding process that is poorly characterized by Q. Instead, we find that a topological coordinate that monitors the residue crossing the loop can identify the TSE of oxidized leptin. By precisely identifying the predicted TSE, one may now reliably calculate theoretical phi-values for the PLT protein, thereby enabling a comparison with experimental measurements. We find the loop-threading constraint leads to noncanonical phi-values that are uniformly small because this PLT protein has a flat energy landscape through the TSE.
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Affiliation(s)
- Jeffrey K Noel
- Structural Biology, Max Delbrück Center for Molecular Medicine, 13125 Berlin, Germany
| | - Ellinor Haglund
- Department of Chemistry, University of Hawaii, Manoa, Honolulu, Hawaii 96822, United States
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8
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Villanueva M, Vostal LE, Cohen DN, Biesbrock D, Kuwaye EP, Driver SG, Hart KM. Differential effects of disulfide bond formation in TEM-1 versus CTX-M-9 β-lactamase. Protein Sci 2024; 33:e4816. [PMID: 37897253 PMCID: PMC10731493 DOI: 10.1002/pro.4816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 08/18/2023] [Accepted: 10/19/2023] [Indexed: 10/30/2023]
Abstract
To investigate how disulfide bonds can impact protein energy landscapes, we surveyed the effects of adding or removing a disulfide in two β-lactamase enzymes, TEM-1 and CTX-M-9. The homologs share a structure and 38% sequence identity, but only TEM-1 contains a native disulfide bond. They also differ in thermodynamic stability and in the number of states populated at equilibrium: CTX-M-9 is two-state whereas TEM-1 has an additional intermediate state. We hypothesized that the disulfide bond is the major underlying determinant for these observed differences in their energy landscapes. To test this, we removed the disulfide bridge from TEM-1 and introduced a disulfide bridge at the same location in CTX-M-9. This modest change to sequence modulates the stabilities-and therefore populations-of TEM-1's equilibrium states and, more surprisingly, creates a novel third state in CTX-M-9. Unlike TEM-1's partially folded intermediate, this third state is a higher-order oligomer with reduced cysteines that retains the native fold and is fully active. Sub-denaturing concentrations of urea shifts the equilibrium to the monomeric form, allowing the disulfide bond to form. Interestingly, comparing the stability of the oxidized monomer with a variant lacking cysteines reveals the disulfide is neither stabilizing nor destabilizing in CTX-M-9, in contrast with the observed stabilization in TEM-1. Thus, we can conclude that engineering disulfide bonds is not always an effective stabilization strategy even when analogous disulfides exist in more stable structural homologs. This study also illustrates how homo-oligomerization can result from a small number of mutations, suggesting complex formation might be easily accessed during a protein family's evolution.
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Affiliation(s)
- Miranda Villanueva
- Department of ChemistryWilliams CollegeWilliamstownMassachusettsUSA
- Present address:
Biological Chemistry DepartmentDavid Geffen School of Medicine, UCLALos AngelesCaliforniaUSA
| | - Lauren E. Vostal
- Department of ChemistryWilliams CollegeWilliamstownMassachusettsUSA
- Present address:
Laboratory of Chemistry and Cell BiologyThe Rockefeller UniversityNew YorkNew YorkUSA
| | - Drew N. Cohen
- Department of ChemistryWilliams CollegeWilliamstownMassachusettsUSA
- Present address:
Feinberg School of MedicineNorthwestern UniversityChicagoIllinoisUSA
| | - Devin Biesbrock
- Department of ChemistryWilliams CollegeWilliamstownMassachusettsUSA
- Present address:
Laboratory of Cellular and Molecular BiologyNational Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of HealthBethesdaMarylandUSA
| | - Elise P. Kuwaye
- Department of ChemistryWilliams CollegeWilliamstownMassachusettsUSA
- Present address:
Department of Biological SciencesColumbia UniversityNew YorkNew YorkUSA
| | - Sasha G. Driver
- Department of ChemistryWilliams CollegeWilliamstownMassachusettsUSA
| | - Kathryn M. Hart
- Department of ChemistryWilliams CollegeWilliamstownMassachusettsUSA
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Luo S, Kong C, Ye D, Liu X, Wang Y, Meng G, Han Y, Xie L, Ji Y. Protein Persulfidation: Recent Progress and Future Directions. Antioxid Redox Signal 2023; 39:829-852. [PMID: 36943282 DOI: 10.1089/ars.2022.0064] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 03/23/2023]
Abstract
Significance: Hydrogen sulfide (H2S) is considered to be a gasotransmitter along with carbon monoxide (CO) and nitric oxide (NO), and is known as a key regulator of physiological and pathological activities. S-sulfhydration (also known as persulfidation), a mechanism involving the formation of protein persulfides by modification of cysteine residues, is proposed here to explain the multiple biological functions of H2S. Investigating the properties of protein persulfides can provide a foundation for further understanding of the potential functions of H2S. Recent Advances: Multiple methods have been developed to determine the level of protein persulfides. It has been demonstrated that protein persulfidation is involved in many biological processes through various mechanisms including the regulation of ion channels, enzymes, and transcription factors, as well as influencing protein-protein interactions. Critical Issues: Some technical and theoretical questions remain to be solved. These include how to improve the specificity of the detection methods for protein persulfidation, why persulfidation typically occurs on one or a few thiols within a protein, how this modification alters protein functions, and whether protein persulfidation has organ-specific patterns. Future Directions: Optimizing the detection methods and elucidating the properties and molecular functions of protein persulfidation would be beneficial for current therapeutics. In this review, we introduce the detailed mechanism of the persulfidation process and discuss persulfidation detection methods. In addition, this review summarizes recent discoveries of the selectivity of protein persulfidation and the regulation of protein functions and cell signaling pathways by persulfidation. Antioxid. Redox Signal. 39, 829-852.
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Affiliation(s)
- Shanshan Luo
- Key Laboratory of Cardiovascular and Cerebrovascular Medicine, Nanjing Medical University, Nanjing, China
| | - Chuiyu Kong
- Key Laboratory of Cardiovascular and Cerebrovascular Medicine, Nanjing Medical University, Nanjing, China
| | - Danyu Ye
- Key Laboratory of Cardiovascular and Cerebrovascular Medicine, Nanjing Medical University, Nanjing, China
| | - Xingeng Liu
- Key Laboratory of Targeted Intervention of Cardiovascular Disease, Nanjing Medical University, Nanjing, China
- Collaborative Innovation Center for Cardiovascular Disease Translational Medicine, Nanjing Medical University, Nanjing, China
| | - Yu Wang
- Key Laboratory of Cardiovascular and Cerebrovascular Medicine, Nanjing Medical University, Nanjing, China
| | - Guoliang Meng
- Department of Pharmacology, School of Pharmacy, Nantong University, Nantong, China
| | - Yi Han
- Department of Geriatrics, First Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Liping Xie
- Key Laboratory of Targeted Intervention of Cardiovascular Disease, Nanjing Medical University, Nanjing, China
- Collaborative Innovation Center for Cardiovascular Disease Translational Medicine, Nanjing Medical University, Nanjing, China
- The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Nanjing, China
| | - Yong Ji
- Key Laboratory of Cardiovascular and Cerebrovascular Medicine, Nanjing Medical University, Nanjing, China
- Key Laboratory of Targeted Intervention of Cardiovascular Disease, Nanjing Medical University, Nanjing, China
- Collaborative Innovation Center for Cardiovascular Disease Translational Medicine, Nanjing Medical University, Nanjing, China
- The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou Municipal Hospital, Gusu School, Nanjing Medical University, Nanjing, China
- National Key Laboratory of Frigid Zone Cardiovascular Diseases (NKLFZCD), Harbin Medical University, Harbin, China
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10
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Doğan Y, Yilmaz Y, Kelesoğlu S, Calapkorur B, Neşelioglu S, Erel Ö, Kalay N. Are Thiols Useful Biomarkers for Coronary Collateral Circulation in Patients with Stable Coronary Artery Disease? J Clin Med 2023; 12:6361. [PMID: 37835005 PMCID: PMC10573799 DOI: 10.3390/jcm12196361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 09/12/2023] [Accepted: 09/28/2023] [Indexed: 10/15/2023] Open
Abstract
Our aim was to investigate the relationship between thiol, which is the main component of the antioxidant system, and coronary collateral circulation (CCC). Our patients consisted of people with stable coronary artery disease (sCAD) and total occlusion in at least one vessel (n = 249). We divided the patients into two groups, good and poor, according to their CCC degree. We determined that DM, total thiol, and disulfide are independent predictors of poor CCC in multivariate logistic regression analysis (OR: 1.012, 95% CI: 1.008-1.017, p < 0.001; OR: 1.022, 95% CI: 1.000-1.044, p = 0.044; OR: 2.671, 95% CI: 1.238-5.761, p = 0.012, respectively). The ROC analysis showed a cut-off value of 328.7 for native thiol regarding the prediction of poor CCC, with 67.4% specificity and 78% sensitivity. For disulfide, it revealed a cut-off value of 15.1 regarding the prediction of poor CCC, with 57.9% specificity and 69.5% sensitivity. In this study, we detected that the patients with sCAD who developed poor CCC had lower levels of native thiol, total thiol, and disulfide compared to those with good CCC. The most interesting finding of our study is that CCC formation is an effective predictor of the antioxidant cascade rather than the inflammation cascade in sCAD patients.
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Affiliation(s)
- Yasemin Doğan
- Department of Cardiology, Kayseri City Training and Research Hospital, University of Health Sciences, Kayseri 38080, Turkey; (Y.Y.); (B.C.)
| | - Yücel Yilmaz
- Department of Cardiology, Kayseri City Training and Research Hospital, University of Health Sciences, Kayseri 38080, Turkey; (Y.Y.); (B.C.)
| | - Saban Kelesoğlu
- Department of Cardiology, Erciyes University Faculty of Medicine, Kayseri 38039, Turkey; (S.K.); (N.K.)
| | - Bekir Calapkorur
- Department of Cardiology, Kayseri City Training and Research Hospital, University of Health Sciences, Kayseri 38080, Turkey; (Y.Y.); (B.C.)
| | - Salim Neşelioglu
- Department of Biochemistry, Yildirim Beyazit University, Ankara 06800, Turkey; (S.N.); (Ö.E.)
| | - Özcan Erel
- Department of Biochemistry, Yildirim Beyazit University, Ankara 06800, Turkey; (S.N.); (Ö.E.)
| | - Nihat Kalay
- Department of Cardiology, Erciyes University Faculty of Medicine, Kayseri 38039, Turkey; (S.K.); (N.K.)
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11
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El Khoury G, Azzam W, Rebehmed J. PyProtif: a PyMol plugin to retrieve and visualize protein motifs for structural studies. Amino Acids 2023; 55:1429-1436. [PMID: 37698713 DOI: 10.1007/s00726-023-03323-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Accepted: 08/24/2023] [Indexed: 09/13/2023]
Abstract
Proteins often possess several motifs and the ones with similar motifs were found to have similar biochemical properties and thus related biological functions. Thereby, multiple databases were developed to store information on such motifs in proteins. For instance, PDBsum stores the results of Promotif's generated structural motifs and Pfam stores pre-computed patterns of functional domains. In addition to the fact that all this stored information is extremely useful, we can further augment its importance if we ought to integrate these motifs into visualization software. In this work, we have developed PyProtif, a plugin for the PyMOL molecular visualization program, which automatically retrieves protein structural and functional motifs from different databases and integrates them in PyMOL for visualization and analyses. Through an expendable menu and a user-friendly interface, the plugin grants the users the ability to study simultaneously multiple proteins and to select and manipulate each motif separately. Thus, this plugin will be of great interest for structural, evolutionary and classification studies of proteins.
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Affiliation(s)
- Gilbert El Khoury
- Department of Computer Science and Mathematics, Lebanese American University, Beirut, Lebanon
| | - Wael Azzam
- Department of Computer Science and Mathematics, Lebanese American University, Beirut, Lebanon
| | - Joseph Rebehmed
- Department of Computer Science and Mathematics, Lebanese American University, Beirut, Lebanon.
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12
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Ye J, Bazzi S, Fritz T, Tittmann K, Mata RA, Uranga J. Mechanisms of Cysteine-Lysine Covalent Linkage-The Role of Reactive Oxygen Species and Competition with Disulfide Bonds. Angew Chem Int Ed Engl 2023; 62:e202304163. [PMID: 37294559 DOI: 10.1002/anie.202304163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 06/09/2023] [Accepted: 06/09/2023] [Indexed: 06/10/2023]
Abstract
Recently, a new naturally occurring covalent linkage was characterised, involving a cysteine and a lysine, bridged through an oxygen atom. The latter was dubbed as the NOS bond, reflecting the individual atoms involved in this uncommon bond which finds little parallel in lab chemistry. It is found to form under oxidising conditions and is reversible upon addition of reducing agents. Further studies have identified the bond in crystal structures across a variety of systems and organisms, potentially playing an important role in regulation, cellular defense and replication. Not only that, double NOS bonds have been identified and even found to be competitive in relation to the formation of disulfide bonds. This raises several questions about how this exotic bond comes to be, what are the intermediates involved in its formation and how it competes with other pathways of sulfide oxidation. With this objective in mind, we revisited our first proposed mechanism for the reaction with model electronic structure calculations, adding information about the reactivity with alternative reactive oxygen species and other potential competing products of oxidation. We present a network with more than 30 reactions which provides one of the most encompassing pictures for cysteine oxidation pathways to date.
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Affiliation(s)
- Jin Ye
- Institute for Physical Chemistry, Georg-August Universität Göttingen, Tammannstraße 6, D-37077, Göttingen, Germany
| | - Sophia Bazzi
- Institute for Physical Chemistry, Georg-August Universität Göttingen, Tammannstraße 6, D-37077, Göttingen, Germany
| | - Tobias Fritz
- Institute for Physical Chemistry, Georg-August Universität Göttingen, Tammannstraße 6, D-37077, Göttingen, Germany
| | - Kai Tittmann
- Department of Molecular Enzymology, Göttingen Center of Molecular Biosciences, Georg-August University Göttingen, Göttingen, Germany
- Department of Structural Dynamics, Max-Planck-Institute for Multidisciplinary Sciences, Göttingen, Germany
| | - Ricardo A Mata
- Institute for Physical Chemistry, Georg-August Universität Göttingen, Tammannstraße 6, D-37077, Göttingen, Germany
| | - Jon Uranga
- Institute for Physical Chemistry, Georg-August Universität Göttingen, Tammannstraße 6, D-37077, Göttingen, Germany
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13
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Molinos M, Fiordalisi MF, Caldeira J, Almeida CR, Barbosa MA, Gonçalves RM. Alterations of bovine nucleus pulposus cells with aging. Aging Cell 2023; 22:e13873. [PMID: 37254638 PMCID: PMC10410011 DOI: 10.1111/acel.13873] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 04/19/2023] [Accepted: 04/29/2023] [Indexed: 06/01/2023] Open
Abstract
Aging is one of the major etiological factors driving intervertebral disc (IVD) degeneration, the main cause of low back pain. The nucleus pulposus (NP) includes a heterogeneous cell population, which is still poorly characterized. Here, we aimed to uncover main alterations in NP cells with aging. For that, bovine coccygeal discs from young (12 months) and old (10-16 years old) animals were dissected and primary NP cells were isolated. Gene expression and proteomics of fresh NP cells were performed. NP cells were labelled with propidium iodide and analysed by flow cytometry for the expression of CD29, CD44, CD45, CD146, GD2, Tie2, CD34 and Stro-1. Morphological cell features were also dissected by imaging flow cytometry. Elder NP cells (up-regulated bIL-6 and bMMP1 gene expression) presented lower percentages of CD29+, CD44+, CD45+ and Tie2+ cells compared with young NP cells (upregulated bIL-8, bCOL2A1 and bACAN gene expression), while GD2, CD146, Stro-1 and CD34 expression were maintained with age. NP cellulome showed an upregulation of proteins related to endoplasmic reticulum (ER) and melanosome independently of age, whereas proteins upregulated in elder NP cells were also associated with glycosylation and disulfide bonds. Flow cytometry analysis of NP cells disclosed the existence of 4 subpopulations with distinct auto-fluorescence and size with different dynamics along aging. Regarding cell morphology, aging increases NP cell area, diameter and vesicles. These results contribute to a better understanding of NP cells aging and highlighting potential anti-aging targets that can help to mitigate age-related disc disease.
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Affiliation(s)
- Maria Molinos
- i3S – Instituto de Investigação e Inovação em SaúdeUniversidade do PortoPortoPortugal
- INEB – Instituto de Engenharia BiomédicaUniversidade do PortoPortoPortugal
- ICBAS – Instituto de Ciências Biomédicas Abel SalazarUniversidade do PortoPortoPortugal
| | - Morena F. Fiordalisi
- i3S – Instituto de Investigação e Inovação em SaúdeUniversidade do PortoPortoPortugal
- INEB – Instituto de Engenharia BiomédicaUniversidade do PortoPortoPortugal
- ICBAS – Instituto de Ciências Biomédicas Abel SalazarUniversidade do PortoPortoPortugal
| | - Joana Caldeira
- i3S – Instituto de Investigação e Inovação em SaúdeUniversidade do PortoPortoPortugal
- INEB – Instituto de Engenharia BiomédicaUniversidade do PortoPortoPortugal
| | - Catarina R. Almeida
- i3S – Instituto de Investigação e Inovação em SaúdeUniversidade do PortoPortoPortugal
- INEB – Instituto de Engenharia BiomédicaUniversidade do PortoPortoPortugal
- iBiMED – Institute of Biomedicine, Department of Medical SciencesUniversity of AveiroAveiroPortugal
| | - Mário A. Barbosa
- i3S – Instituto de Investigação e Inovação em SaúdeUniversidade do PortoPortoPortugal
- INEB – Instituto de Engenharia BiomédicaUniversidade do PortoPortoPortugal
- ICBAS – Instituto de Ciências Biomédicas Abel SalazarUniversidade do PortoPortoPortugal
| | - Raquel M. Gonçalves
- i3S – Instituto de Investigação e Inovação em SaúdeUniversidade do PortoPortoPortugal
- INEB – Instituto de Engenharia BiomédicaUniversidade do PortoPortoPortugal
- ICBAS – Instituto de Ciências Biomédicas Abel SalazarUniversidade do PortoPortoPortugal
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14
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Chen B, Liu X, Zhou K, Xie Y, Wang Y, Zhou H, Bai Y, Xu B. Differentiating the effects of hydrophobic interaction and disulfide bond on the myofibrillar protein emulsion gels at the high temperature and the protein interfacial properties. Food Chem 2023; 412:135472. [PMID: 36731241 DOI: 10.1016/j.foodchem.2023.135472] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 12/30/2022] [Accepted: 01/09/2023] [Indexed: 01/13/2023]
Abstract
The study presented the effects of modulating the hydrophobic interaction and disulfide bond on the properties of myofibrillar protein (MP) emulsion gels at high temperature (95 °C) and the differentiation on the contribution of non-covalent (hydrophobic interaction) and covalent intermolecular interactions (disulfide bond) to the properties of interfacial protein films were also determined. The hydrophobic interactions among MP were modulated by the addition of octenyl succinic anhydride (OSA), and the disulfide bonds were modulated by the SH/SS exchange reactions mediated by GSH. The results showed that the MP emulsion gel properties at 95 °C were improved by modulating the hydrophobic interaction or disulfide bonds, and the dynamic interfacial adsorption of MP and dissipation quartz crystal microbalance experiments showed the interfacial adsorption pattens of protein were also changed. In addition, the hydrophobic interactions putted emphasis on improving the gel matrix, whereas the disulfide bonds focused on increasing the stiffness of interfacial protein films.
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Affiliation(s)
- Bo Chen
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230601, China; Engineering Research Center of Bio-process, Ministry of Education, Hefei University of Technology, Hefei 230601, China; Food Laboratory of Zhongyuan, Luohe 462300, Henan, China
| | - Xiaoyan Liu
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230601, China; Engineering Research Center of Bio-process, Ministry of Education, Hefei University of Technology, Hefei 230601, China
| | - Kai Zhou
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230601, China; Engineering Research Center of Bio-process, Ministry of Education, Hefei University of Technology, Hefei 230601, China
| | - Yong Xie
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230601, China; Engineering Research Center of Bio-process, Ministry of Education, Hefei University of Technology, Hefei 230601, China
| | - Ying Wang
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230601, China; Engineering Research Center of Bio-process, Ministry of Education, Hefei University of Technology, Hefei 230601, China
| | - Hui Zhou
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230601, China; Engineering Research Center of Bio-process, Ministry of Education, Hefei University of Technology, Hefei 230601, China
| | - Yanhong Bai
- College of Food and Bioengineering, Zhengzhou University of Light Industry, Zhengzhou 450001, China; Food Laboratory of Zhongyuan, Luohe 462300, Henan, China
| | - Baocai Xu
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230601, China; Engineering Research Center of Bio-process, Ministry of Education, Hefei University of Technology, Hefei 230601, China; Food Laboratory of Zhongyuan, Luohe 462300, Henan, China.
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15
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Hasegawa Y, Kawasaki T, Yamada M, Hosotani M, Maeda N, Watanabe T, Iwasaki T. Physicochemical properties of wooden breast-extracted myosin and rheological properties of its heat-induced gel. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2023. [PMID: 37066700 DOI: 10.1002/jsfa.12636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 04/12/2023] [Accepted: 04/17/2023] [Indexed: 06/19/2023]
Abstract
BACKGROUND It is reported that broilers with 'wooden breast' have poor processing properties, such as low binding and water-holding capacities. However, the reason for the poor functional characteristics has not been clarified. In this study, myosin was extracted from a wooden breast. Its physicochemical properties were investigated to clarify the relationship between the structure and physicochemical properties of the heating gel of myosin obtained from the wooden breast. RESULTS The turbidity of myosin solution extracted from wooden breast increased with increase in the heat treatment to a higher value than that from the normal breast meat myosin. The solubility of myosin collected from a wooden breast after heating decreased like normal breast muscle myosin. The surface hydrophobicity of myosin removed from wooden breast increased continually above 60 °C, unlike the change in surface hydrophobicity of normal breast myosin. The free thiol group of myosin extracted from the wooden breast was higher than normal breast myosin before and after heating. The apparent elasticity of heat-induced gels and chicken meat sausages was significantly lower in sausages and gel with wooden breast than normal ones (P < 0.05). The microstructure of the heated gel of normal myosin showed a fine network structure. In contrast, the heat-induced gel of wooden breast-extracted myosin showed a structure with loosely connected aggregates and many gaps. CONCLUSION The coarseness of the internal gel structure of myosin extracted from wooden breast was shown to affect the apparent elasticity of the gel and sausages made from the chicken meat. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Yasuhiro Hasegawa
- Department of Food Science and Human Wellness, Rakuno Gakuen University, Ebetsu, Japan
| | - Takeshi Kawasaki
- Research Office Concerning the Health of Humans and Birds, Abashiri, Japan
| | - Michi Yamada
- Department of Sustainable Agriculture, Rakuno Gakuen University, Ebetsu, Japan
| | - Marina Hosotani
- School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu, Japan
| | - Naoyuki Maeda
- Department of Food Science and Human Wellness, Rakuno Gakuen University, Ebetsu, Japan
| | - Takafumi Watanabe
- School of Veterinary Medicine, Rakuno Gakuen University, Ebetsu, Japan
| | - Tomohito Iwasaki
- Department of Food Science and Human Wellness, Rakuno Gakuen University, Ebetsu, Japan
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16
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Tyler TJ, Durek T, Craik DJ. Native and Engineered Cyclic Disulfide-Rich Peptides as Drug Leads. Molecules 2023; 28:molecules28073189. [PMID: 37049950 PMCID: PMC10096437 DOI: 10.3390/molecules28073189] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Revised: 03/27/2023] [Accepted: 03/29/2023] [Indexed: 04/07/2023] Open
Abstract
Bioactive peptides are a highly abundant and diverse group of molecules that exhibit a wide range of structural and functional variation. Despite their immense therapeutic potential, bioactive peptides have been traditionally perceived as poor drug candidates, largely due to intrinsic shortcomings that reflect their endogenous heritage, i.e., short biological half-lives and poor cell permeability. In this review, we examine the utility of molecular engineering to insert bioactive sequences into constrained scaffolds with desired pharmaceutical properties. Applying lessons learnt from nature, we focus on molecular grafting of cyclic disulfide-rich scaffolds (naturally derived or engineered), shown to be intrinsically stable and amenable to sequence modifications, and their utility as privileged frameworks in drug design.
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Affiliation(s)
- Tristan J. Tyler
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Thomas Durek
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
| | - David J. Craik
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
- Australian Research Council Centre of Excellence for Innovations in Peptide and Protein Science, The University of Queensland, Brisbane, QLD 4072, Australia
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17
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Srila W, Min TT, Sumphanapai T, Rangnoi K, Berkmen M, Yamabhai M. Production and applications of fluorobody from redox-engineered Escherichia coli. Appl Microbiol Biotechnol 2023; 107:1959-1970. [PMID: 36729226 PMCID: PMC10050041 DOI: 10.1007/s00253-023-12395-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 01/11/2023] [Accepted: 01/17/2023] [Indexed: 02/03/2023]
Abstract
Efficient selection and production of antibody fragments in microbial systems remain to be a challenging process. To optimize microbial production of single-chain variable fragments (scFvs), we have chosen five model targets, 1) a hapten, Zearalenone (ZEN) mycotoxin, along with infectious agents 2) rabies virus, 3) Propionibacterium acnes, 4) Pseudomonas aeruginosa, and a cancer cell 5) acute myeloid leukemia cell line (HL-60). The scFv binders were affinity selected from a non-immunized human phage display scFv antibody library and genetically fused to the N-terminus of emerald green fluorescent protein (EmGFP). The scFv-EmGFP fusion constructs were subcloned into an expression vector, under the control of T7 promoter, C-terminally tagged with hexa-histidine and expressed in different Escherichia coli (E. coli) hosts. This enabled the detection of cells that expressed the correct scFv-EmGFP fusion, termed fluorobody, via bright fluorescent signal in the cytoplasm. Among the three E. coli hosts tested, an engineered E. coli B strain called SHuffle B that promotes disulfide bond formation in the cytoplasm appeared to be the most appropriate host. The recombinant fluorobodies were well expressed (2-8 mg/L), possessed the fluorescence property of EmGFP, and retained the ability to bind to their cognate targets. Their specific bindings were demonstrated by ELISA, fluorescence-linked immunosorbent assay (FLISA), flow cytometry, and fluorescent microscope imaging. The fluorobody expression platform in this study could be further adopted as a one-step immunostaining technique based on scFv, isolated from phage display library to numerous desired targets. KEY POINTS: • E. coli SHuffle express T7 is a suitable expression host for scFv-EmGFP (fluorobody) • Only the clones harboring scFv-EmGFP plasmid will show bright fluorescent signal • This platform can be used to produce fluorobodies for numerous purposes.
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Affiliation(s)
- Witsanu Srila
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, 30000, Thailand
| | - Thae Thae Min
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, 30000, Thailand
| | - Thitima Sumphanapai
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, 30000, Thailand
| | - Kuntalee Rangnoi
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, 30000, Thailand
| | | | - Montarop Yamabhai
- School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima, 30000, Thailand.
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18
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Zhou X, Wen K, Huang SX, Lu Y, Liu Y, Jin JH, Kale SD, Chen XR. Time-Course Transcriptome Profiling Reveals Differential Resistance Responses of Tomato to a Phytotoxic Effector of the Pathogenic Oomycete Phytophthora cactorum. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12040883. [PMID: 36840230 PMCID: PMC9964705 DOI: 10.3390/plants12040883] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 02/13/2023] [Accepted: 02/13/2023] [Indexed: 05/22/2023]
Abstract
Blight caused by Phytophthora pathogens has a devastating impact on crop production. Phytophthora species secrete an array of effectors, such as Phytophthora cactorum-Fragaria (PcF)/small cysteine-rich (SCR) phytotoxic proteins, to facilitate their infections. Understanding host responses to such proteins is essential to developing next-generation crop resistance. Our previous work identified a small, 8.1 kDa protein, SCR96, as an important virulence factor in Phytophthora cactorum. Host responses to SCR96 remain obscure. Here, we analyzed the effect of SCR96 on the resistance of tomato treated with this recombinant protein purified from yeast cells. A temporal transcriptome analysis of tomato leaves infiltrated with 500 nM SCR96 for 0, 3, 6, and 12 h was performed using RNA-Seq. In total, 36,779 genes, including 2704 novel ones, were detected, of which 32,640 (88.7%) were annotated. As a whole, 5929 non-redundant genes were found to be significantly co-upregulated in SCR96-treated leaves (3, 6, 12 h) compared to the control (0 h). The combination of annotation, enrichment, and clustering analyses showed significant changes in expression beginning at 3 h after treatment in genes associated with defense and metabolism pathways, as well as temporal transcriptional accumulation patterns. Noticeably, the expression levels of resistance-related genes encoding receptor-like kinases/proteins, resistance proteins, mitogen-activated protein kinases (MAPKs), transcription factors, pathogenesis-related proteins, and transport proteins were significantly affected by SCR96. Quantitative reverse transcription PCR (qRT-PCR) validated the transcript changes in the 12 selected genes. Our analysis provides novel information that can help delineate the molecular mechanism and components of plant responses to effectors, which will be useful for the development of resistant crops.
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Affiliation(s)
- Xue Zhou
- College of Plant Protection, Yangzhou University, 48 Eastern Wenhui Road, Yangzhou 225009, China
| | - Ke Wen
- College of Plant Protection, Yangzhou University, 48 Eastern Wenhui Road, Yangzhou 225009, China
| | - Shen-Xin Huang
- College of Plant Protection, Yangzhou University, 48 Eastern Wenhui Road, Yangzhou 225009, China
| | - Yi Lu
- College of Plant Protection, Yangzhou University, 48 Eastern Wenhui Road, Yangzhou 225009, China
| | - Yang Liu
- College of Plant Protection, Yangzhou University, 48 Eastern Wenhui Road, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, 48 Eastern Wenhui Road, Yangzhou 225009, China
| | - Jing-Hao Jin
- College of Plant Protection, Yangzhou University, 48 Eastern Wenhui Road, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, 48 Eastern Wenhui Road, Yangzhou 225009, China
| | - Shiv D. Kale
- Fralin Life Science Institute, Virginia Tech, Blacksburg, VA 24060, USA
| | - Xiao-Ren Chen
- College of Plant Protection, Yangzhou University, 48 Eastern Wenhui Road, Yangzhou 225009, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, 48 Eastern Wenhui Road, Yangzhou 225009, China
- Correspondence:
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19
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Selikhanov G, Atamas A, Yukhimchuk D, Fufina T, Vasilieva L, Gabdulkhakov A. Stabilization of Cereibacter sphaeroides Photosynthetic Reaction Center by the Introduction of Disulfide Bonds. MEMBRANES 2023; 13:154. [PMID: 36837657 PMCID: PMC9967408 DOI: 10.3390/membranes13020154] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 01/19/2023] [Accepted: 01/23/2023] [Indexed: 06/18/2023]
Abstract
The photosynthetic reaction center of the purple nonsulfur bacterium Cereibacter sphaeroides is a useful model for the study of mechanisms of photoinduced electron transfer and a promising component for photo-bio-electrocatalytic systems. The basic research and technological applications of this membrane pigment-protein complex require effective approaches to increase its structural stability. In this work, a rational design approach to genetically modify the reaction centers by introducing disulfide bonds is used. This resulted in significantly increasing the thermal stability of some of the mutant pigment-protein complexes. The formation of the S-S bonds was confirmed by X-ray crystallography as well as SDS-PAGE, and the optical properties of the reaction centers were studied. The genetically modified reaction centers presented here preserved their ability for photochemical charge separation and could be of interest for basic science and biotechnology.
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Affiliation(s)
- Georgii Selikhanov
- Institute of Protein Research, Russian Academy of Sciences, Institutskaya 4, 142290 Pushchino, Moscow Region, Russia
- Federal Research Center Pushchino Scientific Center for Biological Research PSCBR, Institute of Basic Biological Problems, Russian Academy of Sciences, Institutskaya 2, 142290 Pushchino, Moscow Region, Russia
| | - Anastasia Atamas
- Institute of Protein Research, Russian Academy of Sciences, Institutskaya 4, 142290 Pushchino, Moscow Region, Russia
| | - Diana Yukhimchuk
- Institute of Protein Research, Russian Academy of Sciences, Institutskaya 4, 142290 Pushchino, Moscow Region, Russia
| | - Tatiana Fufina
- Federal Research Center Pushchino Scientific Center for Biological Research PSCBR, Institute of Basic Biological Problems, Russian Academy of Sciences, Institutskaya 2, 142290 Pushchino, Moscow Region, Russia
| | - Lyudmila Vasilieva
- Federal Research Center Pushchino Scientific Center for Biological Research PSCBR, Institute of Basic Biological Problems, Russian Academy of Sciences, Institutskaya 2, 142290 Pushchino, Moscow Region, Russia
| | - Azat Gabdulkhakov
- Institute of Protein Research, Russian Academy of Sciences, Institutskaya 4, 142290 Pushchino, Moscow Region, Russia
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20
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Abstract
Environmental agents of exposure can damage proteins, affecting protein function and cellular protein homeostasis. Specific residues are inherently chemically susceptible to damage from individual types of exposure. Amino acid content is not completely predictive of protein susceptibility, as secondary, tertiary, and quaternary structures of proteins strongly influence the reactivity of the proteome to individual exposures. Because we cannot readily predict which proteins will be affected by which chemical exposures, mass spectrometry-based proteomic strategies are necessary to determine the protein targets of environmental toxins and toxicants. This review describes the mechanisms by which environmental exposure to toxins and toxicants can damage proteins and affect their function, and emerging omic methodologies that can be used to identify the protein targets of a given agent. These methods include target identification strategies that have recently revolutionized the drug discovery field, such as activity-based protein profiling, protein footprinting, and protein stability profiling technologies. In particular, we highlight the necessity of multiple, complementary approaches to fully interrogate how protein integrity is challenged by individual exposures.
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Affiliation(s)
- Joseph C Genereux
- Department of Chemistry, University of California, Riverside, CA 92521, USA.
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21
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Macias LA, Brodbelt JS. Investigation of Product Ions Generated by 193 nm Ultraviolet Photodissociation of Peptides and Proteins Containing Disulfide Bonds. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:1315-1324. [PMID: 35736955 DOI: 10.1021/jasms.2c00124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Disulfide bridges are unique post-translational modifications (PTM) that contribute to protein architecture and modulate function. This PTM, however, challenges top-down mass spectrometry by cyclizing stretches of the protein sequence. In order to produce and release detectable product ions that contribute to the assignment of proteoforms, regions of a protein encapsulated by disulfide bonds require two fragmentation events: cleavage of the protein backbone and cleavage of the disulfide bond. Traditional collisional activation methods do not cleave disulfide bonds efficiently, often leading to low sequence coverage of proteins that incorporate this feature. To address this challenge, we have evaluated the fragmentation pathways enabled by 193 nm ultraviolet photodissociation (UVPD) and UVPD coupled to electron transfer dissociation for the characterization of protein structures incorporating disulfide bonds. Cleavage of disulfide bonds by either approach results in S-S and C-S dissociation products that result from a combination of homolytic cleavage and hydrogen-transfer processes. Characterization of these product ions elevates interpretation of complex top-down spectra of proteins that incorporate disulfide bonds.
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Affiliation(s)
- Luis A Macias
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
| | - Jennifer S Brodbelt
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
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22
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Improvement of FGF7 Thermal Stability by Introduction of Mutations in Close Vicinity to Disulfide Bond and Surface Salt Bridge. Int J Pept Res Ther 2022. [DOI: 10.1007/s10989-022-10394-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
AbstractFibroblast Growth Factor 7 (FGF7), a growth factor specific to epithelial cells, has attracted attention as a therapeutic protein. However, FGF7 has a limitation in its use due to low protein stability. Here, the mutations were designed to increase the stability of FGF7 by analyzing its 3D structure and sequence of other FGFs. Palifermin, N-terminal truncated FGF7 is known to have improved stability and was used as control protein in our study. The K126 and K178 were substituted into glutamate to form salt bridge with the neighboring residue R175 respectively and A120C mutation was introduced in close vicinity to disulfide bond between C133 and C137. The data of Circular Dichroism (CD) showed that all mutant proteins tested had higher Tm value than Palifermin and Tm of A120C/K126E/K178E FGF7 mutant protein was 15.24 °C higher than that of Palifermin. The results of cell proliferation activity and soluble protein analyzed by sodium dodecyl sulfate–polyacrylamide gel electrophoresis (SDS-PAGE) after 37 °C or 45 °C incubation exhibited that the stability of A120C mutant protein and A120C-including mutant proteins was improved. These results suggest that the mutation of amino acid in close vicinity to disulfide bond and the salt bridge at the surface of FGF7 enhanced thermal stability and make FGF7 more useful for pharmaceutical and cosmetical application.
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Dong H, Li J, Liu H, Lu S, Wu J, Zhang Y, Yin Y, Zhao Y, Wu C. Design and Ribosomal Incorporation of Noncanonical Disulfide-Directing Motifs for the Development of Multicyclic Peptide Libraries. J Am Chem Soc 2022; 144:5116-5125. [PMID: 35289603 DOI: 10.1021/jacs.2c00216] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The engineering of naturally occurring disulfide-rich peptides (DRPs) has been significantly hampered by the difficulty of manipulating disulfide pairing. New DRPs that take advantage of fold-directing motifs and noncanonical thiol-bearing amino acids are easy-to-fold with expected disulfide connectivities, representing a new class of scaffolds for the development of peptide ligands and therapeutics. However, the limited diversity of the scaffolds and particularly the use of noncanonical amino acids [e.g., penicillamine (Pen)] that are difficult to be translated by ribosomes greatly hamper the further development and application of these DRPs. Here, we designed and synthesized noncanonical bisthiol motifs bearing sterically obstructed thiol groups analogous to the Pen thiol to direct the folding of peptides into specific bicyclic and tricyclic structures. These bisthiol motifs can be ribosomally incorporated into peptides through a commercially available PURE system integrated with genetic code reprograming, which enables, for the first time, the in vitro expression of bicyclic peptides with two noncanonical and orthogonal disulfide bonds. We further constructed a bicyclic peptide library encoded by mRNA, with which new bicyclic peptide ligands with nanomolar affinity to proteins were successfully selected. Therefore, this study provides a new, general, and robust method for discovering de novo DRPs with new structures and functions not derived from natural peptides, which would greatly benefit the field of peptide drug discovery.
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Affiliation(s)
- Huilei Dong
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P.R. China
| | - Jinjing Li
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P.R. China
| | - Hongtan Liu
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P.R. China
| | - Shuaimin Lu
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P.R. China
| | - Junjie Wu
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, P.R. China
| | - Youming Zhang
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, P.R. China
| | - Yizhen Yin
- State Key Laboratory of Microbial Technology, Institute of Microbial Technology, Shandong University, Qingdao 266237, P.R. China
| | - Yibing Zhao
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P.R. China
| | - Chuanliu Wu
- The MOE Key Laboratory of Spectrochemical Analysis and Instrumentation, State Key Laboratory of Physical Chemistry of Solid Surfaces, Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, P.R. China
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Takayama M. Sensitive and resistant of the homologous disulfide-bridged proteins α-lactalbumin and lysozyme to attack of hydrogen-atoms, dithiothreitol and trifluoroacetic acid, examined by matrix-assisted laser desorption/ionization mass spectrometry. Biochem Biophys Rep 2022; 29:101212. [PMID: 35111980 PMCID: PMC8790284 DOI: 10.1016/j.bbrep.2022.101212] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 12/26/2021] [Accepted: 01/13/2022] [Indexed: 12/03/2022] Open
Abstract
Background Evolutionarily homologous proteins bovine α-lactoalbumin (αLA) and hen egg-white lysozyme (HEL) are very similar in primary, secondary and tertiary structures involving the location of disulfide-bridges (S–S), and are resistant to the action of hydrolytic enzymes and reagents. It is of interest to examine and compare the difference in backbone cleavage characteristics, by using reductive and hydrolytic reagents. Methods In-source decay (ISD) combined with matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS), reductive treatment of αLA and HEL with dithiothreitol (DTT) and acid hydrolysis with trifluoroacetic acid (TFA) were employed to examine the difference in the backbone cleavage characteristics of αLA and HEL. Results The treatment of αLA and HEL with DTT/AcOHNH3 resulted in similar cleavage behaviors of the backbone N-Cα and S–S bonds, i.e., the enhancements of the intensity and m/z range of sequence-reflected fragment ions were very similar. However, the treatment of αLA with DTT/TFA resulted in unexpected residue-specific degradation at the peptide bond of the Asp-Xxx, Xxx-Ser/Thr, Gln-Xxx, Xxx-Gly and Gly-Xxx residues, while HEL did not occur such degradation. Conclusions The results obtained above indicate that acidic αLA is very sensitive to acidic additive such as TFA, while basic HEL is resistance to acidic additives. General significance The study demonstrates the sensitive and resistant of evolutionary homologous proteins αLA and HEL to the acid hydrolysis and these characters come from acidic and basic nature of the proteins. Evolutionary homologous proteins bovine alpha-lactoalbumin and hen egg-white lysozyme are quite different in the protection from acidic reagents. Alpha-lactoalbumin is easily hydrolyzed with acidic reagents at the specific Asp, Gly, Thr and Ser residues owing to the acidic protein with pI4.53 Lysozyme is perfectly resistant to acidic reagents due to the presence of strong basic Arg residues owing to the basic protein with pI10.7 Degradation characteristics at the backbone S–S and N-Cα bonds of both proteins are very similar.
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25
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Chin AF, Wrabl JO, Hilser VJ. A thermodynamic atlas of proteomes reveals energetic innovation across the tree of life. Mol Biol Evol 2022; 39:6509521. [PMID: 35038744 PMCID: PMC8896757 DOI: 10.1093/molbev/msac010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Protein stability is a fundamental molecular property enabling organisms to adapt to their biological niches. How this is facilitated and whether there are kingdom specific or more general universal strategies is not known. A principal obstacle to addressing this issue is that the vast majority of proteins lack annotation, specifically thermodynamic annotation, beyond the amino acid and chromosome information derived from genome sequencing. To address this gap and facilitate future investigation into large-scale patterns of protein stability and dynamics within and between organisms, we applied a unique ensemble-based thermodynamic characterization of protein folds to a substantial portion of extant sequenced genomes. Using this approach, we compiled a database resource focused on the position-specific variation in protein stability. Interrogation of the database reveals; 1) domains of life exhibit distinguishing thermodynamic features, with eukaryotes particularly different from both archaea and bacteria, 2) the optimal growth temperature of an organism is proportional to the average apolar enthalpy of its proteome, 3) intrinsic disorder content is also proportional to the apolar enthalpy (but unexpectedly not the predicted stability at 25 °C), and 4) secondary structure and global stability information of individual proteins is extractable. We hypothesize that wider access to residue-specific thermodynamic information of proteomes will result in deeper understanding of mechanisms driving functional adaptation and protein evolution. Our database is free for download at https://afc-science.github.io/thermo-env-atlas/.
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Affiliation(s)
- Alexander F Chin
- Department of Biology, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD, 21218, USA
| | - James O Wrabl
- Department of Biology, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD, 21218, USA
| | - Vincent J Hilser
- Department of Biology, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD, 21218, USA.,T.C. Jenkins Department of Biophysics, Johns Hopkins University, 3400 North Charles Street, Baltimore, MD, 21218, USA
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26
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LEE CW, BAE GY, BAE SH, SUH HJ, JO K. Increased thermal stability of phycocyanin extracted from Spirulina platensis by cysteine addition during enzyme extraction. FOOD SCIENCE AND TECHNOLOGY 2022. [DOI: 10.1590/fst.15021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
- Chi-Woo LEE
- Korea University, Republic of Korea; Jinwi-myeon, Republic of Korea
| | | | | | - Hyung Joo SUH
- Korea University, Republic of Korea; Korea University, Republic of Korea
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27
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Comparison of quality characteristics of six reconstituted whole wheat flour with different modified bran. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2021.112543] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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28
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Insights of the Neofusicoccum parvum- Liquidambar styraciflua Interaction and Identification of New Cysteine-Rich Proteins in Both Species. J Fungi (Basel) 2021; 7:jof7121027. [PMID: 34947009 PMCID: PMC8707630 DOI: 10.3390/jof7121027] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 11/26/2021] [Accepted: 11/26/2021] [Indexed: 11/16/2022] Open
Abstract
Neofusicoccum parvum belongs to the Botryosphaeriaceae family, which contains endophytes and pathogens of woody plants. In this study, we isolated 11 strains from diseased tissue of Liquidambar styraciflua. Testing with Koch's postulates-followed by a molecular approach-revealed that N. parvum was the most pathogenic strain. We established an in vitro pathosystem (L. styraciflua foliar tissue-N. parvum) in order to characterize the infection process during the first 16 days. New CysRPs were identified for both organisms using public transcriptomic and genomic databases, while mRNA expression of CysRPs was analyzed by RT-qPCR. The results showed that N. parvum caused disease symptoms after 24 h that intensified over time. Through in silico analysis, 5 CysRPs were identified for each organism, revealing that all of the proteins are potentially secreted and novel, including two of N. parvum proteins containing the CFEM domain. Interestingly, the levels of the CysRPs mRNAs change during the interaction. This study reports N. parvum as a pathogen of L. styraciflua for the first time and highlights the potential involvement of CysRPs in both organisms during this interaction.
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29
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Zhu J, Avakyan N, Kakkis AA, Hoffnagle AM, Han K, Li Y, Zhang Z, Choi TS, Na Y, Yu CJ, Tezcan FA. Protein Assembly by Design. Chem Rev 2021; 121:13701-13796. [PMID: 34405992 PMCID: PMC9148388 DOI: 10.1021/acs.chemrev.1c00308] [Citation(s) in RCA: 100] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Proteins are nature's primary building blocks for the construction of sophisticated molecular machines and dynamic materials, ranging from protein complexes such as photosystem II and nitrogenase that drive biogeochemical cycles to cytoskeletal assemblies and muscle fibers for motion. Such natural systems have inspired extensive efforts in the rational design of artificial protein assemblies in the last two decades. As molecular building blocks, proteins are highly complex, in terms of both their three-dimensional structures and chemical compositions. To enable control over the self-assembly of such complex molecules, scientists have devised many creative strategies by combining tools and principles of experimental and computational biophysics, supramolecular chemistry, inorganic chemistry, materials science, and polymer chemistry, among others. Owing to these innovative strategies, what started as a purely structure-building exercise two decades ago has, in short order, led to artificial protein assemblies with unprecedented structures and functions and protein-based materials with unusual properties. Our goal in this review is to give an overview of this exciting and highly interdisciplinary area of research, first outlining the design strategies and tools that have been devised for controlling protein self-assembly, then describing the diverse structures of artificial protein assemblies, and finally highlighting the emergent properties and functions of these assemblies.
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Affiliation(s)
| | | | - Albert A. Kakkis
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Alexander M. Hoffnagle
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Kenneth Han
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Yiying Li
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Zhiyin Zhang
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Tae Su Choi
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Youjeong Na
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - Chung-Jui Yu
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
| | - F. Akif Tezcan
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093-0340, United States
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30
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Zhao X, Zhang S, Ma Q, Zhang X, Ma X. Rapid Disulfide Mapping in Peptides and Proteins by meta-Chloroperoxybenzoic Acid ( mCPBA) Oxidation and Tandem Mass Spectrometry. Anal Chem 2021; 93:14618-14625. [PMID: 34704736 DOI: 10.1021/acs.analchem.1c02379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Disulfide bonds are a class of important post-translational modifications that play important roles in modulating the structures and functions of proteins. Therefore, the mapping of disulfide linkages in peptides and proteins is indispensable for complete structure characterization and functional studies. As disulfide bonds in protonated ions do not dissociate readily under low-energy collision-induced dissociation (CID), they are usually chemically cleaved or activated prior to mass spectrometry (MS) or tandem MS (MS/MS) analysis. In this study, we report a new method that allows the mapping of disulfide linkages in peptides and proteins through meta-chloroperoxybenzoic acid (mCPBA)-based disulfide oxidation and MS/MS. Upon oxidation, the disulfide bond is converted to a thiosulfinate group, i.e., S(═O)-S, in a rapid (>60% yield in 1 min) and highly specific approach in an aqueous phase. The thiosulfinate group is then preferentially cleaved by MS/MS. For interchain disulfide linkages, this leads to a facile peptide chain separation and the identification of disulfide-linked peptides. For intrachain disulfide linkages, collisional activation of the thiosulfinate leads to disulfide cleavage and fragmentation of the peptide backbone constrained by the disulfide loop, enabling a near-complete peptide sequencing. The mCPBA oxidation-based disulfide mapping strategy can be readily integrated with bottom-up or top-down protein analysis for comprehensive protein structure elucidation, e.g., digested lysozyme and intact human insulin.
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Affiliation(s)
- Xu Zhao
- Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Sichun Zhang
- Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Qiang Ma
- Chinese Academy of Inspection and Quarantine, Beijing 100176, China
| | - Xinrong Zhang
- Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Xiaoxiao Ma
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instrument, Tsinghua University, Beijing 100084, China
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31
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Hakala T, Yates EV, Challa PK, Toprakcioglu Z, Nadendla K, Matak-Vinkovic D, Dobson CM, Martínez R, Corzana F, Knowles TPJ, Bernardes GJL. Accelerating Reaction Rates of Biomolecules by Using Shear Stress in Artificial Capillary Systems. J Am Chem Soc 2021; 143:16401-16410. [PMID: 34606279 PMCID: PMC8517977 DOI: 10.1021/jacs.1c03681] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Indexed: 12/15/2022]
Abstract
Biomimetics is a design principle within chemistry, biology, and engineering, but chemistry biomimetic approaches have been generally limited to emulating nature's chemical toolkit while emulation of nature's physical toolkit has remained largely unexplored. To begin to explore this, we designed biophysically mimetic microfluidic reactors with characteristic length scales and shear stresses observed within capillaries. We modeled the effect of shear with molecular dynamics studies and showed that this induces specific normally buried residues to become solvent accessible. We then showed using kinetics experiments that rates of reaction of these specific residues in fact increase in a shear-dependent fashion. We applied our results in the creation of a new microfluidic approach for the multidimensional study of cysteine biomarkers. Finally, we used our approach to establish dissociation of the therapeutic antibody trastuzumab in a reducing environment. Our results have implications for the efficacy of existing therapeutic antibodies in blood plasma as well as suggesting in general that biophysically mimetic chemistry is exploited in biology and should be explored as a research area.
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Affiliation(s)
- Tuuli
A. Hakala
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Emma V. Yates
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Pavan K. Challa
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Zenon Toprakcioglu
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Karthik Nadendla
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Dijana Matak-Vinkovic
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Christopher M. Dobson
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Rodrigo Martínez
- Departamento
de Química, Universidad de La Rioja, 26006 Logroño, Spain
| | - Francisco Corzana
- Departamento
de Química, Centro de Investigación en Síntesis
Química, Universidad de La Rioja, 26006 Logroño, Spain
| | - Tuomas P. J. Knowles
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
- Cavendish
Laboratory, University of Cambridge, J. J. Thomson Avenue, CB3 0HE Cambridge, United Kingdom
| | - Gonçalo J. L. Bernardes
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
- Instituto
de Medicina Molecular João Lobo Antunes, Faculdade de Medicina de Universidad de Lisboa, Avenida Prof. Egas Moniz, 1649-028 Lisboa, Portugal
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32
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Yamamoto E, Kawai Y, Takakura K, Kimura M, Murayama H, Matsueda H, Otsuki S, Sakata H, Tokunaga M. Convenient Unsymmetrical Disulfane Synthesis: Basic Zeolite‐Catalyzed Thiol‐Disulfane Exchange Reaction. ChemCatChem 2021. [DOI: 10.1002/cctc.202101092] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Eiji Yamamoto
- Department of Chemistry Graduate School of Science Kyushu University 744 Motooka Nishi-ku Fukuoka 819-0395 Japan
| | - Yasutaka Kawai
- Department of Chemistry Graduate School of Science Kyushu University 744 Motooka Nishi-ku Fukuoka 819-0395 Japan
| | - Kei Takakura
- Department of Chemistry Graduate School of Science Kyushu University 744 Motooka Nishi-ku Fukuoka 819-0395 Japan
| | - Moemi Kimura
- Department of Chemistry Graduate School of Science Kyushu University 744 Motooka Nishi-ku Fukuoka 819-0395 Japan
| | - Haruno Murayama
- Department of Chemistry Graduate School of Science Kyushu University 744 Motooka Nishi-ku Fukuoka 819-0395 Japan
| | - Hironobu Matsueda
- Fine Synthesis Technical Div. 1 DIC Corporation 18 Higashifukashiba Kamisu Ibaraki 314-0193 Japan
| | - Shujiro Otsuki
- Fine Synthesis Technical Div. 1 DIC Corporation 18 Higashifukashiba Kamisu Ibaraki 314-0193 Japan
| | - Hiroshi Sakata
- Fine Synthesis Technical Div. 1 DIC Corporation 18 Higashifukashiba Kamisu Ibaraki 314-0193 Japan
| | - Makoto Tokunaga
- Department of Chemistry Graduate School of Science Kyushu University 744 Motooka Nishi-ku Fukuoka 819-0395 Japan
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33
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Catalano C, AL Mughram MH, Guo Y, Kellogg GE. 3D interaction homology: Hydropathic interaction environments of serine and cysteine are strikingly different and their roles adapt in membrane proteins. Curr Res Struct Biol 2021; 3:239-256. [PMID: 34693344 PMCID: PMC8517007 DOI: 10.1016/j.crstbi.2021.09.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 08/23/2021] [Accepted: 09/23/2021] [Indexed: 12/12/2022] Open
Abstract
Atomic-resolution protein structural models are prerequisites for many downstream activities like structure-function studies or structure-based drug discovery. Unfortunately, this data is often unavailable for some of the most interesting and therapeutically important proteins. Thus, computational tools for building native-like structural models from less-than-ideal experimental data are needed. To this end, interaction homology exploits the character, strength and loci of the sets of interactions that define a structure. Each residue type has its own limited set of backbone angle-dependent interaction motifs, as defined by their environments. In this work, we characterize the interactions of serine, cysteine and S-bridged cysteine in terms of 3D hydropathic environment maps. As a result, we explore several intriguing questions. Are the environments different between the isosteric serine and cysteine residues? Do some environments promote the formation of cystine S-S bonds? With the increasing availability of structural data for water-insoluble membrane proteins, are there environmental differences for these residues between soluble and membrane proteins? The environments surrounding serine and cysteine residues are dramatically different: serine residues are about 50% solvent exposed, while cysteines are only 10% exposed; the latter are more involved in hydrophobic interactions although there are backbone angle-dependent differences. Our analysis suggests that one driving force for -S-S- bond formation is a rather substantial increase in burial and hydrophobic interactions in cystines. Serine and cysteine become less and more, respectively, solvent-exposed in membrane proteins. 3D hydropathic environment maps are an evolving structure analysis tool showing promise as elements in a new protein structure prediction paradigm.
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Affiliation(s)
- Claudio Catalano
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA, USA
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA, USA
| | - Mohammed H. AL Mughram
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA, USA
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA, USA
| | - Youzhong Guo
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA, USA
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA, USA
| | - Glen E. Kellogg
- Department of Medicinal Chemistry, Virginia Commonwealth University, Richmond, VA, USA
- Institute for Structural Biology, Drug Discovery and Development, Virginia Commonwealth University, Richmond, VA, USA
- Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, VA, USA
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34
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Patel KP, Silsby LM, Li G, Bruner SD. Structure-Based Engineering of Peptide Macrocyclases for the Chemoenzymatic Synthesis of Microviridins. J Org Chem 2021; 86:11212-11219. [PMID: 34263606 DOI: 10.1021/acs.joc.1c00785] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Microviridins are cyanobacterial tricyclic depsipeptides with unique ring architectures and function as serine protease inhibitors. In this study, we explore two strategies to probe the structure and mechanism of macrocyclases involved in microviridin biosynthesis. The results both provide approaches for in vitro chemoenzymatic synthesis and insight into the molecular interactions and function of the biosynthetic enzymes. The first strategy involves generating constitutively activated macrocyclases whereby the leader portion of the substrate peptide is covalently attached to the ATP-grasp ligases to examine leader peptide/enzyme interactions. The second strategy uses a structure-based design to create disulfide cross-linked peptide/enzyme complexes. Together, the strategies provide constitutively active enzymes and tools to study the catalysis of the macrocyclizations on synthetic core peptides.
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Affiliation(s)
- Krishna P Patel
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Lily M Silsby
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Gengnan Li
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
| | - Steven D Bruner
- Department of Chemistry, University of Florida, Gainesville, Florida 32611, United States
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35
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Tang P, Tan Z, Ehamparanathan V, Ren T, Hoffman L, Du C, Song Y, Tao L, Lewandowski A, Ghose S, Li ZJ, Liu S. Optimization and kinetic modeling of interchain disulfide bond reoxidation of monoclonal antibodies in bioprocesses. MAbs 2021; 12:1829336. [PMID: 33031716 PMCID: PMC7577745 DOI: 10.1080/19420862.2020.1829336] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Disulfide bonds play a crucial role in folding and structural stabilization of monoclonal antibodies (mAbs). Disulfide bond reduction may happen during the mAb manufacturing process, resulting in low molecular weight species and possible failure to meet product specifications. Although many mitigation strategies have been developed to prevent disulfide reduction, to the best of our knowledge, reforming disulfide bonds from the reduced antibody in manufacturing has not previously been reported. Here, we explored a novel rescue strategy in the downstream process to repair the broken disulfide bonds via in-vitro redox reactions on Protein A resin. Redox conditions including redox pair (cysteine/cystine ratio), pH, temperature, and reaction time were examined to achieve high antibody purity and a high reaction rate. Under the optimal redox condition, >90% reduced antibody could be reoxidized to form an intact antibody on Protein A resin in an hour. In addition, this study showed high flexibility on the range of the intact mAb fraction in the initial reduced mAb sample (the lower limit of intact mAb faction could be 14% based on the data reported in this study). Furthermore, a kinetic model based on elementary oxidative reactions was constructed to help optimize the reoxidation conditions and to predict product purity. Together, the deep understanding of interchain disulfide bond reoxidation, combined with the predictive kinetic model, provided a good foundation to implement a rescue strategy to generate high-purity antibodies with substantial cost savings in manufacturing processes.
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Affiliation(s)
- Peifeng Tang
- Global Product Development and Supply, Bristol-Myers Squibb Company , Devens, MA, USA.,Department of Paper and Bioprocess Engineering, The State University of New York College of Environmental Science and Forestry , Syracuse, NY, USA
| | - Zhijun Tan
- Global Product Development and Supply, Bristol-Myers Squibb Company , Devens, MA, USA
| | - Vivekh Ehamparanathan
- Global Product Development and Supply, Bristol-Myers Squibb Company , Devens, MA, USA
| | - Tingwei Ren
- Global Product Development and Supply, Bristol-Myers Squibb Company , Devens, MA, USA
| | - Laurel Hoffman
- Global Product Development and Supply, Bristol-Myers Squibb Company , Pennington, NJ, USA
| | - Cheng Du
- Global Product Development and Supply, Bristol-Myers Squibb Company , Devens, MA, USA
| | - Yuanli Song
- Global Product Development and Supply, Bristol-Myers Squibb Company , Devens, MA, USA
| | - Li Tao
- Global Product Development and Supply, Bristol-Myers Squibb Company , Pennington, NJ, USA
| | - Angela Lewandowski
- Global Product Development and Supply, Bristol-Myers Squibb Company , Devens, MA, USA
| | - Sanchayita Ghose
- Global Product Development and Supply, Bristol-Myers Squibb Company , Devens, MA, USA
| | - Zheng Jian Li
- Global Product Development and Supply, Bristol-Myers Squibb Company , Devens, MA, USA
| | - Shijie Liu
- Department of Paper and Bioprocess Engineering, The State University of New York College of Environmental Science and Forestry , Syracuse, NY, USA
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Liu Y, Tao F, Miao S, Yang P. Controlling the Structure and Function of Protein Thin Films through Amyloid-like Aggregation. Acc Chem Res 2021; 54:3016-3027. [PMID: 34282883 DOI: 10.1021/acs.accounts.1c00231] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Protein thin films (PTFs) with tunable structure and function can offer multiple opportunities in various fields such as surface modification, biomaterials, packaging, optics, electronics, separation, energy, and environmental science. Although nature may offer a variety of examples of high-level control of structure and function, e.g., the S layer of cells, synthetic alternatives for large-area protein-based thin films with fine control over both biological function and material structure are a key challenge, especially when aiming for facile, low-cost, green, and large-scale preparation as well as a further extension of function, such as the encapsulation and release of functional building blocks.Therefore, regarding the structure and function of PTFs, we will first briefly comment on the problems associated with PTF fabrication, and then, regarding the basis of our long-term research on protein-based thin films, we will summarize the new strategies that we have developed in recent years to explore and control the structure and function of PTFs for frontier research and practical applications.Inspired by naturally occurring protein amyloid fibrillization, we proposed the amyloid-like protein aggregation strategy to assemble proteins into supramolecular 2D films with extremely large sizes and enduring interfacial adhesion stability. This approach opened a new window for PTF fabrication in which the spontaneous interfacial 2D aggregation of protein oligomers instead of traditional 1D protofibril elongation directs the assembly of proteins. As a result, the film morphology, thickness, porosity, and function can be tailored by simply tuning the interfacial aggregation pathways.We further modified amyloid-like protein aggregation to develop chemoselective reaction-induced protein aggregation (CRIPA). It is well known that chemoselective reactions have been employed for protein modification. However, the application of such reactions in PTF fabrication has been overlooked. We initiated this new strategy by employing thiol-disulfide exchange reactions. These reactions are chemoselective toward proteins containing specific disulfide bonds with high redox potentials, resulting in amyloid-like aggregation and thin film formation. Functional proteins with immunity to such reactions can be encapsulated in thin films and released on demand without a loss of activity, opening a new avenue for the development of functional PTFs and coatings.Finally, the resultant amyloid-inspired PTFs, as a new type of biomimetic materials, provide a good platform for integration with various biomedical functions. Here, the creation of bioactive surfaces on virtually arbitrary substrates by amyloid-like PTFs will be discussed, highlighting antimicrobial, antifouling, molecular separation, and interfacial biomineralization activities that exceed those of their native protein precursors and synthetic alternatives.
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Affiliation(s)
- Yongchun Liu
- Key of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi’an 710119, China
| | - Fei Tao
- Key of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi’an 710119, China
| | - Shuting Miao
- Key of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi’an 710119, China
| | - Peng Yang
- Key of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi’an 710119, China
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37
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Arpa M, Sen B, Eren H, Uzun H, Okcu O, Erel O. Total thiol can contribute to differentiating prostate cancer from BPH: Prostate Thiol Index as a new player. Andrologia 2021; 53:e14190. [PMID: 34270802 DOI: 10.1111/and.14190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 06/25/2021] [Accepted: 07/02/2021] [Indexed: 12/24/2022] Open
Abstract
To assess the distinctiveness of serum native thiol (NT), total thiol (TT) and disulfide (SS) levels in PCa patients, we created a new parameter, prostate thiol index (PTI) [tPSA (TTxPVxAge) -1/2 ]. We determined the performance of the PTI on PCa diagnosis. A total of 107 male patients (PCa:65; BPH:42) who were separated according to their Gleason scores, ISUP grades and EAU risk groups and 20 healthy subjects were included. The performances of the tests were determined. The PCa and BPH groups had lower NT and TT levels and higher SS levels than the control group. PCa patients had higher PTI, tPSA, fPSA, PSAD levels, lower fPSA%, PV and PSA-AV levels than BPH patients. TT, PTI, tPSA, fPSA, fPSA%, PSA-AV, PSAD and PV had significant diagnostic performances. PTI had the highest AUC value and accuracy, PSA-AV had the highest specificity, and fPSA had the lowest sensitivity. The performance of the PTI was the best in distinguishing PCa from BPH. PTI, tPSA and PSAD positively and PSA-AV negatively correlated with ISUP grades and EAU groups. TT can contribute to the discrimination of PCa from BPH and PTI may decrease unnecessary biopsies in clinical practice.
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Affiliation(s)
- Medeni Arpa
- Department of Biochemistry, Faculty of Medicine, Recep Tayyip Erdogan University, Rize, Turkey
| | - Bayram Sen
- Department of Biochemistry, Recep Tayyip Erdogan University Training and Research Hospital, Rize, Turkey
| | - Huseyin Eren
- Department of Urology, Faculty of Medicine, Recep Tayyip Erdogan University, Rize, Turkey
| | - Hakkı Uzun
- Department of Urology, Faculty of Medicine, Recep Tayyip Erdogan University, Rize, Turkey
| | - Oguzhan Okcu
- Department of Pathology, Recep Tayyip Erdogan University Training and Research Hospital, Rize, Turkey
| | - Ozcan Erel
- Department of Medical Biochemistry, Yıldırım Beyazıt University Faculty of Medicine, Ankara, Turkey
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Chen B, Zhou K, Xie Y, Nie W, Li P, Zhou H, Xu B. Glutathione-mediated formation of disulfide bonds modulates the properties of myofibrillar protein gels at different temperatures. Food Chem 2021; 364:130356. [PMID: 34147870 DOI: 10.1016/j.foodchem.2021.130356] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 05/24/2021] [Accepted: 06/11/2021] [Indexed: 10/21/2022]
Abstract
The present study illustrated modulation of protein aggregation by affecting disulfide/sulfhydryl exchange reactions by adding different concentrations of free thiol represented by reduced-glutathione (GSH) for modulating myofibrillar protein (MP) gel properties at 75 °C or 95 °C. Gel strength and rheological results showed the effects of GSH were dependent on the concentrations (5, 10, 20, 40, and 80 g/kg) and heating temperatures. SEM results showed that the addition of GSH improved the gel microstructure at 95 °C. AFM and DLS results indicated that protein aggregation was also inhibited. At 75 °C, the addition of GSH influenced both MP aggregation and gel properties. Low concentrations (5, 10 g/kg) of GSH promoted aggregation, whereas high concentrations (20, 40, and 80 g/kg) of GSH inhibited this. By analyzing the protein structure and cross-linking pattern changes of MP and MP/GSH composites, a pathway involving GSH influencing MP gel properties was determined.
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Affiliation(s)
- Bo Chen
- Engineering Research Center of Bio-process, Ministry of Education, Hefei University of Technology, Hefei 230601, China; School of Food and Biological Engineering, Hefei University of Technology, Hefei 230601, China
| | - Kai Zhou
- Engineering Research Center of Bio-process, Ministry of Education, Hefei University of Technology, Hefei 230601, China; School of Food and Biological Engineering, Hefei University of Technology, Hefei 230601, China; Anhui QiangWang Flavouring Food CO., LTD, China
| | - Yong Xie
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230601, China
| | - Wen Nie
- School of Food and Biological Engineering, Hefei University of Technology, Hefei 230601, China
| | - Peijun Li
- Engineering Research Center of Bio-process, Ministry of Education, Hefei University of Technology, Hefei 230601, China; School of Food and Biological Engineering, Hefei University of Technology, Hefei 230601, China
| | - Hui Zhou
- Engineering Research Center of Bio-process, Ministry of Education, Hefei University of Technology, Hefei 230601, China; School of Food and Biological Engineering, Hefei University of Technology, Hefei 230601, China; The Key Laboratory for Agriculture Products Processing of Anhui Province, Hefei 230601, China
| | - Baocai Xu
- Engineering Research Center of Bio-process, Ministry of Education, Hefei University of Technology, Hefei 230601, China; School of Food and Biological Engineering, Hefei University of Technology, Hefei 230601, China.
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Ren T, Tan Z, Ehamparanathan V, Lewandowski A, Ghose S, Li ZJ. Antibody disulfide bond reduction and recovery during biopharmaceutical process development-A review. Biotechnol Bioeng 2021; 118:2829-2844. [PMID: 33844277 DOI: 10.1002/bit.27790] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 04/07/2021] [Accepted: 04/08/2021] [Indexed: 12/29/2022]
Abstract
Antibody disulfide bond reduction has been a challenging issue in monoclonal antibody manufacturing. It could lead to a decrease of product purity and failure to meet the targeted product profile and/or specifications. More importantly, disulfide bond reduction could also impact drug safety and efficacy. Scientists across the industry have been examining the root causes and developing mitigation strategies to address the challenge. In recent years, with the development of high titer mammalian cell culture processes to meet the rapidly growing demand for antibody biopharmaceuticals, disulfide bond reduction has been observed more frequently. Thus, it is necessary to continue evolving the disulfide reduction mitigation strategies and developing novel approaches to maintain high product quality. Additionally, in recent years as more complex molecules (such as bispecific and trispecific antibodies) emerge, the molecular heterogeneity due to incomplete formation of the interchain disulfide bonds becomes a more imperative challenging issue. Given the disulfide reduction challenges that biotech industry is facing, in this review, we provide a comprehensive scientific summary of the root cause analysis of disulfide reduction during process development of antibody therapeutics, mitigation strategies and its potential remediated recovery based on published papers. First, this paper intends to highlight different aspects of the root cause for disulfide reduction. Secondly, to provide a broader understanding of the disulfide bond reduction in downstream process, this paper discusses disulfide bond reduction impact on product stability, associated analytical methods for disulfide bond reduction detection and characterization, process control strategies as well as their manufacturing implementation. In addition, brief perspectives on the development of future mitigation strategies are also reviewed, including platform alignment, mitigation strategy application for the emerging new modalities such as bispecific and trispecific antibodies as well as using machine learning to identify molecule susceptibility of disulfide bond reduction. The data in this review are originated from the published papers.
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Affiliation(s)
- Tingwei Ren
- Biologics Development, Global Product Development and Supply, Bristol-Myers Squibb, Devens, Massachusetts
| | - Zhijun Tan
- Biologics Development, Global Product Development and Supply, Bristol-Myers Squibb, Devens, Massachusetts
| | - Vivekh Ehamparanathan
- Biologics Development, Global Product Development and Supply, Bristol-Myers Squibb, Devens, Massachusetts
| | - Angela Lewandowski
- Biologics Development, Global Product Development and Supply, Bristol-Myers Squibb, Devens, Massachusetts
| | - Sanchayita Ghose
- Biologics Development, Global Product Development and Supply, Bristol-Myers Squibb, Devens, Massachusetts
| | - Zheng Jian Li
- Biologics Development, Global Product Development and Supply, Bristol-Myers Squibb, Devens, Massachusetts
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Yuan W, Casier R, Duhamel J. Unfolding of Helical Poly( L-Glutamic Acid) in N, N-Dimethylformamide Probed by Pyrene Excimer Fluorescence (PEF). Polymers (Basel) 2021; 13:polym13111690. [PMID: 34067276 PMCID: PMC8196828 DOI: 10.3390/polym13111690] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 05/14/2021] [Accepted: 05/18/2021] [Indexed: 11/16/2022] Open
Abstract
The denaturation undergone by α–helical poly(L-glutamic acid) (PLGA) in N,N-dimethylformamide upon addition of guanidine hydrochloride (GdHCl) was characterized by comparing the fluorescence of a series of PLGA constructs randomly labeled with the dye pyrene (Py-PLGA) to that of a series of Py-PDLGA samples prepared from a racemic mixture of D,L-glutamic acid. The process of pyrene excimer formation (PEF) was taken advantage of to probe changes in the conformation of α–helical Py-PLGA. Fluorescence Blob Model (FBM) analysis of the fluorescence decays of the Py-PLGA and Py-PDLGA constructs yielded the average number (<Nblob>) of glutamic acids located inside a blob, which represented the volume probed by an excited pyrenyl label. <Nblob> remained constant for randomly coiled Py-PDLGA but decreased from ~20 to ~10 glutamic acids for the Py-PLGA samples as GdHCl was added to the solution. The decrease in <Nblob> reflected the decrease in the local density of PLGA as the α–helix unraveled in solution. The changes in <Nblob> with GdHCl concentration was used to determine the change in Gibbs energy required to denature the PLGA α–helix in DMF. The relationship between <Nblob> and the local density of macromolecules can now be applied to characterize the conformation of macromolecules in solution.
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Affiliation(s)
| | | | - Jean Duhamel
- Correspondence: ; Tel.: +1-519-888-4567 (ext. 35916)
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41
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Functionally confirmed compound heterozygous ADAM17 missense loss-of-function variants cause neonatal inflammatory skin and bowel disease 1. Sci Rep 2021; 11:9552. [PMID: 33953303 PMCID: PMC8100128 DOI: 10.1038/s41598-021-89063-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Accepted: 04/13/2021] [Indexed: 12/13/2022] Open
Abstract
A disintegrin and metalloprotease 17 (ADAM17) is the major sheddase that processes more than 80 substrates, including tumour necrosis factor-α (TNFα). The homozygous genetic deficiency of ADAM17 causing a complete loss of ADAM17 expression was reported to be linked to neonatal inflammatory skin and bowel disease 1 (NISBD1). Here we report for the first time, a family with NISBD1 caused by functionally confirmed compound heterozygous missense variants of ADAM17, namely c.1699T>C (p.Cys567Arg) and c.1799G>A (p.Cys600Tyr). Both variants were detected in two siblings with clinical features of NISBD1, such as erythroderma with exudate in whole body, recurrent skin infection and sepsis and prolonged diarrhoea. In a cell-based assay using Adam10/17 double-knockout mouse embryonic fibroblasts (Adam10/17−/− mEFs) exogenously expressing each of these mutants, phorbol 12-myristate 13-acetate-stimulated shedding was strongly reduced compared with wild-type ADAM17. Thus, in vitro functional assays demonstrated that both missense variants cause the loss-of-function of ADAM17, resulting in the development of NISBD1. Our study further expands the spectrum of genetic pathology underlying ADAM17 in NISBD1 and establishes functional assay systems for its missense variants.
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Navone L, Vogl T, Luangthongkam P, Blinco JA, Luna-Flores CH, Chen X, von Hellens J, Mahler S, Speight R. Disulfide bond engineering of AppA phytase for increased thermostability requires co-expression of protein disulfide isomerase in Pichia pastoris. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:80. [PMID: 33789740 PMCID: PMC8010977 DOI: 10.1186/s13068-021-01936-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 03/20/2021] [Indexed: 05/07/2023]
Abstract
BACKGROUND Phytases are widely used commercially as dietary supplements for swine and poultry to increase the digestibility of phytic acid. Enzyme development has focused on increasing thermostability to withstand the high temperatures during industrial steam pelleting. Increasing thermostability often reduces activity at gut temperatures and there remains a demand for improved phyases for a growing market. RESULTS In this work, we present a thermostable variant of the E. coli AppA phytase, ApV1, that contains an extra non-consecutive disulfide bond. Detailed biochemical characterisation of ApV1 showed similar activity to the wild type, with no statistical differences in kcat and KM for phytic acid or in the pH and temperature activity optima. Yet, it retained approximately 50% activity after incubations for 20 min at 65, 75 and 85 °C compared to almost full inactivation of the wild-type enzyme. Production of ApV1 in Pichia pastoris (Komagataella phaffi) was much lower than the wild-type enzyme due to the presence of the extra non-consecutive disulfide bond. Production bottlenecks were explored using bidirectional promoters for co-expression of folding chaperones. Co-expression of protein disulfide bond isomerase (Pdi) increased production of ApV1 by ~ 12-fold compared to expression without this folding catalyst and restored yields to similar levels seen with the wild-type enzyme. CONCLUSIONS Overall, the results show that protein engineering for enhanced enzymatic properties like thermostability may result in folding complexity and decreased production in microbial systems. Hence parallel development of improved production strains is imperative to achieve the desirable levels of recombinant protein for industrial processes.
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Affiliation(s)
- Laura Navone
- Faculty of Science, Queensland University of Technology, Brisbane, QLD, Australia.
- ARC Centre of Excellence in Synthetic Biology, Queensland University of Technology, Brisbane, QLD, Australia.
| | - Thomas Vogl
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel
| | | | - Jo-Anne Blinco
- Faculty of Science, Queensland University of Technology, Brisbane, QLD, Australia
| | - Carlos H Luna-Flores
- Faculty of Science, Queensland University of Technology, Brisbane, QLD, Australia
- Bioproton Pty Ltd, Brisbane, QLD, Australia
| | | | | | - Stephen Mahler
- ARC Training Centre for Biopharmaceutical Innovation, The University of Queensland, Brisbane, QLD, Australia
| | - Robert Speight
- Faculty of Science, Queensland University of Technology, Brisbane, QLD, Australia
- ARC Centre of Excellence in Synthetic Biology, Queensland University of Technology, Brisbane, QLD, Australia
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43
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Li X, Lu T, Obenchain DA, Zhang J, Herbers S, Grabow JU, Feng G. The Characteristics of Disulfide-Centered Hydrogen Bonds. Angew Chem Int Ed Engl 2021; 60:5838-5842. [PMID: 33258264 DOI: 10.1002/anie.202014364] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Indexed: 11/10/2022]
Abstract
The disulfide-centered hydrogen bonds in the three different model systems of diethyl disulfide⋅⋅⋅H2 O/H2 CO/HCONH2 clusters were characterized by high-resolution Fourier transform microwave spectroscopy and quantum chemical computations. The global minimum energy structures for each cluster are experimentally observed and are characterized by one of the three different S-S⋅⋅⋅H-C/N/O disulfide-centered hydrogen bonds and two O⋅⋅⋅H-C hydrogen bonds. Non-covalent interaction and natural bond orbital analyses further confirm the experimental observations. The symmetry-adapted perturbation theory (SAPT) analysis reveals that electrostatic is dominant in diethyl disulfide⋅⋅⋅H2 O/HCONH2 clusters being consistent with normal hydrogen bonds, whilst dispersion takes over in diethyl disulfide⋅⋅⋅H2 CO cluster. Our study gives accurate structural parameters for the disulfide bond involved non-covalent clusters providing important benchmarking data for the theoretical evaluation of more complex systems.
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Affiliation(s)
- Xiaolong Li
- School of Chemistry and Chemical Engineering, Chongqing University, Daxuecheng South Rd. 55, 401331, Chongqing, China.,Institut für Physikalische Chemie and Elektrochemie, Gottfried Wilhelm Leibniz Universität Hannover, Callinstraße 3A, 30167, Hannover, Germany
| | - Tao Lu
- School of Chemistry and Chemical Engineering, Chongqing University, Daxuecheng South Rd. 55, 401331, Chongqing, China
| | - Daniel A Obenchain
- Institut für Physikalische Chemie and Elektrochemie, Gottfried Wilhelm Leibniz Universität Hannover, Callinstraße 3A, 30167, Hannover, Germany
| | - Jiaqi Zhang
- School of Chemistry and Chemical Engineering, Chongqing University, Daxuecheng South Rd. 55, 401331, Chongqing, China
| | - Sven Herbers
- Institut für Physikalische Chemie and Elektrochemie, Gottfried Wilhelm Leibniz Universität Hannover, Callinstraße 3A, 30167, Hannover, Germany
| | - Jens-Uwe Grabow
- Institut für Physikalische Chemie and Elektrochemie, Gottfried Wilhelm Leibniz Universität Hannover, Callinstraße 3A, 30167, Hannover, Germany
| | - Gang Feng
- School of Chemistry and Chemical Engineering, Chongqing University, Daxuecheng South Rd. 55, 401331, Chongqing, China
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44
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Chen J, Dai Y, Gong X, Zhang G. Cation-amino acid interactions: Implications for protein destabilization. Biochem Biophys Res Commun 2021; 548:47-52. [PMID: 33631673 DOI: 10.1016/j.bbrc.2021.02.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2020] [Accepted: 02/04/2021] [Indexed: 11/28/2022]
Abstract
The mechanism for protein stabilization or destabilization has long been an open quest. In the present study, we have studied the interactions between amino acids and guanidinium (Gdm+)/ammonium (NH4+) ions by using low field nuclear magnetic resonance (LF-NMR), where Gdm+ and NH4+ are denaturant and stabilizer for proteins, respectively. It shows that Gdm+ favors to bind to the thiol group or the hydroxyl group on the side chain but weakly interacts with the α-carboxyl group. In contrast, NH4+ prefers to bind to the α-carboxyl group but slightly interacts with the thiol group or the hydroxyl group on the side chain of amino acids. 1HNMR reveals the hydrogen bonding between NH4+ and the α-carboxyl group, which is not involved in the interactions between Gdm+ and cysteine. Our study demonstrates that the strong interactions between the denaturant and the sulfur atom or the disulfide bond promote the direct binding of the denaturant toward proteins, leading to the destabilization.
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Affiliation(s)
- Jiantao Chen
- Faculty of Materials Science and Engineering, South China University of Technology, Guangzhou, 510640, PR China
| | - Yingkang Dai
- Faculty of Materials Science and Engineering, South China University of Technology, Guangzhou, 510640, PR China
| | - Xiangjun Gong
- Faculty of Materials Science and Engineering, South China University of Technology, Guangzhou, 510640, PR China; Guangdong Provincial Key Laboratory of Luminescence from Molecular Aggregates, South China University of Technology, PR China.
| | - Guangzhao Zhang
- Faculty of Materials Science and Engineering, South China University of Technology, Guangzhou, 510640, PR China
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45
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Wang T, Zou C, Wen N, Liu X, Meng Z, Feng S, Zheng Z, Meng Q, Wang C. The effect of structural modification of antimicrobial peptides on their antimicrobial activity, hemolytic activity, and plasma stability. J Pept Sci 2021; 27:e3306. [PMID: 33554385 DOI: 10.1002/psc.3306] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 01/19/2021] [Accepted: 01/26/2021] [Indexed: 12/28/2022]
Abstract
In this article, a series of modifications were made on an antimicrobial peptide F2,5,12 W, including altering the amino acid sequence, introducing cysteine and other typical amino acids, developing peptide dimers via disulfide bonds, and conjugating with mPEG, in order to enhance the antimicrobial activity, plasma stability, and reduce the hemolytic activity of peptides. The results showed that mPEG conjugation could significantly improve the plasma stability and reduce the hemolytic activity of peptides, while the antimicrobial activity decreased meanwhile. However, altering the sequence of the peptide without changing its amino acid composition had little impact on its antimicrobial activity and plasma stability. The introduction of cysteine enhanced the plasma stability of peptides conspicuously, but at the same time, the increased hydrophobicity of peptides increased their hemolysis. The antimicrobial mechanism and cytotoxicity of the peptides with relatively high antimicrobial activity were also studied. In general, this study provided some ideas for the rational design and structure optimization of antimicrobial peptides.
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Affiliation(s)
- Taoran Wang
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing, China
| | - Cunbin Zou
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing, China
| | - Na Wen
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing, China
| | - Xingdong Liu
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing, China
| | - Zhao Meng
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing, China
| | - Siliang Feng
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing, China
| | - Zhibing Zheng
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing, China
| | - Qingbin Meng
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing, China.,Key Laboratory of Natural Resources and Functional Molecules of the Changbai Mountain, Affiliated Ministry of Education, College of Pharmacy, Yanbian University, Yanji, Jilin, China
| | - Chenhong Wang
- State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing, China
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Li X, Lu T, Obenchain DA, Zhang J, Herbers S, Grabow J, Feng G. The Characteristics of Disulfide‐Centered Hydrogen Bonds. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202014364] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Xiaolong Li
- School of Chemistry and Chemical Engineering Chongqing University Daxuecheng South Rd. 55 401331 Chongqing China
- Institut für Physikalische Chemie and Elektrochemie Gottfried Wilhelm Leibniz Universität Hannover Callinstraße 3A 30167 Hannover Germany
| | - Tao Lu
- School of Chemistry and Chemical Engineering Chongqing University Daxuecheng South Rd. 55 401331 Chongqing China
| | - Daniel A. Obenchain
- Institut für Physikalische Chemie and Elektrochemie Gottfried Wilhelm Leibniz Universität Hannover Callinstraße 3A 30167 Hannover Germany
| | - Jiaqi Zhang
- School of Chemistry and Chemical Engineering Chongqing University Daxuecheng South Rd. 55 401331 Chongqing China
| | - Sven Herbers
- Institut für Physikalische Chemie and Elektrochemie Gottfried Wilhelm Leibniz Universität Hannover Callinstraße 3A 30167 Hannover Germany
| | - Jens‐Uwe Grabow
- Institut für Physikalische Chemie and Elektrochemie Gottfried Wilhelm Leibniz Universität Hannover Callinstraße 3A 30167 Hannover Germany
| | - Gang Feng
- School of Chemistry and Chemical Engineering Chongqing University Daxuecheng South Rd. 55 401331 Chongqing China
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Mishra A, Kabir MWU, Hoque MT. diSBPred: A machine learning based approach for disulfide bond prediction. Comput Biol Chem 2021; 91:107436. [PMID: 33550156 DOI: 10.1016/j.compbiolchem.2021.107436] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 12/28/2020] [Accepted: 01/10/2021] [Indexed: 12/25/2022]
Abstract
The protein disulfide bond is a covalent bond that forms during post-translational modification by the oxidation of a pair of cysteines. In protein, the disulfide bond is the most frequent covalent link between amino acids after the peptide bond. It plays a significant role in three-dimensional (3D) ab initio protein structure prediction (aiPSP), stabilizing protein conformation, post-translational modification, and protein folding. In aiPSP, the location of disulfide bonds can strongly reduce the conformational space searching by imposing geometrical constraints. Existing experimental techniques for the determination of disulfide bonds are time-consuming and expensive. Thus, developing sequence-based computational methods for disulfide bond prediction becomes indispensable. This study proposed a stacking-based machine learning approach for disulfide bond prediction (diSBPred). Various useful sequence and structure-based features are extracted for effective training, including conservation profile, residue solvent accessibility, torsion angle flexibility, disorder probability, a sequential distance between cysteines, and more. The prediction of disulfide bonds is carried out in two stages: first, individual cysteines are predicted as either bonding or non-bonding; second, the cysteine-pairs are predicted as either bonding or non-bonding by including the results from cysteine bonding prediction as a feature. The examination of the relevance of the features employed in this study and the features utilized in the existing nearest neighbor algorithm (NNA) method shows that the features used in this study improve about 7.39 % in jackknife validation balanced accuracy. Moreover, for individual cysteine bonding prediction and cysteine-pair bonding prediction, diSBPred provides a 10-fold cross-validation balanced accuracy of 82.29 % and 94.20 %, respectively. Altogether, our predictor achieves an improvement of 43.25 % based on balanced accuracy compared to the existing NNA based approach. Thus, diSBPred can be utilized to annotate the cysteine bonding residues of protein sequences whose structures are unknown as well as improve the accuracy of the aiPSP method, which can further aid in experimental studies of the disulfide bond and structure determination.
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Affiliation(s)
- Avdesh Mishra
- Department of Electrical Engineering and Computer Science, Texas A&M University-Kingsville, Kingsville, TX, USA
| | - Md Wasi Ul Kabir
- Department of Computer Science, University of New Orleans, New Orleans, LA, USA
| | - Md Tamjidul Hoque
- Department of Computer Science, University of New Orleans, New Orleans, LA, USA.
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Reddy KKA, Jayashree M, Govindu PCV, Gowd KH. Ligand-induced transition in conformations of vicinal cysteine disulfides in proteins. Proteins 2020; 89:599-613. [PMID: 33378101 DOI: 10.1002/prot.26039] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2020] [Revised: 11/04/2020] [Accepted: 12/12/2020] [Indexed: 01/02/2023]
Abstract
Vicinal cysteine disulfides are thought to be associated with specific conformations of cysteine disulfides due to the restricted rotation of single bonds in an eight-membered cyclic disulfide loop. Conformations of vicinal cysteine disulfides are analyzed using χ1 , χ2 , χ3 , χ2 ', χ1 ' torsion angles in the crystal structures of proteins retrieved from Protein Data Bank (PDB). 85% of vicinal disulfides have (+, -)LHStaple conformation with trans configuration of the peptide bond and 9% have (-, -)RHStaple conformation with cis configured peptide bond. Conformational analysis of dipeptide Cys-Cys vicinal disulfide by density functional theory (DFT) further supported (+, -)LHStaple, (-, -)RHStaple, and (+, +)RHStaple as the preferred conformations of vicinal disulfides. Interestingly, the rare conformations of vicinal disulfides are observed in the ligand-bound forms of proteins and have higher disulfide strain energy. Conformations of vicinal disulfides in palmitoyl protein thioesterase 1, AChBP, and α7 nicotinic receptor are changed from preferred (+, -)LHStaple to rare (+, -)AntiLHHook/(+, -)AntiRHHook/(+, +)RHStaple conformation due to binding of ligands. Surprisingly, ligands are proximal to the vicinal disulfides in protein complexes that exhibited rare conformations of vicinal disulfides. The report has identified (+, -) LHStaple/(-, -) RHStaple as the hallmark conformations of vicinal disulfides and unraveled ligand-induced transition in conformations of vicinal cysteine disulfides in proteins.
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Affiliation(s)
- K Kasi Amarnath Reddy
- Department of Chemistry, School of Chemical Sciences, Central University of Karnataka, Kalaburagi, India
| | - Muddagoni Jayashree
- Department of Chemistry, School of Chemical Sciences, Central University of Karnataka, Kalaburagi, India
| | - Panchada Ch V Govindu
- Department of Chemistry, School of Chemical Sciences, Central University of Karnataka, Kalaburagi, India
| | - Konkallu Hanumae Gowd
- Department of Chemistry, School of Chemical Sciences, Central University of Karnataka, Kalaburagi, India
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Dopp JL, Reuel NF. Simple, functional, inexpensive cell extract for in vitro prototyping of proteins with disulfide bonds. Biochem Eng J 2020. [DOI: 10.1016/j.bej.2020.107790] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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50
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Renawala HK, Chandrababu KB, Topp EM. Fibrillation of Human Calcitonin and Its Analogs: Effects of Phosphorylation and Disulfide Reduction. Biophys J 2020; 120:86-100. [PMID: 33220304 DOI: 10.1016/j.bpj.2020.11.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 10/24/2020] [Accepted: 11/10/2020] [Indexed: 11/16/2022] Open
Abstract
Some therapeutic peptides self-assemble in solution to form ordered, insoluble, β-sheet-rich amyloid fibrils. This physical instability can result in reduced potency, cause immunogenic side effects, and limit options for formulation. Understanding the mechanisms of fibrillation is key to developing rational mitigation strategies. Here, amide hydrogen-deuterium exchange with mass spectrometric analysis (HDX-MS) coupled with proteolytic digestion was used to identify the early stage interactions leading to fibrillation of human calcitonin (hCT), a peptide hormone important in calcium metabolism. hCT fibrillation kinetics was sigmoidal, with lag, growth, and plateau phases as shown by thioflavin T and turbidity measurements. HDX-MS of fibrillating hCT (pH 7.4; 25°C) suggested early involvement of the N-terminal (1-11) and central (12-19) fragments in interactions during the lag phase, whereas C-terminal fragments (20-32 and 26-32) showed limited involvement during this period. The residue-level information was used to develop phosphorylated hCT analogs that showed modified fibrillation that depended on phosphorylation site. Phosphorylation in the central region resulted in complete inhibition of fibrillation for the phospho-Thr-13 hCT analog, whereas phosphorylation in the N-terminal and C-terminal regions inhibited but did not prevent fibrillation. Reduction of the Cys1-Cys7 disulfide bond resulted in faster fibrillation with involvement of different hCT residues as indicated by pulsed HDX-MS. Together, the results demonstrate that small structural changes have significant effects on hCT fibrillation and that understanding these effects can inform the rational development of fibrillation-resistant hCT analogs.
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Affiliation(s)
- Harshil K Renawala
- Department of Industrial and Physical Pharmacy, College of Pharmacy, Purdue University, West Lafayette, Indiana
| | - Karthik B Chandrababu
- Department of Industrial and Physical Pharmacy, College of Pharmacy, Purdue University, West Lafayette, Indiana
| | - Elizabeth M Topp
- Department of Industrial and Physical Pharmacy, College of Pharmacy, Purdue University, West Lafayette, Indiana; National Institute for Bioprocessing Research and Training, Dublin, Ireland.
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