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Liu C, Yu M, Wang M, Yang S, Fu Y, Zhang L, Zhu C, Zhang H. PCAF-mediated acetylation of METTL3 impairs mRNA translation efficiency in response to oxidative stress. SCIENCE CHINA. LIFE SCIENCES 2024; 67:2157-2168. [PMID: 39096338 DOI: 10.1007/s11427-023-2535-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 01/08/2024] [Accepted: 08/01/2024] [Indexed: 08/05/2024]
Abstract
METTL3 methylates RNA and regulates the fate of mRNA through its methyltransferase activity. METTL3 enhances RNA translation independently of its catalytic activity. However, the underlying mechanism is still elusive. Here, we report that METTL3 is both interacted with and acetylated at lysine 177 by the acetyltransferase PCAF and deacetylated by SIRT3. Neither the methyltransferase activity nor the stability of METTL3 is affected by its acetylation at K177. Importantly, acetylation of METTL3 blocks its interaction with EIF3H, a subunit of the translation initiation factor, thereby reducing mRNA translation efficiency. Interestingly, acetylation of METTL3 responds to oxidative stress. Mechanistically, oxidative stress enhances the interaction of PCAF with METTL3, increases METTL3 acetylation, and suppresses the interaction of METTL3 with EIF3H, thereby decreasing the translation efficiency of ribosomes and inhibiting cell proliferation. Altogether, we suggest a mechanism by which oxidative stress regulates RNA translation efficiency by the modulation of METTL3 acetylation mediated by PCAF.
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Affiliation(s)
- Cheng Liu
- Program for Cancer and Cell Biology, Department of Human Anatomy, Histology and Embryology, School of Basic Medical Sciences, Peking University International Cancer Institute, and State Key Laboratory of Molecular Oncology, Peking University Health Science Center, Beijing, 100191, China
| | - Miao Yu
- Program for Cancer and Cell Biology, Department of Human Anatomy, Histology and Embryology, School of Basic Medical Sciences, Peking University International Cancer Institute, and State Key Laboratory of Molecular Oncology, Peking University Health Science Center, Beijing, 100191, China
| | - Mengyuan Wang
- Program for Cancer and Cell Biology, Department of Human Anatomy, Histology and Embryology, School of Basic Medical Sciences, Peking University International Cancer Institute, and State Key Laboratory of Molecular Oncology, Peking University Health Science Center, Beijing, 100191, China
| | - Siyuan Yang
- Program for Cancer and Cell Biology, Department of Human Anatomy, Histology and Embryology, School of Basic Medical Sciences, Peking University International Cancer Institute, and State Key Laboratory of Molecular Oncology, Peking University Health Science Center, Beijing, 100191, China
| | - Yenan Fu
- Program for Cancer and Cell Biology, Department of Human Anatomy, Histology and Embryology, School of Basic Medical Sciences, Peking University International Cancer Institute, and State Key Laboratory of Molecular Oncology, Peking University Health Science Center, Beijing, 100191, China
| | - Lei Zhang
- Program for Cancer and Cell Biology, Department of Human Anatomy, Histology and Embryology, School of Basic Medical Sciences, Peking University International Cancer Institute, and State Key Laboratory of Molecular Oncology, Peking University Health Science Center, Beijing, 100191, China
| | - Chaoyang Zhu
- Department of General Surgery and Urological Surgery, Huaihe Hospital, Henan University, Kaifeng, 100084, China.
| | - Hongquan Zhang
- Program for Cancer and Cell Biology, Department of Human Anatomy, Histology and Embryology, School of Basic Medical Sciences, Peking University International Cancer Institute, and State Key Laboratory of Molecular Oncology, Peking University Health Science Center, Beijing, 100191, China.
- Department of Human Anatomy, Histology, and Embryology, Shenzhen University School of Medicine, Shenzhen, 518055, China.
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2
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Yu R, Wang Y, Zhu J, Yang G. H 2S-mediated blockage of protein acetylation and oxidative stress attenuates lipid overload-induced cardiac senescence. Arch Physiol Biochem 2024; 130:96-109. [PMID: 34511001 DOI: 10.1080/13813455.2021.1976209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 08/30/2021] [Indexed: 10/20/2022]
Abstract
Hydrogen sulphide (H2S), a newly identified gasotransmitter, can be endogenously produced by cystathionine gamma-lyase (CSE) in the cardiovascular system. This study investigated the role of the CSE/H2S system on lipid overload-induced lipotoxicity and cardiac senescence. Lipid overload in rat cardiomyocyte cells (H9C2) promoted intracellular accumulation of lipid, oxidative stress, mitochondrial dysfunctions, lipid peroxidation and inhibited cell viability, all of which could be reversed by exogenously applied H2S. Further data revealed that H2S protected H9C2 cells from lipid overload-induced senescence by altering the expressions of lipid metabolism-related genes and inhibiting cellular acetyl-CoA and global protein acetylation. Enhancement of protein acetylation abolished the protective role of H2S on cardiac senescence. In vivo, knockout of the CSE gene strengthened cardiac lipid accumulation, protein acetylation, and cellular ageing in high fat diet-fed mice. Taken together, the CSE/H2S system is capable of maintaining lipid homeostasis and cellular senescence in heart cells under lipid overload.
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Affiliation(s)
- Ruihuan Yu
- School of Biological, Chemical & Forensic Sciences, Laurentian University, Sudbury, Canada
- Cardiovascular and Metabolic Research Unit, Laurentian University, Sudbury, Canada
| | - Yuehong Wang
- School of Biological, Chemical & Forensic Sciences, Laurentian University, Sudbury, Canada
- Cardiovascular and Metabolic Research Unit, Laurentian University, Sudbury, Canada
| | - Jiechun Zhu
- School of Biological, Chemical & Forensic Sciences, Laurentian University, Sudbury, Canada
- Cardiovascular and Metabolic Research Unit, Laurentian University, Sudbury, Canada
| | - Guangdong Yang
- School of Biological, Chemical & Forensic Sciences, Laurentian University, Sudbury, Canada
- Cardiovascular and Metabolic Research Unit, Laurentian University, Sudbury, Canada
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3
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Zhao Y, Zhang L, Zhang S, Zheng X, Zheng M, Liu J. Maleic anhydride-modified xylanase and its application to the clarification of fruits juices. Food Chem X 2023; 19:100830. [PMID: 37780259 PMCID: PMC10534184 DOI: 10.1016/j.fochx.2023.100830] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2023] [Revised: 07/19/2023] [Accepted: 08/06/2023] [Indexed: 10/03/2023] Open
Abstract
At presently, the catalytic activity of xylanase is sub-optimal, and the required reaction conditions are harsh. To improve its catalytic activity and stability, xylanase (XY) was chemically modified with maleic anhydride (MA). The enzymatic properties of this maleic anhydride-modified xylanase (MA-XY) were then evaluated and analyzed spectroscopically. The results showed that the thermal stability, use of organic solvents, storage stability and the pH range of 3.0 to 9.0 for MA-XY were better than that for XY alone. The kinetic parameters of the enzyme (Km values) decreased from 40.63 to 30.23 mg/mL. Spectroscopic analysis showed that XY had been modified by the acylation reaction to become a tertiary structure. An assay based on clarifying fruit juices showed that the clarification capacity and reducing sugar content using MA-XY increased compared with those using XY. Overall, this study provides a theoretical basis for improving the application of XY in the food industry.
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Affiliation(s)
- Yang Zhao
- College of Food Science and Engineering, Jilin Agricultural University, Changchun, Jilin 130118, China
- National Engineering Research Center for Wheat and Corn Deep Processing Changchun, Jilin 130118, China
| | - Luyue Zhang
- College of Food Science and Engineering, Jilin Agricultural University, Changchun, Jilin 130118, China
- National Engineering Research Center for Wheat and Corn Deep Processing Changchun, Jilin 130118, China
| | - Shiyu Zhang
- College of Food Science and Engineering, Jilin Agricultural University, Changchun, Jilin 130118, China
- National Engineering Research Center for Wheat and Corn Deep Processing Changchun, Jilin 130118, China
| | - Xing Zheng
- College of Food Science and Engineering, Jilin Agricultural University, Changchun, Jilin 130118, China
- National Engineering Research Center for Wheat and Corn Deep Processing Changchun, Jilin 130118, China
| | - Mingzhu Zheng
- College of Food Science and Engineering, Jilin Agricultural University, Changchun, Jilin 130118, China
- National Engineering Research Center for Wheat and Corn Deep Processing Changchun, Jilin 130118, China
| | - Jingsheng Liu
- College of Food Science and Engineering, Jilin Agricultural University, Changchun, Jilin 130118, China
- National Engineering Research Center for Wheat and Corn Deep Processing Changchun, Jilin 130118, China
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4
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Jeevanandam J, Gonçalves M, Castro R, Gallo J, Bañobre-López M, Rodrigues J. Enhanced alpha-amylase inhibition activity of amine-terminated PAMAM dendrimer stabilized pure copper-doped magnesium oxide nanoparticles. BIOMATERIALS ADVANCES 2023; 153:213535. [PMID: 37385162 DOI: 10.1016/j.bioadv.2023.213535] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 06/16/2023] [Accepted: 06/19/2023] [Indexed: 07/01/2023]
Abstract
The present work aims to prepare copper-doped MgO nanoparticles via a sol-gel approach and study their antidiabetic alpha-amylase inhibition activity with undoped MgO nanoparticles. The ability of G5 amine-terminated polyamidoamine (PAMAM) dendrimer for the controlled release of copper-doped MgO nanoparticles to exhibit alpha-amylase inhibition activity was also evaluated. The synthesis of MgO nanoparticles via sol-gel approach and optimization of calcination temperature and time has led to the formation of nanoparticles with different shapes (spherical, hexagonal, and rod-shaped) and a polydispersity in size ranging from 10 to 100 nm with periclase crystalline phase. The presence of copper ions in the MgO nanoparticles has altered their crystallite size, eventually modifying their size, morphology, and surface charge. The efficiency of dendrimer to stabilize spherical copper-doped MgO nanoparticles (ca. 30 %) is higher than in other samples, which was confirmed by UV-Visible, DLS, FTIR, and TEM analysis. The amylase inhibition assay emphasized that the dendrimer nanoparticles stabilization has led to the prolonged enzyme inhibition ability of MgO and copper-doped MgO nanoparticles for up to 24 h.
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Affiliation(s)
- Jaison Jeevanandam
- CQM-Centro de Química da Madeira, Universidade da Madeira, Campus da Penteada, 9020-105 Funchal, Portugal
| | - Mara Gonçalves
- CQM-Centro de Química da Madeira, Universidade da Madeira, Campus da Penteada, 9020-105 Funchal, Portugal
| | - Rita Castro
- CQM-Centro de Química da Madeira, Universidade da Madeira, Campus da Penteada, 9020-105 Funchal, Portugal
| | - Juan Gallo
- Advanced (magnetic) theranostic nanostructures lab (AmTheNa), Nanomedicine group, International Iberian Nanotechnology Laboratory (INL), Braga 4715-330, Portugal
| | - Manuel Bañobre-López
- Advanced (magnetic) theranostic nanostructures lab (AmTheNa), Nanomedicine group, International Iberian Nanotechnology Laboratory (INL), Braga 4715-330, Portugal
| | - João Rodrigues
- CQM-Centro de Química da Madeira, Universidade da Madeira, Campus da Penteada, 9020-105 Funchal, Portugal; School of Materials Science and Engineering, Center for Nano Energy Materials, Northwestern Polytechnical University, Xi'an 710072, China.
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5
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Tang H, Gao Y, Han J. Application Progress of the Single Domain Antibody in Medicine. Int J Mol Sci 2023; 24:ijms24044176. [PMID: 36835588 PMCID: PMC9967291 DOI: 10.3390/ijms24044176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Revised: 02/07/2023] [Accepted: 02/15/2023] [Indexed: 02/22/2023] Open
Abstract
The camelid-derived single chain antibody (sdAb), also termed VHH or nanobody, is a unique, functional heavy (H)-chain antibody (HCAb). In contrast to conventional antibodies, sdAb is a unique antibody fragment consisting of a heavy-chain variable domain. It lacks light chains and a first constant domain (CH1). With a small molecular weight of only 12~15 kDa, sdAb has a similar antigen-binding affinity to conventional Abs but a higher solubility, which exerts unique advantages for the recognition and binding of functional, versatile, target-specific antigen fragments. In recent decades, with their unique structural and functional features, nanobodies have been considered promising agents and alternatives to traditional monoclonal antibodies. As a new generation of nano-biological tools, natural and synthetic nanobodies have been used in many fields of biomedicine, including biomolecular materials, biological research, medical diagnosis and immune therapies. This article briefly overviews the biomolecular structure, biochemical properties, immune acquisition and phage library construction of nanobodies and comprehensively reviews their applications in medical research. It is expected that this review will provide a reference for the further exploration and unveiling of nanobody properties and function, as well as a bright future for the development of drugs and therapeutic methods based on nanobodies.
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Affiliation(s)
- Huaping Tang
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
| | - Yuan Gao
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
- Gansu Key Laboratory of Animal Generational Physiology and Reproductive Regulation, Lanzhou 730070, China
- Correspondence:
| | - Jiangyuan Han
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China
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6
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Koone JC, Dashnaw CM, Gonzalez M, Shaw BF. A method for quantifying how the activity of an enzyme is affected by the net charge of its nearest crowded neighbor. Protein Sci 2022. [PMCID: PMC9601770 DOI: 10.1002/pro.4384] [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: 11/09/2022]
Abstract
The electrostatic effects of protein crowding have not been systematically explored. Rather, protein crowding is generally studied with co‐solvents or crowders that are electrostatically neutral, with no methods to measure how the net charge (Z) of a crowder affects protein function. For example, can the activity of an enzyme be affected electrostatically by the net charge of its neighbor in crowded milieu? This paper reports a method for crowding proteins of different net charge to an enzyme via semi‐random chemical crosslinking. As a proof of concept, RNase A was crowded (at distances ≤ the Debye length) via crosslinking to different heme proteins with Z = +8.50 ± 0.04, Z = +6.39 ± 0.12, or Z = −10.30 ± 1.32. Crosslinking did not disrupt the structure of proteins, according to amide H/D exchange, and did not inhibit RNase A activity. For RNase A, we found that the electrostatic environment of each crowded neighbor had significant effects on rates of RNA hydrolysis. Crowding with cationic cytochrome c led to increases in activity, while crowding with anionic “supercharged” cytochrome c or myoglobin diminished activity. Surprisingly, electrostatic crowding effects were amplified at high ionic strength (I = 0.201 M) and attenuated at low ionic strength (I = 0.011 M). This salt dependence might be caused by a unique set of electric double layers at the dimer interspace (maximum distance of 8 Å, which cannot accommodate four layers). This new method of crowding via crosslinking can be used to search for electrostatic effects in protein crowding.
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Affiliation(s)
- Jordan C. Koone
- Department of Chemistry and Biochemistry Baylor University Waco Texas USA
| | - Chad M. Dashnaw
- Department of Chemistry and Biochemistry Baylor University Waco Texas USA
| | - Mayte Gonzalez
- Department of Chemistry and Biochemistry Baylor University Waco Texas USA
| | - Bryan F. Shaw
- Department of Chemistry and Biochemistry Baylor University Waco Texas USA
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7
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Protein Modifications: From Chemoselective Probes to Novel Biocatalysts. Catalysts 2021. [DOI: 10.3390/catal11121466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Chemical reactions can be performed to covalently modify specific residues in proteins. When applied to native enzymes, these chemical modifications can greatly expand the available set of building blocks for the development of biocatalysts. Nucleophilic canonical amino acid sidechains are the most readily accessible targets for such endeavors. A rich history of attempts to design enhanced or novel enzymes, from various protein scaffolds, has paved the way for a rapidly developing field with growing scientific, industrial, and biomedical applications. A major challenge is to devise reactions that are compatible with native proteins and can selectively modify specific residues. Cysteine, lysine, N-terminus, and carboxylate residues comprise the most widespread naturally occurring targets for enzyme modifications. In this review, chemical methods for selective modification of enzymes will be discussed, alongside with examples of reported applications. We aim to highlight the potential of such strategies to enhance enzyme function and create novel semisynthetic biocatalysts, as well as provide a perspective in a fast-evolving topic.
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8
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Filipe HAL, Fiuza SM, Henriques CA, Antunes FE. Antiviral and antibacterial activity of hand sanitizer and surface disinfectant formulations. Int J Pharm 2021; 609:121139. [PMID: 34592397 DOI: 10.1016/j.ijpharm.2021.121139] [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: 06/21/2021] [Revised: 09/13/2021] [Accepted: 09/24/2021] [Indexed: 01/04/2023]
Abstract
Emergent diseases caused by viral and bacterial infections have proven to be a current and future challenge. The occurrence of these diseases is usually accompanied by the lack of vaccines and dedicated therapies leaving prevention as the best strategy to adopt. In that context, and apart from confinement and physical distancing measures, an increase in hygiene actions, namely hand and surface cleaning and disinfection can reduce the infection spread originated from our day-to-day routines. However, during crisis situations the high disinfectants demand can very likely lead to having them running out of stock. This impels many individuals and companies to produce their own disinfectants. Here, we explore the main components of a disinfection formulation, both for hand-rub and surface cleaning. Alcohol and non-alcohol based formulations are described, including the possibility to fine tune the properties of the final product in order to increase public acceptance while maintaining product efficacy. The action mechanisms of the main active principles are also described conjugating information from experimental and theoretical data. Overall, the main aspects to develop a disinfectant formulation are addressed, as well as their function, helping formulation developers to better understand the impact of their choices.
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Affiliation(s)
- Hugo A L Filipe
- Coimbra Chemistry Centre, Dept. of Chemistry, University of Coimbra, Rua Larga, 3004-535, Coimbra, Portugal; CPIRN-IPG-Center of Potential and Innovation of Natural Resources, Polytechnic Institute of Guarda, 6300-559 Guarda, Portugal.
| | - Sónia M Fiuza
- Science351, IPN (Edifício C) Rua Pedro Nunes, 3030-199 Coimbra, Portugal
| | - César A Henriques
- EcoXperience, HIESE, Quinta Vale do Espinhal, 3230-343 Penela, Portugal
| | - Filipe E Antunes
- Coimbra Chemistry Centre, Dept. of Chemistry, University of Coimbra, Rua Larga, 3004-535, Coimbra, Portugal
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9
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Giri P, Pagar AD, Patil MD, Yun H. Chemical modification of enzymes to improve biocatalytic performance. Biotechnol Adv 2021; 53:107868. [PMID: 34774927 DOI: 10.1016/j.biotechadv.2021.107868] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 11/02/2021] [Accepted: 11/05/2021] [Indexed: 12/23/2022]
Abstract
Improvement in intrinsic enzymatic features is in many instances a prerequisite for the scalable applicability of many industrially important biocatalysts. To this end, various strategies of chemical modification of enzymes are maturing and now considered as a distinct way to improve biocatalytic properties. Traditional chemical modification methods utilize reactivities of amine, carboxylic, thiol and other side chains originating from canonical amino acids. On the other hand, noncanonical amino acid- mediated 'click' (bioorthogoal) chemistry and dehydroalanine (Dha)-mediated modifications have emerged as an alternate and promising ways to modify enzymes for functional enhancement. This review discusses the applications of various chemical modification tools that have been directed towards the improvement of functional properties and/or stability of diverse array of biocatalysts.
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Affiliation(s)
- Pritam Giri
- Department of Systems Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea
| | - Amol D Pagar
- Department of Systems Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea
| | - Mahesh D Patil
- Department of Nanomaterials and Application Technology, Center of Innovative and Applied Bioprocessing (CIAB), Sector-81, PO Manauli, S.A.S. Nagar, Mohali 140306, Punjab, India
| | - Hyungdon Yun
- Department of Systems Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Republic of Korea.
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10
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Loescher CM, Hobbach AJ, Linke WA. Titin (TTN): from molecule to modifications, mechanics and medical significance. Cardiovasc Res 2021; 118:2903-2918. [PMID: 34662387 PMCID: PMC9648829 DOI: 10.1093/cvr/cvab328] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 10/13/2021] [Indexed: 12/19/2022] Open
Abstract
The giant sarcomere protein titin is a major determinant of cardiomyocyte stiffness and contributor to cardiac strain sensing. Titin-based forces are highly regulated in health and disease, which aids in the regulation of myocardial function, including cardiac filling and output. Due to the enormous size, complexity, and malleability of the titin molecule, titin properties are also vulnerable to dysregulation, as observed in various cardiac disorders. This review provides an overview of how cardiac titin properties can be changed at a molecular level, including the role isoform diversity and post-translational modifications (acetylation, oxidation, and phosphorylation) play in regulating myocardial stiffness and contractility. We then consider how this regulation becomes unbalanced in heart disease, with an emphasis on changes in titin stiffness and protein quality control. In this context, new insights into the key pathomechanisms of human cardiomyopathy due to a truncation in the titin gene (TTN) are discussed. Along the way, we touch on the potential for titin to be therapeutically targeted to treat acquired or inherited cardiac conditions, such as HFpEF or TTN-truncation cardiomyopathy.
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Affiliation(s)
- Christine M Loescher
- Institute of Physiology II, University Hospital Münster, Robert-Koch-Str. 27B, Münster, 48149 Germany
| | - Anastasia J Hobbach
- Department of Cardiology I, Coronary, Peripheral Vascular Disease and Heart Failure, University Hospital Münster, Münster, Germany
| | - Wolfgang A Linke
- Institute of Physiology II, University Hospital Münster, Robert-Koch-Str. 27B, Münster, 48149 Germany
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11
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Baumer KM, Cook CD, Zahler CT, Beard AA, Chen Z, Koone JC, Dashnaw CM, Villacob RA, Solouki T, Wood JL, Borchelt DR, Shaw BF. Supercharging Prions via Amyloid‐Selective Lysine Acetylation. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202103548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Katelyn M. Baumer
- Department of Chemistry and Biochemistry Baylor University Waco TX USA
| | | | - Collin T. Zahler
- Department of Chemistry and Biochemistry Baylor University Waco TX USA
| | | | - Zhijuan Chen
- Department of Neuroscience University of Florida Gainesville FL USA
| | - Jordan C. Koone
- Department of Chemistry and Biochemistry Baylor University Waco TX USA
| | - Chad M. Dashnaw
- Department of Chemistry and Biochemistry Baylor University Waco TX USA
| | - Raul A. Villacob
- Department of Chemistry and Biochemistry Baylor University Waco TX USA
| | - Touradj Solouki
- Department of Chemistry and Biochemistry Baylor University Waco TX USA
| | - John L. Wood
- Department of Chemistry and Biochemistry Baylor University Waco TX USA
| | | | - Bryan F. Shaw
- Department of Chemistry and Biochemistry Baylor University Waco TX USA
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12
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Baumer KM, Cook CD, Zahler CT, Beard AA, Chen Z, Koone JC, Dashnaw CM, Villacob RA, Solouki T, Wood JL, Borchelt DR, Shaw BF. Supercharging Prions via Amyloid-Selective Lysine Acetylation. Angew Chem Int Ed Engl 2021; 60:15069-15079. [PMID: 33876528 DOI: 10.1002/anie.202103548] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Indexed: 11/10/2022]
Abstract
Repulsive electrostatic forces between prion-like proteins are a barrier against aggregation. In neuropharmacology, however, a prion's net charge (Z) is not a targeted parameter. Compounds that selectively boost prion Z remain unreported. Here, we synthesized compounds that amplified the negative charge of misfolded superoxide dismutase-1 (SOD1) by acetylating lysine-NH3 + in amyloid-SOD1, without acetylating native-SOD1. Compounds resembled a "ball and chain" mace: a rigid amyloid-binding "handle" (benzothiazole, stilbene, or styrylpyridine); an aryl ester "ball"; and a triethylene glycol chain connecting ball to handle. At stoichiometric excess, compounds acetylated up to 9 of 11 lysine per misfolded subunit (ΔZfibril =-8100 per 103 subunits). Acetylated amyloid-SOD1 seeded aggregation more slowly than unacetylated amyloid-SOD1 in vitro and organotypic spinal cord (these effects were partially due to compound binding). Compounds exhibited reactivity with other amyloid and non-amyloid proteins (e.g., fibrillar α-synuclein was peracetylated; serum albumin was partially acetylated; carbonic anhydrase was largely unacetylated).
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Affiliation(s)
- Katelyn M Baumer
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, USA
| | - Christopher D Cook
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, USA
| | - Collin T Zahler
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, USA
| | - Alexandra A Beard
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, USA
| | - Zhijuan Chen
- Department of Neuroscience, University of Florida, Gainesville, FL, USA
| | - Jordan C Koone
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, USA
| | - Chad M Dashnaw
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, USA
| | - Raul A Villacob
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, USA
| | - Touradj Solouki
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, USA
| | - John L Wood
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, USA
| | - David R Borchelt
- Department of Neuroscience, University of Florida, Gainesville, FL, USA
| | - Bryan F Shaw
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, USA
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13
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Pagar AD, Patil MD, Flood DT, Yoo TH, Dawson PE, Yun H. Recent Advances in Biocatalysis with Chemical Modification and Expanded Amino Acid Alphabet. Chem Rev 2021; 121:6173-6245. [PMID: 33886302 DOI: 10.1021/acs.chemrev.0c01201] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The two main strategies for enzyme engineering, directed evolution and rational design, have found widespread applications in improving the intrinsic activities of proteins. Although numerous advances have been achieved using these ground-breaking methods, the limited chemical diversity of the biopolymers, restricted to the 20 canonical amino acids, hampers creation of novel enzymes that Nature has never made thus far. To address this, much research has been devoted to expanding the protein sequence space via chemical modifications and/or incorporation of noncanonical amino acids (ncAAs). This review provides a balanced discussion and critical evaluation of the applications, recent advances, and technical breakthroughs in biocatalysis for three approaches: (i) chemical modification of cAAs, (ii) incorporation of ncAAs, and (iii) chemical modification of incorporated ncAAs. Furthermore, the applications of these approaches and the result on the functional properties and mechanistic study of the enzymes are extensively reviewed. We also discuss the design of artificial enzymes and directed evolution strategies for enzymes with ncAAs incorporated. Finally, we discuss the current challenges and future perspectives for biocatalysis using the expanded amino acid alphabet.
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Affiliation(s)
- Amol D Pagar
- Department of Systems Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea
| | - Mahesh D Patil
- Department of Systems Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea
| | - Dillon T Flood
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Tae Hyeon Yoo
- Department of Molecular Science and Technology, Ajou University, 206 World cup-ro, Yeongtong-gu, Suwon 16499, Korea
| | - Philip E Dawson
- Department of Chemistry, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California 92037, United States
| | - Hyungdon Yun
- Department of Systems Biotechnology, Konkuk University, 120 Neungdong-ro, Gwangjin-gu, Seoul 05029, Korea
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14
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Srivastava R, Alam MS. The multi-spectroscopic approach on the interaction between rabbit serum albumin and cationic surfactant: Investigation on the formation and solubilization of the protein aggregation. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 239:118542. [PMID: 32502807 DOI: 10.1016/j.saa.2020.118542] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 05/12/2020] [Accepted: 05/23/2020] [Indexed: 06/11/2023]
Abstract
The protein-surfactant interaction studies have great importance in the range of the application like cosmetics, food, pharmaceutical, detergent industries, and many more. In this study, we have studies protein (rabbit serum albumin, RSA) and a cationic surfactant (cetyltrimethylammonium bromide, CTAB) interaction at different physiological conditions (viz., pH, ionic strength, surfactants concentrations, protein concentration, and many more). They form the protein surfactant complexes. The interchange of electrostatic and hydrophobic force monitors the change in complexes. The three different pHs (below (4.0), above (7.0) and at (4.7) the isoelectric point of RSA) of the medium indicate the three different charges on the protein while surfactant is positive in charge. Critical micelle concentration (CMC) plays a significant role in protein-surfactant interaction. CTAB unfolds the protein at its specific concentration range afterward again; it starts refolded. RSA interacted, with the addition of the CTAB is characterized by many spectroscopic methods like UV-visible, fluorescence, fluorescence time-resolved, circular dichroism, and topographical changes monitored by the AFM. In fluorescence spectra, the blue shift shows the unfolding of RSA. The molecular docking indicates the binding energy of 5.8 kcal mol-1. The changes below and above the CMC is significant.
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Affiliation(s)
- Rachana Srivastava
- Council of Scientific and Industrial Research (CSIR) - Central Leather Research Institute (CLRI), Polymer Science & Technology Laboratory, Chennai 600020, India
| | - Md Sayem Alam
- Council of Scientific and Industrial Research (CSIR) - Central Leather Research Institute (CLRI), Polymer Science & Technology Laboratory, Chennai 600020, India; Chemical Science, Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh 201002, India.
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15
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Nwagu TN, Aoyagi H, Okolo B, Moneke A, Yoshida S. Citraconylation and maleylation on the catalytic and thermodynamic properties of raw starch saccharifying amylase from Aspergillus carbonarius. Heliyon 2020; 6:e04351. [PMID: 32671262 PMCID: PMC7339066 DOI: 10.1016/j.heliyon.2020.e04351] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 03/28/2020] [Accepted: 06/25/2020] [Indexed: 01/11/2023] Open
Abstract
Amylase capable of raw starch digestion presents a cheap and easier means of reducing sugar generation from various starch sources. Unfortunately, its potential for use in numerous industrial processes is hindered by poor stability. In this work, chemical modification by acylation using citraconic anhydride (CA) and maleic anhydride (MA) was used to stabilize the raw starch saccharifying amylase from A. carbonarius. The effect of the anhydrides on the pH and thermal stability of the free amylase was investigated. Enzyme kinetics and thermodynamic studies of the free and modified amylase were also carried out. Blue shifts in fluorescent spectra were observed after modification with both anhydrides. Citraconylation led to increased affinity of the enzyme for raw potato starch, unlike maleylation. The activation energy (kJ mol−1) for enzyme inactivation was increased by 94.8% after modification with CA while only 17.9% increase was noted after modification with MA. Acylation led to an increase in Gibb's free energy and enthalpy while a reduction in entropy was observed. At 80 °C the half-life (h) was 5.92, 11.18 and 14.74 for free, MA and CA enzyme samples, respectively. These findings have potential value in all industries interested in starch conversion to sugars.
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Affiliation(s)
- Tochukwu Nwamaka Nwagu
- Department of Microbiology, Faculty of Biological Sciences, University of Nigeria Nsukka, Nigeria
| | - Hideki Aoyagi
- Life Sciences and Bioengineering, Graduate School of Life and Environmental Sciences, University of Tsukuba, Japan
| | - Bartholomew Okolo
- Department of Microbiology, Faculty of Biological Sciences, University of Nigeria Nsukka, Nigeria
| | - Anene Moneke
- Department of Microbiology, Faculty of Biological Sciences, University of Nigeria Nsukka, Nigeria
| | - Shigeki Yoshida
- Life Sciences and Bioengineering, Graduate School of Life and Environmental Sciences, University of Tsukuba, Japan
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16
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Srivastava R, Alam MS. Spectroscopic studies of the aggregation behavior of Human Serum Albumin and cetyltrimethylammonium bromide. Int J Biol Macromol 2020; 158:394-400. [PMID: 32380109 DOI: 10.1016/j.ijbiomac.2020.04.254] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 04/28/2020] [Accepted: 04/28/2020] [Indexed: 11/22/2022]
Abstract
To check the role of micelle in the interaction studies of human serum albumin (HSA) and cetyltrimethylammonium bromide (CTAB), many spectroscopic techniques, like UV-visible, fluorescence, circular dichroism, fluorescence lifetime measurement, and atomic force microscopy (AFM), are employed. The binding affinity of all compound groups depended on the hydrocarbon chain, indicating the predominant role of hydrophobic forces, electrostatic forces and supported by polar interactions on protein surfaces. The protein has a different effect on the polarity of a microenvironment in fluorescence spectra above and below the critical micelle concentration (CMC) of the suractant. The far-UV-CD spectra show unfolding below the CMC and refolding above the CMC. The binding of the surfactant induces changes in the microenvironment at different pHs around the residues of the aromatic amino acid and the disulfide bond of protein. The AFM images show significant changes in the protein's structure. AFM images show dense aggregation below the CMC and above the CMC, some net-like structure formed in the HSA-CTAB complex. To test the experimental results, we used Auto dock Vina to conduct molecular docking. Above and below the CMC, structural changes can be seen.
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Affiliation(s)
- Rachana Srivastava
- Council of Scientific and Industrial Research (CSIR) - Central Leather Research Institute (CLRI), Polymer Science &Technology Laboratory, Chennai 600020, India
| | - Md Sayem Alam
- Council of Scientific and Industrial Research (CSIR) - Central Leather Research Institute (CLRI), Polymer Science &Technology Laboratory, Chennai 600020, India; Chemical Science, Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh- 201 002, India.
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17
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Ma C, Malessa A, Boersma AJ, Liu K, Herrmann A. Supercharged Proteins and Polypeptides. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2020; 32:e1905309. [PMID: 31943419 DOI: 10.1002/adma.201905309] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Revised: 10/10/2019] [Indexed: 06/10/2023]
Abstract
Electrostatic interactions play a vital role in nature. Biomacromolecules such as proteins are orchestrated by electrostatics, among other intermolecular forces, to assemble and organize biochemistry. Natural proteins with a high net charge exist in a folded state or are unstructured and can be an inspiration for scientists to artificially supercharge other protein entities. Recent findings show that supercharging proteins allows for control of their properties such as temperature resistance and catalytic activity. One elegant method to transfer the favorable properties of supercharged proteins to other proteins is the fabrication of fusions. Genetically engineered, supercharged unstructured polypeptides (SUPs) are just one promising fusion tool. SUPs can also be complexed with artificial entities to yield thermotropic and lyotropic liquid crystals and liquids. These architectures represent novel bulk materials that are sensitive to external stimuli. Interestingly, SUPs undergo fluid-fluid phase separation to form coacervates. These coacervates can even be directly generated in living cells or can be combined with dissipative fiber assemblies that induce life-like features. Supercharged proteins and SUPs are developed into exciting classes of materials. Their synthesis, structures, and properties are summarized. Moreover, potential applications are highlighted and challenges are discussed.
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Affiliation(s)
- Chao Ma
- Zernike Institute for Advanced Materials, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Anke Malessa
- Zernike Institute for Advanced Materials, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
| | - Arnold J Boersma
- DWI - Leibniz Institute for Interactive Materials, Forckenbeckstr. 50, 52056, Aachen, Germany
| | - Kai Liu
- State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, 130022, Changchun, China
| | - Andreas Herrmann
- Zernike Institute for Advanced Materials, Nijenborgh 4, 9747 AG, Groningen, The Netherlands
- DWI - Leibniz Institute for Interactive Materials, Forckenbeckstr. 50, 52056, Aachen, Germany
- Institute of Technical and Macromolecular Chemistry, RWTH Aachen University, Worringerweg 2, 52074, Aachen, Germany
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18
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Mercado-Uribe H, Andrade-Medina M, Espinoza-Rodríguez JH, Carrillo-Tripp M, Scheckhuber CQ. Analyzing structural alterations of mitochondrial intermembrane space superoxide scavengers cytochrome-c and SOD1 after methylglyoxal treatment. PLoS One 2020; 15:e0232408. [PMID: 32353034 PMCID: PMC7192434 DOI: 10.1371/journal.pone.0232408] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2020] [Accepted: 04/14/2020] [Indexed: 12/14/2022] Open
Abstract
Mitochondria are quantitatively the most important sources of reactive oxygen species (ROS) which are formed as by-products during cellular respiration. ROS generation occurs when single electrons are transferred to molecular oxygen. This leads to a number of different ROS types, among them superoxide. Although most studies focus on ROS generation in the mitochondrial matrix, the intermembrane space (IMS) is also important in this regard. The main scavengers for the detoxification of superoxide in the IMS are Cu, Zn superoxide dismutase (SOD1) and cytochrome-c. Similar to ROS, certain reactive carbonyl species are known for their high reactivity. The consequences are deleterious modifications to essential components compromising cellular functions and contributing to the etiology of severe pathological conditions like cancer, diabetes and neurodegeneration. In this study, we investigated the susceptibility of SOD1 and cytochrome-c to in vitro glycation by the dicarbonyl methylglyoxal (MGO) and the resulting effects on their structure. We utilized experimental techniques like immunodetection of the MGO-mediated modification 5-hydro-5-methylimidazolone, differential scanning calorimetry, fluorescence emission and circular dichroism measurements. We found that glycation of cytochrome-c leads to monomer aggregation, an altered secondary structure (increase in alpha helical content) and slightly more compact folding. In addition to structural changes, glycated cytochrome-c displays an altered thermal unfolding behavior. Subjecting SOD1 to MGO does not influence its secondary structure. However, similar to cytochrome-c, subunit aggregation is observed under denaturating conditions. Furthermore, the appearance of a second peak in the calorimetry diagram indirectly suggests de-metallation of SOD1 when high MGO levels are used. In conclusion, our data demonstrate that MGO has the potential to alter several structural parameters in important proteins of energy metabolism (cytochrome-c) and antioxidant defense (cytochrome-c, SOD1).
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Affiliation(s)
- Hilda Mercado-Uribe
- Centro de Investigación y de Estudios Avanzados, del Instituto Politécnico Nacional Unidad Monterrey, Parque PIIT, Apodaca, Nuevo León, México
| | - Mariana Andrade-Medina
- Centro de Investigación y de Estudios Avanzados, del Instituto Politécnico Nacional Unidad Monterrey, Parque PIIT, Apodaca, Nuevo León, México
| | | | - Mauricio Carrillo-Tripp
- Centro de Investigación y de Estudios Avanzados, del Instituto Politécnico Nacional Unidad Monterrey, Parque PIIT, Apodaca, Nuevo León, México
| | - Christian Quintus Scheckhuber
- Centro de Investigación y de Estudios Avanzados, del Instituto Politécnico Nacional Unidad Monterrey, Parque PIIT, Apodaca, Nuevo León, México
- * E-mail:
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19
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Srivastava R, Alam MS. Influence of micelles on protein's denaturation. Int J Biol Macromol 2020; 145:252-261. [PMID: 31874269 DOI: 10.1016/j.ijbiomac.2019.12.154] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Revised: 10/05/2019] [Accepted: 12/17/2019] [Indexed: 11/15/2022]
Abstract
To evaluate the role of micelles for protein-surfactant interaction, we have studied the binding modes of serum albumin proteins (human (HSA) and rabbit (RSA)) with anionic-surfactant, sodium dodecyl sulfate (SDS) by using UV-visible, fluorescence, circular dichroism, fluorescence lifetime, atomic force microscopy (AFM) techniques. The study performed with three different pHs (below (4.0), at (4.7), and above (7.0) isoelectric point). Hydrocarbon chain of the surfactant, dominant role of hydrophobic forces and electrostatic interactions helped in polar interaction on protein on binding surfaces. The change above and below the critical micelle concentration (CMC) in fluorescence spectra was due to polarity of the microenvironment. The CD spectra different binding aspects as below CMC and above CMC, explain about folding and unfolding in secondary structure. Surfactant's binding induces fluctuations in the microenvironment of aromatic amino acid's residues of both proteins at different pHs. AFM images clarify the structural changes in both proteins (HSA & RSA). AFM images also indicate some different interesting conformational and structural changes in both proteins below/above the CMC of the surfactant. The molecular docking studies indicate the binding energy -4.8 kcal mol-1 and -4.7 kcal mol-1 for HSA-SDS and RSA-SDS, respectively. Structural changes can be seen above and below the CMC.
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Affiliation(s)
- Rachana Srivastava
- Council of Scientific and Industrial Research (CSIR) - Central Leather Research Institute (CLRI), Polymer Science &Technology Laboratory, Chennai 600020, India
| | - Md Sayem Alam
- Council of Scientific and Industrial Research (CSIR) - Central Leather Research Institute (CLRI), Polymer Science &Technology Laboratory, Chennai 600020, India; Chemical Science, Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201 002, India.
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20
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Giri A, Pant D. Carbonic anhydrase modification for carbon management. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2020; 27:1294-1318. [PMID: 31797268 DOI: 10.1007/s11356-019-06667-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Accepted: 10/01/2019] [Indexed: 06/10/2023]
Abstract
Carbonic anhydrase modification (chemical and biological) is an attractive strategy for its diverse application to accelerate the absorption of CO2 from a flue gas with improved activity and stability. This article reports various possibilities of CA modification using metal-ligand homologous chemistry, cross-linking agents, and residue- and group-specific and genetic modifications, and assesses their role in carbon management. Chemically modified carbonic anhydrase is able to improve the absorption of carbon dioxide from a gas stream into mediation compounds with enhanced sequestration and mineral formation. Genetically modified CA polypeptide can also increase carbon dioxide conversion. Chemical modification of CA can be categorized in terms of (i) residue-specific modification (involves protein-ligand interaction in terms of substitution/addition) and group-specific modifications (based on the functional groups of the target CA). For every sustainable change, there should be no/limited toxic or immunological response. In this review, several CA modification pathways and biocompatibility rules are proposed as a theoretical support for emerging research in this area.
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Affiliation(s)
- Anand Giri
- Department of Environmental Sciences, Central University of Himachal Pradesh, Kangra, India
| | - Deepak Pant
- School of Chemical Sciences, Central University of Haryana, Mahendragarh, Haryana, 123029, India.
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21
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Eldeeb MA, Fahlman RP, Ragheb MA, Esmaili M. Does N‐Terminal Protein Acetylation Lead to Protein Degradation? Bioessays 2019; 41:e1800167. [DOI: 10.1002/bies.201800167] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Revised: 08/12/2019] [Indexed: 12/29/2022]
Affiliation(s)
- Mohamed A. Eldeeb
- Department of Chemistry (Biochemistry Division)Faculty of ScienceCairo University Giza 12613 Egypt
- Department of Neurology and NeurosurgeryMontreal Neurological InstituteMcGill University Montreal Quebec H3A 2B4 Canada
| | - Richard P. Fahlman
- Department of BiochemistryUniversity of Alberta Edmonton Alberta T6G 2R3 Canada
| | - Mohamed A. Ragheb
- Department of Chemistry (Biochemistry Division)Faculty of ScienceCairo University Giza 12613 Egypt
| | - Mansoore Esmaili
- Department of BiochemistryUniversity of Alberta Edmonton Alberta T6G 2R3 Canada
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22
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Zahler CT, Shaw BF. What Are We Missing by Not Measuring the Net Charge of Proteins? Chemistry 2019; 25:7581-7590. [PMID: 30779227 DOI: 10.1002/chem.201900178] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2019] [Indexed: 12/21/2022]
Abstract
The net electrostatic charge (Z) of a folded protein in solution represents a bird's eye view of its surface potentials-including contributions from tightly bound metal, solvent, buffer, and cosolvent ions-and remains one of its most enigmatic properties. Few tools are available to the average biochemist to rapidly and accurately measure Z at pH≠pI. Tools that have been developed more recently seem to go unnoticed. Most scientists are content with this void and estimate the net charge of a protein from its amino acid sequence, using textbook values of pKa . Thus, Z remains unmeasured for nearly all folded proteins at pH≠pI. When marveling at all that has been learned from accurately measuring the other fundamental property of a protein-its mass-one wonders: what are we missing by not measuring the net charge of folded, solvated proteins? A few big questions immediately emerge in bioinorganic chemistry. When a single electron is transferred to a metalloprotein, does the net charge of the protein change by approximately one elementary unit of charge or does charge regulation dominate, that is, do the pKa values of most ionizable residues (or just a few residues) adjust in response to (or in concert with) electron transfer? Would the free energy of charge regulation (ΔΔGz ) account for most of the outer sphere reorganization energy associated with electron transfer? Or would ΔΔGz contribute more to the redox potential? And what about metal binding itself? When an apo-metalloprotein, bearing minimal net negative charge (e.g., Z=-2.0) binds one or more metal cations, is the net charge abolished or inverted to positive? Or do metalloproteins regulate net charge when coordinating metal ions? The author's group has recently dusted off a relatively obscure tool-the "protein charge ladder"-and used it to begin to answer these basic questions.
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Affiliation(s)
- Collin T Zahler
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, 76706, USA
| | - Bryan F Shaw
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX, 76706, USA
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23
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Ramberg KO, Antonik PM, Cheung DL, Crowley PB. Measuring the Impact of PEGylation on a Protein-Polysaccharide Interaction. Bioconjug Chem 2019; 30:1162-1168. [PMID: 30869874 DOI: 10.1021/acs.bioconjchem.9b00099] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
PEGylation is the most widely used half-life extension strategy for protein therapeutics. While it imparts a range of attractive attributes PEGylation can impede protein binding and reduce efficacy. A model system to probe the effects of PEGylation on protein binding has practical applications. Here, we present a system based on complex formation between a hexavalent lectin (RSL) and the globular polysaccharide Ficoll PM70 (a type of glycocluster). Mutants of the lectin were used to generate conjugates with 3, 6, or 12 PEG (1 kDa) chains. Using NMR spectroscopy we monitored how the degree of PEGylation impacted the lectin-Ficoll interaction. The binding propensity was observed to decrease with increasing polymer density. Apparently, the extended PEG chains sterically impede the lectin-Ficoll binding. This deduction was supported by molecular dynamics simulations of the protein-polymer conjugates. The implications for protein-surface interactions are discussed.
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Affiliation(s)
- Kiefer O Ramberg
- School of Chemistry , National University of Ireland Galway , University Road , Galway , H91 TK33 , Ireland
| | - Paweł M Antonik
- School of Chemistry , National University of Ireland Galway , University Road , Galway , H91 TK33 , Ireland
| | - David L Cheung
- School of Chemistry , National University of Ireland Galway , University Road , Galway , H91 TK33 , Ireland
| | - Peter B Crowley
- School of Chemistry , National University of Ireland Galway , University Road , Galway , H91 TK33 , Ireland
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24
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Zhou R, Yang Y, Park SY, Seo YW, Jung SC, Kim KK, Kim K, Kim H. p300/CBP-associated factor promotes autophagic degradation of δ-catenin through acetylation and decreases prostate cancer tumorigenicity. Sci Rep 2019; 9:3351. [PMID: 30833716 PMCID: PMC6399259 DOI: 10.1038/s41598-019-40238-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Accepted: 02/12/2019] [Indexed: 01/21/2023] Open
Abstract
δ-Catenin shares common binding partners with β-catenin. As acetylation and deacetylation regulate β-catenin stability, we searched for histone acetyltransferases (HATs) or histone deacetylases (HDACs) affecting δ-catenin acetylation status and protein levels. We showed that p300/CBP-associated factor (PCAF) directly bound to and acetylated δ-catenin, whereas several class I and class II HDACs reversed this effect. Unlike β-catenin, δ-catenin was downregulated by PCAF-mediated acetylation and upregulated by HDAC-mediated deacetylation. The HDAC inhibitor trichostatin A attenuated HDAC1-mediated δ-catenin upregulation, whereas HAT or autophagy inhibitors, but not proteasome inhibitors, abolished PCAF-mediated δ-catenin downregulation. The results suggested that PCAF-mediated δ-catenin acetylation promotes its autophagic degradation in an Atg5/LC3-dependent manner. Deletions or point mutations identified several lysine residues in different δ-catenin domains involved in PCAF-mediated δ-catenin downregulation. PCAF overexpression in prostate cancer cells markedly reduced δ-catenin levels and suppressed cell growth and motility. PCAF-mediated δ-catenin downregulation inhibited E-cadherin processing and decreased the nuclear distribution of β-catenin, resulting in the suppression of β-catenin/LEF-1-mediated downstream effectors. These data demonstrate that PCAF downregulates δ-catenin by promoting its autophagic degradation and suppresses δ-catenin-mediated oncogenic signals.
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Affiliation(s)
- Rui Zhou
- College of Pharmacy and Research Institute of Life and Pharmaceutical Sciences, Sunchon National University, Sunchon, Republic of Korea
| | - Yi Yang
- College of Pharmacy and Research Institute of Life and Pharmaceutical Sciences, Sunchon National University, Sunchon, Republic of Korea
| | - So-Yeon Park
- College of Pharmacy and Research Institute of Life and Pharmaceutical Sciences, Sunchon National University, Sunchon, Republic of Korea
| | - Young-Woo Seo
- Korea Basic Science Institute, Gwangju Center, Gwangju, Republic of Korea
| | - Sang-Chul Jung
- Department of Environmental Engineering, Sunchon National University, Sunchon, Republic of Korea
| | - Kyung Keun Kim
- Department of Pharmacology, Chonnam National University Medical School, Gwangju, Republic of Korea
| | - Kwonseop Kim
- College of Pharmacy and Research Institute for Drug Development, Chonnam National University, Gwangju, Republic of Korea
| | - Hangun Kim
- College of Pharmacy and Research Institute of Life and Pharmaceutical Sciences, Sunchon National University, Sunchon, Republic of Korea.
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25
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Srivastava R, Alam MS. Role of (single/double chain surfactant) micelles on the protein aggregation. Int J Biol Macromol 2019; 122:72-81. [DOI: 10.1016/j.ijbiomac.2018.10.145] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 10/16/2018] [Accepted: 10/18/2018] [Indexed: 11/16/2022]
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26
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Campbell EC, Grant J, Wang Y, Sandhu M, Williams RJ, Nisbet DR, Perriman AW, Lupton DW, Jackson CJ. Hydrogel‐Immobilized Supercharged Proteins. ACTA ACUST UNITED AC 2018. [DOI: 10.1002/adbi.201700240] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Eleanor C. Campbell
- Research School of Chemistry Australian National University Canberra ACT 2601 Australia
| | - Jacob Grant
- School of Chemistry Monash University Clayton VIC 3800 Australia
| | - Yi Wang
- Laboratory of Advanced Biomaterials Research School of Engineering The Australian National University Canberra ACT 2601 Australia
| | - Mahakaran Sandhu
- Research School of Chemistry Australian National University Canberra ACT 2601 Australia
| | | | - David R. Nisbet
- Laboratory of Advanced Biomaterials Research School of Engineering The Australian National University Canberra ACT 2601 Australia
| | - Adam W. Perriman
- School of Cellular and Molecular Medicine University of Bristol Bristol BS8 1TD UK
| | - David W. Lupton
- School of Chemistry Monash University Clayton VIC 3800 Australia
| | - Colin J. Jackson
- Research School of Chemistry Australian National University Canberra ACT 2601 Australia
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27
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Srivastava R, Alam MS. Effect of pH and surfactant on the protein: A perspective from theory and experiments. Int J Biol Macromol 2018; 107:1519-1527. [DOI: 10.1016/j.ijbiomac.2017.10.019] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 10/04/2017] [Accepted: 10/04/2017] [Indexed: 11/16/2022]
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28
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Ayyadevara S, Balasubramaniam M, Kakraba S, Alla R, Mehta JL, Shmookler Reis RJ. Aspirin-Mediated Acetylation Protects Against Multiple Neurodegenerative Pathologies by Impeding Protein Aggregation. Antioxid Redox Signal 2017; 27:1383-1396. [PMID: 28537433 PMCID: PMC5661865 DOI: 10.1089/ars.2016.6978] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
AIMS Many progressive neurological disorders, including Alzheimer's disease (AD), Huntington's disease, and Parkinson's disease (PD), are characterized by accumulation of insoluble protein aggregates. In prospective trials, the cyclooxygenase inhibitor aspirin (acetylsalicylic acid) reduced the risk of AD and PD, as well as cardiovascular events and many late-onset cancers. Considering the role played by protein hyperphosphorylation in aggregation and neurodegenerative diseases, and aspirin's known ability to donate acetyl groups, we asked whether aspirin might reduce both phosphorylation and aggregation by acetylating protein targets. RESULTS Aspirin was substantially more effective than salicylate in reducing or delaying aggregation in human neuroblastoma cells grown in vitro, and in Caenorhabditis elegans models of human neurodegenerative diseases in vivo. Aspirin acetylates many proteins, while reducing phosphorylation, suggesting that acetylation may oppose phosphorylation. Surprisingly, acetylated proteins were largely excluded from compact aggregates. Molecular-dynamic simulations indicate that acetylation of amyloid peptide energetically disfavors its association into dimers and octamers, and oligomers that do form are less compact and stable than those comprising unacetylated peptides. INNOVATION Hyperphosphorylation predisposes certain proteins to aggregate (e.g., tau, α-synuclein, and transactive response DNA-binding protein 43 [TDP-43]), and it is a critical pathogenic marker in both cardiovascular and neurodegenerative diseases. We present novel evidence that acetylated proteins are underrepresented in protein aggregates, and that aggregation varies inversely with acetylation propensity after diverse genetic and pharmacologic interventions. CONCLUSIONS These results are consistent with the hypothesis that aspirin inhibits protein aggregation and the ensuing toxicity of aggregates through its acetyl-donating activity. This mechanism may contribute to the neuro-protective, cardio-protective, and life-prolonging effects of aspirin. Antioxid. Redox Signal. 27, 1383-1396.
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Affiliation(s)
- Srinivas Ayyadevara
- 1 Central Arkansas Veterans Healthcare System, Research & Development Service , Little Rock, Arkansas.,2 Department of Geriatrics, Reynolds Institute on Aging, University of Arkansas for Medical Sciences , Little Rock, Arkansas
| | - Meenakshisundaram Balasubramaniam
- 1 Central Arkansas Veterans Healthcare System, Research & Development Service , Little Rock, Arkansas.,2 Department of Geriatrics, Reynolds Institute on Aging, University of Arkansas for Medical Sciences , Little Rock, Arkansas
| | - Samuel Kakraba
- 3 Bioinformatics Program, University of Arkansas for Medical Sciences, and University of Arkansas at Little Rock , Little Rock, Arkansas
| | - Ramani Alla
- 1 Central Arkansas Veterans Healthcare System, Research & Development Service , Little Rock, Arkansas.,2 Department of Geriatrics, Reynolds Institute on Aging, University of Arkansas for Medical Sciences , Little Rock, Arkansas
| | - Jawahar L Mehta
- 1 Central Arkansas Veterans Healthcare System, Research & Development Service , Little Rock, Arkansas.,4 Divison of Cardiology, Department of Medicine, University of Arkansas for Medical Sciences , Little Rock, Arkansas
| | - Robert J Shmookler Reis
- 1 Central Arkansas Veterans Healthcare System, Research & Development Service , Little Rock, Arkansas.,2 Department of Geriatrics, Reynolds Institute on Aging, University of Arkansas for Medical Sciences , Little Rock, Arkansas.,3 Bioinformatics Program, University of Arkansas for Medical Sciences, and University of Arkansas at Little Rock , Little Rock, Arkansas
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Birhanu AG, Yimer SA, Holm-Hansen C, Norheim G, Aseffa A, Abebe M, Tønjum T. N ε- and O-Acetylation in Mycobacterium tuberculosis Lineage 7 and Lineage 4 Strains: Proteins Involved in Bioenergetics, Virulence, and Antimicrobial Resistance Are Acetylated. J Proteome Res 2017; 16:4045-4059. [PMID: 28920697 DOI: 10.1021/acs.jproteome.7b00429] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Increasing evidence demonstrates that lysine acetylation is involved in Mycobacterium tuberculosis (Mtb) virulence and pathogenesis. However, previous investigations in Mtb have only monitored acetylation at lysine residues using selected reference strains. We analyzed the global Nε- and O-acetylation of three Mtb isolates: two lineage 7 clinical isolates and the lineage 4 H37Rv reference strain. Quantitative acetylome analysis resulted in identification of 2490 class-I acetylation sites, 2349 O-acetylation and 141 Nε-acetylation sites, derived from 953 unique proteins. Mtb O-acetylation was thereby significantly more abundant than Nε-acetylation. The acetylated proteins were found to be involved in central metabolism, translation, stress responses, and antimicrobial drug resistance. Notably, 261 acetylation sites on 165 proteins were differentially regulated between lineage 7 and lineage 4 strains. A total of 257 acetylation sites on 161 proteins were hypoacetylated in lineage 7 strains. These proteins are involved in Mtb growth, virulence, bioenergetics, host-pathogen interactions, and stress responses. This study provides the first global analysis of O-acetylated proteins in Mtb. This quantitative acetylome data expand the current understanding regarding the nature and diversity of acetylated proteins in Mtb and open a new avenue of research for exploring the role of protein acetylation in Mtb physiology.
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Affiliation(s)
- Alemayehu Godana Birhanu
- Department of Microbiology, University of Oslo , P.O. Box 4950, Nydalen, NO-0424 Oslo, Norway.,Addis Ababa University , Institute of Biotechnology, P.O. Box 1176, Addis Ababa, Ethiopia
| | - Solomon Abebe Yimer
- Department of Microbiology, University of Oslo , P.O. Box 4950, Nydalen, NO-0424 Oslo, Norway.,Department of Microbiology, Oslo University Hospital , P.O. Box 4950, Nydalen, NO-0424 Oslo, Norway
| | - Carol Holm-Hansen
- Infection Control and Environmental Health, Norwegian Institute of Public Health , P.O. Box 4404, Nydalen, NO-0403 Oslo, Norway
| | - Gunnstein Norheim
- Infection Control and Environmental Health, Norwegian Institute of Public Health , P.O. Box 4404, Nydalen, NO-0403 Oslo, Norway
| | - Abraham Aseffa
- Armauer Hansen Research Institute , Jimma Road, P.O. Box 1005, Addis Ababa, Ethiopia
| | - Markos Abebe
- Armauer Hansen Research Institute , Jimma Road, P.O. Box 1005, Addis Ababa, Ethiopia
| | - Tone Tønjum
- Department of Microbiology, University of Oslo , P.O. Box 4950, Nydalen, NO-0424 Oslo, Norway.,Department of Microbiology, Oslo University Hospital , P.O. Box 4950, Nydalen, NO-0424 Oslo, Norway
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30
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Rasouli S, Abdolvahabi A, Croom CM, Plewman DL, Shi Y, Ayers JI, Shaw BF. Lysine acylation in superoxide dismutase-1 electrostatically inhibits formation of fibrils with prion-like seeding. J Biol Chem 2017; 292:19366-19380. [PMID: 28974578 DOI: 10.1074/jbc.m117.805283] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 09/28/2017] [Indexed: 11/06/2022] Open
Abstract
The acylation of lysine residues in superoxide dismutase-1 (SOD1) has been previously shown to decrease its rate of nucleation and elongation into amyloid-like fibrils linked to amyotrophic lateral sclerosis. The chemical mechanism underlying this effect is unclear, i.e. hydrophobic/steric effects versus electrostatic effects. Moreover, the degree to which the acylation might alter the prion-like seeding of SOD1 in vivo has not been addressed. Here, we acylated a fraction of lysine residues in SOD1 with groups of variable hydrophobicity, charge, and conformational entropy. The effect of each acyl group on the rate of SOD1 fibril nucleation and elongation were quantified in vitro with thioflavin-T (ThT) fluorescence, and we performed 594 iterate aggregation assays to obtain statistically significant rates. The effect of the lysine acylation on the prion-like seeding of SOD1 was assayed in spinal cord extracts of transgenic mice expressing a G85R SOD1-yellow fluorescent protein construct. Acyl groups with >2 carboxylic acids diminished self-assembly into ThT-positive fibrils and instead promoted the self-assembly of ThT-negative fibrils and amorphous complexes. The addition of ThT-negative, acylated SOD1 fibrils to organotypic spinal cord failed to produce the SOD1 inclusion pathology that typically results from the addition of ThT-positive SOD1 fibrils. These results suggest that chemically increasing the net negative surface charge of SOD1 via acylation can block the prion-like propagation of oligomeric SOD1 in spinal cord.
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Affiliation(s)
- Sanaz Rasouli
- From the Department of Chemistry and Biochemistry and.,the Institute of Biomedical Studies, Baylor University, Waco, Texas 76706 and
| | | | | | | | - Yunhua Shi
- From the Department of Chemistry and Biochemistry and
| | - Jacob I Ayers
- the Department of Neuroscience, University of Florida, Gainesville, Florida 32611
| | - Bryan F Shaw
- From the Department of Chemistry and Biochemistry and
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31
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Alipour S, Nouri M, Sakhinia E, Samadi N, Roshanravan N, Ghavami A, Khabbazi A. Epigenetic alterations in chronic disease focusing on Behçet's disease: Review. Biomed Pharmacother 2017; 91:526-533. [PMID: 28482290 DOI: 10.1016/j.biopha.2017.04.106] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2017] [Revised: 04/18/2017] [Accepted: 04/23/2017] [Indexed: 12/20/2022] Open
Abstract
OBJECTIVE 'Epigenetics' is specified as the inheritable changes in gene expression with no alterations in DNA sequences. Epigenetics is a rapidly overspreading scientific field, and the study of epigenetic regulation in chronic disease is emerging. This study aims to evaluate epigenetic changes including DNA methylation, histone modification, and non-coding RNAs (ncRNAs) in inflammatory disease, with focus on Behçet's disease. In this review, first we describe the history and classification of epigenetic changes, and then the role of epigenetic alterations in chronic diseases is explained. METHODS Systematic search of MEDLINE, Embase, and Cochrane Library was conducted for all comparative studies since 2000 to 2015 with the limitations of the English language. RESULTS For a notable period of time, researchers have mainly focused on the epigenetic pathways that are involved in the modulation of inflammatory and anti-inflammatory genes. Recent studies have proposed a central role for chronic inflammation in the pathogenesis of chronic disease, including Behçet's disease. CONCLUSION Studies have been reported on the epigenetic of BD showed the role of alterations in the methylation level of IRS elements; histone modifications such as H3K4me27 and H3K4me3; up regulation of miR-182 and miR-3591-3p; down regulation of miR-155, miR-638 and miR-4488 in the pathogenesis of the disease.
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Affiliation(s)
- Shahriar Alipour
- Molecular Medicine, Faculty of Advanced Medical Sciences, Tabriz University of Medical Sciences, Iran; Connective Tissue Diseases Research Center, Tabriz University of Medical Sciences, Iran
| | - Mohammad Nouri
- Dept. of Biochemistry, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Ebrahim Sakhinia
- Dept. of Biochemistry, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Nasser Samadi
- Dept. of Biochemistry, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Neda Roshanravan
- Nutrition Research Center, School of Nutrition, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Abed Ghavami
- Nutrition Research Center, School of Nutrition, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Alireza Khabbazi
- Connective Tissue Diseases Research Center, Tabriz University of Medical Sciences, Iran.
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32
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Zhou Y, Huang T, Huang G, Zhang N, Kong X, Cai YD. Prediction of protein N-formylation and comparison with N-acetylation based on a feature selection method. Neurocomputing 2016. [DOI: 10.1016/j.neucom.2015.10.148] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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33
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Monhemi H, Housaindokht MR. Chemical modification of biocatalyst for function in supercritical CO2: In silico redesign of stable lipase. J Supercrit Fluids 2016. [DOI: 10.1016/j.supflu.2016.06.015] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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34
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Tomita S, Niwa O, Kurita R. Artificial Modification of an Enzyme for Construction of Cross-Reactive Polyion Complexes To Fingerprint Signatures of Proteins and Mammalian Cells. Anal Chem 2016; 88:9079-86. [DOI: 10.1021/acs.analchem.6b02010] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Shunsuke Tomita
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, and DAILAB, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
| | - Osamu Niwa
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, and DAILAB, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
- Advanced
Science Research Laboratory, Saitama Institute of Technology, 1690 Fusaiji, Fukaya, Saitama 369-0293, Japan
| | - Ryoji Kurita
- Biomedical Research Institute, National Institute of Advanced Industrial Science and Technology, and DAILAB, 1-1-1 Higashi, Tsukuba, Ibaraki 305-8566, Japan
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35
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Fukushima A, Lopaschuk GD. Acetylation control of cardiac fatty acid β-oxidation and energy metabolism in obesity, diabetes, and heart failure. Biochim Biophys Acta Mol Basis Dis 2016; 1862:2211-2220. [PMID: 27479696 DOI: 10.1016/j.bbadis.2016.07.020] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Revised: 07/22/2016] [Accepted: 07/25/2016] [Indexed: 12/31/2022]
Abstract
Alterations in cardiac energy metabolism are an important contributor to the cardiac pathology associated with obesity, diabetes, and heart failure. High rates of fatty acid β-oxidation with cardiac insulin resistance represent a cardiac metabolic hallmark of diabetes and obesity, while a marginal decrease in fatty acid oxidation and a prominent decrease in insulin-stimulated glucose oxidation are commonly seen in the early stages of heart failure. Alterations in post-translational control of energy metabolic processes have recently been identified as an important contributor to these metabolic changes. In particular, lysine acetylation of non-histone proteins, which controls a diverse family of mitochondrial metabolic pathways, contributes to the cardiac energy derangements seen in obesity, diabetes, and heart failure. Lysine acetylation is controlled both via acetyltransferases and deacetylases (sirtuins), as well as by non-enzymatic lysine acetylation due to increased acetyl CoA pool size or dysregulated nicotinamide adenine dinucleotide (NAD+) metabolism (which stimulates sirtuin activity). One of the important mitochondrial acetylation targets are the fatty acid β-oxidation enzymes, which contributes to alterations in cardiac substrate preference during the course of obesity, diabetes, and heart failure, and can ultimately lead to cardiac dysfunction in these disease states. This review will summarize the role of lysine acetylation and its regulatory control in the context of mitochondrial fatty acid β-oxidation. The functional contribution of cardiac protein lysine acetylation to the shift in cardiac energy substrate preference that occurs in obesity, diabetes, and especially in the early stages of heart failure will also be reviewed. This article is part of a Special Issue entitled: The role of post-translational protein modifications on heart and vascular metabolism edited by Jason R.B. Dyck & Jan F.C. Glatz.
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Affiliation(s)
- Arata Fukushima
- Cardiovascular Translational Science Institute, University of Alberta, Edmonton, Alberta, Canada
| | - Gary D Lopaschuk
- Cardiovascular Translational Science Institute, University of Alberta, Edmonton, Alberta, Canada.
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36
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Fukushima A, Lopaschuk GD. Cardiac fatty acid oxidation in heart failure associated with obesity and diabetes. Biochim Biophys Acta Mol Cell Biol Lipids 2016; 1861:1525-34. [PMID: 26996746 DOI: 10.1016/j.bbalip.2016.03.020] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Revised: 03/15/2016] [Accepted: 03/16/2016] [Indexed: 12/01/2022]
Abstract
Obesity and diabetes are major public health problems, and are linked to the development of heart failure. Emerging data highlight the importance of alterations in cardiac energy metabolism as a major contributor to cardiac dysfunction related to obesity and diabetes. Increased rates of fatty acid oxidation and decreased rates of glucose utilization are two prominent changes in cardiac energy metabolism that occur in obesity and diabetes. This metabolic profile is probably both a cause and consequence of a prominent cardiac insulin resistance, which is accompanied by a decrease in both cardiac function and efficiency, and by the accumulation of potentially toxic lipid metabolites in the heart that can further exaggerate insulin resistance and cardiac dysfunction. The high cardiac fatty acid oxidation rates seen in obesity and diabetes are attributable to several factors, including: 1) increased fatty acid supply and uptake into the cardiomyocyte, 2) increased transcription of fatty acid metabolic enzymes, 3) decreased allosteric control of mitochondrial fatty acid uptake and fatty acid oxidation, and 4) increased post-translational acetylation control of various fatty acid oxidative enzymes. Emerging evidence suggests that therapeutic approaches aimed at switching the balance of cardiac energy substrate preference from fatty acid oxidation to glucose use can prevent cardiac dysfunction associated with obesity and diabetes. Modulating acetylation control of fatty acid oxidative enzymes is also a potentially attractive strategy, although presently this is limited to precursors of nicotinamide adenine or nonspecific activators of deacetylation such as resveratrol. This review will focus on the metabolic alterations in the heart that occur in obesity and diabetes, as well as on the molecular mechanisms controlling these metabolic changes. This article is part of a Special Issue entitled: Heart Lipid Metabolism edited by G.D. Lopaschuk.
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Affiliation(s)
- Arata Fukushima
- Cardiovascular Translational Science Institute, University of Alberta, Edmonton, Alberta, Canada
| | - Gary D Lopaschuk
- Cardiovascular Translational Science Institute, University of Alberta, Edmonton, Alberta, Canada.
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37
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Abdolvahabi A, Shi Y, Rhodes NR, Cook NP, Martí AA, Shaw BF. Arresting amyloid with coulomb's law: acetylation of ALS-linked SOD1 by aspirin impedes aggregation. Biophys J 2016; 108:1199-212. [PMID: 25762331 DOI: 10.1016/j.bpj.2015.01.014] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2014] [Revised: 12/04/2014] [Accepted: 01/13/2015] [Indexed: 12/15/2022] Open
Abstract
Although the magnitude of a protein's net charge (Z) can control its rate of self-assembly into amyloid, and its interactions with cellular membranes, the net charge of a protein is not viewed as a druggable parameter. This article demonstrates that aspirin (the quintessential acylating pharmacon) can inhibit the amyloidogenesis of superoxide dismutase (SOD1) by increasing the intrinsic net negative charge of the polypeptide, i.e., by acetylation (neutralization) of multiple lysines. The protective effects of acetylation were diminished (but not abolished) in 100 mM NaCl and were statistically significant: a total of 432 thioflavin-T amyloid assays were performed for all studied proteins. The acetylation of as few as three lysines by aspirin in A4V apo-SOD1-a variant that causes familial amyotrophic lateral sclerosis (ALS)-delayed amyloid nucleation by 38% and slowed amyloid propagation by twofold. Lysines in wild-type- and ALS-variant apo-SOD1 could also be peracetylated with aspirin after fibrillization, resulting in supercharged fibrils, with increases in formal net charge of ∼2 million units. Peracetylated SOD1 amyloid defibrillized at temperatures below unacetylated fibrils, and below the melting temperature of native Cu2,Zn2-SOD1 (e.g., fibril Tm = 84.49°C for acetylated D90A apo-SOD1 fibrils). Targeting the net charge of native or misfolded proteins with small molecules-analogous to how an enzyme's Km or Vmax are medicinally targeted-holds promise as a strategy in the design of therapies for diseases linked to protein self-assembly.
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Affiliation(s)
| | - Yunhua Shi
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas
| | - Nicholas R Rhodes
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas
| | - Nathan P Cook
- Department of Chemistry, Rice University, Houston, Texas
| | - Angel A Martí
- Department of Chemistry, Rice University, Houston, Texas; Department of Bioengineering, Rice University, Houston, Texas
| | - Bryan F Shaw
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas.
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38
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Nilvebrant J, Tessier PM, Sidhu SS. Engineered Autonomous Human Variable Domains. Curr Pharm Des 2016; 22:6527-6537. [PMID: 27655414 PMCID: PMC5326600 DOI: 10.2174/1381612822666160921143011] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Revised: 09/16/2016] [Accepted: 09/20/2016] [Indexed: 12/16/2022]
Abstract
BACKGROUND The complex multi-chain architecture of antibodies has spurred interest in smaller derivatives that retain specificity but can be more easily produced in bacteria. Domain antibodies consisting of single variable domains are the smallest antibody fragments and have been shown to possess enhanced ability to target epitopes that are difficult to access using multidomain antibodies. However, in contrast to natural camelid antibody domains, human variable domains typically suffer from low stability and high propensity to aggregate. METHODS This review summarizes strategies to improve the biophysical properties of heavy chain variable domains from human antibodies with an emphasis on aggregation resistance. Several protein engineering approaches have targeted antibody frameworks and complementarity determining regions to stabilize the native state and prevent aggregation of the denatured state. CONCLUSION Recent findings enable the construction of highly diverse libraries enriched in aggregation-resistant variants that are expected to provide binders to diverse antigens. Engineered domain antibodies possess unique advantages in expression, epitope preference and flexibility of formatting over conventional immunoreagents and are a promising class of antibody fragments for biomedical development.
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Affiliation(s)
- Johan Nilvebrant
- Division of Protein Technology, School of Biotechnology, Royal Institute of Technology, Stockholm, Sweden
- Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, Toronto, Canada
| | - Peter M. Tessier
- Center for Biotechnology and Interdisciplinary Studies, Isermann Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York, USA
| | - Sachdev S. Sidhu
- Donnelly Centre for Cellular and Biomolecular Research, Banting and Best Department of Medical Research, University of Toronto, Toronto, Canada
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39
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Development of a rapid high-efficiency scalable process for acetylated Sus scrofa cationic trypsin production from Escherichia coli inclusion bodies. Protein Expr Purif 2015; 116:120-6. [DOI: 10.1016/j.pep.2015.08.025] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Revised: 08/20/2015] [Accepted: 08/21/2015] [Indexed: 11/20/2022]
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40
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Mekonnen T, Mussone P, Bressler D. Valorization of rendering industry wastes and co-products for industrial chemicals, materials and energy: review. Crit Rev Biotechnol 2015; 36:120-31. [DOI: 10.3109/07388551.2014.928812] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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41
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Role of CoA and acetyl-CoA in regulating cardiac fatty acid and glucose oxidation. Biochem Soc Trans 2015; 42:1043-51. [PMID: 25110000 DOI: 10.1042/bst20140094] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
CoA (coenzyme A) and its derivatives have a critical role in regulating cardiac energy metabolism. This includes a key role as a substrate and product in the energy metabolic pathways, as well as serving as an allosteric regulator of cardiac energy metabolism. In addition, the CoA ester malonyl-CoA has an important role in regulating fatty acid oxidation, secondary to inhibiting CPT (carnitine palmitoyltransferase) 1, a key enzyme involved in mitochondrial fatty acid uptake. Alterations in malonyl-CoA synthesis by ACC (acetyl-CoA carboxylase) and degradation by MCD (malonyl-CoA decarboxylase) are important contributors to the high cardiac fatty acid oxidation rates seen in ischaemic heart disease, heart failure, obesity and diabetes. Additional control of fatty acid oxidation may also occur at the level of acetyl-CoA involvement in acetylation of mitochondrial fatty acid β-oxidative enzymes. We find that acetylation of the fatty acid β-oxidative enzymes, LCAD (long-chain acyl-CoA dehydrogenase) and β-HAD (β-hydroxyacyl-CoA dehydrogenase) is associated with an increase in activity and fatty acid oxidation in heart from obese mice with heart failure. This is associated with decreased SIRT3 (sirtuin 3) activity, an important mitochondrial deacetylase. In support of this, cardiac SIRT3 deletion increases acetylation of LCAD and β-HAD, and increases cardiac fatty acid oxidation. Acetylation of MCD is also associated with increased activity, decreases malonyl-CoA levels and an increase in fatty acid oxidation. Combined, these data suggest that malonyl-CoA and acetyl-CoA have an important role in mediating the alterations in fatty acid oxidation seen in heart failure.
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42
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Abdolvahabi A, Gober JL, Mowery RA, Shi Y, Shaw BF. Metal-Ion-Specific Screening of Charge Effects in Protein Amide H/D Exchange and the Hofmeister Series. Anal Chem 2014; 86:10303-10. [DOI: 10.1021/ac502714v] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Alireza Abdolvahabi
- Department of Chemistry and
Biochemistry, Baylor University, Waco, Texas 76706, United States
| | - Jennifer L. Gober
- Department of Chemistry and
Biochemistry, Baylor University, Waco, Texas 76706, United States
| | - Richard A. Mowery
- Department of Chemistry and
Biochemistry, Baylor University, Waco, Texas 76706, United States
| | - Yunhua Shi
- Department of Chemistry and
Biochemistry, Baylor University, Waco, Texas 76706, United States
| | - Bryan F. Shaw
- Department of Chemistry and
Biochemistry, Baylor University, Waco, Texas 76706, United States
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43
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Zhang N, Zhou Y, Huang T, Zhang YC, Li BQ, Chen L, Cai YD. Discriminating between lysine sumoylation and lysine acetylation using mRMR feature selection and analysis. PLoS One 2014; 9:e107464. [PMID: 25222670 PMCID: PMC4164654 DOI: 10.1371/journal.pone.0107464] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2014] [Accepted: 08/10/2014] [Indexed: 11/18/2022] Open
Abstract
Post-translational modifications (PTMs) are crucial steps in protein synthesis and are important factors contributing to protein diversity. PTMs play important roles in the regulation of gene expression, protein stability and metabolism. Lysine residues in protein sequences have been found to be targeted for both types of PTMs: sumoylations and acetylations; however, each PTM has a different cellular role. As experimental approaches are often laborious and time consuming, it is challenging to distinguish the two types of PTMs on lysine residues using computational methods. In this study, we developed a method to discriminate between sumoylated lysine residues and acetylated residues. The method incorporated several features: PSSM conservation scores, amino acid factors, secondary structures, solvent accessibilities and disorder scores. By using the mRMR (Maximum Relevance Minimum Redundancy) method and the IFS (Incremental Feature Selection) method, an optimal feature set was selected from all of the incorporated features, with which the classifier achieved 92.14% accuracy with an MCC value of 0.7322. Analysis of the optimal feature set revealed some differences between acetylation and sumoylation. The results from our study also supported the previous finding that there exist different consensus motifs for the two types of PTMs. The results could suggest possible dominant factors governing the acetylation and sumoylation of lysine residues, shedding some light on the modification dynamics and molecular mechanisms of the two types of PTMs, and provide guidelines for experimental validations.
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Affiliation(s)
- Ning Zhang
- Department of Biomedical Engineering, Tianjin Key Lab of Biomedical Engineering Measurement, Tianjin University, Tianjin, P.R. China
| | - You Zhou
- Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and Shanghai Jiao Tong University School of Medicine, Shanghai, P. R. China
| | - Tao Huang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | - Yu-Chao Zhang
- Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences and Shanghai Jiao Tong University School of Medicine, Shanghai, P. R. China
| | - Bi-Qing Li
- Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, P.R. China
| | - Lei Chen
- College of Information Engineering, Shanghai Maritime University, Shanghai, P.R. China
| | - Yu-Dong Cai
- Institute of Systems Biology, Shanghai University, Shanghai, P.R. China
- * E-mail:
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Shi Y, Abdolvahabi A, Shaw BF. Protein charge ladders reveal that the net charge of ALS-linked superoxide dismutase can be different in sign and magnitude from predicted values. Protein Sci 2014; 23:1417-33. [PMID: 25052939 DOI: 10.1002/pro.2526] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2014] [Revised: 07/19/2014] [Accepted: 07/21/2014] [Indexed: 12/12/2022]
Abstract
This article utilized "protein charge ladders"-chemical derivatives of proteins with similar structure, but systematically altered net charge-to quantify how missense mutations that cause amyotrophic lateral sclerosis (ALS) affect the net negative charge (Z) of superoxide dismutase-1 (SOD1) as a function of subcellular pH and Zn(2+) stoichiometry. Capillary electrophoresis revealed that the net charge of ALS-variant SOD1 can be different in sign and in magnitude-by up to 7.4 units per dimer at lysosomal pH-than values predicted from standard pKa values of amino acids and formal oxidation states of metal ions. At pH 7.4, the G85R, D90A, and G93R substitutions diminished the net negative charge of dimeric SOD1 by up to +2.29 units more than predicted; E100K lowered net charge by less than predicted. The binding of a single Zn(2+) to mutant SOD1 lowered its net charge by an additional +2.33 ± 0.01 to +3.18 ± 0.02 units, however, each protein regulated net charge when binding a second, third, or fourth Zn(2+) (ΔZ < 0.44 ± 0.07 per additional Zn(2+) ). Both metalated and apo-SOD1 regulated net charge across subcellular pH, without inverting from negative to positive at the theoretical pI. Differential scanning calorimetry, hydrogen-deuterium exchange, and inductively coupled plasma mass spectrometry confirmed that the structure, stability, and metal content of mutant proteins were not significantly affected by lysine acetylation. Measured values of net charge should be used when correlating the biophysical properties of a specific ALS-variant SOD1 protein with its observed aggregation propensity or clinical phenotype.
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Affiliation(s)
- Yunhua Shi
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas, 76798-7348
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Molten globule-like partially folded state of Bacillus licheniformis α-amylase at low pH induced by 1,1,1,3,3,3-hexafluoroisopropanol. ScientificWorldJournal 2014; 2014:824768. [PMID: 24977228 PMCID: PMC3996958 DOI: 10.1155/2014/824768] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2014] [Accepted: 02/17/2014] [Indexed: 11/24/2022] Open
Abstract
Effect of 1,1,1,3,3,3-hexafluoroisopropanol (HFIP) on acid-denatured Bacillus licheniformis α-amylase (BLA) at pH 2.0 was investigated by far-UV CD, intrinsic fluorescence, and ANS fluorescence measurements. Addition of increasing HFIP concentrations led to an increase in the mean residue ellipticity at 222 nm (MRE222 nm) up to 1.5 M HFIP concentration beyond which it sloped off. A small increase in the intrinsic fluorescence and a marked increase in the ANS fluorescence were also observed up to 0.4 M HFIP concentration, both of which decreased thereafter. Far- and near-UV CD spectra of the HFIP-induced state observed at 0.4 M HFIP showed significant retention of the secondary structures closer to native BLA but a disordered tertiary structure. Increase in the ANS fluorescence intensity was also observed with the HFIP-induced state, suggesting exposure of the hydrophobic clusters to the solvent. Furthermore, thermal denaturation of HFIP-induced state showed a non-cooperative transition. Taken together, all these results suggested that HFIP-induced state of BLA represented a molten globule-like state at pH 2.0.
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Kim DS, Song HN, Nam HJ, Kim SG, Park YS, Park JC, Woo EJ, Lim HK. Directed evolution of human heavy chain variable domain (VH) using in vivo protein fitness filter. PLoS One 2014; 9:e98178. [PMID: 24892548 PMCID: PMC4043505 DOI: 10.1371/journal.pone.0098178] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Accepted: 04/29/2014] [Indexed: 12/30/2022] Open
Abstract
Human immunoglobulin heavy chain variable domains (VH) are promising scaffolds for antigen binding. However, VH is an unstable and aggregation-prone protein, hindering its use for therapeutic purposes. To evolve the VH domain, we performed in vivo protein solubility selection that linked antibiotic resistance to the protein folding quality control mechanism of the twin-arginine translocation pathway of E. coli. After screening a human germ-line VH library, 95% of the VH proteins obtained were identified as VH3 family members; one VH protein, MG2x1, stood out among separate clones expressing individual VH variants. With further screening of combinatorial framework mutation library of MG2x1, we found a consistent bias toward substitution with tryptophan at the position of 50 and 58 in VH. Comparison of the crystal structures of the VH variants revealed that those substitutions with bulky side chain amino acids filled the cavity in the VH interface between heavy and light chains of the Fab arrangement along with the increased number of hydrogen bonds, decreased solvation energy, and increased negative charge. Accordingly, the engineered VH acquires an increased level of thermodynamic stability, reversible folding, and soluble expression. The library built with the VH variant as a scaffold was qualified as most of VH clones selected randomly were expressed as soluble form in E. coli regardless length of the combinatorial CDR. Furthermore, a non-aggregation feature of the selected VH conferred a free of humoral response in mice, even when administered together with adjuvant. As a result, this selection provides an alternative directed evolution pathway for unstable proteins, which are distinct from conventional methods based on the phage display.
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Affiliation(s)
- Dong-Sik Kim
- Antibody Engineering, Mogam Biotechnology Research Institute, Yongin, Republic of Korea
| | - Hyung-Nam Song
- BioMedical Proteomics Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea; Department of Biotechnology and Bioinformatics, Korea University, Sejong, Republic of Korea
| | - Hyo Jung Nam
- Antibody Engineering, Mogam Biotechnology Research Institute, Yongin, Republic of Korea
| | - Sung-Geun Kim
- Antibody Engineering, Mogam Biotechnology Research Institute, Yongin, Republic of Korea
| | - Young-Seoub Park
- Antibody Engineering, Mogam Biotechnology Research Institute, Yongin, Republic of Korea
| | - Jae-Chan Park
- Antibody Engineering, Mogam Biotechnology Research Institute, Yongin, Republic of Korea
| | - Eui-Jeon Woo
- BioMedical Proteomics Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, Republic of Korea
| | - Hyung-Kwon Lim
- Antibody Engineering, Mogam Biotechnology Research Institute, Yongin, Republic of Korea
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Shi Y, Mowery RA, Shaw BF. Effect of metal loading and subcellular pH on net charge of superoxide dismutase-1. J Mol Biol 2013; 425:4388-404. [PMID: 23871896 DOI: 10.1016/j.jmb.2013.07.018] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2013] [Revised: 07/03/2013] [Accepted: 07/11/2013] [Indexed: 11/17/2022]
Abstract
The net charge of a folded protein is hypothesized to influence myriad biochemical processes (e.g., protein misfolding, electron transfer, molecular recognition); however, few tools exist for measuring net charge and this elusive property remains undetermined--at any pH--for nearly all proteins. This study used lysine-acetyl "protein charge ladders" and capillary electrophoresis to measure the net charge of superoxide dismutase-1 (SOD1)--whose aggregation causes amyotrophic lateral sclerosis (ALS)--as a function of coordinated metal ions and pH. The net negative charge of apo-SOD1 was similar to predicted values; however, the binding of a single Zn(2+) or Cu(2+) ion reduced the net negative charge by a greater magnitude than predicted (i.e., ~4 units, instead of 2), whereas the SOD1 protein underwent charge regulation upon binding 2-4 metal ions. From pH5 to pH8 (i.e., a range consistent with the multiple subcellular loci of SOD1), the holo-SOD1 protein underwent smaller fluctuations in net negative charge than predicted (i.e., ~3 units, instead of ~14) and did not undergo charge inversion at its isoelectric point (pI=5.3) but remained anionic. The regulation of SOD1 net charge along its pathways of metal binding, and across solvent pH, provides insight into its metal-induced maturation and enzymatic activity (which remains diffusion-limited across pH5-8). The anionic nature of holo-SOD1 across subcellular pH suggests that ~45 different ALS-linked mutations to SOD1 will reduce its net negative charge regardless of subcellular localization.
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Affiliation(s)
- Yunhua Shi
- Department of Chemistry and Biochemistry, Baylor University, Waco, TX 76798-7348, USA
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Shi Y, Mowery RA, Ashley J, Hentz M, Ramirez AJ, Bilgicer B, Slunt-Brown H, Borchelt DR, Shaw BF. Abnormal SDS-PAGE migration of cytosolic proteins can identify domains and mechanisms that control surfactant binding. Protein Sci 2012; 21:1197-209. [PMID: 22692797 DOI: 10.1002/pro.2107] [Citation(s) in RCA: 106] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The amino acid substitution or post-translational modification of a cytosolic protein can cause unpredictable changes to its electrophoretic mobility during SDS-PAGE. This type of "gel shifting" has perplexed biochemists and biologists for decades. We identify a mechanism for "gel shifting" that predominates among a set of ALS (amyotrophic lateral sclerosis) mutant hSOD1 (superoxide dismutase) proteins, post-translationally modified hSOD1 proteins, and homologous SOD1 proteins from different organisms. By first comparing how 39 amino acid substitutions throughout hSOD1 affected SDS-PAGE migration, we found that substitutions that caused gel shifting occurred within a single polyacidic domain (residues ~80-101), and were nonisoelectric. Substitutions that decreased the net negative charge of domain 80-101 increased migration; only one substitution increased net negative charge and slowed migration. Capillary electrophoresis, circular dichroism, and size exclusion chromatography demonstrated that amino acid substitutions increase migration during SDS-PAGE by promoting the binding of three to four additional SDS molecules, without significantly altering the secondary structure or Stokes radius of hSOD1-SDS complexes. The high negative charge of domain 80-101 is required for SOD1 gel shifting: neutralizing the polyacidic domain (via chimeric mouse-human SOD1 fusion proteins) inhibited amino acid substitutions from causing gel shifting. These results demonstrate that the pattern of gel shifting for mutant cytosolic proteins can be used to: (i) identify domains in the primary structure that control interactions between denatured cytosolic proteins and SDS and (ii) identify a predominant chemical mechanism for the interaction (e.g., hydrophobic vs. electrostatic).
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Affiliation(s)
- Yunhua Shi
- Department of Chemistry and Biochemistry, Baylor University, Waco, Texas 76706, USA
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Shi SP, Qiu JD, Sun XY, Suo SB, Huang SY, Liang RP. A method to distinguish between lysine acetylation and lysine methylation from protein sequences. J Theor Biol 2012; 310:223-30. [DOI: 10.1016/j.jtbi.2012.06.030] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2012] [Revised: 05/21/2012] [Accepted: 06/25/2012] [Indexed: 01/21/2023]
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Shaw BF, Schneider GF, Arthanari H, Narovlyansky M, Moustakas D, Durazo A, Wagner G, Whitesides GM. Complexes of native ubiquitin and dodecyl sulfate illustrate the nature of hydrophobic and electrostatic interactions in the binding of proteins and surfactants. J Am Chem Soc 2011; 133:17681-95. [PMID: 21939262 DOI: 10.1021/ja205735q] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A previous study, using capillary electrophoresis (CE) [J. Am. Chem. Soc. 2008, 130, 17384-17393], reported that six discrete complexes of ubiquitin (UBI) and sodium dodecyl sulfate (SDS) form at different concentrations of SDS along the pathway to unfolding of UBI in solutions of SDS. One complex (which formed between 0.8 and 1.8 mM SDS) consisted of native UBI associated with approximately 11 molecules of SDS. The current study used CE and (15)N/(13)C-(1)H heteronuclear single quantum coherence (HSQC) NMR spectroscopy to identify residues in folded UBI that associate specifically with SDS at 0.8-1.8 mM SDS, and to correlate these associations with established biophysical and structural properties of this well-characterized protein. The ability of the surface charge and hydrophobicity of folded UBI to affect the association with SDS (at concentrations below the CMC) was studied, using CE, by converting lys-ε-NH(3)(+) to lys-ε-NHCOCH(3) groups. According to CE, the acetylation of lysine residues inhibited the binding of 11 SDS ([SDS] < 2 mM) and decreased the number of complexes of composition UBI-(NHAc)(8)·SDS(n) that formed on the pathway of unfolding of UBI-(NHAc)(8) in SDS. A comparison of (15)N-(1)H HSQC spectra at 0 mM and 1 mM SDS with calculated electrostatic surface potentials of folded UBI (e.g., solutions to the nonlinear Poisson-Boltzmann (PB) equation) suggested, however, that SDS binds preferentially to native UBI at hydrophobic residues that are formally neutral (i.e., Leu and Ile), but that have positive electrostatic surface potential (as predicted from solutions to nonlinear PB equations); SDS did not uniformly interact with residues that have formal positive charge (e.g., Lys or Arg). Cationic functional groups, therefore, promote the binding of SDS to folded UBI because these groups exert long-range effects on the positive electrostatic surface potential (which extend beyond their own van der Waals radii, as predicted from PB theory), and not because cationic groups are necessarily the site of ionic interactions with sulfate groups. Moreover, SDS associated with residues in native UBI without regard to their location in α-helix or β-sheet structure (although residues in hydrogen-bonded loops did not bind SDS). No correlation was observed between the association of an amino acid with SDS and the solvent accessibility of the residue or its rate of amide H/D exchange. This study establishes a few (of perhaps several) factors that control the simultaneous molecular recognition of multiple anionic amphiphiles by a folded cytosolic protein.
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Affiliation(s)
- Bryan F Shaw
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States.
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