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Ajomiwe N, Boland M, Phongthai S, Bagiyal M, Singh J, Kaur L. Protein Nutrition: Understanding Structure, Digestibility, and Bioavailability for Optimal Health. Foods 2024; 13:1771. [PMID: 38890999 PMCID: PMC11171741 DOI: 10.3390/foods13111771] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2024] [Revised: 05/13/2024] [Accepted: 05/23/2024] [Indexed: 06/20/2024] Open
Abstract
This review discusses different protein sources and their role in human nutrition, focusing on their structure, digestibility, and bioavailability. Plant-based proteins, such as those found in legumes, nuts, and seeds, may contain anti-nutritional factors that impact their bioavailability apart from structural and compositional differences from animal proteins. Animal proteins are generally highly digestible and nutritionally superior to plant proteins, with higher amino acid bioavailability. Alternative protein sources are also processed in different ways, which can alter their structure and nutritional value, which is also discussed.
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Affiliation(s)
- Nneka Ajomiwe
- School of Food Technology and Natural Sciences, Massey University, 4442 Palmerston North, New Zealand
| | - Mike Boland
- Riddet Institute, Massey University, 4442 Palmerston North, New Zealand
| | - Suphat Phongthai
- Food Science and Technology Division, School of Agro-Industry, Chiang Mai University, Chiang Mai 50100, Thailand
| | - Manisha Bagiyal
- School of Food Technology and Natural Sciences, Massey University, 4442 Palmerston North, New Zealand
| | - Jaspreet Singh
- School of Food Technology and Natural Sciences, Massey University, 4442 Palmerston North, New Zealand
- Riddet Institute, Massey University, 4442 Palmerston North, New Zealand
| | - Lovedeep Kaur
- School of Food Technology and Natural Sciences, Massey University, 4442 Palmerston North, New Zealand
- Riddet Institute, Massey University, 4442 Palmerston North, New Zealand
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Waghmare S, Guptasarma P. 'Nunchuck' proteins: Short flexible linkers resist proteolysis by facilitating motions in flanking domains to inhibit the approach of proteases. Biochem Biophys Res Commun 2024; 706:149730. [PMID: 38461648 DOI: 10.1016/j.bbrc.2024.149730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 02/18/2024] [Accepted: 02/26/2024] [Indexed: 03/12/2024]
Abstract
Peptides linking well-folded and non-interacting domains in fusion proteins can undergo proteolytic degradation. This leads to physical separation of the domains that were originally sought to be joined. In order to identify characteristics that determine linker degradation propensity, we selected a pair of thermostable, proteolytically-resistant domains, and joined them using five different linkers. We then assessed linker degradation propensities through size-exclusion chromatography, and denaturing and non-denaturing electrophoresis. The domains used were Coh2, an all-beta cohesin from C. thermocellum CipA, and BSX, a beta/alpha barrel xylanase from Bacillus sp. NG-27, while the linkers used were Rigid (3 repeats of N-EAAAK-C), Flexible (two repeats of N-SGGGG-C), Nat-full (42 residues of a Coh2-adjacent linker from CipA), Nat-half (a 21 residues-long derivative of Nat-full) and Nat-quarter (a 9 residues-long derivative of Nat-full). Both with proteolysis effected by proteases present in the environment, and with an exogenously-added protease (Subtilisin A), we found that Flexible underwent little or no degradation, whereas linkers of comparable length like Nat-quarter or Rigid underwent extensive degradation, as did longer linkers like Nat-Half and Nat-Full. Our analyses disfavor the likelihood of the sequence of Flexible being naturally resistant to proteolysis, and instead favor the explanation that the flexibility of Flexible facilitates movements of Coh2 relative to BSX which then serve to sterically prevent the approach of proteases. Thus, the construct incorporating Flexible appears to behave like a 'nunchuck' in which rods/spheres flanking a chain collide with approaching swords that are capable of severing the chain, to prevent severance.
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Affiliation(s)
- Snehal Waghmare
- Centre for Protein Science, Design and Engineering (CPSDE) and Hyperthermophile Enzyme Hydrolase Research Centre (HEHRC), Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Mohali, Knowledge City, Sector-81, SAS Nagar, Punjab, 140306, India
| | - Purnananda Guptasarma
- Centre for Protein Science, Design and Engineering (CPSDE) and Hyperthermophile Enzyme Hydrolase Research Centre (HEHRC), Department of Biological Sciences, Indian Institute of Science Education and Research (IISER), Mohali, Knowledge City, Sector-81, SAS Nagar, Punjab, 140306, India.
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3
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Mayr AL, Hummel K, Leitsch D, Razzazi-Fazeli E. A Comparison of Bottom-Up Proteomic Sample Preparation Methods for the Human Parasite Trichomonas vaginalis. ACS OMEGA 2024; 9:9782-9791. [PMID: 38434803 PMCID: PMC10905575 DOI: 10.1021/acsomega.3c10040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 01/25/2024] [Accepted: 01/31/2024] [Indexed: 03/05/2024]
Abstract
Bottom-up proteomic approaches depend on the efficient digestion of proteins into peptides for mass spectrometric analysis. Sample preparation strategies, based on magnetic beads, filter-aided systems, or in-solution digests, are commonly used for proteomic analysis. Time-intensive methods like filter-aided sample preparation (FASP) have led to the development of new, more time-efficient filter-based strategies like suspension trappings (S-Traps) or magnetic bead-based strategies like SP3. S-Traps have been reported as an alternative proteomic sample preparation method as they allow for high sodium dodecyl sulfate (SDS) concentrations to be present in the sample. In this study, we compare the efficiency of different protocols for FASP, SP3, and S-Trap-based digestion of proteins after extraction from Trichomonas vaginalis. Overall, we found a high number of protein IDs for all tested methods and a high degree of reproducibility within each method type. However, FASP with a 3 kDa cutoff filter unit outperformed the other methods analyzed, referring to the number of protein IDs. This is the first work providing the direct comparison of four different bottom-up proteomic approaches regarding the most efficient proteomic sample preparation protocol for the human parasite T. vaginalis.
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Affiliation(s)
- Anna-Lena Mayr
- VetCore
Facility, University of Veterinary Medicine, Veterinärplatz 1, 1210 Vienna, Austria
| | - Karin Hummel
- VetCore
Facility, University of Veterinary Medicine, Veterinärplatz 1, 1210 Vienna, Austria
| | - David Leitsch
- ISPTM, Medical
University of Vienna, Kinderspitalgasse 15, 1090 Vienna, Austria
| | - Ebrahim Razzazi-Fazeli
- VetCore
Facility, University of Veterinary Medicine, Veterinärplatz 1, 1210 Vienna, Austria
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4
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Höppner S, Schröder B, Fluhrer R. Structure and function of SPP/SPPL proteases: insights from biochemical evidence and predictive modeling. FEBS J 2023; 290:5456-5474. [PMID: 37786993 DOI: 10.1111/febs.16968] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 09/13/2023] [Accepted: 09/29/2023] [Indexed: 10/04/2023]
Abstract
More than 20 years ago, signal peptide peptidase (SPP) and its homologues, the signal peptide peptidase-like (SPPL) proteases have been identified based on their sequence similarity to presenilins, a related family of intramembrane aspartyl proteases. Other than those for the presenilins, no high-resolution structures for the SPP/SPPL proteases are available. Despite this limitation, over the years bioinformatical and biochemical data have accumulated, which altogether have provided a picture of the overall structure and topology of these proteases, their localization in the cell, the process of substrate recognition, their cleavage mechanism, and their function. Recently, the artificial intelligence-based structure prediction tool AlphaFold has added high-confidence models of the expected fold of SPP/SPPL proteases. In this review, we summarize known structural aspects of the SPP/SPPL family as well as their substrates. Of particular interest are the emerging substrate recognition and catalytic mechanisms that might lead to the prediction and identification of more potential substrates and deeper insight into physiological and pathophysiological roles of proteolysis.
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Affiliation(s)
- Sabine Höppner
- Biochemistry and Molecular Biology, Faculty of Medicine, Institute of Theoretical Medicine, University of Augsburg, Germany
| | - Bernd Schröder
- Institute for Physiological Chemistry, Technische Universität Dresden, Germany
| | - Regina Fluhrer
- Biochemistry and Molecular Biology, Faculty of Medicine, Institute of Theoretical Medicine, University of Augsburg, Germany
- Center for Interdisciplinary Health Research, University of Augsburg, Germany
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Kleizen B, de Mattos E, Papaioannou O, Monti M, Tartaglia GG, van der Sluijs P, Braakman I. Transmembrane Helices 7 and 8 Confer Aggregation Sensitivity to the Cystic Fibrosis Transmembrane Conductance Regulator. Int J Mol Sci 2023; 24:15741. [PMID: 37958724 PMCID: PMC10648718 DOI: 10.3390/ijms242115741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 10/18/2023] [Accepted: 10/19/2023] [Indexed: 11/15/2023] Open
Abstract
The Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) is a large multi-spanning membrane protein that is susceptible to misfolding and aggregation. We have identified here the region responsible for this instability. Temperature-induced aggregation of C-terminally truncated versions of CFTR demonstrated that all truncations up to the second transmembrane domain (TMD2), including the R region, largely resisted aggregation. Limited proteolysis identified a folded structure that was prone to aggregation and consisted of TMD2 and at least part of the Regulatory Region R. Only when both TM7 (TransMembrane helix 7) and TM8 were present, TMD2 fragments became as aggregation-sensitive as wild-type CFTR, in line with increased thermo-instability of late CFTR nascent chains and in silico prediction of aggregation propensity. In accord, isolated TMD2 was degraded faster in cells than isolated TMD1. We conclude that TMD2 extended at its N-terminus with part of the R region forms a protease-resistant structure that induces heat instability in CFTR and may be responsible for its limited intracellular stability.
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Affiliation(s)
- Bertrand Kleizen
- Cellular Protein Chemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands; (B.K.); (E.d.M.); (O.P.); (P.v.d.S.)
| | - Eduardo de Mattos
- Cellular Protein Chemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands; (B.K.); (E.d.M.); (O.P.); (P.v.d.S.)
| | - Olga Papaioannou
- Cellular Protein Chemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands; (B.K.); (E.d.M.); (O.P.); (P.v.d.S.)
| | - Michele Monti
- Center for Life Nano- & Neuro-Science, Fondazione Istituto Italiano di Tecnologia (IIT), 00161 Rome, Italy; (M.M.); (G.G.T.)
- Centre for Human Technologies (CHT), Istituto Italiano di Tecnologia (IIT), 16152 Genoa, Italy
| | - Gian Gaetano Tartaglia
- Center for Life Nano- & Neuro-Science, Fondazione Istituto Italiano di Tecnologia (IIT), 00161 Rome, Italy; (M.M.); (G.G.T.)
- Centre for Human Technologies (CHT), Istituto Italiano di Tecnologia (IIT), 16152 Genoa, Italy
| | - Peter van der Sluijs
- Cellular Protein Chemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands; (B.K.); (E.d.M.); (O.P.); (P.v.d.S.)
| | - Ineke Braakman
- Cellular Protein Chemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands; (B.K.); (E.d.M.); (O.P.); (P.v.d.S.)
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6
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Gordon BH, Liu P, Whittington AC, Silvers R, Miller BG. Biochemical methods to map and quantify allosteric motions in human glucokinase. Methods Enzymol 2023; 685:433-459. [PMID: 37245911 PMCID: PMC10308428 DOI: 10.1016/bs.mie.2023.03.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Allosteric regulation of protein function is ubiquitous in biology. Allostery originates from ligand-mediated alterations in polypeptide structure and/or dynamics, which produce a cooperative kinetic or thermodynamic response to changing ligand concentrations. Establishing a mechanistic description of individual allosteric events requires both mapping the relevant changes in protein structure and quantifying the rates of differential conformational dynamics in the absence and presence of effectors. In this chapter, we describe three biochemical approaches to understand the dynamic and structural signatures of protein allostery using the well-established cooperative enzyme glucokinase as a case study. The combined application of pulsed proteolysis, biomolecular nuclear magnetic resonance spectroscopy and hydrogen-deuterium exchange mass spectrometry offers complementary information that can used to establish molecular models for allosteric proteins, especially when differential protein dynamics are involved.
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Affiliation(s)
- Blaine H Gordon
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL, United States; Institute of Molecular Biophysics, Florida State University, Tallahassee, FL, United States
| | - Peilu Liu
- Protein Analytical Chemistry, Genentech Inc., South San Francisco, CA, United States
| | - A Carl Whittington
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL, United States; Department of Biological Science, Florida State University, Tallahassee, FL, United States
| | - Robert Silvers
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL, United States; Institute of Molecular Biophysics, Florida State University, Tallahassee, FL, United States
| | - Brian G Miller
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, FL, United States.
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7
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Zhao J, Ge G, Huang Y, Hou Y, Hu SQ. Butelase 1-Mediated Enzymatic Cyclization of Antimicrobial Peptides: Improvements on Stability and Bioactivity. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2022; 70:15869-15878. [PMID: 36471508 DOI: 10.1021/acs.jafc.2c06588] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Antimicrobial peptides (AMPs) have broad-spectrum antibacterial properties and safety as food preservatives, whereas the stability and antibacterial activity require improvement. Here, the "head-to-tail" cyclization of linear AMP GKE was catalyzed by butelase 1, which resulted in an improved pronouncedly antibacterial effect. Cell morphology and propidium iodide uptake revealed that the increased membrane permeability was one of the bacteriostatic mechanisms of GKE and could be enhanced after cyclization. As cyclic GKE (cGKE) exhibited more stability than the linear counterpart under the microorganism culture environment, the increase in effective bacteriostatic concentration should be a reason for the superior antibacterial effect. Moreover, cGKE exhibited the ordered secondary structure, while GKE possessed a similar structure only in sodium dodecyl sulfate micelles. The structure was also beneficial to improve the antibacterial activity caused by the increased affinity of cGKE to the membranes. Overall, butelase 1-mediated cyclization is a promising strategy for enhancing the antibacterial activity of linear AMPs.
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Affiliation(s)
- Jinsong Zhao
- Overseas Expertise Introduction Center for Discipline Innovation of Food Nutrition and Human Health (111 Center), School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, China
| | - Ge Ge
- Beijing Food Safety Monitoring and Risk Assessment Center, Beijing 100094, China
| | - Yanbo Huang
- State Key Laboratory of Pulp and Paper Engineering, South China University of Technology, Guangzhou, Guangdong 510640, China
| | - Yi Hou
- State Key Laboratory of Pulp and Paper Engineering, South China University of Technology, Guangzhou, Guangdong 510640, China
| | - Song-Qing Hu
- Overseas Expertise Introduction Center for Discipline Innovation of Food Nutrition and Human Health (111 Center), School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, China
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8
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Jaipuria G, Shet D, Malik S, Swain M, Atreya HS, Galea CA, Slomiany MG, Rosenzweig SA, Forbes BE, Norton RS, Mondal S. IGF-dependent dynamic modulation of a protease cleavage site in the intrinsically disordered linker domain of human IGFBP2. Proteins 2022; 90:1732-1743. [PMID: 35443068 PMCID: PMC9357107 DOI: 10.1002/prot.26350] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 03/02/2022] [Accepted: 03/22/2022] [Indexed: 12/29/2022]
Abstract
Functional regulation via conformational dynamics is well known in structured proteins but less well characterized in intrinsically disordered proteins and their complexes. Using NMR spectroscopy, we have identified a dynamic regulatory mechanism in the human insulin-like growth factor (IGF) system involving the central, intrinsically disordered linker domain of human IGF-binding protein-2 (hIGFBP2). The bioavailability of IGFs is regulated by the proteolysis of IGF-binding proteins. In the case of hIGFBP2, the linker domain (L-hIGFBP2) retains its intrinsic disorder upon binding IGF-1, but its dynamics are significantly altered, both in the IGF binding region and distantly located protease cleavage sites. The increase in flexibility of the linker domain upon IGF-1 binding may explain the IGF-dependent modulation of proteolysis of IGFBP2 in this domain. As IGF homeostasis is important for cell growth and function, and its dysregulation is a key contributor to several cancers, our findings open up new avenues for the design of IGFBP analogs inhibiting IGF-dependent tumors.
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Affiliation(s)
- Garima Jaipuria
- NMR Research Centre, Indian Institute of Science, Bangalore-560012, India
| | - Divya Shet
- NMR Research Centre, Indian Institute of Science, Bangalore-560012, India,Nanobiophysics lab, Raman Research Institute, Sadashivnagar, Bangalore-80, India
| | - Shahid Malik
- NMR Research Centre, Indian Institute of Science, Bangalore-560012, India
| | - Monalisa Swain
- NMR Research Centre, Indian Institute of Science, Bangalore-560012, India,Frederick National Laboratory for Cancer Research, Maryland-21701, USA
| | | | - Charles A. Galea
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Parkville 3052, Australia
| | - Mark G. Slomiany
- Department of Cell and Molecular Pharmacology, Medical University of South Carolina, Charleston SC 29425, USA
| | - Steven A. Rosenzweig
- Department of Cell and Molecular Pharmacology, Medical University of South Carolina, Charleston SC 29425, USA
| | - Briony E. Forbes
- Flinders Health and Medical Research Institute, Flinders University, SA 5042, Australia
| | - Raymond S. Norton
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Parkville 3052, Australia,ARC Centre for Fragment-Based Design, Monash University, Parkville 3052, Australia
| | - Somnath Mondal
- NMR Research Centre, Indian Institute of Science, Bangalore-560012, India,Univ. Bordeaux, Institut Européen de Chimie et Biologie and INSERM U1212, ARNA Laboratory, 2 rue Robert Escarpit, 33607 Pessac Cedex, Bordeaux, France
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9
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Hao B, Liu L, Liu N, Sun L, Fan F, Huang J. The Bombyx mori Nucleopolyhedrovirus GP64 Retains the Transmembrane Helix of Signal Peptide to Contribute to Secretion across the Cytomembrane. Microbiol Spectr 2022; 10:e0191322. [PMID: 35938817 PMCID: PMC9430547 DOI: 10.1128/spectrum.01913-22] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Accepted: 07/14/2022] [Indexed: 11/20/2022] Open
Abstract
Bombyx mori nucleopolyhedrovirus (BmNPV) is the primary pathogen of silkworms that causes severe economic losses in sericulture. GP64 is the key membrane fusion protein that mediates budded virus (BV) fusion with the host cell membrane. Previously, we found that the n-region of the GP64 signal peptide (SP) is required for protein secretion and viral pathogenicity; however, our understanding of BmNPV GP64 remains limited. Here, we first reported that BmNPV GP64 retained its SP in the mature protein and virion in only host cells but did not retain in nonhost cells. Uncleaved SP mediates protein targeting to the cytomembrane or secretion in Bombyx mori cells. The exitance of the n-region extended the transmembrane helix length, which resulted in the cleavage site to be located in the helix structure and thus blocked cleavage from signal peptidase (SPase). Without the n-region, the protein fails to be transported to the cytomembrane, but this failure can be rescued by the cleavage site mutation of SP. Helix-breaking mutations in SP abolished protein targeting to the cytomembrane and secretion. Our results revealed a previously unrecognized mechanism by which SP of membrane fusion not only determines protein localization but also determines viral pathogenicity, which highlights the escape mechanism of SP from the cleavage by SPase. IMPORTANCE BmNPV is the primary pathogen of silkworms, which causes severe economic losses in sericulture. BmNPV and Autographa californica multiple nucleopolyhedrovirus (AcMNPV) are closely related group I alphabaculoviruses, but they exhibit nonoverlapping host specificity. Recent studies suppose that GP64 is a determinant of host range, while knowledge remains limited. In this study, we revealed that BmNPV GP64 retained its SP in host cells but not in nonhost cells, and the SP retention is required for GP64 secretion across the cytomembrane. This is the first report that a type I membrane fusion protein retained its SP in mature proteins and virions. Our results unveil the mechanism by which SP GP64 escapes cleavage and the role of SP in protein targeting. This study will help elucidate an important mechanistic understanding of BmNPV infection and host range specificity.
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Affiliation(s)
- Bifang Hao
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, People’s Republic of China
- Key Laboratory of Genetic Improvement of Sericulture in the Ministry of Agriculture, Sericultural Research Institute, Chinese Academy of Agricultural Science, Zhenjiang, Jiangsu, People’s Republic of China
| | - Lin Liu
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, People’s Republic of China
| | - Na Liu
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, People’s Republic of China
| | - Luping Sun
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, People’s Republic of China
| | - Fengxiu Fan
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, People’s Republic of China
| | - Jinshan Huang
- Jiangsu Key Laboratory of Sericultural Biology and Biotechnology, School of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang, Jiangsu, People’s Republic of China
- Key Laboratory of Genetic Improvement of Sericulture in the Ministry of Agriculture, Sericultural Research Institute, Chinese Academy of Agricultural Science, Zhenjiang, Jiangsu, People’s Republic of China
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10
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Vorob'ev MM. Modeling of Proteolysis of β-Lactoglobulin and β-Casein by Trypsin with Consideration of Secondary Masking of Intermediate Polypeptides. Int J Mol Sci 2022; 23:ijms23158089. [PMID: 35897664 PMCID: PMC9331131 DOI: 10.3390/ijms23158089] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 07/20/2022] [Accepted: 07/21/2022] [Indexed: 02/04/2023] Open
Abstract
The opening of protein substrates during degradation by proteases and the corresponding exposure of their internal peptide bonds for a successful enzymatic attack, the so-called demasking effect, was studied for β-lactoglobulin (β-LG) and β-casein (β-CN) hydrolyzed by trypsin. Demasking was estimated by monitoring the redshift in intrinsic tryptophan fluorescence, characterizing the accessibility of polypeptide chains to aqueous medium. The secondary masking of intermediate polypeptides, giving an inverse effect to demasking, caused a restriction of the substrate opening. This led to the limitations in the red shift of fluorescence and the degree of hydrolysis with a long time of hydrolysis of β-LG and β-CN at a constant substrate concentration and reduced trypsin concentrations. The proposed proteolysis model included demasking of initially masked bonds in the protein globule or micelle, secondary masking of intermediate polypeptides, and their subsequent slow demasking. The hydrolysis of peptide bonds was modeled taking into account different hydrolysis rate constants for different peptide bonds. It was demonstrated that demasking competes with secondary masking, which is less noticeable at high trypsin concentrations. Modeling of proteolysis taking into account two demasking processes and secondary masking made it possible to simulate kinetic curves consistent with the experimental data.
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Affiliation(s)
- Mikhail M Vorob'ev
- A. N. Nesmeyanov Institute of Organoelement Compounds, Russian Academy of Sciences, 28 ul. Vavilova, 119991 Moscow, Russia
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11
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Study on activation mechanism and cleavage sites of recombinant butelase-1 zymogen derived from Clitoria ternatea. Biochimie 2022; 199:12-22. [DOI: 10.1016/j.biochi.2022.04.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 04/04/2022] [Accepted: 04/04/2022] [Indexed: 11/15/2022]
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12
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Dobryakova NV, Zhdanov DD, Sokolov NN, Aleksandrova SS, Pokrovskaya MV, Kudryashova EV. Improvement of Biocatalytic Properties and Cytotoxic Activity of L-Asparaginase from Rhodospirillum rubrum by Conjugation with Chitosan-Based Cationic Polyelectrolytes. Pharmaceuticals (Basel) 2022; 15:ph15040406. [PMID: 35455403 PMCID: PMC9029710 DOI: 10.3390/ph15040406] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 03/22/2022] [Accepted: 03/25/2022] [Indexed: 12/04/2022] Open
Abstract
L-asparaginases (L-ASNases, EC 3.5.1.1) are a family of enzymes that are widely used for the treatment of lymphoblastic leukemias. L-ASNase from Rhodospirillum rubrum (RrA) has a low molecular weight, low glutaminase activity, and low immunogenicity, making it a promising enzyme for antitumor drug development. In our work, the complex formation and covalent conjugation of the enzyme with synthetic or natural polycationic polymers was studied. Among non-covalent polyelectrolyte complexes (PEC), polyethyleneimine (PEI) yielded the highest effect on RrA, increasing its activity by 30%. The RrA-PEI complex had increased stability to trypsinolysis, with an inactivation constant decrease up to 10-fold compared to that of the native enzyme. The covalent conjugation of RrA with chitosan-PEI, chitosan-polyethylene glycol (chitosan-PEG), and chitosan-glycol resulted in an increase in the specific activity of L-asparagine (up to 30%). RrA-chitosan-PEG demonstrated dramatically (by 60%) increased cytotoxic activity for human chronic myeloma leukemia K562 cells in comparison to the native enzyme. The antiproliferative activity of RrA and its conjugates was significantly higher (up to 50%) than for that of the commercially available EcA at the same concentration. The results of this study demonstrated that RrA conjugates with polycations can become a promising strategy for antitumor drug development.
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Affiliation(s)
- Natalia V. Dobryakova
- Chemical Faculty, Lomonosov Moscow State University, Leninskie Gory St. 1, 119991 Moscow, Russia;
- Laboratory of Medical Biotechnology, Institute of Biomedical Chemistry, Pogodinskaya St. 10/8, 119121 Moscow, Russia; (N.N.S.); (S.S.A.); (M.V.P.)
| | - Dmitry D. Zhdanov
- Laboratory of Medical Biotechnology, Institute of Biomedical Chemistry, Pogodinskaya St. 10/8, 119121 Moscow, Russia; (N.N.S.); (S.S.A.); (M.V.P.)
- Department of Biochemistry, Peoples’ Friendship University of Russia (RUDN University), Miklukho-Maklaya St. 6, 117198 Moscow, Russia
- Correspondence: (D.D.Z.); (E.V.K.)
| | - Nikolay N. Sokolov
- Laboratory of Medical Biotechnology, Institute of Biomedical Chemistry, Pogodinskaya St. 10/8, 119121 Moscow, Russia; (N.N.S.); (S.S.A.); (M.V.P.)
| | - Svetlana S. Aleksandrova
- Laboratory of Medical Biotechnology, Institute of Biomedical Chemistry, Pogodinskaya St. 10/8, 119121 Moscow, Russia; (N.N.S.); (S.S.A.); (M.V.P.)
| | - Marina V. Pokrovskaya
- Laboratory of Medical Biotechnology, Institute of Biomedical Chemistry, Pogodinskaya St. 10/8, 119121 Moscow, Russia; (N.N.S.); (S.S.A.); (M.V.P.)
| | - Elena V. Kudryashova
- Chemical Faculty, Lomonosov Moscow State University, Leninskie Gory St. 1, 119991 Moscow, Russia;
- Correspondence: (D.D.Z.); (E.V.K.)
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13
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Albuquerque W, Seidel L, Zorn H, Will F, Gand M. Haze Formation and the Challenges for Peptidases in Wine Protein Fining. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:14402-14414. [PMID: 34823353 DOI: 10.1021/acs.jafc.1c05427] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
To meet consumer expectations, white wines must be clear and stable against haze formation. Temperature variations during transport and storage may induce protein aggregation, mainly caused by thaumatin like-proteins (TLPs) and chitinases (CHIs), which thus need to be fined before bottling of the wine. Currently, bentonite clay is employed to inhibit or minimize haze formation in wines. Alternatively, peptidases have emerged as an option for the removal of these thermolabile proteins, although their efficacy under winemaking conditions has not yet been fully demonstrated. The simultaneous understanding of the chemistry behind the cleavage of haze proteins and the haze formation may orchestrate alternative methods of technological and economic importance in winemaking. Therefore, we provide an overview of wine fining by peptidases, and new perspectives are developed to reopen discussions on the aforementioned challenges.
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Affiliation(s)
- Wendell Albuquerque
- Institute of Food Chemistry and Food Biotechnology, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, 35392 Giessen, Germany
| | - Leif Seidel
- Department of Beverage Research, Geisenheim University, Von-Lade-Str. 1, 65366 Geisenheim, Germany
| | - Holger Zorn
- Institute of Food Chemistry and Food Biotechnology, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, 35392 Giessen, Germany
- Fraunhofer Institute for Molecular Biology and Applied Ecology, Ohlebergsweg 12, 35392 Giessen, Germany
| | - Frank Will
- Department of Beverage Research, Geisenheim University, Von-Lade-Str. 1, 65366 Geisenheim, Germany
| | - Martin Gand
- Institute of Food Chemistry and Food Biotechnology, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, 35392 Giessen, Germany
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14
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Structural mapping techniques distinguish the surfaces of fibrillar 1N3R and 1N4R human tau. J Biol Chem 2021; 297:101252. [PMID: 34592311 PMCID: PMC8551503 DOI: 10.1016/j.jbc.2021.101252] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 09/21/2021] [Accepted: 09/24/2021] [Indexed: 12/02/2022] Open
Abstract
The rigid core of intracellular tau filaments from Alzheimer's disease (AD), Pick's disease (PiD), and Corticobasal disease (CBD) brains has been shown to differ in their cryo-EM atomic structure. Despite providing critical information on the intimate arrangement of a fraction of htau molecule within the fibrillar scaffold, the cryo-EM studies neither yield a complete picture of tau fibrillar assemblies structure nor contribute insights into the surfaces that define their interactions with numerous cellular components. Here, using proteomic approaches such as proteolysis and molecular covalent painting, we mapped the exposed amino acid stretches at the surface and those constituting the fibrillar core of in vitro-assembled fibrils of human htau containing one N-terminal domain and three (1N3R) or four (1N4R) C-terminal microtubule-binding repeat domains as a result of alternative splicing. Using limited proteolysis, we identified the proteolytic fragments composing the molecular “bar-code” for each type of fibril. Our results are in agreement with structural data reported for filamentous tau from AD, PiD, and CBD cases predigested with the protease pronase. Finally, we report two amino acid stretches, exposed to the solvent in 1N4R not in 1N3R htau, which distinguish the surfaces of these two kinds of fibrils. Our findings open new perspectives for the design of highly specific ligands with diagnostic and therapeutic potential.
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15
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Sun B, Lv J, Chen J, Liu Z, Zhou Y, Liu L, Jin Y, Wang F. Size-Selective VAILase Proteolysis Provides Dynamic Insights into Protein Structures. Anal Chem 2021; 93:10653-10660. [PMID: 34291915 DOI: 10.1021/acs.analchem.1c02042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Monitoring the dynamic alterations of protein structures within an aqueous solution remains enormously challenging. In this study, we describe a size-selective VAILase proteolysis (SVP)-mass spectrometry (MS) strategy to probe the protein structure changes without strict control of the proteolysis kinetics. The unique conformation selectivity of SVP depends on the uniform nano-sized entrance pores of the VAILase hexameric cage as well as the six inherent molecular rulers in the VAILase-substrate recognition and cleavage. The dynamic insights into subtle conformation alterations of both myoglobin unfolding transition and Aurora kinase A-inhibitor binding are successfully captured using the SVP strategy, which matches well with the results in the molecular dynamics simulation. Our work provides a new paradigm of size-selective native proteolysis for exploring the aqueous protein structure-function relationships.
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Affiliation(s)
- Binwen Sun
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ji Lv
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Jin Chen
- Clinical Center for Molecular Diagnosis and Therapy, The Second Affiliated Hospital of Fujian Medical University, Quanzhou 362000, China
| | - Zheyi Liu
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Ye Zhou
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Lin Liu
- School of Life Sciences, Anhui University, Hefei 230601, Anhui, China
| | - Yan Jin
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Fangjun Wang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China.,University of Chinese Academy of Sciences, Beijing 100049, China
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16
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Lai X, Tang J, ElSayed MEH. Recent advances in proteolytic stability for peptide, protein, and antibody drug discovery. Expert Opin Drug Discov 2021; 16:1467-1482. [PMID: 34187273 DOI: 10.1080/17460441.2021.1942837] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Introduction: To discover and develop a peptide, protein, or antibody into a drug requires overcoming multiple challenges to obtain desired properties. Proteolytic stability is one of the challenges and deserves a focused investigation.Areas covered: This review concentrates on improving proteolytic stability by engineering the amino acids around the cleavage sites of a liable peptide, protein, or antibody. Peptidases are discussed on three levels including all peptidases in databases, mixtures based on organ and tissue types, and individual peptidases. The technique to identify cleavage sites is spotlighted on mass spectrometry-based approaches such as MALDI-TOF and LC-MS. For sequence engineering, the replacements that have been commonly applied with a higher chance of success are highlighted at the beginning, while the rarely used and more complicated replacements are discussed later. Although a one-size-fits-all approach does not exist to apply to different projects, this review provides a 3-step strategy for effectively and efficiently conducting the proteolytic stability experiments to achieve the eventual goal of improving the stability by engineering the molecule itself.Expert opinion: Improving the proteolytic stability is a spiraling up process sequenced by testing and engineering. There are many ways to engineer amino acids, but the choice must consider the cost and properties affected by the changes of the amino acids.
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Affiliation(s)
- Xianyin Lai
- Biotechnology Discovery Research, Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN, USA
| | - Jason Tang
- Biotechnology Discovery Research, Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN, USA
| | - Mohamed E H ElSayed
- Biotechnology Discovery Research, Lilly Research Laboratories, Eli Lilly and Company, Indianapolis, IN, USA
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17
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Albuquerque W, Ghezellou P, Li B, Spengler B, Will F, Zorn H, Gand M. Identification of intact peptides by top-down peptidomics reveals cleavage spots in thermolabile wine proteins. Food Chem 2021; 363:130437. [PMID: 34214891 DOI: 10.1016/j.foodchem.2021.130437] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 06/17/2021] [Accepted: 06/19/2021] [Indexed: 11/25/2022]
Abstract
Prevention of haze formation in wines is challenging for winemakers. Thermolabile proteins in wines, notably thaumatin-like proteins (TLPs) and chitinases (CHIs), undergo structural changes under varying physicochemical conditions, resulting in protein aggregation and visible haze in bottled products. Peptidases are an alternative fining method, although an effective proteolysis under typical winemaking conditions (acidic pH and low temperature) is difficult to achieve. In this study, tryptic peptides from TLPs and CHIs were identified by MS-based peptidomics (top-down proteomics) after exposure of scissile bonds on the protein surface. As proposed by the theory of limited proteolysis, protein conformational changes following temperature and pH variations allowed the detection of enzyme-accessible regions. Protein structure visualization and molecular dynamics simulations were used to highlight cleavage spots and provide the scientific basis for haze formation mechanisms. The described method offers a tool to the search for ideal enzymes to prevent wine haze.
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Affiliation(s)
- Wendell Albuquerque
- Institute of Food Chemistry and Food Biotechnology, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, Giessen 35392, Germany
| | - Parviz Ghezellou
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, Giessen 35392, Germany
| | - Binglin Li
- Institute of Food Chemistry and Food Biotechnology, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, Giessen 35392, Germany; College of Food Science and Engineering, Northwest University, Tai Bai Bei Lu 229, 710000 Shaanxi, China
| | - Bernhard Spengler
- Institute of Inorganic and Analytical Chemistry, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, Giessen 35392, Germany
| | - Frank Will
- Department of Beverage Research, Geisenheim University, Von-Lade-Strasse 1, 65366 Geisenheim, Germany
| | - Holger Zorn
- Institute of Food Chemistry and Food Biotechnology, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, Giessen 35392, Germany; Fraunhofer Institute for Molecular Biology and Applied Ecology, Ohlebergsweg 12, 35392 Giessen, Germany
| | - Martin Gand
- Institute of Food Chemistry and Food Biotechnology, Justus Liebig University Giessen, Heinrich-Buff-Ring 17, Giessen 35392, Germany.
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18
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Zhao J, Fan R, Jia F, Huang Y, Huang Z, Hou Y, Hu SQ. Enzymatic Properties of Recombinant Ligase Butelase-1 and Its Application in Cyclizing Food-Derived Angiotensin I-Converting Enzyme Inhibitory Peptides. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:5976-5985. [PMID: 34003638 DOI: 10.1021/acs.jafc.1c01755] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Butelase-1 is an efficient ligase from Clitoria ternatea with wide applications in the food and biopharmaceutical fields. This research aimed to achieve high-efficiency expression of butelase-1 and explore its application in food-derived angiotensin I-converting enzyme (ACE) inhibitory peptides. The recombinant butelase-1 zymogen was prepared at a yield of 100 mg/L in Escherichia coli and successfully activated at pH 4.5, resulting in a 6973.8 U/L yield of activated butelase-1 with a specific activity of 348.69 U/mg and a catalytic efficiency of 9956 M-1 s-1. Activated butelase-1 exhibited considerable resistance to Tween-20, Triton X-100, and methanol. The "traceless" cyclization of ACE inhibitory peptides was realized using activated butelase-1, which resulted in higher stability and ACE inhibitory activity than those of the linear peptides. Our work proposed an efficient method for the preparation of butelase-1 and provided a promising model for its application in food fields.
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Affiliation(s)
- Jinsong Zhao
- Overseas Expertise Introduction Center for Discipline Innovation of Food Nutrition and Human Health (111 Center), School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, China
| | - Renshui Fan
- Overseas Expertise Introduction Center for Discipline Innovation of Food Nutrition and Human Health (111 Center), School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, China
| | - Feng Jia
- Overseas Expertise Introduction Center for Discipline Innovation of Food Nutrition and Human Health (111 Center), School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, China
| | - Yanbo Huang
- Overseas Expertise Introduction Center for Discipline Innovation of Food Nutrition and Human Health (111 Center), School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, China
- State Key Laboratory of Pulp and Paper Engineering, South China University of Technology, Guangzhou, Guangdong 510640, China
| | - Zhiqiang Huang
- Overseas Expertise Introduction Center for Discipline Innovation of Food Nutrition and Human Health (111 Center), School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, China
| | - Yi Hou
- State Key Laboratory of Pulp and Paper Engineering, South China University of Technology, Guangzhou, Guangdong 510640, China
| | - Song-Qing Hu
- Overseas Expertise Introduction Center for Discipline Innovation of Food Nutrition and Human Health (111 Center), School of Food Science and Engineering, South China University of Technology, Guangzhou 510640, China
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19
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Trimethylamine N-oxide alters structure-function integrity of β-casein: Structural disorder co-regulates the aggregation propensity and chaperone activity. Int J Biol Macromol 2021; 182:921-930. [PMID: 33872615 DOI: 10.1016/j.ijbiomac.2021.04.060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 03/31/2021] [Accepted: 04/09/2021] [Indexed: 11/23/2022]
Abstract
Intrinsically disordered proteins (IDPs), involved in the regulation and function of various cellular processes like transcription, translation, cell cycle etc., exist as ensembles of rapidly interconverting structures with functional plasticity. Among numerous cellular regulatory mechanisms involved in structural and functional regulation of IDPs, osmolytes are emerging as promising regulatory agents due to their ability to affect the structure-function integrity of IDPs. The present study investigated the effect of methylamine osmolytes on β-casein, an IDP essential for maintaining the overall stability of casein complex in milk. It was observed that trimethylamine N-oxide induces a compact structural state in β-casein with slightly decreased chaperone activity and insignificant aggregation propensity. However, the other two osmolytes from this group, i.e., sarcosine and betaine, had no significant effect on the overall structure and chaperone activity of the IDP. The present study hints towards the possible evolutionary selection of higher structural disorder in β-casein, compared to α-casein, for stability of the casein complex and prevention of amyloidosis in the mammary gland.
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20
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Yang J, Gao Z, Ren X, Sheng J, Xu P, Chang C, Fu Y. DeepDigest: Prediction of Protein Proteolytic Digestion with Deep Learning. Anal Chem 2021; 93:6094-6103. [DOI: 10.1021/acs.analchem.0c04704] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Jinghan Yang
- CEMS, NCMIS, RCSDS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100190, P. R. China
- School of Mathematical Sciences, University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Zhiqiang Gao
- CEMS, NCMIS, RCSDS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100190, P. R. China
- School of Mathematical Sciences, University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Xiuhan Ren
- School of Sciences, China University of Mining & Technology, Beijing 100083, P. R. China
| | - Jie Sheng
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, P. R. China
| | - Ping Xu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, P. R. China
| | - Cheng Chang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, P. R. China
| | - Yan Fu
- CEMS, NCMIS, RCSDS, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100190, P. R. China
- School of Mathematical Sciences, University of Chinese Academy of Sciences, Beijing 100049, P. R. China
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21
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Petrovich GD, Corradi GR, Pavan CH, Noli Truant S, Adamo HP. Highly exposed segment of the Spf1p P5A-ATPase near transmembrane M5 detected by limited proteolysis. PLoS One 2021; 16:e0245679. [PMID: 33507968 PMCID: PMC7842927 DOI: 10.1371/journal.pone.0245679] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Accepted: 01/05/2021] [Indexed: 11/20/2022] Open
Abstract
The yeast Spf1p protein is a primary transporter that belongs to group 5 of the large family of P-ATPases. Loss of Spf1p function produces ER stress with alterations of metal ion and sterol homeostasis and protein folding, glycosylation and membrane insertion. The amino acid sequence of Spf1p shows the characteristic P-ATPase domains A, N, and P and the transmembrane segments M1-M10. In addition, Spf1p exhibits unique structures at its N-terminus (N-T region), including two putative additional transmembrane domains, and a large insertion connecting the P domain with transmembrane segment M5 (D region). Here we used limited proteolysis to examine the structure of Spf1p. A short exposure of Spf1p to trypsin or proteinase K resulted in the cleavage at the N and C terminal regions of the protein and abrogated the formation of the catalytic phosphoenzyme and the ATPase activity. In contrast, limited proteolysis of Spf1p with chymotrypsin generated a large N-terminal fragment containing most of the M4-M5 cytosolic loop, and a minor fragment containing the C-terminal region. If lipids were present during chymotryptic proteolysis, phosphoenzyme formation and ATPase activity were preserved. ATP slowed Spf1p proteolysis without detectable changes of the generated fragments. The analysis of the proteolytic peptides by mass spectrometry and Edman degradation indicated that the preferential chymotryptic site was localized near the cytosolic end of M5. The susceptibility to proteolysis suggests an unexpected exposure of this region of Spf1p that may be an intrinsic feature of P5A-ATPases.
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Affiliation(s)
- Guido D. Petrovich
- Facultad de Farmacia y Bioquímica, Departamento de Química Biológica, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)-Universidad de Buenos Aires, Instituto de Química y Fisicoquímica Biológicas (IQUIFIB), Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Gerardo R. Corradi
- Facultad de Farmacia y Bioquímica, Departamento de Química Biológica, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)-Universidad de Buenos Aires, Instituto de Química y Fisicoquímica Biológicas (IQUIFIB), Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Carlos H. Pavan
- Facultad de Farmacia y Bioquímica, Departamento de Química Biológica, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)-Universidad de Buenos Aires, Instituto de Química y Fisicoquímica Biológicas (IQUIFIB), Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Sofia Noli Truant
- Facultad de Farmacia y Bioquímica, Cátedra de Inmunología and Instituto de Estudios de la Inmunidad Humoral Prof. Dr. Ricardo A. Margni (IDEHU), UBA-CONICET, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Hugo P. Adamo
- Facultad de Farmacia y Bioquímica, Departamento de Química Biológica, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET)-Universidad de Buenos Aires, Instituto de Química y Fisicoquímica Biológicas (IQUIFIB), Universidad de Buenos Aires, Buenos Aires, Argentina
- * E-mail:
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Zhu T, Wang SH, Li D, Wang SY, Liu X, Song J, Wang YT, Zhang SY. Progress of tubulin polymerization activity detection methods. Bioorg Med Chem Lett 2021; 37:127698. [PMID: 33468346 DOI: 10.1016/j.bmcl.2020.127698] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 11/05/2020] [Accepted: 11/14/2020] [Indexed: 12/13/2022]
Abstract
Tubulin, an important target in tumor therapy, is one of the hotspots in the field of antineoplastic drugs in recent years, and it is of great significance to design and screen new inhibitors for this target. Natural products and chemical synthetic drugs are the main sources of tubulin inhibitors. However, due to the variety of compound structure types, it has always been difficult for researchers to screen out polymerization inhibitors with simple operation, high efficiency and low cost. A large number of articles have reported the screening methods of tubulin inhibitors and their biological activity. In this article, the biological activity detection methods of tubulin polymerization inhibitors are reviewed. Thus, it provides a theoretical basis for the further study of tubulin polymerization inhibitors and the selection of methods for tubulin inhibitors.
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Affiliation(s)
- Ting Zhu
- School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, China; Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Sheng-Hui Wang
- School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Dong Li
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Shu-Yu Wang
- School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Xu Liu
- Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China
| | - Jian Song
- School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, China; Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou 450001, China.
| | - Ya-Ting Wang
- School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, China.
| | - Sai-Yang Zhang
- School of Basic Medical Sciences, Zhengzhou University, Zhengzhou 450001, China; Henan Institute of Advanced Technology, Zhengzhou University, Zhengzhou 450001, China.
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23
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Tryptophan Fluorescence and Time-Lag Hydrolysis of Peptide Bonds during Degradation of β-Lactoglobulin by Trypsin. Catalysts 2020. [DOI: 10.3390/catal10121368] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The opening of protein globules and corresponding exposure of their internal peptide bonds, the so-called demasking effect, is required for successful hydrolysis of peptide bonds by proteases. Under the proteolytic action of trypsin on β-lactoglobulin (β-LG), the evolution of tryptophan fluorescence spectra showed that the demasking process consists of two stages with different demasking rate constants for each stage. It was found that the ratio of these constants depends on the concentration of trypsin and changes are approximately threefold when the concentration of trypsin changes in the range of 0.3–15 mg/L. Simulation of hydrolysis taking into account the demasking effect demonstrated how the apparent first-order rate constants obtained experimentally are related to the true hydrolysis rate constants and demasking parameters. The lag phase in the kinetic curves corresponding to the hydrolysis of various peptide bonds in β-LG was also analyzed. The increased lag times indicated sites that are hydrolyzed by a two-stage demasking mechanism.
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24
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Payandeh Z, Rahbar MR, Jahangiri A, Hashemi ZS, Zakeri A, Jafarisani M, Rasaee MJ, Khalili S. Design of an engineered ACE2 as a novel therapeutics against COVID-19. J Theor Biol 2020; 505:110425. [PMID: 32735992 PMCID: PMC7387268 DOI: 10.1016/j.jtbi.2020.110425] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 07/05/2020] [Accepted: 07/27/2020] [Indexed: 01/02/2023]
Abstract
The interaction between the angiotensin-converting enzyme 2 (ACE2) and the receptor binding domain (RBD) of the spike protein from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) plays a pivotal role in virus entry into the host cells. Since recombinant ACE2 protein has been suggested as an anti-SARS-CoV-2 therapeutic agent, this study was conducted to design an ACE2 protein with more desirable properties. In this regard, the amino acids with central roles in enzymatic activity of the ACE2 were substituted. Moreover, saturation mutagenesis at the interaction interface between the ACE2 and RBD was performed to increase their interaction affinity. The best mutations to increase the structural and thermal stability of the ACE2 were also selected based on B factors and mutation effects. The obtained resulted revealed that the Arg273Gln and Thr445Gly mutation have drastically reduced the binding affinity of the angiotensin-II into the active site of ACE2. The Thr27Arg mutation was determined to be the most potent mutation to increase the binding affinity. The Asp427Arg mutation was done to decrease the flexibility of the region with high B factor. The Pro451Met mutation along with the Gly448Trp mutation was predicted to increase the thermodynamic stability and thermostability of the ACE2. The designed therapeutic ACE2 would have no enzymatic activity while it could bear stronger interaction with Spike glycoprotein of the SARS-CoV-2. Moreover, decreased in vivo enzymatic degradation would be anticipated due to increased thermostability. This engineered ACE2 could be exploited as a novel therapeutic agent against COVID-19 after necessary evaluations.
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Affiliation(s)
- Zahra Payandeh
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohammad Reza Rahbar
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Abolfazl Jahangiri
- Applied Microbiology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Zahra Sadat Hashemi
- ATMP Department, Breast Cancer Research Center, Motamed Cancer Institute, ACECR, Tehran, Iran
| | - Alireza Zakeri
- Department of Biology Sciences, Shahid Rajaee Teacher Training University, Tehran, Iran
| | - Moslem Jafarisani
- Clinical Biochemistry, School of Medicine, Shahroud University of Medical Sciences, Shahroud, Iran
| | - Mohammad Javad Rasaee
- Department of Medical Biotechnology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Saeed Khalili
- Department of Biology Sciences, Shahid Rajaee Teacher Training University, Tehran, Iran.
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Dai L, Li Z, Chen D, Jia L, Guo J, Zhao T, Nordlund P. Target identification and validation of natural products with label-free methodology: A critical review from 2005 to 2020. Pharmacol Ther 2020; 216:107690. [PMID: 32980441 DOI: 10.1016/j.pharmthera.2020.107690] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 09/22/2020] [Accepted: 09/22/2020] [Indexed: 02/08/2023]
Abstract
Natural products (NPs) have been an important source of therapeutic drugs in clinic use and contributed many chemical probes for research. The usefulness of NPs is however often marred by the incomplete understanding of their direct cellular targets. A number of experimental methods for drug target identification have been developed over the years. One class of methods, termed "label-free" methodology, exploits the energetic and biophysical features accompanying the association of macromolecules with drugs and other compounds in their native forms. Herein we review the working principles, assay implementations, and key applications of the most important approaches, and also give examples where they have been applied to NPs. We also assess the key advantages and limitations of each method. Furthermore, we address when and how the label-free methodology can be particularly useful considering some of the unique features of NP chemistry and bioactivation.
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Affiliation(s)
- Lingyun Dai
- Department of Urology, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen Urology Minimally Invasive Engineering Center, Shenzhen 518020, Guangdong, China; Department of Geriatrics, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen 518020, Guangdong, China; Institute of Molecular and Cell Biology, A*STAR, Singapore 138673, Singapore.
| | - Zhijie Li
- Department of Urology, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen Urology Minimally Invasive Engineering Center, Shenzhen 518020, Guangdong, China; Department of Geriatrics, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen 518020, Guangdong, China
| | - Dan Chen
- Institute of Molecular and Cell Biology, A*STAR, Singapore 138673, Singapore
| | - Lin Jia
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong 999077, China
| | - Jinan Guo
- Department of Urology, Shenzhen People's Hospital (The Second Clinical Medical College, Jinan University, The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen Urology Minimally Invasive Engineering Center, Shenzhen 518020, Guangdong, China
| | - Tianyun Zhao
- Institute of Molecular and Cell Biology, A*STAR, Singapore 138673, Singapore
| | - Pär Nordlund
- Institute of Molecular and Cell Biology, A*STAR, Singapore 138673, Singapore; Department of Oncology and Pathology, Karolinska Institutet, 171 77 Stockholm, Sweden.
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Spagnolli G, Requena JR, Biasini E. Understanding prion structure and conversion. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2020; 175:19-30. [PMID: 32958233 DOI: 10.1016/bs.pmbts.2020.07.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Since their original identification, prions have represented enigmatic agents that defy the classical concept of genetic inheritance. For almost four decades, the high-resolution structure of PrPSc, the infectious and misfolded counterpart of the cellular prion protein (PrPC), has remained elusive, mostly due to technical challenges posed by its high insolubility and aggregation propensity. As a result, such a lack of information has critically hampered the search for an effective therapy against prion diseases. Nevertheless, multiple attempts to get insights into the structure of PrPSc have provided important experimental constraints that, despite being at limited resolution, are paving the way for the application of computer-aided technologies to model the three-dimensional architecture of prions and their templated replication mechanism. Here, we review the most relevant studies carried out so far to elucidate the conformation of infectious PrPSc and offer an overview of the most advanced molecular models to explain prion structure and conversion.
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Affiliation(s)
- Giovanni Spagnolli
- Department of Cellular, Computational and Integrative Biology (CIBIO), Trento, TN, Italy; Dulbecco Telethon Institute, University of Trento, Trento, TN, Italy
| | - Jesús R Requena
- CIMUS Biomedical Research Institute & Department of Medical Sciences, University of Santiago de Compostela-IDIS, Santiago, Spain
| | - Emiliano Biasini
- Department of Cellular, Computational and Integrative Biology (CIBIO), Trento, TN, Italy; Dulbecco Telethon Institute, University of Trento, Trento, TN, Italy.
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27
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Padín-González E, Navarro-Palomares E, Valdivia L, Iturrioz-Rodríguez N, Correa MA, Valiente R, Fanarraga ML. A custom-made functionalization method to control the biological identity of nanomaterials. NANOMEDICINE-NANOTECHNOLOGY BIOLOGY AND MEDICINE 2020; 29:102268. [PMID: 32663511 DOI: 10.1016/j.nano.2020.102268] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Revised: 06/24/2020] [Accepted: 07/06/2020] [Indexed: 12/12/2022]
Abstract
Here we propose a one-step strategy to endow nanomaterials with a custom-designed bio-identity. This study designs a universal 'nanomaterial binding domain' that can be genetically attached to any protein ensuring precise and spontaneous protein orientation. We demonstrate how, despite the simplicity of the method, the bioconjugation achieved: (i) is highly efficient, even in the presence of competing proteins, (ii) is stable at extreme physiological conditions (pH ranges 5.2-9.0; NaCl concentrations 0-1 M); (iii) prevents unwanted protein biofouling days after incubation in biologically-relevant conditions; and finally, (iv) avoids nanoparticle interaction with promiscuous unspecific receptors. In summary, this protein biocoating technique, applicable to a wide array of nano-designs, integrates material science and molecular biology procedures to create hybrid nanodevices with well-defined surfaces and predictable biological behaviors, opening a chapter in precision nanodiagnostics, nanosensing or nanotherapeutic applications.
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Affiliation(s)
| | | | - Lourdes Valdivia
- Group of Nanomedicina-IDIVAL University of Cantabria, Santander, Spain
| | | | - Miguel Angel Correa
- Department of Physical Chemistry, Centre for Biomedical Research (CINBIO), Southern Galicia Institute of Health Research (IISGS), and Biomedical Research Networking Center for Mental Health (CIBERSAM), Universidad de Vigo, Vigo, Spain
| | - Rafael Valiente
- Group of Nanomedicina-IDIVAL University of Cantabria, Santander, Spain; Department of Applied Physics, Facultad de Ciencias, Santander, Spain
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28
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Harman JL, Loes AN, Warren GD, Heaphy MC, Lampi KJ, Harms MJ. Evolution of multifunctionality through a pleiotropic substitution in the innate immune protein S100A9. eLife 2020; 9:e54100. [PMID: 32255429 PMCID: PMC7213983 DOI: 10.7554/elife.54100] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 04/03/2020] [Indexed: 12/16/2022] Open
Abstract
Multifunctional proteins are evolutionary puzzles: how do proteins evolve to satisfy multiple functional constraints? S100A9 is one such multifunctional protein. It potently amplifies inflammation via Toll-like receptor four and is antimicrobial as part of a heterocomplex with S100A8. These two functions are seemingly regulated by proteolysis: S100A9 is readily degraded, while S100A8/S100A9 is resistant. We take an evolutionary biochemical approach to show that S100A9 evolved both functions and lost proteolytic resistance from a weakly proinflammatory, proteolytically resistant amniote ancestor. We identify a historical substitution that has pleiotropic effects on S100A9 proinflammatory activity and proteolytic resistance but has little effect on S100A8/S100A9 antimicrobial activity. We thus propose that mammals evolved S100A8/S100A9 antimicrobial and S100A9 proinflammatory activities concomitantly with a proteolytic 'timer' to selectively regulate S100A9. This highlights how the same mutation can have pleiotropic effects on one functional state of a protein but not another, thus facilitating the evolution of multifunctionality.
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Affiliation(s)
- Joseph L Harman
- Department of Chemistry and Biochemistry, University of OregonEugeneUnited States
- Institute of Molecular Biology, University of OregonEugeneUnited States
| | - Andrea N Loes
- Department of Chemistry and Biochemistry, University of OregonEugeneUnited States
- Institute of Molecular Biology, University of OregonEugeneUnited States
| | - Gus D Warren
- Department of Chemistry and Biochemistry, University of OregonEugeneUnited States
- Institute of Molecular Biology, University of OregonEugeneUnited States
| | - Maureen C Heaphy
- Department of Chemistry and Biochemistry, University of OregonEugeneUnited States
- Institute of Molecular Biology, University of OregonEugeneUnited States
| | | | - Michael J Harms
- Department of Chemistry and Biochemistry, University of OregonEugeneUnited States
- Institute of Molecular Biology, University of OregonEugeneUnited States
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29
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Lyu J, Wang K, Ye M. Modification-free approaches to screen drug targets at proteome level. Trends Analyt Chem 2020. [DOI: 10.1016/j.trac.2019.06.024] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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Permyakov SE, Yundina EN, Kazakov AS, Permyakova ME, Uversky VN, Permyakov EA. Mouse S100G protein exhibits properties characteristic of a calcium sensor. Cell Calcium 2020; 87:102185. [PMID: 32114281 DOI: 10.1016/j.ceca.2020.102185] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 02/10/2020] [Accepted: 02/21/2020] [Indexed: 01/09/2023]
Abstract
Bovine S100 G (calbindin D9k, small Ca2+-binding protein of the EF-hand superfamily) is considered as a calcium buffer protein; i.e., the binding of Ca2+ practically does not change its general conformation. A set of experimental approaches has been used to study structural properties of apo- and Ca2+-loaded forms of mouse S100 G (81.4% identity in amino acid sequence with bovine S100 G). This analysis revealed that, in contrast to bovine S100 G, the removal of calcium ions increases α-helices content of mouse S100 G protein and enhances its accessibility to digestion by α-chymotrypsin. Furthermore, mouse apo-S100 G is characterized by a decreased surface hydrophobicity and reduced tendency for oligomerization. Such behavior is typical of calcium sensor proteins. Apo-state of mouse S100 G still has rather compact structure, which can be cooperatively unfolded by temperature and GdnHCl. Computational analysis of amino acid sequences of S100 G proteins shows that these proteins could be in a disordered state upon a removal of the bound calcium ions. The experimental data show that, although mouse apo-S100 G is flexible compared to the Ca2+-loaded state, the apo-form is not completely disordered and preserves some cooperatively meting structure. The origin of the unexpectedly high stability of mouse S100 G can be rationalized by an exceptionally strong association of its N- and C-terminal parts containing the EF-hands I and II, respectively.
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Affiliation(s)
- Sergei E Permyakov
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia.
| | - Elena N Yundina
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - Alexei S Kazakov
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - Maria E Permyakova
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
| | - Vladimir N Uversky
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia; Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, 33612, USA.
| | - Eugene A Permyakov
- Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russia
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31
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de la Fuente M, Han X, Miyagi M, Nieman MT. Expression and Purification of Protease-Activated Receptor 4 (PAR4) and Analysis with Histidine Hydrogen-Deuterium Exchange. Biochemistry 2020; 59:671-681. [PMID: 31957446 DOI: 10.1021/acs.biochem.9b00987] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Protease-activated receptors (PARs) are G-protein-coupled receptors that are activated by proteolysis of the N-terminus, which exposes a tethered ligand that interacts with the receptor. Numerous studies have focused on the signaling pathways mediated by PARs. However, the structural basis for initiation of these pathways is unknown. Here, we describe a strategy for the expression and purification of PAR4. This is the first PAR family member to be isolated without stabilizing modifications for biophysical studies. We monitored PAR4 activation with histidine hydrogen-deuterium exchange. PAR4 has nine histidines that are spaced throughout the protein, allowing a global view of solvent accessible and nonaccessible regions. Peptides containing each of the nine His residues were used to determine the t1/2 for each His residue in apo or thrombin-activated PAR4. The thrombin-cleaved PAR4 exhibited a 2-fold increase (p > 0.01) in t1/2 values observed for four histidine residues (His180, His229, His240, and His380), demonstrating that these regions have decreased solvent accessibility upon thrombin treatment. In agreement, thrombin-cleaved PAR4 also was resistant to thermolysin digestion. In contrast, the rate of thermolysin proteolysis following stimulation with the PAR4 activation peptide was the same as that of unstimulated PAR4. Further analysis showed the C-terminus is protected in thrombin-activated PAR4 compared to uncleaved or agonist peptide-treated PAR4. The studies described here are the first to examine the tethered ligand activation mechanism for a PAR family member biophysically and shed light on the overall conformational changes that follow activation of PARs by a protease.
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Affiliation(s)
- Maria de la Fuente
- Department of Pharmacology , Case Western Reserve University , Cleveland , Ohio 44106-4965 , United States
| | - Xu Han
- Department of Pharmacology , Case Western Reserve University , Cleveland , Ohio 44106-4965 , United States
| | - Masaru Miyagi
- Department of Pharmacology , Case Western Reserve University , Cleveland , Ohio 44106-4965 , United States
| | - Marvin T Nieman
- Department of Pharmacology , Case Western Reserve University , Cleveland , Ohio 44106-4965 , United States
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32
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Sandoval DR, Gomez Toledo A, Painter CD, Tota EM, Sheikh MO, West AMV, Frank MM, Wells L, Xu D, Bicknell R, Corbett KD, Esko JD. Proteomics-based screening of the endothelial heparan sulfate interactome reveals that C-type lectin 14a (CLEC14A) is a heparin-binding protein. J Biol Chem 2020; 295:2804-2821. [PMID: 31964714 DOI: 10.1074/jbc.ra119.011639] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 01/10/2020] [Indexed: 12/21/2022] Open
Abstract
Animal cells express heparan sulfate proteoglycans that perform many important cellular functions by way of heparan sulfate-protein interactions. The identification of membrane heparan sulfate-binding proteins is challenging because of their low abundance and the need for extensive enrichment. Here, we report a proteomics workflow for the identification and characterization of membrane-anchored and extracellular proteins that bind heparan sulfate. The technique is based on limited proteolysis of live cells in the absence of denaturation and fixation, heparin-affinity chromatography, and high-resolution LC-MS/MS, and we designate it LPHAMS. Application of LPHAMS to U937 monocytic and primary murine and human endothelial cells identified 55 plasma membrane, extracellular matrix, and soluble secreted proteins, including many previously unidentified heparin-binding proteins. The method also facilitated the mapping of the heparin-binding domains, making it possible to predict the location of the heparin-binding site. To validate the discovery feature of LPHAMS, we characterized one of the newly-discovered heparin-binding proteins, C-type lectin 14a (CLEC14A), a member of the C-type lectin family that modulates angiogenesis. We found that the C-type lectin domain of CLEC14A binds one-to-one to heparin with nanomolar affinity, and using molecular modeling and mutagenesis, we mapped its heparin-binding site. CLEC14A physically interacted with other glycosaminoglycans, including endothelial heparan sulfate and chondroitin sulfate E, but not with neutral or sialylated oligosaccharides. The LPHAMS technique should be applicable to other cells and glycans and provides a way to expand the repertoire of glycan-binding proteins for further study.
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Affiliation(s)
- Daniel R Sandoval
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California 92093; Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, California 92093
| | - Alejandro Gomez Toledo
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California 92093
| | - Chelsea D Painter
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California 92093; Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, California 92093
| | - Ember M Tota
- Department of Chemistry and Biochemistry, University of California, San Diego, La Jolla, California 92093
| | - M Osman Sheikh
- Department of Biochemistry and Molecular Biology, Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602
| | - Alan M V West
- Biomedical Sciences Graduate Program, University of California, San Diego, La Jolla, California 92093
| | | | - Lance Wells
- Department of Biochemistry and Molecular Biology, Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia 30602
| | - Ding Xu
- Department of Oral Biology, School of Dental Medicine, University at Buffalo, Buffalo, New York 14214
| | - Roy Bicknell
- College of Medicine and Dentistry, University of Birmingham, Birmingham B15 2TT, United Kingdom
| | - Kevin D Corbett
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California 92093
| | - Jeffrey D Esko
- Department of Cellular and Molecular Medicine, University of California, San Diego, La Jolla, California 92093; Glycobiology Research and Training Center, University of California, San Diego, La Jolla, California 92093.
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Wang H, Lin X, Li S, Lin J, Xie C, Liu D, Yao D. Rational molecular design for improving digestive enzyme resistance of beta-glucosidase from Trichoderma viride based on inhibition of bound state formation. Enzyme Microb Technol 2019; 133:109465. [PMID: 31874695 DOI: 10.1016/j.enzmictec.2019.109465] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 11/05/2019] [Accepted: 11/06/2019] [Indexed: 11/18/2022]
Abstract
Beta-glucosidase (BGL1) is widely used in animal feed industries. However, degradation caused by digestive enzymes in the intestine hampers its application. Improving the resistance of feed enzymes against proteases is crucial in livestock farming. To improve the resistance of beta-glucosidase against pepsin and trypsin, a rational molecular design based on the inhibition of bound-state formation and secondary design was developed. The strategy includes: (1) prediction of the interaction surface of the pepsin-BGL1 complex structure, (2) prediction of key amino acids affecting the formation of the complex, (3) optimization of pepsin-resistant mutants by structural evaluation, (4) secondary molecular design based on pepsin-resistant mutants, and optimization of pepsin and trypsin-resistant mutants. Two BGL1 protein mutants (BGL1Q627C and BGL1Q627C/R543H/R646W) were constructed, and then mutated and wild-type BGL1s were expressed in Pichia pastoris. The half-life of BGL1Q627C and BGL1Q627C/R543H/R646W were 1.36 and 1.51 times that of the wild type upon pepsin exposure, respectively. For trypsin resistance, the half-life were 0.93 and 1.53 times that of the wild type, respectively. Compare to those of the wild type, most of the basic enzymatic properties of both mutants were not significantly changed except for increased Michaelis constants. The rational design method can be used as a guide for modifying other feed enzymes.
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Affiliation(s)
- Hao Wang
- Institute of Microbial Biotechnology, Jinan University, Guangzhou City, Guangdong Province, 510632, China; Department of Bioengineering, Jinan University, Guangzhou City, Guangdong Province, 510632, China
| | - Xiangna Lin
- Institute of Microbial Biotechnology, Jinan University, Guangzhou City, Guangdong Province, 510632, China; National Engineering Research Center of Genetic Medicine, Guangzhou City, Guangdong Province, 510632, China
| | - Shuang Li
- Institute of Microbial Biotechnology, Jinan University, Guangzhou City, Guangdong Province, 510632, China; Department of Bioengineering, Jinan University, Guangzhou City, Guangdong Province, 510632, China
| | - Jianlin Lin
- Institute of Microbial Biotechnology, Jinan University, Guangzhou City, Guangdong Province, 510632, China
| | - Chunfang Xie
- Institute of Microbial Biotechnology, Jinan University, Guangzhou City, Guangdong Province, 510632, China; Department of Bioengineering, Jinan University, Guangzhou City, Guangdong Province, 510632, China
| | - Daling Liu
- Institute of Microbial Biotechnology, Jinan University, Guangzhou City, Guangdong Province, 510632, China; Department of Bioengineering, Jinan University, Guangzhou City, Guangdong Province, 510632, China.
| | - Dongsheng Yao
- Institute of Microbial Biotechnology, Jinan University, Guangzhou City, Guangdong Province, 510632, China; National Engineering Research Center of Genetic Medicine, Guangzhou City, Guangdong Province, 510632, China.
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Structural modeling and role of HAX-1 as a positive allosteric modulator of human serine protease HtrA2. Biochem J 2019; 476:2965-2980. [PMID: 31548268 DOI: 10.1042/bcj20190569] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Revised: 09/18/2019] [Accepted: 09/23/2019] [Indexed: 11/17/2022]
Abstract
HAX-1, a multifunctional protein involved in cell proliferation, calcium homeostasis, and regulation of apoptosis, is a promising therapeutic target. It regulates apoptosis through multiple pathways, understanding of which is limited by the obscurity of its structural details and its intricate interaction with its cellular partners. Therefore, using computational modeling, biochemical, functional enzymology and spectroscopic tools, we predicted the structure of HAX-1 as well as delineated its interaction with one of it pro-apoptotic partner, HtrA2. In this study, three-dimensional structure of HAX-1 was predicted by threading and ab initio tools that were validated using limited proteolysis and fluorescence quenching studies. Our pull-down studies distinctly demonstrate that the interaction of HtrA2 with HAX-1 is directly through its protease domain and not via the conventional PDZ domain. Enzymology studies further depicted that HAX-1 acts as an allosteric activator of HtrA2. This 'allosteric regulation' offers promising opportunities for the specific control and functional modulation of a wide range of biological processes associated with HtrA2. Hence, this study for the first time dissects the structural architecture of HAX-1 and elucidates its role in PDZ-independent activation of HtrA2.
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35
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Gao Z, Chang C, Yang J, Zhu Y, Fu Y. AP3: An Advanced Proteotypic Peptide Predictor for Targeted Proteomics by Incorporating Peptide Digestibility. Anal Chem 2019; 91:8705-8711. [DOI: 10.1021/acs.analchem.9b02520] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Zhiqiang Gao
- National Center for Mathematics and Interdisciplinary Sciences, Key Laboratory of Random Complex Structures and Data Science, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100190, China
- School of Mathematical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Cheng Chang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
| | - Jinghan Yang
- National Center for Mathematics and Interdisciplinary Sciences, Key Laboratory of Random Complex Structures and Data Science, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100190, China
- School of Mathematical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yunping Zhu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, National Center for Protein Sciences (Beijing), Beijing Institute of Lifeomics, Beijing 102206, China
- Anhui Medical University, Hefei 230032, China
| | - Yan Fu
- National Center for Mathematics and Interdisciplinary Sciences, Key Laboratory of Random Complex Structures and Data Science, Academy of Mathematics and Systems Science, Chinese Academy of Sciences, Beijing 100190, China
- School of Mathematical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
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36
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Alavi SE, Cabot PJ, Moyle PM. Glucagon-Like Peptide-1 Receptor Agonists and Strategies To Improve Their Efficiency. Mol Pharm 2019; 16:2278-2295. [PMID: 31050435 DOI: 10.1021/acs.molpharmaceut.9b00308] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Type 2 diabetes mellitus (T2DM) is increasing in global prevalence and is associated with serious health problems (e.g., cardiovascular disease). Various treatment options are available for T2DM, including the incretin hormone glucagon-like peptide-1 (GLP-1). GLP-1 is a therapeutic peptide secreted from the intestines following food intake, which stimulates the secretion of insulin from the pancreas. The native GLP-1 has a very short plasma half-life, owning to renal clearance and degradation by the enzyme dipeptidyl peptidase-4. To overcome this issue, various GLP-1 agonists with increased resistance to proteolytic degradation and reduced renal clearance have been developed, with several currently marketed. Strategies, such as controlled release delivery systems, methods to reduce renal clearance (e.g., PEGylation and conjugation to antibodies), and methods to improve proteolytic stability (e.g., stapling, cyclization, and glycosylation) provide means to further improve the ability of GLP-1 analogs. These will be discussed in this literature review.
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Affiliation(s)
- Seyed Ebrahim Alavi
- School of Pharmacy , The University of Queensland , Woolloongabba , 4102 , Australia
| | - Peter J Cabot
- School of Pharmacy , The University of Queensland , Woolloongabba , 4102 , Australia
| | - Peter M Moyle
- School of Pharmacy , The University of Queensland , Woolloongabba , 4102 , Australia
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37
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Chatterjee S, Das A, Raghuraman H. Biochemical and biophysical characterization of a prokaryotic Mg 2+ ion channel: Implications for cost-effective purification of membrane proteins. Protein Expr Purif 2019; 161:8-16. [PMID: 31028884 DOI: 10.1016/j.pep.2019.04.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 04/19/2019] [Indexed: 10/26/2022]
Abstract
Although magnesium is the second most abundant cation present in the cell, the transport mechanism of Mg2+ across membranes is poorly understood. Importantly, the prokaryotic MgtE Mg2+ channel is related to mammalian SLC41A1 transporters and, therefore, biochemical and biophysical characterization of MgtE and its orthologs assumes significance. To date, the purification and structure determination of MgtE from Thermus thermophilus has been carried out using the widely used nonionic detergent, n-dodecyl-β-d-maltopyranoside (DDM). However, DDM is an expensive detergent and alternative methods to produce high-quality proteins in stable and functional form will be practically advantageous to carry out structural studies in a cost-effective manner. In this work, we have utilized 'dual-detergent strategy' to successfully purify MgtE channel in a stable and functional form by employing relatively inexpensive detergents (Triton X-100 and Anzergent 3-14) for membrane solubilization and subsequently changed to DDM during purification. Our results show that Triton X-100 and Anzergent 3-14 extract MgtE well and the quality of purified protein is comparable to DDM-extracted MgtE. Interestingly, addition of high concentration of salt and glycerol during solubilization does not significantly affect the quantity and quality of MgtE. Importantly, limited proteolysis assay, circular dichroism spectroscopy and ensemble tryptophan fluorescence strongly support the use of Triton X-100, in particular, as an inexpensive, alternative detergent for the purification of MgtE without compromising the structural integrity of the channel and Mg2+-induced gating-related conformational dynamics. Overall, these results are relevant for the cost-effective purification of stable and functional membrane proteins in general, and magnesium channels, in particular.
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Affiliation(s)
- Satyaki Chatterjee
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, Homi Bhabha National Institute, 1/AF Bidhannagar, Kolkata, 700 064, India
| | - Anindita Das
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, Homi Bhabha National Institute, 1/AF Bidhannagar, Kolkata, 700 064, India
| | - H Raghuraman
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, Homi Bhabha National Institute, 1/AF Bidhannagar, Kolkata, 700 064, India.
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38
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Brown MC, Abdine A, Chavez J, Schaffner A, Torres-Arancivia C, Lada B, JiJi RD, Osman R, Cooley JW, Ubarretxena-Belandia I. Unwinding of the Substrate Transmembrane Helix in Intramembrane Proteolysis. Biophys J 2019; 114:1579-1589. [PMID: 29642028 DOI: 10.1016/j.bpj.2018.01.043] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2017] [Revised: 12/19/2017] [Accepted: 01/08/2018] [Indexed: 10/17/2022] Open
Abstract
Intramembrane-cleaving proteases (I-CLiPs) activate pools of single-pass helical membrane protein signaling precursors that are key in the physiology of prokaryotic and eukaryotic cells. Proteases typically cleave peptide bonds within extended or flexible regions of their substrates, and thus the mechanism underlying the ability of I-CLiPs to hydrolyze the presumably α-helical transmembrane domain (TMD) of these membrane proteins is unclear. Using deep-ultraviolet resonance Raman spectroscopy in combination with isotopic labeling, we show that although predominantly in canonical α-helical conformation, the TMD of the established I-CLiP substrate Gurken displays 310-helical geometry. As measured by microscale thermophoresis, this substrate binds with high affinity to the I-CLiPs GlpG rhomboid and MCMJR1 presenilin homolog in detergent micelles. Binding results in deep-ultraviolet resonance Raman spectra, indicating conformational changes consistent with unwinding of the 310-helical region of the substrate's TMD. This 310-helical conformation is key for intramembrane proteolysis, as the substitution of a single proline residue in the TMD of Gurken by alanine suppresses 310-helical content in favor of α-helical geometry and abolishes cleavage without affecting binding to the I-CLiP. Complemented by molecular dynamics simulations of the TMD of Gurken, our vibrational spectroscopy data provide biophysical evidence in support of a model in which the transmembrane region of cleavable I-CLiP substrates displays local deviations in canonical α-helical conformation characterized by chain flexibility, and binding to the enzyme results in conformational changes that facilitate local unwinding of the transmembrane helix for cleavage.
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Affiliation(s)
- Mia C Brown
- Department of Chemistry, University of Missouri, Columbia, Missouri
| | - Alaa Abdine
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Jose Chavez
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Adam Schaffner
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Celia Torres-Arancivia
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Brian Lada
- Department of Chemistry, University of Missouri, Columbia, Missouri
| | - Renee D JiJi
- Department of Chemistry, University of Missouri, Columbia, Missouri
| | - Roman Osman
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Jason W Cooley
- Department of Chemistry, University of Missouri, Columbia, Missouri.
| | - Iban Ubarretxena-Belandia
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, New York; Biofisika Institute (CSIC, UPV/EHU), University of the Basque Country, Leioa, Spain.
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39
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Ma KM, Thomas ES, Wereszczynski J, Menhart N. Empirical and Computational Comparison of Alternative Therapeutic Exon Skip Repairs for Duchenne Muscular Dystrophy. Biochemistry 2019; 58:2061-2076. [PMID: 30896926 DOI: 10.1021/acs.biochem.9b00062] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Duchenne muscular dystrophy (DMD) is a common and devastating genetic disease primarily caused by exon deletions that create a genetic frameshift in dystrophin. Exon skipping therapy seeks to correct this by masking an exon during the mRNA maturation process, restoring dystrophin expression, but creating an edited protein missing both the original defect and the therapeutically skipped region. Crucially, it is possible to correct many defects in alternative ways, by skipping an exon either before or after the patient's defect. This results in alternatively edited, hybrid proteins that might have different properties and therapeutic consequences. We examined three such dystrophin exon-skipped edits, Δe45-53, Δe46-54, and Δe47-55, comprising two pairs of alternative repairs of Δe46-53 and Δe47-54 DMD defects. We found that in both cases, Δe46-54 was the more stable repair as determined by a variety of thermodynamic and biochemical measurements. We also examined the origin of these differences with molecular dynamics simulations, which showed that these stability differences were the result of different types of structural perturbations. For example, in one edit there was partial unfolding at the edit site that caused domain-localized perturbations while in another there was unfolding at the protein domain junctions distal to the edit site that increased molecular flexibility. These results demonstrate that alternative exon skip repairs of the same underlying defect can have very different consequences at the level of protein structure and stability and furthermore that these can arise by different mechanisms, either locally or by more subtle long-range perturbations.
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40
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Omidi-Ardali H, Aminian M, Golestani A, Shahaboddin ME, Maleki M. N∆89 and C∆274 Truncated Enzymes of Chondroitinase ABC I Regain More Imperturbable Microenvironments Around Structural Components in Comparison to their Wild Type. Protein J 2019; 38:151-159. [DOI: 10.1007/s10930-019-09821-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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41
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Whittington AC, Mason AJ, Rokyta DR. A Single Mutation Unlocks Cascading Exaptations in the Origin of a Potent Pitviper Neurotoxin. Mol Biol Evol 2019; 35:887-898. [PMID: 29329419 DOI: 10.1093/molbev/msx334] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Evolutionary innovations and complex phenotypes seemingly require an improbable amount of genetic change to evolve. Rattlesnakes display two dramatically different venom phenotypes. Type I venoms are hemorrhagic with low systemic toxicity and high expression of tissue-destroying snake venom metalloproteinases. Type II venoms are highly neurotoxic and lack snake venom metalloproteinase expression and associated hemorrhagic activity. This dichotomy hinges on Mojave toxin (MTx), a phospholipase A2 (PLA2) based β-neurotoxin expressed in Type II venoms. MTx is comprised of a nontoxic acidic subunit that undergoes extensive proteolytic processing and allosterically regulates activity of a neurotoxic basic subunit. Evolution of the acidic subunit presents an evolutionary challenge because the need for high expression of a nontoxic venom component and the proteolytic machinery required for processing suggests genetic changes of seemingly little immediate benefit to fitness. We showed that MTx evolved through a cascading series of exaptations unlocked by a single nucleotide change. The evolution of one new cleavage site in the acidic subunit unmasked buried cleavage sites already present in ancestral PLA2s, enabling proteolytic processing. Snake venom serine proteases, already present in the venom to disrupt prey hemostasis, possess the requisite specificities for MTx acidic subunit proteolysis. The dimerization interface between MTx subunits evolved by exploiting a latent, but masked, hydrophobic interaction between ancestral PLA2s. The evolution of MTx through exaptation of existing functional and structural features suggests complex phenotypes that depend on evolutionary innovations can arise from minimal genetic change enabled by prior evolution.
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Affiliation(s)
- A Carl Whittington
- Department of Biological Science, Florida State University, Tallahassee, FL
| | - Andrew J Mason
- Department of Biology, University of Central Florida, Orlando, FL
- Department of Biological Sciences, Clemson University, Clemson, SC
| | - Darin R Rokyta
- Department of Biological Science, Florida State University, Tallahassee, FL
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42
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Krasinski CA, Zheng Q, Ivancic VA, Spratt DE, Lazo ND. The Longest Amyloid-β Precursor Protein Intracellular Domain Produced with Aβ42 Forms β-Sheet-Containing Monomers That Self-Assemble and Are Proteolyzed by Insulin-Degrading Enzyme. ACS Chem Neurosci 2018; 9:2892-2897. [PMID: 30067897 DOI: 10.1021/acschemneuro.8b00305] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Alzheimer's disease (AD) is the most common neurodegenerative disease resulting in dementia. It is characterized pathologically by extracellular amyloid plaques composed mainly of deposited Aβ42 and intracellular neurofibrillary tangles formed by hyperphosphorylated tau protein. Recent clinical trials targeting Aβ have failed, suggesting that other polypeptides produced from the amyloid-β precursor protein (APP) may be involved in AD. An attractive polypeptide is AICD57, the longest APP intracellular domain (AICD) coproduced with Aβ42. Here, we show that AICD57 forms micelle-like assemblies that are proteolyzed by insulin-degrading enzyme (IDE), indicating that AICD57 monomers are in dynamic equilibrium with AICD57 assemblies. The N-terminal part of AICD57 monomer is not degraded, but its C-terminal part is hydrolyzed, particularly in the YENPTY motif that has been associated with the hyperphosphorylation of tau. Therefore, sustaining IDE activity well into old age holds promise for regulating levels of not only Aβ but also AICD in the aging brain.
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Affiliation(s)
- Claire A. Krasinski
- Carlson School of Chemistry and Biochemistry, Clark University, 950 Main Street, Worcester, Massachusetts 01610, United States
| | - Qiuchen Zheng
- Carlson School of Chemistry and Biochemistry, Clark University, 950 Main Street, Worcester, Massachusetts 01610, United States
| | - Valerie A. Ivancic
- Carlson School of Chemistry and Biochemistry, Clark University, 950 Main Street, Worcester, Massachusetts 01610, United States
| | - Donald E. Spratt
- Carlson School of Chemistry and Biochemistry, Clark University, 950 Main Street, Worcester, Massachusetts 01610, United States
| | - Noel D. Lazo
- Carlson School of Chemistry and Biochemistry, Clark University, 950 Main Street, Worcester, Massachusetts 01610, United States
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43
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Limatola A, Eichmann C, Jacob RS, Ben-Nissan G, Sharon M, Binolfi A, Selenko P. Time-Resolved NMR Analysis of Proteolytic α-Synuclein Processing in vitro and in cellulo. Proteomics 2018; 18:e1800056. [PMID: 30260559 DOI: 10.1002/pmic.201800056] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 09/14/2018] [Indexed: 11/07/2022]
Abstract
Targeted proteolysis of the disordered Parkinson's disease protein alpha-synuclein (αSyn) constitutes an important event under physiological and pathological cell conditions. In this work, site-specific αSyn cleavage by different endopeptidases in vitro and by endogenous proteases in extracts of challenged and unchallenged cells was studied by time-resolved NMR spectroscopy. Specifically, proteolytic processing was monitored under neutral and low pH conditions and in response to Rotenone-induced oxidative stress. Further, time-dependent degradation of electroporation-delivered αSyn in intact SH-SY5Y and A2780 cells was analyzed. Results presented here delineate a general framework for NMR-based proteolysis studies in vitro and in cellulo, and confirm earlier reports pertaining to the exceptional proteolytic stability of αSyn under physiological cell conditions. However, experimental findings also reveal altered protease susceptibilities in selected mammalian cell lines and upon induced cell stress.
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Affiliation(s)
- Antonio Limatola
- Leibniz Institute of Molecular Pharmacology (FMP-Berlin), In-cell NMR Group,, Robert-Rössle Strasse 10, 13125, Berlin, Germany.,Department of Biology, Stanford University, Stanford, CA, 94305-5430, USA
| | - Cédric Eichmann
- Leibniz Institute of Molecular Pharmacology (FMP-Berlin), In-cell NMR Group,, Robert-Rössle Strasse 10, 13125, Berlin, Germany
| | - Reeba Susan Jacob
- Leibniz Institute of Molecular Pharmacology (FMP-Berlin), In-cell NMR Group,, Robert-Rössle Strasse 10, 13125, Berlin, Germany.,Department of Biological Regulation, Weizmann Institute of Science, 234 Herzl Street, 761000, Rehovot, Israel
| | - Gili Ben-Nissan
- Department of Biomolecular Sciences, Weizmann Institute of Science, 234 Herzl Street, 761000, Rehovot, Israel
| | - Michal Sharon
- Department of Biomolecular Sciences, Weizmann Institute of Science, 234 Herzl Street, 761000, Rehovot, Israel
| | - Andres Binolfi
- Leibniz Institute of Molecular Pharmacology (FMP-Berlin), In-cell NMR Group,, Robert-Rössle Strasse 10, 13125, Berlin, Germany.,Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET) and Plataforma Argentina de Biología Estructural y Metabolómica (PLABEM), Ocampo y Esmeralda, 2000, Rosario, Argentina
| | - Philipp Selenko
- Leibniz Institute of Molecular Pharmacology (FMP-Berlin), In-cell NMR Group,, Robert-Rössle Strasse 10, 13125, Berlin, Germany.,Department of Biological Regulation, Weizmann Institute of Science, 234 Herzl Street, 761000, Rehovot, Israel
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44
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Wang X, Du J, Zhang ZY, Fu YJ, Wang WM, Liang AH. A rational design to enhance the resistance of Escherichia coli phytase appA to trypsin. Appl Microbiol Biotechnol 2018; 102:9647-9656. [DOI: 10.1007/s00253-018-9327-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2018] [Revised: 08/07/2018] [Accepted: 08/10/2018] [Indexed: 10/28/2022]
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45
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Clemente N, Abdine A, Ubarretxena-Belandia I, Wang C. Coupled Transmembrane Substrate Docking and Helical Unwinding in Intramembrane Proteolysis of Amyloid Precursor Protein. Sci Rep 2018; 8:12411. [PMID: 30120254 PMCID: PMC6098081 DOI: 10.1038/s41598-018-30015-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2018] [Accepted: 07/23/2018] [Indexed: 12/03/2022] Open
Abstract
Intramembrane-cleaving proteases (I-CLiPs) play crucial roles in physiological and pathological processes, such as Alzheimer’s disease and cancer. However, the mechanisms of substrate recognition by I-CLiPs remain poorly understood. The aspartic I-CLiP presenilin is the catalytic subunit of the γ-secretase complex, which releases the amyloid-β peptides (Aβs) through intramembrane proteolysis of the transmembrane domain of the amyloid precursor protein (APPTM). Here we used solution NMR to probe substrate docking of APPTM to the presenilin homologs (PSHs) MCMJR1 and MAMRE50, which cleaved APPTM in the NMR tube. Chemical shift perturbation (CSP) showed juxtamembrane regions of APPTM mediate its docking to MCMJR1. Binding of the substrate to I-CLiP decreased the magnitude of amide proton chemical shifts δH at the C-terminal half of the substrate APPTM, indicating that the docking to the enzyme weakens helical hydrogen bonds and unwinds the substrate transmembrane helix around the initial ε-cleavage site. The APPTM V44M substitution linked to familial AD caused more CSP and helical unwinding around the ε-cleavage site. MAMRE50, which cleaved APPTM at a higher rate, also caused more CSP and helical unwinding in APPTM than MCMJR1. Our data suggest that docking of the substrate transmembrane helix and helical unwinding is coupled in intramembrane proteolysis and FAD mutation modifies enzyme/substrate interaction, providing novel insights into the mechanisms of I-CLiPs and AD drug discovery.
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Affiliation(s)
- Nicolina Clemente
- Biochemistry and Biophysics Graduate Program, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York, 12180, USA
| | - Alaa Abdine
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Iban Ubarretxena-Belandia
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA.,Biofisika Institute (CSIC, UPV/EHU), Universidad del País Vasco (UPV/EHU), E-48940, Leioa, Spain
| | - Chunyu Wang
- Biochemistry and Biophysics Graduate Program, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York, 12180, USA. .,Department of Biological Sciences, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York, 12180, USA.
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46
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Jarchi S, Ataei F, Hosseinkhani S. Mutation of conserved residues K329 and R330 on the surface of firefly luciferase: Effect on proteolytic degradation. Int J Biol Macromol 2018; 115:324-330. [DOI: 10.1016/j.ijbiomac.2018.04.050] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 04/08/2018] [Accepted: 04/10/2018] [Indexed: 10/17/2022]
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47
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Kar B, Verma P, den Haan R, Sharma AK. Effect of N-linked glycosylation on the activity and stability of a β-glucosidase from Putranjiva roxburghii. Int J Biol Macromol 2018; 112:490-498. [DOI: 10.1016/j.ijbiomac.2018.01.201] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 01/06/2018] [Accepted: 01/30/2018] [Indexed: 12/31/2022]
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48
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Samanta A, Kiselar J, Pumroy RA, Han S, Moiseenkova-Bell VY. Structural insights into the molecular mechanism of mouse TRPA1 activation and inhibition. J Gen Physiol 2018; 150:751-762. [PMID: 29703838 PMCID: PMC5940248 DOI: 10.1085/jgp.201711876] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2017] [Revised: 02/26/2018] [Accepted: 04/06/2018] [Indexed: 12/13/2022] Open
Abstract
Pain, though serving the beneficial function of provoking a response to dangerous situations, is an unpleasant sensory and emotional experience. Transient receptor potential ankyrin 1 (TRPA1) is a member of the transient receptor potential (TRP) cation channel family and is localized in "nociceptors," where it plays a key role in the transduction of chemical, inflammatory, and neuropathic pain. TRPA1 is a Ca2+-permeable, nonselective cation channel that is activated by a large variety of structurally unrelated electrophilic and nonelectrophilic chemical compounds. Electrophilic ligands are able to activate TRPA1 channels by interacting with critical cysteine residues on the N terminus of the channels via covalent modification and/or disulfide bonds. Activation by electrophilic compounds is dependent on their thiol-reactive moieties, accounting for the structural diversity of the group. On the other hand, nonelectrophilic ligands do not interact with critical cysteines on the channel, so the structural diversity of this group is unexplained. Although near-atomic-resolution structures of TRPA1 were resolved recently by cryo-electron microscopy, in the presence of both agonists and antagonists, detailed mechanisms of channel activation and inhibition by these modulators could not be determined. Here, we investigate the effect of both electrophilic and nonelectrophilic ligands on TRPA1 channel conformational rearrangements with limited proteolysis and mass spectrometry. Collectively, our results reveal that channel modulation results in conformational rearrangements in the N-terminal ankyrin repeats, the pre-S1 helix, the TRP-like domain, and the linker regions of the channel.
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Affiliation(s)
- Amrita Samanta
- Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University, Cleveland, OH
| | - Janna Kiselar
- Center for Proteomics, School of Medicine, Case Western Reserve University, Cleveland, OH
| | - Ruth A Pumroy
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA
| | | | - Vera Y Moiseenkova-Bell
- Department of Physiology and Biophysics, School of Medicine, Case Western Reserve University, Cleveland, OH .,Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, Philadelphia, PA
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49
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Wang H, Yong G, Brown SL, Lee HE, Zenaidee MA, Supuran CT, Donald WA. Supercharging protein ions in native mass spectrometry using theta capillary nanoelectrospray ionization mass spectrometry and cyclic alkylcarbonates. Anal Chim Acta 2018; 1003:1-9. [DOI: 10.1016/j.aca.2017.11.075] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 11/22/2017] [Accepted: 11/25/2017] [Indexed: 12/27/2022]
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50
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The Structure of PrP Sc Prions. Pathogens 2018; 7:pathogens7010020. [PMID: 29414853 PMCID: PMC5874746 DOI: 10.3390/pathogens7010020] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 01/31/2018] [Accepted: 02/03/2018] [Indexed: 12/14/2022] Open
Abstract
PrPSc (scrapie isoform of the prion protein) prions are the infectious agent behind diseases such as Creutzfeldt–Jakob disease in humans, bovine spongiform encephalopathy in cattle, chronic wasting disease in cervids (deer, elk, moose, and reindeer), as well as goat and sheep scrapie. PrPSc is an alternatively folded variant of the cellular prion protein, PrPC, which is a regular, GPI-anchored protein that is present on the cell surface of neurons and other cell types. While the structure of PrPC is well studied, the structure of PrPSc resisted high-resolution determination due to its general insolubility and propensity to aggregate. Cryo-electron microscopy, X-ray fiber diffraction, and a variety of other approaches defined the structure of PrPSc as a four-rung β-solenoid. A high-resolution structure of PrPSc still remains to be solved, but the four-rung β-solenoid architecture provides a molecular framework for the autocatalytic propagation mechanism that gives rise to the alternative conformation of PrPSc. Here, we summarize the current knowledge regarding the structure of PrPSc and speculate about the molecular conversion mechanisms that leads from PrPC to PrPSc.
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