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Bhopatkar AA, Bhatt N, Haque MA, Xavier R, Fung L, Jerez C, Kayed R. MAPT mutations associated with familial tauopathies lead to formation of conformationally distinct oligomers that have cross-seeding ability. Protein Sci 2024; 33:e5099. [PMID: 39145409 PMCID: PMC11325167 DOI: 10.1002/pro.5099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2024] [Revised: 06/13/2024] [Accepted: 06/18/2024] [Indexed: 08/16/2024]
Abstract
The microtubule associated protein, tau, is implicated in a multitude of neurodegenerative disorders that are collectively termed as tauopathies. These disorders are characterized by the presence of tau aggregates within the brain of afflicted individuals. Mutations within the MAPT gene that encodes the tau protein form the genetic backdrop for familial forms of tauopathies, such as frontotemporal dementia (FTD), but the molecular consequences of such alterations and their pathological effects are unclear. We sought to investigate the conformational properties of the aggregates of three tau mutants: A152T, P301L, and R406W, all implicated within FTD, and compare them to those of the native form (WT-Tau 2N4R). Our immunochemical analysis reveals that mutants and WT tau oligomers exhibit similar affinity for conformation-specific antibodies but have distinct morphology and secondary structure. Additionally, these oligomers possess different dye-binding properties and varying sensitivity to proteolytic processing. These results point to conformational variety among them. We then tested the ability of the mutant oligomers to cross-seed the aggregation of WT tau monomer. Using similar array of experiments, we found that cross-seeding with mutant aggregates leads to the formation of conformationally unique WT oligomers. The results discussed in this paper provide a novel perspective on the structural properties of oligomeric forms of WT tau 2N4R and its mutant, along with shedding some light on their cross-seeding behavior.
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Affiliation(s)
- Anukool A. Bhopatkar
- Department of Neurology, Mitchell Center for Neurodegenerative DiseasesUniversity of Texas Medical BranchGalvestonTexasUSA
- Departments of Neurology, Neuroscience and Cell BiologyUniversity of Texas Medical BranchGalvestonTexasUSA
- Present address:
Department of Pharmacology and ToxicologyUniversity of Mississippi Medical CenterJacksonMississippiUSA
| | - Nemil Bhatt
- Department of Neurology, Mitchell Center for Neurodegenerative DiseasesUniversity of Texas Medical BranchGalvestonTexasUSA
- Departments of Neurology, Neuroscience and Cell BiologyUniversity of Texas Medical BranchGalvestonTexasUSA
| | - Md Anzarul Haque
- Department of Neurology, Mitchell Center for Neurodegenerative DiseasesUniversity of Texas Medical BranchGalvestonTexasUSA
- Departments of Neurology, Neuroscience and Cell BiologyUniversity of Texas Medical BranchGalvestonTexasUSA
| | - Rhea Xavier
- Department of Neurology, Mitchell Center for Neurodegenerative DiseasesUniversity of Texas Medical BranchGalvestonTexasUSA
- Departments of Neurology, Neuroscience and Cell BiologyUniversity of Texas Medical BranchGalvestonTexasUSA
| | - Leiana Fung
- Department of Neurology, Mitchell Center for Neurodegenerative DiseasesUniversity of Texas Medical BranchGalvestonTexasUSA
- Departments of Neurology, Neuroscience and Cell BiologyUniversity of Texas Medical BranchGalvestonTexasUSA
- Present address:
Neuroscience Graduate Program, UT Southwestern Medical CenterDallasTexasUSA
| | - Cynthia Jerez
- Department of Neurology, Mitchell Center for Neurodegenerative DiseasesUniversity of Texas Medical BranchGalvestonTexasUSA
- Departments of Neurology, Neuroscience and Cell BiologyUniversity of Texas Medical BranchGalvestonTexasUSA
| | - Rakez Kayed
- Department of Neurology, Mitchell Center for Neurodegenerative DiseasesUniversity of Texas Medical BranchGalvestonTexasUSA
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Zürcher D, Wuchner K, Arosio P. Real-Time Observation of Protein Aggregation at Liquid-Liquid Interfaces in a Microfluidic Device. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024:e2401085. [PMID: 39175118 DOI: 10.1002/smll.202401085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 07/04/2024] [Indexed: 08/24/2024]
Abstract
A droplet microfluidic device to capture in real-time protein aggregation at liquid-liquid interfaces is described. In contrast to conventional methods, typically characterized by a lag time between the application of interfacial stress and the measurement of protein aggregation, here protein adsorption, the formation of a viscoelastic protein layer, aggregation, and shedding of protein particles into solution is simultaneously monitored. The device is applied to analyze the stability of antibody formulations over a wide range of concentrations (1-180 mg mL-1) at the silicone oil (SO)-water interface under controlled mechanical deformation. The adsorption onto oil droplets induces the formation of a viscoelastic protein layer on a subsecond timescale, which progressively restricts the relaxation of the droplets within the chip. Upon mechanical rupture, the protein layer releases particles in solution. The rate of particle formation increases strongly with concentration, similar to the bulk viscosity. Concentrations above 120 mg mL-1 lead to aggregation in seconds and drastically decrease the mechanical perturbations required to shed protein particles in solution. These results are important for the development of formulations at high-protein concentrations (>100 mg mL-1) and indicate that particular attention should be given to interface-induced particle formation in this concentration range. In this context, low-volume microfluidic platforms allow the assessment of protein physical instabilities early in development and represent attractive tools to optimize antibody stability and formulation design consuming limited amounts of material.
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Affiliation(s)
- Dominik Zürcher
- ETH Zürich, Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, Zürich, 8093, Switzerland
| | - Klaus Wuchner
- Cilag GmbH International, a division of Johnson & Johnson, TDS-Biologics, Analytical Development, Schaffhausen, 8200, Switzerland
| | - Paolo Arosio
- ETH Zürich, Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, Zürich, 8093, Switzerland
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3
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Vishwakarma P, Puri S, Banerjee M, Chang CY, Chang CC, Chaudhuri TK. Deciphering the Thermal Stability of Bacteriophage MS2-Derived Virus-like Particle and Its Engineered Variant. ACS Biomater Sci Eng 2024; 10:4812-4822. [PMID: 38976823 DOI: 10.1021/acsbiomaterials.4c00770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
RNA bacteriophage MS2-derived virus-like particles (VLPs) have been widely used in biomedical research as model systems to study virus assembly, structure-function relationships, vaccine development, and drug delivery. Considering the diverse utility of these VLPs, a systemic engineering approach has been utilized to generate smaller particles with optimal serum stability and tissue penetrance. Additionally, it is crucial to demonstrate the overall stability of these mini MS2 VLPs, ensuring cargo protection until they reach their target cell/organ. However, no detailed analysis of the thermal stability and heat-induced disassembly of MS2 VLPs has yet been attempted. In this work, we investigated the thermal stability of both wild-type (WT) MS2 VLP and its "mini" variant containing S37P mutation (mini MS2 VLP). The mini MS2 VLP exhibits a higher capsid melting temperature (Tm) when compared to its WT MS2 VLP counterpart, possibly attributed to its smaller interdimer angle. Our study presents that the thermal unfolding of MS2 VLPs follows a sequential process involving particle destabilization, nucleic acid exposure/melting, and disassembly of VLP. This observation underscores the disruption of cooperative intersubunit interactions and protein-nucleic acid interactions, shedding light on the mechanism of heat-induced VLP disassembly.
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Affiliation(s)
- Pragati Vishwakarma
- Kusuma School of Biological Science, Indian Institute of Technology Delhi, New Delhi 110016, India
| | - Sarita Puri
- Department of Bioscience, University of Milan, Milan 20133, Italy
| | - Manidipa Banerjee
- Kusuma School of Biological Science, Indian Institute of Technology Delhi, New Delhi 110016, India
| | - Chia-Yu Chang
- Department of Biological Sciences and Technology, National Yang-Ming Chiao Tsung University, Hsinchu 30068, Taiwan
| | - Chia-Ching Chang
- Department of Biological Sciences and Technology, National Yang-Ming Chiao Tsung University, Hsinchu 30068, Taiwan
- Department of Electrophysics, National Yang-Ming Chiao Tung University, Hsinchu 30010, Taiwan
- Center for Intelligent Drug Systems and Smart Bio-devices (IDS2B), National Yang-Ming Chiao Tung University, Hsinchu 30068, Taiwan
- International College of Semiconductor Technology, National Yang-Ming Chiao Tung University, Hsinchu 30068, Taiwan
- Institute of Physics, Academia Sinica, Taipei 11529, Taiwan
| | - Tapan K Chaudhuri
- Kusuma School of Biological Science, Indian Institute of Technology Delhi, New Delhi 110016, India
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4
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Dyagala S, Mukherjee N, Halder S, Charaya H, Muzaffar-Ur-Rehman M, Murugesan S, Chakraborty S, Chatterjee T, Saha SK. Presenting a new fluorescent probe, methyl(10-phenylphenanthren-9-yl)sulfane sensitive to the polarity and rigidity of the microenvironment: applications toward microheterogeneous systems. RSC Adv 2024; 14:25865-25888. [PMID: 39156745 PMCID: PMC11328280 DOI: 10.1039/d4ra05565a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2024] [Accepted: 08/06/2024] [Indexed: 08/20/2024] Open
Abstract
A molecule, methyl(10-phenylphenanthren-9-yl)sulfane (MPPS), with a straightforward structure, has been synthesized, characterized, and explored as a new fluorescent probe for microheterogeneous systems. The photophysical properties of MPPS have been studied through experimental and theoretical calculations using the range-separated hybrid functional CAM-B3LYP in conjunction with a 6-311++g(d,p) basis set. Theoretical calculations show that the freely rotating phenyl ring forms a 94° dihedral angle with the phenanthrene ring in the ground state. Experimentally found two absorption bands correspond to the n → π* and π → π* transitions supported by the frontier molecular orbital calculations. Two excited singlet states, E-1 and E-2 (the former being more stable than the latter in the gas phase), exist with dihedral angles between the phenyl and phenanthrene rings as 142° and 133°, respectively, in the gas phase. Two emitting states in a condensed medium of varying polarities are supported by the steady-state fluorescence and fluorescence intensity decay data. Emission energies, fluorescence intensities, and excited singlet state lifetimes change with the polarity of the solvents. To support that the free rotation in the molecule is responsible for these changes, the fluorescence properties of another molecule, methyl(10-(o-tolyl)phenanthren-9-yl)sulfane (MTPS), with restricted rotation of the substituted benzene, i.e., o-tolyl ring have been studied. The fast-intensity decay component of MPPS is ascribed to the conformer in the E-1 state. The molecule has proved to be an excellent polarity probe explored to determine the critical micelle concentrations (cmc) values of different surfactants, which agree well with the literature reports. Different regions of binding isotherm (specific, non-cooperative, cooperative, and massive binding) of a gemini surfactant, 12-6-12,2Br- with bovine serum albumin (BSA) have been successfully demonstrated by the steady-state and time-resolved fluorescence and fluorescence anisotropic properties of MPPS. Docking results show that MPPS resides in the hydrophobic pocket of BSA. The fluorescence quenching of BSA by MPPS reveals the location of Trp residues of BSA. Thus, a polarity and molecular rigidity-sensitive fluorescent molecule, MPPS has been presented here that can potentially be used to monitor the changes in the microenvironment of biomolecules in different processes.
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Affiliation(s)
- Shalini Dyagala
- Department of Chemistry, Birla Institute of Technology & Science (BITS) Pilani, Hyderabad Campus Hyderabad Telangana 500078 India +91-40-66303643 +91-40-66303-680
| | - Nilanjana Mukherjee
- Department of Chemistry, Birla Institute of Technology & Science (BITS) Pilani, Hyderabad Campus Hyderabad Telangana 500078 India +91-40-66303643 +91-40-66303-680
| | - Sayantan Halder
- Department of Chemistry, Birla Institute of Technology & Science (BITS) Pilani, Hyderabad Campus Hyderabad Telangana 500078 India +91-40-66303643 +91-40-66303-680
| | - Heena Charaya
- Department of Chemistry, Birla Institute of Technology & Science (BITS) Pilani, Pilani Campus Rajasthan 333031 India +91 1596 515716
| | - Mohammed Muzaffar-Ur-Rehman
- Department of Pharmacy, Birla Institute of Technology & Science (BITS) Pilani, Pilani Campus Rajasthan 333031 India
| | - Sankaranarayanan Murugesan
- Department of Pharmacy, Birla Institute of Technology & Science (BITS) Pilani, Pilani Campus Rajasthan 333031 India
| | - Shamik Chakraborty
- Department of Chemistry, Birla Institute of Technology & Science (BITS) Pilani, Pilani Campus Rajasthan 333031 India +91 1596 515716
| | - Tanmay Chatterjee
- Department of Chemistry, Birla Institute of Technology & Science (BITS) Pilani, Hyderabad Campus Hyderabad Telangana 500078 India +91-40-66303643 +91-40-66303-680
| | - Subit Kumar Saha
- Department of Chemistry, Birla Institute of Technology & Science (BITS) Pilani, Hyderabad Campus Hyderabad Telangana 500078 India +91-40-66303643 +91-40-66303-680
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5
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Chatterjee C, Mohan GR, C HV, Biswas B, Sundaram V, Srivastava A, Matheshwaran S. Anti-mutagenic agent targeting LexA to combat antimicrobial resistance in mycobacteria. J Biol Chem 2024:107650. [PMID: 39122002 DOI: 10.1016/j.jbc.2024.107650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Revised: 07/17/2024] [Accepted: 07/29/2024] [Indexed: 08/12/2024] Open
Abstract
Antimicrobial resistance (AMR) is a serious global threat demanding innovations for effective control of pathogens. The bacterial SOS response, regulated by the master regulators, LexA and RecA, contributes to AMR through advantageous mutations. Targeting the LexA/RecA system with a novel inhibitor could suppress the SOS response and potentially reduce the occurrence of AMR. RecA presents a challenge as a therapeutic target due to its conserved structure and function across species, including humans. Conversely, LexA which is absent in eukaryotes, can be potentially targeted, due to its involvement in SOS response that is majorly responsible for adaptive mutagenesis and AMR. Our studies combining bioinformatic, biochemical, biophysical, molecular, and cell-based assays present a unique inhibitor of mycobacterial LexA, wherein we show that the inhibitor interacts directly with the catalytic site residues of LexA of Mycobacterium tuberculosis (Mtb), consequently hindering its cleavage, suppressing SOS response thereby reducing mutation frequency and AMR.
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Affiliation(s)
- Chitral Chatterjee
- Department of Biological Sciences and Bioengineering; Indian Institute of Technology Kanpur, Kanpur-208016, UP, India
| | - Gokul Raj Mohan
- Department of Biological Sciences and Bioengineering; Indian Institute of Technology Kanpur, Kanpur-208016, UP, India
| | - Hariharan V C
- Department of Biological Sciences and Bioengineering; Indian Institute of Technology Kanpur, Kanpur-208016, UP, India
| | - Bhumika Biswas
- Department of Biological Sciences and Bioengineering; Indian Institute of Technology Kanpur, Kanpur-208016, UP, India
| | - Vidya Sundaram
- Department of Biological Sciences and Engineering, Indian Institute of Technology, Gandhinagar-382355, Gujarat, India
| | - Ashutosh Srivastava
- Department of Biological Sciences and Engineering, Indian Institute of Technology, Gandhinagar-382355, Gujarat, India
| | - Saravanan Matheshwaran
- Department of Biological Sciences and Bioengineering; Indian Institute of Technology Kanpur, Kanpur-208016, UP, India; Centre for Environmental Sciences and Engineering, Indian Institute of Technology Kanpur, Kanpur-208016, UP, India; Mehta Family Centre for Engineering in Medicine, Indian Institute of Technology, Kanpur-208016, UP, India; Kotak School of Sustainability, Indian Institute of Technology, Kanpur-208016, UP, India.
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6
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Goswami V, Das SM, Deep S. Quercetin-Loaded Nanocarriers as Effective Inhibitors for Copper Metal Ion-Induced γD-Crystallin Aggregation. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:16093-16102. [PMID: 39046313 DOI: 10.1021/acs.langmuir.4c00933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/25/2024]
Abstract
Cataract is one of the leading causes of blindness worldwide. Till date, the only solution for cataracts is surgery, which is a resource-intensive solution. A much simpler solution is to find a potential drug that could inhibit aggregation. It is well established that nonamyloid aggregates of eye lens protein result in cataract. γD-Crystallin, a thermodynamically stable protein, is one of the most abundant proteins in the core of the eye lens and is found to aggregate under stress conditions, leading to the cataract. It has also been found that in cataractous lens, the concentration of metals like copper is elevated significantly as compared to healthy eye lens, suggesting their role in inducing aggregation. In our present study, aggregation of γD-Crystallin was carried out in the presence of Cu (II). Using techniques like turbidity assay, CD spectroscopy, ANS binding assay, and microscopic studies like TEM, it could be confirmed that protein aggregates in the presence of Cu (II) and the nature of aggregates is amorphous. Various polyphenols were tested to suppress aggregation of the protein. Quercetin was observed to be the most efficient. To overcome the problems associated with the delivery of polyphenols, such as solubility and bioavailability, quercetin was encapsulated in two types of nanocarriers. Their characterization was done using TEM, DLS, and other techniques. The potency of quercetin-loaded CS-TPP/CS-PLGA NPs as inhibitors of γD-Crystallin aggregation was confirmed by various experiments.
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Affiliation(s)
- Vishakha Goswami
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Sony Moni Das
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
| | - Shashank Deep
- Department of Chemistry, Indian Institute of Technology Delhi, Hauz Khas, New Delhi 110016, India
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7
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Zhan Y, Li N, Qin T, Peng L, Deng W, Xu Z, Wang L, Charles ID, Liu B. A smartphone-based supramolecular biosensor for portable and rapid detection of buprofezin in real food samples. Food Chem 2024; 460:140779. [PMID: 39121778 DOI: 10.1016/j.foodchem.2024.140779] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Revised: 08/01/2024] [Accepted: 08/04/2024] [Indexed: 08/12/2024]
Abstract
Buprofezin (BUP) is an insect growth regulator widely used in agriculture to control hemipteran pests, particularly the melon aphid, Aphis gossypii, due to its efficiency and low toxicity. Although approved by the Chinese government, its maximum residue limit (MRL) in food is strictly regulated, and conventional techniques for detecting BUP have several limitations. Our study reports successful BUP detection using a supramolecular fluorescent probe DP@ALB, constructed with chalcone-based fluorescent dye DP and albumin as the host. The probe offers advantages such as low cost, visual signal output with high fluorescence color variation, rapid response, and high sensitivity. Additionally, portable test strips enable convenient on-site BUP detection and simplifying field monitoring of spiked real samples. The study achieves precise qualitative and quantitative BUP analysis in grape fruit, groundwater, and soil with satisfactory recoveries. Further, the biological applicability of sensor for the in vitro detection of BUP in L929 living cells was demonstrated. This research breakthrough overcomes the limitations of traditional analytical methods, offering an efficient and reliable approach for food and environmental monitoring and pesticide residue detection.
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Affiliation(s)
- Yilin Zhan
- College of Material Science and Engineering, Guangdong Research Center for Interfacial Engineering of Functional Materials, Guangdong Provincial Key Laboratory of New Energy Materials Service Safety, Shenzhen University, Shenzhen 518060, China
| | - Na Li
- College of Material Science and Engineering, Guangdong Research Center for Interfacial Engineering of Functional Materials, Guangdong Provincial Key Laboratory of New Energy Materials Service Safety, Shenzhen University, Shenzhen 518060, China
| | - Tianyi Qin
- School of Biomedical Engineering, Hainan University, Sanya, Hainan 572025, China
| | - Linhui Peng
- School of Biomedical Engineering, Hainan University, Sanya, Hainan 572025, China
| | - Weihua Deng
- College of Material Science and Engineering, Guangdong Research Center for Interfacial Engineering of Functional Materials, Guangdong Provincial Key Laboratory of New Energy Materials Service Safety, Shenzhen University, Shenzhen 518060, China
| | - Zhongyong Xu
- College of Material Science and Engineering, Guangdong Research Center for Interfacial Engineering of Functional Materials, Guangdong Provincial Key Laboratory of New Energy Materials Service Safety, Shenzhen University, Shenzhen 518060, China
| | - Lei Wang
- College of Material Science and Engineering, Guangdong Research Center for Interfacial Engineering of Functional Materials, Guangdong Provincial Key Laboratory of New Energy Materials Service Safety, Shenzhen University, Shenzhen 518060, China
| | - Immanuel David Charles
- College of Material Science and Engineering, Guangdong Research Center for Interfacial Engineering of Functional Materials, Guangdong Provincial Key Laboratory of New Energy Materials Service Safety, Shenzhen University, Shenzhen 518060, China..
| | - Bin Liu
- College of Material Science and Engineering, Guangdong Research Center for Interfacial Engineering of Functional Materials, Guangdong Provincial Key Laboratory of New Energy Materials Service Safety, Shenzhen University, Shenzhen 518060, China..
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8
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Albaghlany RM, Shahsavani MB, Hoshino M, Moosavi-Movahedi AA, Ghasemi Y, Yousefi R. Optimizing expression, purification, structural and functional assessments of a novel dimeric incretin (GLP-1cpGLP-1). Biochimie 2024; 223:133-146. [PMID: 37931794 DOI: 10.1016/j.biochi.2023.10.020] [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: 09/19/2023] [Revised: 10/28/2023] [Accepted: 10/31/2023] [Indexed: 11/08/2023]
Abstract
Glucagon-like peptide-1 (GLP-1) is an incretin hormone that reduces postprandial glycemic excursions by enhancing insulin secretion. In this study, a new dimeric GLP-1 analogue (GLP-1cpGLP-1) was designed by inserting human insulin C-peptide (CP) in the middle of a dimer of [Gly8] GLP-1 (7-36). Then, the dimeric incretin (GLP-1cpGLP-1) was ligated to human αB-crystallin (αB-Cry) to create a hybrid protein, abbreviated as αB-GLP-1cpGLP-1. The constructed gene was well expressed in the bacterial host system. After specific chemical release from the hybrid protein, the dimeric incretin was purified by size exclusion chromatography (SEC). Finally, the RP-HPLC analysis indicated a purity of >99 % for the dimeric incretin. The secondary structure assessments by various spectroscopic methods, and in silico analysis suggested that the dimeric incretin has α-helical rich structure. The dynamic light scattering (DLS) analysis indicates that our dimeric incretin forms large oligomeric structures. This incretin analogue significantly reduced blood glucose levels in both healthy and diabetic mice while effectively triggering insulin release. The size exclusion HPLC also indicates the interaction of the new incretin analogue with human serum albumin, the main carrier protein in the bloodstream. Consistent with the results obtained from the biological activity assessments, this significant interaction indicates its potential as a viable therapeutic agent with a long-lasting effect. The results of our research represent a significant breakthrough in the successful design of an active incretin dimer capable of effectively controlling blood sugar levels and inducing insulin secretion in the realm of diabetes treatment.
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Affiliation(s)
- Rawayh Muslim Albaghlany
- Protein Chemistry Laboratory (PCL), Department of Biology, College of Sciences, Shiraz University, Shiraz, Iran
| | - Mohammad Bagher Shahsavani
- Protein Chemistry Laboratory (PCL), Department of Biology, College of Sciences, Shiraz University, Shiraz, Iran
| | - Masaru Hoshino
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, 606-8501, Japan
| | | | - Younes Ghasemi
- Department of Pharmaceutical Biotechnology and Pharmaceutical Sciences Research Center, Faculty of Pharmacy, Shiraz University of Medical Sciences, Shiraz, 71345, Iran
| | - Reza Yousefi
- Protein Chemistry Laboratory (PCL), Department of Biology, College of Sciences, Shiraz University, Shiraz, Iran; Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran.
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9
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Azevedo AM, Nunes C, Moniz T, Pérez RL, Ayala CE, Rangel M, Reis S, Santos JL, Warner IM, Saraiva MLM. Studies of Protein Binding to Biomimetic Membranes Using a Group of Uniform Materials Based on Organic Salts Derived From 8-Anilino-1-naphthalenesulfonic Acid. APPLIED SPECTROSCOPY 2024; 78:806-814. [PMID: 38747750 PMCID: PMC11340245 DOI: 10.1177/00037028241249768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 03/27/2024] [Indexed: 08/22/2024]
Abstract
Tuning the 8-anilino-1-naphthalenesulfonic acid (ANS) structure usually requires harsh conditions and long reaction times, which can result in low yields. Herein, ANS was modified to form an ANS group of uniform materials based on organic salts (GUMBOS), prepared with simple metathesis reactions and distinct cations, namely tetrabutylammonium (N4444), tetrahexylammonium (N6666), and tetrabutylphosphonium (P4444). These ANS-based GUMBOS were investigated as fluorescent probes for membrane binding studies with four proteins having distinct physicochemical properties. Liposomes of 1,2-dimyristoyl-sn-glycero-3-phosphocholine were employed as membrane models as a result of their ability to mimic the structure and chemical composition of cell membranes. Changes in fluorescence intensity were used to monitor protein binding to liposomes, and adsorption data were fitted to a Freundlich-like isotherm. It was determined that [N4444][ANS] and [P4444][ANS] GUMBOS have enhanced optical properties and lipophilicity as compared to parent ANS. As a result, these two GUMBOS were selected for subsequent protein-membrane binding studies. Both [N4444][ANS] and [P4444][ANS] GUMBOS and parent ANS independently reached membrane saturation within the same concentration range. Furthermore, distinct fluorescence responses were observed upon the addition of proteins to each probe, which demonstrates the impact of properties such as lipophilicity on the binding process. The relative maintenance of binding cooperativity and maximum fluorescence intensity suggests that proteins compete with ANS-based probes for the same membrane binding sites. Finally, this GUMBOS-based approach is simple, rapid, and involves relatively small amounts of reagents, making it attractive for high-throughput purposes. These results presented herein can also provide relevant information for designing GUMBOS with ameliorated properties.
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Affiliation(s)
- Ana M.O. Azevedo
- LAQV, REQUIMTE, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Cláudia Nunes
- LAQV, REQUIMTE, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Tânia Moniz
- LAQV, REQUIMTE, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade do Porto, Porto, Portugal
- LAQV, REQUIMTE, Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
| | - Rocío L. Pérez
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana, USA
- Department of Chemistry and Biochemistry, Georgia Southern University, Statesboro, Georgia, USA
| | - Caitlan E. Ayala
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana, USA
| | - Maria Rangel
- LAQV, REQUIMTE, Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
| | - Salette Reis
- LAQV, REQUIMTE, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - João L.M. Santos
- LAQV, REQUIMTE, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
| | - Isiah M. Warner
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana, USA
| | - M. Lúcia M.F.S. Saraiva
- LAQV, REQUIMTE, Departamento de Ciências Químicas, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal
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10
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Li JY, Zhou CM, Jin RL, Song JH, Yang KC, Li SL, Tan BH, Li YC. The detection methods currently available for protein aggregation in neurological diseases. J Chem Neuroanat 2024; 138:102420. [PMID: 38626816 DOI: 10.1016/j.jchemneu.2024.102420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 03/30/2024] [Accepted: 04/13/2024] [Indexed: 04/21/2024]
Abstract
Protein aggregation is a pathological feature in various neurodegenerative diseases and is thought to play a crucial role in the onset and progression of neurological disorders. This pathological phenomenon has attracted increasing attention from researchers, but the underlying mechanism has not been fully elucidated yet. Researchers are increasingly interested in identifying chemicals or methods that can effectively detect protein aggregation or maintain protein stability to prevent aggregation formation. To date, several methods are available for detecting protein aggregates, including fluorescence correlation spectroscopy, electron microscopy, and molecular detection methods. Unfortunately, there is still a lack of methods to observe protein aggregation in situ under a microscope. This article reviews the two main aspects of protein aggregation: the mechanisms and detection methods of protein aggregation. The aim is to provide clues for the development of new methods to study this pathological phenomenon.
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Affiliation(s)
- Jing-Yi Li
- Department of Histology and Embryology, College of Basic Medical Sciences, Norman Bethune Health Science Center of Jilin University, Changchun city, Jilin Province 130021, PR China
| | - Cheng-Mei Zhou
- Department of Histology and Embryology, College of Basic Medical Sciences, Norman Bethune Health Science Center of Jilin University, Changchun city, Jilin Province 130021, PR China
| | - Rui-Lin Jin
- Department of Histology and Embryology, College of Basic Medical Sciences, Norman Bethune Health Science Center of Jilin University, Changchun city, Jilin Province 130021, PR China
| | - Jia-Hui Song
- Department of Histology and Embryology, College of Basic Medical Sciences, Norman Bethune Health Science Center of Jilin University, Changchun city, Jilin Province 130021, PR China; Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Changchun 130021, PR China
| | - Ke-Chao Yang
- Department of Histology and Embryology, College of Basic Medical Sciences, Norman Bethune Health Science Center of Jilin University, Changchun city, Jilin Province 130021, PR China
| | - Shu-Lei Li
- Department of Histology and Embryology, College of Basic Medical Sciences, Norman Bethune Health Science Center of Jilin University, Changchun city, Jilin Province 130021, PR China
| | - Bai-Hong Tan
- Laboratory Teaching Center of Basic Medicine, Norman Bethune Health Science Center of Jilin University, Changchun city, Jilin Province 130021, PR China
| | - Yan-Chao Li
- Department of Histology and Embryology, College of Basic Medical Sciences, Norman Bethune Health Science Center of Jilin University, Changchun city, Jilin Province 130021, PR China; Key Laboratory of Pathobiology, Ministry of Education, Jilin University, Changchun 130021, PR China.
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11
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Ling B, Gungoren B, Yao Y, Dutka P, Vassallo R, Nayak R, Smith CAB, Lee J, Swift MB, Shapiro MG. Truly Tiny Acoustic Biomolecules for Ultrasound Imaging and Therapy. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2307106. [PMID: 38409678 DOI: 10.1002/adma.202307106] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 02/01/2024] [Indexed: 02/28/2024]
Abstract
Nanotechnology offers significant advantages for medical imaging and therapy, including enhanced contrast and precision targeting. However, integrating these benefits into ultrasonography is challenging due to the size and stability constraints of conventional bubble-based agents. Here bicones, truly tiny acoustic contrast agents based on gas vesicles (GVs), a unique class of air-filled protein nanostructures naturally produced in buoyant microbes, are described. It is shown that these sub-80 nm particles can be effectively detected both in vitro and in vivo, infiltrate tumors via leaky vasculature, deliver potent mechanical effects through ultrasound-induced inertial cavitation, and are easily engineered for molecular targeting, prolonged circulation time, and payload conjugation.
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Affiliation(s)
- Bill Ling
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Bilge Gungoren
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Yuxing Yao
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Przemysław Dutka
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
- Division of Biology and Bioengineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Reid Vassallo
- School of Biomedical Engineering, University of British Columbia, Vancouver, BC, V6T 1K2, Canada
| | - Rohit Nayak
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Cameron A B Smith
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Justin Lee
- Division of Biology and Bioengineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Margaret B Swift
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
| | - Mikhail G Shapiro
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, 91125, USA
- Division of Engineering and Applied Science, California Institute of Technology, Pasadena, CA, 91125, USA
- Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA, 91125, USA
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12
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Lan T, Dong Y, Jiang L, Zhang Y, Sui X. Analytical approaches for assessing protein structure in protein-rich food: A comprehensive review. Food Chem X 2024; 22:101365. [PMID: 38623506 PMCID: PMC11016869 DOI: 10.1016/j.fochx.2024.101365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 03/24/2024] [Accepted: 04/05/2024] [Indexed: 04/17/2024] Open
Abstract
This review focuses on changes in nutrition and functional properties of protein-rich foods, primarily attributed to alterations in protein structures. We provide a comprehensive overview and comparison of commonly used laboratory methods for protein structure identification, aiming to offer readers a convenient understanding of these techniques. The review covers a range of detection technologies employed in food protein analysis and conducts an extensive comparison to identify the most suitable method for various proteins. While these techniques offer distinct advantages for protein structure determination, the inherent complexity of food matrices presents ongoing challenges. Further research is necessary to develop and enhance more robust detection methods to improve accuracy in protein conformation and structure analysis.
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Affiliation(s)
- Tian Lan
- College of Food Science, Northeast Agricultural University, Harbin 150030, China
| | - Yabo Dong
- College of Food Science, Northeast Agricultural University, Harbin 150030, China
| | - Lianzhou Jiang
- College of Food Science, Northeast Agricultural University, Harbin 150030, China
| | - Yan Zhang
- College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin 150030, China
| | - Xiaonan Sui
- College of Food Science, Northeast Agricultural University, Harbin 150030, China
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13
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Lira RB, Dillingh LS, Schuringa JJ, Yahioglu G, Suhling K, Roos WH. Fluorescence lifetime imaging microscopy of flexible and rigid dyes probes the biophysical properties of synthetic and biological membranes. Biophys J 2024; 123:1592-1609. [PMID: 38702882 PMCID: PMC11214022 DOI: 10.1016/j.bpj.2024.04.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 03/22/2024] [Accepted: 04/30/2024] [Indexed: 05/06/2024] Open
Abstract
Sensing of the biophysical properties of membranes using molecular reporters has recently regained widespread attention. This was elicited by the development of new probes of exquisite optical properties and increased performance, combined with developments in fluorescence detection. Here, we report on fluorescence lifetime imaging of various rigid and flexible fluorescent dyes to probe the biophysical properties of synthetic and biological membranes at steady state as well as upon the action of external membrane-modifying agents. We tested the solvatochromic dyes Nile red and 1,2-dimyristoyl-sn-glycero-3-phosphoethanolamine-N-(7-nitro-2-1,3-benzoxadiazol-4-yl) (ammonium salt) (NBD), the viscosity sensor Bodipy C12, the flipper dye FliptR, as well as the dyes 3,3'-dioctadecyloxacarbocyanine perchlorate (DiO), Bodipy C16, lissamine-rhodamine, and Atto647, which are dyes with no previous reported environmental sensitivity. The performance of the fluorescent probes, many of which are commercially available, was benchmarked with well-known environmental reporters, with Nile red and Bodipy C12 being specific reporters of medium hydration and viscosity, respectively. We show that some widely used ordinary dyes with no previous report of sensing capabilities can exhibit competing performance compared to highly sensitive commercially available or custom-based solvatochromic dyes, molecular rotors, or flipper in a wide range of biophysics experiments. Compared to other methods, fluorescence lifetime imaging is a minimally invasive and nondestructive method with optical resolution. It enables biophysical mapping at steady state or assessment of the changes induced by membrane-active molecules at subcellular level in both synthetic and biological membranes when intensity measurements fail to do so. The results have important consequences for the specific choice of the sensor and take into consideration factors such as probe sensitivity, response to environmental changes, ease and speed of data analysis, and the probe's intracellular distribution, as well as potential side effects induced by labeling and imaging.
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Affiliation(s)
- Rafael B Lira
- Moleculaire Biofysica, Zernike Instituut, Rijksuniversiteit Groningen, Groningen, the Netherlands.
| | - Laura S Dillingh
- Moleculaire Biofysica, Zernike Instituut, Rijksuniversiteit Groningen, Groningen, the Netherlands; Department of Hematology, Universitair Medisch Centrum Groningen & Rijksuniversiteit Groningen, Groningen, the Netherlands
| | - Jan-Jacob Schuringa
- Department of Hematology, Universitair Medisch Centrum Groningen & Rijksuniversiteit Groningen, Groningen, the Netherlands
| | | | - Klaus Suhling
- Department of Physics, King's College London, Strand, London, UK.
| | - Wouter H Roos
- Moleculaire Biofysica, Zernike Instituut, Rijksuniversiteit Groningen, Groningen, the Netherlands
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14
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Jain A, Judy E, Kishore N. Analytical Aspects of ANSA-BSA Association: A Thermodynamic and Conformational Approach. J Phys Chem B 2024; 128:5344-5362. [PMID: 38773936 DOI: 10.1021/acs.jpcb.4c01751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/24/2024]
Abstract
Many studies have demonstrated the manner in which ANS interacts with bovine serum albumin (BSA), although they are limited by the extremely low solubility of dye. The present study demonstrates the binding of ANSA dye with BSA, and since this dye can easily replace ANS, it not only simplifies research but also improves sensor accuracy for serum albumin. A combination of calorimetry and spectroscopy has been employed to establish the thermodynamic signatures associated with the interaction of ANSA with the protein and the consequent conformational changes in the latter. The results of differential scanning calorimetry reveal that when the concentration of ANSA in solution is increased, the thermal stability of the protein increases substantially. The fluorescence data demonstrated a decrease in the binding affinity of ANSA with the protein when pH increased but was unable to identify a change in the mode of interaction of the ligand. ITC has demonstrated that the mode of interaction between ANSA and the protein varies from a single set of binding sites at pH 5 and 7.4 to a sequential binding site at pH 10, emphasizing the potential relevance of protein conformational changes. TCSPC experiments suggested a dynamic type in the presence of ANSA. Molecular docking studies suggest that ANSA molecules are able to find ionic centers in the hydrophobic pockets of BSA. The findings further imply that given its ease of use in experiments, ANSA may be a useful probe for tracking the presence of serum albumin and partially folded protein states.
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Affiliation(s)
- Anu Jain
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Eva Judy
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Nand Kishore
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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15
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Polat MS, Nadaroglu H. Utilizing Copper Nanoclusters as a Fluorescent Probe for Quantitative Monitoring of Doxorubicin Anticancer Drug. J Fluoresc 2024:10.1007/s10895-024-03779-6. [PMID: 38842793 DOI: 10.1007/s10895-024-03779-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 05/19/2024] [Indexed: 06/07/2024]
Abstract
Monitoring the amount of chemotherapeutic drugs in biological fluids is extremely important for dose adjustment or control of side effects during the treatment process. In this study, copper nanoclusters (Cu NCs) were synthesized via a one-pot method using ammonium citrate as the reducing agent. Cu NCs exhibited bright blue fluorescence, good optical properties and outstanding photostability. The produced Cu NCs were characterized in detail by UV‒vis absorption, fluorescence spectroscopy and transmission electron microscopy (TEM). The produced Cu NCs showed a high quantum yield of 0.97. A fluorescence system was used for doxorubicin (DOX) determination using Cu NCs as a nanoprobe. The presence of DOX decreased the fluorescence intensity of the CuNCs at 445 nm but increased the fluorescence intensity of the CuNCs at 619 nm. As a result, quantitative detection of DOX can be achieved by measuring the ratio of fluorescence intensities at 445 and 619 nm (F619/F445). The fluorescence quenching activity of the Cu NCs was determined to have a linear relationship with the amount of DOX anticancer drug in the range of 1-15 ppb, and the usability of the Cu NCs as a sensor for detection in biological fluids was demonstrated. It was determined that this method can be used to measure the amount of DOX in biological samples effectively.
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Affiliation(s)
- Muhammed Seyid Polat
- Department of Nano-Science and Nano-Engineering, Institute of Science and Technology, Ataturk University, Erzurum, 25240, Turkey
| | - Hayrunnisa Nadaroglu
- Department of Nano-Science and Nano-Engineering, Institute of Science and Technology, Ataturk University, Erzurum, 25240, Turkey.
- Department of Food Technology, Erzurum Vocational College of Technical Sciences, Ataturk University, Erzurum, 25240, Turkey.
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16
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Feng RR, Wang M, Zhang W, Gai F. Unnatural Amino Acids for Biological Spectroscopy and Microscopy. Chem Rev 2024; 124:6501-6542. [PMID: 38722769 DOI: 10.1021/acs.chemrev.3c00944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2024]
Abstract
Due to advances in methods for site-specific incorporation of unnatural amino acids (UAAs) into proteins, a large number of UAAs with tailored chemical and/or physical properties have been developed and used in a wide array of biological applications. In particular, UAAs with specific spectroscopic characteristics can be used as external reporters to produce additional signals, hence increasing the information content obtainable in protein spectroscopic and/or imaging measurements. In this Review, we summarize the progress in the past two decades in the development of such UAAs and their applications in biological spectroscopy and microscopy, with a focus on UAAs that can be used as site-specific vibrational, fluorescence, electron paramagnetic resonance (EPR), or nuclear magnetic resonance (NMR) probes. Wherever applicable, we also discuss future directions.
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Affiliation(s)
- Ran-Ran Feng
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Manxi Wang
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Wenkai Zhang
- Department of Physics and Applied Optics Beijing Area Major Laboratory, Beijing Normal University, Beijing 100875, China
| | - Feng Gai
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
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17
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Nascimento ALA, Guimarães AS, Rocha TDS, Goulart MOF, Xavier JDA, Santos JCC. Structural changes in hemoglobin and glycation. VITAMINS AND HORMONES 2024; 125:183-229. [PMID: 38997164 DOI: 10.1016/bs.vh.2024.02.001] [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: 07/14/2024]
Abstract
Hemoglobin (Hb) is a hemeprotein found inside erythrocytes and is crucial in transporting oxygen and carbon dioxide in our bodies. In erythrocytes (Ery), the main energy source is glucose metabolized through glycolysis. However, a fraction of Hb can undergo glycation, in which a free amine group from the protein spontaneously binds to the carbonyl of glucose in the bloodstream, resulting in the formation of glycated hemoglobin (HbA1c), widely used as a marker for diabetes. Glycation leads to structural and conformational changes, compromising the function of proteins, and is intensified in the event of hyperglycemia. The main changes in Hb include structural alterations to the heme group, compromising its main function (oxygen transport). In addition, amyloid aggregates can form, which are strongly related to diabetic complications and neurodegenerative diseases. Therefore, this chapter discusses in vitro protocols for producing glycated Hb, as well as the main techniques and biophysical assays used to assess changes in the protein's structure before and after the glycation process. This more complete understanding of the effects of glycation on Hb is fundamental for understanding the complications associated with hyperglycemia and for developing more effective prevention and treatment strategies.
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Affiliation(s)
- Amanda Luise Alves Nascimento
- Federal University of Alagoas, Institute of Chemistry and Biotechnology, Campus A. C. Simões, Maceió, Alagoas, Brazil
| | - Ari Souza Guimarães
- Federal University of Alagoas, Institute of Chemistry and Biotechnology, Campus A. C. Simões, Maceió, Alagoas, Brazil
| | - Tauane Dos Santos Rocha
- Federal University of Alagoas, Institute of Chemistry and Biotechnology, Campus A. C. Simões, Maceió, Alagoas, Brazil
| | | | - Jadriane de Almeida Xavier
- Federal University of Alagoas, Institute of Chemistry and Biotechnology, Campus A. C. Simões, Maceió, Alagoas, Brazil.
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18
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Carabadjac I, Vormittag LC, Muszer T, Wuth J, Ulbrich MH, Heerklotz H. Transfer of ANS-Like Drugs from Micellar Drug Delivery Systems to Albumin Is Highly Favorable and Protected from Competition with Surfactant by "Reserved" Binding Sites. Mol Pharm 2024; 21:2198-2211. [PMID: 38625037 DOI: 10.1021/acs.molpharmaceut.3c00875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/17/2024]
Abstract
Micellar drug delivery systems (MDDS) for the intravenous administration of poorly soluble drugs have great advantages over alternative formulations in terms of the safety of their excipients, storage stability, and straightforward production. A classic example is mixed micelles of glycocholate (GC) and lecithin, both endogenous substances in human blood. What limits the use of MDDS is the complexity of the transitions after injection. In particular, as the MDDS disintegrate partially or completely after injection, the drug has to be transferred safely to endogenous carriers in the blood, such as human serum albumin (HSA). If this transfer is compromised, the drug might precipitate─a process that needs to be excluded under all circumstances. The key question of this paper is whether the high local concentration of GC at the moment and site of MDDS dissolution might transiently saturate HSA binding sites and, hence, endanger quick drug transfer. To address this question, we have used a new approach, which is time-resolved fluorescence spectroscopy of the single tryptophan in HSA, Trp-214, to characterize the competitive binding of GC and the drug substitute anilinonaphthalenesulfonate (ANS) to HSA. Time-resolved fluorescence of Trp-214 showed important advantages over established methods for tackling this problem. ANS has been the standard "model drug" to study albumin binding for decades, given its structural similarity to the class of naphthalene-containing acidic drugs and the fact that it is displaced from HSA by numerous drugs (which presumably bind to the same sites). Our complex global fit uses the critical approximation that the average lifetimes behave similarly to a single lifetime, but the resulting errors are found to be moderate and the results provide a convincing explanation of the, at first glance, counterintuitive behavior. Accordingly, and largely in line with the literature, we observed two types of sites binding ANS at HSA: 3 type A, rather peripheral, and 2 type B, likely more central sites. The latter quench Trp-214 by Förster Resonance Energy Transfer (FRET) with a rate constant of ≈0.4 ns-1 per ANS. Adding millimolar concentrations of GC displaces ANS from the A sites but not from B sites. At incomplete ANS saturation, this causes a GC-induced translocation of ANS from A to the more FRET-active B sites. This leads to the apparent paradox that the partial displacement of ANS from HSA increases its quenching effect on Trp-214. The most important conclusion is that (ANS-like) drugs cannot be displaced from the type-B sites, and consequently, drug transfer to these sites is not impaired by competitive binding of GC in the vicinity of a dissolving micelle. The second conclusion is that for unbound GC above the CMC (9 mM), ANS equilibrates between HSA and GC micelles but with a strong preference for free sites on HSA. That means that even persisting micelles would lose their cargo readily once exposed to HSA. For all MDDS sharing this property, targeted drug delivery approaches involving them as the nanocarrier would be pointless.
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Affiliation(s)
- Iulia Carabadjac
- Institute of Pharmaceutical Sciences, University of Freiburg, Hermann-Herder-Str. 9, 79104 Freiburg, Germany
| | - Leonie C Vormittag
- Institute of Pharmaceutical Sciences, University of Freiburg, Hermann-Herder-Str. 9, 79104 Freiburg, Germany
| | - Thomas Muszer
- Institute of Pharmaceutical Sciences, University of Freiburg, Hermann-Herder-Str. 9, 79104 Freiburg, Germany
| | - Jakob Wuth
- Institute of Pharmaceutical Sciences, University of Freiburg, Hermann-Herder-Str. 9, 79104 Freiburg, Germany
| | - Maximilian H Ulbrich
- Department of Neuroanatomy, Institute of Anatomy and Cell Biology, Faculty of Medicine, University of Freiburg, Albertstr. 17, 79104 Freiburg, Germany
- BIOSS Centre for Biological Signalling Studies, Schan̈zlestr. 18, Freiburg 79104, Germany
| | - Heiko Heerklotz
- Institute of Pharmaceutical Sciences, University of Freiburg, Hermann-Herder-Str. 9, 79104 Freiburg, Germany
- Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto M5s 3M2, Ontario, Canada
- BIOSS Centre for Biological Signalling Studies, Schan̈zlestr. 18, Freiburg 79104, Germany
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19
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Singh SL, Bhat R. Cyclic-NDGA Effectively Inhibits Human γ-Synuclein Fibrillation, Forms Nontoxic Off-Pathway Species, and Disintegrates Preformed Mature Fibrils. ACS Chem Neurosci 2024; 15:1770-1786. [PMID: 38637513 DOI: 10.1021/acschemneuro.3c00793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2024] Open
Abstract
Parkinson's disease arises from protein misfolding, aggregation, and fibrillation and is characterized by LB (Lewy body) deposits, which contain the protein α-synuclein (α-syn) as their major component. Another synuclein, γ-synuclein (γ-syn), coexists with α-syn in Lewy bodies and is also implicated in various types of cancers, especially breast cancer. It is known to seed α-syn fibrillation after its oxidation at methionine residue, thereby contributing in synucleinopathy. Despite its involvement in synucleinopathy, the search for small molecule inhibitors and modulators of γ-syn fibrillation remains largely unexplored. This work reveals the modulatory properties of cyclic-nordihydroguaiaretic acid (cNDGA), a natural polyphenol, on the structural and aggregational properties of human γ-syn employing various biophysical and structural tools, namely, thioflavin T (ThT) fluorescence, Rayleigh light scattering, 8-anilinonaphthalene-1-sulfonic acid binding, far-UV circular dichroism (CD), Fourier transform infrared spectroscopy (FTIR) spectroscopy, atomic force microscopy, ITC, molecular docking, and MTT-toxicity assay. cNDGA was observed to modulate the fibrillation of γ-syn to form off-pathway amorphous species that are nontoxic in nature at as low as 75 μM concentration. The modulation is dependent on oxidizing conditions, with cNDGA weakly interacting (Kd ∼10-5 M) with the residues at the N-terminal of γ-syn protein as investigated by isothermal titration calorimetry and molecular docking, respectively. Increasing cNDGA concentration results in an increased recovery of monomeric γ-syn as shown by sodium dodecyl sulfate and native-polyacrylamide gel electrophoresis. The retention of native structural properties of γ-syn in the presence of cNDGA was further confirmed by far-UV CD and FTIR. In addition, cNDGA is most effective in suppression of fibrillation when added at the beginning of the fibrillation kinetics and is also capable of disintegrating the preformed mature fibrils. These findings could, therefore, pave the ways for further exploring cNDGA as a potential therapeutic against γ-synucleinopathies.
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Affiliation(s)
- Sneh Lata Singh
- School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
| | - Rajiv Bhat
- School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
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20
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Siddiqui U, Khan AB, Ahmad T, Rehman AA, Jairajpuri MA. A common protein C inhibitor exosite partially controls the heparin induced activation and inhibition of serine proteases. Int J Biol Macromol 2024; 266:131065. [PMID: 38521329 DOI: 10.1016/j.ijbiomac.2024.131065] [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: 01/06/2024] [Revised: 03/04/2024] [Accepted: 03/20/2024] [Indexed: 03/25/2024]
Abstract
Protein C inhibitor (PCI) maintains hemostasis by inhibiting both procoagulant and anticoagulant serine proteases, and plays important roles in coagulation, fibrinolysis, reproduction, and anti-angiogenesis. The reactive site loop of PCI traps and irreversibly inhibits the proteases like APC (activating protein C), thrombin (FIIa) and factor Xa (FXa). Previous studies on antithrombin (ATIII) had identified Tyr253 and Glu255 as functional exosites that interact and aid in the inhibition of factor IXa and FXa. Presence of exosite in PCI is not known, however a sequence comparison with the PCI from different vertebrate species and ATIII identified Glu239 to be absolutely conserved. PCI residues analogous to ATIII exosite residues were mutated to R238A and E239A. Purified variant PCI in the presence of heparin (10 μg/ml) showed a 2-4 fold decrease in the rate of inhibition of the proteases. However, the stoichiometry of inhibition of FIIa, APC, and FXa by native PCI, R238A and E239A variants were found to be close to 1.0, which also indicated the formation of stable complexes based on SDS-PAGE and western blot analysis with thrombin and APC. Our findings revealed the possible presence of an exosite in PCI that influences the protease inhibition rates.
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Affiliation(s)
- Urfi Siddiqui
- Department of Bioscience, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Abdul Burhan Khan
- Department of Bioscience, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Tahif Ahmad
- Department of Bioscience, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
| | - Ahmed Abdur Rehman
- Department of Bioscience, Jamia Millia Islamia, Jamia Nagar, New Delhi 110025, India
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21
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Park JH, Park AR, Kim K, Shin SH, Jeon Y, Lee WK, Lee D, Baek JH. Prediction of the minimum amount of anti-adhesive agent required for entire intra-abdominal cavity using fluorescent dye. KOREAN JOURNAL OF CLINICAL ONCOLOGY 2024; 20:18-26. [PMID: 38988015 PMCID: PMC11261179 DOI: 10.14216/kjco.24004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 04/19/2024] [Accepted: 04/30/2024] [Indexed: 07/12/2024]
Abstract
PURPOSE Studies on the appropriate amount of anti-adhesive agents for preventing postoperative adhesion are lacking. This animal study aimed to investigate the distribution of an anti-adhesive agent in the abdominal cavity and estimate the necessary amount to cover the entire cavity. METHODS Fluorescent dye Flamma-552 was conjugated to Guardix-sol to create Guardix-Flamma, which was laparoscopically applied to the abdominal cavity of two 10-kg pigs in different amounts: 15 mL for G1 and 35 mL for G2. After 24 hours, the distribution of Guardix-Flamma was examined under the near-infrared mode of the laparoscope, and the thickness was measured in tissues from the omentum, small, and large intestine by immunohistochemistry. RESULTS The average area of the abdominal cavity in 10 kg pigs was 2,755 cm2. Guardix-Flamma fluorescence was detected in the greater omentum, ascites in the pelvis, and right quadrant area in G1, whereas in G2, it was detected everywhere. On average, the total thickness of G1 and G2 were 12.68 ± 9.80 μm and 18.16 ± 15.57 μm, respectively. Guardix-Flamma thickness applied to the omentum, small, and large intestines of G2 were 1.31-, 1.45-, and 1.49-times thicker than those of G1, respectively, and were all statistically significant (P < 0.05). CONCLUSION The entire abdominal cavity of the 10 kg pig was not evenly covered with 15 mL of Guardix. Although 35 mL of Guardix is sufficient to cover the same area with an average thickness of 18 µm, further studies should evaluate the minimum thickness required for an effective anti-adhesive function.
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Affiliation(s)
- Ji-Hyeon Park
- Department of Surgery, Gachon University Gil Medical Center, Gachon University College of Medicine, Incheon,
Korea
| | - A Reum Park
- Department of Biomedical Engineering, Graduate School of Gachon University, Seongnam,
Korea
| | - Kiwon Kim
- Department of Technical Support, BioActs Co., Ltd., Incheon,
Korea
| | - Seo Hyun Shin
- Department of Testing and Research, KNOTUS Co., Ltd., Incheon,
Korea
| | - Youngbae Jeon
- Department of Surgery, Gachon University Gil Medical Center, Gachon University College of Medicine, Incheon,
Korea
| | - Woon Kee Lee
- Department of Surgery, Gachon University Gil Medical Center, Gachon University College of Medicine, Incheon,
Korea
| | - Donghyuk Lee
- Department of Premedicine, Gachon University, Seongnam,
Korea
| | - Jeong-Heum Baek
- Department of Surgery, Gachon University Gil Medical Center, Gachon University College of Medicine, Incheon,
Korea
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22
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Juković M, Ratkaj I, Kalafatovic D, Bradshaw NJ. Amyloids, amorphous aggregates and assemblies of peptides - Assessing aggregation. Biophys Chem 2024; 308:107202. [PMID: 38382283 DOI: 10.1016/j.bpc.2024.107202] [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: 11/29/2023] [Revised: 01/31/2024] [Accepted: 02/14/2024] [Indexed: 02/23/2024]
Abstract
Amyloid and amorphous aggregates represent the two major categories of aggregates associated with diseases, and although exhibiting distinct features, researchers often treat them as equivalent, which demonstrates the need for more thorough characterization. Here, we compare amyloid and amorphous aggregates based on their biochemical properties, kinetics, and morphological features. To further decipher this issue, we propose the use of peptide self-assemblies as minimalistic models for understanding the aggregation process. Peptide building blocks are significantly smaller than proteins that participate in aggregation, however, they make a plausible means to bridge the gap in discerning the aggregation process at the more complex, protein level. Additionally, we explore the potential use of peptide-inspired models to research the liquid-liquid phase separation as a feasible mechanism preceding amyloid formation. Connecting these concepts can help clarify our understanding of aggregation-related disorders and potentially provide novel drug targets to impede and reverse these serious illnesses.
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Affiliation(s)
- Maja Juković
- Faculty of Biotechnology and Drug Development, University of Rijeka, 51000 Rijeka, Croatia
| | - Ivana Ratkaj
- Faculty of Biotechnology and Drug Development, University of Rijeka, 51000 Rijeka, Croatia
| | - Daniela Kalafatovic
- Faculty of Biotechnology and Drug Development, University of Rijeka, 51000 Rijeka, Croatia.
| | - Nicholas J Bradshaw
- Faculty of Biotechnology and Drug Development, University of Rijeka, 51000 Rijeka, Croatia.
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23
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Siddiqui S, Ahmad R, Ahmad Y, Faizy AF, Moin S. Biophysical insight into the binding mechanism of epigallocatechin-3-gallate and cholecalciferol to albumin and its preventive effect against AGEs formation: An in vitro and in silico approach. Int J Biol Macromol 2024; 267:131474. [PMID: 38599429 DOI: 10.1016/j.ijbiomac.2024.131474] [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: 01/18/2024] [Revised: 03/24/2024] [Accepted: 04/06/2024] [Indexed: 04/12/2024]
Abstract
Advanced glycation end products (AGEs) are produced non-enzymatically through the process of glycation. Increased AGEs production has been linked to several diseases including polycystic ovary syndrome (PCOS). PCOS contributes to the development of secondary comorbidities, such as diabetes, cardiovascular complications, infertility, etc. Consequently, research is going on AGEs-inhibiting phytochemicals for their potential to remediate and impede the progression of hyperglycaemia associated disorders. In this study human serum albumin is used as a model protein, as albumin is predominantly present in follicular fluid. This article focusses on the interaction and antiglycating potential of (-)-Epigallocatechin-3-gallate (EGCG) and vitamin D in combination using various techniques. The formation of the HSA-EGCG and HSA-vitamin D complex was confirmed by UV and fluorescence spectroscopy. Thermodynamic analysis verified the spontaneity of reaction, and presence of hydrogen bonds and van der Waals interactions. FRET confirms high possibility of energy transfer. Cumulative antiglycation resulted in almost 60 % prevention in AGEs formation, decreased alterations at lysine and arginine, and reduced protein carbonylation. Secondary and tertiary structural changes were analysed by circular dichroism, Raman spectroscopy and ANS binding assay. Type and size of aggregates were confirmed by Rayleigh and dynamic light scattering, ThT fluorescence, SEM and SDS-PAGE. Effect on cellular redox status, DNA integrity and cytotoxicity was analysed in lymphocytes using dichlorofluorescein (DCFH-DA), DAPI and MTT assay which depicted an enhancement in antioxidant level by cumulative treatment. These findings indicate that EGCG and vitamin D binds strongly to HSA and have antiglycation ability which enhances upon synergism.
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Affiliation(s)
- Sana Siddiqui
- Department of Biochemistry, J.N.M.C., Faculty of Medicine, Aligarh Muslim University, Aligarh 202002, U.P., India
| | - Rizwan Ahmad
- Department of Biochemistry, J.N.M.C., Faculty of Medicine, Aligarh Muslim University, Aligarh 202002, U.P., India
| | - Yusra Ahmad
- Department of Biochemistry, J.N.M.C., Faculty of Medicine, Aligarh Muslim University, Aligarh 202002, U.P., India
| | - Abul Faiz Faizy
- Department of Biochemistry, J.N.M.C., Faculty of Medicine, Aligarh Muslim University, Aligarh 202002, U.P., India
| | - Shagufta Moin
- Department of Biochemistry, J.N.M.C., Faculty of Medicine, Aligarh Muslim University, Aligarh 202002, U.P., India.
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24
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Dash BR, Gardas RL, Mishra AK. Probing the heterogeneity of molecular level organization of ionic liquids: a comparative study using neutral Nile red and cationic Nile blue sulfate as fluorescent probes for butyrolactam-based protic ionic liquids. Phys Chem Chem Phys 2024; 26:13350-13363. [PMID: 38639928 DOI: 10.1039/d4cp00520a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/20/2024]
Abstract
Ionic liquids (ILs) are liquid salts composed of cations and anions, known for their significant local heterogeneity at the molecular level. To understand the microheterogeneity with regard to their local polarity and local viscosity, we have used two structurally similar but chemically distinguishable fluorescent probes: Nile red (NR), a neutral molecule, and Nile blue sulfate (NBS), a charged molecule. A comparative study of the response of the two probes to the molecular level heterogeneity of ILs is expected to provide a better clarity of understanding regarding the charged polar domain and the uncharged hydrophobic domain of ILs. Towards this, we synthesized two butyrolactam-based protic ionic liquids (PILs), i.e., BTF and BTD, with the same ionic headgroup ([BT]+) and different alkyl tails ([RCOO]-), where {R = H, C11H23}. BTF has no significant hydrophobic domain, whereas BTD has a larger hydrophobic domain. Temperature-dependent fluorescence parameters such as fluorescence intensity, lifetime, and anisotropy were measured for both NR and NBS molecules. The use of a pair of structurally similar but ionically different probes enables differential estimation of parameters like the microviscosity of a domain using the fluorescence anisotropy parameter (r). The absorption and emission spectra of both probe molecules are observed to be blue shifted upon going from BTF to BTD. NR showed a significant blue shift in absorption and emission band maxima. Conversely, NBS exhibited a small wavelength shift, possibly influenced by the preferred location of their charged head group domain. Temperature-dependent rotational relaxation time (θ) of NR in BTD is smaller than that of NBS by 60-70%, indicating that stronger charge-charge interactions exist between the polar domain of BTD and NBS. Moreover, it is observed that the local viscosity of the BTF IL around both probes is similar, whereas there is a considerable difference for the BTD IL. These results are an indication that NBS being charged prefers to locate itself in the charged head group region of the IL, whereas NR being neutral tends to reside both in the hydrophobic domain and in the head group but is predominantly located in the hydrophobic domain.
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Affiliation(s)
- Bignya Rani Dash
- Department of Chemistry, Indian Institute of Technology Madras, Chennai 600036, India.
| | - Ramesh L Gardas
- Department of Chemistry, Indian Institute of Technology Madras, Chennai 600036, India.
| | - Ashok Kumar Mishra
- Department of Chemistry, Indian Institute of Technology Madras, Chennai 600036, India.
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25
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Masroor A, Zaidi N, Nabi F, Malik S, Zehra S, Arjmand F, Naseem N, Khan RH. Biophysical insight into anti-amyloidogenic nature of novel ionic Co(II)(phen)(H 2O) 4] +[glycinate] - chemotherapeutic drug candidate against human lysozyme aggregation. Biophys Chem 2024; 308:107214. [PMID: 38428228 DOI: 10.1016/j.bpc.2024.107214] [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: 11/21/2023] [Revised: 02/10/2024] [Accepted: 02/25/2024] [Indexed: 03/03/2024]
Abstract
In the recent past, there has been an ever-increasing interest in the search for metal-based therapeutic drug candidates for protein misfolding disorders (PMDs) particularly neurodegenerative disorders such as Alzheimer's, Parkinson's, Prion's diseases, and amyotrophic lateral sclerosis. Also, different amyloidogenic variants of human lysozyme (HL) are involved in hereditary systemic amyloidosis. Metallo-therapeutic agents are extensively studied as antitumor agents, however, they are relatively unexplored for the treatment of non-neuropathic amyloidoses. In this work, inhibition potential of a novel ionic cobalt(II) therapeutic agent (CoTA) of the formulation [Co(phen)(H2O)4]+[glycinate]- is evaluated against HL fibrillation. Various biophysical techniques viz., dye-binding assays, dynamic light scattering (DLS), differential scanning calorimetry (DSC), electron microscopy, and molecular docking experiments validate the proposed mechanism of inhibition of HL fibrillation by CoTA. The experimental corroborative results of these studies reveal that CoTA can suppress and slow down HL fibrillation at physiological temperature and pH. DLS and 1-anilino-8-naphthalenesulfonate (ANS) assay show that reduced fibrillation in the presence of CoTA is marked by a significant decrease in the size and hydrophobicity of the aggregates. Fluorescence quenching and molecular docking results demonstrate that CoTA binds moderately to the aggregation-prone region of HL (Kb = 6.6 × 104 M-1), thereby, inhibiting HL fibrillation. In addition, far-UV CD and DSC show that binding of CoTA to HL does not cause any change in the stability of HL. More importantly, CoTA attenuates membrane damaging effects of HL aggregates against RBCs. This study identifies inorganic metal complexes as a therapeutic intervention for systemic amyloidosis.
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Affiliation(s)
- Aiman Masroor
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, U.P 202002, India
| | - Nida Zaidi
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, U.P 202002, India
| | - Faisal Nabi
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, U.P 202002, India
| | - Sadia Malik
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, U.P 202002, India
| | - Siffeen Zehra
- Department of Chemistry, Aligarh Muslim University, Aligarh, U.P 202002, India
| | - Farukh Arjmand
- Department of Chemistry, Aligarh Muslim University, Aligarh, U.P 202002, India
| | - Nida Naseem
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, U.P 202002, India
| | - Rizwan Hasan Khan
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, U.P 202002, India.
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26
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Nuñez E, Muguruza-Montero A, Alicante SM, Villarroel A. Fluorometric Measurement of Calmodulin-Dependent Peptide-Protein Interactions Using Dansylated Calmodulin. Bio Protoc 2024; 14:e4963. [PMID: 38618173 PMCID: PMC11006803 DOI: 10.21769/bioprotoc.4963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 02/07/2024] [Accepted: 02/07/2024] [Indexed: 04/16/2024] Open
Abstract
The assessment of peptide-protein interactions is a pivotal aspect of studying the functionality and mechanisms of various bioactive peptides. In this context, it is essential to employ methods that meet specific criteria, including sensitivity, biocompatibility, versatility, simplicity, and the ability to offer real-time monitoring. In cellular contexts, only a few proteins naturally possess inherent fluorescence, specifically those containing aromatic amino acids, particularly tryptophan. Nonetheless, by covalently attaching fluorescent markers, almost all proteins can be modified for monitoring purposes. Among the early extrinsic fluorescent probes designed for this task, dansyl chloride (DNSC) is a notable option due to its versatile nature and reliable performance. DNSC has been the primary choice as a fluorogenic derivatizing reagent for analyzing amino acids in proteins and peptides for an extended period of time. In our work, we have effectively utilized the distinctive properties of dansylated-calmodulin (D-CaM) for monitoring the interaction dynamics between proteins and peptides, particularly in the context of their association with calmodulin (CaM), a calcium-dependent regulatory protein. This technique not only enables us to scrutinize the affinity of diverse ligands but also sheds light on the intricate role played by calcium in these interactions. Key features • Dynamic fluorescence and real-time monitoring: dansyl-modified CaM enables sensitive, real-time fluorescence, providing valuable insights into the dynamics of molecular interactions and ligand binding. • Selective interaction and stable fluorescent adducts: DNSC selectively interacts with primary amino groups, ensuring specific detection and forming stable fluorescent sulfonamide adducts. • Versatility in research and ease of identification: D-CaM is a versatile tool in biological research, facilitating identification, precise quantification, and drug assessment for therapeutic development. • Sensitivity to surrounding alterations: D-CaM exhibits sensitivity to its surroundings, particularly ligand-induced changes, offering subtle insights into molecular interactions and environmental influences.
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Affiliation(s)
- Eider Nuñez
- Instituto Biofisika, CSIC-UPV/EHU, Leioa, Spain
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27
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Ansari NK, Rais A, Naeem A. Methotrexate for Drug Repurposing as an Anti-Aggregatory Agent to Mercuric Treated α-Chymotrypsinogen-A. Protein J 2024; 43:362-374. [PMID: 38431536 DOI: 10.1007/s10930-024-10187-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/24/2024] [Indexed: 03/05/2024]
Abstract
Protein aggregation is related to numerous pathological conditions like Alzheimer's and Parkinson's disease. In our study, we have shown that an already existing FDA-approved drug; methotrexate (MTX) can be reprofiled on preformed α-chymotrypsinogen A (α-Cgn A) aggregates. The zymogen showed formation of aggregates upon interaction with mercuric ions, with increasing concentration of Hg2Cl2 (0-150 µM). The hike in ThT and ANS fluorescence concomitant with blue shift, bathochromic shift and the hyperchromic effect in the CR absorbance, RLS and turbidity measurements, substantiate the zymogen β-rich aggregate formation. The secondary structural alterations of α- Cgn A as analyzed by CD measurements, FTIR and Raman spectra showed the transformation of native β-barrel conformation to β-inter-molecular rich aggregates. The native α- Cgn A have about 30% α-helical content which was found to be about 3% in presence of mercuric ions suggesting the formation of aggregates. The amorphous aggregates were visualized by SEM. On incubation of Hg2Cl2 treated α- Cgn A with increasing concentration of the MTX resulted in reversing aggregates to the native-like structure. These results were supported by remarkable decrease in ThT and ANS fluorescence intensities and CR absorbance and also consistent with CD, FTIR, and Raman spectroscopy data. MTX was found to increase the α-helical content of the zymogen from 3 to 15% proposing that drug is efficient in disrupting the β-inter-molecular rich aggregates and reverting it to native like structure. The SEM images are in accordance with CD data showing the disintegration of aggregates. The most effective concentration of the drug was found to be 120 µM. Molecular docking analysis showed that MTX molecule was surrounded by the hydrophobic residues including Phe39, His40, Arg145, Tyr146, Thr151, Gly193, Ser195, and Gly216 and conventional hydrogen bonds, including Gln73 (bond length: 2.67Å), Gly142 (2.59Å), Thr144 (2.81Å), Asn150 (2.73Å), Asp153 (2.71Å), and Cys191 (2.53Å). This investigation will help to find the use of already existing drugs to cure protein misfolding-related abnormalities.
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Affiliation(s)
- Neha Kausar Ansari
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, U.P, 202002, India
| | - Amaan Rais
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, U.P, 202002, India
| | - Aabgeena Naeem
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, U.P, 202002, India.
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28
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Prout-Holm RA, van Walstijn CC, Hitsman A, Rowley MJ, Olsen JE, Page BDG, Frankel A. Investigating Protein Binding with the Isothermal Ligand-induced Resolubilization Assay. Chembiochem 2024; 25:e202300773. [PMID: 38266114 DOI: 10.1002/cbic.202300773] [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: 11/13/2023] [Revised: 01/24/2024] [Accepted: 01/24/2024] [Indexed: 01/26/2024]
Abstract
Target engagement assays typically detect and quantify the direct physical interaction of a protein of interest and its ligand through stability changes upon ligand binding. Commonly used target engagement methods detect ligand-induced stability by subjecting samples to thermal or proteolytic stress. Here we describe a new variation to these approaches called Isothermal Ligand-induced Resolubilization Assay (ILIRA), which utilizes lyotropic solubility stress to measure ligand binding through changes in target protein solubility. We identified distinct buffer systems and salt concentrations that compromised protein solubility for four diverse proteins: dihydrofolate reductase (DHFR), nucleoside diphosphate-linked moiety X motif 5 (NUDT5), poly [ADP-ribose] polymerase 1 (PARP1), and protein arginine N-methyltransferase 1 (PRMT1). Ligand-induced solubility rescue was demonstrated for these proteins, suggesting that ILIRA can be used as an additional target engagement technique. Differences in ligand-induced protein solubility were assessed by Coomassie blue staining for SDS-PAGE and dot blot, as well as by NanoOrange, Thioflavin T, and Proteostat fluorescence, thus offering flexibility for readout and assay throughput.
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Affiliation(s)
- Riley A Prout-Holm
- Faculty of Pharmaceutical Sciences, The University of British Columbia, 2405 Wesbrook Mall, Vancouver, BC V6T 1Z3, Canada
| | - Cerissa C van Walstijn
- Faculty of Science, Utrecht University, Heidelberglaan 8, 3584 CS, Utrecht, The Netherlands
| | - Alana Hitsman
- Faculty of Pharmaceutical Sciences, The University of British Columbia, 2405 Wesbrook Mall, Vancouver, BC V6T 1Z3, Canada
| | - Michael J Rowley
- Faculty of Pharmaceutical Sciences, The University of British Columbia, 2405 Wesbrook Mall, Vancouver, BC V6T 1Z3, Canada
| | - Jonas E Olsen
- Faculty of Pharmaceutical Sciences, The University of British Columbia, 2405 Wesbrook Mall, Vancouver, BC V6T 1Z3, Canada
| | - Brent D G Page
- Faculty of Pharmaceutical Sciences, The University of British Columbia, 2405 Wesbrook Mall, Vancouver, BC V6T 1Z3, Canada
| | - Adam Frankel
- Faculty of Pharmaceutical Sciences, The University of British Columbia, 2405 Wesbrook Mall, Vancouver, BC V6T 1Z3, Canada
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29
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Natarajan A, Vadrevu LR, Rangan K. DRGD-linked charged EKKE dimeric dodecapeptide: pH-based amyloid nanostructures and their application in lead and uranium binding. RSC Adv 2024; 14:9200-9217. [PMID: 38505393 PMCID: PMC10949120 DOI: 10.1039/d3ra08261j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 03/04/2024] [Indexed: 03/21/2024] Open
Abstract
Peptides have been reported to undergo self-assembly into diverse nanostructures, influenced by several parameters, including their amino acid sequence, pH, charge, solvent, and temperature. Inspired by natural systems, researchers have developed biomimetic peptides capable of self-assembling into supramolecular functional structures. The present study explored a newly designed peptide sequence, EKKEDRGDEKKE, where E = glutamic acid, K = lysine, D = aspartic acid, G = glycine, and R = arginine, with a metal binding DRGD sequence incorporated between the exclusively charged EKKE peptide. We investigated the formation and the potential of the EKKEDRGDEKKE peptide in retaining the structure and morphology adopted by the individual EKKE peptide. According to a combination of experimental techniques such as thioflavin T fluorescence, field emission-scanning electron microscopy, atomic force microscopy, and circular dichroism, it was evident that the EKKEDRGDEKKE peptide displayed a pH-dependent propensity to adopt amyloid-like structures. Furthermore, the self-assembled entities formed under acidic, basic, and neutral conditions exhibited morphological variations, which resembled that observed for the exclusively charged EKKE peptide. Furthermore, the incorporation of the functional DRGD motif resulted in promising binding to two toxic metal ions, lead (Pb) and uranium (U), as evidenced by a range of spectroscopic techniques, including UV-visible spectroscopy, atomic absorption spectroscopy, fluorescence spectroscopy, and X-ray photoelectron spectroscopy. The use of the amyloid-forming EKKEDRGDEKKE scaffold can also be extended to potential biomedical applications.
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Affiliation(s)
- Aishwarya Natarajan
- Department of Chemistry, Birla Institute of Technology and Science Pilani, Hyderabad Campus Jawahar Nagar Hyderabad 500 078 Telangana India
- Department of Biological Sciences, Birla Institute of Technology and Science Pilani, Hyderabad Campus Jawahar Nagar Hyderabad 500 078 Telangana India
| | - Late Ramakrishna Vadrevu
- Department of Biological Sciences, Birla Institute of Technology and Science Pilani, Hyderabad Campus Jawahar Nagar Hyderabad 500 078 Telangana India
| | - Krishnan Rangan
- Department of Chemistry, Birla Institute of Technology and Science Pilani, Hyderabad Campus Jawahar Nagar Hyderabad 500 078 Telangana India
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30
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Stepanchuk AA, Stys PK. Spectral Fluorescence Pathology of Protein Misfolding Disorders. ACS Chem Neurosci 2024; 15:898-908. [PMID: 38407017 DOI: 10.1021/acschemneuro.3c00798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2024] Open
Abstract
Protein misfolding has been extensively studied in the context of neurodegenerative disorders and systemic amyloidoses. Due to misfolding and aggregation of proteins being highly heterogeneous and generating a variety of structures, a growing body of evidence illustrates numerous ways how the aggregates contribute to progression of diseases such as Alzheimer's disease, Parkinson's disease, and prion disorders. Different misfolded species of the same protein, commonly referred to as strains, appear to play a significant role in shaping the disease clinical phenotype and clinical progression. The distinct toxicity profiles of various misfolded proteins underscore their importance. Current diagnostics struggle to differentiate among these strains early in the disease course. This review explores the potential of spectral fluorescence approaches to illuminate the complexities of protein misfolding pathology and discusses the applications of advanced spectral methods in the detection and characterization of protein misfolding disorders. By examining spectrally variable probes, current data analysis approaches, and important considerations for the use of these techniques, this review aims to provide an overview of the progress made in this field and highlights directions for future research.
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Affiliation(s)
- Anastasiia A Stepanchuk
- Department of Clinical Neurosciences, Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Peter K Stys
- Department of Clinical Neurosciences, Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
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31
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Dasnoy S, Illartin M, Queffelec J, Nkunku A, Peerboom C. Combined Effect of Shaking Orbit and Vial Orientation on the Agitation-Induced Aggregation of Proteins. J Pharm Sci 2024; 113:669-679. [PMID: 37611666 DOI: 10.1016/j.xphs.2023.08.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 08/15/2023] [Accepted: 08/15/2023] [Indexed: 08/25/2023]
Abstract
Orbital shaking in a glass vial is a commonly used forced degradation test to evaluate protein propensity for agitation-induced aggregation. Vial shaking in horizontal orientation has been widely recommended to maximize the air-liquid interface area while ensuring solution contact with the stopper. We evaluated the impact of shaking orbit diameter and frequency, and glass vial orientation (horizontal versus vertical) on the aggregation of three proteins prepared in surfactant-free formulation buffers. As soon as an orbit-specific frequency threshold was reached, an increase in turbidity was observed for the three proteins in vertical orientation only when using a 3 mm agitation orbit, and in horizontal orientation only when using a 30 mm agitation orbit. Orthogonal analyses confirmed turbidity was linked to protein aggregation. The most turbid samples had a visually more homogeneous appearance in vertical than in horizontal orientation, in line with the predicted dispersion of air and liquid phases obtained from computational fluid dynamics agitation simulations. Both shaking orbits were used to assess the performance of nonionic surfactants. We show that the propensity of a protein to aggregate in a vial agitated in horizontal or vertical orientation depends on the shaking orbit, and confirm that Brij® 58 and FM1000 prevent proteins from agitation-induced aggregation at lower concentrations than polysorbate 80.
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Affiliation(s)
| | - Marion Illartin
- UCB Pharma, Chemin du Foriest, 1420 Braine-l'Alleud, Belgium; Institut Mines-Télécom (IMT) Mines Albi, Allée des Sciences, 81000 Albi, France
| | - Julie Queffelec
- UCB Pharma, Chemin du Foriest, 1420 Braine-l'Alleud, Belgium; Institut Mines-Télécom (IMT) Mines Albi, Allée des Sciences, 81000 Albi, France
| | - Aubrey Nkunku
- UCB Pharma, Chemin du Foriest, 1420 Braine-l'Alleud, Belgium; ALTEN Belgium, Chaussée de Charleroi 112, 1060 Bruxelles, Belgium
| | - Claude Peerboom
- UCB Pharma, Chemin du Foriest, 1420 Braine-l'Alleud, Belgium
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Sonkar KS, Pachauri M, Kumar A, Choudhary H, Jagannadham MV. Conformational stability of peroxidase from the latex of Artocarpus lakoocha: influence of pH, chaotropes, and temperature. FRONTIERS IN PLANT SCIENCE 2024; 15:1341454. [PMID: 38476686 PMCID: PMC10929713 DOI: 10.3389/fpls.2024.1341454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 02/02/2024] [Indexed: 03/14/2024]
Abstract
The latex of the medicinal plant Artocarpus lakoocha (A. lakoocha), which has been shown to have potential anti-inflammatory and wound-healing capabilities, contains a novel heme-peroxidase. This protein was subjected to activity assays, fluorescence spectroscopy, and far-UV circular dichroism to investigate its structure, dynamics, and stability. The results demonstrated the presence of three folding states: the native state (N) at neutral pH, intermediate states including molten globule (MG) at pH 2 and acid-unfolded (UA) at pH 1.5 or lower, and acid-refolded (A) at pH 0.5, along with alkaline denatured (UB) at pH 8-12 and the third denatured state (D) at GuHCl concentrations exceeding 5 M. Absorbance studies indicated the presence of loosely associated form of heme in the pH range of 1-2. The protein showed stability and structural integrity across a wide pH range (3-10), temperature (70°C), and high concentrations of GuHCl (5 M) and urea (8 M). This study is the first to report multiple 'partially folded intermediate states' of A. lakoocha peroxidase, with varying amounts of secondary structure, stability, and compactness. These results demonstrate the high stability of A. lakoocha peroxidase and its potential for biotechnological and industrial applications, making it a valuable model system for further studies on its structure-function relationship.
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Affiliation(s)
- Kirti Shila Sonkar
- Molecular Biology Unit, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
| | | | - Amit Kumar
- Department of Biochemistry, University of Delhi, New Delhi, India
| | - Himanshi Choudhary
- Molecular Pathology Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), Trieste, Italy
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Bharti, Nair MS. Molecular cloning, biophysical and in silico studies of Human papillomavirus 33 E2 DNA binding domain. J Biomol Struct Dyn 2024:1-20. [PMID: 38385450 DOI: 10.1080/07391102.2024.2317996] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 02/07/2024] [Indexed: 02/23/2024]
Abstract
Human papillomavirus 33, a high-risk HPV strain, is mainly responsible for HPV infection and cervical cancer in Asian countries. The E2 protein of HPV 33 is a DNA-binding protein that plays a crucial role in viral replication and transcription. We have cloned, overexpressed, and purified the DNA binding domain of the E2 protein. Size exclusion chromatography results suggested that the protein exists in a homodimeric state in the native form. Circular dichroism data showed that the protein has a higher content of β-sheet. The melting temperature obtained from differential scanning calorimetry is 52.59 °C, and the protein is stable at pH 8 and is in a dimeric form at basic pH. The protein is monomeric or unfolded at a very low pH. Chemical denaturation studies suggested that the protein denatured and dissociated simultaneously. The DNA binding activity of the protein was also confirmed and it showed binding affinity in the order of 106 M-1. The protein structure was modeled using homology modeling and other bioinformatic tools. The virtual screening and molecular dynamic simulation studies were performed to find compounds that can act as potent inhibitors against E2 DBD. This study expands the understanding of the conserved structural and binding properties of HPV33 E2 DBD and provides the first report on the characterization of the viral protein.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Bharti
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Haridwar Uttarakhand, India
| | - Maya S Nair
- Department of Biosciences and Bioengineering, Indian Institute of Technology Roorkee, Roorkee, Haridwar Uttarakhand, India
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Gooran N, Kopra K. Fluorescence-Based Protein Stability Monitoring-A Review. Int J Mol Sci 2024; 25:1764. [PMID: 38339045 PMCID: PMC10855643 DOI: 10.3390/ijms25031764] [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: 12/31/2023] [Revised: 01/26/2024] [Accepted: 01/29/2024] [Indexed: 02/12/2024] Open
Abstract
Proteins are large biomolecules with a specific structure that is composed of one or more long amino acid chains. Correct protein structures are directly linked to their correct function, and many environmental factors can have either positive or negative effects on this structure. Thus, there is a clear need for methods enabling the study of proteins, their correct folding, and components affecting protein stability. There is a significant number of label-free methods to study protein stability. In this review, we provide a general overview of these methods, but the main focus is on fluorescence-based low-instrument and -expertise-demand techniques. Different aspects related to thermal shift assays (TSAs), also called differential scanning fluorimetry (DSF) or ThermoFluor, are introduced and compared to isothermal chemical denaturation (ICD). Finally, we discuss the challenges and comparative aspects related to these methods, as well as future opportunities and assay development directions.
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Affiliation(s)
| | - Kari Kopra
- Department of Chemistry, University of Turku, Henrikinkatu 2, 20500 Turku, Finland;
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35
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Chen YL, Lee J, Liu Z, Strych U, Bottazzi ME, Lin YP, Chen WH. Biophysical and biochemical characterization of a recombinant Lyme disease vaccine antigen, CspZ-YA. Int J Biol Macromol 2024; 259:129295. [PMID: 38211914 DOI: 10.1016/j.ijbiomac.2024.129295] [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: 10/19/2023] [Revised: 12/19/2023] [Accepted: 01/05/2024] [Indexed: 01/13/2024]
Abstract
Lyme disease, caused by Lyme Borrelia spirochetes, is the most common vector-borne illness in the United States. Despite its global significance, with an estimated 14.5 % seroprevalence, there is currently no licensed vaccine. Previously, we demonstrated that CspZ-YA protein conferred protection against Lyme Borrelia infection, making it a promising vaccine candidate. However, such a protein was tagged with hexahistidine, and thus not preferred for vaccine development; furthermore, the formulation to stabilize the protein was understudied. In this work, we developed a two-step purification process for tag-free E. coli-expressed recombinant CspZ-YA. We further utilized various bioassays to analyze the protein and determine the suitable buffer system for long-term storage and formulation as a vaccine immunogen. The results indicated that a buffer with a pH between 6.5 and 8.5 stabilized CspZ-YA by reducing its surface hydrophobicity and colloidal interactions. Additionally, low pH values induced a change in local spatial conformation and resulted in a decrease in α-helix content. Lastly, an optimal salinity of 22-400 mM at pH 7.5 was found to be important for its stability. Collectively, this study provides a fundamental biochemical and biophysical understanding and insights into the ideal stabilizing conditions to produce CspZ-YA recombinant protein for use in vaccine formulation and development.
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Affiliation(s)
- Yi-Lin Chen
- Department of Pediatrics, Division of Tropical Medicine, National School of Tropical Medicine, Baylor College of Medicine, Houston, TX, USA; Texas Children's Hospital Center for Vaccine Development, Houston, TX, USA
| | - Jungsoon Lee
- Department of Pediatrics, Division of Tropical Medicine, National School of Tropical Medicine, Baylor College of Medicine, Houston, TX, USA; Texas Children's Hospital Center for Vaccine Development, Houston, TX, USA
| | - Zhuyun Liu
- Department of Pediatrics, Division of Tropical Medicine, National School of Tropical Medicine, Baylor College of Medicine, Houston, TX, USA; Texas Children's Hospital Center for Vaccine Development, Houston, TX, USA
| | - Ulrich Strych
- Department of Pediatrics, Division of Tropical Medicine, National School of Tropical Medicine, Baylor College of Medicine, Houston, TX, USA; Texas Children's Hospital Center for Vaccine Development, Houston, TX, USA
| | - Maria Elena Bottazzi
- Department of Pediatrics, Division of Tropical Medicine, National School of Tropical Medicine, Baylor College of Medicine, Houston, TX, USA; Texas Children's Hospital Center for Vaccine Development, Houston, TX, USA; Department of Biology, Baylor University, Waco, TX, USA
| | - Yi-Pin Lin
- Division of Infectious Diseases, Wadsworth Center, NYSDOH, Albany, NY, USA; Department of Biomedical Sciences, SUNY Albany, Albany, NY, USA.
| | - Wen-Hsiang Chen
- Department of Pediatrics, Division of Tropical Medicine, National School of Tropical Medicine, Baylor College of Medicine, Houston, TX, USA; Texas Children's Hospital Center for Vaccine Development, Houston, TX, USA.
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Kyrychenko A, Ladokhin AS. Fluorescent Probes and Quenchers in Studies of Protein Folding and Protein-Lipid Interactions. CHEM REC 2024; 24:e202300232. [PMID: 37695081 PMCID: PMC11113672 DOI: 10.1002/tcr.202300232] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 08/20/2023] [Indexed: 09/12/2023]
Abstract
Fluorescence spectroscopy provides numerous methodological tools for structural and functional studies of biological macromolecules and their complexes. All fluorescence-based approaches require either existence of an intrinsic probe or an introduction of an extrinsic one. Moreover, studies of complex systems often require an additional introduction of a specific quencher molecule acting in combination with a fluorophore to provide structural or thermodynamic information. Here, we review the fundamentals and summarize the latest progress in applications of different classes of fluorescent probes and their specific quenchers, aimed at studies of protein folding and protein-membrane interactions. Specifically, we discuss various environment-sensitive dyes, FRET probes, probes for short-distance measurements, and several probe-quencher pairs for studies of membrane penetration of proteins and peptides. The goals of this review are: (a) to familiarize the readership with the general concept that complex biological systems often require both a probe and a quencher to decipher mechanistic details of functioning and (b) to provide example of the immediate applications of the described methods.
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Affiliation(s)
- Alexander Kyrychenko
- Institute of Chemistry and School of Chemistry, V. N. Karazin Kharkiv National University, 4 Svobody sq., Kharkiv, 61022, Ukraine
| | - Alexey S Ladokhin
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, 3901 Rainbow Boulevard, Kansas City, KS, 66160, United States
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Siri M, Mangiarotti A, Vázquez-Dávila M, Bidan CM. Curli Amyloid Fibers in Escherichia coli Biofilms: The Influence of Water Availability on their Structure and Functional Properties. Macromol Biosci 2024; 24:e2300234. [PMID: 37776075 DOI: 10.1002/mabi.202300234] [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: 05/24/2023] [Revised: 09/22/2023] [Indexed: 10/01/2023]
Abstract
Escherichia coli biofilms consist of bacteria embedded in a self-produced matrix mainly made of protein fibers and polysaccharides. The curli amyloid fibers found in the biofilm matrix are promising versatile building blocks to design sustainable bio-sourced materials. To exploit this potential, it is crucial to understand i) how environmental cues during biofilm growth influence the molecular structure of these amyloid fibers, and ii) how this translates at higher length scales. To explore these questions, the effect of water availability during biofilm growth on the conformation and functions of curli is studied. Microscopy and spectroscopy are used to characterize the amyloid fibers purified from biofilms grown on nutritive substrates with different water contents, and micro-indentation to measure the rigidity of the respective biofilms. The purified curli amyloid fibers present differences in the yield, structure, and functional properties upon biofilm growth conditions. Fiber packing and β-sheets content correlate with their hydrophobicity and chemical stability, and with the rigidity of the biofilms. This study highlights how E. coli biofilm growth conditions impact curli structure and functions contributing to macroscopic materials properties. These fundamental findings infer an alternative strategy to tune curli structure, which will ultimately benefit engineering hierarchical and functional curli-based materials.
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Affiliation(s)
- Macarena Siri
- Max Planck Institute of Colloids and Interfaces, Department of Biomaterials, 14476, Potsdam, Germany
| | - Agustín Mangiarotti
- Max Planck Institute of Colloids and Interfaces, Department of Sustainable and Bio-inspired Materials, 14476, Potsdam, Germany
| | - Mónica Vázquez-Dávila
- Max Planck Institute of Colloids and Interfaces, Department of Biomaterials, 14476, Potsdam, Germany
| | - Cécile M Bidan
- Max Planck Institute of Colloids and Interfaces, Department of Biomaterials, 14476, Potsdam, Germany
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38
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Pan S, Manabe N, Ohno S, Komatsu S, Fujimura T, Yamaguchi Y. Each N-glycan on human IgA and J-chain uniquely affects oligomericity and stability. Biochim Biophys Acta Gen Subj 2024; 1868:130536. [PMID: 38070292 DOI: 10.1016/j.bbagen.2023.130536] [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: 10/28/2023] [Revised: 11/24/2023] [Accepted: 11/30/2023] [Indexed: 01/03/2024]
Abstract
BACKGROUND Immunoglobulin A (IgA) plays a pivotal role in various immune responses, especially that of mucosal immunity. IgA is usually assembled into dimers with the contribution of J-chains. There are two N-glycosylation sites in human IgA1-Fc and one in the J-chain. There is no consensus as yet on the functional role of the N-glycosylation. METHODS To gain a better understanding of their role, we designed a series of IgA1-Fc mutants, which were expressed in the absence or presence of the J-chain. RESULTS IgA1-Fc without the J-chain, was predominantly expressed as a monomer, and in its presence dimers and some polymers appeared. N263 (Fc Cα2), N459 (Fc tailpiece) and N49 (J-chain) were shown to be site-specifically modified with N-glycans by mass spectrometry analysis. Mutant IgA1-Fc N459Q failed to form a proper dimer in the presence of the J-chain, instead higher-order aggregates appeared. Fluorescence experiments suggest that the N459-glycans cover a hydrophobic surface at the Fc tailpiece that prevents other Fc molecules from approaching the dimeric IgA. A thermofluor assay revealed that the N-glycans at N263 (Fc) and N49 (J-chain) both contribute in different ways to the thermal stability of the Fc-J-chain complex. NMR analysis of 13C-labeled Fc suggests that the N459-glycan is relatively flexible while the N263-glycan is more rigid. CONCLUSIONS We conclude that the N459-glycan of IgA1-Fc is essential for dimer formation and prevention of higher-order aggregates while those at N263 (Fc) and N49 (J-chain) stabilize the Fc-J-chain complex. GENERAL SIGNIFICANCE Site-specific role for N-glycan in molecular assembly is addressed.
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Affiliation(s)
- Shunli Pan
- Division of Structural Glycobiology, Institute of Molecular Biomembrane and Glycobiology, Tohoku Medical and Pharmaceutical University, 4-4-1 Komatsushima, Aoba-ku, Sendai 981-8558, Miyagi, Japan
| | - Noriyoshi Manabe
- Division of Structural Glycobiology, Institute of Molecular Biomembrane and Glycobiology, Tohoku Medical and Pharmaceutical University, 4-4-1 Komatsushima, Aoba-ku, Sendai 981-8558, Miyagi, Japan
| | - Shiho Ohno
- Division of Structural Glycobiology, Institute of Molecular Biomembrane and Glycobiology, Tohoku Medical and Pharmaceutical University, 4-4-1 Komatsushima, Aoba-ku, Sendai 981-8558, Miyagi, Japan
| | - Sachiko Komatsu
- Division of Bioanalytical Chemistry, Tohoku Medical and Pharmaceutical University, 4-4-1 Komatsushima, Aoba-ku, Sendai 981-8558, Miyagi, Japan
| | - Tsutomu Fujimura
- Division of Bioanalytical Chemistry, Tohoku Medical and Pharmaceutical University, 4-4-1 Komatsushima, Aoba-ku, Sendai 981-8558, Miyagi, Japan
| | - Yoshiki Yamaguchi
- Division of Structural Glycobiology, Institute of Molecular Biomembrane and Glycobiology, Tohoku Medical and Pharmaceutical University, 4-4-1 Komatsushima, Aoba-ku, Sendai 981-8558, Miyagi, Japan.
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Ghahramani M, Shahsavani MB, Khaleghinejad SH, Niazi A, Moosavi-Movahedi AA, Yousefi R. Efficient Expression in the Prokaryotic Host System, Purification and Structural Analyses of the Recombinant Human ACE2 Catalytic Subunit as a Hybrid Protein with the B Subunit of Cholera Toxin (CTB-ACE2). Protein J 2024; 43:24-38. [PMID: 38017315 DOI: 10.1007/s10930-023-10164-y] [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] [Accepted: 10/10/2023] [Indexed: 11/30/2023]
Abstract
Angiotensin-converting enzyme 2 (ACE2) has a specific interaction with the coronavirus spike protein, enabling its entry into human cells. This membrane enzyme converts angiotensin II into angiotensin 1-7, which has an essential role in protecting the heart and improving lung function. Many therapeutic properties have been attributed to the human recombinant ACE2 (hrACE2), especially in combating complications related to diabetes mellitus and hypertension, as well as, preventing the coronavirus from entering the target tissues. In the current study, we designed an appropriate gene construct for the hybrid protein containing the ACE2 catalytic subunit and the B subunit of cholera toxin (CTB-ACE2). This structural feature will probably help the recombinant hybrid protein enter the mucosal tissues, including the lung tissue. Optimization of this hybrid protein expression was investigated in BL21 bacterial host cells. Also, the hybrid protein was identified with an appropriate antibody using the ELISA method. A large amount of the hybrid protein (molecular weight of ~ 100 kDa) was expressed as the inclusion body when the induction was performed in the presence of 0.25 mM IPTG and 1% sucrose for 10 h. Finally, the protein structural features were assessed using several biophysical methods. The fluorescence emission intensity and oligomeric size distribution of the CTB-ACE2 suggested a temperature-dependent alteration. The β-sheet and α-helix were also dominant in the hybrid protein structure, and this protein also displays acceptable chemical stability. In overall, according to our results, the efficient expression and successful purification of the CTB-ACE2 protein may pave the path for its therapeutic applications against diseases such as covid-19, diabetes mellitus and hypertension.
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Affiliation(s)
- Maryam Ghahramani
- Protein Chemistry Laboratory (PCL), Department of Biology, College of Sciences, Shiraz University, Shiraz, Iran
| | - Mohammad Bagher Shahsavani
- Protein Chemistry Laboratory (PCL), Department of Biology, College of Sciences, Shiraz University, Shiraz, Iran
| | - Seyed Hossein Khaleghinejad
- Protein Chemistry Laboratory (PCL), Department of Biology, College of Sciences, Shiraz University, Shiraz, Iran
| | - Ali Niazi
- Institute of Biotechnology, Shiraz University, Shiraz, Iran
| | | | - Reza Yousefi
- Protein Chemistry Laboratory (PCL), Department of Biology, College of Sciences, Shiraz University, Shiraz, Iran.
- Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Iran.
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40
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Wang F, Zhang Y. Physiology and pharmacological targeting of phase separation. J Biomed Sci 2024; 31:11. [PMID: 38245749 PMCID: PMC10800077 DOI: 10.1186/s12929-024-00993-z] [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: 08/30/2023] [Accepted: 01/04/2024] [Indexed: 01/22/2024] Open
Abstract
Liquid-liquid phase separation (LLPS) in biology describes a process by which proteins form membraneless condensates within a cellular compartment when conditions are met, including the concentration and posttranslational modifications of the protein components, the condition of the aqueous solution (pH, ionic strength, pressure, and temperature), and the existence of assisting factors (such as RNAs or other proteins). In these supramolecular liquid droplet-like inclusion bodies, molecules are held together through weak intermolecular and/or intramolecular interactions. With the aid of LLPS, cells can assemble functional sub-units within a given cellular compartment by enriching or excluding specific factors, modulating cellular function, and rapidly responding to environmental or physiological cues. Hence, LLPS is emerging as an important means to regulate biology and physiology. Yet, excessive inclusion body formation by, for instance, higher-than-normal concentrations or mutant forms of the protein components could result in the conversion from dynamic liquid condensates into more rigid gel- or solid-like aggregates, leading to the disruption of the organelle's function followed by the development of human disorders like neurodegenerative diseases. In summary, well-controlled formation and de-formation of LLPS is critical for normal biology and physiology from single cells to individual organisms, whereas abnormal LLPS is involved in the pathophysiology of human diseases. In turn, targeting these aggregates or their formation represents a promising approach in treating diseases driven by abnormal LLPS including those neurodegenerative diseases that lack effective therapies.
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Affiliation(s)
- Fangfang Wang
- Department of Pharmacology, School of Medicine, Case Comprehensive Cancer Center, Case Western Reserve University, 2109 Adelbert Road, W309A, Cleveland, OH, 44106, USA
| | - Youwei Zhang
- Department of Pharmacology, School of Medicine, Case Comprehensive Cancer Center, Case Western Reserve University, 2109 Adelbert Road, W309A, Cleveland, OH, 44106, USA.
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41
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Gorecki J, Krause S. Numerical investigation of a graphene-on-semiconductor device for optical monitoring of cell electrophysiology. iScience 2024; 27:108554. [PMID: 38188511 PMCID: PMC10770480 DOI: 10.1016/j.isci.2023.108554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 09/19/2023] [Accepted: 11/20/2023] [Indexed: 01/09/2024] Open
Abstract
Spatially resolved sensing devices for electrostatic potentials are extremely useful for characterization of living cells, however, many current techniques lack the speed necessary to capture spatially resolved, functional information of cells in real-time. Here, an optical sensing technique is proposed based on graphene on a semiconductor stack operating in the near-infrared spectrum. By modeling coherent interference of multiply reflected beam paths within the semiconductor stack, we demonstrate how the device produces a continuous reflectivity change in response to graphene Fermi energy which is ideal for sensing changes in local electrostatic fields produced by action potentials of living cells. By coupling the device with a high-speed camera, we propose this platform will allow for high-speed imaging of action potentials over a large sensing area with micron scale resolution.
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Affiliation(s)
- Jon Gorecki
- Department of Bioengineering, Imperial College London, Exhibition Road, London SW7 2BX, UK
| | - Steffi Krause
- School of Engineering and Materials Science, Queen Mary University of London, Mile End Road, London E1 4NS, UK
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42
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Mohammadi S, Seyedalipour B, Hashemi SZ, Hosseinkhani S, Mohseni M. Implications of ALS-Associated Mutations on Biochemical and Biophysical Features of hSOD1 and Aggregation Formation. Biochem Genet 2024:10.1007/s10528-023-10619-y. [PMID: 38196030 DOI: 10.1007/s10528-023-10619-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 12/02/2023] [Indexed: 01/11/2024]
Abstract
One of the recognized motor neuron degenerative disorders is amyotrophic lateral sclerosis (ALS). By now, several mutations have been reported and linked to ALS patients, some of which are induced by mutations in the human superoxide dismutase (hSOD1) gene. The ALS-provoking mutations are located throughout the structure of hSOD1 and promote the propensity to aggregate. Despite numerous investigations, the underlying mechanism related to the toxicity of mutant hSOD1 through the gain of a toxic function is still vague. We surveyed two mutant forms of hSOD1 by removing and adding cysteine at positions 146 and 72, respectively, to investigate the biochemical characterization and amyloid formation. Our findings predicted the harmful and destabilizing impact of two SOD1 mutants using multiple programs. The specific activity of the wild-type form was about 1.42- and 1.92-fold higher than that of C146R and G72C mutants, respectively. Comparative structural studies using CD spectropolarimetry, and intrinsic and ANS fluorescence showed alterations in secondary structure content, exposure of hydrophobic patches, and structural compactness of WT-hSOD1 vs. mutants. We demonstrated that two mutants were able to promote amyloid-like aggregates under amyloid induction circumstances (50-mM Tris-HCl pH 7.4, 0.2-M KSCN, 50-mM DTT, 37 °C, 190 rpm). Monitoring aggregates were done using an enhancement in thioflavin T fluorescence and alterations in Congo red absorption. The mutants accelerated fibrillation with subsequently greater fluorescence amplitude and a shorter lag time compared to WT-SOD1. These findings support the aggregation of ALS-associated SOD1 mutants as an integral part of ALS pathology.
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Affiliation(s)
- Saeede Mohammadi
- Department of Molecular and Cell Biology, Faculty of Basic Science, University of Mazandaran, Babolsar, Iran
| | - Bagher Seyedalipour
- Department of Molecular and Cell Biology, Faculty of Basic Science, University of Mazandaran, Babolsar, Iran.
| | - Seyedeh Zohreh Hashemi
- Department of Molecular and Cell Biology, Faculty of Basic Science, University of Mazandaran, Babolsar, Iran
| | - Saman Hosseinkhani
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Mojtaba Mohseni
- Department of Microbiology, Faculty of Basic Science, University of Mazandaran, Babolsar, Iran
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Ota C, Konishi T, Tanaka SI, Takano K. Induced Circular Dichroism Analysis of Thermally Induced Conformational Changes on Protein Binding Sites Under a Crowding Environment. Chemphyschem 2024; 25:e202300593. [PMID: 37845184 DOI: 10.1002/cphc.202300593] [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: 08/20/2023] [Revised: 10/15/2023] [Accepted: 10/16/2023] [Indexed: 10/18/2023]
Abstract
Protein-ligand interactions in crowded cellular environments play a crucial role in biological functions. The crowded environment can perturb the overall protein structure and local conformation, thereby influencing the binding pathway of protein-ligand reactions within the cellular milieu. Therefore, a detailed understanding of the local conformation is crucial for elucidating the intricacies of protein-ligand interactions in crowded cellular environments. In this study, we investigated the feasibility of induced circular dichroism (ICD) using 8-anilinonaphthalene-1-sulfonic acid (ANS) for local conformational analysis at the binding site in a crowding environment. Bovine serum albumin (BSA) concentration-dependent measurements were performed to assess the feasibility of ANS-ICD for analyzing protein interior binding sites. The results showed distinct changes in the ANS-ICD spectra of BSA solutions, indicating their potential for analyzing the internal conformation of proteins. Moreover, temperature-dependent measurements were performed in dilute and crowding environments, revealing distinct denaturation pathways of BSA binding sites. Principal component analysis of ANS-ICD spectral changes revealed lower temperature pre-denaturation in the crowded solution than that in the diluted solution, suggesting destabilization of binding sites owing to self-crowding repulsive interactions. The established ANS-ICD method can provide valuable conformational insights into protein-ligand interactions in crowded cellular environments.
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Affiliation(s)
- Chikashi Ota
- College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga, 525-8577, Japan
| | - Tomoya Konishi
- Department of Biomolecular Chemistry, Kyoto Prefectural University, Sakyo-ku, Kyoto, 606-8522, Japan
| | - Shun-Ichi Tanaka
- Department of Biomolecular Chemistry, Kyoto Prefectural University, Sakyo-ku, Kyoto, 606-8522, Japan
| | - Kazufumi Takano
- Department of Biomolecular Chemistry, Kyoto Prefectural University, Sakyo-ku, Kyoto, 606-8522, Japan
- Kazufumi Takano - Department of Biomolecular Chemistry, Kyoto Prefectural University, Sakyo-ku, Kyoto, 606-8522, Japan
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44
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Kumar V, Kaushik V, Kumar S, Levkovich SA, Gupta P, Laor Bar-Yosef D, Gazit E, Segal D. The von Hippel-Lindau protein forms fibrillar amyloid assemblies that are mitigated by the anti-amyloid molecule Purpurin. Biochem Biophys Res Commun 2024; 690:149250. [PMID: 38039781 DOI: 10.1016/j.bbrc.2023.149250] [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: 10/03/2023] [Revised: 11/03/2023] [Accepted: 11/13/2023] [Indexed: 12/03/2023]
Abstract
The von Hippel-Lindau protein (pVHL) is a tumor suppressor involved in oxygen regulation via dynamic nucleocytoplasmic shuttling. It plays a crucial role in cell survival by degrading hypoxia-inducible factors (HIFs). Mutations in the VHL gene cause angiogenic tumors, characterized as VHL syndrome. However, aggressive tumors involving wild-type pVHL have also been described but the underlying mechanism remains to be revealed. We have previously shown that pVHL possesses several short amyloid-forming motifs, making it aggregation-prone. In this study, using a series of biophysical assays, we demonstrated that a pVHL-derived fragment (pVHL104-140) that harbors the nuclear export motif and HIF binding site, forms amyloid-like fibrillar structures in vitro by following secondary-nucleation-based kinetics. The peptide also formed amyloids at acidic pH that mimics the tumor microenvironment. We, subsequently, validated the amyloid formation by pVHL in vitro. Using the Curli-dependent amyloid generator (C-DAG) expression system, we confirmed the amyloidogenesis of pVHL in bacterial cells. The pVHL amyloids are an attractive target for therapeutics of the VHL syndrome. Accordingly, we demonstrated in vitro that Purpurin is a potent inhibitor of pVHL fibrillation. The amyloidogenic behavior of wild-type pVHL and its inhibition provide novel insights into the molecular underpinning of the VHL syndrome and its possible treatment.
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Affiliation(s)
- Vijay Kumar
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Vibha Kaushik
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Sourav Kumar
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Shon A Levkovich
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Priya Gupta
- School of Plant Sciences and Food Security, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Dana Laor Bar-Yosef
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Ehud Gazit
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 6997801, Israel; BLAVATNIK CENTER for Drug Discovery, Tel Aviv University, Tel Aviv, 6997801, Israel; Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, 6997801, Israel
| | - Daniel Segal
- Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, 6997801, Israel; BLAVATNIK CENTER for Drug Discovery, Tel Aviv University, Tel Aviv, 6997801, Israel; Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, 6997801, Israel.
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45
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Gao K, Zha F, Rao J, Chen B. Nonenzymatic glycation as a tunable technique to modify plant proteins: A comprehensive review on reaction process, mechanism, conjugate structure, and functionality. Compr Rev Food Sci Food Saf 2024; 23:e13269. [PMID: 38284590 DOI: 10.1111/1541-4337.13269] [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: 07/27/2023] [Revised: 10/10/2023] [Accepted: 10/25/2023] [Indexed: 01/30/2024]
Abstract
Plant proteins are expected to become a major protein source to replace currently used animal-derived proteins in the coming years. However, there are always challenges when using these proteins due to their low water solubility induced by the high molecular weight storage proteins. One approach to address this challenge is to modify proteins through Maillard glycation, which involves the reaction between proteins and carbohydrates. In this review, we discuss various chemical methods currently available for determining the indicators of the Maillard reaction in the early stage, including the graft degree of glycation and the available lysine or sugar, which are involved in the very beginning of the reaction. We also provide a detailed description of the most popular methods for determining graft sites and assessing different plant protein structures and functionalities upon non-enzymatic glycation. This review offers valuable insights for researchers and food scientists in order to develop plant-based protein ingredients with improved functionality.
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Affiliation(s)
- Kun Gao
- Department of Plant Sciences, North Dakota State University, Fargo, North Dakota, USA
| | - Fengchao Zha
- Department of Plant Sciences, North Dakota State University, Fargo, North Dakota, USA
| | - Jiajia Rao
- Department of Plant Sciences, North Dakota State University, Fargo, North Dakota, USA
| | - Bingcan Chen
- Department of Plant Sciences, North Dakota State University, Fargo, North Dakota, USA
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Shakilanishi S, Mrudula P, Shanthi C. Production of dehairing protease by Bacillus cereus VITSN04: a model cradle-to-cradle approach for sustainable greener production of leathers. ENVIRONMENTAL TECHNOLOGY 2024; 45:180-191. [PMID: 35848414 DOI: 10.1080/09593330.2022.2102938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 07/09/2022] [Indexed: 06/15/2023]
Abstract
Despite several attempts over decades, process scalability and sustainability remain a challenge to produce an environmental-friendly enzyme to gain industrial attention. In the present study, microbial degradation of chrome shavings (chromium-collagen leather waste) and the resulting collagen hydrolysate for producing the dehairing protease by Bacillus cereus VITSN04 were investigated in a lab-scale fermentor. Scale-up degradation of shavings resulted in higher recovery of collagen hydrolysate (76%) within 72 h compared to shake flasks (68% in 120 h). Earlier achieved medium composition of collagen hydrolysate (12 g L-1) and molasses (15 g L-1) appeared to induce amylase at the high rate, despite the maximal production of protease (203.8 ± 0.18 U mL-1), which was analysed by ANS fluorescence spectroscopy. Optimization of the media containing collagen hydrolysate (12 g L-1) and molasses (5 g L-1) was effective in producing protease (170.6 ± 0.1 U mL-1) and reduced the co-synthesis of amylase (48.2 ± 0.09 U mL-1). The controlled fermentation process by feeding molasses during the exponential growth phase had enhanced the dehairing protease production (∼2.96 fold). The produced protease then partitioned through the biphasic system and showed significant dehairing of goat skins on the pilot scale. Thus, the scalability of the process to produce dehairing enzymes using waste, generated at the site of its use, offers hope for sustainable greener production of leathers.
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Affiliation(s)
- S Shakilanishi
- Department of Biotechnology, School of BioSciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - P Mrudula
- Centre for Nanobiotechnology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
| | - C Shanthi
- Department of Biotechnology, School of BioSciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
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Khan S, Naeem A. Bovine serum albumin prevents human hemoglobin aggregation and retains its chaperone-like activity. J Biomol Struct Dyn 2024; 42:346-361. [PMID: 36974939 DOI: 10.1080/07391102.2023.2192802] [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: 02/03/2023] [Accepted: 03/13/2023] [Indexed: 03/29/2023]
Abstract
This study investigates the ability of bovine serum albumin (BSA) to act as an extracellular chaperone (EC) on human hemoglobin (Hb) at a pH of 7.4. The best temperature for studying this behavior was determined by analyzing Hb's aggregation kinetics at multiple temperatures. 55 °C was chosen as the optimal temperature for forming Hb amyloids. BSA was then tested at various concentrations (20-100 μM) to assess its chaperone-like activity on Hb at 55 °C. At a concentration of 100 μM, BSA exhibits chaperone-like activity with a client protein:BSA ratio of 1:10. The high ratio implies that the chaperone activity of BSA is favored by the effects of macromolecular crowding. The results showed that BSA has the potential to inhibit Hb's dissociation into alpha and beta subunits and protein aggregation by inhibiting secondary nucleation. BSA also causes the depolymerization of fibrils over time. The results were validated using molecular docking and all-atom molecular dynamics simulations. MD analysis such as RMSD, RMSF, Rg, SASA, Hydrogen bond, PCA, Free energy landscape (FEL) revealed that the stability of hemoglobin is greater when it is bound to BSA compared to unbound state. The study suggests that BSA can potentially bind to Hb dimers and reduce excitonic interactions, which reduces Hb aggregation. These results are consistent with the aggregation kinetics experiments.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Sadaf Khan
- Department of Biochemistry, Aligarh Muslim University, Aligarh, India
| | - Aabgeena Naeem
- Department of Biochemistry, Aligarh Muslim University, Aligarh, India
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48
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Otun SO, Graca R, Achilonu I. Combating Aminoglycoside Resistance: From Structural and Functional Characterisation to Therapeutic Challenges with RKAAT. Curr Protein Pept Sci 2024; 25:454-468. [PMID: 38314602 DOI: 10.2174/0113892037278814231226104509] [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: 09/18/2023] [Revised: 12/04/2023] [Accepted: 12/07/2023] [Indexed: 02/06/2024]
Abstract
A comprehensive knowledge of aminoglycoside-modifying enzymes (AMEs) and their role in bacterial resistance mechanisms is urgently required due to the rising incidence of antibiotic resistance, particularly in Klebsiella pneumoniae infections. This study explores the essential features of AMEs, including their structural and functional properties, the processes by which they contribute to antibiotic resistance, and the therapeutic importance of aminoglycosides. The study primarily examines the Recombinant Klebsiella pneumoniae Aminoglycoside Adenylyl Transferase (RKAAT), particularly emphasizing its biophysical characteristics and the sorts of resistance it imparts. Furthermore, this study examines the challenges presented by RKAAT-mediated resistance, an evaluation of treatment methods and constraints, and options for controlling infection. The analysis provides a prospective outlook on strategies to address and reduce antibiotic resistance. This extensive investigation seeks to provide vital insights into the continuing fight against bacterial resistance, directing future research efforts and medicinal approaches.
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Affiliation(s)
- Sarah Oluwatobi Otun
- Department of Molecular and Cell Biology, Protein Structure-function Unit, University of Witwatersrand, Johannesburg, South Africa
| | - Richard Graca
- Department of Molecular and Cell Biology, Protein Structure-function Unit, University of Witwatersrand, Johannesburg, South Africa
| | - Ikechukwu Achilonu
- Department of Molecular and Cell Biology, Protein Structure-function Unit, University of Witwatersrand, Johannesburg, South Africa
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Wang C, Teng L, Liu ZS, Kamalova A, McMenimen KA. HspB5 Chaperone Structure and Activity Are Modulated by Chemical-Scale Interactions in the ACD Dimer Interface. Int J Mol Sci 2023; 25:471. [PMID: 38203641 PMCID: PMC10778692 DOI: 10.3390/ijms25010471] [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: 11/20/2023] [Revised: 12/24/2023] [Accepted: 12/27/2023] [Indexed: 01/12/2024] Open
Abstract
Small heat shock proteins (sHsps) are a family of ATP-independent molecular chaperones that function as "holdases" and prevent protein aggregation due to changes in temperature, pH, or oxidation state. sHsps have a conserved α-crystallin domain (ACD), which forms the dimer building block, flanked by variable N- and C-terminal regions. sHsps populate various oligomeric states as a function of their sequestrase activity, and these dynamic structural features allow the proteins to interact with a plethora of cellular substrates. However, the molecular mechanisms of their dynamic conformational assembly and the interactions with various substrates remains unclear. Therefore, it is important to gain insight into the underlying physicochemical properties that influence sHsp structure in an effort to understand their mechanism(s) of action. We evaluated several disease-relevant mutations, D109A, F113Y, R116C, R120G, and R120C, in the ACD of HspB5 for changes to in vitro chaperone activity relative to that of wildtype. Structural characteristics were also evaluated by ANS fluorescence and CD spectroscopy. Our results indicated that mutation Y113F is an efficient holdase, while D109A and R120G, which are found in patients with myofibrillar myopathy and cataracts, respectively, exhibit a large reduction in holdase activity in a chaperone-like light-scattering assay, which indicated alterations in substrate-sHsp interactions. The extent of the reductions in chaperone activities are different among the mutants and specific to the substrate protein, suggesting that while sHsps are able to interact with many substrates, specific interactions provide selectivity for some substrates compared to others. This work is consistent with a model for chaperone activity where key electrostatic interactions in the sHsp dimer provide structural stability and influence both higher-order sHsp interactions and facilitate interactions with substrate proteins that define chaperone holdase activity.
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Affiliation(s)
- Chenwei Wang
- Program in Biochemistry, Mount Holyoke College, South Hadley, MA 01075, USA; (C.W.); (L.T.); (Z.S.L.)
| | - Lilong Teng
- Program in Biochemistry, Mount Holyoke College, South Hadley, MA 01075, USA; (C.W.); (L.T.); (Z.S.L.)
| | - Zhiyan Silvia Liu
- Program in Biochemistry, Mount Holyoke College, South Hadley, MA 01075, USA; (C.W.); (L.T.); (Z.S.L.)
| | - Aichurok Kamalova
- Program in Neuroscience and Behavior, Mount Holyoke College, South Hadley, MA 01075, USA;
| | - Kathryn A. McMenimen
- Program in Biochemistry, Mount Holyoke College, South Hadley, MA 01075, USA; (C.W.); (L.T.); (Z.S.L.)
- Program in Neuroscience and Behavior, Mount Holyoke College, South Hadley, MA 01075, USA;
- Department of Chemistry, Mount Holyoke College, South Hadley, MA 01075, USA
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Day EC, Chittari SS, Bogen MP, Knight AS. Navigating the Expansive Landscapes of Soft Materials: A User Guide for High-Throughput Workflows. ACS POLYMERS AU 2023; 3:406-427. [PMID: 38107416 PMCID: PMC10722570 DOI: 10.1021/acspolymersau.3c00025] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 11/02/2023] [Accepted: 11/07/2023] [Indexed: 12/19/2023]
Abstract
Synthetic polymers are highly customizable with tailored structures and functionality, yet this versatility generates challenges in the design of advanced materials due to the size and complexity of the design space. Thus, exploration and optimization of polymer properties using combinatorial libraries has become increasingly common, which requires careful selection of synthetic strategies, characterization techniques, and rapid processing workflows to obtain fundamental principles from these large data sets. Herein, we provide guidelines for strategic design of macromolecule libraries and workflows to efficiently navigate these high-dimensional design spaces. We describe synthetic methods for multiple library sizes and structures as well as characterization methods to rapidly generate data sets, including tools that can be adapted from biological workflows. We further highlight relevant insights from statistics and machine learning to aid in data featurization, representation, and analysis. This Perspective acts as a "user guide" for researchers interested in leveraging high-throughput screening toward the design of multifunctional polymers and predictive modeling of structure-property relationships in soft materials.
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Affiliation(s)
| | | | - Matthew P. Bogen
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Abigail S. Knight
- Department of Chemistry, The University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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