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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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Hatai J, Prasad PK, Lahav-Mankovski N, Oppenheimer-Low N, Unger T, Sirkis YF, Dadosh T, Motiei L, Margulies D. Assessing changes in the expression levels of cell surface proteins with a turn-on fluorescent molecular probe. Chem Commun (Camb) 2021; 57:1875-1878. [PMID: 33427257 DOI: 10.1039/d0cc07095e] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Tri-nitrilotriacetic acid (NTA)-based fluorescent probes were developed and used to image His-tagged-labelled outer membrane protein C (His-OmpC) in live Escherichia coli. One of these probes was designed to light up upon binding, which provided the means to assess changes in the His-OmpC expression levels by taking a simple fluorescence spectrum.
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Affiliation(s)
- Joydev Hatai
- Department of Organic Chemistry, Weizmann Institute of Science, Rehovot 7610001, Israel.
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Adeola HA, Soyele OO, Adefuye AO, Jimoh SA, Butali A. Omics-based molecular techniques in oral pathology centred cancer: prospect and challenges in Africa. Cancer Cell Int 2017; 17:61. [PMID: 28592923 PMCID: PMC5460491 DOI: 10.1186/s12935-017-0432-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Accepted: 05/29/2017] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The completion of the human genome project and the accomplished milestones in the human proteome project; as well as the progress made so far in computational bioinformatics and "big data" processing have contributed immensely to individualized/personalized medicine in the developed world. MAIN BODY At the dawn of precision medicine, various omics-based therapies and bioengineering can now be applied accurately for the diagnosis, prognosis, treatment, and risk stratification of cancer in a manner that was hitherto not thought possible. The widespread introduction of genomics and other omics-based approaches into the postgraduate training curriculum of diverse medical and dental specialties, including pathology has improved the proficiency of practitioners in the use of novel molecular signatures in patient management. In addition, intricate details about disease disparity among different human populations are beginning to emerge. This would facilitate the use of tailor-made novel theranostic methods based on emerging molecular evidences. CONCLUSION In this review, we examined the challenges and prospects of using currently available omics-based technologies vis-à-vis oral pathology as well as prompt cancer diagnosis and treatment in a resource limited setting.
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Affiliation(s)
- Henry A. Adeola
- Department of Oral and Maxillofacial Pathology, Faculty of Dentistry, University of the Western Cape and Tygerberg Hospital, Cape Town, South Africa
- International Centre for Genetic Engineering and Biotechnology, Cape Town, South Africa
- Division of Dermatology, Department of Medicine, Faculty of Health Sciences and Groote Schuur Hospital, University of Cape Town, Cape Town, South Africa
| | - Olujide O. Soyele
- Department of Oral Maxillo-facial Surgery and Oral Pathology, Obafemi Awolowo University, Ile-Ife, Nigeria
| | - Anthonio O. Adefuye
- Division of Health Sciences Education, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa
| | - Sikiru A. Jimoh
- Department of Anatomical Sciences, Faculty of Health Sciences, Walter Sisulu University, Mthatha, Eastern Cape South Africa
| | - Azeez Butali
- Department of Oral Pathology, Radiology and Medicine, University of Iowa, Iowa City, IA USA
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Uzoma I, Zhu H. Interactome mapping: using protein microarray technology to reconstruct diverse protein networks. GENOMICS PROTEOMICS & BIOINFORMATICS 2013; 11:18-28. [PMID: 23395178 PMCID: PMC3968920 DOI: 10.1016/j.gpb.2012.12.005] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2012] [Accepted: 12/20/2012] [Indexed: 12/22/2022]
Abstract
A major focus of systems biology is to characterize interactions between cellular components, in order to develop an accurate picture of the intricate networks within biological systems. Over the past decade, protein microarrays have greatly contributed to advances in proteomics and are becoming an important platform for systems biology. Protein microarrays are highly flexible, ranging from large-scale proteome microarrays to smaller customizable microarrays, making the technology amenable for detection of a broad spectrum of biochemical properties of proteins. In this article, we will focus on the numerous studies that have utilized protein microarrays to reconstruct biological networks including protein–DNA interactions, posttranslational protein modifications (PTMs), lectin–glycan recognition, pathogen–host interactions and hierarchical signaling cascades. The diversity in applications allows for integration of interaction data from numerous molecular classes and cellular states, providing insight into the structure of complex biological systems. We will also discuss emerging applications and future directions of protein microarray technology in the global frontier.
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Affiliation(s)
- Ijeoma Uzoma
- Department of Pharmacology and Molecular Sciences, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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Biophysical Characterization and Folding Studies of Plant Protease, Wrightin: Identification of Folding Intermediate Under Different Conditions. Protein J 2009; 28:213-23. [DOI: 10.1007/s10930-009-9186-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Zanivan S, Cascone I, Peyron C, Molineris I, Marchio S, Caselle M, Bussolino F. A new computational approach to analyze human protein complexes and predict novel protein interactions. Genome Biol 2008; 8:R256. [PMID: 18053208 PMCID: PMC2246258 DOI: 10.1186/gb-2007-8-12-r256] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2007] [Revised: 11/14/2007] [Accepted: 12/04/2007] [Indexed: 11/20/2022] Open
Abstract
A new approach to identifying interacting proteins based on gene-expression data uses hypergeometric distribution and Monte-Carlo simulations. We propose a new approach to identify interacting proteins based on gene expression data. By using hypergeometric distribution and extensive Monte-Carlo simulations, we demonstrate that looking at synchronous expression peaks in a single time interval is a high sensitivity approach to detect co-regulation among interacting proteins. Combining gene expression and Gene Ontology similarity analyses enabled the extraction of novel interactions from microarray datasets. Applying this approach to p21-activated kinase 1, we validated α-tubulin and early endosome antigen 1 as its novel interactors.
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Affiliation(s)
- Sara Zanivan
- Department of Oncological Sciences and Division of Molecular Angiogenesis, Institute for Cancer Research and Treatment (IRCC), University of Torino Medical School, Strada Provinciale, I-10060 Candiolo (Turin), Italy.
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Pande M, Dubey VK, Sahu V, Jagannadham MV. Conformational plasticity of cryptolepain: accumulation of partially unfolded states in denaturants induced equilibrium unfolding. J Biotechnol 2007; 131:404-17. [PMID: 17825936 DOI: 10.1016/j.jbiotec.2007.08.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2007] [Revised: 07/25/2007] [Accepted: 08/01/2007] [Indexed: 11/23/2022]
Abstract
pH and chemical denaturant dependent conformational changes of a serine protease cryptolepain from Cryptolepis buchanani are presented in this paper. Activity measurements, near UV, far UV CD, fluorescence emission spectroscopy, and ANS binding studies have been carried out to understand the folding mechanism of the protein in the presence of denaturants. pH and chemical denaturants have a marked effect on the stability, structure, and function of many globular proteins due to their ability to influence the electrostatic interactions. The preliminary biophysical study on cryptolepain shows that major elements of secondary structure are beta-sheets. Under neutral conditions the enzyme was stable in urea while GuHCl-induced equilibrium unfolding was cooperative. Cryptolepain shows little ANS binding even under neutral conditions due to more hydrophobicity of beta-sheets. Multiple intermediates were populated during the pH-induced unfolding of cryptolepain. Temperature-induced denaturation of cryptolepain in the molten globule like state is non-cooperative, contrary to the cooperativity seen with the native protein, suggesting the presence of two parts, possibly domains, in the molecular structure of cryptolepain, with different stability that unfolds in steps. Interestingly, the GuHCl-induced unfolding of A state (molten globule state) of cryptolepain is unique, as lower concentration of denaturant, not only induces structure but also facilitate transition from one molten globule like state (MG(1)) into another (MG(2)). The increase of pH drives the protein into alkaline denatured state characterized by the absence of any ANS binding. GuHCl- and urea-induced unfolding transition curves at pH 12.0 were non-coincidental indicating the presence of an intermediate in the unfolding pathway.
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Affiliation(s)
- Monu Pande
- Molecular Biology Unit, Institute of Medical Sciences, Banaras Hindu University, Varanasi, India
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Ciulli A, Abell C. Biophysical tools to monitor enzyme-ligand interactions of enzymes involved in vitamin biosynthesis. Biochem Soc Trans 2005; 33:767-71. [PMID: 16042595 DOI: 10.1042/bst0330767] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Knowledge of biomolecular interactions is of importance to our understanding of biological processes such as enzyme catalysis and inhibition. Biophysical techniques enable sensitive detection and accurate characterization of binding and are therefore powerful tools in enzymology and rational drug design. The applications of NMR spectroscopy and isothermal titration calorimetry to study enzyme-ligand interactions will be discussed. Recent work on ketopantoate reductase, which catalyses an important step on the biosynthetic pathway to vitamin B5, is used to illustrate the potential of this approach.
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Affiliation(s)
- A Ciulli
- University Chemical Laboratory, Lensfield Road, Cambridge CB2 1EW, UK.
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Rich RL, Myszka DG. A survey of the year 2002 commercial optical biosensor literature. J Mol Recognit 2004; 16:351-82. [PMID: 14732928 DOI: 10.1002/jmr.649] [Citation(s) in RCA: 70] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
We have compiled 819 articles published in the year 2002 that involved commercial optical biosensor technology. The literature demonstrates that the technology's application continues to increase as biosensors are contributing to diverse scientific fields and are used to examine interactions ranging in size from small molecules to whole cells. Also, the variety of available commercial biosensor platforms is increasing and the expertise of users is improving. In this review, we use the literature to focus on the basic types of biosensor experiments, including kinetics, equilibrium analysis, solution competition, active concentration determination and screening. In addition, using examples of particularly well-performed analyses, we illustrate the high information content available in the primary response data and emphasize the impact of including figures in publications to support the results of biosensor analyses.
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Affiliation(s)
- Rebecca L Rich
- Center for Biomolecular Interaction Analysis, University of Utah, Salt Lake City, UT 84132, USA
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Kumar DP, Tiwari A, Bhat R. Effect of pH on the stability and structure of yeast hexokinase A. Acidic amino acid residues in the cleft region are critical for the opening and the closing of the structure. J Biol Chem 2004; 279:32093-9. [PMID: 15145950 DOI: 10.1074/jbc.m313449200] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
pH and salts have a marked effect on the stability, structure, and function of many globular proteins due to their ability to influence the electrostatic interactions. In this work, calorimetry, CD, and fluorescence studies have been carried out to understand the pH-dependent conformational changes of the two-domain protein yeast hexokinase A. In conjunction with the crystal structural data available, the present results have enabled the complete characterization and analysis of the pH-dependent conformational changes of the enzyme that have strong implications in understanding its structure-function relationship. The calorimetric profiles show a single thermal transition in the acidic pH range, whereas two independent transitions were observed in the alkaline pH range, suggesting the structural merger of the domains at the acidic pH. Comparison of the thermal transitions at pH 8.5 studied by different techniques suggests that the first transition corresponds to the smaller domain, and the second transition corresponds to the larger domain. The acid-denatured state of hexokinase A has high secondary structure content with little or no tertiary interactions and binds to the hydrophobic dye 8-anilinonaphthalene-1-sulfonic acid, suggesting that it is a molten globule-like state, whereas the alkali-denatured state is less structured than the acid-denatured state but more structured than the urea-denatured state, suggestive of a premolten globule-like state. Structural analysis using the published hexokinase B structure as well as the hexokinase A structure with the revised amino acid sequence in conjunction with the results obtained by us suggests that the ionization state of the acidic residues at the active site could regulate domain movements that are responsible for the opening and the closure of the cleft between the two domains and in turn affect the structure and function of the enzyme.
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Affiliation(s)
- D Prasanna Kumar
- Centre for Biotechnology, Jawaharlal Nehru University, New Delhi 110 067, India
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