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Mishra S, Ghosh A, Hansda B, Mondal TK, Biswas T, Das B, Roy D, Kumari P, Mondal S, Mandal B. Activation of Inert Supports for Enzyme(s) Immobilization Harnessing Biocatalytic Sustainability for Perennial Utilization. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:18377-18406. [PMID: 39171729 DOI: 10.1021/acs.langmuir.4c00488] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/23/2024]
Abstract
Although Nature's evolution and intelligence have gifted humankind with noteworthy enzyme candidates to simplify complex reactions with ultrafast, overselective, effortless, mild biological reactions for millions of years, their availability at minute-scale, short-range time-temperature stability, and purification costs hardly justify recycling/or reuse. Covalent immobilization, particularly via multipoint bonds, prevents denaturing, maintains activities for long-range time, pH, and temperature, and makes catalysts available for repetitive usages; which attracts researchers and industries to bring more immobilized enzyme contenders in science and commercial progressions. Inert-support activation, the most crucial step, needs appropriate activators; under mild conditions, the activator's functional group(s) still present on the activated support rapidly couples the enzyme, preventing unfolding and keeping the active site alive. This review summarizes exciting experimental advances, from the 1950s until today, in the activation strategies of various inert supports with five different surface activators, the cyanogen bromide, the isocyanate/isothiocyanate, the glutaraldehyde, the carbodiimide (with or without N-hydroxysuccinimide (NHS)), and the diazo group, for the immobilization of diverse enzymes for broader applications. These activators under mild pH (7.5 ± 0.5) and temperature (27 ± 3 °C) and ordinary stirring witnessed support activation and enzyme coupling and put off unfolding, harnessing addressable activities (CNBr: 40 ± 10%; -N═C═O/-N═C═S: 32 ± 7%; GA: 70 ± 15%; CDI: 60 ± 10%; -N+≡N: 80 ± 15%), while underprivileged stability, longevity, and reusabilities keep future investigations alive.
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Affiliation(s)
- Shailja Mishra
- Analytical and Bio-analytical Laboratory, Department of Chemistry, Visva-Bharati, Santiniketan, West Bengal, India 731235
| | - Ankit Ghosh
- Analytical and Bio-analytical Laboratory, Department of Chemistry, Visva-Bharati, Santiniketan, West Bengal, India 731235
| | - Biswajit Hansda
- Analytical and Bio-analytical Laboratory, Department of Chemistry, Visva-Bharati, Santiniketan, West Bengal, India 731235
| | - Tanay K Mondal
- Analytical and Bio-analytical Laboratory, Department of Chemistry, Visva-Bharati, Santiniketan, West Bengal, India 731235
| | - Tirtha Biswas
- Analytical and Bio-analytical Laboratory, Department of Chemistry, Visva-Bharati, Santiniketan, West Bengal, India 731235
| | - Basudev Das
- Analytical and Bio-analytical Laboratory, Department of Chemistry, Visva-Bharati, Santiniketan, West Bengal, India 731235
| | - Dipika Roy
- Department of Chemistry, Jadavpur University, Main Campus 188, Raja S.C. Mallick Rd, Kolkata, West Bengal, India 700032
| | - Pallavi Kumari
- University Department of Chemistry, T.M.B.U., Bhagalpur, Bihar-812007, India
| | - Sneha Mondal
- Analytical and Bio-analytical Laboratory, Department of Chemistry, Visva-Bharati, Santiniketan, West Bengal, India 731235
| | - Bhabatosh Mandal
- Analytical and Bio-analytical Laboratory, Department of Chemistry, Visva-Bharati, Santiniketan, West Bengal, India 731235
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Guo WY, Fu YX, Mei LC, Chen Z, Zhang ZY, Wang F, Yang WC, Liu G, Yang GF. Rational Design of Esterase-Insensitive Fluorogenic Probes for In Vivo Imaging. ACS Sens 2023; 8:2041-2049. [PMID: 37146071 DOI: 10.1021/acssensors.3c00264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Small-molecule fluorogenic probes are indispensable tools for performing research in biomedical fields and chemical biology. Although numerous cleavable fluorogenic probes have been developed to investigate various bioanalytes, few of them meet the baseline requirements for in vivo biosensing for disease diagnosis due to their insufficient specificity resulted from the remarkable esterase interferences. To address this critical issue, we developed a general approach called fragment-based fluorogenic probe discovery (FBFPD) to design esterase-insensitive probes for in vitro and in vivo applications. With the designed esterase-insensitive fluorogenic probe, we successfully achieved light-up in vivo imaging and quantitative analysis of cysteine. This strategy was further extended to design highly specific fluorogenic probes for other representative targets, sulfites, and chymotrypsin. The present study expands the bioanalytical toolboxes available and offers a promising platform to develop esterase-insensitive cleavable fluorogenic probes for in vivo biosensing and bioimaging for the early diagnosis of diseases.
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Affiliation(s)
- Wu-Yingzheng Guo
- National Key Laboratory of Green Pesticide, Central China Normal University, Wuhan 430079, P.R. China
| | - Yi-Xuan Fu
- National Key Laboratory of Green Pesticide, Central China Normal University, Wuhan 430079, P.R. China
| | - Long-Can Mei
- National Key Laboratory of Green Pesticide, Central China Normal University, Wuhan 430079, P.R. China
| | - Zhao Chen
- National Key Laboratory of Green Pesticide, Central China Normal University, Wuhan 430079, P.R. China
| | - Zi-Ye Zhang
- National Key Laboratory of Green Pesticide, Central China Normal University, Wuhan 430079, P.R. China
| | - Fan Wang
- National Key Laboratory of Green Pesticide, Central China Normal University, Wuhan 430079, P.R. China
| | - Wen-Chao Yang
- National Key Laboratory of Green Pesticide, Central China Normal University, Wuhan 430079, P.R. China
| | - Guozhen Liu
- School of Medicine, The Chinese University of Hong Kong, Shenzhen 518172, P.R. China
| | - Guang-Fu Yang
- National Key Laboratory of Green Pesticide, Central China Normal University, Wuhan 430079, P.R. China
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3
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Biswas P, Adhikari A, Pal U, Mondal S, Mukherjee D, Ghosh R, Obaid RJ, Moussa Z, Choudhury SS, Ahmed SA, Das R, Pal SK. A combined spectroscopic and molecular modeling Study on structure-function-dynamics under chemical modification: Alpha-chymotrypsin with formalin preservative. Front Chem 2022; 10:978668. [PMID: 36118312 PMCID: PMC9473634 DOI: 10.3389/fchem.2022.978668] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 08/01/2022] [Indexed: 11/13/2022] Open
Abstract
Enzyme function can be altered via modification of its amino acid residues, side chains and large-scale domain modifications. Herein, we have addressed the role of residue modification in catalytic activity and molecular recognition of an enzyme alpha-chymotrypsin (CHT) in presence of a covalent cross-linker formalin. Enzyme assay reveals reduced catalytic activity upon increased formalin concentration. Polarization gated anisotropy studies of a fluorophore 8-Anilino-1-naphthalenesulfonic acid (ANS) in CHT show a dip rise pattern in presence of formalin which is consistent with the generation of multiple ANS binding sites in the enzyme owing to modifications of its local amino acid residues. Molecular docking study on amino acid residue modifications in CHT also indicate towards the formation of multiple ANS binding site. The docking model also predicted no change in binding behavior for the substrate Ala-Ala-Phe-7-amido-4-methylcoumarin (AMC) at the active site upon formalin induced amino acid cross-linking.
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Affiliation(s)
- Pritam Biswas
- Department of Microbiology, St. Xavier’s College, Kolkata, India
| | - Aniruddha Adhikari
- Department of Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Kolkata, India
| | - Uttam Pal
- Technical Research Centre, S. N. Bose National Centre for Basic Sciences, Kolkata, India
| | - Susmita Mondal
- Department of Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Kolkata, India
| | - Dipanjan Mukherjee
- Department of Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Kolkata, India
| | - Ria Ghosh
- Technical Research Centre, S. N. Bose National Centre for Basic Sciences, Kolkata, India
| | - Rami J. Obaid
- Department of Chemistry, Faculty of Applied Sciences, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Ziad Moussa
- Department of Chemistry, College of Science, United Arab Emirates University, Al Ain, Abu Dhabi, United Arab Emirates
| | - Sudeshna Shyam Choudhury
- Department of Microbiology, St. Xavier’s College, Kolkata, India
- *Correspondence: Sudeshna Shyam Choudhury, ; Saleh A. Ahmed, ; Ranjan Das, ; Samir Kumar Pal,
| | - Saleh A. Ahmed
- Department of Chemistry, Faculty of Applied Sciences, Umm Al-Qura University, Makkah, Saudi Arabia
- Chemistry Department, Faculty of Science, Assiut University, Assiut, Egypt
- *Correspondence: Sudeshna Shyam Choudhury, ; Saleh A. Ahmed, ; Ranjan Das, ; Samir Kumar Pal,
| | - Ranjan Das
- Department of Chemistry, West Bengal State University, Barasat, Kolkata, India
- *Correspondence: Sudeshna Shyam Choudhury, ; Saleh A. Ahmed, ; Ranjan Das, ; Samir Kumar Pal,
| | - Samir Kumar Pal
- Department of Chemical, Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Kolkata, India
- Technical Research Centre, S. N. Bose National Centre for Basic Sciences, Kolkata, India
- *Correspondence: Sudeshna Shyam Choudhury, ; Saleh A. Ahmed, ; Ranjan Das, ; Samir Kumar Pal,
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Biswas P, Pal U, Adhikari A, Mondal S, Ghosh R, Mukherjee D, Saha‐Dasgupta T, Choudhury SS, Das R, Pal SK. Essential Loop Dynamics Modulates Catalytic Activity in α‐Chymotrypsin. ChemistrySelect 2022. [DOI: 10.1002/slct.202104262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Pritam Biswas
- Department of Microbiology St. Xavier's College, 30, Mother Teresa Sarani Kolkata 700016 India
| | - Uttam Pal
- Technical Research Centre S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake Kolkata 700106 India
| | - Aniruddha Adhikari
- Department of Chemical Biological and Macromolecular Sciences S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake Kolkata 700106 India
| | - Susmita Mondal
- Department of Chemical Biological and Macromolecular Sciences S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake Kolkata 700106 India
| | - Ria Ghosh
- Technical Research Centre S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake Kolkata 700106 India
| | - Dipanjan Mukherjee
- Department of Chemical Biological and Macromolecular Sciences S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake Kolkata 700106 India
| | - Tanusri Saha‐Dasgupta
- Department of Condensed Matter Physics and Material Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake Kolkata 700106 India
| | | | - Ranjan Das
- Department of Chemistry West Bengal state University, Barasat Kolkata 700126 India
| | - Samir Kumar Pal
- Technical Research Centre S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake Kolkata 700106 India
- Department of Chemical Biological and Macromolecular Sciences S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt Lake Kolkata 700106 India
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5
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Lan T, Tian QQ, Li MH, He W. Activatable endoplasmic reticulum-targeted NIR fluorescent probe with a large Stokes shift for detecting and imaging chymotrypsin. Analyst 2022; 147:4098-4104. [DOI: 10.1039/d2an01013e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this work, the first endoplasmic reticulum-targeted near-infrared fluorescent probe, ISO-Chy, with a large Stokes shift is reported by introducing a recognition group of 4-bromobutyl for chymotrypsin detection.
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Affiliation(s)
- Ting Lan
- Department of Chemistry, School of Pharmacy, The Fourth Military Medical University, 169 Changle West Road, Xi'an, 710032, P. R. China
| | - Qin-qin Tian
- Department of Chemistry, School of Pharmacy, The Fourth Military Medical University, 169 Changle West Road, Xi'an, 710032, P. R. China
| | - Ming-hua Li
- Department of Chemistry, School of Pharmacy, The Fourth Military Medical University, 169 Changle West Road, Xi'an, 710032, P. R. China
| | - Wei He
- Department of Chemistry, School of Pharmacy, The Fourth Military Medical University, 169 Changle West Road, Xi'an, 710032, P. R. China
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6
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Zou X, Zhao Y, Lai C, Liang Y, Lin W. A non-peptide probe for detecting chymotrypsin activity based on protection-deprotection strategy in living systems. J Mater Chem B 2021; 9:8417-8423. [PMID: 34545893 DOI: 10.1039/d1tb01509e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Chymotrypsin (CHT) plays a vital role in the metabolism of organisms and affects cell proliferation and apoptosis. Abnormal levels of CHT will lead to a variety of diseases, such as inflammatory arthritis, diabetes, pharyngitis, indigestion, and pancreatic cancer. Therefore, it is significant to design an effective method for the detection of CHT in living systems. Here, we synthesized a specific deep-red non-peptide probe DT by effectively combining isophorone and p-hydroxybenzaldehyde for the detection of CHT using 3-phenylpropionate chloride as the recognition group based on a protection-deprotection strategy. The DT probe exhibited an emission range of 525-700 nm and showed excellent photostability, high sensitivity (LOD = 0.071 U mL-1), and selectivity for CHT detection. The cellular experiments demonstrated that DT could sensitively recognize CHT activity in three cell lines and the content of CHT was much higher in P815 cells than in MCF-7 and 3T3 cells. Also, DT was successfully used to visualize the endogenous CHT in zebrafish. Notably, the DT probe provided an intuitive way to visualize endogenous CHT in mouse pancreas for the first time, demonstrating the potential for application in the future clinical diagnosis of pancreatic diseases. Therefore, the small-molecule probe DT is expected to be a useful molecular tool for CHT-related disease diagnosis and drug discovery.
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Affiliation(s)
- Xiang Zou
- Guangxi Key Laboratory of Electrochemical Energy Materials, Institute of Optical Materials and Chemical Biology, School of Chemistry and Chemical Engineering, Guangxi University, Nanning, Guangxi 530004, P. R. China.
| | - Yuping Zhao
- Guangxi Key Laboratory of Electrochemical Energy Materials, Institute of Optical Materials and Chemical Biology, School of Chemistry and Chemical Engineering, Guangxi University, Nanning, Guangxi 530004, P. R. China.
| | - Chaofeng Lai
- Guangxi Key Laboratory of Electrochemical Energy Materials, Institute of Optical Materials and Chemical Biology, School of Chemistry and Chemical Engineering, Guangxi University, Nanning, Guangxi 530004, P. R. China.
| | - Yun Liang
- Guangxi Key Laboratory of Electrochemical Energy Materials, Institute of Optical Materials and Chemical Biology, School of Chemistry and Chemical Engineering, Guangxi University, Nanning, Guangxi 530004, P. R. China.
| | - Weiying Lin
- Guangxi Key Laboratory of Electrochemical Energy Materials, Institute of Optical Materials and Chemical Biology, School of Chemistry and Chemical Engineering, Guangxi University, Nanning, Guangxi 530004, P. R. China.
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7
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Prabodh A, Wang Y, Sinn S, Albertini P, Spies C, Spuling E, Yang LP, Jiang W, Bräse S, Biedermann F. Fluorescence detected circular dichroism (FDCD) for supramolecular host-guest complexes. Chem Sci 2021; 12:9420-9431. [PMID: 34349916 PMCID: PMC8278969 DOI: 10.1039/d1sc01411k] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 06/08/2021] [Indexed: 11/30/2022] Open
Abstract
Fluorescence-detected circular dichroism (FDCD) spectroscopy is applied for the first time to supramolecular host-guest and host-protein systems and compared to the more known electronic circular dichroism (ECD). We find that FDCD can be an excellent choice for common supramolecular applications, e.g. for the detection and chirality sensing of chiral organic analytes, as well as for reaction monitoring. Our comprehensive investigations demonstrate that FDCD can be conducted in favorable circumstances at much lower concentrations than ECD measurements, even in chromophoric and auto-emissive biofluids such as blood serum, overcoming the sensitivity limitation of absorbance-based chiroptical spectroscopy. Besides, the combined use of FDCD and ECD can provide additional valuable information about the system, e.g. the chemical identity of an analyte or hidden aggregation phenomena. We believe that simultaneous FDCD- and ECD-based chiroptical characterization of emissive supramolecular systems will be of general benefit for characterizing fluorescent, chiral supramolecular systems due to the higher information content obtained by their combined use.
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Affiliation(s)
- Amrutha Prabodh
- Karlsruhe Institute of Technology (KIT), Institute of Nanotechnology (INT) Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen Germany
| | - Yichuan Wang
- Karlsruhe Institute of Technology (KIT), Institute of Nanotechnology (INT) Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen Germany
- Karlsruhe Institute of Technology (KIT), Institute of Organic Chemistry Fritz-Haber-Weg 6 76131 Karlsruhe Germany
| | - Stephan Sinn
- Karlsruhe Institute of Technology (KIT), Institute of Nanotechnology (INT) Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen Germany
| | | | - Christian Spies
- JASCO Deutschland GmbH Robert-Bosch-Str. 14, 64319 Pfungstadt Germany
| | - Eduard Spuling
- Karlsruhe Institute of Technology (KIT), Institute of Organic Chemistry Fritz-Haber-Weg 6 76131 Karlsruhe Germany
| | - Liu-Pan Yang
- Southern University of Science and Technology, Department of Chemistry Xueyuan Boulevard 1088, Nanshan District 518055 Shenzhen China
| | - Wei Jiang
- Southern University of Science and Technology, Department of Chemistry Xueyuan Boulevard 1088, Nanshan District 518055 Shenzhen China
| | - Stefan Bräse
- Karlsruhe Institute of Technology (KIT), Institute of Organic Chemistry Fritz-Haber-Weg 6 76131 Karlsruhe Germany
- Karlsruhe Institute of Technology (KIT), Institute of Biological and Chemical Systems - Functional Molecular Systems (ICBS-FMS) Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Germany
| | - Frank Biedermann
- Karlsruhe Institute of Technology (KIT), Institute of Nanotechnology (INT) Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen Germany
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8
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Rajapaksha AA, Fu YX, Guo WY, Liu SY, Li ZW, Xiong CQ, Yang WC, Yang GF. Review on the recent progress in the development of fluorescent probes targeting enzymes. Methods Appl Fluoresc 2021; 9. [PMID: 33873170 DOI: 10.1088/2050-6120/abf988] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Accepted: 04/19/2021] [Indexed: 02/07/2023]
Abstract
Enzymes are very important for biological processes in a living being, performing similar or multiple tasks in and out of cells, tissues and other organisms at a particular location. The abnormal activity of particular enzyme usually caused serious diseases such as Alzheimer's disease, Parkinson's disease, cancers, diabetes, cardiovascular diseases, arthritis etc. Hence, nondestructive and real-time visualization for certain enzyme is very important for understanding the biological issues, as well as the drug administration and drug metabolism. Fluorescent cellular probe-based enzyme detectionin vitroandin vivohas become broad interest for human disease diagnostics and therapeutics. This review highlights the recent findings and designs of highly sensitive and selective fluorescent cellular probes targeting enzymes for quantitative analysis and bioimaging.
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Affiliation(s)
- Asanka Amith Rajapaksha
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, People's Republic of China.,Department of Nano Science Technology, Faculty of Technology, Wayamba University of Sri Lanka, Kuliyapitiya, Sri Lanka
| | - Yi-Xuan Fu
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, People's Republic of China
| | - Wu Yingzheng Guo
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, People's Republic of China
| | - Shi-Yu Liu
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, People's Republic of China
| | - Zhi-Wen Li
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, People's Republic of China
| | - Cui-Qin Xiong
- Department of Interventional Medicine, Wuhan Third Hospital-Tongren Hospital of Wuhan University, Wuhan 430070, People's Republic of China
| | - Wen-Chao Yang
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, People's Republic of China
| | - Guang-Fu Yang
- Key Laboratory of Pesticide & Chemical Biology of Ministry of Education, International Joint Research Center for Intelligent Biosensor Technology and Health, College of Chemistry, Central China Normal University, Wuhan 430079, People's Republic of China
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Biswas P, Adhikari A, Pal U, Singh P, Das M, Saha-Dasgupta T, Choudhury SS, Das R, Pal SK. Flexibility modulates the catalytic activity of a thermostable enzyme: key information from optical spectroscopy and molecular dynamics simulation. SOFT MATTER 2020; 16:3050-3062. [PMID: 32133476 DOI: 10.1039/c9sm02479d] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Enzymes are dynamical macromolecules and their conformation can be altered via local fluctuations of side chains, large scale loop and even domain motions which are intimately linked to their function. Herein, we have addressed the role of dynamic flexibility in the catalytic activity of a thermostable enzyme almond beta-glucosidase (BGL). Optical spectroscopy and classical molecular dynamics (MD) simulation were employed to study the thermal stability, catalytic activity and dynamical flexibility of the enzyme. An enzyme assay reveals high thermal stability and optimum catalytic activity at 333 K. Polarization-gated fluorescence anisotropy measurements employing 8-anilino-1-napthelenesulfonic acid (ANS) have indicated increasing flexibility of the enzyme with an increase in temperature. A study of the atomic 3D structure of the enzyme shows the presence of four loop regions (LRs) strategically placed over the catalytic barrel as a lid. MD simulations have indicated that the flexibility of BGL increases concurrently with temperature through different fluctuating characteristics of the enzyme's LRs. Principal Component Analysis (PCA) and the Steered Molecular Dynamics (SMD) simulation manifest the gatekeeper role of the four LRs through their dynamic fluctuations surrounding the active site which controls the catalytic activity of BGL.
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Affiliation(s)
- Pritam Biswas
- Department of Microbiology, St. Xavier's College, 30, Mother Teresa Sarani, Kolkata 700016, India.
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10
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Abstract
Chymotrypsin is one of the most extensively known proteases participating in the pathogenesis of various diseases, which can be used in drug discovery and clinical diagnosis.
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Affiliation(s)
- Haixia Shi
- P. E. Department
- Jiangsu University
- Zhenjiang 212013
- P. R. China
| | - Cheng Liu
- School of Life Sciences
- Jiangsu University
- Zhenjiang 212013
- P. R. China
| | - Jingjie Cui
- School of Automation
- Hangzhou Dianzi University
- Hangzhou
- P. R. China
| | - Jia Cheng
- School of Life Sciences
- Jiangsu University
- Zhenjiang 212013
- P. R. China
| | - Yuanwei Lin
- School of Life Sciences
- Jiangsu University
- Zhenjiang 212013
- P. R. China
| | - Li Gao
- School of Life Sciences
- Jiangsu University
- Zhenjiang 212013
- P. R. China
| | - Rong Luo
- Institute of Geriatric Cardiovascular Disease
- Chengdu Medical College
- Chengdu
- China
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11
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Mu S, Xu Y, Zhang Y, Guo X, Li J, Wang Y, Liu X, Zhang H. A non-peptide NIR fluorescent probe for detection of chymotrypsin and its imaging application. J Mater Chem B 2019. [DOI: 10.1039/c9tb00085b] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
A novel non-peptide NIR fluorescent probe for the detection of chymotrypsin and its imaging application.
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Affiliation(s)
- Shuai Mu
- State Key Laboratory of Applied Organic Chemistry
- Key Laboratory of Nonferrous Metals Chemistry and Resources Utilization of Gansu Province and College of Chemistry and Chemical Engineering
- Lanzhou University
- Lanzhou 730000
- China
| | - Yixuan Xu
- State Key Laboratory of Applied Organic Chemistry
- Key Laboratory of Nonferrous Metals Chemistry and Resources Utilization of Gansu Province and College of Chemistry and Chemical Engineering
- Lanzhou University
- Lanzhou 730000
- China
| | - Yintang Zhang
- Henan Key Laboratory of Biomolecular Recognition and Sensing
- College of Chemistry and Chemical Engineering
- Shangqiu Normal University
- Shangqiu 476000
- China
| | - Xiumei Guo
- State Key Laboratory of Applied Organic Chemistry
- Key Laboratory of Nonferrous Metals Chemistry and Resources Utilization of Gansu Province and College of Chemistry and Chemical Engineering
- Lanzhou University
- Lanzhou 730000
- China
| | - Jian Li
- State Key Laboratory of Applied Organic Chemistry
- Key Laboratory of Nonferrous Metals Chemistry and Resources Utilization of Gansu Province and College of Chemistry and Chemical Engineering
- Lanzhou University
- Lanzhou 730000
- China
| | - Yali Wang
- Key Laboratory of Traditional Chinese medicine quality and standard
- Gansu University of Chinese Medicine
- Lanzhou
- China
| | - Xiaoyan Liu
- State Key Laboratory of Applied Organic Chemistry
- Key Laboratory of Nonferrous Metals Chemistry and Resources Utilization of Gansu Province and College of Chemistry and Chemical Engineering
- Lanzhou University
- Lanzhou 730000
- China
| | - Haixia Zhang
- State Key Laboratory of Applied Organic Chemistry
- Key Laboratory of Nonferrous Metals Chemistry and Resources Utilization of Gansu Province and College of Chemistry and Chemical Engineering
- Lanzhou University
- Lanzhou 730000
- China
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12
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Ultrafast dynamics-driven biomolecular recognition where fast activities dictate slow events. J Biosci 2018. [DOI: 10.1007/s12038-018-9776-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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13
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Enzyme activity of α-chymotrypsin: Deactivation by gold nano-cluster and reactivation by glutathione. J Colloid Interface Sci 2017; 494:74-81. [DOI: 10.1016/j.jcis.2017.01.027] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2016] [Revised: 01/07/2017] [Accepted: 01/09/2017] [Indexed: 11/15/2022]
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14
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Xin L, Li Y, Wu L, Zhao J, Song Z. Quantitative Monitoring of Rutin in Human Urine by Flow Injection-Chemiluminescence Analysis. J CHIN CHEM SOC-TAIP 2017. [DOI: 10.1002/jccs.201600884] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Ladi Xin
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, College of Chemistry and Materials Science; Northwest University; Xi'an 710127 China
| | - Yajuan Li
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, College of Chemistry and Materials Science; Northwest University; Xi'an 710127 China
| | - Lingmin Wu
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, College of Chemistry and Materials Science; Northwest University; Xi'an 710127 China
| | - Jingchan Zhao
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, College of Chemistry and Materials Science; Northwest University; Xi'an 710127 China
| | - Zhenghua Song
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, College of Chemistry and Materials Science; Northwest University; Xi'an 710127 China
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15
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Wu L, Yang SH, Xiong H, Yang JQ, Guo J, Yang WC, Yang GF. Nonpeptide-Based Small-Molecule Probe for Fluorogenic and Chromogenic Detection of Chymotrypsin. Anal Chem 2017; 89:3687-3693. [DOI: 10.1021/acs.analchem.6b05115] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Lei Wu
- Key
Laboratory of Pesticide and Chemical Biology of Ministry of Education,
College of Chemistry, Central China Normal University, Wuhan 430079, P.R. China
| | - Shu-Hou Yang
- Key
Laboratory of Pesticide and Chemical Biology of Ministry of Education,
College of Chemistry, Central China Normal University, Wuhan 430079, P.R. China
| | - Hao Xiong
- Key
Laboratory of Pesticide and Chemical Biology of Ministry of Education,
College of Chemistry, Central China Normal University, Wuhan 430079, P.R. China
| | - Jia-Qian Yang
- Key
Laboratory of Pesticide and Chemical Biology of Ministry of Education,
College of Chemistry, Central China Normal University, Wuhan 430079, P.R. China
| | - Jun Guo
- Key
Laboratory of Pesticide and Chemical Biology of Ministry of Education,
College of Chemistry, Central China Normal University, Wuhan 430079, P.R. China
| | - Wen-Chao Yang
- Key
Laboratory of Pesticide and Chemical Biology of Ministry of Education,
College of Chemistry, Central China Normal University, Wuhan 430079, P.R. China
| | - Guang-Fu Yang
- Key
Laboratory of Pesticide and Chemical Biology of Ministry of Education,
College of Chemistry, Central China Normal University, Wuhan 430079, P.R. China
- Collaborative Innovation Center of Chemical Science
and Engineering, Tianjin 30071, P.R. China
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16
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Wei G, Xi W, Nussinov R, Ma B. Protein Ensembles: How Does Nature Harness Thermodynamic Fluctuations for Life? The Diverse Functional Roles of Conformational Ensembles in the Cell. Chem Rev 2016; 116:6516-51. [PMID: 26807783 PMCID: PMC6407618 DOI: 10.1021/acs.chemrev.5b00562] [Citation(s) in RCA: 253] [Impact Index Per Article: 31.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
All soluble proteins populate conformational ensembles that together constitute the native state. Their fluctuations in water are intrinsic thermodynamic phenomena, and the distributions of the states on the energy landscape are determined by statistical thermodynamics; however, they are optimized to perform their biological functions. In this review we briefly describe advances in free energy landscape studies of protein conformational ensembles. Experimental (nuclear magnetic resonance, small-angle X-ray scattering, single-molecule spectroscopy, and cryo-electron microscopy) and computational (replica-exchange molecular dynamics, metadynamics, and Markov state models) approaches have made great progress in recent years. These address the challenging characterization of the highly flexible and heterogeneous protein ensembles. We focus on structural aspects of protein conformational distributions, from collective motions of single- and multi-domain proteins, intrinsically disordered proteins, to multiprotein complexes. Importantly, we highlight recent studies that illustrate functional adjustment of protein conformational ensembles in the crowded cellular environment. We center on the role of the ensemble in recognition of small- and macro-molecules (protein and RNA/DNA) and emphasize emerging concepts of protein dynamics in enzyme catalysis. Overall, protein ensembles link fundamental physicochemical principles and protein behavior and the cellular network and its regulation.
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Affiliation(s)
- Guanghong Wei
- State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (MOE), and Department of Physics, Fudan University, Shanghai, P. R. China
| | - Wenhui Xi
- State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (MOE), and Department of Physics, Fudan University, Shanghai, P. R. China
| | - Ruth Nussinov
- Basic Science Program, Leidos Biomedical Research, Inc. Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland 21702, USA
- Sackler Inst. of Molecular Medicine Department of Human Genetics and Molecular Medicine Sackler School of Medicine, Tel Aviv University, Tel Aviv 69978, Israel
| | - Buyong Ma
- Basic Science Program, Leidos Biomedical Research, Inc. Cancer and Inflammation Program, National Cancer Institute, Frederick, Maryland 21702, USA
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17
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Ward K, Stuckey DC. Refractive index matching to develop transparent polyaphrons: Characterization of immobilized proteins. Colloids Surf B Biointerfaces 2016; 142:159-164. [DOI: 10.1016/j.colsurfb.2016.02.054] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 02/11/2016] [Accepted: 02/16/2016] [Indexed: 11/29/2022]
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18
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Ward K, Xi J, Stuckey DC. Immobilization of enzymes using non-ionic colloidal liquid aphrons (CLAs): Activity kinetics, conformation, and energetics. Biotechnol Bioeng 2015; 113:970-8. [DOI: 10.1002/bit.25865] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Revised: 10/12/2015] [Accepted: 10/19/2015] [Indexed: 11/06/2022]
Affiliation(s)
- Keeran Ward
- Department of Chemical Engineering; Imperial College London; SW7 2AZ London United Kingdom
| | - Jingshu Xi
- Department of Chemical Engineering; Imperial College London; SW7 2AZ London United Kingdom
| | - David C. Stuckey
- Department of Chemical Engineering; Imperial College London; SW7 2AZ London United Kingdom
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19
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Recovery of chymotrypsin using magnetic particles and aqueous micellar two-phase systems: Influence of non-ionic surfactants on enzyme activity. ACTA ACUST UNITED AC 2014. [DOI: 10.1016/j.molcatb.2014.10.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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20
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Menegatti M, Vangone A, Palla R, Milano G, Cavallo L, Oliva R, De Cristofaro R, Peyvandi F. A recurrent Gly43Asp substitution in coagulation Factor X rigidifies its catalytic pocket and impairs catalytic activity and intracellular trafficking. Thromb Res 2014; 133:481-7. [DOI: 10.1016/j.thromres.2013.12.020] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Revised: 11/28/2013] [Accepted: 12/16/2013] [Indexed: 11/30/2022]
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21
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Maxwell CI, Mosey NJ, Stan Brown R. DFT Computational Study of the Methanolytic Cleavage of DNA and RNA Phosphodiester Models Promoted by the Dinuclear Zn(II) Complex of 1,3-Bis(1,5,9-triazacyclododec-1-yl)propane. J Am Chem Soc 2013; 135:17209-22. [DOI: 10.1021/ja4088264] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
| | - Nicholas J. Mosey
- Department
of Chemistry, Queen’s University, Kingston, Ontario, Canada K7L 3N6
| | - R. Stan Brown
- Department
of Chemistry, Queen’s University, Kingston, Ontario, Canada K7L 3N6
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22
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Abstract
Macromolecular crowding decreases the diffusion rate, shifts the equilibrium of protein-protein and protein-substrate interactions, and changes protein conformational dynamics. Collectively, these effects contribute to enzyme catalysis. Here we describe how crowding may bias the conformational change and dynamics of enzyme populations and in this way affect catalysis. Crowding effects have been studied using artificial crowding agents and in vivo-like environments. These studies revealed a correlation between protein dynamics and function in the crowded environment. We suggest that crowded environments be classified into uniform crowding and structured crowding. Uniform crowding represents random crowding conditions created by synthetic particles with a narrow size distribution. Structured crowding refers to the highly coordinated cellular environment, where proteins and other macromolecules are clustered and organized. In structured crowded environments the perturbation of protein thermal stability may be lower; however, it may still be able to modulate functions effectively and dynamically. Dynamic, allosteric enzymes could be more sensitive to cellular perturbations if their free energy landscape is flatter around the native state; on the other hand, if their free energy landscape is rougher, with high kinetic barriers separating deep minima, they could be more robust. Above all, cells are structured; and this holds both for the cytosol and for the membrane environment. The crowded environment is organized, which limits the search, and the crowders are not necessarily inert. More likely, they too transmit allosteric effects, and as such play important functional roles. Overall, structured cellular crowding may lead to higher enzyme efficiency and specificity.
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Affiliation(s)
- Judith Klinman
- Department of Chemistry Department of Molecular and Cell Biology, University of California The california institute for Quantitativ, Berkeley, CA, USA
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23
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Makhal A, Sarkar S, Pal SK. Protein-Mediated Synthesis of Nanosized Mn-Doped ZnS: A Multifunctional, UV-Durable Bio-Nanocomposite. Inorg Chem 2012; 51:10203-10. [DOI: 10.1021/ic301083g] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Abhinandan Makhal
- Department of Chemical,
Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt
Lake, Kolkata 700 098, India
| | - Soumik Sarkar
- Department of Chemical,
Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt
Lake, Kolkata 700 098, India
| | - Samir Kumar Pal
- Department of Chemical,
Biological and Macromolecular Sciences, S. N. Bose National Centre for Basic Sciences, Block JD, Sector III, Salt
Lake, Kolkata 700 098, India
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24
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Kumar A, Venkatesu P. Overview of the stability of α-chymotrypsin in different solvent media. Chem Rev 2012; 112:4283-307. [PMID: 22506806 DOI: 10.1021/cr2003773] [Citation(s) in RCA: 176] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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25
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Verma SK, Ghosh KK. Effect of cationic surfactants on the enzymatic activity of α-chymotrypsin. KINETICS AND CATALYSIS 2011. [DOI: 10.1134/s0023158411010216] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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26
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Verma PK, Giri A, Thanh NTK, Tung LD, Mondal O, Pal M, Pal SK. Superparamagnetic fluorescent nickel–enzyme nanobioconjugates: synthesis and characterization of a novel multifunctional biological probe. ACTA ACUST UNITED AC 2010. [DOI: 10.1039/b925477c] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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27
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Chen AY, Jani AS, Zheng L, Burke PJ, Brody JP. Microfabricated arrays of cylindrical wells facilitate single-molecule enzymology of α-chymotrypsin. Biotechnol Prog 2009; 25:929-37. [DOI: 10.1002/btpr.283] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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