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Wang Z, Li W, Hou X. Probing the interaction mechanism of SDBS with AtPrxQ from Arabidopsis thaliana: Insight into the molecular toxicity to plants. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 313:124118. [PMID: 38461562 DOI: 10.1016/j.saa.2024.124118] [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: 12/04/2023] [Revised: 02/28/2024] [Accepted: 03/03/2024] [Indexed: 03/12/2024]
Abstract
As the most universally used anionic surfactant, ubiquitous existence and accumulation of sodium dodecyl benzene sulfonate (SDBS) in the environment has inevitably imposed the associated harmful impacts to plants due to producing excessive reactive oxygen species. However, the underlying hazardous mechanism of the SDBS-induced oxidative stress to plants at molecular level has never been reported. Here, the molecular interaction of AtPrxQ with SDBS was explored for the first time. The intrinsic fluorescence of AtPrxQ was quenched based on static quenching, and a single binding site of AtPrxQ towards SDBS and the potential interaction forces driven by hydrophobic interactions were predicted from thermodynamic parameters and molecular docking results. Besides, the interaction pattern of AtPrxQ and SDBS was also confirmed by the bio-layer interferometry with moderate binding affinity. Moreover, the structural changes of AtPrxQ along with the destructions of the protein framework and the hydrophobic enhancement around aromatic amino acids were observed upon binding with SDBS. At last, the toxic effects produced by SDBS on peroxidase activities and Arabidopsis seedlings growth were also characterized. Thus this work may provide insights on the molecular interactions of AtPrxQ with SDBS and assessments on the biological hazards of SDBS to plants even for the agriculture.
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Affiliation(s)
- Zhong Wang
- Shandong Province Key Laboratory of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, China
| | - Wanting Li
- Shandong Province Key Laboratory of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, China
| | - Xiaomin Hou
- Shandong Province Key Laboratory of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, China.
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2
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Vahedi SZ, Farhadian S, Shareghi B, Asgharzadeh S. Thermodynamic and functional changes of alpha-chymotrypsin after interaction with gallic acid. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 313:124109. [PMID: 38447443 DOI: 10.1016/j.saa.2024.124109] [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: 10/31/2023] [Revised: 02/24/2024] [Accepted: 03/02/2024] [Indexed: 03/08/2024]
Abstract
In the present study, the interaction mechanism between gallic acid (GA) and α-Chymotrypsin (α-CT) was investigated by employing a series ofspectroscopic methods, computational docking and molecular dynamic (MD) simulation. Fluorescence spectra analysis indicated the formation of a stable complex between GA and α-CT, where the quenching of the fluorescence emission was predominantly characterized by a static mechanism. TheCA obtained binding constants for the α-CT-GA complex were in the order of 103 M-1, indicating the moderate binding affinity of GA for α-CT. The corresponding CD findings showed that the interaction between GA and α-CT resulted in an alteration of the protein's secondary structure. The findings of the enzyme activity investigation clearly showed that the presence of GA led to a notable decline in the enzymatic activity of α-CT, highlighting GA's function as an effective inhibitor for α-CT. The molecular docking simulations revealed the optimal binding site for the GA molecule within the α-CT structure and MD simulations confirmed the stability of the α-CT-GA complex. This research expands our comprehension regarding the behavior of enzymes in the presence of small-molecule ligands and opens avenues for food safety.
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Affiliation(s)
- Seyedeh Zohreh Vahedi
- Department of Biology, Faculty of Science, Shahrekord University, Shahrekord, P. O. Box.115, Iran; Central Laboratory, Shahrekord University, Shahrekord, Iran
| | - Sadegh Farhadian
- Department of Biology, Faculty of Science, Shahrekord University, Shahrekord, P. O. Box.115, Iran; Central Laboratory, Shahrekord University, Shahrekord, Iran.
| | - Behzad Shareghi
- Department of Biology, Faculty of Science, Shahrekord University, Shahrekord, P. O. Box.115, Iran; Central Laboratory, Shahrekord University, Shahrekord, Iran
| | - Sanaz Asgharzadeh
- Department of Biology, Faculty of Science, Shahrekord University, Shahrekord, P. O. Box.115, Iran; Central Laboratory, Shahrekord University, Shahrekord, Iran
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3
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Lin C, Du H. Interactions between forsythoside E and two cholinesterases at the different conditions: fluorescence sections. Methods Appl Fluoresc 2024; 12:025003. [PMID: 38428023 DOI: 10.1088/2050-6120/ad2f3a] [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: 09/26/2023] [Accepted: 03/01/2024] [Indexed: 03/03/2024]
Abstract
Forsythoside E is one secondary metabolite ofForsythia suspensa(Thunb.) Vahl. In the study, the interactions between forsythoside E and two types of cholinesterases, acetylcholinesterase and butyrylcholinesterase were investigated in the different conditions. Forsythoside E increased the fluorescence intensity of acetylcholinesterase but quenched the fluorescence of butyrylcholinesterase. Aβ25-35used in the study may not form complexes with cholinesterases, and did not affect the interaction between forsythoside E and cholinesterases. The charged quaternary group of AsCh interacted with the 'anionic' subsite in acetylcholinesterase, which did not affect the interaction between forsythoside E and acetylcholinesterase. The enhancement rate of forsythoside E to acetylcholinesterase fluorescence from high to low was acid solution (pH 6.4), neutral solution (pH 7.4) and alkaline solution (pH 8.0), while the reduction rate of forsythoside E to butyrylcholinesterase fluorescence was in reverse order. Metal ions may interact with cholinesterases, and increased the effects of forsythoside E to cholinesterases fluorescence, in order that Fe3+was the highest, followed by Cu2+, and Mg2+. A forsythoside E-butyrylcholinesterase complex at stoichiometric ratio of 1:1 was spontaneously formed, and the static quenching was the main quenching mode in the process of forsythoside E binding with butyrylcholinesterase. TheKvalues of two complexes were pretty much the same, suggesting that the interaction between cholinesterases and forsythoside E was almost unaffected by acid-base environment and metal ions. Thennumbers of two cholinesterases approximately equaled to one, indicating that there was only one site on each cholinesterase applicable for forsythoside E to bind to.
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Affiliation(s)
- Conghuan Lin
- Institute of Molecular Science, Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan 030006, People's Republic of China
| | - Huizhi Du
- Institute of Molecular Science, Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Shanxi University, Taiyuan 030006, People's Republic of China
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Ghorai S, Jana B, Ganguly J. Network-supported and adaptable binding efficacy for flexible and multi-functionalized chitosan/phenolic carbaldehyde hydrogels. Int J Biol Macromol 2023; 253:127004. [PMID: 37734526 DOI: 10.1016/j.ijbiomac.2023.127004] [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: 06/02/2023] [Revised: 09/12/2023] [Accepted: 09/18/2023] [Indexed: 09/23/2023]
Abstract
A thoughtful strategy has been intended to control the hydrogel networking to assess the binding efficacy of multifunctional hydrogel. The processing of two distinct network-supported hydrogels has portrayed to express the operating interactions involved during co-existence with solvents, small molecules, biomolecules, etc. Herein, chitosan has separately functionalized in semisynthetic approaches with 4-hydroxyisopthalaldehyde (ChDA) and 2-hydroxybenzene-1,3,5-tricarbaldehyde (ChTA) to construct different gel networks. The disposition of gel networks ChDA adapts more flexible chain or spine, whereas ChTA possesses restricted movements within gel networks. The gel networks of hydrogels have a significant role in their distinct physical activities. Their gel-bonding elucidations have performed to establish the variation in mechanical, swelling photophysical properties, etc. Remarkable self-fluorescence behaviors are used as a tool for binding study. Distinctive gel networks and their flexibility have investigated against self-fluorescence, UV-Vis, and FTIR against small molecule, Boron trifluoride and biomolecule, and Bovine serum albumin. Hydrogel/BF3 shows variation in fluorescence due to the disposition of gel networks. Hydrogel/BSA quenching of fluorescence at three different temperatures provides the binding constant and Stern-Volmer quenching constant. Theoretical DFT and docking studies successfully established the flexibility against binding study. The controlling of cross-linking or functionalization is very crucial for the development of hydrogel-mediated applications.
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Affiliation(s)
- Shubhankar Ghorai
- Department of Chemistry, Indian Institute of Engineering Science and Technology, Howrah 711103, WB, India.
| | - Biswajit Jana
- Department of Chemistry, Indian Institute of Engineering Science and Technology, Howrah 711103, WB, India.
| | - Jhuma Ganguly
- Department of Chemistry, Indian Institute of Engineering Science and Technology, Howrah 711103, WB, India.
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5
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Cui J, Fan Y, Lian D, Wang S, Wang M, Du Y, Li Y, Li L. Interaction of narcissoside with α-amylase from Bacillus subtilis and Porcine pancreatic by multi-spectral analysis and molecular dynamics simulation. LUMINESCENCE 2023. [PMID: 38038156 DOI: 10.1002/bio.4637] [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: 08/26/2023] [Revised: 09/23/2023] [Accepted: 11/11/2023] [Indexed: 12/02/2023]
Abstract
In this work, interaction mechanism of narcissoside with two α-amylase from Bacillus subtilis (BSA) and Porcine pancreatic (PPA) are comparatively studied by multi-spectral analysis, molecular docking and molecular dynamics simulation. The results prove that narcissoside can statically quench fluorescence of BSA/PPA. Two complexes are mainly formed by hydrogen bond and van der Waals force. With the increase of temperature, the two complexes formed by narcissoside and two enzymes become unstable. At the same experimental temperature, the binding force of narcissoside to PPA is higher than that of BSA. The binding of narcissoside to PPA/BSA increases the hydrophobicity of microenvironment. Moreover, the secondary structure of PPA/BSA is mainly changed by decreasing the α-helix. The optimal binding modes of narcissoside with BSA/PPA are predicted by molecular docking, and the stability of the two complexes is evaluated by molecular dynamics simulations.
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Affiliation(s)
- Jingjing Cui
- The College of Chemistry, Changchun Normal University, Changchun, China
| | - Yangyang Fan
- The College of Chemistry, Changchun Normal University, Changchun, China
| | - Di Lian
- The College of Chemistry, Changchun Normal University, Changchun, China
| | - Suqing Wang
- The College of Chemistry, Changchun Normal University, Changchun, China
| | - Meizi Wang
- The College of Chemistry, Changchun Normal University, Changchun, China
| | - Yutong Du
- The College of Chemistry, Changchun Normal University, Changchun, China
| | - Yuan Li
- The College of Chemistry, Changchun Normal University, Changchun, China
| | - Li Li
- The College of Chemistry, Changchun Normal University, Changchun, China
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Konevtsova OV, Golushko IY, Podgornik R, Rochal SB. Integration of Cypoviruses into polyhedrin matrix. NANOSCALE ADVANCES 2023; 5:4140-4148. [PMID: 37560430 PMCID: PMC10408579 DOI: 10.1039/d3na00393k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Accepted: 07/14/2023] [Indexed: 08/11/2023]
Abstract
Unlike in other viruses, in Cypoviruses the genome is doubly protected since their icosahedral capsids are embedded into a perfect polyhedrin crystal. Current experimental methods cannot resolve the resulting interface structure and we propose a symmetry-based approach to predict it. We reveal a remarkable match between the surfaces of Cypovirus and the outer polyhedrin matrix. The match arises due to the preservation of the common tetragonal symmetry, allowing perfect contacts of polyhedrin trimers with VP1 and VP5 capsid proteins. We highlight a crucial role of the VP5 proteins in embedding the Cypovirus into the polyhedrin matrix and discuss the relationship between the nucleoside triphosphatase activity of the proteins and their role in the superstructure formation. Additionally, we propose an electrostatic mechanism that drives the viral superstructure disassembly occurring in the alkaline environment of the insect intestines. Our study may underpin novel strategies for engineering proteinaceous nanocontainers in diverse biotechnological and chemical applications.
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Affiliation(s)
| | - Ivan Yu Golushko
- Physics Faculty, Southern Federal University Rostov-on-Don Russia
| | - Rudolf Podgornik
- School of Physical Sciences and Kavli Institute for Theoretical Sciences, University of Chinese Academy of Sciences Beijing 100049 China
- CAS Key Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences Beijing 100190 China
- Wenzhou Institute of the University of Chinese Academy of Sciences Wenzhou Zhejiang 325000 China
| | - Sergei B Rochal
- Physics Faculty, Southern Federal University Rostov-on-Don Russia
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7
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Barik S, Mahapatra A, Preeyanka N, Sarkar M. Assessing the impact of choline chloride and benzyltrimethylammonium chloride-based deep eutectic solvents on the structure and conformational dynamics of bovine serum albumin: a combined steady-state, time-resolved fluorescence and fluorescence correlation spectroscopic study. Phys Chem Chem Phys 2023; 25:20093-20108. [PMID: 37462948 DOI: 10.1039/d3cp01380d] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2023]
Abstract
Although deep eutectic solvents (DESs) are regarded as useful substitutes for both ionic liquids and common organic solvents for storage and applications of biomolecules, it is still unclear whether all DESs or only specific types of DESs will be suitable for the said purpose. In view of this, the current study aims to report on the structure and conformational dynamics of BSA in the presence of two DESs, namely ethaline (choline chloride:ethylene glycol) and BMEG (benzyltrimethyl ammonium chloride:ethylene glycol), having the same hydrogen bond donor but with a distinct hydrogen bond acceptor, so that how small changes in one constituent of a DES alter the protein-DES interaction at the molecular level can be understood. The protein-DES interaction is investigated by exploiting both ensemble-averaged measurements like steady-state and time-resolved fluorescence spectroscopy, circular dichroism (CD) spectroscopy, and single-molecule sensitive techniques based on fluorescence correlation spectroscopy (FCS). Interestingly, the results obtained from these studies have demonstrated that while a very small quantity of BMEG completely unfolds the native structure of the protein, it remains in a partially unfolded state even at very high ethaline content. More interestingly, it has been found that at very high concentrations of BMEG, the unfolded protein undergoes enhanced protein-protein interaction resulting in the aggregation of BSA. All of the results obtained from these investigations have essentially suggested that both protein-DES interaction and interspecies interaction among the constituent of DESs play a crucial role in governing the overall stability and conformational dynamics of the protein in DESs.
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Affiliation(s)
- Sahadev Barik
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), An OCC of Homi Bhabha National Institute, Jatni, Khurda, Bhubaneswar 752050, Odisha, India.
- Centre of Interdisciplinary Science (CIS), NISER, Bhubaneswar, Jatni, Khurda, 752050, Odisha, India
| | - Amita Mahapatra
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), An OCC of Homi Bhabha National Institute, Jatni, Khurda, Bhubaneswar 752050, Odisha, India.
- Centre of Interdisciplinary Science (CIS), NISER, Bhubaneswar, Jatni, Khurda, 752050, Odisha, India
| | - Naupada Preeyanka
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), An OCC of Homi Bhabha National Institute, Jatni, Khurda, Bhubaneswar 752050, Odisha, India.
- Centre of Interdisciplinary Science (CIS), NISER, Bhubaneswar, Jatni, Khurda, 752050, Odisha, India
| | - Moloy Sarkar
- School of Chemical Sciences, National Institute of Science Education and Research (NISER), An OCC of Homi Bhabha National Institute, Jatni, Khurda, Bhubaneswar 752050, Odisha, India.
- Centre of Interdisciplinary Science (CIS), NISER, Bhubaneswar, Jatni, Khurda, 752050, Odisha, India
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8
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Chen J, Bian X, Zhang S, Yang G. Study on the interaction of two quinazoline derivatives as novel PI3K/mTOR dual inhibitors and anticancer agents to human serum albumin utilizing spectroscopy and docking. LUMINESCENCE 2023; 38:260-268. [PMID: 36648974 DOI: 10.1002/bio.4444] [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: 07/13/2022] [Revised: 11/25/2022] [Accepted: 01/15/2023] [Indexed: 01/18/2023]
Abstract
Interactions of human serum albumin (HSA) with two structurally similar quinazoline derivatives, S1 and S2 , which are potential anticancer drugs acting on PI3K/mTOR targets, were investigated in vitro utilizing multiple spectroscopy as well as molecular docking. The fluorescence quenching study demonstrated that HSA fluorescence could be statically quenched by S1 and S2 through the formation of an HSA-drug complex. Furthermore, the details of the binding site number, binding constant, as well as the thermodynamic parameters, were estimated at 298, 303, and 310 K. The results revealed that hydrogen bond interactions, as well as van der Waals forces, were the predominant factors responsible for binding HSA to S1 or S2 . Synchronous fluorescence and ultraviolet (UV) absorption spectra suggested that S1 and S2 had little effect on the polarity of the microenvironment and conformation of HSA. Energy transfer from HSA to S1 or S2 most probably occurred. The docking study revealed that S1 and S2 were able to bind to the hydrophobic cavity that was located in the HSA subdomain IIA and formed varying numbers of hydrogen bonds with amino acid residues nearby. Due to the subtle difference in the chemical structure, the binding of S1 and S2 to HSA was slightly different.
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Affiliation(s)
- Jiangang Chen
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, Shaanxi Province, China
| | - Xiaoli Bian
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, Shaanxi Province, China
| | - Sanqi Zhang
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, Shaanxi Province, China
| | - Guangde Yang
- School of Pharmacy, Xi'an Jiaotong University, Xi'an, Shaanxi Province, China
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Yelamanda Rao K, Jeelan Basha S, Monika K, Sreelakshmi M, Sivakumar I, Mallikarjuna G, Yadav RM, Kumar S, Subramanyam R, Damu AG. Synthesis and anti-Alzheimer potential of novel α-amino phosphonate derivatives and probing their molecular interaction mechanism with acetylcholinesterase. Eur J Med Chem 2023; 253:115288. [PMID: 37031527 DOI: 10.1016/j.ejmech.2023.115288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Revised: 03/14/2023] [Accepted: 03/14/2023] [Indexed: 04/03/2023]
Abstract
Pleiotropic interference may be a prerequisite for the efficient limitation of the progression of multi-factorial diseases such as Alzheimer's disease (AD). Concept of designing the single chemical entity acting on two or more targets of interest has potential advantage in AD therapy. In line with this, rational design and synthesis of frame work of hybrids bearing 2,3-disubstituted quinazolinone, vanillin and α-amino phosphonate scaffolds (5a─v) were carried out. A congeneric set of twenty-two synthetic derivatives (5a─v) were evaluated for their cholinesterase inhibitory, antioxidant, DNA nicking, DNA protection, neuroprotective and Aβ aggregation modulatory activities. Amongst tested activities, the most significant and worth mentioning is that the analogues 5m, 5p and 5u were found to be the most potent, selective, and mixed type inhibitors of EeAChE with IC50 values of 0.296 ± 0.030, 0.289 ± 0.027, and 0.306 ± 0.028 μM, respectively. Further, the biophysical approaches indicated that the compounds 5m, 5p, and 5u have a strong binding affinity towards AChE. Kinetic and Molecular docking studies have revealed that the most active congeners were well oriented in the AChE active site by interacting with both catalytic active site (CAS) and peripheral anionic site (PAS). A few parameters derived from molecular dynamics (MD) simulation trajectories emphasized the stability of AChE-5p and 5m complexes throughout the 100 ns simulations, and the local conformational changes of the residues of AChE validate the stability of AChE-5p and 5m complexes. Further, these derivatives significantly impacted ABTS radical scavenging capacities and maximal DNA protection activity. Importantly, Thioflavin T (ThT) assay and FE-SEM study demonstrated compounds 5m, 5p and 5u as effective Aβ1-42 fibril modulators at molecular level by the formation of micro size co-assembled mature structures, thus efficiently abolishing the cytotoxicity of Aβ1-42. Finally, these active compounds are determined to be non-toxic and highly neuroprotective against H2O2-induced cell death in SK-N-SH cell lines. Furthermore, in silico ADMET prediction studies have revealed that the targeted analogues satisfied most of the characteristics of CNS acting drugs. These multi-functional efficacies indicated worthiness of these α-amino phosphonate derivatives being chosen for further pharmacokinetics, toxicity, and behavioral research to test their potential for AD treatment.
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Dixit R, Khambhati K, Supraja KV, Singh V, Lederer F, Show PL, Awasthi MK, Sharma A, Jain R. Application of machine learning on understanding biomolecule interactions in cellular machinery. BIORESOURCE TECHNOLOGY 2023; 370:128522. [PMID: 36565819 DOI: 10.1016/j.biortech.2022.128522] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 12/17/2022] [Accepted: 12/20/2022] [Indexed: 06/17/2023]
Abstract
Machine learning (ML) applications have become ubiquitous in all fields of research including protein science and engineering. Apart from protein structure and mutation prediction, scientists are focusing on knowledge gaps with respect to the molecular mechanisms involved in protein binding and interactions with other components in the experimental setups or the human body. Researchers are working on several wet-lab techniques and generating data for a better understanding of concepts and mechanics involved. The information like biomolecular structure, binding affinities, structure fluctuations and movements are enormous which can be handled and analyzed by ML. Therefore, this review highlights the significance of ML in understanding the biomolecular interactions while assisting in various fields of research such as drug discovery, nanomedicine, nanotoxicity and material science. Hence, the way ahead would be to force hand-in hand of laboratory work and computational techniques.
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Affiliation(s)
- Rewati Dixit
- Waste Treatment Laboratory, Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Haus-khas, New Delhi 110016, India
| | - Khushal Khambhati
- Department of Biosciences, School of Science, Indrashil University, Rajpur, Mehsana 382715, Gujarat, India
| | - Kolli Venkata Supraja
- Waste Treatment Laboratory, Department of Biochemical Engineering and Biotechnology, Indian Institute of Technology Delhi, Haus-khas, New Delhi 110016, India
| | - Vijai Singh
- Department of Biosciences, School of Science, Indrashil University, Rajpur, Mehsana 382715, Gujarat, India
| | - Franziska Lederer
- Helmholtz-Zentrum Dresden-Rossendorf, Helmholtz Institute Freiberg for Resource Technology, Bautzner landstrasse 400, 01328 Dresden, Germany
| | - Pau-Loke Show
- Zhejiang Provincial Key Laboratory for Subtropical Water Environment and Marine Biological Resources Protection, Wenzhou University, Wenzhou 325035, China; Department of Sustainable Engineering, Saveetha School of Engineering, SIMATS, Chennai 602105, India; Department of Chemical and Environmental Engineering, University of Nottingham, Malaysia, 43500 Semenyih, Selangor Darul Ehsan, Malaysia
| | - Mukesh Kumar Awasthi
- College of Natural Resources and Environment, Northwest A&F University, Yangling 712100, China
| | - Abhinav Sharma
- Institute Theory of Polymers, Leibniz Institute for Polymer Research, Hohe Strasse 6, 01069 Dresden, Germany
| | - Rohan Jain
- Helmholtz-Zentrum Dresden-Rossendorf, Helmholtz Institute Freiberg for Resource Technology, Bautzner landstrasse 400, 01328 Dresden, Germany.
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11
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Surface chemistry of graphene tailoring the activity of digestive enzymes by modulating interfacial molecular interactions. J Colloid Interface Sci 2023; 630:179-192. [DOI: 10.1016/j.jcis.2022.10.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Revised: 09/26/2022] [Accepted: 10/10/2022] [Indexed: 11/06/2022]
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12
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Zhu R, Liang Y, Luo H, Cao H, Liu Y, Huang S, Xiao Q. Investigations of interaction mechanism and conformational variation of serum albumin affected by artemisinin and dihydroartemisinin. J Mol Recognit 2023; 36:e3000. [PMID: 36315411 DOI: 10.1002/jmr.3000] [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: 09/07/2022] [Revised: 10/14/2022] [Accepted: 10/26/2022] [Indexed: 11/05/2022]
Abstract
In this work, binding interactions of artemisinin (ART) and dihydroartemisinin (DHA) with human serum albumin (HSA) and bovine serum albumin (BSA) were investigated thoroughly to illustrate the conformational variation of serum albumin. Experimental results indicated that ART and DHA bound strongly with the site I of serum albumins via hydrogen bond (H-bond) and van der Waals force and subsequently statically quenched the intrinsic fluorescence of serum albumins through concentration-dependent manner. The quenching abilities of two drugs on the intrinsic fluorescence of HSA were much higher than the quenching abilities of two drugs on the intrinsic fluorescence of BSA. Both ART and DHA, especially DHA, caused the conformational variation of serum albumins and reduced the α-helix structure content of serum albumins. DHA with hydrophilic hydroxyl group bound with HSA more strongly, suggesting the important roles of the chemical polarity and the hydrophilicity during the binding interactions of two drugs with serum albumins. These results reveal the molecular understanding of binding interactions between ART derivatives and serum albumins, providing vital information for the future application of ART derivatives in biological and clinical areas.
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Affiliation(s)
- Rukui Zhu
- Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, College of Chemistry and Materials, Nanning Normal University, Nanning, People's Republic of China
| | - Yu Liang
- Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, College of Chemistry and Materials, Nanning Normal University, Nanning, People's Republic of China
| | - Huajian Luo
- Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, College of Chemistry and Materials, Nanning Normal University, Nanning, People's Republic of China
| | - Huishan Cao
- Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, College of Chemistry and Materials, Nanning Normal University, Nanning, People's Republic of China
| | - Yi Liu
- Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, College of Chemistry and Materials, Nanning Normal University, Nanning, People's Republic of China.,State Key Laboratory of Separation Membranes and Membrane Processes, School of Chemistry and Chemical Engineering, Tiangong University, Tianjin, People's Republic of China
| | - Shan Huang
- Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, College of Chemistry and Materials, Nanning Normal University, Nanning, People's Republic of China
| | - Qi Xiao
- Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, College of Chemistry and Materials, Nanning Normal University, Nanning, People's Republic of China
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Yeggoni DP, Dubey S, Mohammad YZ, Rachamallu A, Subramanyam R. Elucidation of binding mechanism of stigmasterol with human serum albumin: a biophysical and molecular dynamics simulation approach. J Biomol Struct Dyn 2022; 40:12135-12147. [PMID: 34463217 DOI: 10.1080/07391102.2021.1968498] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
In the present study, we have analyzed the interaction of a phytochemical, stigmasterol (Stig), with human serum albumin (HSA) under physiological conditions using fluorescence quenching, circular dichroism and molecular modeling methods. Cytotoxic studies with Stig in mouse macrophages (RAW 246.7) and HeLa cell lines showed anti-inflammatory and anti-cancer properties. Further, the intrinsic fluorescence of HSA was quenched by Stig, which was considered a static quenching mechanism. The site-specific marker experiments revealed that Stig binds to the IIIA subdomain of HSA with a binding constant of KStig=1.8 ± 0.03 × 105 M-1 and free energy of -7.26 ± 0.031 Kcal/mol. The secondary structure of HSA was partially unfolded after binding of Stig, which indicates an alteration in the microenvironment of the protein binding site. Molecular docking experiments found that Stig binds strongly with HSA at the IIIA domain of the hydrophobic pocket with one hydrogen bond. The rigidity of the protein-Stig complex and free energies were analyzed by molecular dynamic simulation (MDS) for 100 ns, where the HSA-Stig was stabilized after 40 ns. MDS studies revealed that HSA does not significantly change the secondary structure when it binds with Stig, which is in agreement with the circular dichroism data. Overall, the results obtained gave qualitative and quantitative insight into the binding interaction between HSA and Stig, which is essential in understanding the latter as a therapeutic molecule.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - Shreya Dubey
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | - Yusuf Zamal Mohammad
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, India
| | | | - Rajagopal Subramanyam
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad, India
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14
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Investigation of the Effect of Molecular Weight, Density, and Initiator Structure Size on the Repulsive Force between a PNIPAM Polymer Brush and Protein. ADVANCES IN POLYMER TECHNOLOGY 2022. [DOI: 10.1155/2022/9741080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
This paper focuses on the effect of degree of polymerization (N), density (
), and pattern size (
) on the interaction force between a periodically patterned Poly(N-isopropylacrylamide) (PNIPAM) brush and protein. The hydrophobic interaction, the Van der Waals attractive force, and the steric repulsive force were expressed in terms of
,
, and
. The osmotic constant (k1) and the entropic constant (k2) were determined from the fit of the steric repulsive force to an experimentally obtained force distance curve. The osmotic constant was 0.105, and the entropic constant was 0.255. Using these constants, the steric repulsive force was plotted as a function of the separation distance(s) between the substrate and the protein. The forces were determined at a separation distance equal to 0.3 nm, where L0 is the equilibrium thickness of the PNIPAM brush. At this separation distance, the value of the steric repulsive force was much higher than the value of the sum of the hydrophobic interaction and the Van der Waals attractive force for large degree of polymerization (
) and density (
chains/nm2). However, the repulsive force was comparable to the sum of the hydrophobic interaction and the Van der Waals attractive force for a small degree of polymerization (
) and density (
). Furthermore, the steric repulsive force was plotted as a function of pattern size
. The plot indicated that the steric repulsive force becomes nearly zero for all degrees of polymerization and density when the value of the initiator structure size was less than 200 nm. In addition to the steric repulsive force, the lateral extension of the chains in the periodically patterned PNIPAM brush was calculated by scaling low and compared with the experimental data taken from previously published literatures. The polymer brush structure was modelled as if the immediate bare substrate is so wide that even a stretched polymer segment cannot reach to the next polymer brush structure. In such models, the value of the lateral extension was equal to the thickness of the homogenous brush. It was independent of the pattern size. However, when the polymer brush structure was modelled as if there is another polymer brush structure at a distance half of the size of the period, the lateral extension was found to be dependent on the size of the initiator structure size due to chain bridging. This was witnessed by the patterning of polymer brushes using the interferometric patterning of PNIPAM brushes and an atomic force microscopy imaging of the polymer brush structures both in air and in water. The polymer brush structure resolution in water was much lower than the resolution in air, which indicates the lateral extension of the polymer chains in water. For such kind of periodic polymer brush structures, the gap between them was calculated, and it was found dependent on the degree of polymerization, density, and initiator structure size.
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Murali M, Latha J, Prakash PA, Sangeetha S, Selvakumaran B, Jaabir MSM. Characterization of [Ru(bpy)2(diamine)]2+ complexes and their DNA binding and cleavage, BSA interaction, cytotoxic, and anticancer mechanistic properties. Polyhedron 2022. [DOI: 10.1016/j.poly.2022.115925] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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16
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Wang L, Liang YS, Wu ZB, Liu YS, Xiao YH, Hu T, Gao R, Fang J, Liu J, Wu AP. Exploring the interaction between Cry1Ac protein and Zn 2+, Cd 2+ metal ions by fluorescence quenching and molecular docking approaches. CHEMOSPHERE 2022; 297:134105. [PMID: 35245590 DOI: 10.1016/j.chemosphere.2022.134105] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 02/19/2022] [Accepted: 02/22/2022] [Indexed: 06/14/2023]
Abstract
Bacillus Thuringiensis (Bt) protein has a strong ability to complex with metal ions, which may increase the transport of metal ions in the soil multi-media system. In this study, the interactions between Cry1Ac protein and metal ions (Zn2+ and Cd2+) were investigated through spectroscopies and molecular docking methods. The spectra results showed that both Zn2+ and Cd2+ quenched the fluorescence intensity of Cry1Ac protein through the static quenching. The binding constants with 4-5 orders of magnitude also indicated the interactions between the ions and the Cry1Ac protein. The thermodynamic analysis showed that hydrogen bonds and van der Waals forces were predominant during the processes. In terms of the Förster non-radiation energy transfer theory, the binding distances between metal ions and Cry1Ac protein were approximately 0.21-0.24 nm, indicating the existence of a non-radiative energy transfer between them. Furthermore, molecular docking revealed that the metal ions participated in ligand binding with the Cry1Ac at the locations Asp569, Thr560, Asn564 and Gln566. The present work provided reasonable models helping us further understand the transport effect of heavy metals in the presence of Cry1Ac. The results could provide mechanistic insights into the nature of metal ions-Cry1Ac interactions and offer important information on the toxicity risk of metal ions-Cry1Ac binding interactions.
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Affiliation(s)
- Li Wang
- College of Resources and Environment, Hunan Agricultural University and Hunan Provincial Key Laboratory of Rural Ecosystem Health in Dongting Lake Area, Changsha, 410128, PR China
| | - Yun-Shan Liang
- College of Resources and Environment, Hunan Agricultural University and Hunan Provincial Key Laboratory of Rural Ecosystem Health in Dongting Lake Area, Changsha, 410128, PR China.
| | - Zhi-Bin Wu
- College of Resources and Environment, Hunan Agricultural University and Hunan Provincial Key Laboratory of Rural Ecosystem Health in Dongting Lake Area, Changsha, 410128, PR China
| | - Yi-Song Liu
- College of Veterinary Medicine, Hunan Agricultural University and National and Local Union Engineering Research Center of Veterinary Herbal Medicine Resource and Initiative, Changsha, 410128, PR China
| | - Yun-Hua Xiao
- College of Bioscience and Biotechnology, Hunan Agricultural University and Hunan Engineering Laboratory for Pollution Control and Waste Utilization in Swine Production, Changsha, 410128, PR China
| | - Teng Hu
- College of Resources and Environment, Hunan Agricultural University and Hunan Provincial Key Laboratory of Rural Ecosystem Health in Dongting Lake Area, Changsha, 410128, PR China
| | - Rong Gao
- College of Resources and Environment, Hunan Agricultural University and Hunan Provincial Key Laboratory of Rural Ecosystem Health in Dongting Lake Area, Changsha, 410128, PR China
| | - Jun Fang
- College of Bioscience and Biotechnology, Hunan Agricultural University and Hunan Engineering Laboratory for Pollution Control and Waste Utilization in Swine Production, Changsha, 410128, PR China
| | - Jiao Liu
- College of Resources and Environment, Hunan Agricultural University and Hunan Provincial Key Laboratory of Rural Ecosystem Health in Dongting Lake Area, Changsha, 410128, PR China
| | - Ai Ping Wu
- College of Resources and Environment, Hunan Agricultural University and Hunan Provincial Key Laboratory of Rural Ecosystem Health in Dongting Lake Area, Changsha, 410128, PR China
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17
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Zhao L, Jin X, Li Y, Yu Y, He L, Liu R. Effects of A-type oligomer procyanidins on protein glycation using two glycation models coupled with spectroscopy, chromatography, and molecular docking. Food Res Int 2022; 155:111068. [DOI: 10.1016/j.foodres.2022.111068] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 02/07/2022] [Accepted: 02/23/2022] [Indexed: 11/04/2022]
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18
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Li J, Liu Y, Li T, Gantumur MA, Qayum A, Bilawal A, Jiang Z, Wang L. Non-covalent interaction and digestive characteristics between α-lactalbumin and safflower yellow: Impacts of microwave heating temperature. Lebensm Wiss Technol 2022. [DOI: 10.1016/j.lwt.2022.113206] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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19
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Vyas P, Kumar PBS, Das SL. Sorting of proteins with shape and curvature anisotropy on a lipid bilayer tube. SOFT MATTER 2022; 18:1653-1665. [PMID: 35132986 DOI: 10.1039/d2sm00077f] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Curvature induced sorting of lipid membrane bound proteins has been widely studied through experiments that induce curvature variation in a giant unilamellar lipid-bilayer vesicle with adsorbed proteins by pulling thin cylindrical tethers. In the theoretical space, this has been supplemented with models that capture curvature dependent interaction between membrane and idealized protein particles, through free energy contributions. Many membrane proteins such as the BAR domain proteins are known to have extremely anisotropic shapes and soft interacting potentials, whereas the idealizations of protein particles explored in models have only assumed them as hard disk-like particles with curvature anisotropy. Here, we present a model of sorting of the proteins while including the effects of softness in their interaction potentials, shape anisotropy in the protein structure, and curvature anisotropy in the interactions with the membrane. This is based on a clean separation of free energy contributions from non-ideal fluid behavior of soft anisotropic particles and curvature interactions between proteins and membranes. We probe the behavior of the sorting function under limiting conditions and show that it converges to the previously derived models. In addition to this, we present a comparison of the variation in sorting ratio due to the observed variation in the shape parameter values in known membrane proteins. Finally, using published experimental data for membrane proteins, we perform fitting and derive model parameters. We observe that shape anisotropy adversely affects the sorting of proteins to a high curvature region, whereas curvature anisotropy and softer interaction between proteins favor sorting.
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Affiliation(s)
- Pranav Vyas
- Department of Bioengineering, Stanford University, Stanford, California 94305, USA.
| | - P B Sunil Kumar
- Department of Physics, Indian Institute of Technology Palakkad, Palakkad 678623, India
| | - Sovan Lal Das
- Physical and Chemical Biology Laboratory and Department of Mechanical Engineering, Indian Institute of Technology Palakkad, Palakkad 678623, India
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20
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Wang X, Zhang Z, Liu Z, Ma X, Dai Q, Wang X, Ge B, He H, Huang F. Spectroscopic investigation on the binding interactions between graphene quantum dots and carbonic anhydrase. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 265:120369. [PMID: 34547684 DOI: 10.1016/j.saa.2021.120369] [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: 06/14/2021] [Revised: 08/28/2021] [Accepted: 09/04/2021] [Indexed: 06/13/2023]
Abstract
As a new member of the nanomaterials family, ultrasmall graphene quantum dots (GQDs) have shown broad application prospects in the field of biomedicine, but the analysis of their biological effects at the molecular level is yet limited. Herein, carbonic anhydrase (CA) was selected as a model protein to assess the interactions between GQDs and biomacromolecules. A range of spectroscopic techniques were employed to systematically investigate the binding interactions between GQDs and CA and the catalytic function of CA in the presence of GQDs was evaluated. Experimental results showed that GQDs could quench the intrinsic fluorescence of CA and the concentration dependent quenching efficiency exhibited an obvious deviation from the linear plot, indicating a static binding mode. Further investigation suggested that van der Waal interactions and hydrogen bonding were the main driving forces. Additionally, circular dichroism measurement showed that the binding of GQDs induced slight conformational changes of CA. The catalytic capability assessment proved that these binding interactions resulted in the reduction of the biological functions of CA. This comprehensive study provided important insight into the interaction of GQDs with biomacromolecules, which would be crucial for the further applications of GQDs and other nanomaterials in the biomedical field.
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Affiliation(s)
- Xiaojuan Wang
- State Key Laboratory of Heavy Oil Processing, College of Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China.
| | - Zhixiong Zhang
- State Key Laboratory of Heavy Oil Processing, College of Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China
| | - Zhenzhen Liu
- State Key Laboratory of Heavy Oil Processing, College of Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China
| | - Xiqi Ma
- State Key Laboratory of Heavy Oil Processing, College of Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China
| | - Qi Dai
- State Key Laboratory of Heavy Oil Processing, College of Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China
| | - Xiaoqiang Wang
- State Key Laboratory of Heavy Oil Processing, College of Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China
| | - Baosheng Ge
- State Key Laboratory of Heavy Oil Processing, College of Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China
| | - Hua He
- State Key Laboratory of Heavy Oil Processing, College of Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China
| | - Fang Huang
- State Key Laboratory of Heavy Oil Processing, College of Chemical Engineering, China University of Petroleum (East China), Qingdao 266580, China.
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21
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Li B, Hao C, Liu H, Yang H, Zhong K, Zhang M, Sun R. Interaction of graphene oxide with lysozyme:Insights from conformational structure and surface charge investigations. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2022; 264:120207. [PMID: 34419829 DOI: 10.1016/j.saa.2021.120207] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Revised: 06/26/2021] [Accepted: 07/16/2021] [Indexed: 06/13/2023]
Abstract
Lysozyme (Lyz) is an important antibacterial protein that exists widely in nature. In recent years, the application of graphene oxide (GO) in the field of biotechnology electronics, optics, chemistry and energy storage has been extensively studied. However, due to the unique properties of GO, the mechanism of its interaction with biomacromolecule proteins is very complex. To further explore the interaction between GO and proteins we explore the influence of different pH and heat treatment conditions on the interaction between GO and Lyz, the GO (0-20 μg/mL) was added at a fixed Lyz concentration (0.143 mg/mL) under different pHs. The structure and surface charge changes of Lyz were measured by spectroscopic analysis and zeta potential. The results showed that the interaction between GO and Lyz depends on temperature and pH, significant changes have taken place in its tertiary and secondary structures. By analyzing the UV absorption spectrum, it was found that lysozyme and GO formed a stable complex, and the conformation of the enzyme was changed. In acidic pH conditions (i.e., pH < pI), a high density of Lyz were found to adsorb on the GO surface, whereas an increase in pH resulted in a progressive decrease in the density of the adsorbed Lyz. This pH-dependent adsorption is ascribed to the electrostatic interactions between the negatively charged GO surface and the tunable ionization of the Lyz molecules. The secondary structure of Lyz adsorbed on GO was also found to be highly dependent on the pH. In this paper, we investigated the exact mechanism of pH-influenced GO binding to lysozyme, which has important guidance significance for the potential toxicity of GO biology and its applications in biomedical fields such as structure-based drug design.
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Affiliation(s)
- Binbin Li
- School of Physics and Information Technology, Shaanxi Normal University, Xi'an 710062, China
| | - Changchun Hao
- School of Physics and Information Technology, Shaanxi Normal University, Xi'an 710062, China.
| | - Hengyu Liu
- School of Physics and Information Technology, Shaanxi Normal University, Xi'an 710062, China
| | - Haiyan Yang
- School of Physics and Information Technology, Shaanxi Normal University, Xi'an 710062, China
| | - Kunfeng Zhong
- School of Physics and Information Technology, Shaanxi Normal University, Xi'an 710062, China
| | - Mingduo Zhang
- School of Physics and Information Technology, Shaanxi Normal University, Xi'an 710062, China.
| | - Runguang Sun
- School of Physics and Information Technology, Shaanxi Normal University, Xi'an 710062, China
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22
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Su Y, Sun Y, Zhai Y, Gu L, Li J, Gong L, Chang C, Yang Y. Effects of surfactants on activity and structure of egg yolk antibody. FOOD AND BIOPRODUCTS PROCESSING 2022. [DOI: 10.1016/j.fbp.2022.01.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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23
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Parreira P, Martins MCL. The biophysics of bacterial infections: Adhesion events in the light of force spectroscopy. Cell Surf 2021; 7:100048. [PMID: 33665520 PMCID: PMC7898176 DOI: 10.1016/j.tcsw.2021.100048] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2018] [Revised: 08/10/2020] [Accepted: 12/03/2020] [Indexed: 02/08/2023] Open
Abstract
Bacterial infections are the most eminent public health challenge of the 21st century. The primary step leading to infection is bacterial adhesion to the surface of host cells or medical devices, which is mediated by a multitude of molecular interactions. At the interface of life sciences and physics, last years advances in atomic force microscopy (AFM)-based force spectroscopy techniques have made possible to measure the forces driving bacteria-cell and bacteria-materials interactions on a single molecule/cell basis (single molecule/cell force spectroscopy). Among the bacteria-(bio)materials surface interactions, the life-threatening infections associated to medical devices involving Staphylococcus aureus and Escherichia coli are the most eminent. On the other hand, Pseudomonas aeruginosa binding to the pulmonary and urinary tract or the Helicobacter pylori binding to the gastric mucosa, are classical examples of bacteria-host cell interactions that end in serious infections. As we approach the end of the antibiotic era, acquisition of a deeper knowledge of the fundamental forces involved in bacteria - host cells/(bio)materials surface adhesion is crucial for the identification of new ligand-binding events and its assessment as novel targets for alternative anti-infective therapies. This article aims to highlight the potential of AFM-based force spectroscopy for new targeted therapies development against bacterial infections in which adhesion plays a pivotal role and does not aim to be an extensive overview on the AFM technical capabilities and theory of single molecule force spectroscopy.
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Affiliation(s)
- Paula Parreira
- INEB – Instituto de Engenharia Biomédica, Universidade do Porto, Portugal
- i3S – Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal
| | - M. Cristina L. Martins
- INEB – Instituto de Engenharia Biomédica, Universidade do Porto, Portugal
- i3S – Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal
- ICBAS – Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Portugal
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24
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Yeggoni DP, Rachamallu A, Subramanyam R. Comparative binding studies of bacosine with human serum albumin and α-1-acid glycoprotein biophysical evaluation and computational approach. J Pharm Biomed Anal 2021; 209:114478. [PMID: 34894460 DOI: 10.1016/j.jpba.2021.114478] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Revised: 11/03/2021] [Accepted: 11/11/2021] [Indexed: 01/25/2023]
Abstract
Bacosine (BAC) is a natural product isolated from a herb and used in the Ayurvedic system of medicine. It is reported to have a wide array of biological activities, which has generated interest in its therapeutic potential. To better understand how BAC may operate as a potential anti-cancer therapeutic, we examined its anti-cancer properties in the human breast cancer cell line, MCF-7. In order to get an idea of how it may behave in vivo, we also evaluated its interaction with human serum albumin (HSA) and α-1-acid glycoprotein (AGP) using fluorescence spectroscopy and in silico molecular modelling. Based on our in vitro studies, we found that BAC inhibited MCF-7 cell growth in a dose-dependent manner with an IC50 value of 9 µM. In addition, the intrinsic fluorescence of HSA and AGP was quenched by BAC, consistent with a static quenching mechanism. Fluorescence emission spectroscopy revealed a binding of 2.97 ± 0.01 × 104 M-1 for HSA-BAC which corresponded to a free energy change of - 6.07 kcal/mol at 25 °C. In addition, we found that BAC had a binding constant of 1.8 ± 0.02 × 103 M-1 to AGP which corresponded to a change in free energy - 4.42 kcal/mol at 25 °C. We also identified the site of BAC binding to the HSA protein using the site-specific marker, phenylbutazone, along with molecular docking studies. Circular dichroism spectra revealed partial changes in the secondary structure of HSA in the presence of BAC suggesting direct interactions. Molecular dynamics simulations demonstrated that the HSA-BAC complex reaches an equilibration state at around 4 ns, suggesting that the HSA-BAC complex is quite stable. Our results provide evidence that serum proteins can act as a carrier protein for BAC, potentially impacting its development as an anti-cancer agent.
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Affiliation(s)
- Daniel Pushparaju Yeggoni
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India
| | - Aparna Rachamallu
- National Institute of Animal Biotechnology, Q City Road, Gachibowli, Hyderabad, Telangana 500032, India
| | - Rajagopal Subramanyam
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad 500046, India.
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25
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Luo H, Li B, Liu J, Liu Y, Xiao Q, Huang S. Investigation on conformational variation and fibrillation of human serum albumin affected by molybdenum disulfide quantum dots. Int J Biol Macromol 2021; 190:999-1006. [PMID: 34487782 DOI: 10.1016/j.ijbiomac.2021.08.215] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 08/27/2021] [Accepted: 08/30/2021] [Indexed: 11/25/2022]
Abstract
In this work, binding interaction between molybdenum disulfide quantum dots (MoS2 QDs) and human serum albumin (HSA) was researched deeply to dissect the conformational variation and fibrillation of HSA affected by MoS2 QDs. The results revealed that MoS2 QDs bound strongly with HSA with molar ratio of 1:1 under the joint actions of hydrogen bond and van der Waals force, leading to the static fluorescence quenching of HSA. MoS2 QDs caused the secondary structure transition of HSA from α-helix stepwise to β-turn, β-sheet, and random coil gradually. MoS2 QDs reduced both the molar enthalpy change and the melting temperature of HSA, reducing the thermal stability of HSA significantly. It is worth noting that MoS2 QDs inhibited the fibrillation process of HSA according to the reduced hydrophobic environment and the disturbance of disulfide bonds in HSA network structure. These results reveal the precise binding mechanism of MoS2 QDs with HSA at molecular level, providing indispensable information for the potential application of MoS2 QDs in biological fields.
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Affiliation(s)
- Huajian Luo
- Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, College of Chemistry and Materials, Nanning Normal University, Nanning 530001, PR China
| | - Bo Li
- Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, College of Chemistry and Materials, Nanning Normal University, Nanning 530001, PR China
| | - Jiajia Liu
- Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, College of Chemistry and Materials, Nanning Normal University, Nanning 530001, PR China
| | - Yi Liu
- Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, College of Chemistry and Materials, Nanning Normal University, Nanning 530001, PR China
| | - Qi Xiao
- Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, College of Chemistry and Materials, Nanning Normal University, Nanning 530001, PR China.
| | - Shan Huang
- Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, College of Chemistry and Materials, Nanning Normal University, Nanning 530001, PR China.
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26
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Luo H, Liang Y, Zhang H, Liu Y, Xiao Q, Huang S. Comparison on binding interactions of quercetin and its metal complexes with calf thymus DNA by spectroscopic techniques and viscosity measurement. J Mol Recognit 2021; 34:e2933. [PMID: 34432328 DOI: 10.1002/jmr.2933] [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: 07/16/2021] [Revised: 08/10/2021] [Accepted: 08/12/2021] [Indexed: 11/08/2022]
Abstract
Quercetin (Qu) and its metal complexes have received great attention during the last years, due to their good antioxidant, antibacterial, and anticancer activities. In this contribution, binding interactions of Qu and Qu-metal complexes with calf thymus DNA (ctDNA) were investigated and compared systematically by using spectroscopic techniques and viscosity measurement. UV-vis absorption spectra of ctDNA-compound systems showed obvious hypochromic effect. Relative viscosity and melting temperature of ctDNA increased after the addition of Qu and Qu-metal complexes, and the change tendency is Qu-Cr(III) > Qu-Mn(II) > Qu-Zn(II) > Qu-Cu(II) > Qu. Fluorescence competition experiments show that hydrogen bonds and van der Waals interaction play an important role in the intercalative binding of Qu and Qu-metal complexes with ctDNA. Qu and Qu-metal complexes could unwind the right-handed B-form helicity of ctDNA and further affect its base pair stacking. Space steric hindrance might be responsible for the differences in the intercalative binding between ctDNA and different Qu-metal complexes. These results provide new information for the molecular understanding of binding interactions of Qu-metal complexes with DNA and the strategy for research of structural influences.
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Affiliation(s)
- Huajian Luo
- Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, College of Chemistry and Materials, Nanning Normal University, Nanning, China
| | - Yu Liang
- Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, College of Chemistry and Materials, Nanning Normal University, Nanning, China
| | - Huiying Zhang
- College of Chemistry and Biological Engineering, Hechi University, Hechi, China
| | - Yi Liu
- Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, College of Chemistry and Materials, Nanning Normal University, Nanning, China.,State Key Laboratory of Separation Membranes and Membrane Processes, School of Chemistry and Chemical Engineering, Tiangong University, Tianjin, China
| | - Qi Xiao
- Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, College of Chemistry and Materials, Nanning Normal University, Nanning, China
| | - Shan Huang
- Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, College of Chemistry and Materials, Nanning Normal University, Nanning, China
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27
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Chen X, Zhang Y, Arora P, Guan X. Nanopore Stochastic Sensing Based on Non-covalent Interactions. Anal Chem 2021; 93:10974-10981. [PMID: 34319076 DOI: 10.1021/acs.analchem.1c02102] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A variety of species could be detected by using nanopores engineered with various recognition sites based upon non-covalent interactions, including electrostatic, aromatic, and hydrophobic interactions. The existence of these engineered non-covalent bonding sites was supported by the single-channel recording technique. The advantage of the non-covalent interaction-based sensing strategy was that the recognition site of the engineered nanopore was not specific for a particular molecule but instead selective for a class of species (e.g., cationic, anionic, aromatic, and hydrophobic). Since different species produce current modulations with quite different signatures represented by amplitude, residence time, and even characteristic voltage-dependence curve, the non-covalent interaction-based nanopore sensor could not only differentiate individual molecules in the same category but also enable differentiation between species with similar structures or molecular weights. Hence, our developed non-covalent interaction-based nanopore sensing strategy may find useful application in the detection of molecules of medical and/or environmental importance.
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Affiliation(s)
- Xiaohan Chen
- Department of Chemistry, Illinois Institute of Technology, 3101 S. Dearborn Street, Chicago, Illinois 60616, United States
| | - Youwen Zhang
- Department of Chemistry, Illinois Institute of Technology, 3101 S. Dearborn Street, Chicago, Illinois 60616, United States
| | - Pearl Arora
- Department of Chemistry, Illinois Institute of Technology, 3101 S. Dearborn Street, Chicago, Illinois 60616, United States
| | - Xiyun Guan
- Department of Chemistry, Illinois Institute of Technology, 3101 S. Dearborn Street, Chicago, Illinois 60616, United States
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Luo H, Li H, Liu Y, Yang L, Xiao Q, Huang S. Investigation on conformational variation and activity of trypsin affected by black phosphorus quantum dots via multi-spectroscopy and molecular modeling. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 256:119746. [PMID: 33819763 DOI: 10.1016/j.saa.2021.119746] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 03/22/2021] [Accepted: 03/22/2021] [Indexed: 06/12/2023]
Abstract
Binding interaction between black phosphorus quantum dots (BPQDs) and trypsin was researched deeply to illustrate the variations on conformation and activity of trypsin affected by BPQDs via multi-spectroscopy and molecular modeling. Experimental results implied that inherent fluorescence of trypsin was quenched by BPQDs via static fluorescence quenching mode. BPQDs bound with trypsin to construct ground-state complex under the binding forces of van der Waal interaction and hydrophobic interaction, resulting in the conformational change of trypsin to be more hydrophilic and incompact. The result of molecular modeling indicated that BPQDs interacted with trypsin at its allosteric site and inhibited the activity of trypsin via non-competitive manner. Finally, BPQDs efficiently inhibited the digestion activity of trypsin on human serum albumin, human cervical carcinoma HeLa cells, and human lung adenocarcinoma A549 cells. This work not only explores the in-depth understanding on the influence of BPQDs on proteinases but also paves the way for further application of BPQDs on human beings for diseases treatments.
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Affiliation(s)
- Huajian Luo
- Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, College of Chemistry and Materials, Nanning Normal University, Nanning 530001, PR China
| | - Haimei Li
- Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, College of Chemistry and Materials, Nanning Normal University, Nanning 530001, PR China
| | - Yi Liu
- Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, College of Chemistry and Materials, Nanning Normal University, Nanning 530001, PR China
| | - Liyun Yang
- Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, College of Chemistry and Materials, Nanning Normal University, Nanning 530001, PR China
| | - Qi Xiao
- Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, College of Chemistry and Materials, Nanning Normal University, Nanning 530001, PR China.
| | - Shan Huang
- Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, College of Chemistry and Materials, Nanning Normal University, Nanning 530001, PR China.
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29
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El-Bindary AA, Anwar ZM, El-Shafaie T. Effect of some amino acids on the binding of quercetin and rutin flavonoids with DNA. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.116131] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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30
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Santos FC, Costa PJ, Garcia MH, Morais TS. Binding of RuCp complexes with human apo-transferrin: fluorescence spectroscopy and molecular docking methods. Biometals 2021; 34:1029-1042. [PMID: 34155581 DOI: 10.1007/s10534-021-00325-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 06/14/2021] [Indexed: 11/25/2022]
Abstract
The interaction between human serum transferrin (hTf) and three promising organometallic Ru (II)- (η5-C5H5) derived complexes, that have already shown strong in vitro cytotoxicity towards human cancer cell lines, has been investigated using fluorescence spectroscopic techniques. The results suggested that the formation of Ru-hTf systems involves a dynamic collision. The binding process occurs spontaneously (ΔG < 0), mainly driven by hydrophobic interactions. Additional docking studies show that all complexes bind preferably to a specific hydrophobic pocket in the C2-subdomain as already observed for other metal-cyclopentadienyl (MCp) complexes and are in agreement with the experimental results. With these studies we hope to contribute to the understanding of the mechanism of action of these promising cytotoxic agents, thus providing clues for a more rational design.
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Affiliation(s)
- Filipa C Santos
- Centro de Química Estrutural, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal
| | - Paulo J Costa
- BioISI - Biosystems & Integrative Sciences Institute, Faculty of Sciences, University of Lisboa, 1749-016, Lisboa, Portugal
| | - M Helena Garcia
- Centro de Química Estrutural, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal
| | - Tânia S Morais
- Centro de Química Estrutural, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016, Lisboa, Portugal.
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31
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Zhu ZM, Zhang WJ. Spectroscopic Analysis of the Interaction Between the Antiparasitic Drug Nitazoxanide and Bovine Serum Albumin. IRANIAN JOURNAL OF SCIENCE AND TECHNOLOGY, TRANSACTIONS A: SCIENCE 2021. [DOI: 10.1007/s40995-021-01102-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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32
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Zhang J, Zhao N, Xu J, Qi Y, Wei X, Fan M. Exploring the catalytic mechanism of a novel β-glucosidase BGL0224 from Oenococcus oeni SD-2a: Kinetics, spectroscopic and molecular simulation. Enzyme Microb Technol 2021; 148:109814. [PMID: 34116760 DOI: 10.1016/j.enzmictec.2021.109814] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 04/14/2021] [Accepted: 04/29/2021] [Indexed: 11/25/2022]
Abstract
The β-glucosidase derived from microorganisms has attracted worldwide interest for their industrial applications, but studies on β-glucosidases from Oenococcus oeni are rare. In this paper, catalytic mechanism of a novel β-glucosidase BGL0224 of Oenococcus oeni SD-2a was explored for the first time by kinetic parameters determination, fluorescence spectroscopy and quenching mechanism analysis, molecular dynamics simulation. The results indicated that BGL0224 had universal catalytic effect on different types of glycoside substrates, but the catalytic efficiencies were different. Fluorescence quenching analysis results suggested that the quenching processes between BGL0224 and seven kinds of substrates were predominated by the static quenching mechanism. A reasonable three-dimensional model of BGL0224 was obtained using the crystal structure of E.coli BglA as a template. The analysis results of molecular simulation (RMSD, Rg, RMSF and hydrogen bonding) showed that the composite system 'BGL0224-pNPG' was very stable after 40 ns. The catalytic process of BGL0224 acting on 'p-Nitrophenyl β-d-glucopyranoside' conformed to the double displacement mechanism. Two glutamic acid residues 'Glu178 and Glu377' played a vital role in the whole catalytic process. Overall, this study gave specific insights on the catalytic mechanism of BGL0224, which was of great significance for developing its potential applications in food industry.
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Affiliation(s)
- Jie Zhang
- College of Food Science and Engineering, Northwest A & F University, Yangling, Shaanxi, 712100, China
| | - Ning Zhao
- College of Food Science and Engineering, Northwest A & F University, Yangling, Shaanxi, 712100, China
| | - Junnan Xu
- College of Food Science and Engineering, Northwest A & F University, Yangling, Shaanxi, 712100, China
| | - Yiman Qi
- College of Food Science and Engineering, Northwest A & F University, Yangling, Shaanxi, 712100, China
| | - Xinyuan Wei
- College of Food Science and Engineering, Northwest A & F University, Yangling, Shaanxi, 712100, China
| | - Mingtao Fan
- College of Food Science and Engineering, Northwest A & F University, Yangling, Shaanxi, 712100, China.
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33
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Tang SF, Hou X. Probing the toxic interactions between bisphenol A and glutathione S-transferase Phi8 from Arabidopsis thaliana. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 213:112029. [PMID: 33578103 DOI: 10.1016/j.ecoenv.2021.112029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 01/28/2021] [Accepted: 02/02/2021] [Indexed: 06/12/2023]
Abstract
As primary polymer material in industrial products, bisphenol A (BPA) has become one of the most productive chemicals. Excluding its endocrine-disrupting property, BPA can also produce excessive reactive oxygen species (ROS). Nevertheless, the underlying toxic mechanisms of BPA-induced oxidative damages to plants are still unknown. In this work, glutathione S-transferase Phi8 was used as biomarker to evaluate the hazardous oxidative effects of BPA at the molecular level. Firstly, the intrinsic fluorescence of AtGSTF8 was statically quenched along with complex formation and structural and conformational changes, which led to the loosening and unfolding of the framework of AtGSTF8 as well as the increase of hydrophilicity around Trp residues. Then a single binding site was predicted for AtGSTF8 towards BPA and the complex formation was predominantly driven by hydrophobic interactions owing to the positive ΔH and ΔS. Besides, the predicted binding site of BPA was close to the H-site of AtGSTF8 which was surrounded by several hydrophobic amino acids based on the molecular docking results. The activity of glutathione S-transferase was declined and the plant growth was destroyed upon complex formation. The investigation of the binding mechanism of BPA with AtGSTF8 at molecular level would provide experimental assessments on toxicological effects of BPA on plants.
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Affiliation(s)
- Si-Fu Tang
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao 266109, China
| | - Xiaomin Hou
- Shandong Province Key Laboratory of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, China.
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34
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Wei J, Huang F, Feng H, Massey IY, Clara T, Long D, Cao Y, Luo J, Yang F. Characterization and Mechanism of Linearized-Microcystinase Involved in Bacterial Degradation of Microcystins. Front Microbiol 2021; 12:646084. [PMID: 33859631 PMCID: PMC8042282 DOI: 10.3389/fmicb.2021.646084] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Accepted: 02/22/2021] [Indexed: 01/17/2023] Open
Abstract
Microcystins (MCs) are extremely hazardous to the ecological environment and public health. How to control and remove MCs is an unsolved problem all over the world. Some microbes and their enzymes are thought to be effective in degrading MCs. Microcystinase can linearize microcystin-leucine-arginine (MC-LR) via a specific locus. However, linearized MC-LR is also very toxic and needs to be removed. How linearized MC-LR was metabolized by linearized-microcystinase, especially how linearized-microcystinase binds to linearized MC-LR, has not been defined. A combination of in vitro experiments and computer simulation was applied to explore the characterization and molecular mechanisms for linearized MC-LR degraded by linearized-microcystinase. The purified linearized-microcystinase was obtained by recombinant Escherichia coli overexpressing. The concentration of linearized MC-LR was detected by high-performance liquid chromatography, and linearized MC-LR degradation products were analyzed by the mass spectrometer. Homology modeling was used to predict the structure of the linearized-microcystinase. Molecular docking techniques on the computer were used to simulate the binding sites of linearized-microcystinase and linearized MC-LR. The purified linearized-microcystinase was obtained successfully. The linearized-microcystinase degraded linearized MC-LR to tetrapeptide efficiently. The second structure of linearized-microcystinase consisted of many alpha-helices, beta-strands, and colis. Linearized-microcystinase interacted the linearized MC-LR with hydrogen bond, hydrophobic interaction, electrostatic forces, and the Van der Waals force. This study firstly reveals the characterization and specific enzymatic mechanism of linearized-microcystinase for catalyzing linearized MC-LR. These findings encourage the application of MC-degrading engineering bacteria and build a great technique for MC-LR biodegradation in environmental engineering.
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Affiliation(s)
- Jia Wei
- Hunan Provincial Key Laboratory of Clinical Epidemiology, Xiangya School of Public Health, Central South University, Changsha, China
| | - Feiyu Huang
- Hunan Provincial Key Laboratory of Clinical Epidemiology, Xiangya School of Public Health, Central South University, Changsha, China
| | - Hai Feng
- Hunan Provincial Key Laboratory of Clinical Epidemiology, Xiangya School of Public Health, Central South University, Changsha, China
| | - Isaac Yaw Massey
- Hunan Provincial Key Laboratory of Clinical Epidemiology, Xiangya School of Public Health, Central South University, Changsha, China
| | - Tezi Clara
- Hunan Provincial Key Laboratory of Clinical Epidemiology, Xiangya School of Public Health, Central South University, Changsha, China
| | - Dingxin Long
- Hunan Province Key Laboratory of Typical Environmental Pollution and Health Hazards, School of Public Health, University of South China, Hengyang, China
| | - Yi Cao
- Hunan Province Key Laboratory of Typical Environmental Pollution and Health Hazards, School of Public Health, University of South China, Hengyang, China
| | - Jiayou Luo
- Hunan Provincial Key Laboratory of Clinical Epidemiology, Xiangya School of Public Health, Central South University, Changsha, China
| | - Fei Yang
- Hunan Provincial Key Laboratory of Clinical Epidemiology, Xiangya School of Public Health, Central South University, Changsha, China.,Hunan Province Key Laboratory of Typical Environmental Pollution and Health Hazards, School of Public Health, University of South China, Hengyang, China.,Key Laboratory of Environmental Medicine Engineering, School of Public Health Southeast University, Ministry of Education, Nanjing, China
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35
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Li X, Zhao R, Shao D, Yuan Y, Bi S. Multispectral and molecular modeling investigations on the binding behaviors of two anticoccidials with serum albumins. J Biomol Struct Dyn 2021; 40:6522-6533. [PMID: 33583333 DOI: 10.1080/07391102.2021.1886173] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
The interaction properties of monensin/clopidol with bovine/human serum albumin (BSA/HSA) were determined via multispectral together with molecular modeling techniques in the report. Fluorescence quenching spectra at different temperatures and fluorescence lifetime determination demonstrated that the fluorescence quenching belonged to a static quenching type. In the case of monensin-BSA, clopidol-BSA, monensin-HSA and clopidol-HSA, the binding constants Ka (291 K) were 5.42 × 104, 4.96 × 104, 3.22 × 104 and 2.99 × 104 M-1, respectively; the binding distances r0 were 1.88, 2.53, 2.19 and 2.02 nm, respectively. Monensin and clopidol bound strongly with BSA/HSA with binding free energies equal to -26.37/-25.11 and -26.11/-24.93 kJ mol-1, respectively. The spontaneous binding process was dominated by hydrogen bonds and van der Waals forces as reflected in thermodynamic parameters analyses. Synchronous, CD, FTIR and UV-vis spectra assays confirmed that serum albumins conformations were altered. Using competitive experiment, monensin/clopidol was observed to bind at site I of serum albumins, which were reconfirmed by the results of molecular modeling.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Xu Li
- College of Chemistry, Changchun Normal University, Changchun, China
| | - Rui Zhao
- College of Chemistry, Changchun Normal University, Changchun, China
| | - Di Shao
- College of Chemistry, Changchun Normal University, Changchun, China
| | - Yue Yuan
- College of Chemistry, Changchun Normal University, Changchun, China
| | - Shuyun Bi
- College of Chemistry, Changchun Normal University, Changchun, China
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36
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Akhuli A, Chakraborty D, Agrawal AK, Sarkar M. Probing the Interaction of Bovine Serum Albumin with Copper Nanoclusters: Realization of Binding Pathway Different from Protein Corona. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021; 37:1823-1837. [PMID: 33502208 DOI: 10.1021/acs.langmuir.0c03176] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
With an aim to understand the interaction mechanism of bovine serum albumin (BSA) with copper nanoclusters (CuNCs), three different types CuNCs having chemically different surface ligands, namely, tannic acid (TA), chitosan, and cysteine (Cys), have been fabricated, and investigations are carried out in the absence and presence of protein (BSA) at ensemble-averaged and single-molecule levels. The CuNCs, capped with different surface ligands, are consciously chosen so that the role of surface ligands in the overall protein-NCs interactions is clearly understood, but, more importantly, to find whether these CuNCs can interact with protein in a new pathway without forming the "protein corona", which otherwise has been observed in relatively larger nanoparticles when they are exposed to biological fluids. Analysis of the data obtained from fluorescence, ζ-potential, and ITC measurements has clearly indicated that the BSA protein in the presence of CuNCs does not attain the binding stoichiometry (BSA/CuNCs > 1) that is required for the formation of "protein corona". This conclusion is further substantiated by the outcome of the fluorescence correlation spectroscopy (FCS) study. Further analysis of data and thermodynamic calculations have revealed that the surface ligands of the CuNCs play an important role in the protein-NCs binding events, and they can alter the mode and thermodynamics of the process. Specifically, the data have demonstrated that the binding of BSA with TA-CuNCs and Chitosan-CuNCs follows two types of binding modes; however, the same with Cys-CuNCs goes through only one type of binding mode. Circular dichroism (CD) measurements have indicated that the basic structure of BSA remains almost unaltered in the presence of CuNCs. The outcome of the present study is expected to encourage and enable better application of NCs in biological applications.
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Affiliation(s)
- Amit Akhuli
- School of Chemical Sciences, National Institute of Science Education and Research, HBNI, Bhimpur-Padanpur, Jatni, Khorda, Bhubaneswar 752050, Odisha, India
| | - Debabrata Chakraborty
- School of Chemical Sciences, National Institute of Science Education and Research, HBNI, Bhimpur-Padanpur, Jatni, Khorda, Bhubaneswar 752050, Odisha, India
| | - Aman Kumar Agrawal
- School of Chemical Sciences, National Institute of Science Education and Research, HBNI, Bhimpur-Padanpur, Jatni, Khorda, Bhubaneswar 752050, Odisha, India
| | - Moloy Sarkar
- School of Chemical Sciences, National Institute of Science Education and Research, HBNI, Bhimpur-Padanpur, Jatni, Khorda, Bhubaneswar 752050, Odisha, India
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37
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Sangeetha S, Ajaykamal T, Murali M. Copper( ii) complexes of 2-methyl-8-hydroxyquinoline and tri/diimine co-ligand: DFT calculations, DNA and BSA binding, DNA cleavage, cytotoxicity and induction of apoptosis. NEW J CHEM 2021. [DOI: 10.1039/d1nj00392e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Four-coordinate copper(ii) complex cleaves supercoiled ϕX174 RF DNA without reductant while five-coordinate complex cleaves with reductant. The cytotoxicity against cancer cells are higher than cisplatin, less-toxic to normal cells and induce apoptosis.
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Affiliation(s)
- Somasundaram Sangeetha
- Coordination and Bioinorganic Chemistry Research Laboratory
- Department of Chemistry
- National College (Autonomous)
- Tiruchirappalli 620 001
- India
| | | | - Mariappan Murali
- Coordination and Bioinorganic Chemistry Research Laboratory
- Department of Chemistry
- National College (Autonomous)
- Tiruchirappalli 620 001
- India
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38
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Xiao Q, Liang J, Luo H, Li H, Yang J, Huang S. Investigations of conformational structures and activities of trypsin and pepsin affected by food colourant allura red. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.114359] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
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39
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Huang S, Luo H, Liu Y, Su W, Xiao Q. Comparable investigation of binding interactions between three arene ruthenium(II) thiosemicarbazone complexes and calf thymus DNA. Polyhedron 2020. [DOI: 10.1016/j.poly.2020.114864] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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40
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Huang S, Luo H, Su W, Xiao Q, Xie J. Comparative study of binding interactions between three organometallic rhodium(III) complexes with curcuminoid ligands and human serum albumin. J Mol Recognit 2020; 34:e2876. [PMID: 32974948 DOI: 10.1002/jmr.2876] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 08/21/2020] [Accepted: 09/02/2020] [Indexed: 11/06/2022]
Abstract
Organometallic rhodium(III) complexes with curcuminoid ligands attracted considerable attention in biological-related fields and the variation of curcuminoid ligands may regulate the biological activity of these organometallic rhodium(III) complexes. To deeply evaluate the biological influences of these complexes, the binding interactions between three rhodium(III) complexes with curcuminoid ligands and human serum albumin (HSA) were comparably investigated by spectroscopic and electrochemical techniques. The results suggested that the intrinsic fluorescence of HSA was quenched by three complexes through static fluorescence quenching mode. Three complexes bonded with Sudlow's site I of HSA to form ground-state compounds under the binding forces of van der Waals interactions, hydrogen bonds formation, and protonation. Finally, the native conformational structure and the thermal stability of HSA were all changed. Space steric hindrance of complexes took part in the differences of the fluorescence quenching processes, and the chemical polarity of the complexes played a vital role in the variations of the structure and biological activity of HSA. These results illustrated the molecular interactions between protein and organometallic rhodium(III) complexes with curcuminoid ligands, offering new insight about the prospective applications of analogical rhodium(III) complexes in biomedicine areas.
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Affiliation(s)
- Shan Huang
- Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, College of Chemistry and Materials, Nanning Normal University, Nanning, P. R. China
| | - Huajian Luo
- Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, College of Chemistry and Materials, Nanning Normal University, Nanning, P. R. China
| | - Wei Su
- Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, College of Chemistry and Materials, Nanning Normal University, Nanning, P. R. China
| | - Qi Xiao
- Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, College of Chemistry and Materials, Nanning Normal University, Nanning, P. R. China
| | - Jiangning Xie
- Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, College of Chemistry and Materials, Nanning Normal University, Nanning, P. R. China
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41
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Andersson J, Bilotto P, Mears LLE, Fossati S, Ramach U, Köper I, Valtiner M, Knoll W. Solid-supported lipid bilayers - A versatile tool for the structural and functional characterization of membrane proteins. Methods 2020; 180:56-68. [PMID: 32920130 DOI: 10.1016/j.ymeth.2020.09.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 09/07/2020] [Accepted: 09/08/2020] [Indexed: 02/07/2023] Open
Abstract
The cellular membrane is central to the development of single-and multicellular life, as it separates the delicate cellular interior from the hostile environment. It exerts tight control over entry and exit of substances, is responsible for signaling with other cells in multicellular organisms and prevents pathogens from entering the cell. In the case of bacteria and viruses, the cellular membrane also hosts the proteins enabling invasion of the host organism. In a very real sense therefore, the cellular membrane is central to all life. The study of the cell membrane and membrane proteins in particular has therefore attracted significant attention. Due to the enormous variety of tasks performed by the membrane, it is a highly complex and challenging structure to study. Ideally, membrane components would be studied in isolation from this environment, but unlike water soluble proteins, the amphiphilic environment provided by the cellular membrane is key to the structure and function of the cell membrane. Therefore, model membranes have been developed to provide an environment in which a membrane protein can be studied. This review presents a set of tools that enable the comprehensive characterization of membrane proteins: electrochemical tools, surface plasmon resonance, neutron scattering, the surface forces apparatus and atomic force microscopy are discussed, with a particular focus on experimental technique and data evaluation.
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Affiliation(s)
| | - Pierluigi Bilotto
- Institute of Applied Physics, Vienna University of Technology, Vienna 1040, Austria
| | - Laura L E Mears
- Institute of Applied Physics, Vienna University of Technology, Vienna 1040, Austria
| | - Stefan Fossati
- AIT Austrian Institute of Technology, 1210 Vienna, Austria; Institute of Applied Physics, Vienna University of Technology, Vienna 1040, Austria
| | - Ulrich Ramach
- Institute of Applied Physics, Vienna University of Technology, Vienna 1040, Austria; CEST Kompetenzzentrum für elektrochemische Oberflächentechnologie, Wiener Neustadt 2700, Austria
| | - Ingo Köper
- Flinders Institute for Nanoscale Science and Technology, College of Science and Engineering, Flinders University, Adelaide, SA, Australia
| | - Markus Valtiner
- Institute of Applied Physics, Vienna University of Technology, Vienna 1040, Austria; CEST Kompetenzzentrum für elektrochemische Oberflächentechnologie, Wiener Neustadt 2700, Austria
| | - Wolfgang Knoll
- AIT Austrian Institute of Technology, 1210 Vienna, Austria; CEST Kompetenzzentrum für elektrochemische Oberflächentechnologie, Wiener Neustadt 2700, Austria
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42
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Mahanthappa M, Savanur MA, Yellappa S. Molecular interaction studies of zinc sulphide nanoparticles with DNA and its consequence: a multitechnique approach. LUMINESCENCE 2020; 36:45-56. [DOI: 10.1002/bio.3912] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2019] [Revised: 05/24/2020] [Accepted: 07/05/2020] [Indexed: 12/27/2022]
Affiliation(s)
- Mallappa Mahanthappa
- Department of Chemistry Bangalore University Jnanabharathi Campus Bengaluru India
- Research Resource Centre Visvesvaraya Technological University Belagavi India
- School of Applied Sciences REVA University Bengaluru 560064 India
| | - Mohammed Azharuddin Savanur
- Department of Biochemistry Karnatak University Dharwad India
- Department of Biochemistry Indian Institute of Science Bengaluru India
| | - Shivaraj Yellappa
- Department of Chemistry Bangalore University Jnanabharathi Campus Bengaluru India
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Huang S, Li H, Liu Y, Yang L, Wang D, Xiao Q. Investigations of conformational structure and enzymatic activity of trypsin after its binding interaction with graphene oxide. JOURNAL OF HAZARDOUS MATERIALS 2020; 392:122285. [PMID: 32105952 DOI: 10.1016/j.jhazmat.2020.122285] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 12/07/2019] [Accepted: 02/10/2020] [Indexed: 06/10/2023]
Abstract
Herein, interaction between graphene oxide (GO) and trypsin was systematically characterized for deep investigations of conformational structure and enzymatic activity of trypsin affected by GO. Results indicated that GO bound with trypsin to form ground state complex with molar ratio of 1 to 1. Intrinsic fluorescence of trypsin was statically quenched by GO through van der Waal interaction, hydrophobic interaction, hydrogen bond, and electrostatic interaction. Both tertiary structure and secondary structure of trypsin were changed obviously after its binding with trypsin, resulting in the structure transformation of trypsin from the β-sheet structure to the α-helix structure. Since GO bound with the allosteric site of trypsin to inhibit its enzymatic activity via non-competitive manner, GO efficiently protected human serum albumin and human cervical carcinoma HeLa cells from the digestion of trypsin. These results explored the exact binding mechanism of GO with protease, which provides more important information for possible biological risk of GO on human beings.
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Affiliation(s)
- Shan Huang
- Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, College of Chemistry and Materials, Nanning Normal University, Guangxi Teachers Education University, Nanning, 530001, PR China
| | - Haimei Li
- Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, College of Chemistry and Materials, Nanning Normal University, Guangxi Teachers Education University, Nanning, 530001, PR China
| | - Yi Liu
- Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, College of Chemistry and Materials, Nanning Normal University, Guangxi Teachers Education University, Nanning, 530001, PR China
| | - Liyun Yang
- Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, College of Chemistry and Materials, Nanning Normal University, Guangxi Teachers Education University, Nanning, 530001, PR China
| | - Dan Wang
- Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, College of Chemistry and Materials, Nanning Normal University, Guangxi Teachers Education University, Nanning, 530001, PR China
| | - Qi Xiao
- Guangxi Key Laboratory of Natural Polymer Chemistry and Physics, College of Chemistry and Materials, Nanning Normal University, Guangxi Teachers Education University, Nanning, 530001, PR China.
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Wang C, Shi D, Zhang F, Yu X, Lin G, Zhou Z. Characterization of binding interaction between magnesium isoglycyrrhizinate and human serum albumin. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 234:118245. [PMID: 32179463 DOI: 10.1016/j.saa.2020.118245] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 02/24/2020] [Accepted: 03/07/2020] [Indexed: 06/10/2023]
Abstract
Magnesium isoglycyrrhizinate (MgIG) is the magnesium salt of 18β-glycyrrhizic acid extracted from licorice, a Chinese traditional medicine. The pharmacokinetic characteristics of MgIG have been widely studied; nevertheless, its target protein and mechanism of action remain unclear. Therefore, the objective of present work was to determine the characteristics of binding between human serum albumin (HSA) and MgIG. The formation of HSA-MgIG complex was studied using spectrometric techniques, LC-MS/MS, and molecular docking calculations. The results of fluorescence study demonstrated the quenching mechanism is definitely static. The negative thermodynamic parameters suggested that the interaction is enthalpically driven and occurs spontaneously. Binding density and probe displacement analysis suggested that MgIG bound to HSA at a single site, determined to be site I. The mean albumin binding rate of MgIG with HSA concentration ranged from 35 to 50 g·L-1 reached 85.6%. Molecular docking analysis revealed the major residues and interaction forces involved in formation of HSA-MgIG complex, corresponding with the experimental results.
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Affiliation(s)
- Chenxiang Wang
- Department of Pharmacy, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, China
| | - Dawei Shi
- Department of Pharmacy, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, China
| | - Fangfang Zhang
- Department of Pharmacy, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, China
| | - Xuben Yu
- Department of Pharmacy, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, China
| | - Guanyang Lin
- Department of Pharmacy, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, China.
| | - Ziye Zhou
- Department of Pharmacy, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, China.
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Han X, Hao H, Li Q, Liu C, Lei J, Yu F, Chen K, Liu Y, Huang T. The interaction mechanism between fludarabine and human serum albumin researched by comprehensive spectroscopic methods and molecular docking technique. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 233:118170. [PMID: 32143170 DOI: 10.1016/j.saa.2020.118170] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 02/03/2020] [Accepted: 02/16/2020] [Indexed: 06/10/2023]
Abstract
Fludarabine (Flu) is widely used to treat B-cell chronic lymphocytic leukemia. HSA is of the essence to human, especially in blood circulation system. The interaction mechanism between Flu and HSA was studied by comprehensive spectroscopic methods and molecular docking technique. UV-vis and FL spectrum results indicated that Flu bond with HSA, and there was a new complex produced at the binding site I in subdomain IIA. Association constants at 298 K were 1.637 × 104 M-1 and 1.552 × 104 M-1 at 310 K, respectively. The negative enthalpy (ΔH) and positive entropy (ΔS) values for the interaction revealed that the binding behavior was driven by hydrophobic forces and hydrogen bonds. The results obtained from UV, RLS spectra, 3D fluorescence and CD spectrum illustrated that Flu could change the secondary structure of HSA. According to molecule docking result, the binding energy of interaction is -11.15 kcal/mol.
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Affiliation(s)
- XiaoLe Han
- Key Laboratory of Catalysis and Energy Materials Chemistry of Ministry of Education & Hubei Key Laboratory of Catalysis and Materials Science, South-Central University for Nationalities, Wuhan 430074, China.
| | - Hao Hao
- Key Laboratory of Catalysis and Energy Materials Chemistry of Ministry of Education & Hubei Key Laboratory of Catalysis and Materials Science, South-Central University for Nationalities, Wuhan 430074, China
| | - QingYu Li
- Key Laboratory of Catalysis and Energy Materials Chemistry of Ministry of Education & Hubei Key Laboratory of Catalysis and Materials Science, South-Central University for Nationalities, Wuhan 430074, China
| | - ChenYin Liu
- Key Laboratory of Catalysis and Energy Materials Chemistry of Ministry of Education & Hubei Key Laboratory of Catalysis and Materials Science, South-Central University for Nationalities, Wuhan 430074, China
| | - JiaWen Lei
- Key Laboratory of Catalysis and Energy Materials Chemistry of Ministry of Education & Hubei Key Laboratory of Catalysis and Materials Science, South-Central University for Nationalities, Wuhan 430074, China
| | - Fan Yu
- Key Laboratory of Catalysis and Energy Materials Chemistry of Ministry of Education & Hubei Key Laboratory of Catalysis and Materials Science, South-Central University for Nationalities, Wuhan 430074, China
| | - Ke Chen
- Key Laboratory of Catalysis and Energy Materials Chemistry of Ministry of Education & Hubei Key Laboratory of Catalysis and Materials Science, South-Central University for Nationalities, Wuhan 430074, China
| | - Yi Liu
- State Key Laboratory of Virology & Key laboratory of Analytical Chemistry for Biology and Medicine (MOE), College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Tao Huang
- Key Laboratory of Catalysis and Energy Materials Chemistry of Ministry of Education & Hubei Key Laboratory of Catalysis and Materials Science, South-Central University for Nationalities, Wuhan 430074, China.
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Song C, Luo H, Lin X, Peng Z, Weng L, Tang X, Xu S, Song M, Jin L, Zheng X. Study on AgInZnS-Graphene Oxide Non-toxic Quantum Dots for Biomedical Sensing. Front Chem 2020; 8:331. [PMID: 32432079 PMCID: PMC7215081 DOI: 10.3389/fchem.2020.00331] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Accepted: 03/31/2020] [Indexed: 11/20/2022] Open
Abstract
In recent years, non-toxic quantum dot has caught the attention of biomedical fields. However, the inherent cytotoxicity of QDs makes its biomedical application painful, and is a major drawback of this method. In this paper, a non-toxic and water-soluble quantum dot AgInZnS-GO using graphene oxide was synthesized. A simple model of state complex was also established, which is produced through a combination of quantum dots and protein. The interaction between AIZS-GO QDs and human serum albumin (HSA) has significant meaning in vivo biological application. Herein, the binding of AIZS-GO QDs and HSA were researched using fluorescence spectra, Uv-visible absorption spectra, FT-IR spectra, and circular dichroism (CD) spectra. The results of fluorescence spectra demonstrate that AIZS-GO QDs have an obvious fluorescence quenching effect on HSA. The quenching mechanism is static quenching, which implies that some type of complex was produced by the binding of QDs and HSA. These results were further proved by Uv-visible absorption spectroscopy. The Stern-Volmer quenching constant Ksv at various temperatures (298 K, 303 K, 308 K) were acquired from analyzing Stern-Volmer plots of the fluorescence quenching information. The Van't Hoff equation could describe the thermodynamic parameters, which demonstrated that the van der Waals and hydrogen bonds had an essential effect on the interaction. FT-IR spectra and CD spectra further indicate that AIZS-GO QDs can alter the structure of HSA. These spectral methods show that the quantum dot can combine well with HSA. The experimental results showed that AgInZn-GO water-soluble quantum dots have good biocompatibility, which can be combined with proteins to form new compounds which have no cytotoxicity and biological practicability. It provides an important basis for the combination of quantum dots and specific proteins as well as fluorescent labeling.
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Affiliation(s)
- Chi Song
- Department of Life Science and Technology, Changshu Institute of Technology, Changshu, China
| | - Haoyue Luo
- Key Laboratory of Optoelectronic Technology and Systems of Ministry of Education of China, Chongqing University, Chongqing, China
| | - Xiaogang Lin
- Key Laboratory of Optoelectronic Technology and Systems of Ministry of Education of China, Chongqing University, Chongqing, China
| | - Zhijia Peng
- Key Laboratory of Optoelectronic Technology and Systems of Ministry of Education of China, Chongqing University, Chongqing, China
| | - Lingdong Weng
- Key Laboratory of Optoelectronic Technology and Systems of Ministry of Education of China, Chongqing University, Chongqing, China
| | - Xiaosheng Tang
- Key Laboratory of Optoelectronic Technology and Systems of Ministry of Education of China, Chongqing University, Chongqing, China
| | - Shibin Xu
- Key Laboratory of Optoelectronic Technology and Systems of Ministry of Education of China, Chongqing University, Chongqing, China
| | - Ming Song
- Key Laboratory of Optoelectronic Technology and Systems of Ministry of Education of China, Chongqing University, Chongqing, China
| | - Lifeng Jin
- Key Laboratory of Optoelectronic Technology and Systems of Ministry of Education of China, Chongqing University, Chongqing, China
| | - Xiaodong Zheng
- Chongqing University Cancer Hospital, Chongqing University, Chongqing, China
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Li J, Wang J, Fan J, Huang G, Yan L. Binding characteristics of aflatoxin B 1 with free DNA in vitro. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 230:118054. [PMID: 32006841 DOI: 10.1016/j.saa.2020.118054] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Revised: 01/07/2020] [Accepted: 01/09/2020] [Indexed: 06/10/2023]
Abstract
In this paper, the binding characteristics of aflatoxin B1 (AFB1) with the herring sperm deoxyribonucleic acid (DNA) in vitro were investigated through different analytical methods. The ultraviolet-visible spectroscopy (UV-vis), fluorescence, and circular dichroism (CD) spectra results showed that a new AFB1-DNA complex was formed. All the results suggested that AFB1 interacted with free DNA in vitro in an intercalating binding mode. The results of the DNA melting experiments also showed that the melting temperature of DNA increased by about 12.1 °C due to the addition of AFB1, which was supposed to be closely related to the intercalation of AFB1 into DNA. The agar gel electrophoresis experiments further confirmed that the binding mode of AFB1 and free DNA in vitro was indeed intercalation. In addition, the fluorescence quenching induced by adding AFB1 to the ethidium bromide-DNA (EB-DNA) mixture indicated the presence of competitive non-covalent intercalating binding interaction with a competitive binding constant of 5.58 L/mol between AFB1, EB, and DNA. The thermodynamic data demonstrated that the main driving forces of the binding reaction were van der Waals forces and hydrogen bond. The resonance light scattering (RLS) assay results showed that the DNA binding saturation values of AFB1, EB, psoralen (PSO), and angelicin (ANG) were 2.14, 15.59, 0.74, and 0.74, respectively. These results indicated that the DNA binding capacity of AFB1 was weaker than that of EB, but stronger than those of PSO and ANG.
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Affiliation(s)
- Junsheng Li
- Guangxi Key Laboratory of Green Processing of Sugar Resources, Guangxi University of Science and Technology, Donghuan Road 268, Liuzhou 545006, Guangxi, PR China.
| | - Jingting Wang
- Guangxi Key Laboratory of Green Processing of Sugar Resources, Guangxi University of Science and Technology, Donghuan Road 268, Liuzhou 545006, Guangxi, PR China
| | - Junfu Fan
- Guangxi Key Laboratory of Green Processing of Sugar Resources, Guangxi University of Science and Technology, Donghuan Road 268, Liuzhou 545006, Guangxi, PR China
| | - Guoxia Huang
- Guangxi Key Laboratory of Green Processing of Sugar Resources, Guangxi University of Science and Technology, Donghuan Road 268, Liuzhou 545006, Guangxi, PR China
| | - Liujuan Yan
- Guangxi Key Laboratory of Green Processing of Sugar Resources, Guangxi University of Science and Technology, Donghuan Road 268, Liuzhou 545006, Guangxi, PR China
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Wang Z, Tang SF, Hou X. Glutathione peroxidase 6 from Arabidopsis thaliana as potential biomarker for plants exposure assessment to di-(2-ethylhexyl) phthalate. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 229:117955. [PMID: 31887676 DOI: 10.1016/j.saa.2019.117955] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2019] [Revised: 12/11/2019] [Accepted: 12/12/2019] [Indexed: 06/10/2023]
Abstract
As a most abundant plasticizer, Di-(2-ethylhexyl) phthalate (DEHP) has been widely used in agriculture with an associated potential toxicity to many species including plants via the production of the excessive reactive oxygen species (ROS). However, the potential toxic mechanisms of the plasticizer DEHP-induced oxidative damage to plants remain unknown. The antioxidant enzyme glutathione peroxidase has been suggested as biomarkers to reflect over excessive oxidative stress. In this study, the effect of DEHP on AtGPX6 was evaluated by multi-spectroscopic techniques and molecular docking method. The fluorescence intensity of AtGPX6 was reduced by the static quenching mechanism upon the addition of DEHP. The predominant forces in complex formation was mainly impelled by hydrogen bonding and Van der Waals forces based on the negative ΔH and ΔS, which was in accordance with the molecular docking results. In addition, the secondary structural changes resulted from the complex formation were investigated in presence of different amounts of DEHP by the combination of fluorescence, UV-vis absorption and Circular dichroism spectra, which revealed the loosening and unfolding of the framework of AtGPX6 accompanied with the enhancement of the hydrophilicity around the tryptophan residues. The exploration of the interaction mechanism of DEHP with AtGPX6 at molecular level would help to evaluate the toxicity of the plasticizers and forecast the related adverse effects on plants.
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Affiliation(s)
- Zhong Wang
- Shandong Province Key Laboratory of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, China
| | - Si-Fu Tang
- College of Chemistry and Pharmaceutical Sciences, Qingdao Agricultural University, Qingdao 266109, China
| | - Xiaomin Hou
- Shandong Province Key Laboratory of Applied Mycology, College of Life Sciences, Qingdao Agricultural University, Qingdao 266109, China.
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Huang S, Li H, Luo H, Yang L, Zhou Z, Xiao Q, Liu Y. Conformational structure variation of human serum albumin after binding interaction with black phosphorus quantum dots. Int J Biol Macromol 2020; 146:405-414. [DOI: 10.1016/j.ijbiomac.2020.01.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Revised: 12/31/2019] [Accepted: 01/01/2020] [Indexed: 01/02/2023]
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