1
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Wei X, Huang W, Han Y, Chen L, Wang Y, Yu S, Yang F. Allosteric mechanism of synergistic effect in α- and β-amylase mixtures. Int J Biol Macromol 2024; 280:135653. [PMID: 39278430 DOI: 10.1016/j.ijbiomac.2024.135653] [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: 07/08/2024] [Revised: 09/12/2024] [Accepted: 09/12/2024] [Indexed: 09/18/2024]
Abstract
Alpha-amylase and beta-amylase coexist as mixtures in industrial production, and the two amylases have active synergistic effects when they approach each other. These effects are due to enhanced enzyme binding affinity for the substrate and the rate of particle hydrolysis. Here, we report the allosteric mechanism of this synergistic effect in α- and β-amylase mixtures. The assay showed higher activity after mixing α- and β-amylase. Molecular docking showed that α- and β-amylase create a stable dual-enzyme complex with high binding energy, and that complex formation does not affect the exposure of respective active sites. β-Amylase is specifically bound to the B domain of α-amylase, and the dynamic plasticity of the B domain makes it move spatially, and this adjustment leads to a more open conformation in the active site of α-amylase. Because the enzymes binding make the complex more stable, the degree to which the relative activity of the dual-enzyme complex is inhibited is significantly reduced. After enzyme hydrolysis, the products maltose and glucose accumulate and produce competitive inhibition, which explains the relative activity decrease of the later-stage dual-enzyme cooperation. Structural characterization by FT-IR and CD spectroscopy did not reveal significant changes in respective secondary structures after enzyme binding.
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Affiliation(s)
- Xinfei Wei
- Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Wanqiu Huang
- Kweichow Moutai Group, Renhuai, Guizhou 564501, China; Guizhou Key Laboratory of Microbial Resources Exploration in Fermentation Industry, Kweichow Moutai Group, Zunyi 564501, China
| | - Ying Han
- Kweichow Moutai Group, Renhuai, Guizhou 564501, China; Guizhou Key Laboratory of Microbial Resources Exploration in Fermentation Industry, Kweichow Moutai Group, Zunyi 564501, China
| | - Liangqiang Chen
- Kweichow Moutai Group, Renhuai, Guizhou 564501, China; Guizhou Key Laboratory of Microbial Resources Exploration in Fermentation Industry, Kweichow Moutai Group, Zunyi 564501, China
| | - Yanlin Wang
- Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Shaoning Yu
- Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China.
| | - Fan Yang
- Kweichow Moutai Group, Renhuai, Guizhou 564501, China; Guizhou Key Laboratory of Microbial Resources Exploration in Fermentation Industry, Kweichow Moutai Group, Zunyi 564501, China.
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2
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Bhattacharya S, Page A, Shinde P. Capecitabine loaded potato starch-chitosan nanoparticles: A novel approach for targeted therapy and improved outcomes in aggressive colon cancer. Eur J Pharm Biopharm 2024; 200:114328. [PMID: 38763329 DOI: 10.1016/j.ejpb.2024.114328] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Revised: 05/08/2024] [Accepted: 05/14/2024] [Indexed: 05/21/2024]
Abstract
Aggressive colon cancer treatment poses significant challenges. This study investigates the potential of innovative carbohydrate-based nanoparticles for targeted Capecitabine (CTB) delivery. CTB nanoparticles were synthesized by conjugating CTB with potato starch and chitosan using ultrasonication, hydrolysis, and ionotropic gelation. Characterization included drug loading, rheology, Surface-Enhanced Raman Spectroscopy (SERS), Fourier-Transform Infrared Spectroscopy (FTIR), Differential Scanning Calorimetry (DSC), X-ray Diffraction (XRD), and Thermogravimetric Analysis (TGA). In vitro and in vivo antitumor activity was evaluated using HT-29 cells and N, N-dimethylhydrazine-induced Balb/c mice, respectively. Cellular assays assessed angiogenesis, migration, proliferation, and apoptosis. Nanoparticles exhibited a mean size of 245 nm, positive zeta potential (+30 mV), high loading efficacy (76 %), and sustained drug release (92 % over 100 h). CTB-loaded nanoparticles displayed superior colon histology, reduced tumour scores, and inhibited VEGD and CD31 expression compared to free CTB. Cellular assays confirmed significant antitumor effects, including reduced tube formation, migration, and proliferation, and increased apoptosis. This study demonstrates the promise of CTB-loaded potato starch-chitosan nanoparticles for aggressive colon cancer treatment. These findings highlight the potential of these nanoparticles for further evaluation in diverse cancer models.
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Affiliation(s)
- Sankha Bhattacharya
- Department of Pharmaceutics, School of Pharmacy & Technology Management, SVKM'S NMIMS Deemed-to-be University, Shirpur, Maharashtra 425405, India.
| | - Amit Page
- Department of Pharmaceutics, School of Pharmacy & Technology Management, SVKM'S NMIMS Deemed-to-be University, Shirpur, Maharashtra 425405, India
| | - Prafull Shinde
- Shobhaben Pratapbhai Patel School of Pharmacy & Technology Management, NMIMS Deemed-to-be-University, India
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3
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Huang Y, Zhang T, Hu H, Duan X, Wu K, Chai X, He D. Trans-cinnamaldehyde fumigation inhibits Escherichia coli by affecting the mechanism of intracellular biological macromolecules. Nat Prod Res 2024:1-12. [PMID: 38516726 DOI: 10.1080/14786419.2024.2331611] [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: 08/08/2023] [Accepted: 03/10/2024] [Indexed: 03/23/2024]
Abstract
This study aimed to determine the antibacterial mechanism of cinnamaldehyde fumigation in Escherichia coli (E. coli). Through vapour fumigation, cinnamaldehyde was confirmed to exhibit effective antibacterial activity against E. coli. The minimum inhibitory concentration (MIC) and minimum bacterial concentration (MBC) were 0.25 μL/mL and 0.5 μL/mL, respectively. Based on transmission electron microscopy, the wrinkled bacterial cells observed after fumigation could be related to the leakage of intracellular substances. Laser tweezers Raman spectroscopy revealed changes in the main chain of proteins, the hydrogen bond system and spatial structure, and single- and double-stranded DNA breaks. In addition, breakage of the fatty acyl chain backbone was found to affect the vertical order degree of the lipid bilayer and cell membrane fluidity, thereby inhibiting the growth of E. coli. Overall, our findings indicate that cinnamaldehyde fumigation inhibits E. coli growth by inducing changes in intracellular biological macromolecules.
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Affiliation(s)
- Yuqiang Huang
- Department of Food Science and Engineering, Faculty of Chemical Engineering and Light Industry, Guangdong University of Technology, Guangzhou, China
| | - Tong Zhang
- Department of Food Science and Engineering, Faculty of Chemical Engineering and Light Industry, Guangdong University of Technology, Guangzhou, China
| | - Huiying Hu
- Department of Food Science and Engineering, Faculty of Chemical Engineering and Light Industry, Guangdong University of Technology, Guangzhou, China
| | - Xuejuan Duan
- Department of Food Science and Engineering, Faculty of Chemical Engineering and Light Industry, Guangdong University of Technology, Guangzhou, China
| | - Kegang Wu
- Department of Food Science and Engineering, Faculty of Chemical Engineering and Light Industry, Guangdong University of Technology, Guangzhou, China
| | - Xianghua Chai
- Department of Food Science and Engineering, Faculty of Chemical Engineering and Light Industry, Guangdong University of Technology, Guangzhou, China
| | - Dong He
- Department of Food Science and Engineering, Faculty of Chemical Engineering and Light Industry, Guangdong University of Technology, Guangzhou, China
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4
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Shen H, Fu C, Zhang J, Feng B, Yu S. Protocol for determining protein dynamics using FT-IR spectroscopy. STAR Protoc 2023; 4:102587. [PMID: 38043057 PMCID: PMC10701451 DOI: 10.1016/j.xpro.2023.102587] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 07/05/2023] [Accepted: 08/31/2023] [Indexed: 12/05/2023] Open
Abstract
In biological systems, protein function depends on spatial and temporal changes known as protein dynamics, which can be probed by amide hydrogen/deuterium (H/D) exchange. Here, we present a protocol for determining protein dynamics by Fourier-transform infrared (FT-IR) spectroscopy. We describe steps for protein sample preparation and FT-IR spectra collection. We then detail procedures for spectra analysis. Applications include the effects of protein mutation or protein and metal ion or ligand interactions on the protein H/D exchange rate. For complete details on the use and execution of this protocol, please refer to Yu et al. (2013).1.
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Affiliation(s)
- Hao Shen
- Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China; State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, China
| | - Cuiping Fu
- Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Junting Zhang
- Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Bin Feng
- Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China; State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, China.
| | - Shaoning Yu
- Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China; State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ningbo University, Ningbo, 315211, China.
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5
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Zhang J, Zhou F, Liang X, Yang G. SCAMPER: Accurate Type-Specific Prediction of Calcium-Binding Residues Using Sequence-Derived Features. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2023; 20:1406-1416. [PMID: 35536812 DOI: 10.1109/tcbb.2022.3173437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Understanding molecular mechanisms involved in calcium-protein interactions and modeling corresponding docking rely on the accurate identification of calcium-binding residues (CaBRs). The defects of experimentally annotating protein functions enhances the development of computational approaches that correctly identify calcium-binding interactions. Studies have reported that current methods severely cross-predict residues that interact with other types of molecules (e.g., nucleic acids, proteins, and small ligands) as CaBRs. In this study, a novel predictor named SCAMPER (Selective CAlciuM-binding PrEdictoR) is proposed for the accurate and specific prediction of CaBRs. SCAMPER is designed using newly compiled dataset with complete UniProt sequences and annotations, which include calcium-binding, nucleic acid-binding, protein-binding, and small ligand-binding residues. We use a novel designed two-layer scheme to perform predictions as well as penalize cross-predictions. Empirical tests on an independent test dataset reveals that the proposed method significantly outperforms state-of-the-art predictors. SCAMPER is proved to be capable of distinguishing CaBRs from different types of metal-ion binding residues. We further perform CaBRs predictions on the whole human proteome, and use the results to hypothesize calcium-binding proteins (CaBPs). The latest experimental verified CaBPs and GO analysis prove the accuracy of our predictions. We implement the proposed method and share the data at http://www.inforstation.com/webservers/SCAMPER/.
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6
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Stewart AM, Shanmugam M, Kutta RJ, Scrutton NS, Lovett JE, Hay S. Combined Pulsed Electron Double Resonance EPR and Molecular Dynamics Investigations of Calmodulin Suggest Effects of Crowding Agents on Protein Structures. Biochemistry 2022; 61:1735-1742. [PMID: 35979922 PMCID: PMC9454100 DOI: 10.1021/acs.biochem.2c00099] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
![]()
Calmodulin (CaM) is a highly dynamic Ca2+-binding
protein
that exhibits large conformational changes upon binding Ca2+ and target proteins. Although it is accepted that CaM exists in
an equilibrium of conformational states in the absence of target protein,
the physiological relevance of an elongated helical linker region
in the Ca2+-replete form has been highly debated. In this
study, we use PELDOR (pulsed electron–electron double resonance)
EPR measurements of a doubly spin-labeled CaM variant to assess the
conformational states of CaM in the apo-, Ca2+-bound, and
Ca2+ plus target peptide-bound states. Our findings are
consistent with a three-state conformational model of CaM, showing
a semi-open apo-state, a highly extended Ca2+-replete state,
and a compact target protein-bound state. Molecular dynamics simulations
suggest that the presence of glycerol, and potentially other molecular
crowding agents, has a profound effect on the relative stability of
the different conformational states. Differing experimental conditions
may explain the discrepancies in the literature regarding the observed
conformational state(s) of CaM, and our PELDOR measurements show good
evidence for an extended conformation of Ca2+-replete CaM
similar to the one observed in early X-ray crystal structures.
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Affiliation(s)
- Andrew M Stewart
- The Roy J. Carver Department of Biochemistry, Biophysics and Molecular Biology, Iowa State University, Ames 50011, Iowa, United States.,Manchester Institute of Biotechnology and Department of Chemistry, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| | - Muralidharan Shanmugam
- Manchester Institute of Biotechnology and Department of Chemistry, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| | - Roger J Kutta
- Manchester Institute of Biotechnology and Department of Chemistry, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K.,Institute of Physical and Theoretical Chemistry, University of Regensburg, Regensburg 93040, Germany
| | - Nigel S Scrutton
- Manchester Institute of Biotechnology and Department of Chemistry, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| | - Janet E Lovett
- SUPA School of Physics and Astronomy and BSRC, The University of St Andrews, St Andrews KY16 9SS, U.K
| | - Sam Hay
- Manchester Institute of Biotechnology and Department of Chemistry, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
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7
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Structural and functional properties of soluble Antarctic krill proteins covalently modified by rutin. Food Chem 2022; 379:132159. [DOI: 10.1016/j.foodchem.2022.132159] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Revised: 01/10/2022] [Accepted: 01/12/2022] [Indexed: 12/31/2022]
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8
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Yang S, Zhang Q, Yang H, Shi H, Dong A, Wang L, Yu S. Progress in infrared spectroscopy as an efficient tool for predicting protein secondary structure. Int J Biol Macromol 2022; 206:175-187. [PMID: 35217087 DOI: 10.1016/j.ijbiomac.2022.02.104] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 02/14/2022] [Accepted: 02/17/2022] [Indexed: 12/21/2022]
Abstract
Infrared (IR) spectroscopy is a highly sensitive technique that provides complete information on chemical compositions. The IR spectra of proteins or peptides give rise to nine characteristic IR absorption bands. The amide I bands are the most prominent and sensitive vibrational bands and widely used to predict protein secondary structures. The interference of H2O absorbance is the greatest challenge for IR protein secondary structure prediction. Much effort has been made to reduce/eliminate the interference of H2O, simplify operation steps, and increase prediction accuracy. Progress in sampling and equipment has rendered the Fourier transform infrared (FTIR) technique suitable for determining the protein secondary structure in broader concentration ranges, greatly simplifying the operating steps. This review highlights the recent progress in sample preparation, data analysis, and equipment development of FTIR in A/T mode, with a focus on recent applications of FTIR spectroscopy in the prediction of protein secondary structure. This review also provides a brief introduction of the progress in ATR-FTIR for predicting protein secondary structure and discusses some combined IR methods, such as AFM-based IR spectroscopy, that are used to analyze protein structural dynamics and protein aggregation.
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Affiliation(s)
- Shouning Yang
- Zhejiang Provincial Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China
| | | | - Huayan Yang
- Zhejiang Provincial Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Haimei Shi
- Zhejiang Provincial Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Aichun Dong
- Department of Chemistry and Biochemistry, University of Northern Colorado, Greeley, CO, USA.
| | - Li Wang
- Kweichow Moutai Group, Renhuai, Guizhou 564501, China.
| | - Shaoning Yu
- Zhejiang Provincial Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China.
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9
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Zhang N, Zhou S, Ji HH, Li XD. Effects of the IQ1 motif of Drosophila myosin-5 on the calcium interaction of calmodulin. Cell Calcium 2022; 103:102549. [DOI: 10.1016/j.ceca.2022.102549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 01/24/2022] [Accepted: 02/02/2022] [Indexed: 11/26/2022]
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10
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Nde J, Zhang P, Ezerski JC, Lu W, Knapp K, Wolynes PG, Cheung MS. Coarse-Grained Modeling and Molecular Dynamics Simulations of Ca 2+-Calmodulin. Front Mol Biosci 2021; 8:661322. [PMID: 34504868 PMCID: PMC8421859 DOI: 10.3389/fmolb.2021.661322] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Accepted: 07/21/2021] [Indexed: 12/21/2022] Open
Abstract
Calmodulin (CaM) is a calcium-binding protein that transduces signals to downstream proteins through target binding upon calcium binding in a time-dependent manner. Understanding the target binding process that tunes CaM’s affinity for the calcium ions (Ca2+), or vice versa, may provide insight into how Ca2+-CaM selects its target binding proteins. However, modeling of Ca2+-CaM in molecular simulations is challenging because of the gross structural changes in its central linker regions while the two lobes are relatively rigid due to tight binding of the Ca2+ to the calcium-binding loops where the loop forms a pentagonal bipyramidal coordination geometry with Ca2+. This feature that underlies the reciprocal relation between Ca2+ binding and target binding of CaM, however, has yet to be considered in the structural modeling. Here, we presented a coarse-grained model based on the Associative memory, Water mediated, Structure, and Energy Model (AWSEM) protein force field, to investigate the salient features of CaM. Particularly, we optimized the force field of CaM and that of Ca2+ ions by using its coordination chemistry in the calcium-binding loops to match with experimental observations. We presented a “community model” of CaM that is capable of sampling various conformations of CaM, incorporating various calcium-binding states, and carrying the memory of binding with various targets, which sets the foundation of the reciprocal relation of target binding and Ca2+ binding in future studies.
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Affiliation(s)
- Jules Nde
- Department of Physics, University of Houston, Houston, TX, United States.,Center for Theoretical Biological Physics, Rice University, Houston, TX, United States
| | - Pengzhi Zhang
- Department of Physics, University of Houston, Houston, TX, United States
| | - Jacob C Ezerski
- Department of Physics, University of Houston, Houston, TX, United States
| | - Wei Lu
- Center for Theoretical Biological Physics, Rice University, Houston, TX, United States
| | - Kaitlin Knapp
- Center for Theoretical Biological Physics, Rice University, Houston, TX, United States
| | - Peter G Wolynes
- Center for Theoretical Biological Physics, Rice University, Houston, TX, United States
| | - Margaret S Cheung
- Department of Physics, University of Houston, Houston, TX, United States.,Center for Theoretical Biological Physics, Rice University, Houston, TX, United States
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11
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Bakhsheshi-Rad HR, Ismail AF, Aziz M, Akbari M, Hadisi Z, Omidi M, Chen X. Development of the PVA/CS nanofibers containing silk protein sericin as a wound dressing: In vitro and in vivo assessment. Int J Biol Macromol 2020; 149:513-521. [PMID: 31954780 DOI: 10.1016/j.ijbiomac.2020.01.139] [Citation(s) in RCA: 96] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 01/12/2020] [Accepted: 01/13/2020] [Indexed: 02/09/2023]
Abstract
Skin and soft tissue infections are major concerns with respect to wound repair. Recently, anti-bacterial wound dressings have been emerging as promising candidates to reduce infection, thus accelerating the wound healing process. This paper presents our work to develop and characterize poly(vinyl alcohol) (PVA)/chitosan (CS)/silk sericin (SS)/tetracycline (TCN) porous nanofibers, with diameters varying from 305 to 425 nm, both in vitro and in vivo for potential applications as wound dressings. The fabricated nanofibers possess a considerable capacity to take up water through swelling (~325-650%). Sericin addition leads to increased hydrophilicity and elongation at break while decreasing fiber diameter and mechanical strength. Moreover, fibroblasts (L929) cultured on the nanofibers with low sericin content (PVA/CS/1-2SS) displayed greater proliferation compared to those on nanofibers without sericin (PVA/CS). Nanofibers loaded with high sericin and tetracycline content significantly inhibited the growth of Escherichia coli and Staphylococcus aureus. In vivo examination revealed that PVA/CS/2SS-TCN nanofibers enhance wound healing, re-epithelialization, and collagen deposition compared to traditional gauze and nanofibers without sericin. The results of this study demonstrate that the PVA/CS/2SS-TCN nanofiber creates a promising alternative to traditional wound dressing materials.
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Affiliation(s)
- Hamid Reza Bakhsheshi-Rad
- Advanced Materials Research Center, Department of Materials Engineering, Najafabad Branch, Islamic Azad University, Najafabad, Iran; Advanced Membrane Technology Research Center (AMTEC), Universiti Teknologi Malaysia, 81310, Skudai, Johor Bahru, Johor, Malaysia.
| | - Ahmad Fauzi Ismail
- Advanced Membrane Technology Research Center (AMTEC), Universiti Teknologi Malaysia, 81310, Skudai, Johor Bahru, Johor, Malaysia
| | - Madzlan Aziz
- Advanced Membrane Technology Research Center (AMTEC), Universiti Teknologi Malaysia, 81310, Skudai, Johor Bahru, Johor, Malaysia
| | - Mohsen Akbari
- Laboratory for Innovations in MicroEngineering (LiME), Department of Mechanical Engineering, University of Victoria, Victoria, BC V8P 5C2, Canada
| | - Zhina Hadisi
- Laboratory for Innovations in MicroEngineering (LiME), Department of Mechanical Engineering, University of Victoria, Victoria, BC V8P 5C2, Canada
| | - Mahdi Omidi
- Advanced Materials Research Center, Department of Materials Engineering, Najafabad Branch, Islamic Azad University, Najafabad, Iran
| | - Xiongbiao Chen
- Department of Mechanical Engineering, College of Engineering, University of Saskatchewan, Saskatoon, SK, Canada
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12
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Trande M, Pedretti M, Bonza MC, Di Matteo A, D'Onofrio M, Dominici P, Astegno A. Cation and peptide binding properties of CML7, a calmodulin-like protein from Arabidopsis thaliana. J Inorg Biochem 2019; 199:110796. [PMID: 31419675 DOI: 10.1016/j.jinorgbio.2019.110796] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 07/26/2019] [Accepted: 07/31/2019] [Indexed: 12/12/2022]
Abstract
Plants contain a large family of so-called calmodulin-like proteins (CMLs) which differ from canonical calmodulin in that they show greater variability in sequence, length, and number of EF-hand domains. The presence of this extended CML family has raised questions regarding the role of these proteins: are they functionally redundant or do they play specific functions in physiological plant processes? To answer these questions, comprehensive biochemical and structural information on CML proteins is fundamental. Among the 50 CMLs from Arabidopsis thaliana, herein we described the ability of CML7 to bind metal ions focusing on the Ca2+ and Mg2+ sensing properties, as well as on metal-induced conformational changes. Circular dichroism and nuclear magnetic resonance (NMR) studies indicated that both Ca2+ and Mg2+ stabilize CML7, as reflected in conformational rearrangements in secondary and tertiary structure and in increases in thermal stability of the protein. However, the conformational changes that binding induces differ between the two metal ions, and only Ca2+ binding controls a structural transition that leads to hydrophobic exposure, as suggested by 8-anilino-1-naphthalenesulfonic acid fluorescence. Isothermal titration calorimetry data coupled with NMR experiments revealed the presence of two high affinity Ca2+-binding sites in the C-lobe of CML7 and two weaker sites in the N-lobe. The paired nature of these CML7 EF-hands enables them to bind Ca2+ with positive cooperativity within each globular domain. Our results clearly place CML7 in the category of Ca2+ sensors. Along with this, the protein can bind to a model target peptide (melittin) in a Ca2+-dependent manner.
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Affiliation(s)
- Matteo Trande
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy
| | - Marco Pedretti
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy
| | - Maria Cristina Bonza
- Department of Biosciences, University of Milano, Via Celoria 26, 20133 Milano, Italy
| | - Adele Di Matteo
- Institute of Molecular Biology and Pathology, CNR, Piazzale Aldo Moro 5, Roma 00185, Italy
| | - Mariapina D'Onofrio
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy
| | - Paola Dominici
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy
| | - Alessandra Astegno
- Department of Biotechnology, University of Verona, Strada Le Grazie 15, 37134 Verona, Italy.
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13
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Wei CC, Fabry E, Hay E, Lloyd L, Kaufman N, Yang YP, Stuehr DJ. Metal binding and conformational studies of the calcium binding domain of NADPH oxidase 5 reveal its similarity and difference to calmodulin. J Biomol Struct Dyn 2019; 38:2352-2368. [DOI: 10.1080/07391102.2019.1633409] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Chin-Chuan Wei
- Department of Chemistry, Southern Illinois University Edwardsville, Edwardsville, Illinois, USA
| | - Emily Fabry
- Department of Chemistry, Southern Illinois University Edwardsville, Edwardsville, Illinois, USA
| | - Evan Hay
- Department of Chemistry, Southern Illinois University Edwardsville, Edwardsville, Illinois, USA
| | - Laura Lloyd
- Department of Chemistry, Southern Illinois University Edwardsville, Edwardsville, Illinois, USA
| | - Nichole Kaufman
- Department of Chemistry, Southern Illinois University Edwardsville, Edwardsville, Illinois, USA
| | - Ya-Ping Yang
- Department of Pathobiology, the Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, Ohio, USA
| | - Dennis J. Stuehr
- Department of Pathobiology, the Lerner Research Institute, Cleveland Clinic Foundation, Cleveland, Ohio, USA
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14
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Zhao L, Lai L, Zhang Z. How calcium ion binding induces the conformational transition of the calmodulin N-terminal domain—an atomic level characterization. Phys Chem Chem Phys 2019; 21:19795-19804. [DOI: 10.1039/c9cp03917a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The Ca2+binding and triggering conformation transition of nCaM were detected in unbiased molecular dynamics simulations.
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Affiliation(s)
- Likun Zhao
- College of Life Science
- University of Chinese Academy of Sciences
- Beijing
- China
| | - Luhua Lai
- BNLMS, and Peking-Tsinghua Center for Life Sciences at the College of Chemistry and Molecular Engineering
- Peking University
- Beijing
- China
- Center for Quantitative Biology
| | - Zhuqing Zhang
- College of Life Science
- University of Chinese Academy of Sciences
- Beijing
- China
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15
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Lin L, Liu C, Nayak BC, He W, You M, Yuchi Z. A two-step purification strategy using calmodulin as an affinity tag. J Chromatogr A 2018; 1544:16-22. [PMID: 29499842 DOI: 10.1016/j.chroma.2018.02.045] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Revised: 02/01/2018] [Accepted: 02/21/2018] [Indexed: 11/19/2022]
Abstract
Calmodulin (CaM) is a Ca2+-binding protein that plays an important role in cellular Ca2+-signaling. CaM interacts with diverse downstream target proteins and regulates their functions in a Ca2+-dependent manner. CaM changes its conformation and hydrophobicity upon [Ca2+] change and consequently changes its interaction with CaM-binding domains from the targets. Based on these special properties of CaM, it was used as an affinity tag to develop a novel purification strategy by using it for two sequential orthogonal purification steps: 1) an affinity purification step, in which CaM-tag interacts with an immobilized CaM-binding domain; and 2) a hydrophobic interaction chromatography step, during which CaM binds to a phenyl sepharose column. In both steps, the CaM-tagged protein binds in the presence of Ca2+ and unbinds in the presence of ethylenediaminetetraacetic acid (EDTA). An optional third step can be added to remove the CaM-tag if necessary. We used green fluorescent protein (GFP) as a test protein to demonstrate the effectiveness of the method. High yield and high purity of GFP with proper function was obtained using this novel strategy. We believe that this method can be applied to a wide range of protein targets for structural and functional studies.
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Affiliation(s)
- Lianyun Lin
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China; Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, 350002, China; Fujian-Taiwan Joint Centre for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Chen Liu
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China
| | - Bidhan Chandra Nayak
- Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China
| | - Weiyi He
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, 350002, China; Fujian-Taiwan Joint Centre for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Minsheng You
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; Joint International Research Laboratory of Ecological Pest Control, Ministry of Education, Fuzhou, 350002, China; Fujian-Taiwan Joint Centre for Ecological Control of Crop Pests, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| | - Zhiguang Yuchi
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Institute of Applied Ecology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China; Tianjin Key Laboratory for Modern Drug Delivery & High-Efficiency, Collaborative Innovation Center of Chemical Science and Engineering, School of Pharmaceutical Science and Technology, Tianjin University, Tianjin, 300072, China.
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16
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Zhang J, Zhang X, Zhang F, Yu S. Solid-film sampling method for the determination of protein secondary structure by Fourier transform infrared spectroscopy. Anal Bioanal Chem 2017; 409:4459-4465. [PMID: 28526999 DOI: 10.1007/s00216-017-0390-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Revised: 04/23/2017] [Accepted: 05/02/2017] [Indexed: 10/19/2022]
Abstract
Fourier transform infrared (FTIR) spectroscopy is one of the widely used vibrational spectroscopic methods in protein structural analysis. The protein solution sample loaded in demountable CaF2 liquid cell presents a challenge and is limited to high concentrations. Some researchers attempted the simpler solid-film sampling method for the collection of protein FTIR spectra. In this study, the solid-film sampling FTIR method was studied in detail. The secondary structure components of some globular proteins were determined by this sampling method, and the results were consistent with those data determined by the traditional solution sampling FTIR method and X-ray crystallography, indicating that this sampling method is feasible and efficient for the structural characterization of proteins. Furthermore, much lower protein concentrations (~0.5 mg/mL) were needed to obtain high-quality FTIR spectra, which expands the application of FTIR spectroscopy to almost the same concentration range used for circular dichroism and fluorescence spectroscopy, making comparisons among three commonly used techniques possible in protein studies. Graphical Abstract ᅟ.
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Affiliation(s)
- Junting Zhang
- Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Xiaoning Zhang
- Department of Chemistry, Fudan University, Shanghai, 200433, China
| | - Fan Zhang
- Zhejiang BioHarmonious SciTech. Co. LTD., Hangzhou, Zhejiang, 310018, China
| | - Shaoning Yu
- Department of Chemistry, Fudan University, Shanghai, 200433, China.
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17
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Lin Z, Hu R, Zhou J, Ye Y, Xu Z, Lin C. A further insight into the adsorption mechanism of protein on hydroxyapatite by FTIR-ATR spectrometry. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2017; 173:527-531. [PMID: 27744063 DOI: 10.1016/j.saa.2016.09.050] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Revised: 08/24/2016] [Accepted: 09/26/2016] [Indexed: 06/06/2023]
Abstract
The adsorption mechanism of bovine serum albumin (BSA) on hydroxyapatite (HA) for different time intervals has been studied by Fourier transform infrared (FTIR)-attenuated total internal reflectance (ATR) spectrometry in this paper. The difference spectra obtained in HA and BSA frequency regions demonstrate that the binding of PO, from the phosphate (PO43-) of HA, to the hydrogen of methyl (-CH3), methene (-CH2) and amideII (-CNH) in the protein appears to be much faster and stronger than that of the PO group. In addition, Ca2+ must serve as a key role in the interaction of BSA with HA. The binding of Ca2+ to the oxygen of the peptide bond seems to induce a significant reconformation of polypeptide backbones from β-pleated sheet to α-helix and β-turn of helical circles. This alteration seems to have been accompanied by much hydrogen of polypeptides driven to bind PO43- and OH- of the HA actively and much -C=O and HN groups of the peptide bond freed from inter-chain hydrogen bonding to react on Ca2+ and combine strongly with the HA surface. This might be well expected to promote the HA biomineralization.
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Affiliation(s)
- Zhongyu Lin
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, PR China.
| | - Ren Hu
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, PR China
| | - Jianzhang Zhou
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, PR China
| | - Yiwen Ye
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, PR China
| | - Zhaoxi Xu
- Xiamen A ER TE System Engineering CO., LTD, Xiamen 361005, PR China
| | - Changjian Lin
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 361005, PR China
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18
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Makiyama RK, Fernandes CAH, Dreyer TR, Moda BS, Matioli FF, Fontes MRM, Maia IG. Structural and thermodynamic studies of the tobacco calmodulin-like rgs-CaM protein. Int J Biol Macromol 2016; 92:1288-1297. [PMID: 27514444 DOI: 10.1016/j.ijbiomac.2016.08.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 07/08/2016] [Accepted: 08/07/2016] [Indexed: 11/23/2022]
Abstract
The tobacco calmodulin-like protein rgs-CaM is involved in host defense against virus and is reported to possess an associated RNA silencing suppressor activity. Rgs-CaM is also believed to act as an antiviral factor by interacting and targeting viral silencing suppressors for autophagic degradation. Despite these functional data, calcium interplay in the modulation of rgs-CaM is still poorly understood. Here we show that rgs-CaM displays a prevalent alpha-helical conformation and possesses three functional Ca2+-binding sites. Using computational modeling and molecular dynamics simulation, we demonstrate that Ca2+ binding to rgs-CaM triggers expansion of its tertiary structure with reorientation of alpha-helices within the EF-hands. This conformational change leads to the exposure of a large negatively charged region that may be implicated in the electrostatic interactions between rgs-CaM and viral suppressors. Moreover, the kd values obtained for Ca2+ binding to the three functional sites are not within the affinity range of a typical Ca2+ sensor.
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Affiliation(s)
- Rodrigo K Makiyama
- Universidade Estadual Paulista (UNESP), Instituto de Biociências, Departamento de Genética, Botucatu, SP, Brazil
| | - Carlos A H Fernandes
- Universidade Estadual Paulista (UNESP), Instituto de Biociências, Departamento de Física e Biofísica, Botucatu, SP, Brazil
| | - Thiago R Dreyer
- Universidade Estadual Paulista (UNESP), Instituto de Biociências, Departamento de Física e Biofísica, Botucatu, SP, Brazil
| | - Bruno S Moda
- Universidade Estadual Paulista (UNESP), Instituto de Biociências, Departamento de Genética, Botucatu, SP, Brazil
| | - Fabio F Matioli
- Universidade Estadual Paulista (UNESP), Instituto de Biociências, Departamento de Física e Biofísica, Botucatu, SP, Brazil
| | - Marcos R M Fontes
- Universidade Estadual Paulista (UNESP), Instituto de Biociências, Departamento de Física e Biofísica, Botucatu, SP, Brazil
| | - Ivan G Maia
- Universidade Estadual Paulista (UNESP), Instituto de Biociências, Departamento de Genética, Botucatu, SP, Brazil.
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19
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Calmodulin in complex with the first IQ motif of myosin-5a functions as an intact calcium sensor. Proc Natl Acad Sci U S A 2016; 113:E5812-E5820. [PMID: 27647889 DOI: 10.1073/pnas.1607702113] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The motor function of vertebrate myosin-5a is inhibited by its tail in a Ca2+-dependent manner. We previously demonstrated that the calmodulin (CaM) bound to the first isoleucine-glutamine (IQ) motif (IQ1) of myosin-5a is responsible for the Ca2+-dependent regulation of myosin-5a. We have solved the crystal structure of a truncated myosin-5a containing the motor domain and IQ1 (MD-IQ1) complexed with Ca2+-bound CaM (Ca2+-CaM) at 2.5-Å resolution. Compared with the structure of the MD-IQ1 complexed with essential light chain (an equivalent of apo-CaM), MD-IQ1/Ca2+-CaM displays large conformational differences in IQ1/CaM and little difference in the motor domain. In the MD-IQ1/Ca2+-CaM structure, the N-lobe and the C-lobe of Ca2+-CaM adopt an open conformation and grip the C-terminal and the N-terminal portions of the IQ1, respectively. Remarkably, the interlobe linker of CaM in IQ1/Ca2+-CaM is in a position opposite that in IQ1/apo-CaM, suggesting that CaM flip-flops relative to the IQ1 during the Ca2+ transition. We demonstrated that CaM continuously associates with the IQ1 during the Ca2+ transition and that the binding of CaM to IQ1 increases Ca2+ affinity and substantially changes the kinetics of the Ca2+ transition, suggesting that the IQ1/CaM complex functions as an intact Ca2+ sensor responding to distinct calcium signals.
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20
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Astegno A, La Verde V, Marino V, Dell'Orco D, Dominici P. Biochemical and biophysical characterization of a plant calmodulin: Role of the N- and C-lobes in calcium binding, conformational change, and target interaction. BIOCHIMICA ET BIOPHYSICA ACTA 2016; 1864:297-307. [PMID: 26708477 DOI: 10.1016/j.bbapap.2015.12.003] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Revised: 11/29/2015] [Accepted: 12/09/2015] [Indexed: 12/22/2022]
Abstract
In plants, transient elevation of intracellular Ca(2+) concentration in response to abiotic stress is responsible for glutamate decarboxylase (GAD) activation via association with calmodulin (CaM), an EF-hand protein consisting of two homologous domains (N and C). An unusual 1:2 binding mode of CaM to CaM-binding domains of GAD has long been known, however the contribution of the two CaM domains in target recognition and activation remains to be clarified. Here, we explored the coupling between physicochemical properties of Arabidopsis CaM1 (AtCaM1) and Arabidopsis GAD1 activation, focusing on each AtCaM1 lobe. We found that the four EF-loops of AtCaM1 differently contribute to the ~20 μM apparent affinity for Ca(2+) and the C-lobe shows a ~6-fold higher affinity than N-lobe (Kd(app) 5.6 μM and 32 μM for C- and N-lobes, respectively). AtCaM1 responds structurally to Ca(2+) in a manner similar to vertebrate CaM based on comparison of Ca(2+)-induced changes in hydrophobicity exposure, secondary structure, and hydrodynamic behavior. Molecular dynamics simulations of AtCaM1 apo and Ca(2+)-bound reveal that the latter state is significantly less flexible, although regions of the N-lobe remain quite flexible; this suggests the importance of N-lobe for completing the transition to the extended structure of holoprotein, consistent with data from ANS fluorescence, CD spectroscopy, and SEC analysis. Moreover, enzymatic analysis reveal that mutations in the two lobes affect GAD1 activation in similar ways and only intact AtCaM1 can fully activate GAD1. Taken together, our data provide new insights into the CaM lobes role in interactions between CaM and plant GAD.
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Affiliation(s)
| | | | - Valerio Marino
- Department of Neurological, Biomedical and Movement Sciences, University of Verona, Verona, Italy
| | - Daniele Dell'Orco
- Department of Neurological, Biomedical and Movement Sciences, University of Verona, Verona, Italy
| | - Paola Dominici
- Department of Biotechnology, University of Verona, Verona, Italy
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21
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Thermodynamics of Calcium binding to the Calmodulin N-terminal domain to evaluate site-specific affinity constants and cooperativity. J Biol Inorg Chem 2015; 20:905-19. [DOI: 10.1007/s00775-015-1275-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2015] [Accepted: 05/31/2015] [Indexed: 10/23/2022]
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22
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Yu Y, Wang J, Shao Q, Shi J, Zhu W. Increasing the sampling efficiency of protein conformational transition using velocity-scaling optimized hybrid explicit/implicit solvent REMD simulation. J Chem Phys 2015; 142:125105. [PMID: 25833612 DOI: 10.1063/1.4916118] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The application of temperature replica exchange molecular dynamics (REMD) simulation on protein motion is limited by its huge requirement of computational resource, particularly when explicit solvent model is implemented. In the previous study, we developed a velocity-scaling optimized hybrid explicit/implicit solvent REMD method with the hope to reduce the temperature (replica) number on the premise of maintaining high sampling efficiency. In this study, we utilized this method to characterize and energetically identify the conformational transition pathway of a protein model, the N-terminal domain of calmodulin. In comparison to the standard explicit solvent REMD simulation, the hybrid REMD is much less computationally expensive but, meanwhile, gives accurate evaluation of the structural and thermodynamic properties of the conformational transition which are in well agreement with the standard REMD simulation. Therefore, the hybrid REMD could highly increase the computational efficiency and thus expand the application of REMD simulation to larger-size protein systems.
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Affiliation(s)
- Yuqi Yu
- ACS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Jinan Wang
- ACS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Qiang Shao
- ACS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Jiye Shi
- UCB Pharma, 216 Bath Road, Slough SL1 4EN, United Kingdom
| | - Weiliang Zhu
- ACS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
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23
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Optimized orthogonal translation of unnatural amino acids enables spontaneous protein double-labelling and FRET. Nat Chem 2014; 6:393-403. [PMID: 24755590 DOI: 10.1038/nchem.1919] [Citation(s) in RCA: 203] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Accepted: 03/12/2014] [Indexed: 12/13/2022]
Abstract
The ability to introduce different biophysical probes into defined positions in target proteins will provide powerful approaches for interrogating protein structure, function and dynamics. However, methods for site-specifically incorporating multiple distinct unnatural amino acids are hampered by their low efficiency. Here we provide a general solution to this challenge by developing an optimized orthogonal translation system that uses amber and evolved quadruplet-decoding transfer RNAs to encode numerous pairs of distinct unnatural amino acids into a single protein expressed in Escherichia coli with a substantial increase in efficiency over previous methods. We also provide a general strategy for labelling pairs of encoded unnatural amino acids with different probes via rapid and spontaneous reactions under physiological conditions. We demonstrate the utility of our approach by genetically directing the labelling of several pairs of sites in calmodulin with fluorophores and probing protein structure and dynamics by Förster resonance energy transfer.
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24
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Zhao Y, Yang H, Meng K, Yu S. Probing the Ca2+/CaM-induced secondary structural and conformational changes in calcineurin. Int J Biol Macromol 2014; 64:453-7. [DOI: 10.1016/j.ijbiomac.2013.12.036] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Revised: 12/24/2013] [Accepted: 12/27/2013] [Indexed: 10/25/2022]
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25
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Wang J, Shao Q, Xu Z, Liu Y, Yang Z, Cossins BP, Jiang H, Chen K, Shi J, Zhu W. Exploring transition pathway and free-energy profile of large-scale protein conformational change by combining normal mode analysis and umbrella sampling molecular dynamics. J Phys Chem B 2013; 118:134-43. [PMID: 24350625 DOI: 10.1021/jp4105129] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Large-scale conformational changes of proteins are usually associated with the binding of ligands. Because the conformational changes are often related to the biological functions of proteins, understanding the molecular mechanisms of these motions and the effects of ligand binding becomes very necessary. In the present study, we use the combination of normal-mode analysis and umbrella sampling molecular dynamics simulation to delineate the atomically detailed conformational transition pathways and the associated free-energy landscapes for three well-known protein systems, viz., adenylate kinase (AdK), calmodulin (CaM), and p38α kinase in the absence and presence of respective ligands. For each protein under study, the transient conformations along the conformational transition pathway and thermodynamic observables are in agreement with experimentally and computationally determined ones. The calculated free-energy profiles reveal that AdK and CaM are intrinsically flexible in structures without obvious energy barrier, and their ligand binding shifts the equilibrium from the ligand-free to ligand-bound conformation (population shift mechanism). In contrast, the ligand binding to p38α leads to a large change in free-energy barrier (ΔΔG ≈ 7 kcal/mol), promoting the transition from DFG-in to DFG-out conformation (induced fit mechanism). Moreover, the effect of the protonation of D168 on the conformational change of p38α is also studied, which reduces the free-energy difference between the two functional states of p38α and thus further facilitates the conformational interconversion. Therefore, the present study suggests that the detailed mechanism of ligand binding and the associated conformational transition is not uniform for all kinds of proteins but correlated to their respective biological functions.
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Affiliation(s)
- Jinan Wang
- Drug Discovery and Design Center, CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , 555 Zuchongzhi Road, Shanghai, 201203, China
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26
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Potvin-Fournier K, Lefèvre T, Picard-Lafond A, Valois-Paillard G, Cantin L, Salesse C, Auger M. The thermal stability of recoverin depends on calcium binding and its myristoyl moiety as revealed by infrared spectroscopy. Biochemistry 2013; 53:48-56. [PMID: 24359287 DOI: 10.1021/bi401336g] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
To evaluate the structural stability of recoverin, a member of the neuronal calcium sensor family, the effect of temperature, myristoylation, and calcium:protein molar ratio on its secondary structure has been studied by transmission infrared spectroscopy. On the basis of the data, the protein predominantly adopts α-helical structures (∼50-55%) with turns, unordered structures, and β-sheets at 25 °C. The data show no significant impact of the presence of calcium and myristoylation on secondary structure. It is found that, in the absence of calcium, recoverin denatures and self-aggregates while being heated, with the formation of intermolecular antiparallel β-sheets. The nonmyristoylated protein (Rec-nMyr) exhibits a lower temperature threshold of aggregation and a higher intermolecular β-sheet content at 65 °C than the myristoylated protein (Rec-Myr). The former thus appears to be less thermally stable than the latter. In the presence of excess calcium ions (calcium:protein ratio of 10), the protein is thermally stable up to 65 °C with no significant conformational change, the presence of the myristoyl chain having no effect on the thermal stability of recoverin under these conditions. A decrease in the thermal stability of recoverin is observed as the calcium:protein molar ratio decreases, with Rec-nMyr being less stable than Rec-Myr. The data overall suggest that a minimal number of coordinated calcium ions is necessary to fully stabilize the structure of recoverin and that, when bound to the membrane, i.e., when the myristoyl chain protrudes from the interior pocket, recoverin should be more stable than in a Ca-free solution, i.e., when the myristoyl chain is sequestered in the interior.
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Affiliation(s)
- Kim Potvin-Fournier
- Département de chimie, Regroupement québécois de recherche sur la fonction, la structure et l'ingénierie des protéines (PROTEO), Centre de recherche sur les matériaux avancés (CERMA), Université Laval , Pavillon Alexandre-Vachon, 1045 avenue de la médecine, Québec, Québec G1V 0A6, Canada
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27
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Li F, Yu T, Yu S. Structural dynamic and thermodynamic analysis of calcineurin B subunit induced by calcium/magnesium binding. Int J Biol Macromol 2013; 60:122-7. [DOI: 10.1016/j.ijbiomac.2013.05.009] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2013] [Revised: 05/10/2013] [Accepted: 05/13/2013] [Indexed: 10/26/2022]
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28
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Das A, Chakrabarti J, Ghosh M. Conformational thermodynamics of metal-ion binding to a protein. Chem Phys Lett 2013. [DOI: 10.1016/j.cplett.2013.07.022] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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29
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Overestimated accuracy of circular dichroism in determining protein secondary structure. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2013; 42:455-61. [PMID: 23467783 DOI: 10.1007/s00249-013-0896-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2012] [Revised: 01/22/2013] [Accepted: 02/19/2013] [Indexed: 10/27/2022]
Abstract
Circular dichroism (CD) is a spectroscopic technique widely used for estimating protein secondary structures in aqueous solution, but its accuracy has been doubted in recent work. In the present paper, the contents of nine globular proteins with known secondary structures were determined by CD spectroscopy and Fourier transform infrared spectroscopy (FTIR) in aqueous solution. A large deviation was found between the CD spectra and X-ray data, even when the experimental conditions were optimized. The content determined by FTIR was in good agreement with the X-ray crystallography data. Therefore, CD spectra are not recommended for directly calculating the content of a protein's secondary structure.
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30
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Calcium-dependent conformational transition of calmodulin determined by Fourier transform infrared spectroscopy. Int J Biol Macromol 2013; 56:57-61. [PMID: 23403030 DOI: 10.1016/j.ijbiomac.2013.02.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2012] [Revised: 02/01/2013] [Accepted: 02/01/2013] [Indexed: 11/21/2022]
Abstract
The Ca(2+)-induced conformational changes in calmodulin (CaM) were monitored by Fourier transform infrared spectroscopy (FT-IR) at different molar ratios of Ca(2+) to CaM. The results show that these changes occur in two distinctive transitions. The first transition involves significant changes in the overall secondary structure with a small gain in solvent accessibility, and is completed after the second Ca(2+) binds to both EF-hands of its C-terminal domain. The second transition is accompanied by CaM folding into a tighter, less hydrogen-exchangeable structure, and is completed by the addition of the fourth Ca(2+) to have four Ca(2+) per molecule. Particularly, α-helices in CaM-nCa(2+)(n=0, 1, 2) are less stable than those in CaM-nCa(2+)(n=3, 4).
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31
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Nara M, Morii H, Tanokura M. Coordination to divalent cations by calcium-binding proteins studied by FTIR spectroscopy. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2012. [PMID: 23201542 DOI: 10.1016/j.bbamem.2012.11.025] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
We review the Fourier-transform infrared (FTIR) spectroscopy of side-chain COO(-) groups of Ca(2+)-binding proteins: parvalbumins, bovine calmodulin, akazara scallop troponin C and related calcium binding proteins and peptide analogues. The COO(-) stretching vibration modes can be used to identify the coordination modes of COO(-) groups of Ca(2+)-binding proteins to metal ions: bidentate, unidentate, and pseudo-bridging. FTIR spectroscopy demonstrates that the coordination structure of Mg(2+) is distinctly different from that of Ca(2+) in the Ca(2+)-binding site in solution. The interpretation of COO(-) stretches is ensured on the basis of the spectra of calcium-binding peptide analogues. The implication of COO(-) stretches is discussed for Ca(2+)-binding proteins. This article is part of a Special Issue entitled: FTIR in membrane proteins and peptide studies.
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Affiliation(s)
- Masayuki Nara
- Laboratory of Chemistry, College of Liberal Arts and Sciences, Tokyo Medical and Dental University, Chiba 272-0827, Japan.
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