1
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Grigas AT, Liu Z, Regan L, O'Hern CS. Core packing of well‐defined X‐ray and
NMR
structures is the same. Protein Sci 2022; 31:e4373. [PMID: 35900019 PMCID: PMC9277709 DOI: 10.1002/pro.4373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 05/06/2022] [Accepted: 06/02/2022] [Indexed: 11/10/2022]
Abstract
Numerous studies have investigated the differences and similarities between protein structures determined by solution NMR spectroscopy and those determined by X-ray crystallography. A fundamental question is whether any observed differences are due to differing methodologies or to differences in the behavior of proteins in solution versus in the crystalline state. Here, we compare the properties of the hydrophobic cores of high-resolution protein crystal structures and those in NMR structures, determined using increasing numbers and types of restraints. Prior studies have reported that many NMR structures have denser cores compared with those of high-resolution X-ray crystal structures. Our current work investigates this result in more detail and finds that these NMR structures tend to violate basic features of protein stereochemistry, such as small non-bonded atomic overlaps and few Ramachandran and sidechain dihedral angle outliers. We find that NMR structures solved with more restraints, and which do not significantly violate stereochemistry, have hydrophobic cores that have a similar size and packing fraction as their counterparts determined by X-ray crystallography at high resolution. These results lead us to conclude that, at least regarding the core packing properties, high-quality structures determined by NMR and X-ray crystallography are the same, and the differences reported earlier are most likely a consequence of methodology, rather than fundamental differences between the protein in the two different environments.
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Affiliation(s)
- Alex T. Grigas
- Graduate Program in Computational Biology and Bioinformatics Yale University New Haven Connecticut USA
- Integrated Graduate Program in Physical and Engineering Biology Yale University New Haven Connecticut USA
| | - Zhuoyi Liu
- Integrated Graduate Program in Physical and Engineering Biology Yale University New Haven Connecticut USA
- Department of Mechanical Engineering and Materials Science Yale University New Haven Connecticut USA
| | - Lynne Regan
- Institute of Quantitative Biology, Biochemistry and Biotechnology Centre for Synthetic and Systems Biology, School of Biological Sciences, University of Edinburgh Edinburgh UK
| | - Corey S. O'Hern
- Graduate Program in Computational Biology and Bioinformatics Yale University New Haven Connecticut USA
- Integrated Graduate Program in Physical and Engineering Biology Yale University New Haven Connecticut USA
- Department of Mechanical Engineering and Materials Science Yale University New Haven Connecticut USA
- Department of Physics Yale University New Haven Connecticut USA
- Department of Applied Physics Yale University New Haven Connecticut USA
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2
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Li C, Wang W, Lee J, Zeng L, Yang Y, Yin SJ, Park YD, Qian GY. Comparative studies of the expression of creatine kinase isoforms under immune stress in Pelodiscus sinensis. Int J Biol Macromol 2020; 162:11-23. [PMID: 32531365 PMCID: PMC7282771 DOI: 10.1016/j.ijbiomac.2020.06.036] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 06/04/2020] [Accepted: 06/04/2020] [Indexed: 01/12/2023]
Abstract
The expression and localization of different isoforms of creatine kinase in Pelodiscus sinensis (PSCK) were studied to reveal the role of PSCK isozymes (PSCK-B, PSCK-M, PSCK-S) under bacterial infection-induced immunologic stress. The computational molecular dynamics simulations predicted that PSCK-S would mostly possess a kinase function in a structural aspect when compared to PSCK-B and PSCK-M. The assay of biochemical parameters such as total superoxide dismutase (T-SOD), lactate dehydrogenase (LDH), malondialdehyde (MDA), catalase (CAT), and the content of ATP were measured along with total PSCK activity in different tissue samples under bacterial infection. The expression detections of PSCK isozymes in vitro and in vivo were overall well-matched where PSCK isozymes were expressed differently in P. sinensis tissues. The results showed that PSCK-B mostly contributes to the spleen, followed by the liver and myocardium; PSCK-M mostly contributes to the liver, followed by the myocardium and skeletal muscle, while PSCK-S contributes to the spleen and is uniquely expressed in skeletal muscle. Our study suggests that the various alterations of PSCK isozymes in tissues of P. sinensis are prone to defense the bacterial infection and blocking energetic imbalance before severe pathogenesis turned on in P. sinensis.
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Affiliation(s)
- Caiyan Li
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, PR China
| | - Wei Wang
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, PR China
| | - Jinhyuk Lee
- Genome Editing Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Gwahak-ro, Yuseong-gu, Daejeon 34141, Republic of Korea
| | - Lifang Zeng
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, PR China
| | - Yufei Yang
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, PR China
| | - Shang-Jun Yin
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, PR China
| | - Yong-Doo Park
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, PR China; Skin Diseases Research Center, Yangtze Delta Region Institute of Tsinghua University, 705 Yatai Road, Jiaxing 314006, PR China.
| | - Guo-Ying Qian
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo 315100, PR China.
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3
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Li B, Fooksa M, Heinze S, Meiler J. Finding the needle in the haystack: towards solving the protein-folding problem computationally. Crit Rev Biochem Mol Biol 2018; 53:1-28. [PMID: 28976219 PMCID: PMC6790072 DOI: 10.1080/10409238.2017.1380596] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Revised: 08/22/2017] [Accepted: 09/13/2017] [Indexed: 12/22/2022]
Abstract
Prediction of protein tertiary structures from amino acid sequence and understanding the mechanisms of how proteins fold, collectively known as "the protein folding problem," has been a grand challenge in molecular biology for over half a century. Theories have been developed that provide us with an unprecedented understanding of protein folding mechanisms. However, computational simulation of protein folding is still difficult, and prediction of protein tertiary structure from amino acid sequence is an unsolved problem. Progress toward a satisfying solution has been slow due to challenges in sampling the vast conformational space and deriving sufficiently accurate energy functions. Nevertheless, several techniques and algorithms have been adopted to overcome these challenges, and the last two decades have seen exciting advances in enhanced sampling algorithms, computational power and tertiary structure prediction methodologies. This review aims at summarizing these computational techniques, specifically conformational sampling algorithms and energy approximations that have been frequently used to study protein-folding mechanisms or to de novo predict protein tertiary structures. We hope that this review can serve as an overview on how the protein-folding problem can be studied computationally and, in cases where experimental approaches are prohibitive, help the researcher choose the most relevant computational approach for the problem at hand. We conclude with a summary of current challenges faced and an outlook on potential future directions.
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Affiliation(s)
- Bian Li
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN, USA
| | - Michaela Fooksa
- Center for Structural Biology, Vanderbilt University, Nashville, TN, USA
- Chemical and Physical Biology Graduate Program, Vanderbilt University, Nashville, TN, USA
| | - Sten Heinze
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN, USA
| | - Jens Meiler
- Department of Chemistry, Vanderbilt University, Nashville, TN, USA
- Center for Structural Biology, Vanderbilt University, Nashville, TN, USA
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4
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Bermejo GA, Clore GM, Schwieters CD. Improving NMR Structures of RNA. Structure 2016; 24:806-815. [PMID: 27066747 DOI: 10.1016/j.str.2016.03.007] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Revised: 02/26/2016] [Accepted: 03/04/2016] [Indexed: 01/27/2023]
Abstract
Here, we show that modern solution nuclear magnetic resonance (NMR) structures of RNA exhibit more steric clashes and conformational ambiguities than their crystallographic X-ray counterparts. To tackle these issues, we developed RNA-ff1, a new force field for structure calculation with Xplor-NIH. Using seven published NMR datasets, RNA-ff1 improves covalent geometry and MolProbity validation criteria for clashes and backbone conformation in most cases, relative to both the previous Xplor-NIH force field and the original structures associated with the experimental data. In addition, with smaller base-pair step rises in helical stems, RNA-ff1 structures enjoy more favorable base stacking. Finally, structural accuracy improves in the majority of cases, as supported by complete residual dipolar coupling cross-validation. Thus, the reported advances show great promise in bridging the quality gap that separates NMR and X-ray structures of RNA.
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Affiliation(s)
- Guillermo A Bermejo
- Division of Computational Bioscience, Center for Information Technology, National Institutes of Health, Bethesda, MD 20892-5624, USA
| | - G Marius Clore
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892-0520, USA
| | - Charles D Schwieters
- Division of Computational Bioscience, Center for Information Technology, National Institutes of Health, Bethesda, MD 20892-5624, USA.
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5
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Ryu H, Lim G, Sung BH, Lee J. NMRe: a web server for NMR protein structure refinement with high-quality structure validation scores. Bioinformatics 2015; 32:611-3. [DOI: 10.1093/bioinformatics/btv595] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 10/10/2015] [Indexed: 11/12/2022] Open
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6
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Ryu H, Kim TR, Ahn S, Ji S, Lee J. Protein NMR structures refined without NOE data. PLoS One 2014; 9:e108888. [PMID: 25279564 PMCID: PMC4184813 DOI: 10.1371/journal.pone.0108888] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2014] [Accepted: 09/04/2014] [Indexed: 12/31/2022] Open
Abstract
The refinement of low-quality structures is an important challenge in protein structure prediction. Many studies have been conducted on protein structure refinement; the refinement of structures derived from NMR spectroscopy has been especially intensively studied. In this study, we generated flat-bottom distance potential instead of NOE data because NOE data have ambiguity and uncertainty. The potential was derived from distance information from given structures and prevented structural dislocation during the refinement process. A simulated annealing protocol was used to minimize the potential energy of the structure. The protocol was tested on 134 NMR structures in the Protein Data Bank (PDB) that also have X-ray structures. Among them, 50 structures were used as a training set to find the optimal "width" parameter in the flat-bottom distance potential functions. In the validation set (the other 84 structures), most of the 12 quality assessment scores of the refined structures were significantly improved (total score increased from 1.215 to 2.044). Moreover, the secondary structure similarity of the refined structure was improved over that of the original structure. Finally, we demonstrate that the combination of two energy potentials, statistical torsion angle potential (STAP) and the flat-bottom distance potential, can drive the refinement of NMR structures.
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Affiliation(s)
- Hyojung Ryu
- Korean Bioinformation Center (KOBIC), Korea Research Institute of Bioscience and Biotechnology, Daejeon, The Republic of Korea
- Department of Bioinformatics, University of Science and Technology, Daejeon, The Republic of Korea
| | - Tae-Rae Kim
- Department of Chemistry, Seoul National University, Seoul, The Republic of Korea
| | - SeonJoo Ahn
- Korean Bioinformation Center (KOBIC), Korea Research Institute of Bioscience and Biotechnology, Daejeon, The Republic of Korea
| | - Sunyoung Ji
- Korean Bioinformation Center (KOBIC), Korea Research Institute of Bioscience and Biotechnology, Daejeon, The Republic of Korea
- Department of Bioinformatics, University of Science and Technology, Daejeon, The Republic of Korea
| | - Jinhyuk Lee
- Korean Bioinformation Center (KOBIC), Korea Research Institute of Bioscience and Biotechnology, Daejeon, The Republic of Korea
- Department of Bioinformatics, University of Science and Technology, Daejeon, The Republic of Korea
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7
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Zhang X, Shen D, Lü ZR, Zhan Y, Si N, Li MM, Yang JM, Zhou HM, Park YD, Zhang Q, Lee J. Effects of hydroxysafflor yellow A on ALDH1: Inhibition kinetics and molecular dynamics simulation. Process Biochem 2014. [DOI: 10.1016/j.procbio.2014.06.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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8
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Effects of osmolytes on arginine kinase from Euphausia superba: A study on thermal denaturation and aggregation. Process Biochem 2014. [DOI: 10.1016/j.procbio.2014.03.019] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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9
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Mao B, Tejero R, Baker D, Montelione GT. Protein NMR structures refined with Rosetta have higher accuracy relative to corresponding X-ray crystal structures. J Am Chem Soc 2014; 136:1893-906. [PMID: 24392845 PMCID: PMC4129517 DOI: 10.1021/ja409845w] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have found that refinement of protein NMR structures using Rosetta with experimental NMR restraints yields more accurate protein NMR structures than those that have been deposited in the PDB using standard refinement protocols. Using 40 pairs of NMR and X-ray crystal structures determined by the Northeast Structural Genomics Consortium, for proteins ranging in size from 5-22 kDa, restrained Rosetta refined structures fit better to the raw experimental data, are in better agreement with their X-ray counterparts, and have better phasing power compared to conventionally determined NMR structures. For 37 proteins for which NMR ensembles were available and which had similar structures in solution and in the crystal, all of the restrained Rosetta refined NMR structures were sufficiently accurate to be used for solving the corresponding X-ray crystal structures by molecular replacement. The protocol for restrained refinement of protein NMR structures was also compared with restrained CS-Rosetta calculations. For proteins smaller than 10 kDa, restrained CS-Rosetta, starting from extended conformations, provides slightly more accurate structures, while for proteins in the size range of 10-25 kDa the less CPU intensive restrained Rosetta refinement protocols provided equally or more accurate structures. The restrained Rosetta protocols described here can improve the accuracy of protein NMR structures and should find broad and general for studies of protein structure and function.
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Affiliation(s)
- Binchen Mao
- Center for Advanced Biotechnology and Medicine, and Department of Molecular Biology and Biochemistry, and Department of Biochemistry and Molecular Biology of Robert Wood Johnson Medical School, and Northeast Structural Genomics Consortium, Rutgers, The State University of New Jersey , Piscataway, New Jersey 08854, United States
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10
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Kim TR, Yang JS, Shin S, Lee J. Statistical torsion angle potential energy functions for protein structure modeling: a bicubic interpolation approach. Proteins 2013; 81:1156-65. [PMID: 23408564 DOI: 10.1002/prot.24265] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2012] [Revised: 01/20/2013] [Accepted: 01/24/2013] [Indexed: 11/09/2022]
Abstract
A set of grid type knowledge-based energy functions is introduced for ϕ-χ₁ , ψ-χ₁ , ϕ-ψ, and χ₁ -χ₂ torsion angle combinations. Boltzmann distribution is assumed for the torsion angle populations from protein X-ray structures, and the functions are named as statistical torsion angle potential energy functions. The grid points around periodic boundaries are duplicated to force periodicity, and the remedy relieves the derivative discontinuity problem. The devised functions rapidly improve the quality of model structures. The potential bias in the functions and the usefulness of additional secondary structure information are also investigated. The proposed guiding functions are expected to facilitate protein structure modeling, such as protein structure prediction, protein design, and structure refinement.
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Affiliation(s)
- Tae-Rae Kim
- Department of Chemistry, Seoul National University, Seoul 151-747, Republic of Korea
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11
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Kim TR, Ji S, Lee S, Chu IS, Shin S, Lee J. A hybrid modeling strategy using Nuclear Overhauser Effect data with contact information. Chem Phys Lett 2012. [DOI: 10.1016/j.cplett.2012.09.074] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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12
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Bermejo GA, Clore GM, Schwieters CD. Smooth statistical torsion angle potential derived from a large conformational database via adaptive kernel density estimation improves the quality of NMR protein structures. Protein Sci 2012; 21:1824-36. [PMID: 23011872 DOI: 10.1002/pro.2163] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Revised: 09/14/2012] [Accepted: 09/17/2012] [Indexed: 11/09/2022]
Abstract
Statistical potentials that embody torsion angle probability densities in databases of high-quality X-ray protein structures supplement the incomplete structural information of experimental nuclear magnetic resonance (NMR) datasets. By biasing the conformational search during the course of structure calculation toward highly populated regions in the database, the resulting protein structures display better validation criteria and accuracy. Here, a new statistical torsion angle potential is developed using adaptive kernel density estimation to extract probability densities from a large database of more than 10⁶ quality-filtered amino acid residues. Incorporated into the Xplor-NIH software package, the new implementation clearly outperforms an older potential, widely used in NMR structure elucidation, in that it exhibits simultaneously smoother and sharper energy surfaces, and results in protein structures with improved conformation, nonbonded atomic interactions, and accuracy.
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Affiliation(s)
- Guillermo A Bermejo
- Division of Computational Bioscience, Center for Information Technology, National Institutes of Health, Bethesda, Maryland 20892-5624, USA
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13
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Wang SF, Lee J, Wang W, Si YX, Li C, Kim TR, Yang JM, Yin SJ, Qian GY. The effect of Zn(2+) on Pelodiscus sinensis creatine kinase: unfolding and aggregation studies. J Biomol Struct Dyn 2012; 31:572-90. [PMID: 22888913 DOI: 10.1080/07391102.2012.706074] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
We studied the effects of Zn(2+) on creatine kinase from the Chinese soft-shelled turtle, Pelodiscus sinensis (PSCK). Zn(2+) inactivated the activity of PSCK (IC(50) = .079 ± .004 mM) following first-order kinetics consistent with multiple phases. The spectrofluorimetry results showed that Zn(2+) induced significant tertiary structural changes of PSCK with exposure to hydrophobic surfaces and that Zn(2+) directly induced PSCK aggregation. The addition of osmolytes such as glycine, proline, and liquaemin successfully blocked PSCK aggregation, recovering the conformation and activity of PSCK. We measured the ORF gene sequence of PSCK by rapid amplification of cDNA end and simulated the 3D structure of PSCK. The results of molecular dynamics simulations showed that eight Zn(2+) bind to PSCK and one Zn(2+) is predicted to bind in a plausible active site of creatine and ATP. The interaction of Zn(2+) with the active site could mostly block the activity of PSCK. Our study provides important insight into the action of Zn(2+) on PSCK as well as more insights into the PSCK folding and ligand-binding mechanisms, which could provide important insight into the metabolic enzymes of P. sinensis.
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Affiliation(s)
- Su-Fang Wang
- College of Biological and Environmental Sciences, Zhejiang Wanli University, Ningbo, 315100, PR China
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