1
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Meng C, Pei Y, Zou Q, Yuan L. DP-AOP: A novel SVM-based antioxidant proteins identifier. Int J Biol Macromol 2023; 247:125499. [PMID: 37414318 DOI: 10.1016/j.ijbiomac.2023.125499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 06/01/2023] [Accepted: 06/19/2023] [Indexed: 07/08/2023]
Abstract
The identification of antioxidant proteins is a challenging yet meaningful task, as they can protect against the damage caused by some free radicals. In addition to time-consuming, laborious, and expensive experimental identification methods, efficient identification of antioxidant proteins through machine learning algorithms has become increasingly common. In recent years, researchers have proposed models for identifying antioxidant proteins; unfortunately, although the accuracy of models is already high, their sensitivity is too low, indicating the possibility of overfitting in the model. Therefore, we developed a new model called DP-AOP for the recognition of antioxidant proteins. We used the SMOTE algorithm to balance the dataset, selected Wei's proposed feature extraction algorithm to obtain 473 dimensional feature vectors, and based on the sorting function in MRMD, scored and ranked each feature to obtain a feature set with contribution values ranging from high to low. To effectively reduce the feature dimension, we combined the dynamic programming idea to make the local eight features the optimal subset. After obtaining the 36 dimensional feature vectors, we finally selected 17 features through experimental analysis. The SVM classification algorithm was used to implement the model through the libsvm tool. The model achieved satisfactory performance, with an accuracy rate of 91.076 %, SN of 96.4 %, SP of 85.8 %, MCC of 82.6 %, and F1 core of 91.5 %. Furthermore, we built a free web server to facilitate researchers' subsequent unfolding studies of antioxidant protein recognition. The website is http://112.124.26.17:8003/#/.
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Affiliation(s)
- Chaolu Meng
- College of Computer and Information Engineering, Inner Mongolia Agricultural University, Hohhot, China; Inner Mongolia Autonomous Region Key Laboratory of Big Data Research and Application of Agriculture and Animal Husbandry, China.
| | - Yue Pei
- College of Computer and Information Engineering, Inner Mongolia Agricultural University, Hohhot, China
| | - Quan Zou
- Institute of Fundamental and Frontier Sciences, University of Electronic Science and Technology of China, China.
| | - Lei Yuan
- Department of Hepatobiliary Surgery, Quzhou People's Hospital, China.
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2
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Serebryany E, Zhao VY, Park K, Bitran A, Trauger SA, Budnik B, Shakhnovich EI. Systematic conformation-to-phenotype mapping via limited deep sequencing of proteins. Mol Cell 2023; 83:1936-1952.e7. [PMID: 37267908 DOI: 10.1016/j.molcel.2023.05.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 01/29/2023] [Accepted: 05/03/2023] [Indexed: 06/04/2023]
Abstract
Non-native conformations drive protein-misfolding diseases, complicate bioengineering efforts, and fuel molecular evolution. No current experimental technique is well suited for elucidating them and their phenotypic effects. Especially intractable are the transient conformations populated by intrinsically disordered proteins. We describe an approach to systematically discover, stabilize, and purify native and non-native conformations, generated in vitro or in vivo, and directly link conformations to molecular, organismal, or evolutionary phenotypes. This approach involves high-throughput disulfide scanning (HTDS) of the entire protein. To reveal which disulfides trap which chromatographically resolvable conformers, we devised a deep-sequencing method for double-Cys variant libraries of proteins that precisely and simultaneously locates both Cys residues within each polypeptide. HTDS of the abundant E. coli periplasmic chaperone HdeA revealed distinct classes of disordered hydrophobic conformers with variable cytotoxicity depending on where the backbone was cross-linked. HTDS can bridge conformational and phenotypic landscapes for many proteins that function in disulfide-permissive environments.
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Affiliation(s)
- Eugene Serebryany
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA.
| | - Victor Y Zhao
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Kibum Park
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Amir Bitran
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA
| | - Sunia A Trauger
- Center for Mass Spectrometry, Harvard University, Cambridge, MA 02138, USA
| | - Bogdan Budnik
- Center for Mass Spectrometry, Harvard University, Cambridge, MA 02138, USA
| | - Eugene I Shakhnovich
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA.
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3
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Zhou J, Lan Q, Li W, Ji LN, Wang K, Xia XH. Single Molecule Protein Segments Sequencing by a Plasmonic Nanopore. Nano Lett 2023; 23:2800-2807. [PMID: 36927001 DOI: 10.1021/acs.nanolett.3c00086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Obtaining sequential and conformational information on proteins is vital to understand their functions. Although the nanopore-based electrical detection can sense single molecule (SM) protein and distinguish among different amino acids, this approach still faces difficulties in slowing down protein translocation and improving ionic current signal-to-noise ratio. Here, we observe the unfolding and multistep sequential translocation of SM cytochrome c (cyt c) through a surface enhanced Raman scattering (SERS) active conical gold nanopore. High bias voltage unfolds SM protein causing more exposure of amino acid residues to the nanopore, which slows down the protein translocation. Specific SERS traces of different SM cyt c segments are then recorded sequentially when they pass through the hotspot inside the gold nanopore. This study shows that the combination of SM SERS with a nanopore can provide a direct insight into protein segments and expedite the development of nanopore toward SM protein sequencing.
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Affiliation(s)
- Juan Zhou
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Qing Lan
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Wang Li
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Li-Na Ji
- State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210023, China
| | - Kang Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
| | - Xing-Hua Xia
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, China
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4
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Dhanalakshmi K, Kuramitsu S, Yokoyama S, Kumarevel T, Ponnuraj K. Crystal structure analysis of pyrrolidone carboxyl peptidase from Thermus thermophilus. Biophys Chem 2023; 293:106946. [PMID: 36563626 DOI: 10.1016/j.bpc.2022.106946] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Revised: 12/06/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022]
Abstract
Pyrrolidone carboxyl peptidase (PCP) hydrolytically removes the L-pyroglutamic acid from the amino terminal region of pyroglutamyl proteins or peptides. So far, only a limited number of structures of PCP have been solved. Here we report the crystal structure of pyrrolidone carboxyl peptidase from Thermus thermophilus (TtPCP) which has been solved using the molecular replacement method and refined at 1.9 Å resolution. TtPCP follows the α/β/α architecture in which the central β-sheets are surrounded by α-helices on both sides. The inter subunit contact between two monomers consists of two short antiparallel β-strands and part of a long protrusion loop. By comparing the TtPCP with its structural homologs, we identified the putative catalytic triad residues as Glu76, Cys139 and His160. A unique disulfide link found in some homologs of TtPCP, formed between two monomers that provide thermal stability to the protein, is not observed in TtPCP. Hence, being a thermophilic protein, the putative thermal stability of TtPCP could be due to more intra and inter-molecular hydrogen bonds, hydrophobic and ion pair interactions when compared with its mesophilic counterpart. The structural details of TtPCP will be helpful to understand the basis of the intrinsic stability of thermophilic proteins. Also, it could be useful for protein engineering.
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Affiliation(s)
- K Dhanalakshmi
- Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai 600 025, India
| | - Seiki Kuramitsu
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka 560-0043, Japan
| | - Shigeyuki Yokoyama
- Structural Biology Laboratory, RIKEN Yokohama Institute, RIKEN, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan
| | - Thirumananseri Kumarevel
- Structural Biology Laboratory, RIKEN Yokohama Institute, RIKEN, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan; Laboratory for Transcription Structural Biology, RIKEN Center for Biosystems Dynamic Research, RIKEN Yokohama Institute, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan.
| | - Karthe Ponnuraj
- Centre of Advanced Study in Crystallography and Biophysics, University of Madras, Guindy Campus, Chennai 600 025, India.
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5
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He H, Wu C, Saqib M, Hao R. Single-molecule fluorescence methods for protein biomarker analysis. Anal Bioanal Chem 2023:10.1007/s00216-022-04502-9. [PMID: 36609860 DOI: 10.1007/s00216-022-04502-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 12/07/2022] [Accepted: 12/20/2022] [Indexed: 01/09/2023]
Abstract
Proteins have been considered key building blocks of life. In particular, the protein content of an organism and a cell offers significant information for the in-depth understanding of the disease and biological processes. Single-molecule protein detection/sequencing tools will revolutionize clinical (proteomics) research, offering ultrasensitivity for low-abundance biomarker (protein) detection, which is important for the realization of early-stage disease diagnosis and single-cell proteomics. This improved detection/measurement capability delivers new sets of techniques to explore new frontiers and address important challenges in various interdisciplinary areas including nanostructured materials, molecular medicine, molecular biology, and chemistry. Importantly, fluorescence-based methods have emerged as indispensable tools for single protein detection/sequencing studies, providing a higher signal-to-noise ratio (SNR). Improvements in fluorescent dyes/probes and detector capabilities coupled with advanced (image) analysis strategies have fueled current developments for single protein biomarker detections. For example, in comparison to conventional ELISA (i.e., based on ensembled measurements), single-molecule fluorescence detection is more sensitive, faster, and more accurate with reduced background, high-throughput, and so on. In comparison to MS sequencing, fluorescence-based single-molecule protein sequencing can achieve the sequencing of peptides themselves with higher sensitivity. This review summarizes various typical single-molecule detection technologies including their methodology (modes of operation), detection limits, advantages and drawbacks, and current challenges with recent examples. We describe the fluorescence-based single-molecule protein sequencing/detection based on five kinds of technologies such as fluorosequencing, N-terminal amino acid binder, nanopore light sensing, and DNA nanotechnology. Finally, we present our perspective for developing high-performance fluorescence-based sequencing/detection techniques.
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Affiliation(s)
- Haihan He
- Department of Chemistry, Southern University of Science and Technology, Shenzhen, 518055, China.,Research Center for Chemical Biology and Omics Analysis, School of Science, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Chuhong Wu
- Department of Chemistry, Southern University of Science and Technology, Shenzhen, 518055, China.,Research Center for Chemical Biology and Omics Analysis, School of Science, Southern University of Science and Technology, Shenzhen, 518055, China
| | - Muhammad Saqib
- Department of Chemistry, Southern University of Science and Technology, Shenzhen, 518055, China.,Research Center for Chemical Biology and Omics Analysis, School of Science, Southern University of Science and Technology, Shenzhen, 518055, China.,Institute of Chemistry, Khwaja Fareed University of Engineering & Information Technology, Rahim Yar Khan 64200, Pakistan
| | - Rui Hao
- Department of Chemistry, Southern University of Science and Technology, Shenzhen, 518055, China. .,Research Center for Chemical Biology and Omics Analysis, School of Science, Southern University of Science and Technology, Shenzhen, 518055, China.
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6
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He Q, Tang L. Sub-5 nm nanogap electrodes towards single-molecular biosensing. Biosens Bioelectron 2022; 213:114486. [PMID: 35749816 DOI: 10.1016/j.bios.2022.114486] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 06/10/2022] [Accepted: 06/14/2022] [Indexed: 11/02/2022]
Abstract
Nanogap electrodes (NGEs) with sub-5 nm gap has been widely used in single-molecule sensing and sequencing, with the characteristics of label-free, high sensitivity, rapid detection and low-cost. However, the fabrication of sub-5 nm gap electrodes with high controllability and reproducibility still remains a great challenge that impedes the experimental research and the commercialization of the nanogap device. Here, we review the common currently used fabrication methods of nanogap electrodes, such as gap narrowing deposition, mechanical controllable break junctions and the fabrication methods combined with nanopore or nanochannel. We then highlight the typical applications of nanogap electrodes in biological/chemical sensing fields, including single molecule recognition, single molecule sequencing and chemical kinetics analysis. Finally, the challenges of nanogap electrodes in single molecule sensing/sequencing are outlined and the future directions for sensing perspectives are suggested.
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Affiliation(s)
- Qiuxiang He
- State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou, 310027, China
| | - Longhua Tang
- State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou, 310027, China.
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7
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Chislett M, Guo J, Bond PL, Wang Y, Donose BC, Yuan Z. Reactive nitrogen species from free nitrous acid (FNA) cause cell lysis. Water Res 2022; 217:118401. [PMID: 35427827 DOI: 10.1016/j.watres.2022.118401] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Revised: 04/01/2022] [Accepted: 04/04/2022] [Indexed: 06/14/2023]
Abstract
Free nitrous acid (FNA, i.e. HNO2) has been demonstrated to have broad biocidal effects on a range of microorganisms, which has direct implications for wastewater management. However, the biocidal mechanisms still remain largely unknown. This study aims to test the hypothesis that FNA will induce cell lysis via cell membrane perforations, and consequently cause cell death via proteolysis, through the use of two model organisms namely Escherichia coli K12 and Pseudomonas putida KT2440. A combination of analytical techniques that included viability assays, atomic force microscopy (AFM), protein abundance assays and proteomic analysis using Quadruple-Orbitrap™ Mass spectrometry was used to evaluate the extent of cell death and possible cell lysis mechanisms. FNA treatment at 6.09 mg/L for 24 h (conditions typically applied in applications) induced 36 ± 4.2% and 91 ± 3.5% cell death/lysis of E. coli and P. putida, respectively. AFM showed that the lysis of cells was observed via perforations in the cell membrane; cells also appeared to shrink and become flat following FNA treatment. By introducing a reactive nitrogen species (RNS) scavenger to act as a treatment control, we further revealed that it was the nitrosative decomposition species of FNA, such as .NO that caused the cell lysis through the destruction of protein macromolecules found in the cell membrane (proteolysis). Subsequently, the RNS went on to cause the destruction of protein macromolecules within the cells. The death of these model organisms E. coli and P. putida following exposure to FNA treatment provides insights into the use of FNA as an antimicrobial agent in wastewater treatment.
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Affiliation(s)
- Mariella Chislett
- Australian Centre for Water and Environmental Biotechnology (ACWEB, formerly AWMC), The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Jianhua Guo
- Australian Centre for Water and Environmental Biotechnology (ACWEB, formerly AWMC), The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Philip L Bond
- Australian Centre for Water and Environmental Biotechnology (ACWEB, formerly AWMC), The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Yue Wang
- Australian Centre for Water and Environmental Biotechnology (ACWEB, formerly AWMC), The University of Queensland, St. Lucia, Queensland 4072, Australia
| | - Bogdan C Donose
- School of Information Technology and Electrical Engineering, The University of Queensland, St Lucia, Brisbane, QLD 4072, Australia
| | - Zhiguo Yuan
- Australian Centre for Water and Environmental Biotechnology (ACWEB, formerly AWMC), The University of Queensland, St. Lucia, Queensland 4072, Australia
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8
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Arbita AA, Paul NA, Cox J, Zhao J. Amino acid sequence of two new milk-clotting proteases from the macroalga Gracilaria edulis. Int J Biol Macromol 2022; 211:499-505. [PMID: 35561860 DOI: 10.1016/j.ijbiomac.2022.05.038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 04/08/2022] [Accepted: 05/05/2022] [Indexed: 11/05/2022]
Abstract
This study is aimed at identifying and characterising the proteases we previously extracted from the red seaweed Gracilaria edulis with the potential as milk-clotting enzymes. The protease extract was first analysed by sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE) and zymography. Two protease bands with a molecular weight of 44 and 108 kDa were identified, and analysed using in-gel digestion and liquid chromatography-tandem mass spectrometry/mass spectrometry (LC-MS/MS). Eight peptides from the LC-MS/MS analysis matched those in existing protein databases but they were not related to any protease of the genera Gracilaria and Hydropuntia. Further analysis revealed that more than 80% of the peptide sequence of the algal proteases matched with those from members of the bacteria kingdom, including Gallaecimonas and Alteromonas. Among these, twelve matching homolog proteases were identified as metalloprotease and serine protease. The results indicated that the algal proteases have a close relationship with both algae and bacteria, and suggest that the proteases might have resulted from past bacterial colonisation of the algae and subsequent horizontal gene transfer between bacteria and algae.
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Affiliation(s)
- Ariestya Arlene Arbita
- School of Chemical Engineering, The University of New South Wales, Sydney, NSW 2052, Australia; School of Chemical Engineering, Faculty of Industrial and Technology, Parahyangan Catholic University, Ciumbuleuit 94, Bandung 40141, Indonesia
| | - Nicholas A Paul
- School of Science and Engineering, University of the Sunshine Coast, Maroochydore, Queensland 4558, Australia
| | - Julian Cox
- School of Chemical Engineering, The University of New South Wales, Sydney, NSW 2052, Australia
| | - Jian Zhao
- School of Chemical Engineering, The University of New South Wales, Sydney, NSW 2052, Australia.
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9
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Zheng JS, Liang J, Shi WW, Li Y, Hu HG, Tian CL, Liu L. A mirror-image protein-based information barcoding and storage technology. Sci Bull (Beijing) 2021; 66:1542-1549. [PMID: 36654283 DOI: 10.1016/j.scib.2021.03.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2021] [Revised: 02/12/2021] [Accepted: 03/02/2021] [Indexed: 02/03/2023]
Abstract
A mirror-image protein-based information barcoding and storage technology wherein D-amino acids are used to encode information into mirror-image proteins that are chemically synthesized is described. These mirror-image proteins were then fused into various materials from which information-encoded objects were produced. Subsequently, the mirror-image proteins were extracted from the objects using biotin-streptavidin resin-mediated specific enrichment and cleaved using an Ni(II)-mediated selective peptide cleavage. Protein sequencing was accomplished using liquid chromatography/tandem mass spectrometry (LC-MS/MS) and then transcoded into the recorded information. We demonstrated the use of this technology to encode Chinese words into mirror-image proteins, which were then fused onto a poly(ethylene terephthalate) (PET) film and retrieved and decoded by LC-MS/MS sequencing. Compared to information barcoding and storage technologies using natural biopolymers, the mirror-image biopolymers used in our technology may be more stable and durable.
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Affiliation(s)
- Ji-Shen Zheng
- Tsinghua-Peking Joint Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China; Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Jun Liang
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Wei-Wei Shi
- Tsinghua-Peking Joint Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Ying Li
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Hong-Gang Hu
- Institute of Translational Medicine, Shanghai University, Shanghai 200444, China
| | - Chang-Lin Tian
- Hefei National Laboratory for Physical Sciences at the Microscale, School of Life Sciences, University of Science and Technology of China, Hefei 230027, China
| | - Lei Liu
- Tsinghua-Peking Joint Center for Life Sciences, Ministry of Education Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Center for Synthetic and Systems Biology, Department of Chemistry, Tsinghua University, Beijing 100084, China.
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10
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Rodriguez-Larrea D. Single-aminoacid discrimination in proteins with homogeneous nanopore sensors and neural networks. Biosens Bioelectron 2021; 180:113108. [PMID: 33690101 DOI: 10.1016/j.bios.2021.113108] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 02/08/2021] [Accepted: 02/19/2021] [Indexed: 12/18/2022]
Abstract
A technology capable of sequencing individual protein molecules would revolutionize our understanding of biological processes. Nanopore technology can analyze single heteropolymer molecules such as DNA by measuring the ionic current flowing through a single nanometer hole made in an electrically insulating membrane. This current is sensitive to the monomer sequence. However, proteins are remarkably complex and identifying a single residue change in a protein remains a challenge. In this work, I show that simple neural networks can be trained to recognize protein mutants. Although these networks are quickly and efficiently trained, their ability to generalize in an independent experiment is poor. Using a thermal annealing protocol on the nanopore sample, and examining many mutants with the same nanopore sensor are measures aimed at reducing training data variability which produce an increase in the generalizability of the trained neural network. Using this approach, we obtain a 100% correct assignment among 9 mutants in >50% of the experiments. Interestingly, the neural network performance, compared to a random guess, improves as more mutants are included in the dataset for discrimination. Engineered nanopores prepared with high homogeneity coupled with state-of-the-art analysis of the ionic current signals may enable single-molecule protein sequencing.
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Affiliation(s)
- David Rodriguez-Larrea
- Biofisika Institute (CSIC, UPV/EHU) and Department of Biochemistry and Molecular Biology (UPV/EHU), Barrio Sarriena S/n, Leioa, 48940, Spain.
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11
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Nivala J, Mulroney L, Luan Q, Abu-Shumays R, Akeson M. Unfolding and Translocation of Proteins Through an Alpha-Hemolysin Nanopore by ClpXP. Methods Mol Biol 2021; 2186:145-155. [PMID: 32918735 DOI: 10.1007/978-1-0716-0806-7_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Proteins present a significant challenge for nanopore-based sequence analysis. This is partly due to their stable tertiary structures that must be unfolded for linear translocation, and the absence of regular charge density. To address these challenges, here we describe how ClpXP, an ATP-dependent protein unfoldase, can be harnessed to unfold and processively translocate multi-domain protein substrates through an alpha-hemolysin nanopore sensor. This process results in ionic current patterns that are diagnostic of protein sequence and structure at the single-molecule level.
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Affiliation(s)
- Jeff Nivala
- Paul G. Allen School of Computer Science and Engineering, University of Washington, Seattle, WA, USA.
| | - Logan Mulroney
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Qing Luan
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN, USA
| | - Robin Abu-Shumays
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
| | - Mark Akeson
- UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, CA, USA
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12
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Tullman J, Marino JP, Kelman Z. Leveraging nature's biomolecular designs in next-generation protein sequencing reagent development. Appl Microbiol Biotechnol 2020; 104:7261-71. [PMID: 32617618 DOI: 10.1007/s00253-020-10745-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 06/09/2020] [Accepted: 06/15/2020] [Indexed: 01/18/2023]
Abstract
Next-generation approaches for protein sequencing are now emerging that could have the potential to revolutionize the field in proteomics. One such sequencing method involves fluorescence-based imaging of immobilized peptides in which the N-terminal amino acid of a polypeptide is readout sequentially by a series of fluorescently labeled biomolecules. When selectively bound to a specific N-terminal amino acid, the NAAB (N-terminal amino acid binder) affinity reagent identifies the amino acid through its associated fluorescence tag. A key technical challenge in implementing this fluoro-sequencing approach is the need to develop NAAB affinity reagents with the high affinity and selectivity for specific N-terminal amino acids required for this biotechnology application. One approach to develop such a NAAB affinity reagent is to leverage naturally occurring biomolecules that bind amino acids and/or peptides. Here, we describe several candidate biomolecules that could be considered for this purpose and discuss the potential for developability of each. Key points • Next-generation sequencing methods are emerging that could revolutionize proteomics. • Sequential readout of N-terminal amino acids by fluorescent-tagged affinity reagents. • Native peptide/amino acid binders can be engineered into affinity reagents. • Protein size and structure contribute to feasibility of reagent developability.
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13
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Skowron PM, Krefft D, Brodzik R, Kasperkiewicz P, Drag M, Koller KP. An alternative for proteinase K-heat-sensitive protease from fungus Onygena corvina for biotechnology: cloning, engineering, expression, characterization and special application for protein sequencing. Microb Cell Fact 2020; 19:135. [PMID: 32580707 PMCID: PMC7313183 DOI: 10.1186/s12934-020-01392-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Accepted: 06/15/2020] [Indexed: 12/19/2022] Open
Abstract
Background A neutral, heat-sensitive serine protease (NHSSP) originating from the feather-degrading fungus Onygena corvina (O. corvina) was described and defined as an alkaline serine protease of the subtilisin type S8 family, exhibiting an enzymatic activity at neutral pH. Generally, broad specificity proteases, such as proteinase K or trypsin, have found numerous applications in research and biotechnology. Results We report the cloning and expression in the yeast PichiaPink™ system, as well as purification, and characterization of the NHSSP. Recombinant, His6-tagged NHSSP was efficiently expressed from an optimized, synthetic gene and purified using a simple protocol based on ammonium sulfate fractionation and hydrophobic interaction chromatography. The enzyme shows atypical C-terminal processing, the coded preproprotein undergoes signal peptide removal and maturation through the clipping of a propeptide section and 10 amino acids (aa) from the C-terminus, including the His6-tag. The deletion variant has been constructed, devoid of the C-terminal ORF segment, thus eliminating the need for C-terminal processing. Both NHSSP variants exhibit very similar enzymatic characteristics. The purified enzymes were characterized to determine the optimal proteolytic conditions. We revealed that the mature NHSSP is reproducibly active over a wide pH range from neutral to mild acidic (pH of 5.0 to 8.5), with an optimum at pH 6.8, and at temperatures of 15 to 50 °C with an optimum at 38–42 °C. Interestingly, we demonstrated that the protease can be fully deactivated by a moderate increase in temperature of about 15 °C from the optimum to over 50 °C. The protease was partially sensitive to serine protease inhibitors, and not inhibited by chelating or reducing agents and detergents. SDS induced autolysis of NHSSP, which points to a high stimulation of its proteolytic activity. Conclusions The NHSSP was produced as a recombinant protein with high efficiency. Compared to proteinase K, the most common serine protease used, NHSSP shows an approx. twofold higher specific activity. Protein sequencing can be a valuable technical application for the protease. The protein coverage is significantly higher in comparison to trypsin and reaches about 84–100% for β-lactoglobulin (BLG), antibody (mAb) light and heavy chains. Furthermore, the option to perform digestions at neutral to slightly acidic pH-values down to pH 5.0 avoids modification of peptides, e.g. due to deamidation.
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Affiliation(s)
- Piotr M Skowron
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63 Street, 80-308, Gdansk, Poland.
| | - Daria Krefft
- Department of Molecular Biotechnology, Faculty of Chemistry, University of Gdansk, Wita Stwosza 63 Street, 80-308, Gdansk, Poland
| | - Robert Brodzik
- BLIRT S.A., Trzy Lipy 3/1.38 Street, 80-172, Gdansk, Poland
| | - Paulina Kasperkiewicz
- Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27 Street, 50-370, Wroclaw, Poland
| | - Marcin Drag
- Department of Chemical Biology and Bioimaging, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27 Street, 50-370, Wroclaw, Poland
| | - Klaus-Peter Koller
- Institute for Molecular Bio Science, University Frankfurt, Max-von-Laue-Str. 9, 60438, Frankfurt, Germany
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Liu GT, Jiang JF, Liu XN, Jiang JZ, Sun L, Duan W, Li RM, Wang Y, Lecourieux D, Liu CH, Li SH, Wang LJ. New insights into the heat responses of grape leaves via combined phosphoproteomic and acetylproteomic analyses. Hortic Res 2019; 6:100. [PMID: 31666961 PMCID: PMC6804945 DOI: 10.1038/s41438-019-0183-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 06/03/2019] [Accepted: 06/04/2019] [Indexed: 05/04/2023]
Abstract
Heat stress is a serious and widespread threat to the quality and yield of many crop species, including grape (Vitis vinifera L.), which is cultivated worldwide. Here, we conducted phosphoproteomic and acetylproteomic analyses of leaves of grape plants cultivated under four distinct temperature regimes. The phosphorylation or acetylation of a total of 1011 phosphoproteins with 1828 phosphosites and 96 acetyl proteins with 148 acetyl sites changed when plants were grown at 35 °C, 40 °C, and 45 °C in comparison with the proteome profiles of plants grown at 25 °C. The greatest number of changes was observed at the relatively high temperatures. Functional classification and enrichment analysis indicated that phosphorylation, rather than acetylation, of serine/arginine-rich splicing factors was involved in the response to high temperatures. This finding is congruent with previous observations by which alternative splicing events occurred more frequently in grapevine under high temperature. Changes in acetylation patterns were more common than changes in phosphorylation patterns in photosynthesis-related proteins at high temperatures, while heat-shock proteins were associated more with modifications involving phosphorylation than with those involving acetylation. Nineteen proteins were identified with changes associated with both phosphorylation and acetylation, which is consistent with crosstalk between these posttranslational modification types.
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Affiliation(s)
- Guo-Tian Liu
- Beijing Key Laboratory of Grape Science and Enology and Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093 China
- College of Horticulture, Northwest A&F University, Yangling, 712100 China
- University of Chinese Academy of Sciences, Beijing, 100093 China
| | - Jian-Fu Jiang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009 China
| | - Xin-Na Liu
- Beijing Key Laboratory of Grape Science and Enology and Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093 China
- University of Chinese Academy of Sciences, Beijing, 100093 China
| | - Jin-Zhu Jiang
- Beijing Key Laboratory of Grape Science and Enology and Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093 China
- University of Chinese Academy of Sciences, Beijing, 100093 China
| | - Lei Sun
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009 China
| | - Wei Duan
- Beijing Key Laboratory of Grape Science and Enology and Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093 China
| | - Rui-Min Li
- College of Horticulture, Northwest A&F University, Yangling, 712100 China
| | - Yi Wang
- Beijing Key Laboratory of Grape Science and Enology and Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093 China
- University of Chinese Academy of Sciences, Beijing, 100093 China
| | - David Lecourieux
- Universite´ de Bordeaux, ISVV, Ecophysiologie et Ge´nomique Fonctionnelle de la Vigne, UMR 1287, F-33140 Villenave d’Ornon, France
- INRA, ISVV, Ecophysiologie et Ge´nomique Fonctionnelle de la Vigne, UMR 1287, F-33140 Villenave d’Ornon, France
| | - Chong-Huai Liu
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou, 450009 China
| | - Shao-Hua Li
- Beijing Key Laboratory of Grape Science and Enology and Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093 China
- University of Chinese Academy of Sciences, Beijing, 100093 China
| | - Li-Jun Wang
- Beijing Key Laboratory of Grape Science and Enology and Key Laboratory of Plant Resources, Institute of Botany, the Chinese Academy of Sciences, Beijing, 100093 China
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15
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Xu X, Liu X, Yan Y, Wang W, Gebretsadik K, Qi X, Xu Q, Chen X. Comparative proteomic analysis of cucumber powdery mildew resistance between a single-segment substitution line and its recurrent parent. Hortic Res 2019; 6:115. [PMID: 31645969 PMCID: PMC6804742 DOI: 10.1038/s41438-019-0198-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 07/04/2019] [Accepted: 08/27/2019] [Indexed: 05/04/2023]
Abstract
Powdery mildew (PM) is considered a major cause of yield losses and reduced quality in cucumber worldwide, but the molecular basis of PM resistance remains poorly understood. A segment substitution line, namely, SSL508-28, was developed with dominant PM resistance in the genetic background of PM-susceptible cucumber inbred line D8. The substituted segment contains 860 genes. An iTRAQ-based comparative proteomic technology was used to map the proteomes of PM-inoculated and untreated (control) D8 and SSL508-28. The number of differentially regulated proteins (DRPs) in SSL508-28 was almost three times higher than that in D8. Fourteen DRPs were located in the substituted segment interval. Comparative gene expression analysis revealed that nodulin-related protein 1 (NRP1) may be a good candidate for PM resistance. Gene Ontology enrichment analysis showed that DRPs functioning in tetrapyrrole biosynthetic process, sulfur metabolic process and cell redox homeostasis were specifically enriched in the resistant line SSL508-28. DRPs categorized in the KEGG term photosynthesis increased in both lines upon PM infection, suggesting that the strategies used by cucumber may be different from those used by other crops to react to PM attacks at the initial stage. The measurement of hydrogen peroxide and superoxide anion production and net photosynthetic rate were consistent with the changes in protein abundance, suggesting that the proteomic results were reliable. There was a poor correlation between DRPs measured by iTRAQ and the corresponding gene expression changes measured by RNA-seq with the same experimental design. Taken together, these findings improve the understanding of the molecular mechanisms underlying the response of cucumber to PM infection.
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Affiliation(s)
- Xuewen Xu
- School of Horticulture and Plant Protection, Yangzhou University, 225009 Yangzhou, Jiangsu China
| | - Xueli Liu
- School of Horticulture and Plant Protection, Yangzhou University, 225009 Yangzhou, Jiangsu China
| | - Yali Yan
- School of Horticulture and Plant Protection, Yangzhou University, 225009 Yangzhou, Jiangsu China
| | - Wei Wang
- School of Horticulture and Plant Protection, Yangzhou University, 225009 Yangzhou, Jiangsu China
| | - Kiros Gebretsadik
- School of Horticulture and Plant Protection, Yangzhou University, 225009 Yangzhou, Jiangsu China
| | - Xiaohua Qi
- School of Horticulture and Plant Protection, Yangzhou University, 225009 Yangzhou, Jiangsu China
| | - Qiang Xu
- School of Horticulture and Plant Protection, Yangzhou University, 225009 Yangzhou, Jiangsu China
| | - Xuehao Chen
- School of Horticulture and Plant Protection, Yangzhou University, 225009 Yangzhou, Jiangsu China
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16
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Ji Z, Kang X, Wang S, Guo P. Nano-channel of viral DNA packaging motor as single pore to differentiate peptides with single amino acid difference. Biomaterials 2018; 182:227-233. [PMID: 30138785 DOI: 10.1016/j.biomaterials.2018.08.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2018] [Revised: 07/17/2018] [Accepted: 08/02/2018] [Indexed: 12/23/2022]
Abstract
Detection, differentiation, mapping, and sequencing of proteins are important in proteomics for the assessment of cell development such as protein methylation or phosphorylation as well as the diagnosis of diseases including metabolic disorder, mental illness, immunological ailments, and malignant cancers. Nanopore technology has demonstrated the potential for the sequencing or sensing of DNA, RNA, chemicals, or other macromolecules. Due to the diversity of protein in shape, structure and charge and the composition versatility of 20 amino acids, the sequencing of proteins remains challenging. Herein, we report the application of the channel of bacteriophage T7 DNA packaging motor for the differentiation of an assortment of peptides of a single amino acid difference. Explicit fingerprints or signatures were obtained based on current blockage and dwell time of individual peptide. Data from the clear mapping of small proteins after protease digestion suggests the potential of using T7 motor channel for proteomics including protein sequencing.
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Affiliation(s)
- Zhouxiang Ji
- Center for RNA Nanobiotechnology and Nanomedicine, Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, College of Medicine, Dorothy M. Davis Heart and Lung Research Institute and James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Xinqi Kang
- Center for RNA Nanobiotechnology and Nanomedicine, Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, College of Medicine, Dorothy M. Davis Heart and Lung Research Institute and James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Shaoying Wang
- Center for RNA Nanobiotechnology and Nanomedicine, Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, College of Medicine, Dorothy M. Davis Heart and Lung Research Institute and James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA
| | - Peixuan Guo
- Center for RNA Nanobiotechnology and Nanomedicine, Division of Pharmaceutics and Pharmaceutical Chemistry, College of Pharmacy, College of Medicine, Dorothy M. Davis Heart and Lung Research Institute and James Comprehensive Cancer Center, The Ohio State University, Columbus, OH, USA.
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17
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Epstein JA, Blank PS, Searle BC, Catlin AD, Cologna SM, Olson MT, Backlund PS, Coorssen JR, Yergey AL. ProteinProcessor: A probabilistic analysis using mass accuracy and the MS spectrum. Proteomics 2017; 16:2480-90. [PMID: 27546229 DOI: 10.1002/pmic.201600137] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Revised: 07/29/2016] [Accepted: 08/17/2016] [Indexed: 11/05/2022]
Abstract
Current approaches to protein identification rely heavily on database matching of fragmentation spectra or precursor peptide ions. We have developed a method for MALDI TOF-TOF instrumentation that uses peptide masses and their measurement errors to confirm protein identifications from a first pass MS/MS database search. The method uses MS1-level spectral data that have heretofore been ignored by most search engines. This approach uses the distribution of mass errors of peptide matches in the MS1 spectrum to develop a probability model that is independent of the MS/MS database search identifications. Peptide mass matches can come from both precursor ions that have been fragmented as well as those that are tentatively identified by accurate mass alone. This additional corroboration enables us to confirm protein identifications to MS/MS-based scores that are otherwise considered to be only of moderate quality. Straightforward and easily applicable to current proteomic analyses, this tool termed "ProteinProcessor" provides a robust and invaluable addition to current protein identification tools.
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Affiliation(s)
- Jonathan A Epstein
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, USA
| | - Paul S Blank
- Section on Integrative Biophysics, Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, USA
| | | | - Aaron D Catlin
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, USA
| | - Stephanie M Cologna
- Department of Chemistry, University of Illinois at Chicago, Chicago, IL, USA
| | - Matthew T Olson
- Department of Pathology, The Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Peter S Backlund
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, USA
| | - Jens R Coorssen
- Faculty of Graduate Studies and the Departments of Health Sciences and Biological Sciences, Brock University, St. Catharines, ON, Canada
| | - Alfred L Yergey
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, NIH, Bethesda, MD, USA.
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18
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Brito-Argáez L, Tamayo-Sansores JA, Madera-Piña D, García-Villalobos FJ, Moo-Puc RE, Kú-González Á, Villanueva MA, Islas-Flores I. Biochemical characterization and immunolocalization studies of a Capsicum chinense Jacq. protein fraction containing DING proteins and anti-microbial activity. Plant Physiol Biochem 2016; 109:502-514. [PMID: 27835848 DOI: 10.1016/j.plaphy.2016.10.031] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 10/24/2016] [Accepted: 10/25/2016] [Indexed: 06/06/2023]
Abstract
The DING protein family consists of proteins of great biological importance due to their ability to inhibit carcinogenic cell growth. A DING peptide with Mr ∼7.57 kDa and pI ∼5.06 was detected in G10P1.7.57, a protein fraction from Capsicum chinense Jacq. seeds. Amino acid sequencing of the peptide produced three smaller peptides showing identity to the DING protein family. G10P1.7.57 displayed a phosphatase activity capable of dephosphorylating different phosphorylated substrates and inhibited the growth of Saccharomyces cerevisiae cells. Western immunoblotting with a custom-made polyclonal antibody raised against a sequence (ITYMSPDYAAPTLAGLDDATK), derived from the ∼7.57 kDa polypeptide, immunodetected an ∼ 39 kDa polypeptide in G10P1.7.57. Purification by electroelution followed by amino acid sequencing of the ∼39 kDa polypeptide yielded seven new peptide sequences and an additional one identical to that of the initially identified peptide. Western immunoblotting of soluble proteins from C. chinense seeds and leaves revealed the presence of the ∼39 kDa polypeptide at all developmental stages, with increased accumulation when the organs reached maturity. Immunolocalization using Dabsyl chloride- or Alexa fluor 488-conjugated antibodies revealed a specific fluorescent signal in the cell cytoplasm at all developmental stages, giving support to the idea that the ∼39 kDa polypeptide is a soluble DING protein. Thus, we have identified and characterized a protein fraction with a DING protein from C. chinense.
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Affiliation(s)
- Ligia Brito-Argáez
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán A.C., Calle 43 No. 130, Colonia Chuburná de Hidalgo, C.P. 97200, Mérida, Yucatán, Mexico
| | - José A Tamayo-Sansores
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán A.C., Calle 43 No. 130, Colonia Chuburná de Hidalgo, C.P. 97200, Mérida, Yucatán, Mexico
| | - Dianeli Madera-Piña
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán A.C., Calle 43 No. 130, Colonia Chuburná de Hidalgo, C.P. 97200, Mérida, Yucatán, Mexico
| | - Francisco J García-Villalobos
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán A.C., Calle 43 No. 130, Colonia Chuburná de Hidalgo, C.P. 97200, Mérida, Yucatán, Mexico
| | - Rosa E Moo-Puc
- Unidad de Investigación, Instituto Mexicano del Seguro Social, IMSS, T1, C.P. 97150, Mérida, Yucatán, Mexico
| | - Ángela Kú-González
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán A.C., Calle 43 No. 130, Colonia Chuburná de Hidalgo, C.P. 97200, Mérida, Yucatán, Mexico
| | - Marco A Villanueva
- Unidad Académica de Sistemas Arrecifales, Instituto de Ciencias del Mar y Limnología, Universidad Nacional Autónoma de México, Puerto Morelos, Quintana Roo, C.P. 77580, Mexico
| | - Ignacio Islas-Flores
- Unidad de Bioquímica y Biología Molecular de Plantas, Centro de Investigación Científica de Yucatán A.C., Calle 43 No. 130, Colonia Chuburná de Hidalgo, C.P. 97200, Mérida, Yucatán, Mexico.
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19
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Kanthala S, Mill CP, Riese DJ 2nd, Jaiswal M, Jois S. Expression and purification of HER2 extracellular domain proteins in Schneider2 insect cells. Protein Expr Purif 2016; 125:26-33. [PMID: 26363121 DOI: 10.1016/j.pep.2015.09.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Revised: 08/27/2015] [Accepted: 09/03/2015] [Indexed: 02/07/2023]
Abstract
Overexpression of human epidermal growth factor receptor 2 (HER2/ErbB2/Neu) results in ligand independent activation of kinase signaling and is found in about 30% of human breast cancers, and is correlated with a more aggressive tumor phenotype. The HER2 extracellular domain (ECD) consists of four domains - I, II, III and IV. Although the role of each domain in the dimerization and activation of the receptor has been extensively studied, the role of domain IV (DIV) is not clearly understood yet. In our previous studies, we reported peptidomimetic molecules inhibit HER2:HER3 heterodimerization. In order to study the binding interactions of peptidomimetics with HER2 DIV in detail, properly folded recombinant HER2 protein in pure form is important. We have expressed and purified HER2 ECD and DIV proteins in the Drosophila melanogaster Schneider2 (S2) cell line. Using the commercial Drosophila expression system (DES), we transfected S2 cells with plasmids designed to direct the expression of secreted recombinant HER2 ECD and DIV proteins. The secreted proteins were purified from the conditioned medium by filtration, ultrafiltration, dialysis and nickel affinity chromatography techniques. The purified HER2 proteins were then analyzed using Western blot, mass spectrometry and circular dichroism (CD) spectroscopy.
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20
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Gholami D, Goodarzi T, Aminzadeh S, Alavi SM, Kazemipour N, Farrokhi N. Bacterial Secretome Analysis in Hunt for Novel Bacteriocins with Ability to Control Xanthomonas citri subsp. Citri. Iran J Biotechnol 2015; 13:10-19. [PMID: 28959294 PMCID: PMC5435018 DOI: 10.15171/ijb.1123] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2015] [Revised: 06/27/2015] [Accepted: 08/27/2015] [Indexed: 11/09/2022]
Abstract
BACKGROUND Xanthomonas citri subsp. citri (Xcc), the causative agent of bacterial citrus canker, has affected citriculture worldwide. Varieties of means have been used to minimize its devastating effects, but no attention has been given to bacteriocins. OBJECTIVES Here and for the first time, we report the isolation and characterization of two novel bacteriocins. MATERIALS AND METHODS Secretome containing bacteriocins of isolated bacteria was separated via SDS-PAGE. Each isolated protein band was characterized and checked for its efficacy in controlling two pathogenic isolates of Xcc via disk diffusion assay. The effects of varieties of carbon, nitrogen and phosphate sources were evaluated on both bacterial growth and bacteriocin production via Taguchi orthogonal method. RESULTS The two bacteriocins showed an activity up to 55ºC that were sensitive to proteases suggesting being protein in nature. Analysis of SDS-PAGE purified protein bands of bacterial secretomes with demonstrated potency against Xcc revealed the presence of peptides with relative molecular masses of 16.9 and 17 kDa for Cronobacter and Enterobacter, respectively. Sequence analysis of peptides revealed an HCP1 family VI secretion system homologue for Cronobacter (YP_001439956) and pilin FimA homologue for Enterobacter (CBK85798.1). A Taguchi orthogonal array was also implemented to determine the effect of temperature and eight other chemical factors on bacteriocin production for each bacterium. CONCLUSIONS Two peptides with novel antibacterial activities effective against Xcc were isolated, characterized and conditions were optimized for their higher production.
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Affiliation(s)
- Dariush Gholami
- Department of Bioprocess Engineering, National Institute for Genetic Engineering and Biotechnology, Tehran, Iran
- Science Department, Sistan-Baluchistan University, Zahedan, Iran
| | - Tannaz Goodarzi
- Department of Bioprocess Engineering, National Institute for Genetic Engineering and Biotechnology, Tehran, Iran
| | - Saeed Aminzadeh
- Department of Bioprocess Engineering, National Institute for Genetic Engineering and Biotechnology, Tehran, Iran
| | - Seyed Mehdi Alavi
- Department of Bioprocess Engineering, National Institute for Genetic Engineering and Biotechnology, Tehran, Iran
| | | | - Naser Farrokhi
- Department of Biotechnology, Faculty of New Technologies and Energy Engineering, Shahid Beheshti University, Tehran, Iran
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21
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Chen L, Wang N, Sun D, Li L. Microwave-assisted acid hydrolysis of proteins combined with peptide fractionation and mass spectrometry analysis for characterizing protein terminal sequences. J Proteomics 2014; 100:68-78. [PMID: 24145141 DOI: 10.1016/j.jprot.2013.10.014] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Revised: 09/24/2013] [Accepted: 10/09/2013] [Indexed: 12/17/2022]
Abstract
We report a relatively simple mass spectrometric technique for characterizing the terminal amino acid sequences of proteins. It is based on the use of microwave-assisted acid hydrolysis (MAAH) with 3M HCl to hydrolyze a protein into polypeptide ladders with varying sizes of up to the molecular mass of the protein. The hydrolysate is then fractionated by isocratic reversed phase liquid chromatography (RPLC) to produce a low-mass-peptide fraction mainly consisting of the terminal peptides. This fraction is subjected to LC tandem mass spectrometry (MS/MS) analysis to generate the terminal peptide sequence information. Using bovine serum albumin as an example, it is shown that more than 10 terminal peptides of each end could be identified using as little as 0.5μg (7.5pmol) of protein. This method was applied for the characterization of a recombinant protein (mCherry with an additional sequence tag added to the N-terminal for expression and purification) and its truncated form (mCherry treated with enterokinase to cleave off the tag). Sequence errors and unexpected by-products with different terminal sequences were determined from these two samples, illustrating that this method of HCl MAAH with peptide fractionation and LC-MS/MS analysis should be useful for detailed characterization of protein terminal sequences. BIOLOGICAL SIGNIFICANCE Protein terminal truncation or modification plays an important role in determining the biological functions of a protein. Detailed characterization of protein terminal sequences is critical in biological studies as well as in the development and quality control of protein-based therapeutics and vaccines. In this work, we report a relatively simple method for analyzing protein terminal sequences based on microwave-assisted acid hydrolysis to generate the peptide ladder of a protein, liquid chromatography fractionation of the resultant ladder to collect the low-mass-peptide fraction which mainly contains terminal peptides, and LC-ESI MS/MS sequencing of the collected peptides. This article is part of a Special Issue entitled: Can Proteomics Fill the Gap Between Genomics and Phenotypes?
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Affiliation(s)
- Lu Chen
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Nan Wang
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Difei Sun
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Liang Li
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada.
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22
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Zheng Q, Zhang H, Chen H. Integration of online digestion and electrolytic reduction with mass spectrometry for rapid disulfide-containing protein structural analysis. Int J Mass Spectrom 2013; 353:84-92. [PMID: 25419170 PMCID: PMC4240030 DOI: 10.1016/j.ijms.2013.04.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Bottom-up structural analysis of disulfide-bond containing proteins usually involves time-consuming offline enzymatic digestion, chemical reduction and thiol protection prior to mass spectrometric detection, which takes many hours. This paper presents an expedited bottom-up approach, employing desorption electrospray ionization-mass spectrometry (DESI-MS) coupled with online pepsin digestion and online electrochemical reduction of disulfide bonds. Peptides are generated in high digestion yield as its precursor protein in acidic aqueous solution flows through a pepsin column, which can undergo direct electrolysis. The electrolytic behaviors of peptides, as online monitored by DESI-MS, suggest the presence or absence of disulfide bonds in the peptides, and also provide information to relate disulfide bond-containing peptide precursors to their corresponding reduced products. Furthermore, selective electrolysis simply using different reduction potentials can be adopted to generate either partially or fully reduced peptides to assist disulfide bond mapping. In addition, it turns out that DESI is suitable for ionizing peptides in water without organic solvent additives (organic solvent additives would not be compatible with the use of pepsin column). The feasibility of this method was demonstrated using insulin, a protein carrying three pairs of disulfide-bonds as an example, in which all disulfide bond linkages and most of the protein sequence were successfully determined. Strikingly, this method shortens the sample digestion, reduction and MS detection from hours to less than 7 min, which could be of high value in high-throughput proteomics research.
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Affiliation(s)
- Qiuling Zheng
- Center for Intelligent Chemical Instrumentation, Department of Chemistry and Biochemistry, Ohio University, Athens, OH 45701, USA
| | - Hao Zhang
- Department of Chemistry, Washington University, St. Louis, MO 63130, USA
- Corresponding author. Tel.: +1 314 935 7486
| | - Hao Chen
- Center for Intelligent Chemical Instrumentation, Department of Chemistry and Biochemistry, Ohio University, Athens, OH 45701, USA
- Corresponding author. Tel.: +1 740 593 0719; fax: +1 740 597 3157
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