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Polańska O, Szulc N, Stottko R, Olek M, Nadwodna J, Gąsior-Głogowska M, Szefczyk M. Challenges in Peptide Solubilization - Amyloids Case Study. CHEM REC 2024:e202400053. [PMID: 39023378 DOI: 10.1002/tcr.202400053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 05/23/2024] [Indexed: 07/20/2024]
Abstract
Peptide science has been a rapidly growing research field because of the enormous potential application of these biocompatible and bioactive molecules. However, many factors limit the widespread use of peptides in medicine, and low solubility is among the most common problems that hamper drug development in the early stages of research. Solubility is a crucial, albeit poorly understood, feature that determines peptide behavior. Several different solubility predictors have been proposed, and many strategies and protocols have been reported to dissolve peptides, but none of them is a one-size-fits-all method for solubilization of even the same peptide. In this review, we look for the reasons behind the difficulties in dissolving peptides, analyze the factors influencing peptide aggregation, conduct a critical analysis of solubilization strategies and protocols available in the literature, and give some tips on how to deal with the so-called difficult sequences. We focus on amyloids, which are particularly difficult to dissolve and handle such as amyloid beta (Aβ), insulin, and phenol-soluble modulins (PSMs).
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Affiliation(s)
- Oliwia Polańska
- Department of Biomedical Engineering, Faculty of Fundamental Problems of Technology, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Natalia Szulc
- Department of Physics and Biophysics, Wroclaw University of Environmental and Life Sciences, Norwida 25, 50-375, Wrocław, Poland
| | - Rafał Stottko
- Faculty of Chemistry, Wrocław University of Science and Technology, Gdanska 7/9, 50-344, Wrocław, Poland
| | - Mateusz Olek
- Faculty of Medical Sciences in Zabrze, Medical University of Silesia in Katowice, Traugutta 2, 41-800 Zabrze, Poland
| | - Julita Nadwodna
- Department of Biomedical Engineering, Faculty of Fundamental Problems of Technology, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Marlena Gąsior-Głogowska
- Department of Biomedical Engineering, Faculty of Fundamental Problems of Technology, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370, Wroclaw, Poland
| | - Monika Szefczyk
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370, Wroclaw, Poland
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2
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Seifert B, Baudis S, Wischke C. Composition-Dependent Protein-Material Interaction of Poly(Methyl Methacrylate- co-styrene) Nanoparticle Series. Int J Mol Sci 2023; 24:16390. [PMID: 38003579 PMCID: PMC10671716 DOI: 10.3390/ijms242216390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 11/09/2023] [Accepted: 11/14/2023] [Indexed: 11/26/2023] Open
Abstract
Polymer nanoparticles continue to be of high interest in life science applications. Still, adsorption processes occurring in protein-containing media and their implications for biological responses are not generally predictable. Here, the effect of nanoparticle composition on the adsorption of bovine serum albumin (BSA), fibronectin (FN) and immunoglobulin G (IgG) as structurally and functionally different model proteins was explored by systematically altering the composition of poly(methyl methacrylate-co-styrene) nanoparticles with sizes in a range of about 550 nm. As determined by protein depletion from the suspension medium via a colorimetric assay, BSA and IgG adsorbed at similar quantities, while FN reached larger masses of adsorbed protein (up to 0.4 ± 0.06 µg·cm-2 BSA, 0.42 ± 0.09 µg·cm-2 IgG, 0.72 ± 0.04 µg·cm-2 FN). A higher content of styrene as the more hydrophobic polymer component enhanced protein binding, which suggests a contribution of hydrophobic interactions despite the particles exhibiting strongly negatively charged surfaces with zeta potentials of -44 to -52 mV. The quantities of adsorbed proteins were estimated to correspond to a confluent surface coverage. Overall, this study illustrated how protein binding can be controlled by systematically varying the nanoparticle bulk composition and may serve as a basis for establishing interfaces with a targeted level of protein retention and/or presentation.
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3
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Mohanta TK, Kamran MS, Omar M, Anwar W, Choi GS. PlantMWpIDB: a database for the molecular weight and isoelectric points of the plant proteomes. Sci Rep 2022; 12:7421. [PMID: 35523906 PMCID: PMC9076895 DOI: 10.1038/s41598-022-11077-z] [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] [Received: 06/22/2021] [Accepted: 04/11/2022] [Indexed: 01/14/2023] Open
Abstract
The molecular weight and isoelectric point of the proteins are very important parameters that control their subcellular localization and subsequent function. Although the genome sequence data of the plant kingdom improved enormously, the proteomic details have been poorly elaborated. Therefore, we have calculated the molecular weight and isoelectric point of the plant proteins and reported them in this database. A database, PlantMWpIDB, containing protein data from 342 plant proteomes was created to provide information on plant proteomes for hypothesis formulation in basic research and for biotechnological applications. The Molecular weight and isoelectric point (pI) are important molecular parameters of proteins that are useful when conducting protein studies involving 2D gel electrophoresis, liquid chromatography-mass spectrometry, and X-ray protein crystallography. PlantMWpIDB provides an easy-to-use and efficient interface for search options and generates a summary of basic protein parameters. The database represents a virtual 2D proteome map of plants, and the molecular weight and pI of a protein can be obtained by searching on the name of a protein, a keyword, or by a list of accession numbers. The PlantMWpIDB database also allows one to query protein sequences. The database can be found in the following link https://plantmwpidb.com/ . The individual 2D virtual proteome map of the plant kingdom will enable us to understand the proteome diversity between different species. Further, the molecular weight and isoelectric point of individual proteins can enable us to understand their functional significance in different species.
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Affiliation(s)
- Tapan Kumar Mohanta
- Natural and Medical Sciences Research Center, University of Nizwa, Nizwa, 616, Oman.
| | - Muhammad Shahzad Kamran
- Department of Computer Science and IT, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Muhammad Omar
- Department of Data Science, Faculty of Computing, The Islamia University of Bahawalpur, Bahawalpur, Pakistan.,Department of Information and Communication Engineering, Yeungnam University, 214-1, Gyeongsan-si, 712-749, South Korea
| | - Waheed Anwar
- Department of Computer Science and IT, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Gyu Sang Choi
- Department of Information and Communication Engineering, Yeungnam University, 214-1, Gyeongsan-si, 712-749, South Korea.
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Shahrear S, Afroj Zinnia M, Sany MRU, Islam ABMMK. Functional Analysis of Hypothetical Proteins of Vibrio parahaemolyticus Reveals the Presence of Virulence Factors and Growth-Related Enzymes With Therapeutic Potential. Bioinform Biol Insights 2022; 16:11779322221136002. [PMID: 36386863 PMCID: PMC9661560 DOI: 10.1177/11779322221136002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 09/30/2022] [Indexed: 11/11/2022] Open
Abstract
Vibrio parahaemolyticus, an aquatic pathogen, is a major concern in the shrimp aquaculture industry. Several strains of this pathogen are responsible for causing acute hepatopancreatic necrosis disease as well as other serious illness, both of which result in severe economic losses. The genome sequence of two pathogenic strains of V. parahaemolyticus, MSR16 and MSR17, isolated from Bangladesh, have been reported to gain a better understanding of their diversity and virulence. However, the prevalence of hypothetical proteins (HPs) makes it challenging to obtain a comprehensive understanding of the pathogenesis of V. parahaemolyticus. The aim of the present study is to provide a functional annotation of the HPs to elucidate their role in pathogenesis employing several in silico tools. The exploration of protein domains and families, similarity searches against proteins with known function, gene ontology enrichment, along with protein-protein interaction analysis of the HPs led to the functional assignment with a high level of confidence for 656 proteins out of a pool of 2631 proteins. The in silico approach used in this study was important for accurately assigning function to HPs and inferring interactions with proteins with previously described functions. The HPs with function predicted were categorized into various groups such as enzymes involved in small-compound biosynthesis pathway, iron binding proteins, antibiotics resistance proteins, and other proteins. Several proteins with potential druggability were identified among them. In addition, the HPs were investigated in search of virulent factors, which led to the identification of proteins that have the potential to be exploited as vaccine candidate. The findings of the study will be effective in gaining a better understanding of the molecular mechanisms of bacterial pathogenesis. They may also provide an insight into the process of evaluating promising targets for the development of drugs and vaccines against V. parahaemolyticus.
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Affiliation(s)
- Sazzad Shahrear
- Department of Genetic Engineering and Biotechnology, University of Dhaka, Dhaka, Bangladesh
| | | | - Md. Rabi Us Sany
- Department of Genetic Engineering and Biotechnology, University of Dhaka, Dhaka, Bangladesh
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5
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Reis PBPS, Clevert DA, Machuqueiro M. pKPDB: a protein data bank extension database of pKa and pI theoretical values. Bioinformatics 2021; 38:297-298. [PMID: 34260689 DOI: 10.1093/bioinformatics/btab518] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 07/02/2021] [Accepted: 07/08/2021] [Indexed: 02/03/2023] Open
Abstract
SUMMARY pKa values of ionizable residues and isoelectric points of proteins provide valuable local and global insights about their structure and function. These properties can be estimated with reasonably good accuracy using Poisson-Boltzmann and Monte Carlo calculations at a considerable computational cost (from some minutes to several hours). pKPDB is a database of over 12 M theoretical pKa values calculated over 120k protein structures deposited in the Protein Data Bank. By providing precomputed pKa and pI values, users can retrieve results instantaneously for their protein(s) of interest while also saving countless hours and resources that would be spent on repeated calculations. Furthermore, there is an ever-growing imbalance between experimental pKa and pI values and the number of resolved structures. This database will complement the experimental and computational data already available and can also provide crucial information regarding buried residues that are under-represented in experimental measurements. AVAILABILITY AND IMPLEMENTATION Gzipped csv files containing p Ka and isoelectric point values can be downloaded from https://pypka.org/pKPDB. To query a single PDB code please use the PypKa free server at https://pypka.org. The pKPDB source code can be found at https://github.com/mms-fcul/pKPDB. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Pedro B P S Reis
- Department of Chemistry and Biochemistry, Faculty of Sciences, University of Lisbon, 1749-016 Lisboa, Portugal.,Bayer AG, Research & Development, Pharmaceuticals. Machine Learning Research, 13353 Berlin, Germany
| | - Djork-Arné Clevert
- Bayer AG, Research & Development, Pharmaceuticals. Machine Learning Research, 13353 Berlin, Germany
| | - Miguel Machuqueiro
- Department of Chemistry and Biochemistry, Faculty of Sciences, University of Lisbon, 1749-016 Lisboa, Portugal
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Tokmakov AA, Kurotani A, Sato KI. Protein pI and Intracellular Localization. Front Mol Biosci 2021; 8:775736. [PMID: 34912847 PMCID: PMC8667598 DOI: 10.3389/fmolb.2021.775736] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Accepted: 11/11/2021] [Indexed: 11/13/2022] Open
Abstract
The protein isoelectric point (pI) can be calculated from an amino acid sequence using computational analysis in a good agreement with experimental data. Availability of whole-genome sequences empowers comparative studies of proteome-wide pI distributions. It was found that the whole-proteome distributions of protein pI values are multimodal in different species. It was further hypothesized that the observed multimodality is associated with subcellular localization-specific differences in local pI distributions. Here, we overview the multimodality of proteome-wide pI distributions in different organisms focusing on the relationships between protein pI and subcellular localization. We also discuss the probable factors responsible for variation of the intracellular localization-specific pI profiles.
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Affiliation(s)
- Alexander A Tokmakov
- Department of Genetic Engineering, Faculty of Biology-Oriented Science and Technology, Kindai University, Wakayama, Japan
| | - Atsushi Kurotani
- Center for Sustainable Resource Science, RIKEN Yokohama Institute, Yokohama, Japan
| | - Ken-Ichi Sato
- Laboratory of Cell Signaling and Development, Faculty of Life Sciences, Kyoto Sangyo University, Kyoto, Japan
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7
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Kozlowski LP. IPC 2.0: prediction of isoelectric point and pKa dissociation constants. Nucleic Acids Res 2021; 49:W285-W292. [PMID: 33905510 PMCID: PMC8262712 DOI: 10.1093/nar/gkab295] [Citation(s) in RCA: 56] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2021] [Revised: 04/03/2021] [Accepted: 04/12/2021] [Indexed: 01/05/2023] Open
Abstract
The isoelectric point is the pH at which a particular molecule is electrically neutral due to the equilibrium of positive and negative charges. In proteins and peptides, this depends on the dissociation constant (pKa) of charged groups of seven amino acids and NH+ and COO− groups at polypeptide termini. Information regarding isoelectric point and pKa is extensively used in two-dimensional gel electrophoresis (2D-PAGE), capillary isoelectric focusing (cIEF), crystallisation, and mass spectrometry. Therefore, there is a strong need for the in silico prediction of isoelectric point and pKa values. In this paper, I present Isoelectric Point Calculator 2.0 (IPC 2.0), a web server for the prediction of isoelectric points and pKa values using a mixture of deep learning and support vector regression models. The prediction accuracy (RMSD) of IPC 2.0 for proteins and peptides outperforms previous algorithms: 0.848 versus 0.868 and 0.222 versus 0.405, respectively. Moreover, the IPC 2.0 prediction of pKa using sequence information alone was better than the prediction from structure-based methods (0.576 versus 0.826) and a few folds faster. The IPC 2.0 webserver is freely available at www.ipc2-isoelectric-point.org
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Affiliation(s)
- Lukasz Pawel Kozlowski
- Institute of Informatics, Faculty of Mathematics, Informatics, and Mechanics, University of Warsaw, Warsaw, Mazovian Voivodeship 02-097, Poland
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8
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Abass OA, Timofeev VI, Sarkar B, Onobun DO, Ogunsola SO, Aiyenuro AE, Aborode AT, Aigboje AE, Omobolanle BN, Imolele AG, Abiodun AA. Immunoinformatics analysis to design novel epitope based vaccine candidate targeting the glycoprotein and nucleoprotein of Lassa mammarenavirus (LASMV) using strains from Nigeria. J Biomol Struct Dyn 2021; 40:7283-7302. [PMID: 33719908 DOI: 10.1080/07391102.2021.1896387] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Lassa mammarenavirus (LASMV) is responsible for a specific type of acute viral hemorrhagic fever known as Lassa fever. Lack of effective treatments and counter-measures against the virus has resulted in a high mortality rate in its endemic regions. Therefore, in this study, a novel epitope-based vaccine has been designed using the methods of immunoinformatics targeting the glycoprotein and nucleoprotein of the virus. After numerous robust analyses, two CTL epitopes, eight HTL epitopes and seven B-cell epitopes were finally selected for constructing the vaccine. All these most promising epitopes were found to be antigenic, non-allergenic, nontoxic and non-human homolog, which made them suitable for designing the subunit vaccine. Furthermore, the selected T-cell epitopes which were found to be fully conserved across different isolates of the virus, were also considered for final vaccine construction. After that, numerous validation experiments, i.e. molecular docking, molecular dynamics simulation and immune simulation were conducted, which predicted that our designed vaccine should be stable within the biological environment and effective in combating the LASMV infection. In the end, codon adaptation and in silico cloning studies were performed to design a recombinant plasmid for producing the vaccine industrially. However, further in vitro and in vivo assessments should be done on the constructed vaccine to finally confirm its safety and efficacy.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Ohilebo Abdulateef Abass
- Department of Bioinformatics & Computational Biology, Centre for BioCode, Benin, Nigeria.,Department of Biochemistry, Faculty of Life Sciences, Ambrose Alli University, Ekpoma, Nigeria
| | - Vladimir I Timofeev
- Shubnikov Institute of Crystallography of Federal Scientific Research Centre "Crystallography and Photonics" of Russian Academy of Sciences, Moscow, Russian Federation
| | - Bishajit Sarkar
- Department of Biotechnology & Genetic Engineering, Faculty of Biological Sciences, Jahangirnagar University, Dhaka, Bangladesh
| | - Desmond Odiamehi Onobun
- Department of Bioinformatics & Computational Biology, Centre for BioCode, Benin, Nigeria.,Department of Biochemistry, Faculty of Life Sciences, Ambrose Alli University, Ekpoma, Nigeria
| | | | | | - Abdullahi Tunde Aborode
- Research & Development, Shaping Women in STEM (SWIS) Africa, Lagos, Nigeria.,Research & Development, Healthy Africans Platform, Ibadan, Nigeria
| | | | | | | | - Alade Adebowale Abiodun
- Bio-Computing Research Unit, Molecular Biology & Simulations (Mols & Sims) Centre, Ado-Ekiti, Nigeria
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9
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Odhar HA, Ahjel SW, Humadi SS. Towards the design of multiepitope-based peptide vaccine candidate against SARS-CoV-2.. [DOI: 10.1101/2020.07.07.186122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
AbstractCoronavirus disease 2019 is a current pandemic health threat especially for elderly patients with comorbidities. This respiratory disease is caused by a beta coronavirus known as severe acute respiratory syndrome coronavirus 2. The disease can progress into acute respiratory distress syndrome that can be fatal. Currently, no specific drug or vaccine are available to combat this pandemic outbreak. Social distancing and lockdown have been enforced in many places worldwide. The spike protein of coronavirus 2 is essential for viral entry into host target cells via interaction with angiotensin converting enzyme 2. This viral protein is considered a potential target for design and development of a drug or vaccine. Previously, we have reported several potential epitopes on coronavirus 2 spike protein with high antigenicity, low allergenicity and good stability against specified proteases. In the current study, we have constructed and evaluated a peptide vaccine from these potential epitopes by using in silico approach. This construct is predicted to have a protective immunogenicity, low allergenicity and good stability with minor structural flaws in model build. The population coverage of the used T-cells epitopes is believed to be high according to the employed restricted alleles. The vaccine construct can elicit efficient and long-lasting immune response as appeared through simulation analysis. This multiepitope-based peptide vaccine may represent a potential candidate against coronavirus 2. However, further in vitro and in vivo verification are required.
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10
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Odhar HA, Ahjel SW, Humadi SS. Towards the design of epitope candidates for Coronavirus 2. Bioinformation 2020; 16:375-386. [PMID: 32831518 PMCID: PMC7434951 DOI: 10.6026/97320630016375] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Revised: 04/12/2020] [Accepted: 04/12/2020] [Indexed: 01/21/2023] Open
Abstract
The severe acute respiratory syndrome coronavirus-2, formerly known as 2019 novel coronavirus, is a pandemic public health threat. This beta coronavirus potentially infects the alveolar cells of the lung leading to pneumonia. The disease may progress into acute respiratory distress syndrome especially in elderly patients with comorbidities. Therefore, it is of interest to design and develop candidates for treatment, therapy and prevention. The spike glycoprotein of the virus known to potentially interact with angiotensin converting enzyme 2 as a cell entry receptor is a suitable candidate for further consideration as vaccine and treatment candidate. Hence, we screened the spike protein of coronavirus-2 for potential B-cell and T-cell epitopes for further deliberation. Thus, we document several peptides on the spike protein with predicted high antigenicity, low allergenicity and good stability against selected proteases. The linear B-cell epitope with sequence 'GFNCYFPLQSYGF' is of particular interest in this context towards the design and development of short peptide vaccine candidates for combat and care against the virus.
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Affiliation(s)
| | | | - Suhad Sami Humadi
- Department of pharmacy, Al-Zahrawi University College, Karbala, Iraq
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11
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Füssl F, Criscuolo A, Cook K, Scheffler K, Bones J. Cracking Proteoform Complexity of Ovalbumin with Anion-Exchange Chromatography–High-Resolution Mass Spectrometry under Native Conditions. J Proteome Res 2019; 18:3689-3702. [DOI: 10.1021/acs.jproteome.9b00375] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Florian Füssl
- NIBRT—The National Institute for Bioprocessing Research and Training, Foster Avenue,
Mount Merrion, Blackrock, Co. Dublin A94 X099, Ireland
| | - Angela Criscuolo
- Thermo Fisher Scientific, Hanna-Kunath-Strasse 11, 28199 Bremen, Germany
| | - Ken Cook
- Thermo Fisher Scientific, Stafford House, 1 Boundary Park, Hemel Hempstead HP2 7GE, United Kingdom
| | - Kai Scheffler
- Thermo Fisher Scientific, Dornierstrasse 4, 82110 Germering, Germany
| | - Jonathan Bones
- NIBRT—The National Institute for Bioprocessing Research and Training, Foster Avenue,
Mount Merrion, Blackrock, Co. Dublin A94 X099, Ireland
- School of Chemical and Bioprocess Engineering, University College Dublin, Belfield, Dublin 4 D04 V1W8, Ireland
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12
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Guckeisen T, Hosseinpour S, Peukert W. Isoelectric Points of Proteins at the Air/Liquid Interface and in Solution. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:5004-5012. [PMID: 30892047 DOI: 10.1021/acs.langmuir.9b00311] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Electrostatic interactions play essential roles in determining the function, colloidal stability, and adsorption of proteins on different surfaces and interfaces. Therefore, a molecular-level understanding of the charge state of the proteins under different conditions is required to explain their macroscopic properties. In this study, we have employed an inherently surface-sensitive spectroscopic tool, sum frequency generation spectroscopy, to determine the charge state of a wide range of proteins as a function of pH at the air/liquid interface via measurement of the degree of orientation of water molecules. We compared the isoelectric point (IEP) of the 12 investigated proteins at the air/liquid interface with that in the bulk solution obtained through zeta potential measurements. Ellipsometry is performed to determine the film thickness at the air/liquid interface at different charge states. In particular, protein aggregation at the IEP is reflected by increased film thickness. For all proteins, the interfacial point of zero charge is close (with less than 1 pH unit variation) to that in the bulk solution.
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Affiliation(s)
- Tobias Guckeisen
- Institute of Particle Technology (LFG) , Friedrich-Alexander-Universität-Erlangen-Nürnberg (FAU) , Cauerstraße 4 , 91058 Erlangen , Germany
| | - Saman Hosseinpour
- Institute of Particle Technology (LFG) , Friedrich-Alexander-Universität-Erlangen-Nürnberg (FAU) , Cauerstraße 4 , 91058 Erlangen , Germany
| | - Wolfgang Peukert
- Institute of Particle Technology (LFG) , Friedrich-Alexander-Universität-Erlangen-Nürnberg (FAU) , Cauerstraße 4 , 91058 Erlangen , Germany
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13
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Determination of 5-fluorouracil and tegafur in tear fluid of patients treated with oral fluoropyrimidine anticancer agent, S-1. Jpn J Ophthalmol 2018; 62:432-437. [DOI: 10.1007/s10384-018-0603-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2017] [Accepted: 05/01/2018] [Indexed: 11/27/2022]
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14
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Htwe EE, Nakama Y, Imanaka H, Ishida N, Imamura K. Influence of an external electric field on removal of protein fouling on a stainless steel surface by proteolytic enzymes. Colloids Surf B Biointerfaces 2017; 159:118-124. [PMID: 28780458 DOI: 10.1016/j.colsurfb.2017.07.074] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 07/20/2017] [Accepted: 07/26/2017] [Indexed: 10/19/2022]
Abstract
Enzymatic cleaning is a potentially useful method for removing proteinaceous fouling from solid surfaces under mild conditions. Herein, the influence of an external electric field on the enzymatic cleaning of a metal surface fouled with a protein was investigated. The model fouling protein (BSA; lysozyme) was prepared on a stainless steel (St) surface, and the resulting surface subjected to enzymatic cleaning with an electric potential being applied to the St plate. Trypsin, α-chymotrypsin, and thermolysin were used as model proteases. The amounts of protein remaining on the plate before and during the cleaning process were measured by means of a reflection absorption technique using Fourier transform infrared spectroscopy. In the case for BSA fouling, the cleaning efficiency of the protease tended to increase at more negative applied potentials. Whereas, there was an optimum applied potential for removing the lysozyme fouling. Atomic force microscopy analyses indicated that applying an adequate range of electric potential enhanced the enzymatic removal of protein fouling inside scratches on the St plate surface. These findings suggest the existence of two modes of electrostatic interactions for the external electric field, one with protease molecules and the other with digested fragments of the fouling protein.
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Affiliation(s)
- Ei Ei Htwe
- Division of Chemistry and Biochemistry, Graduate School of Natural Science and Technology, Okayama University, 3-1-1 Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
| | - Yuhi Nakama
- Division of Chemistry and Biochemistry, Graduate School of Natural Science and Technology, Okayama University, 3-1-1 Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
| | - Hiroyuki Imanaka
- Division of Chemistry and Biochemistry, Graduate School of Natural Science and Technology, Okayama University, 3-1-1 Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
| | - Naoyuki Ishida
- Division of Chemistry and Biochemistry, Graduate School of Natural Science and Technology, Okayama University, 3-1-1 Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
| | - Koreyoshi Imamura
- Division of Chemistry and Biochemistry, Graduate School of Natural Science and Technology, Okayama University, 3-1-1 Tsushima-naka, Kita-ku, Okayama 700-8530, Japan.
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15
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Kašička V. Recent developments in capillary and microchip electroseparations of peptides (2015-mid 2017). Electrophoresis 2017; 39:209-234. [PMID: 28836681 DOI: 10.1002/elps.201700295] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 08/15/2017] [Accepted: 08/16/2017] [Indexed: 12/17/2022]
Abstract
The review brings a comprehensive overview of recent developments and applications of high performance capillary and microchip electroseparation methods (zone electrophoresis, isotachophoresis, isoelectric focusing, affinity electrophoresis, electrokinetic chromatography, and electrochromatography) to analysis, microscale isolation, purification, and physicochemical and biochemical characterization of peptides in the years 2015, 2016, and ca. up to the middle of 2017. Advances in the investigation of electromigration properties of peptides and in the methodology of their analysis (sample preseparation, preconcentration and derivatization, adsorption suppression and EOF control, and detection) are described. New developments in particular CE and CEC methods are presented and several types of their applications to peptide analysis are reported: qualitative and quantitative analysis, determination in complex (bio)matrices, monitoring of chemical and enzymatical reactions and physical changes, amino acid, sequence and chiral analysis, and peptide mapping of proteins. Some micropreparative peptide separations are shown and capabilities of CE and CEC methods to provide important physicochemical characteristics of peptides are demonstrated.
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Affiliation(s)
- Václav Kašička
- Institute of Organic Chemistry and Biochemistry, The Czech Academy of Sciences, Prague, Czech Republic
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16
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Kozlowski LP. Proteome-pI: proteome isoelectric point database. Nucleic Acids Res 2016; 45:D1112-D1116. [PMID: 27789699 PMCID: PMC5210655 DOI: 10.1093/nar/gkw978] [Citation(s) in RCA: 169] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Revised: 10/07/2016] [Accepted: 10/13/2016] [Indexed: 11/13/2022] Open
Abstract
Proteome-pI is an online database containing information about predicted
isoelectric points for 5029 proteomes calculated using 18 methods. The isoelectric point,
the pH at which a particular molecule carries no net electrical charge, is an important
parameter for many analytical biochemistry and proteomics techniques, especially for 2D
gel electrophoresis (2D-PAGE), capillary isoelectric focusing, liquid chromatography–mass
spectrometry and X-ray protein crystallography. The database, available at http://isoelectricpointdb.org
allows the retrieval of virtual 2D-PAGE plots and the development of customised fractions
of proteome based on isoelectric point and molecular weight. Moreover,
Proteome-pI facilitates statistical comparisons of the various
prediction methods as well as biological investigation of protein isoelectric point space
in all kingdoms of life. For instance, using Proteome-pI data, it is
clear that Eukaryotes, which evolved tight control of homeostasis, encode proteins with
pI values near the cell pH. In contrast, Archaea living frequently in
extreme environments can possess proteins with a wide range of isoelectric points. The
database includes various statistics and tools for interactive browsing, searching and
sorting. Apart from data for individual proteomes, datasets corresponding to major protein
databases such as UniProtKB/TrEMBL and the NCBI non-redundant (nr)
database have also been precalculated and made available in CSV format.
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Affiliation(s)
- Lukasz P Kozlowski
- Quantitative and Computational Biology Group, Max Planck Institute for Biophysical Chemistry, Göttingen, Lower Saxony, 37077, Germany
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17
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Abstract
BACKGROUND Accurate estimation of the isoelectric point (pI) based on the amino acid sequence is useful for many analytical biochemistry and proteomics techniques such as 2-D polyacrylamide gel electrophoresis, or capillary isoelectric focusing used in combination with high-throughput mass spectrometry. Additionally, pI estimation can be helpful during protein crystallization trials. RESULTS Here, I present the Isoelectric Point Calculator (IPC), a web service and a standalone program for the accurate estimation of protein and peptide pI using different sets of dissociation constant (pKa) values, including two new computationally optimized pKa sets. According to the presented benchmarks, the newly developed IPC pKa sets outperform previous algorithms by at least 14.9 % for proteins and 0.9 % for peptides (on average, 22.1 % and 59.6 %, respectively), which corresponds to an average error of the pI estimation equal to 0.87 and 0.25 pH units for proteins and peptides, respectively. Moreover, the prediction of pI using the IPC pKa's leads to fewer outliers, i.e., predictions affected by errors greater than a given threshold. CONCLUSIONS The IPC service is freely available at http://isoelectric.ovh.org Peptide and protein datasets used in the study and the precalculated pI for the PDB and some of the most frequently used proteomes are available for large-scale analysis and future development. REVIEWERS This article was reviewed by Frank Eisenhaber and Zoltán Gáspári.
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18
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Audain E, Ramos Y, Hermjakob H, Flower DR, Perez-Riverol Y. Accurate estimation of isoelectric point of protein and peptide based on amino acid sequences. ACTA ACUST UNITED AC 2015; 32:821-7. [PMID: 26568629 PMCID: PMC5939969 DOI: 10.1093/bioinformatics/btv674] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2015] [Accepted: 11/10/2015] [Indexed: 12/02/2022]
Abstract
Motivation: In any macromolecular polyprotic system—for example protein, DNA or RNA—the isoelectric point—commonly referred to as the pI—can be defined as the point of singularity in a titration curve, corresponding to the solution pH value at which the net overall surface charge—and thus the electrophoretic mobility—of the ampholyte sums to zero. Different modern analytical biochemistry and proteomics methods depend on the isoelectric point as a principal feature for protein and peptide characterization. Protein separation by isoelectric point is a critical part of 2-D gel electrophoresis, a key precursor of proteomics, where discrete spots can be digested in-gel, and proteins subsequently identified by analytical mass spectrometry. Peptide fractionation according to their pI is also widely used in current proteomics sample preparation procedures previous to the LC-MS/MS analysis. Therefore accurate theoretical prediction of pI would expedite such analysis. While such pI calculation is widely used, it remains largely untested, motivating our efforts to benchmark pI prediction methods. Results: Using data from the database PIP-DB and one publically available dataset as our reference gold standard, we have undertaken the benchmarking of pI calculation methods. We find that methods vary in their accuracy and are highly sensitive to the choice of basis set. The machine-learning algorithms, especially the SVM-based algorithm, showed a superior performance when studying peptide mixtures. In general, learning-based pI prediction methods (such as Cofactor, SVM and Branca) require a large training dataset and their resulting performance will strongly depend of the quality of that data. In contrast with Iterative methods, machine-learning algorithms have the advantage of being able to add new features to improve the accuracy of prediction. Contact: yperez@ebi.ac.uk Availability and Implementation: The software and data are freely available at https://github.com/ypriverol/pIR. Supplementary information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Enrique Audain
- Department of Proteomics, Center of Molecular Immunology
| | - Yassel Ramos
- Department of Proteomics, Center for Genetic Engineering and Biotechnology, Ciudad de la Habana, Cuba
| | - Henning Hermjakob
- Department European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK and
| | - Darren R Flower
- School of Life and Health Sciences, Aston University, Aston Triangle, Birmingham, B4 7ET, UK
| | - Yasset Perez-Riverol
- Department European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SD, UK and
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