1
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Zhang L, Yang L, Li Y, Ma J, Du X, Cao C, Jia Y, Li R. Ultrasonic treatment of foam for the prevention of foam-induced pepsin inactivation. Colloids Surf B Biointerfaces 2022; 221:113021. [DOI: 10.1016/j.colsurfb.2022.113021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 11/10/2022] [Accepted: 11/12/2022] [Indexed: 11/16/2022]
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2
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Lee YJ, Yi YC, Lin YC, Chen CC, Hung JH, Lin JY, Ng IS. Purification and biofabrication of 5-aminolevulinic acid for photodynamic therapy against pathogens and cancer cells. BIORESOUR BIOPROCESS 2022; 9:68. [PMID: 38647835 PMCID: PMC10992327 DOI: 10.1186/s40643-022-00557-9] [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: 04/12/2022] [Accepted: 06/03/2022] [Indexed: 11/10/2022] Open
Abstract
5-Aminolevulinic acid (5-ALA) is a non-proteinogenic amino acid which has involved in heme metabolism of organisms, and has been widely applied in agriculture, and medical fields nowadays. 5-ALA is used in the elimination of pathogens or cancer cells by photodynamic therapy (PDT) owing to the photosensitizer reaction which releases the reactive oxygen species (ROS). Currently, biofabrication of 5-ALA is regarded as the most efficient and eco-friendly approach, but the complicated ingredient of medium causes the nuisance process of purification, resulting in low recovery and high producing cost. In this study, hydrogen chloride, sodium acetate, and ammonia were examined to maximize the recovery of 5-ALA from ion-exchange chromatography (IEC), thus a 92% recovery in 1 M ammonia at pH 9.5 was obtained. Afterward, the activated carbon was used for decolorization to further remove the pigments from the eluent. Four organic solvents, i.e., diethyl ether, methanol, ethanol, and acetone were compared to extract and form 5-ALA precipitation. The purified 5-ALA was verified to eliminate 74% of A549 human lung cancer and 83% of A375 melanoma skin cancer cell. Moreover, Proteus hauseri, Aeromonas hydrophila, Bacillus cereus, and Staphylococcus aureus were killed via anti-microbial PDT with 1% 5-ALA and reached 100% killing rate at optimal condition. With the addition of 0.05% 5-ALA during the culture, the growth of microalgae Chlorella sorokiniana was improved to against a common aquatic pathogen, A. hydrophila. The broad application of 5-ALA was demonstrated in this study for the first time.
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Affiliation(s)
- Yen-Ju Lee
- Department of Chemical Engineering, National Cheng Kung University, Tainan, Taiwan
| | - Ying-Chen Yi
- Department of Chemical Engineering, National Cheng Kung University, Tainan, Taiwan
| | - Yu-Chieh Lin
- Department of Chemical Engineering, National Cheng Kung University, Tainan, Taiwan
| | - Chao-Chung Chen
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Jia-Horung Hung
- Institute of Clinical Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Department of Ophthalmology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Jia-Yi Lin
- Department of Chemical Engineering, National Cheng Kung University, Tainan, Taiwan
| | - I-Son Ng
- Department of Chemical Engineering, National Cheng Kung University, Tainan, Taiwan.
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3
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Kozlowski LP. Proteome-pI 2.0: proteome isoelectric point database update. Nucleic Acids Res 2022; 50:D1535-D1540. [PMID: 34718696 PMCID: PMC8728302 DOI: 10.1093/nar/gkab944] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Revised: 09/28/2021] [Accepted: 10/04/2021] [Indexed: 11/18/2022] Open
Abstract
Proteome-pI 2.0 is an update of an online database containing predicted isoelectric points and pKa dissociation constants of proteins and peptides. 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. Additionally, it can be obtained directly from the pKa values of individual charged residues of the protein. The Proteome-pI 2.0 database includes data for over 61 million protein sequences from 20 115 proteomes (three to four times more than the previous release). The isoelectric point for proteins is predicted by 21 methods, whereas pKa values are inferred by one method. To facilitate bottom-up proteomics analysis, individual proteomes were digested in silico with the five most commonly used proteases (trypsin, chymotrypsin, trypsin + LysC, LysN, ArgC), and the peptides' isoelectric point and molecular weights were calculated. The database enables the retrieval of virtual 2D-PAGE plots and customized fractions of a proteome based on the isoelectric point and molecular weight. In addition, isoelectric points for proteins in NCBI non-redundant (nr), UniProt, SwissProt, and Protein Data Bank are available in both CSV and FASTA formats. The database can be accessed at http://isoelectricpointdb2.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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4
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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: 50] [Impact Index Per Article: 16.7] [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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5
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Lunkad R, Murmiliuk A, Tošner Z, Štěpánek M, Košovan P. Role of p KA in Charge Regulation and Conformation of Various Peptide Sequences. Polymers (Basel) 2021; 13:E214. [PMID: 33435335 PMCID: PMC7827592 DOI: 10.3390/polym13020214] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 12/31/2020] [Accepted: 01/02/2021] [Indexed: 12/15/2022] Open
Abstract
Peptides containing amino acids with ionisable side chains represent a typical example of weak ampholytes, that is, molecules with multiple titratable acid and base groups, which generally exhibit charge regulating properties upon changes in pH. Charged groups on an ampholyte interact electrostatically with each other, and their interaction is coupled to conformation of the (macro)molecule, resulting in a complex feedback loop. Their charge-regulating properties are primarily determined by the pKA of individual ionisable side-chains, modulated by electrostatic interactions between the charged groups. The latter is determined by the amino acid sequence in the peptide chain. In our previous work we introduced a simple coarse-grained model of a flexible peptide. We validated it against experiments, demonstrating its ability to quantitatively predict charge on various peptides in a broad range of pH. In the current work, we investigated two types of peptide sequences: diblock and alternating, each of them consisting of an equal number of amino acids with acid and base side-chains. We showed that changing the sequence while keeping the same overall composition has a profound effect on the conformation, whereas it practically does not affect total charge on the peptide. Nevertheless, the sequence significantly affects the charge state of individual groups, showing that the zero net effect on the total charge is a consequence of unexpected cancellation of effects. Furthermore, we investigated how the difference between the pKA of acid and base side chains affects the charge and conformation of the peptide, showing that it is possible to tune the charge-regulating properties by following simple guiding principles based on the pKA and on the amino acid sequence. Our current results provide a theoretical basis for understanding of the complex coupling between the ionisation and conformation in flexible polyampholytes, including synthetic polymers, biomimetic materials and biological molecules, such as intrinsically disordered proteins, whose function can be regulated by changes in the pH.
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Affiliation(s)
| | | | | | | | - Peter Košovan
- Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University, 128 43 Prague, Czech Republic; (R.L.); (A.M.); (Z.T.); (M.Š.)
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6
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Ladwig JE, Zhu X, Rolandi P, Hart R, Robinson J, Rydholm A. Mechanistic model of
pH
and excipient concentration during ultrafiltration and diafiltration processes of therapeutic antibodies. Biotechnol Prog 2020; 36:e2993. [DOI: 10.1002/btpr.2993] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 02/15/2020] [Accepted: 03/12/2020] [Indexed: 11/09/2022]
Affiliation(s)
| | - XiaoXiang Zhu
- Process Development Amgen, Cambridge Massachusetts USA
| | - Pablo Rolandi
- Process Development Amgen, Cambridge Massachusetts USA
| | - Roger Hart
- Process Development Amgen, Cambridge Massachusetts USA
| | | | - Amber Rydholm
- Process Engineering, Alcami Corporation Wilmington North Carolina USA
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7
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Sandoval-Lira J, Mondragón-Solórzano G, Lugo-Fuentes LI, Barroso-Flores J. Accurate Estimation of p Kb Values for Amino Groups from Surface Electrostatic Potential ( VS,min) Calculations: The Isoelectric Points of Amino Acids as a Case Study. J Chem Inf Model 2020; 60:1445-1452. [PMID: 32108480 DOI: 10.1021/acs.jcim.9b01173] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Theoretical calculation of equilibrium dissociation constants is a very computationally demanding and time-consuming process since it requires an extremely accurate computation of the solvation free energy changes for each of the species involved. By correlating the minimum surface electrostatic potential (VS,min) on the nitrogen atom of several aliphatic amino groups-calculated at the density functional theory (DFT) ωB97X-D/cc-pVDZ level of theory-we obtained regression models for each kind of substitution pattern from which we interpolate their corresponding pKb values with remarkable accuracy: primary R2 = 0.9519; secondary R2 = 0.9112; and tertiary R2 = 0.8172 (N = 20 for each family). These models were validated with tests sets (N = 5) with mean absolute error (MAE) values of 0.1213 (primary), 0.4407 (secondary), and 0.3057 (tertiary). Combining this ansatz with another previously reported by our group to estimate pKa values [Caballero-García, G.; et al. Molecules 2019, 24(1), 79] we are able to reproduce the isoelectric points of 13 amino acids with no titrable side chains with MAE = 0.4636 pI units.
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Affiliation(s)
- Jacinto Sandoval-Lira
- Centro Conjunto de Investigación en Quı́mica Sustentable UAEM-UNAM, Carretera Toluca-Atlacomulco Km. 14.5, Unidad San Cayetano, Toluca de Lerdo 50200, México.,Instituto de Quı́mica, Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria, CDMX 04510, México
| | - Gustavo Mondragón-Solórzano
- Centro Conjunto de Investigación en Quı́mica Sustentable UAEM-UNAM, Carretera Toluca-Atlacomulco Km. 14.5, Unidad San Cayetano, Toluca de Lerdo 50200, México.,Instituto de Quı́mica, Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria, CDMX 04510, México
| | - Leonardo I Lugo-Fuentes
- Departamento de Quı́mica, División de Ciencias Naturales y Exactas, Universidad de Guanajuato, Noria Alta S/N, Guanajuato 36050, México
| | - Joaquín Barroso-Flores
- Centro Conjunto de Investigación en Quı́mica Sustentable UAEM-UNAM, Carretera Toluca-Atlacomulco Km. 14.5, Unidad San Cayetano, Toluca de Lerdo 50200, México.,Instituto de Quı́mica, Universidad Nacional Autónoma de México, Circuito Exterior, Ciudad Universitaria, CDMX 04510, México
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8
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Hong Y, Truong AD, Lee J, Lee K, Kim GB, Heo KN, Lillehoj HS, Hong YH. Identification of duck liver-expressed antimicrobial peptide 2 and characterization of its bactericidal activity. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2018; 32:1052-1061. [PMID: 30381731 PMCID: PMC6601062 DOI: 10.5713/ajas.18.0571] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/28/2018] [Accepted: 10/26/2018] [Indexed: 01/22/2023]
Abstract
Objective This study was conducted to identify duck liver-expressed antimicrobial peptide 2 (LEAP-2) and demonstrate its antimicrobial activity against various pathogens. Methods Tissue samples were collected from 6 to 8-week-old Pekin ducks (Anas platyrhynchos domesticus), total RNA was extracted, and cDNA was synthesized. To confirm the duck LEAP-2 transcript expression levels, quantitative real-time polymerase chain reaction was conducted. Two kinds of peptides (a linear peptide and a disulfide-type peptide) were synthesized to compare the antimicrobial activity. Then, antimicrobial activity assay and fluorescence microscopic analysis were conducted to demonstrate duck LEAP-2 bactericidal activity. Results The duck LEAP-2 peptide sequence showed high identity with those of other avian species (>85%), as well as more than 55% of identity with mammalian sequences. LEAP-2 mRNA was highly expressed in the liver with duodenum next, and then followed by lung, spleen, bursa and jejunum and was the lowest in the muscle. Both of LEAP-2 peptides efficiently killed bacteria, although the disulfide-type LEAP-2 showed more powerful bactericidal activity. Also, gram-positive bacteria was more susceptible to duck LEAP-2 than gram-negative bacteria. Using microscopy, we confirmed that LEAP-2 peptides could kill bacteria by disrupting the bacterial cell envelope. Conclusion Duck LEAP-2 showed its antimicrobial activity against both gram-positive and gram-negative bacteria. Disulfide bonds were important for the powerful killing effect by disrupting the bacterial cell envelope. Therefore, duck LEAP-2 can be used for effective antibiotics alternatives.
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Affiliation(s)
- Yeojin Hong
- Department of Animal Science and Technology, Chung-Ang University, Anseong 17546, Korea
| | - Anh Duc Truong
- Department of Animal Science and Technology, Chung-Ang University, Anseong 17546, Korea.,Department of Biochemistry and Immunology, National Institute of Veterinary Research, Dong Da, Hanoi 10000, Vietnam
| | - Janggeun Lee
- Department of Animal Science and Technology, Chung-Ang University, Anseong 17546, Korea
| | - Kyungbaek Lee
- Department of Animal Science and Technology, Chung-Ang University, Anseong 17546, Korea
| | - Geun-Bae Kim
- Department of Animal Science and Technology, Chung-Ang University, Anseong 17546, Korea
| | - Kang-Nyeong Heo
- Poultry Research Institute, National Institute of Animal Science, RDA, Pyeongchang 25342, Korea
| | - Hyun S Lillehoj
- Animal Biosciences and Biotechnology Laboratory, Agricultural Research Services, United States Department of Agriculture, Beltsville, MD 20705, USA
| | - Yeong Ho Hong
- Department of Animal Science and Technology, Chung-Ang University, Anseong 17546, Korea
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9
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Maddigan NK, Tarzia A, Huang DM, Sumby CJ, Bell SG, Falcaro P, Doonan CJ. Protein surface functionalisation as a general strategy for facilitating biomimetic mineralisation of ZIF-8. Chem Sci 2018; 9:4217-4223. [PMID: 29780551 PMCID: PMC5942038 DOI: 10.1039/c8sc00825f] [Citation(s) in RCA: 103] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 03/09/2018] [Indexed: 12/17/2022] Open
Abstract
The surface charge and chemistry of a protein determines its ability to facilitate biomimetic mineralisation.
The durability of enzymes in harsh conditions can be enhanced by encapsulation within metal–organic frameworks (MOFs) via a process called biomimetic mineralisation. Herein we show that the surface charge and chemistry of a protein determines its ability to seed MOF growth. We demonstrate that chemical modification of amino acids on the protein surface is an effective method for systematically controlling biomimetic mineralisation by zeolitic imidazolate framework-8 (ZIF-8). Reaction of surface lysine residues with succinic (or acetic) anhydride facilitates biomimetic mineralisation by increasing the surface negative charge, whereas reaction of surface carboxylate moieties with ethylenediamine affords a more positively charged protein and hinders the process. Moreover, computational studies confirm that the surface electrostatic potential of a protein is a good indicator of its ability to induce biomimetic mineralisation. This study highlights the important role played by protein surface chemistry in encapsulation and outlines a general method for facilitating the biomimetic mineralisation of proteins.
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Affiliation(s)
- Natasha K Maddigan
- Department of Chemistry and the Centre for Advanced Nanomaterials , The University of Adelaide , Adelaide , South Australia 5005 , Australia .
| | - Andrew Tarzia
- Department of Chemistry and the Centre for Advanced Nanomaterials , The University of Adelaide , Adelaide , South Australia 5005 , Australia .
| | - David M Huang
- Department of Chemistry and the Centre for Advanced Nanomaterials , The University of Adelaide , Adelaide , South Australia 5005 , Australia .
| | - Christopher J Sumby
- Department of Chemistry and the Centre for Advanced Nanomaterials , The University of Adelaide , Adelaide , South Australia 5005 , Australia .
| | - Stephen G Bell
- Department of Chemistry and the Centre for Advanced Nanomaterials , The University of Adelaide , Adelaide , South Australia 5005 , Australia .
| | - Paolo Falcaro
- Department of Chemistry and the Centre for Advanced Nanomaterials , The University of Adelaide , Adelaide , South Australia 5005 , Australia . .,Institute of Physical and Theoretical Chemistry , Graz University of Technology , Stremayrgasse 9 , Graz 8010 , Austria
| | - Christian J Doonan
- Department of Chemistry and the Centre for Advanced Nanomaterials , The University of Adelaide , Adelaide , South Australia 5005 , Australia .
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10
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Tovar G. Design of a software for calculating isoelectric point of a polypeptide according to their net charge using the graphical programming language LabVIEW. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2018; 46:39-46. [PMID: 29105959 DOI: 10.1002/bmb.21088] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Revised: 06/23/2017] [Accepted: 10/06/2017] [Indexed: 06/07/2023]
Abstract
A software to calculate the net charge and to predict the isoelectric point (pI) of a polypeptide is developed in this work using the graphical programming language LabVIEW. Through this instrument the net charges of the ionizable residues of the polypeptide chains of the proteins are calculated at different pH values, tabulated, pI is predicted and an Excel (-xls) type file is generated. In this work, the experimental values of the pIs (pI) of different proteins are compared with the values of the pIs (pI) calculated graphically, achieving a correlation coefficient (R) of 0.934746 which represents a good reliability for a p < 0.01. In this way the generated program can constitute an instrument applicable in the laboratory, facilitating the calculation to graduate students and junior researchers. © 2017 by The International Union of Biochemistry and Molecular Biology, 46(1):39-46, 2018.
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Affiliation(s)
- Glomen Tovar
- Instituto de Investigaciones Biomédicas (BIOMED), Universidad de Carabobo, Núcleo Aragua, Las Delicias Maracay, Venezuela 2101
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11
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Xu G, Wang C, Yao P. Stable emulsion produced from casein and soy polysaccharide compacted complex for protection and oral delivery of curcumin. Food Hydrocoll 2017. [DOI: 10.1016/j.foodhyd.2017.05.010] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
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12
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A combined experimental and molecular simulation study of factors influencing interaction of quinoa proteins-carrageenan. Int J Biol Macromol 2017; 107:949-956. [PMID: 28943441 DOI: 10.1016/j.ijbiomac.2017.09.076] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 08/29/2017] [Accepted: 09/18/2017] [Indexed: 11/22/2022]
Abstract
The interaction between quinoa proteins isolate (QP isolate) and the negatively charged polysaccharide ι-Carragennan (Carr) as a function of pH was studied. Experimental measurements as turbidity, hydrophobic surface, ζ-potential, and hydrodynamic size were carried out. Associative interaction between QP and Carr was found in the pH range between 1 and 2.9. When both molecules are negatively charged (pH>5,5), a pure Coulombic repulsion regime is observed and the self-association of QP due to the Carr exclusion is proposed. In the intermediate pH range, the experimental data suggests that the charge regulation mechanism can overcome the electrostatic repulsion that may take place (and an attraction between QP and Carr can still be observed). Computational simulations by means of free energy derivatives using the Monte Carlo method were carried out to better understand the interaction mechanism between QP and Carr. QP was modeled as a single protein using one of the major proteins, Chenopodin (Ch), and Carr was modeled as a negatively charged polyelectrolyte (NCP) chain, both in the cell model framework. Simulation results showed attractive interactions in agreement with the experimental data.
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13
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Requião RD, Fernandes L, de Souza HJA, Rossetto S, Domitrovic T, Palhano FL. Protein charge distribution in proteomes and its impact on translation. PLoS Comput Biol 2017; 13:e1005549. [PMID: 28531225 PMCID: PMC5460897 DOI: 10.1371/journal.pcbi.1005549] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2016] [Revised: 06/06/2017] [Accepted: 05/02/2017] [Indexed: 11/25/2022] Open
Abstract
As proteins are synthesized, the nascent polypeptide must pass through a negatively charged exit tunnel. During this stage, positively charged stretches can interact with the ribosome walls and slow the translation. Therefore, charged polypeptides may be important factors that affect protein expression. To determine the frequency and distribution of positively and negatively charged stretches in different proteomes, the net charge was calculated for every 30 consecutive amino acid residues, which corresponds to the length of the ribosome exit tunnel. The following annotated and reviewed proteins in the UniProt database (Swiss-Prot) were analyzed: 551,705 proteins from different organisms and a total of 180 million protein segments. We observed that there were more negative than positive stretches and that super-charged positive sequences (i.e., net charges ≥ 14) were underrepresented in the proteomes. Overall, the proteins were more positively charged at their N-termini and C-termini, and this feature was present in most organisms and subcellular localizations. To investigate whether the N-terminal charges affect the elongation rates, previously published ribosomal profiling data obtained from S. cerevisiae, without translation-interfering drugs, were analyzed. We observed a nonlinear effect of the charge on the ribosome occupancy in which values ≥ +5 and ≤ -6 showed increased and reduced ribosome densities, respectively. These groups also showed different distributions across 80S monosomes and polysomes. Basic polypeptides are more common within short proteins that are translated by monosomes, whereas negative stretches are more abundant in polysome-translated proteins. These findings suggest that the nascent peptide charge impacts translation and can be one of the factors that regulate translation efficiency and protein expression. Which factors shape the sequence of amino acids that will form a protein? The biochemical features of amino acids, such as their charge and hydrophobicity, are important drivers of protein tridimensional folding, which creates interaction sites for binding other molecules and directs proteins to specific cellular compartments. These features all impact the activity of the proteins after they are produced. Another less obvious factor that influences the protein’s primary structure may be how efficiently a given amino acid sequence is produced by the ribosome. It is known that a repetitive stretch of positively charged amino acids may interact with the negative charges in the ribosome exit tunnel, slowing, or even halting, translation. By analyzing the charge of protein stretches in different organisms, we observed that proteins tend to present positively charged stretches at their extremities, and high charge values can slow (for positive charges) or speed (for negative charges) translation. An interesting consequence of this trend is that proteins that are translated in high quantities by several ribosomes at the same RNA (polysomes) tend to have more negatively charged stretches than proteins that are translated by a single ribosome per RNA (monosomes).
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Affiliation(s)
- Rodrigo D. Requião
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Luiza Fernandes
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Henrique José Araujo de Souza
- Programa de Pós-Graduação em Informática, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Silvana Rossetto
- Programa de Pós-Graduação em Informática, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Tatiana Domitrovic
- Departamento de Virologia, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- * E-mail: (FLP); (TD)
| | - Fernando L. Palhano
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
- * E-mail: (FLP); (TD)
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14
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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: 165] [Impact Index Per Article: 20.6] [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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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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Achilleos DS, Hatton TA, Vamvakaki M. Photoreponsive Hybrid Nanoparticles with Inherent FRET Activity. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:5981-5989. [PMID: 27222922 DOI: 10.1021/acs.langmuir.6b00875] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The photoactivated inherent fluorescence resonance energy transfer (FRET) properties of a hard-and-soft hybrid nanosystem comprising poly(1'-(2-methacryloxyethyl)-3',3'-dimethyl-6-nitrospiro-(2H-1-benzopyran-2,2'-indoline))-co-poly[2-(dimethylamino)ethyl methacrylate] (PSPMA-co-PDMAEMA) random copolymer brushes on silica nanoparticles are described. This unique FRET process is switched on by the simultaneous generation of isomer X and merocyanine (MC), which are bipolar in nature and comprise donor-acceptor dyads, from a single spiropyran (SP) chromophore upon UV irradiation. These X-MC species exhibit sufficient lifetimes to allow the read-out of the FRET process. The phenomenon is gradually switched off because of the thermal relaxation of the bipolar chromophores. This inherent property of the nanoemitters is employed in the development of biosensors of high specificity by monitoring variations in the FRET efficiency and lifetime of the hybrids in the presence of biological substances. More specifically, bovine serum albumin (BSA) augments the formation of MC species and retards the MC photobleaching process, leading to the enhancement of the FRET efficiency and lifetime, respectively. On the other hand, amino acid l-histidine further retards the MC thermal relaxation and prolongs the FRET process. We envisage that this platform opens new perspectives in the development of novel, optical nanosensors for applications in various fields including healthcare products and environmental monitoring.
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Affiliation(s)
- Demetra S Achilleos
- Institute of Electronic Structure and Laser (IESL), Foundation for Research and Technology-Hellas (FORTH), 711 10 Heraklion, Crete, Greece
- Department of Materials Science and Technology, University of Crete , 710 03 Heraklion, Crete, Greece
| | - T Alan Hatton
- Department of Chemical Engineering, Massachusetts Institute of Technology , Cambridge, Massachusetts 02139, United States
| | - Maria Vamvakaki
- Institute of Electronic Structure and Laser (IESL), Foundation for Research and Technology-Hellas (FORTH), 711 10 Heraklion, Crete, Greece
- Department of Materials Science and Technology, University of Crete , 710 03 Heraklion, Crete, Greece
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Constantinou AP, Elladiou M, Patrickios CS. Regular and Inverse Polyampholyte Hydrogels: A Detailed Comparison. Macromolecules 2016. [DOI: 10.1021/acs.macromol.6b00538] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
| | - Marios Elladiou
- Department of Chemistry University of Cyprus P.O.
Box 20537 1678 Nicosia Cyprus
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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: 38] [Impact Index Per Article: 4.2] [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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Przybylski C, Mokaddem M, Prull-Janssen M, Saesen E, Lortat-Jacob H, Gonnet F, Varenne A, Daniel R. On-line capillary isoelectric focusing hyphenated to native electrospray ionization mass spectrometry for the characterization of interferon-γ and variants. Analyst 2015; 140:543-50. [DOI: 10.1039/c4an01305k] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The on-line hyphenation of Capillary IsoElectric Focusing (CIEF) with ElectroSpray Ionization Mass Spectrometry (ESI/MS) has been carried out in a non-denaturing detection mode at the CIEF-MS interface.
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Affiliation(s)
- Cédric Przybylski
- CNRS
- Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement (UMR 8587)
- Evry
- France
- Université Evry-Val-D'Essonne
| | - Meriem Mokaddem
- Chimie ParisTech
- Ecole Nationale Supérieure de Chimie
- Unité de Technologies Chimiques et Biologiques pour la Santé
- Paris
- France
| | - Mehdi Prull-Janssen
- CNRS
- Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement (UMR 8587)
- Evry
- France
- Université Evry-Val-D'Essonne
| | - Els Saesen
- Université Grenoble Alpes
- Institut de Biologie Structurale (IBS)
- Grenoble
- France
- CNRS
| | - Hugues Lortat-Jacob
- Université Grenoble Alpes
- Institut de Biologie Structurale (IBS)
- Grenoble
- France
- CNRS
| | - Florence Gonnet
- CNRS
- Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement (UMR 8587)
- Evry
- France
- Université Evry-Val-D'Essonne
| | - Anne Varenne
- Chimie ParisTech
- Ecole Nationale Supérieure de Chimie
- Unité de Technologies Chimiques et Biologiques pour la Santé
- Paris
- France
| | - Régis Daniel
- CNRS
- Laboratoire Analyse et Modélisation pour la Biologie et l'Environnement (UMR 8587)
- Evry
- France
- Université Evry-Val-D'Essonne
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Visnevskij C, Ciuta G, Ketleriute S, Savickaite M, Makuska R. ISARA ATRP of methacrylic acid neutralized by simple amines yielding linear polymers and anionic molecular brushes. Eur Polym J 2014. [DOI: 10.1016/j.eurpolymj.2014.03.031] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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21
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Pafiti KS, Elladiou M, Patrickios CS. “Inverse Polyampholyte” Hydrogels from Double-Cationic Hydrogels: Synthesis by RAFT Polymerization and Characterization. Macromolecules 2014. [DOI: 10.1021/ma500084c] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kyriaki S. Pafiti
- Department of Chemistry, University of Cyprus,
P.O. Box 20537, 1678 Nicosia, Cyprus
| | - Marios Elladiou
- Department of Chemistry, University of Cyprus,
P.O. Box 20537, 1678 Nicosia, Cyprus
| | - Costas S. Patrickios
- Department of Chemistry, University of Cyprus,
P.O. Box 20537, 1678 Nicosia, Cyprus
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22
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Chen L, Chen T, Fang W, Wen Y, Lin S, Lin J, Cai C. Synthesis and pH-Responsive “Schizophrenic” Aggregation of a Linear-Dendron-Like Polyampholyte Based on Oppositely Charged Polypeptides. Biomacromolecules 2013; 14:4320-30. [DOI: 10.1021/bm401215w] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Lili Chen
- Shanghai Key Laboratory of
Advanced Polymeric Materials, Key Laboratory for Ultrafine Materials
of Ministry of Education, School of Materials Science and Engineering, East China University of Science and Technology, Shanghai 200237, People’s Republic of China
| | - Tao Chen
- Shanghai Key Laboratory of
Advanced Polymeric Materials, Key Laboratory for Ultrafine Materials
of Ministry of Education, School of Materials Science and Engineering, East China University of Science and Technology, Shanghai 200237, People’s Republic of China
| | - Wenxiang Fang
- Shanghai Key Laboratory of
Advanced Polymeric Materials, Key Laboratory for Ultrafine Materials
of Ministry of Education, School of Materials Science and Engineering, East China University of Science and Technology, Shanghai 200237, People’s Republic of China
| | - Ying Wen
- Shanghai Key Laboratory of
Advanced Polymeric Materials, Key Laboratory for Ultrafine Materials
of Ministry of Education, School of Materials Science and Engineering, East China University of Science and Technology, Shanghai 200237, People’s Republic of China
| | - Shaoliang Lin
- Shanghai Key Laboratory of
Advanced Polymeric Materials, Key Laboratory for Ultrafine Materials
of Ministry of Education, School of Materials Science and Engineering, East China University of Science and Technology, Shanghai 200237, People’s Republic of China
| | - Jiaping Lin
- Shanghai Key Laboratory of
Advanced Polymeric Materials, Key Laboratory for Ultrafine Materials
of Ministry of Education, School of Materials Science and Engineering, East China University of Science and Technology, Shanghai 200237, People’s Republic of China
| | - Chunhua Cai
- Shanghai Key Laboratory of
Advanced Polymeric Materials, Key Laboratory for Ultrafine Materials
of Ministry of Education, School of Materials Science and Engineering, East China University of Science and Technology, Shanghai 200237, People’s Republic of China
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23
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Hammami R, Fliss I. Use of SciDBMaker as Tool for the Design of Specialized Biological Databases. Bioinformatics 2013. [DOI: 10.4018/978-1-4666-3604-0.ch093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The exponential growth of molecular biology research in recent decades has brought concomitant growth in the number and size of genomic and proteomic databases used to interpret experimental findings. Particularly, growth of protein sequence records created the need for smaller and manually annotated databases. Since scientists are continually developing new specific databases to enhance their understanding of biological processes, the authors created SciDBMaker to provide a tool for easy building of new specialized protein knowledge bases. This chapter also suggests best practices for specialized biological databases design, and provides examples for the implementation of these practices.
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SYNTHESIS AND pH REVERSIBLE AGGREGATING BEHAVIOR OF POLY(AMINO ACID) BASED LINEAR-DENDRON-LIKE POLYAMPHOLYTE. ACTA POLYM SIN 2013. [DOI: 10.3724/sp.j.1105.2013.12270] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Pafiti KS, Philippou Z, Loizou E, Porcar L, Patrickios CS. End-Linked Poly[2-(dimethylamino)ethyl Methacrylate]–Poly(methacrylic acid) Polyampholyte Conetworks: Synthesis by Sequential RAFT Polymerization and Swelling and SANS Characterization. Macromolecules 2011. [DOI: 10.1021/ma200668v] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kyriaki S. Pafiti
- Department of Chemistry, University of Cyprus, P.O. Box 20537, 1678 Nicosia, Cyprus
| | - Zelina Philippou
- Department of Chemistry, University of Cyprus, P.O. Box 20537, 1678 Nicosia, Cyprus
| | - Elena Loizou
- Department of Chemistry, University of Cyprus, P.O. Box 20537, 1678 Nicosia, Cyprus
| | - Lionel Porcar
- Institute Max von Laue−Paul Langevin, BP 156, F-38042, Grenoble, Cedex 9, France
| | - Costas S. Patrickios
- Department of Chemistry, University of Cyprus, P.O. Box 20537, 1678 Nicosia, Cyprus
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Comparisons of protein extraction procedures and quantification methods for the proteomic analysis of Gram-positive Paenibacillus sp. strain D9. World J Microbiol Biotechnol 2010. [DOI: 10.1007/s11274-010-0621-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Long WF, Labute P. Calibrative approaches to protein solubility modeling of a mutant series using physicochemical descriptors. J Comput Aided Mol Des 2010; 24:907-16. [PMID: 20842408 PMCID: PMC2956060 DOI: 10.1007/s10822-010-9383-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2009] [Accepted: 08/31/2010] [Indexed: 11/25/2022]
Abstract
A set of physicochemical properties describing a protein of known structure is employed for a calibrative approach to protein solubility. Common hydrodynamic and electrophoretic properties routinely measured in the bio-analytical laboratory such as zeta potential, dipole moment, the second osmotic virial coefficient are first estimated in silico as a function a pH and solution ionic strength starting with the protein crystal structure. The utility of these descriptors in understanding the solubility of a series of ribonuclease Sa mutants is investigated. A simple two parameter model was trained using solubility data of the wild type protein measured at a restricted number of solution pHs. Solubility estimates of the mutants demonstrate that zeta potential and dipole moment may be used to rationalize solubility trends over a wide pH range. Additionally a calibrative model based on the protein's second osmotic virial coefficient, B₂₂ was developed. A modified DVLO type potential along with a simplified representation of the protein allowed for efficient computation of the second viral coefficient. The standard error of prediction for both models was on the order of 0.3 log S units. These results are very encouraging and demonstrate that these models may be trained with a small number of samples and employed extrapolatively for estimating mutant solubilities.
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Widmann M, Trodler P, Pleiss J. The isoelectric region of proteins: a systematic analysis. PLoS One 2010; 5:e10546. [PMID: 20479870 PMCID: PMC2866324 DOI: 10.1371/journal.pone.0010546] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2010] [Accepted: 04/13/2010] [Indexed: 11/25/2022] Open
Abstract
Background Binding of proteins in ion exchange chromatography is dominated by electrostatic interactions and can be tuned by adjusting pH and ionic strength of the solvent. Therefore, the isoelectric region (IER), the pH region of almost zero charge near the pI, has been used to predict the binding properties of proteins. Principal findings Usually the IER is small and binding and elution is carried out at pH values near to the pI. However, some proteins with an extended IER have been shown to bind and elute far away from its pI. To analyze factors that mediate the size of the IER and to identify proteins with an extended IER, two protein families consisting of more than 7000 proteins were systematically investigated. Most proteins were found to have a small IER and thus are expected to bind or elute near to their pI, while only a small fraction of less than 2% had a large IER. Conclusions Only four factors, the number of histidines, the pI, the number of titratable amino acids and the ratio of acidic to basic residues, are sufficient to reliably classify proteins by their IER based on their sequence only, and thus to predict their binding and elution behaviour in ion exchange chromatography.
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Affiliation(s)
- Michael Widmann
- Institute of Technical Biochemistry, University of Stuttgart, Stuttgart, Germany
| | - Peter Trodler
- Institute of Technical Biochemistry, University of Stuttgart, Stuttgart, Germany
| | - Jürgen Pleiss
- Institute of Technical Biochemistry, University of Stuttgart, Stuttgart, Germany
- * E-mail:
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29
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Temperature and pH-responsive properties of poly(styrene-co-maleic anhydride)-grafting poly(oxypropylene)-amines. J Colloid Interface Sci 2009; 336:82-9. [DOI: 10.1016/j.jcis.2009.03.064] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2009] [Revised: 03/26/2009] [Accepted: 03/27/2009] [Indexed: 11/21/2022]
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30
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Robinson CM, Shariati F, Gillaspy AF, Dyer DW, Chodosh J. Genomic and bioinformatics analysis of human adenovirus type 37: new insights into corneal tropism. BMC Genomics 2008; 9:213. [PMID: 18471294 PMCID: PMC2397415 DOI: 10.1186/1471-2164-9-213] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2007] [Accepted: 05/09/2008] [Indexed: 01/22/2023] Open
Abstract
Background Human adenovirus type 37 (HAdV-37) is a major etiologic agent of epidemic keratoconjunctivitis, a common and severe eye infection associated with long-term visual morbidity due to persistent corneal inflammation. While HAdV-37 has been known for over 20 years as an important cause, the complete genome sequence of this serotype has yet to be reported. A detailed bioinformatics analysis of the genome sequence of HAdV-37 is extremely important to understanding its unique pathogenicity in the eye. Results We sequenced and annotated the complete genome of HAdV-37, and performed genomic and bioinformatics comparisons with other HAdVs to identify differences that might underlie the unique corneal tropism of HAdV-37. Global pairwise genome alignment with HAdV-9, a human species D adenovirus not associated with corneal infection, revealed areas of non-conserved sequence principally in genes for the virus fiber (site of host cell binding), penton (host cell internalization signal), hexon (principal viral capsid structural protein), and E3 (site of several genes that mediate evasion of the host immune system). Phylogenetic analysis revealed close similarities between predicted proteins from HAdV-37 of species D and HAdVs from species B and E. However, virtual 2D gel analyses of predicted viral proteins uncovered unexpected differences in pI and/or size of specific proteins thought to be highly similar by phylogenetics. Conclusion This genomic and bioinformatics analysis of the HAdV-37 genome provides a valuable tool for understanding the corneal tropism of this clinically important virus. Although disparities between HAdV-37 and other HAdV within species D in genes encoding structural and host receptor-binding proteins were to some extent expected, differences in the E3 region suggest as yet unknown roles for this area of the genome. The whole genome comparisons and virtual 2D gel analyses reported herein suggest potent areas for future studies.
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Affiliation(s)
- Christopher M Robinson
- Molecular Pathogenesis of Eye Infection Research Center, Dean A. McGee Eye Institute, 608 Stanton L, Young Blvd., Oklahoma City, OK 73104, USA.
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Hammami R, Zouhir A, Naghmouchi K, Ben Hamida J, Fliss I. SciDBMaker: new software for computer-aided design of specialized biological databases. BMC Bioinformatics 2008; 9:121. [PMID: 18298861 PMCID: PMC2267701 DOI: 10.1186/1471-2105-9-121] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2007] [Accepted: 02/25/2008] [Indexed: 12/22/2022] Open
Abstract
Background The exponential growth of research in molecular biology has brought concomitant proliferation of databases for stocking its findings. A variety of protein sequence databases exist. While all of these strive for completeness, the range of user interests is often beyond their scope. Large databases covering a broad range of domains tend to offer less detailed information than smaller, more specialized resources, often creating a need to combine data from many sources in order to obtain a complete picture. Scientific researchers are continually developing new specific databases to enhance their understanding of biological processes. Description In this article, we present the implementation of a new tool for protein data analysis. With its easy-to-use user interface, this software provides the opportunity to build more specialized protein databases from a universal protein sequence database such as Swiss-Prot. A family of proteins known as bacteriocins is analyzed as 'proof of concept'. Conclusion SciDBMaker is stand-alone software that allows the extraction of protein data from the Swiss-Prot database, sequence analysis comprising physicochemical profile calculations, homologous sequences search, multiple sequence alignments and the building of new and more specialized databases. It compiles information with relative ease, updates and compares various data relevant to a given protein family and could solve the problem of dispersed biological search results.
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Affiliation(s)
- Riadh Hammami
- Unité de Protéomie Fonctionnelle & Biopréservation Alimentaire, Institut Supérieur des Sciences Biologiques Appliquées de Tunis, Université El Manar, Tunisie.
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Maldonado A, Vara F, Sillero A. Improved application of the oscillating method for the isoelectric point determination of protein: Potential connection with protein data banks. Comput Biol Med 2008; 38:23-30. [PMID: 17655838 DOI: 10.1016/j.compbiomed.2007.06.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2006] [Revised: 05/23/2007] [Accepted: 06/11/2007] [Indexed: 10/23/2022]
Abstract
The oscillating method (OM) for the theoretical determination of the pI values, one by one, of proteins and other macromolecules has been previously published [Sillero and Maldonado, Comput. Biol. Med 36 (2006) 157-166]. An improved application of the method, here named as improved oscillating method (IOM), allows the pI determination of group of proteins. This characteristic may be useful to explore the pI value and electric charge of family of enzymes. As an example the pI values of 1630 enzymes collected in a Swiss-Prot data bank (www.expasy.org), as belonging to the enzymes ligases (EC 6. 2. 1. *) is presented. The method also permits the determination of the pI value of any group of proteins stored in data banks provided that they can be supplied to the program in a FASTA format. Free access to IOM can be reached at http://www.bq.uam.es/otros/pical3.zip.
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Affiliation(s)
- Andrés Maldonado
- Departmento de Bioquímica, Facultad de Medicina, Instituto de Investigaciones Biomédicas Alberto Sols (UAM/CSIC), Arzobispo Morcillo 4, 28029 Madrid, Spain
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Georgiou TK, Patrickios CS. Synthesis, characterization, and DNA adsorption studies of ampholytic model conetworks based on cross-linked star copolymers. Biomacromolecules 2007; 9:574-82. [PMID: 18163576 DOI: 10.1021/bm701123s] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Five model conetworks based on cross-linked star ampholytic copolymers were synthesized by group transfer polymerization. The ampholytic copolymers were based on two hydrophilic monomers: the positively ionizable 2-(dimethylamino)ethyl methacrylate (DMAEMA) and the negatively ionizable methacrylic acid (MAA). Ethylene glycol dimethacrylate was used as the cross-linker. These five ampholytic model conetworks were isomers based on equimolar DMAEMA-MAA copolymer stars of different architectures: heteroarm (two), star block (two), and statistical. The two networks based on the homopolymer stars were also synthesized. The MAA units were introduced via the polymerization of tetrahydropyranyl methacrylate and the acid hydrolysis of the latter after network formation. All the precursors to the (co)networks were characterized in terms of their molecular weights using gel permeation chromatography (GPC). The mass of the extractables from the (co)networks was measured and characterized in terms of molecular weight and composition using GPC and proton nuclear magnetic resonance (1H NMR) spectroscopy, respectively. The degrees of swelling (DS) of all the ampholytic conetworks were measured as a function of pH and were found to present a minimum at a pH value which was taken as the isoelectric point, pI. The DS and the pI values did not present a dependence on conetwork architecture. Finally, DNA adsorption studies onto the ampholyte conetworks indicated that DNA binding was governed by electrostatics.
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Affiliation(s)
- Theoni K Georgiou
- Department of Chemistry, University of Cyprus, P.O. Box 20537, 1678 Nicosia, Cyprus
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Dong R, Krishnan S, Baird BA, Lindau M, Ober CK. Patterned Biofunctional Poly(acrylic acid) Brushes on Silicon Surfaces. Biomacromolecules 2007; 8:3082-92. [PMID: 17880179 DOI: 10.1021/bm700493v] [Citation(s) in RCA: 131] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Protein patterning was carried out using a simple procedure based on photolithography wherein the protein was not subjected to UV irradiation and high temperatures or contacted with denaturing solvents or strongly acidic or basic solutions. Self-assembled monolayers of poly(ethylene glycol) (PEG) on silicon surfaces were exposed to oxygen plasma through a patterned photoresist. The etched regions were back-filled with an initiator for surface-initiated atom transfer radical polymerization (ATRP). ATRP of sodium acrylate was readily achieved at room temperature in an aqueous medium. Protonation of the polymer resulted in patterned poly(acrylic acid) (PAA) brushes. A variety of biomolecules containing amino groups could be covalently tethered to the dense carboxyl groups of the brush, under relatively mild conditions. The PEG regions surrounding the PAA brush greatly reduced nonspecific adsorption. Avidin was covalently attached to PAA brushes, and biotin-tagged proteins could be immobilized through avidin-biotin interaction. Such an immobilization method, which is based on specific interactions, is expected to better retain protein functionality than direct covalent binding. Using biotin-tagged bovine serum albumin (BSA) as a model, a simple strategy was developed for immobilization of small biological molecules using BSA as linkages, while BSA can simultaneously block nonspecific interactions.
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Affiliation(s)
- Rong Dong
- Department of Chemistry, Materials Science and Engineering, and Applied and Engineering Physics, Cornell University, Ithaca, NY 14853, USA
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35
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Zhu K, Zhao J, Lubman DM, Miller FR, Barder TJ. Protein pI shifts due to posttranslational modifications in the separation and characterization of proteins. Anal Chem 2007; 77:2745-55. [PMID: 15859589 DOI: 10.1021/ac048494w] [Citation(s) in RCA: 137] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Proteins from breast cancer cell lines are characterized using a 2-D liquid separation technique in which protein pI is used as the first-dimension separation parameter. To effect this protein pI separation, chromatofocusing(CF) is employed whereby a pH gradient is generated on-column using a weak anion exchange medium with the intact proteins fractionated and collected every 0.2 pH unit. It is demonstrated that the pI for expressed intact proteins as generated by CF is an important parameter for identification and characterization of the actual protein modifications occurring in the cancer cell. For most proteins, the experimentally determined pI is very close to that predicted by the databases. In other cases, however, where the pI is observed to be shifted from the expected value, it is shown that this shift is often correlated to protein modifications. The modifications that cause such shifts include truncations and deletions often observed in cancer cells or phosphorylations that can shift the pI by several pH units. It is also shown that the effects of phosphorylation on the observed shift can vary depending upon the protein and the amount of phosphorylation. Moreover, large changes in the pI are often observed for proteins with a pI above 7.0 upon phosphorylation, whereas little change is observed for proteins with a pI of approximately 5.0. The expressed protein's pI value thus becomes an important parameter together with the intact MW value, peptide map, and MS/MS results for identification of the presence and type of posttranslational modifications occurring in the cancer cell.
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Affiliation(s)
- Kan Zhu
- Department of Chemistry, The University of Michigan, Ann Arbor, Michigan 48109-1055, USA
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36
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Abstract
Proper validation can accelerate sequence-based discovery of proteins and protein-coding genes. Databases currently contain a backlog of experimentally unverified gene models and tentative assignments of observed transcripts to coding or noncoding RNA. We present and apply a general principle, founded on base composition and the genetic code and validated here by bulk 2-D gels, that can improve the reliability of such classifications and of the algorithms or pipelines that lead to them.
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Affiliation(s)
- Stéphane Cruveiller
- Atelier de Génomique Comparative, Genoscope, Centre National de Séquençage, Evry, France
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37
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Vo CD, Armes SP, Randall DP, Sakai K, Biggs S. Synthesis of Zwitterionic Diblock Copolymers without Protecting Group Chemistry. Macromolecules 2006. [DOI: 10.1021/ma062648n] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | | | - David P. Randall
- School of Life Sciences, The University of Sussex, Brighton BN1 9QG, United Kingdom
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38
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Colinge J, Masselot A, Carbonell P, Appel RD. InSilicoSpectro: An Open-Source Proteomics Library. J Proteome Res 2006; 5:619-24. [PMID: 16512677 DOI: 10.1021/pr0504236] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We present a new proteomics open-source project, InSilicoSpectro, aimed at implementing recurrent computations that are necessary for proteomics data analysis. Illustrative examples are mass list file format conversions, protein sequence digestion, theoretical peptide and fragment mass computations, graphical display, matching with experimental data, isoelectric point estimation, and peptide retention time prediction. The project library is written in Perl, a widely used scripting language in bioinformatics, and it offers a unique framework of integrated objects to implement complex proteomics data analyses. For instance, only a few lines of code are required to digest a protein with fixed and variable modifications, label peptides with 18O, compute the fragmentation spectra and display their match with experimental spectra. We believe that InSilicoSpectro will be of great help to bioinformaticians, without detailed knowledge of proteomics specifics, and to mass spectrometrists with computer programming interest as well.
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Affiliation(s)
- Jacques Colinge
- Upper Austria University of Applied Sciences at Hagenberg, Bioinformatics Department, Hauptstrasse 117, A-4232 Hagenberg, Austria.
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Mao B, Gan L, Gan Y, Tam K, Tan O. Controlled one-pot synthesis of pH-sensitive self-assembled diblock copolymers and their aggregation behavior. POLYMER 2005. [DOI: 10.1016/j.polymer.2005.08.048] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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40
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Gilsdorf J, Gul N, Smith LA. Expression, purification, and characterization of Clostridium botulinum type B light chain. Protein Expr Purif 2005; 46:256-67. [PMID: 16297638 DOI: 10.1016/j.pep.2005.09.024] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2005] [Revised: 09/13/2005] [Accepted: 09/17/2005] [Indexed: 10/25/2022]
Abstract
A full-length synthetic gene encoding the light chain of botulinum neurotoxin serotype B, approximately 50 kDa (BoNT/B LC), has been cloned into a bacterial expression vector pET24a+. BoNT/B LC was expressed in Escherichia coli BL21.DE3.pLysS and isolated from the soluble fraction. The resultant protein was purified to homogeneity by cation chromatography and was determined to be >98% pure as assessed by SDS-polyacrylamide gel stained with SilverXpress and analyzed by densitometry. Mass spectroscopic analysis indicated the protein to be 50.8 kDa, which equaled the theoretically expected mass. N-terminal sequencing of the purified protein showed the sequence corresponded to the known reported sequence. The recombinant BoNT/B light chain was found to be highly stable, catalytically active, and has been used to prepare antisera that neutralizes against BoNT/B challenge. Characterization of the protein including pH, temperature, and the stability of the protein in the presence or absence of zinc is described within. The influence of pH differences, buffer, and added zinc on secondary and tertiary structure of BoNT/B light chain was analyzed by circular dichroism and tryptophan fluorescence measurements. Optimal conditions for obtaining maximum metalloprotease activity and stabilizing the protein for long term storage were determined. We further analyzed the thermal denaturation of BoNT/B LC as a function of temperature to probe the pH and added zinc effects on light chain stability. The synthetic BoNT/B LC has been found to be highly active on its substrate (vesicle associated membrane protein-2) and, therefore, can serve as a useful reagent for BoNT/B research.
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Affiliation(s)
- Janice Gilsdorf
- Integrated Toxicology Division, U.S. Army Medical Research Institute of Infectious Diseases, 1425 Porter Street, Frederick, MD 21702-5011, USA
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41
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Khachane A, Kumar R, Jain S, Jain S, Banumathy G, Singh V, Nagpal S, Tatu U. “Plasmo2D”: An Ancillary Proteomic Tool to Aid Identification of Proteins from Plasmodium falciparum. J Proteome Res 2005; 4:2369-74. [PMID: 16335988 DOI: 10.1021/pr050289p] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Bioinformatics tools to aid gene and protein sequence analysis have become an integral part of biology in the post-genomic era. Release of the Plasmodium falciparum genome sequence has allowed biologists to define the gene and the predicted protein content as well as their sequences in the parasite. Using pI and molecular weight as characteristics unique to each protein, we have developed a bioinformatics tool to aid identification of proteins from Plasmodium falciparum. The tool makes use of a Virtual 2-DE generated by plotting all of the proteins from the Plasmodium database on a pI versus molecular weight scale. Proteins are identified by comparing the position of migration of desired protein spots from an experimental 2-DE and that on a virtual 2-DE. The procedure has been automated in the form of user-friendly software called "Plasmo2D". The tool can be downloaded from http://144.16.89.25/Plasmo2D.zip.
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Affiliation(s)
- Amit Khachane
- Department of Biochemistry, Indian Institute of Science, Bangalore 560012, India
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42
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Ermakova E. Lysozyme dimerization: Brownian dynamics simulation. J Mol Model 2005; 12:34-41. [PMID: 16133093 DOI: 10.1007/s00894-005-0001-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2004] [Accepted: 05/12/2005] [Indexed: 10/25/2022]
Abstract
The lysozyme dimerization reaction has been studied within the framework of encounter-complex (EC) formation theory using the MacroDox software package. Two types of energetically favorite ECs were determined. In the first of them, active-center amino acids of lysozyme take part in the complex formation or the second molecule blocks accessibility to active center sterically. Epitope amino-acid residues are involved in the complex of type II. The existence of both types of complexes does not contradict experimental data. Dimer-formation rate constants for different kinds of EC were calculated. Increasing the pH from 2.0 to 10.0 decreases the total positive lysozyme charge and eliminates the unfavorable repulsive electrostatic interaction. The rate constant of EC formation is inversely proportional to the protein total charge. The association rate constant was also enhanced by an increase of ionic strength that screened repulsive electrostatic interaction between positively charged proteins.
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Affiliation(s)
- Elena Ermakova
- Kazan Institute of Biochemistry and Biophysics RAS, 420111 Kazan, P.O. Box 30, Russia.
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43
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44
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Sillero A, Maldonado A. Isoelectric point determination of proteins and other macromolecules: oscillating method. Comput Biol Med 2005; 36:157-66. [PMID: 16389075 DOI: 10.1016/j.compbiomed.2004.09.006] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2004] [Accepted: 09/07/2004] [Indexed: 10/26/2022]
Abstract
A program written in Visual Basic has been developed to calculate the isoelectric point of proteins and other macromolecules bearing acid-basic residues. The pI value can be theoretically calculated with the precision required. The computer automatically supplies a representation of the charge of the protein versus pH values. The corresponding values can also be obtained, on command, in the form of table.
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Affiliation(s)
- Antonio Sillero
- Facultad de Medicina, Departamento de Bioquímica, Instituto de Investigaciones Biomédicas Alberto Sols, CSIC/UAM, Madrid, Spain.
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45
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Cai Y, Armes SP. Synthesis of Well-Defined Y-Shaped Zwitterionic Block Copolymers via Atom-Transfer Radical Polymerization. Macromolecules 2004. [DOI: 10.1021/ma048511j] [Citation(s) in RCA: 94] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yuanli Cai
- Department of Chemistry, University of Sheffield, Brook Hill, Sheffield, South Yorkshire, S3 7HF, U.K. and Institute of Polymer Science, College of Chemistry, Xiangtan University, Xiangtan, Hunan, 411105, P. R. China
| | - Steven P. Armes
- Department of Chemistry, University of Sheffield, Brook Hill, Sheffield, South Yorkshire, S3 7HF, U.K. and Institute of Polymer Science, College of Chemistry, Xiangtan University, Xiangtan, Hunan, 411105, P. R. China
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46
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Bories-Azeau X, Mérian T, Weaver JVM, Armes SP, van den Haak HJW. Synthesis of Near-Monodisperse Acidic Homopolymers and Block Copolymers from Hydroxylated Methacrylic Copolymers Using Succinic Anhydride under Mild Conditions. Macromolecules 2004. [DOI: 10.1021/ma048726t] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Xavier Bories-Azeau
- Department of Chemistry, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QJ, United Kingdom
| | - Tiphaine Mérian
- Department of Chemistry, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QJ, United Kingdom
| | - Jonathan V. M. Weaver
- Department of Chemistry, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QJ, United Kingdom
| | - Steven P. Armes
- Department of Chemistry, School of Life Sciences, University of Sussex, Falmer, Brighton BN1 9QJ, United Kingdom
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47
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Bories-Azeau X, Armes SP, van den Haak HJW. Facile Synthesis of Zwitterionic Diblock Copolymers without Protecting Group Chemistry. Macromolecules 2004. [DOI: 10.1021/ma035904u] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Xavier Bories-Azeau
- Department of Chemistry, School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9QJ, UK
| | - Steven P. Armes
- Department of Chemistry, School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9QJ, UK
| | - Henk J. W. van den Haak
- Department of Chemistry, School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9QJ, UK
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48
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Loizou E, Triftaridou AI, Georgiou TK, Vamvakaki M, Patrickios CS. Cationic double-hydrophilic model networks: synthesis, characterization, modeling and protein adsorption studies. Biomacromolecules 2003; 4:1150-60. [PMID: 12959578 DOI: 10.1021/bm020102c] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Group transfer polymerization (GTP) was used for the preparation of eight networks based on two hydrophilic monomers, 2-(dimethylamino)ethyl methacrylate (DMAEMA) and poly(ethylene glycol) methacrylate (PEGMA). Ethylene glycol dimethacrylate (EGDMA) served as the cross-linker, whereas 1,4-bis(methoxytrimethylsiloxymethylene)cyclohexane (MTSMC) was used as a bifunctional initiator. Seven of the networks had linear segments of accurate molecular weight between the cross-links, i.e., they were model networks, whereas the eighth was an equimolar randomly cross-linked network. Five of the seven model networks were based on ABA triblock copolymers with PEGMA midblocks and DMAEMA endblocks, in which the DMAEMA/PEGMA ratio was varied. The remaining two model networks were equimolar isomers, the one based on BAB triblocks (with a DMAEMA midblock) and the other based on the statistical copolymer. The degrees of swelling of all of the networks were measured as a function of pH and were found to increase below pH 7. The degrees of swelling at low pH values increased with the percentage of the DMAEMA monomer, which is ionized under these conditions. These swelling results were confirmed qualitatively by theoretical calculations. Finally, the pH-dependence of the adsorption of the proteins pepsin, bovine serum albumin, and lysozyme onto one of the model networks was studied.
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Affiliation(s)
- Elena Loizou
- Department of Chemistry, University of Cyprus, PO Box 20537, 1678 Nicosia, Cyprus
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49
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Hiller K, Schobert M, Hundertmark C, Jahn D, Münch R. JVirGel: Calculation of virtual two-dimensional protein gels. Nucleic Acids Res 2003; 31:3862-5. [PMID: 12824438 PMCID: PMC168943 DOI: 10.1093/nar/gkg536] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
We developed JVirGel, a collection of tools for the simulation and analysis of proteomics data. The software creates and visualizes virtual two-dimensional (2D) protein gels based on the migration behaviour of proteins in dependence of their theoretical molecular weights in combination with their calculated isoelectric points. The utilization of all proteins of an organism of interest deduced from genes of the corresponding genome project in combination with the elimination of obvious membrane proteins permits the creation of an optimized calculated proteome map. The electrophoretic separation behaviour of single proteins is accessible interactively in a Java(TM) applet (small application in a web browser) by selecting a pI/MW range and an electrophoretic timescale of interest. The calculated pattern of protein spots helps to identify unknown proteins and to localize known proteins during experimental proteomics approaches. Differences between the experimentally observed and the calculated migration behaviour of certain proteins provide first indications for potential protein modification events. When possible, the protein spots are directly linked via a mouse click to the public databases SWISS-PROT and PRODORIC. Additionally, we provide tools for the serial calculation and visualization of specific protein properties like pH dependent charge curves and hydrophobicity profiles. These values are helpful for the rational establishment of protein purification procedures. The proteomics tools are available on the World Wide Web at http://prodoric.tu-bs.de/proteomics.php.
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Affiliation(s)
- Karsten Hiller
- Institut für Mikrobiologie, Technische Universität Braunschweig, Spielmannstrasse 7, D-38106 Braunschweig, Germany
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50
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Ehebauer MT, Mans BJ, Gaspar ARM, Neitz AWH. Identification of extrinsic blood coagulation pathway inhibitors from the tick Ornithodoros savignyi (Acari: Argasidae). Exp Parasitol 2002; 101:138-48. [PMID: 12427468 DOI: 10.1016/s0014-4894(02)00102-9] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The salt BaSO(4) selectively adsorbs two proteins from crude Ornithodoros savignyi salivary gland extract. They co-purify during reversed-phase HPLC, but can be separated by hydrophobic-interaction chromatography. Their molecular masses are 9333 and 9173Da. The 9.3kDa protein was designated BSAP1 and the 9.1kDa protein BSAP2. Their amino acid compositions show significant differences, in particular the presence of seven and eight cysteine residues in BSAP1 and BSAP2, respectively. The proteins do not contain gamma-carboxyglutamic acid, hydroxyproline, or hydroxylysine. The proteins do not inhibit the intrinsic coagulation cascade, but inhibit the extrinsic pathway. The observed inhibition is not due to inhibition of factor VII. Both proteins bind to membranes. BSAP1 binds neutral and negatively charged membranes more strongly than BSAP2. Its affinity for negative membranes is, however, much lower than for neutral membranes. In contrast, BSAP2 binds both membranes equally strongly. The binding of the proteins to the membranes was significantly lowered upon pre-incubation with Ca(2+).
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Affiliation(s)
- M T Ehebauer
- Department of Biochemistry, University of Pretoria, Pretoria, South Africa
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