1
|
Masson P, Lushchekina S. Conformational Stability and Denaturation Processes of Proteins Investigated by Electrophoresis under Extreme Conditions. Molecules 2022; 27:6861. [PMID: 36296453 PMCID: PMC9610776 DOI: 10.3390/molecules27206861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2022] [Revised: 10/10/2022] [Accepted: 10/10/2022] [Indexed: 11/17/2022] Open
Abstract
The functional structure of proteins results from marginally stable folded conformations. Reversible unfolding, irreversible denaturation, and deterioration can be caused by chemical and physical agents due to changes in the physicochemical conditions of pH, ionic strength, temperature, pressure, and electric field or due to the presence of a cosolvent that perturbs the delicate balance between stabilizing and destabilizing interactions and eventually induces chemical modifications. For most proteins, denaturation is a complex process involving transient intermediates in several reversible and eventually irreversible steps. Knowledge of protein stability and denaturation processes is mandatory for the development of enzymes as industrial catalysts, biopharmaceuticals, analytical and medical bioreagents, and safe industrial food. Electrophoresis techniques operating under extreme conditions are convenient tools for analyzing unfolding transitions, trapping transient intermediates, and gaining insight into the mechanisms of denaturation processes. Moreover, quantitative analysis of electrophoretic mobility transition curves allows the estimation of the conformational stability of proteins. These approaches include polyacrylamide gel electrophoresis and capillary zone electrophoresis under cold, heat, and hydrostatic pressure and in the presence of non-ionic denaturing agents or stabilizers such as polyols and heavy water. Lastly, after exposure to extremes of physical conditions, electrophoresis under standard conditions provides information on irreversible processes, slow conformational drifts, and slow renaturation processes. The impressive developments of enzyme technology with multiple applications in fine chemistry, biopharmaceutics, and nanomedicine prompted us to revisit the potentialities of these electrophoretic approaches. This feature review is illustrated with published and unpublished results obtained by the authors on cholinesterases and paraoxonase, two physiologically and toxicologically important enzymes.
Collapse
Affiliation(s)
- Patrick Masson
- Biochemical Neuropharmacology Laboratory, Kazan Federal University, Kremlievskaya Str. 18, 420111 Kazan, Russia
| | - Sofya Lushchekina
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Kosygin Str. 4, 119334 Moscow, Russia
| |
Collapse
|
2
|
Improved gel electrophoresis matrix for hydrophobic protein separation and identification. Anal Biochem 2011; 410:98-109. [DOI: 10.1016/j.ab.2010.11.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2010] [Revised: 11/06/2010] [Accepted: 11/08/2010] [Indexed: 12/26/2022]
|
3
|
Variations on a theme: Changes to electrophoretic separations that can make a difference. J Proteomics 2010; 73:1562-72. [DOI: 10.1016/j.jprot.2010.04.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2010] [Revised: 04/01/2010] [Accepted: 04/03/2010] [Indexed: 11/19/2022]
|
4
|
Rabilloud T, Vaezzadeh AR, Potier N, Lelong C, Leize-Wagner E, Chevallet M. Power and limitations of electrophoretic separations in proteomics strategies. MASS SPECTROMETRY REVIEWS 2009; 28:816-843. [PMID: 19072760 DOI: 10.1002/mas.20204] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Proteomics can be defined as the large-scale analysis of proteins. Due to the complexity of biological systems, it is required to concatenate various separation techniques prior to mass spectrometry. These techniques, dealing with proteins or peptides, can rely on chromatography or electrophoresis. In this review, the electrophoretic techniques are under scrutiny. Their principles are recalled, and their applications for peptide and protein separations are presented and critically discussed. In addition, the features that are specific to gel electrophoresis and that interplay with mass spectrometry (i.e., protein detection after electrophoresis, and the process leading from a gel piece to a solution of peptides) are also discussed.
Collapse
|
5
|
Lindberg P, Roeraade J. GEL MATRICES IN N-METHYLFORMAMIDE FOR SEPARATION OF DNA FRAGMENTS. J LIQ CHROMATOGR R T 2007. [DOI: 10.1081/jlc-100101662] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- P. Lindberg
- a Department of Analytical Chemistry , Royal Institute of Technology , Stockholm , S-100 44 , Sweden
| | - J. Roeraade
- a Department of Analytical Chemistry , Royal Institute of Technology , Stockholm , S-100 44 , Sweden
| |
Collapse
|
6
|
Galvani M, Hamdan M, Righetti PG. Investigating the reaction of a number of gel electrophoresis cross-linkers with beta-lactoglobulin by matrix assisted laser desorption/ionization-mass spectrometry. Electrophoresis 2000; 21:3684-92. [PMID: 11271487 DOI: 10.1002/1522-2683(200011)21:17<3684::aid-elps3684>3.0.co;2-e] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
A number of cross-linkers that are commonly used in polyacrylamide gels have been incubated with bovine beta-lactoglobulin B and the resulting reaction mixtures were examined by matrix assisted laser desorption/ionization-mass spectrometry. At concentrations of 0.1, 1, and 20 mM of each cross-linker incubated for 1 h with 50 pmol/microL of the protein, a reactivity scale can be expressed as polyethylene glycol diacrylate > N,N'-bisacrylylcystamine > bisacrylyl piperazine > N,N'-methylenebisacrylamide >> N,N'-diallyltartardiamide (PEGDA>BAC>BAP>Bis>>DATD). Relatively short incubation times indicated one of the five Cys residues as the target of reaction, which was confirmed by post-source decay measurements. Longer incubation times (24 h) with bisacrylamide extended the reaction to all five Cys residues and a number of Lys residues. A second consequence of longer reaction time is the involvement of both terminals of the cross-linker in the observed reaction. This experimental evidence is the first to demonstrate a different reactivity of both ends of one of the most commonly used cross-linkers. Investigation of solutions containing a cross-linker and acrylamide monomers provided useful information on the competition between the two identities for reaction with the protein. Possible implications of these experimental observations for isoelectric focusing separations in polyacrylamide gels are discussed.
Collapse
Affiliation(s)
- M Galvani
- GlaxoWellcome Medicines Research Center, Verona, Italy
| | | | | |
Collapse
|
7
|
Abstract
Agarose and polyacrylamide are the gels used for most analytical and micropreparative electrophoresis of biopolymers. In an alternative approach that offers different physico-chemical properties from these standard gels, nonionic hydrogels and amphigels composed of poly(N-acetylethylenimine) (PAEI) and a variety of cross-linkers were prepared and used as anticonvective matrices for isoelectric focusing. PAEI was prepared from the ring opening, ionic polymerization of 2-methyl-2-oxazoline. The N-acetyl side chains were hydrolyzed with aqueous sodium hydroxide to produce secondary amine sites which were used for the attachment of cross-linkers. Several cross-linkers were tested for their suitability for electrophoresis, and the cross-linker system based on the Diels-Alder reaction between a furan and maleimide tethered to PAEI gave a moldable gel that can be reversibly converted to a sol at 80 degrees C. This gel was used for isoelectric focusing under both denaturing and nondenaturing conditions. Several protein standards were resolved as well as was achieved with polyacrylamide.
Collapse
Affiliation(s)
- T E Zewert
- The Beckman Institute, California Institute of Technology, Division of Biology, Pasadena, USA
| | | |
Collapse
|
8
|
Righetti PG, Gelfi C. Electrophoresis gel media: the state of the art. JOURNAL OF CHROMATOGRAPHY. B, BIOMEDICAL SCIENCES AND APPLICATIONS 1997; 699:63-75. [PMID: 9392368 DOI: 10.1016/s0378-4347(96)00207-1] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Some unique events have occurred in the last few years which might revolutionize the field of polyacrylamide gel electrophoresis. While it was widely recognized that such matrices could normally be cast with a small pore size distribution, typically of the order of a few nanometers diameter (for protein sieving), recent developments suggest that "macroporous" gels could also be produced in the domain of polyacrylamides. If constraints to chain motion are imposed during gel polymerization, large-pore structures can be grown. Such constraints can originate either from low temperatures or from the presence of preformed polymers in the gelling solution; in both cases, the growing chains are forced to "laterally aggregate" via inter-chain hydrogen bond formation. Upon consumption of pendant double bonds, such bundles are frozen in the three-dimensional space by permanent cross-links. As an additional development, a novel photopolymerization system is described, comprising a cationic dye (methylene blue) and a redox couple (sodium toluene sulfinate, a reducer, and diphenyliodonium chloride, a mild oxidizer). Methylene blue catalysis is characterized by a unique efficiency, ensuring >96% conversion of monomers, even in hydro-organic solvents and in the presence of surfactants, which normally quench or completely inhibit the persulphate-driven reaction. In addition, methylene blue-sustained photopolymerization can be operated in the entire pH 3-10 interval, where most other systems fail. Perhaps the most striking novelty in the field is the appearance of a novel monomer (N-acryloylaminopropanol, AAP) coupling a high hydrophilicity with a unique resistance to alkaline hydrolysis. Given the fact that a poly(AAP) matrix is 500 times more stable than a poly(acrylamide) gel, while being twice as hydrophilic, it is anticipated that this novel chemistry will have no difficulties in replacing the old electrophoretic anticonvective media. The review ends with a glimpse at novel sieving media in capillary zone electrophoresis: polymer networks. Such media, by providing an almost infinite range of pore sizes, due to the absence of a rigid support, allow sieving mechanisms to be operative over a wide interval of particle sizes, even up to genomic DNA. Viscous solutions of polymer networks, made with the novel poly(AAP) chemistry, allow repeated use of the same separation column, well above 50 injections. Silica-bound poly(AAP) chains provide effective quenching of electroosmosis and >200 analyses by isoelectric focusing.
Collapse
Affiliation(s)
- P G Righetti
- Department of Agricultural and Industrial Biotechnologies, University of Verona, Italy
| | | |
Collapse
|
9
|
Adessi C, Miege C, Albrieux C, Rabilloud T. Two-dimensional electrophoresis of membrane proteins: a current challenge for immobilized pH gradients. Electrophoresis 1997; 18:127-35. [PMID: 9059834 DOI: 10.1002/elps.1150180124] [Citation(s) in RCA: 111] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Membrane proteins were separated by high resolution two-dimensional (2-D) electrophoresis. On isoelectric focusing (IEF) with immobilized pH gradients severe protein losses in the resulting 2-D map were observed when compared with carrier ampholyte-based IEF. This has been noticed for two different biological systems, namely the chloroplast envelope of spinach and the endocytic vesicles from Dictyostelium discoideum. The possible mechanisms of these losses on immobilized pH gradients are discussed.
Collapse
Affiliation(s)
- C Adessi
- Laboratoire de Chimie des Protéines, CEA, Grenoble, France
| | | | | | | |
Collapse
|
10
|
|
11
|
Simò-Alfonso E, Gelfi C, Sebastiano R, Citterio A, Righetti PG. Novel acrylamido monomers with higher hydrophilicity and improved hydrolytic stability: I. Synthetic route and product characterization. Electrophoresis 1996; 17:723-31. [PMID: 8738335 DOI: 10.1002/elps.1150170418] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The novel acrylamido monomer reported by our group (N-acryloylaminoethoxyethanol, AAEE; Chiari et al., Electrophoresis 1994, 15, 177-186), found to combine high hydrophilicity with extraordinary resistance to alkaline hydrolysis, has come under closer scrutiny due to unexpected and random autopolymerization while stored as a 1/1 v/v water solution at 4 degrees C (possibly due to a greater oxidability of the ether group). We have additionally found a unique degradation pathway of the monomer, called "1-6 H-transfer", by which the C1 (on the double bond site), by constantly ramming against the C6, next to the ether oxygen (O7, which in fact favors the transfer of the hydrogen atom by C1), produces radicals which more efficiently add to the monomer favoring autopolymerization and cross-linking. A number of novel monomers is proposed while maintaining the other unique characteristics of AAEE. One of them, N-acryloylaminopropanol, offers all the unique, special qualities of AAEE, without the noxious aspects of autopolymerization. Additionally, a synthetic route was optimized, yielding an essentially pure product in a single reaction step, with a yield > 99% and an equivalent purity (> 99%). The synthesis consists in reacting acryloyl chloride at -40 degrees C in presence of a twofold molar excess of aminopropanol and in ethanol (instead of methanol) as solvent. Other solvents, as well as the use of triethylamine for neutralizing the HCl produced, were found to give a variety of undesired byproducts.
Collapse
Affiliation(s)
- E Simò-Alfonso
- Universitat de Valencia, Departamento de Quimica Analitica, Facultad de Quimica, Burjassot, Spain
| | | | | | | | | |
Collapse
|
12
|
Esteve-Romero J, Simò-Alfonso E, Bossi A, Bresciani F, Righetti PG. Sample-streaks and smears in immobilized pH gradient gels. Electrophoresis 1996; 17:704-8. [PMID: 8738331 DOI: 10.1002/elps.1150170414] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
In immobilized pH gradient (IPG) gel formulations as wide as pH 4-9, encompassing neutrality and containing the pK 7.0 acrylamido buffer as one of the buffering ions, smears are directly proportional to the total amount of the pK 7.0 species. At a total level of 10 mM pK 7.0 in these gel formulations, severe smears occur not only for mildly hydrophobic proteins (e.g., recombinant alcalase and termamylase) but also for the relatively hydrophilic pI marker proteins. Streaks and smears are essentially abolished in recipes devoid of the pK 7.0 compound or in formulations containing a maximum of 3 mM of this component. Although partitioning in water/n-octanol has shown the pK 7.0 acrylamido buffer to be quite hydrophobic (P = 0.5), the occurrence of smears could be to the presence of oligomers in some commercial preparations. Even when dissolved in n-propanol, some batches of acrylamido buffers might still contain oligomers, probably formed during the synthetic step.
Collapse
Affiliation(s)
- J Esteve-Romero
- Universitat Jaume I, Departament de Ciencies Experimentals, Area de Quimica Analitica, Castellò, Spain
| | | | | | | | | |
Collapse
|
13
|
van Sinderen D, Karsens H, Kok J, Terpstra P, Ruiters MH, Venema G, Nauta A. Sequence analysis and molecular characterization of the temperate lactococcal bacteriophage r1t. Mol Microbiol 1996; 19:1343-55. [PMID: 8730875 DOI: 10.1111/j.1365-2958.1996.tb02478.x] [Citation(s) in RCA: 155] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
The temperate lactococcal bacteriophage r1t was isolated from its lysogenic host and its genome was subjected to nucleotide sequence analysis. The linear r1t genome is composed of 33,350 bp and was shown to possess 3' staggered cohesive ends. Fifty open reading frames (ORFs) were identified which are, probably, organized in a life-cycle-specific manner. Nucleotide sequence comparisons, N-terminal amino acid sequencing and functional analyses enabled the assignment of possible functions to a number of DNA sequences and ORFs. In this way, ORFs specifying regulatory proteins, proteins involved in DNA replication, structural proteins, a holin, a lysin, an integrase, and a dUTPase were putatively identified. One ORF seems to be contained within a self-splicing group I intron. In addition, the bacteriophage att site required for site-specific integration into the host chromosome was determined.
Collapse
Affiliation(s)
- D van Sinderen
- Department of Genetics, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, NN Haren, The Netherlands
| | | | | | | | | | | | | |
Collapse
|
14
|
Affiliation(s)
- M Chiari
- Istituto di Chimica degli Ormoni, CNR, Milano, Italy
| | | |
Collapse
|
15
|
Sanders JW, Leenhouts KJ, Haandrikman AJ, Venema G, Kok J. Stress response in Lactococcus lactis: cloning, expression analysis, and mutation of the lactococcal superoxide dismutase gene. J Bacteriol 1995; 177:5254-60. [PMID: 7665513 PMCID: PMC177316 DOI: 10.1128/jb.177.18.5254-5260.1995] [Citation(s) in RCA: 117] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
In an analysis of the stress response of Lactococcus lactis, three proteins that were induced under low pH culture conditions were detected. One of these was identified as the lactococcal superoxide dismutase (SodA) by N-terminal amino acid sequence analysis. The gene encoding this protein, designated sodA, was cloned by the complementation of a sodA sodB Escherichia coli strain. The deduced amino acid sequence of L. lactis SodA showed the highest degree of similarity to the manganese-containing Sod (MnSod) of Bacillus stearothermophilus. A promoter upstream of the sodA gene was identified by primer extension analysis, and an inverted repeat surrounding the -35 hexanucleotide of this promoter is possibly involved in the regulation of the expression of sodA. The expression of sodA was analyzed by transcriptional fusions with a promoterless lacZ gene. The induction of beta-galactosidase activity occurred in aerated cultures. Deletion experiments revealed that a DNA fragment of more than 130 bp surrounding the promoter was needed for the induction of lacZ expression by aeration. The growth rate of an insertion mutant of sodA did not differ from that of the wild type in standing cultures but was decreased in aerated cultures.
Collapse
Affiliation(s)
- J W Sanders
- Department of Genetics, University of Groningen, NN Haren, The Netherlands
| | | | | | | | | |
Collapse
|
16
|
|
17
|
Rabilloud T, Valette C, Lawrence JJ. Sample application by in-gel rehydration improves the resolution of two-dimensional electrophoresis with immobilized pH gradients in the first dimension. Electrophoresis 1994; 15:1552-8. [PMID: 7536671 DOI: 10.1002/elps.11501501223] [Citation(s) in RCA: 285] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
We describe a modification in the sample application mode for isoelectric focusing with immobilized pH gradients. Instead of being applied at the surface of the gel in a sample cup, the sample is introduced into the gel during the immobilized pH gradient strip rehydration step. This modification implies the use of low percentage gels (below 3.5% T) and specially designed, but simple, rehydration chambers. The main advantages are a uniform resolution without side effects and the possibility of handling large sample volumes (500 microL for a standard 3 x 160 x 0.5 mm strip), allowing micropreparative work (milligram samples) with a simple experimental design.
Collapse
Affiliation(s)
- T Rabilloud
- CEA-Laboratoire de Biologie, Moléculaire du Cycle Cellulaire, INSERM U309, Grenoble
| | | | | |
Collapse
|
18
|
Wiersma JA, Bos M, Pennings AJ. High strength poly(meth)acrylamide copolymer hydrogels. Polym Bull (Berl) 1994. [DOI: 10.1007/bf00296073] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
19
|
|
20
|
Chiari M, Micheletti C, Nesi M, Fazio M, Righetti PG. Towards new formulations for polyacrylamide matrices: N-acryloylaminoethoxyethanol, a novel monomer combining high hydrophilicity with extreme hydrolytic stability. Electrophoresis 1994; 15:177-86. [PMID: 8026432 DOI: 10.1002/elps.1150150131] [Citation(s) in RCA: 115] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Matrices for electrokinetic separations, based on a unique class of mono- and disubstituted (on the amido nitrogen) acrylamides such as e.g., N-acryloylaminoethoxyethanol (AAEE) and acrylamido-N,N-diethoxyethanol, offer the following advantages: (i) strong resistance to alkaline hydrolysis (most zone separations occurring at basic pH values), (ii) high hydrophilicity and (iii) greater porosity, due to the higher molecular weight of the monomers. When compared with conventional poly(acrylamide), a poly(AAEE) matrix, when subjected to mild alkaline hydrolysis (0.1 N NaOH, 70 degrees C) appears to be 500 times more stable. Such stability is also confirmed under strong alkaline hydrolysis (1 N NaOH, 100 degrees C) as well as under mild and strong acidic hydrolysis. Mildly hydrolyzed poly(AAEE) matrices still perform extremely well in both conventional isoelectric focusing and immobilized pH gradients, techniques which are quite sensitive to traces of acrylate in the polymer coil. Conversely, mildly hydrolyzed poly(acrylamide) matrices, when used in isoelectric focusing, generate pH gradients between pH 4 and 5, having an inflection point (pH 4.6) equivalent to the pK value of acrylic acid. This novel class of monomers shows great promise for future applications in all electrokinetic methodologies.
Collapse
Affiliation(s)
- M Chiari
- Instituto di Chimica degli Ormoni, CNR, Milano, Italy
| | | | | | | | | |
Collapse
|
21
|
Abstract
Behavior of serum albumins of different species was compared with regard to electrophoretic mobility under native conditions, molecular mass and isoelectric point in presence or absence of denaturing agents. In addition to serum samples from human, horse, cow, pig, cat, dog, sheep, goat, chicken, rabbit, mouse, and rat, commercially available standards or albumin preparations obtained by chromatographic procedures were analyzed. Feline and canine albumins showed marked differences in all investigated methods. Our experiments also revealed several factors influencing albumin patterns, especially during isoelectric focusing in immobilized pH gradients or in the presence of carrier ampholytes.
Collapse
Affiliation(s)
- I Miller
- Protein and Peptide Chemistry Group, University for Veterinary Medicine, Vienna, Austria
| | | |
Collapse
|
22
|
Caglio S, Righetti PG. On the efficiency of methylene blue versus persulfate catalysis of polyacrylamide gels, as investigated by capillary zone electrophoresis. Electrophoresis 1993; 14:997-1003. [PMID: 8125068 DOI: 10.1002/elps.11501401159] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
The efficiency of a novel method of photopolymerization, based on photoinitiating the reaction with methylene blue (MB), in presence of a redox couple (sodium toluenesulfinate and diphenyliodonium chloride), vs, the conventional persulfate--N,N,N',N'-tetramethylethylenediamine redox couple was investigated as a function of different effectors in solution. Oxygen dissolved in the gelling mixture strongly quenches persulfate catalysis, while leaving essentially unaltered the process initiated by photopolymerization. On the contrary, the presence of 8 M urea substantially accelerates a persulfate-driven reaction, boosting the conversion of monomers to near completion (> 98%) while leaving the photopolymerization process largely unaffected. Polyacrylamide polymerization has also been performed in a number of hydroorganic solvents (all in a 50:50 v/v ratio): dimethyl sulfoxide (DMSO), tetramethylurea, formamide and dimethylformamide. In all cases, the persulfate-catalyzed reaction was strongly quenched and even completely inhibited (in DMSO), whereas the photopolymerization process was essentially unaffected by any of these organic solvents. The reaction kinetics of the methylene blue-driven reaction could not be ameliorated when admixing an anionic dye (e.g., eosin Y) to the cationic MB, even when amply changing their molar ratios. Thus, it appears that photocatalysis with MB (and the redox couple sodium toluene-sulfinate and diphenyliodonium chloride) is a unique process, proceeding at optimum rate under the most adverse conditions, completely insensitive to any kind of positive and negative effectors and able to ensure at least 95% monomer conversion under the standard conditions of 1 h reaction time at room temperature.(ABSTRACT TRUNCATED AT 250 WORDS)
Collapse
Affiliation(s)
- S Caglio
- Chair of Biochemistry, Faculty of Pharmacy, University of Milano, Italy
| | | |
Collapse
|
23
|
Giorgio Righetti P, Chiari M, Nesi M, Caglio S. Towards new formulations for polyacrylamide matrices, as investigated by capillary zone electrophoresis. J Chromatogr A 1993. [DOI: 10.1016/0021-9673(93)83425-r] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
24
|
Hibner U, Rabilloud T, Lutfalla G. Interaction of two DNA-binding factors expressed in B- and T-lymphocyte precursors. RESEARCH IN IMMUNOLOGY 1993; 144:93-109. [PMID: 8516560 DOI: 10.1016/0923-2494(93)80065-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Two DNA-binding factors detected in pre-B and pre-T cells and absent from mature lymphocytes are described. Factor A displayed no appreciable sequence selectivity but bound only to DNA fragments longer than 120 base pairs. The minimal size of a binding site was lower on an intrinsically curved DNA, suggesting formation of tertiary structures on DNA. Factor B interacted with sequences, other than consensus recombination signals, present in the vicinity of unrearranged immunoglobulin genes. Binding of factor B inhibited the interaction of factor A with the same DNA fragment. The presence of the factor-B-binding site in an episomal V(D)J recombinase substrate lowered the frequency of recombination in vivo. We propose that the two factors described here may function as accessory proteins in V(D)J recombination, possibly modulating accessibility of genes to the recombinase.
Collapse
Affiliation(s)
- U Hibner
- Unité de Génétique et Biochimie du Développement, Institut Pasteur, Paris, France
| | | | | |
Collapse
|
25
|
Lyubimova T, Caglio S, Gelfi C, Righetti PG, Rabilloud T. Photopolymerization of polyacrylamide gels with methylene blue. Electrophoresis 1993; 14:40-50. [PMID: 8462514 DOI: 10.1002/elps.1150140108] [Citation(s) in RCA: 45] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Photopolymerization of polyacrylamide gels in the presence of methylene blue (100 microM) and a redox couple (1 mM sodium toluenesulfinate, a reducer, and 50 microM diphenyliodonium chloride, an oxidizer) has been investigated. The gel point, i.e. the time needed for onset of gelation upon illumination, has been found to lengthen progressively at lower temperatures and at lower light intensities. If the three catalysts are progressively diluted, the gel point does not vary for a threefold dilution, but gelation is greatly hampered below a 1:5 dilution of the three effectors. Photobleaching has been assessed as a function of liquid layer thickness (from 0.5 to 2 mm), of a progressive dye dilution (down to a fourfold dilution) and as a function of temperature. A maximum of elastic modulus is located in correspondence to a minimum of permeability (both situated at 5% cross-linker). It is found that methylene blue-activated polymerization produces polyacrylamide gels with elastic properties which are higher than in persulfate-activated gels, so far the most popular matrices for electrokinetic separations. Due to the ease of preparation, the full control of all experimental parameters, and the lack of oxidizing power of this catalyst system (as opposed to the strong oxidation power of persulfate catalysis), methylene blue catalysis is advocated as a valid alternative to other redox systems.
Collapse
Affiliation(s)
- T Lyubimova
- Institute of Continuous Media Mechanics of UB Academy of Sciences, Perm
| | | | | | | | | |
Collapse
|
26
|
Zewert T, Harrington M. Polyethyleneglycol methacrylate 200 as an electrophoresis matrix in hydroorganic solvents. Electrophoresis 1992; 13:824-31. [PMID: 1483423 DOI: 10.1002/elps.11501301182] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The properties of gels composed of poly(polyethyleneglycol methacrylate) and copolymers of polyethyleneglycol methacrylate and acrylamide were studied. These novel electrophoresis matrices are amphigels (swellable in water and organic solvents) that have unprecedented organic solvent compatibility. Hydrophobic proteins which are poorly solubilized in aqueous detergent systems (e.g., zein) are well-resolved in these gels with hydro-organic solvents. This is especially relevant for isoelectric focusing, to avoid using either ionic detergents that may interfere with the focusing, or urea that may cause carbamylation of proteins. Variations of crosslinker, buffer, and solvent systems in these gels were explored.
Collapse
Affiliation(s)
- T Zewert
- NSF Center for Molecular Biotechnology, Beckman Institute, Pasadena, CA 91125
| | | |
Collapse
|
27
|
Zewert T, Harrington M. Polyhydroxy and polyethyleneglycol (meth)acrylate polymers: physical properties and general studies for their use as electrophoresis matrices. Electrophoresis 1992; 13:817-24. [PMID: 1483422 DOI: 10.1002/elps.11501301181] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
A new series of materials have been tested for their suitability as electrophoresis matrices. The mechanical and optical properties of gels composed of polyethyleneglycol (meth)acrylate esters or polyhydroxy (meth)acrylate esters in water and in various concentrations of organic solvents are described. Several crosslinkers including polyethyleneglycol and polyhydroxy di(meth)acrylates, piperazine diacrylate, and bisacrylamide were used in these studies. Electrophoretic migration and separation of a series of protein standards through polyethyleneglycol methacrylate (PEGM) 200, PEGM 400, and glyceryl methacrylate is demonstrated. Further, copolymerization of all of the monomers with acrylamide was performed and the distribution of monomer incorporation into the polymer network calculated. All monomers and copolymers that were examined by IR spectroscopy showed greater than 99% polymerization. These results justify their further study for biomolecule separations.
Collapse
Affiliation(s)
- T Zewert
- NSF Center for Molecular Biotechnology, Beckman Institute, Pasadena, CA 91125
| | | |
Collapse
|
28
|
Gelfi C, de Besi P, Alloni A, Righetti PG. Investigation of the properties of novel acrylamido monomers by capillary zone electrophoresis. J Chromatogr A 1992. [DOI: 10.1016/0021-9673(92)87140-4] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
|
29
|
Investigation of the properties of acrylamide bifunctional monomers (cross-linkers) by capillary zone electrophoresis. J Chromatogr A 1992. [DOI: 10.1016/0021-9673(92)87141-t] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
|
30
|
Chiari M, Ettori C, Manzocchi A, Righetti PG. Structure-stability relationship of Immobiline chemicals for isoelectric focusing as monitored by capillary zone electrophoresis. J Chromatogr A 1991. [DOI: 10.1016/s0021-9673(01)88621-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
|
31
|
Gelfi C, Canali A, Righetti PC, Vezzoni P, Smith C, Mellon M, Jain T, Shorr R. DNA sequencing in HydroLink matrices: extension of reading ability to greater than 600 nucleotides. Electrophoresis 1990; 11:595-600. [PMID: 2289457 DOI: 10.1002/elps.1150110802] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
All the systems for optimizing DNA sequencing published so far have introduced modifications regarding: (i) linearization of band migration via ionic strength gradients or wedge-shaped gels; (ii) automatization of band reading via introduction of fluorescent probes; (iii) direct blotting analysis; (iv) pulsed electric fields and (v) discontinuous buffer systems. In all these systems, DNA sequence reading with an accuracy of ca. 98% rarely exceeds a length of 350 bases. We have chosen, in order to increase the reading ability of a single gel, to manipulate the characteristics of the gel matrix. The Seq-HydroLink gel formation here reported allows optimal reading, from a single gel run, of at least 600 bases. In order to guarantee this reading ability in a single run, the upper and lower ends of the ladder are time-resolved, i.e. the same sample is applied to the gel matrix at three different time intervals. The present system represents an increase of at least 30% in reading ability as compared with any type of polyacrylamide gel formulation so far reported.
Collapse
Affiliation(s)
- C Gelfi
- Department Biomedical Sciences and Technologies, University of Milano
| | | | | | | | | | | | | | | |
Collapse
|
32
|
Righetti PG, Chiari M, Casale E, Chiesa C, Jain T, Shorr R. HydroLink gel electrophoresis (HLGE). I. Matrix characterization. JOURNAL OF BIOCHEMICAL AND BIOPHYSICAL METHODS 1989; 19:37-49. [PMID: 2809066 DOI: 10.1016/0165-022x(89)90049-3] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
A new gelatinous matrix is reported, having intermediate properties between those of polyacrylamide and agarose gels. The matrix has the unique property of being amphiphilic, i.e. of swelling in both plain water and polar organic solvents, and seems particularly well suited for electrophoresis of DNA. The compatibility with organic solvents includes 50% dimethyl sulphoxide, 50% tetramethyl urea, 50% acetonitrile and 50% tetrahydrofuran, the latter having a dielectric constant of 20. The matrix is hypothesized to consist of brush-like pillars, having a hydrophobic core and a hydrophilic coating. The latter is formed by short chains protruding in the surrounding liquid and able to coordinate large amounts of water.
Collapse
Affiliation(s)
- P G Righetti
- Department of Biomedical Sciences and Technologies, University of Milano, Italy
| | | | | | | | | | | |
Collapse
|
33
|
Abstract
Matrices used in modern electrokinetic techniques are surveyed. They are essentially three: cellulose acetate, agarose and polyacrylamide gels. The use of cellulose acetate is confined mostly to analyses in clinical chemistry labs. The properties of agarose are discussed, in particular its capacity of forming large-pore structures via supercoiling, i.e. formation of suprafibers with average radii of approximately 20-25 nm. Several modified agaroses are reviewed, in particular the SeaPlaque, SeaPrep, NuSieve, NuFix, Seakem and Isogel brands and a composite agarose-polyacrylamide matrix, quite popular in the seventies for DNA and RNA separations. The field of polyacrylamide gels seems to be bursting, with the large number of crosslinkers described, imparting special properties to such matrices. The properties of new, modified acrylamide monomers, little known in the field of electrophoresis, are evaluated; in particular: trisacryl gels, hydroxyalkyl methacrylate gels and acryloylmorpholine-bisacrylylpiperazine gels, the latter formed by amphiphilic monomers, highly resistant to alkaline hydrolysis. The properties and formulas of a host of acidic and basic acrylamido derivatives (11 of them) used as buffers and titrants for isoelectric focusing in immobilized pH gradients are reviewed here for the first time. The review culminates with a glimpse at a new generation of amphiphatic matrices, such as HydroLink and 'shielded hydrophobic phase' gels, which appear to be the latest developments in the fields of electrophoresis and chromatography, respectively.
Collapse
Affiliation(s)
- P G Righetti
- Chair of Biochemistry, Faculty of Pharmacy, University of Milan, Italy
| |
Collapse
|
34
|
Hochstrasser DF, Patchornik A, Merril CR. Development of polyacrylamide gels that improve the separation of proteins and their detection by silver staining. Anal Biochem 1988; 173:412-23. [PMID: 3189819 DOI: 10.1016/0003-2697(88)90208-4] [Citation(s) in RCA: 257] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Background staining that is associated with silver detection of proteins and nucleic acids in polyacrylamide gels has been shown to be due mostly to the amide groups in methylenebisacrylamide, a commonly used gel crosslinker. In attempts to reduce this background staining, eight existing crosslinking agents were tested. All of these proved to be unsuitable. Six new crosslinking agents were synthesized and tested. Of these, diacrylylpiperazine provided increased physical strength, improved electrophoretic separation of proteins, and silver staining detection of proteins with reduced background stain.
Collapse
Affiliation(s)
- D F Hochstrasser
- Biochemical Genetics Section, National Institute of Mental Health, Bethesda, Maryland 20892
| | | | | |
Collapse
|
35
|
Kozulić M, Kozulić B, Mosbach K. Poly-N-acryloyl-Tris gels as anticonvection media for electrophoresis and isoelectric focusing. Anal Biochem 1987; 163:506-12. [PMID: 3662000 DOI: 10.1016/0003-2697(87)90255-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
We describe in detail the synthesis of an acrylic monomer, N-acryloyl-tris(hydroxy-methyl)aminomethane (NAT), which was successfully used for the preparation of gels for electrophoresis and isoelectric focusing. The polymerization kinetics and transparency of the poly(NAT) gels crosslinked by N,N'-methylenebisacrylamide (Bis) are also shown. Poly(NAT)-Bis gradient (4-24%) gel resolves proteins according to their size. The exclusion limit of this gel is slightly over 3 X 10(6), which is more than threefold higher than the exclusion limit of the polyacrylamide gradient gel of the same concentration. The gel made of 6% NAT and 3% Bis represents a suitable matrix for isoelectric focusing. These results demonstrate that poly(NAT)-Bis gels could be advantageously used in those applications where the extensive sieving by the polyacrylamide matrix is not desir desirable.
Collapse
Affiliation(s)
- M Kozulić
- Institute of Biotechnology, ETH Hönggerberg, HPT, Zurich, Switzerland
| | | | | |
Collapse
|
36
|
Rabilloud T, Hubert M, Tarroux P. Procedures for two-dimensional electrophoretic analysis of nuclear proteins. J Chromatogr A 1986. [DOI: 10.1016/s0021-9673(01)83474-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
|
37
|
Vecchio G, Righetti PG, Zanoni M, Artoni G, Gianazza E. Fractionation techniques in a hydro-organic environment. I. Sulfolane as a solvent for hydrophobic proteins. Anal Biochem 1984; 137:410-9. [PMID: 6731825 DOI: 10.1016/0003-2697(84)90107-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Sulfolane (thiophene, tethrahydro-1,1-dioxide), at concentrations of 4 M or above, is an efficient solubilizing agent for water-insoluble proteins (e.g., zein or globin chains). In comparison with urea, it appears indefinitely stable in aqueous solutions and does not chemically modify proteins upon storage. Moreover, it favors protein structure, i.e., it increases their alpha-helix content, while urea decreases it. Sulfolane is compatible with electrophoretic techniques (it only slightly reduces polyacrylamide polymerization efficiency and it does not interfere with protein and peptide detection methods) and with chromatographic methods (it has negligible A280 nm). With hydrophilic proteins, sulfolane behaves as a mild denaturant and precipitates them at concentrations between 5 and 7 M.
Collapse
|