1
|
dos Santos ACF, Ahmadzadegan A, Ximenes E, Vlachos P, Ardekani A, Kapur S, Corvari V, Ladisch MR. In vitro measurement of concentration of unlabeled protein within a hyaluronic acid matrix. Biotechnol Bioeng 2022; 119:3647-3656. [PMID: 36131370 PMCID: PMC9828174 DOI: 10.1002/bit.28243] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Revised: 09/16/2022] [Accepted: 09/17/2022] [Indexed: 01/12/2023]
Abstract
There are currently more than 560 therapeutic monoclonal antibodies (mAbs) at various stages of research and clinical testing, including candidates for administration by subcutaneous (SC) injection. Preclinical studies based on in vitro measurements of high molecular weight proteins within simulated SC matrices are assisting laboratory studies of interactions of injectable biotherapeutic proteins within the SC environment in relation to bioavailability. We report a new method for directly measuring diffusion of unlabeled, high molecular weight proteins injected into an in vitro matrix that simulates the negatively charged environment of the SC. The matrix consists of 10 mg/ml HA in a repurposed cell culture chamber. The measurement consists of pipetting triplicate 20 μl protein samples into the matrix, placing the chamber in a laboratory scanner, activating tryptophan residues in the protein at 280 nm, and imaging the resulting protein fluorescence at 384 nm over a 0.5-4 h time period thus tracking protein movement. This facile approach enables mapping of protein concentration as a function of time and distance within the matrix, and determination of diffusion coefficients, D, within ±10%. Bovine IgG and BSA gave D = 2.3 ± 0.2*10-7 and 4.6 ± 0.2*10-7 cm2 /s at 24°C, respectively, for initial protein concentrations of 21 mg/mL.
Collapse
Affiliation(s)
- Antonio C. F. dos Santos
- Laboratory of Renewable Resources EngineeringPurdue UniversityWest LafayetteIndianaUSA,Department of Agricultural and Biological EngineeringPurdue UniversityWest LafayetteIndianaUSA
| | - Adib Ahmadzadegan
- School of Mechanical EngineeringPurdue UniversityWest LafayetteIndianaUSA
| | - Eduardo Ximenes
- Laboratory of Renewable Resources EngineeringPurdue UniversityWest LafayetteIndianaUSA,Department of Agricultural and Biological EngineeringPurdue UniversityWest LafayetteIndianaUSA
| | - Pavlos Vlachos
- School of Mechanical EngineeringPurdue UniversityWest LafayetteIndianaUSA,Weldon School of Biomedical EngineeringPurdue UniversityWest LafayetteIndianaUSA
| | - Arezoo Ardekani
- School of Mechanical EngineeringPurdue UniversityWest LafayetteIndianaUSA
| | - Shiven Kapur
- Bioproduct Research and DevelopmentEli LillyIndianapolisIndianaUSA
| | - Vince Corvari
- Bioproduct Research and DevelopmentEli LillyIndianapolisIndianaUSA
| | - Michael R. Ladisch
- Laboratory of Renewable Resources EngineeringPurdue UniversityWest LafayetteIndianaUSA,Department of Agricultural and Biological EngineeringPurdue UniversityWest LafayetteIndianaUSA,Weldon School of Biomedical EngineeringPurdue UniversityWest LafayetteIndianaUSA
| |
Collapse
|
2
|
Sasikumar D, Vinod K, Sunny J, Hariharan M. Exciton interactions in helical crystals of a hydrogen-bonded eumelanin monomer. Chem Sci 2022; 13:2331-2338. [PMID: 35310511 PMCID: PMC8864807 DOI: 10.1039/d1sc06755a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 01/19/2022] [Indexed: 12/04/2022] Open
Abstract
Eumelanin, a naturally occurring group of heterogeneous polymers/aggregates providing photoprotection to living organisms, consist of 5,6-dihydroxyindole (DHI) and 5,6-dihydroxyindole-2-carboxylic acid (DHICA) building blocks. Despite their prevalence in the animal world, the structure and therefore the mechanism behind the photoprotective broadband absorption and non-radiative decay of eumelanin remain largely unknown. As a small step towards solving the incessant mystery, DHI is crystallized in a non-protic solvent environment to obtain DHI crystals having a helical packing motif. The present approach reflects the solitary directional effect of hydrogen bonds between the DHI chromophores for generating the crystalline assembly and filters out any involvement of the surrounding solvent environment. The DHI single crystals having an atypical chiral packing motif (P212121 Sohncke space group) incorporate enantiomeric zig-zag helical stacks arranged in a herringbone fashion with respect to each other. Each of the zig-zag helical stacks originates from a bifurcated hydrogen bonding interaction between the hydroxyl substituents in adjacent DHI chromophores which act as the backbone structure for the helical assembly. Fragment-based excited state analysis performed on the DHI crystalline assembly demonstrates exciton delocalization along the DHI units that connect each enantiomeric helical stack while, within each stack, the excitons remain localized. Fascinatingly, over the time evolution for generation of single-crystals of the DHI-monomer, mesoscopic double-helical crystals are formed, possibly attributed to the presence of covalently connected DHI trimers in chloroform solution. The oligomeric DHI (in line with the chemical disorder model) along with the characteristic crystalline packing observed for DHI provides insights into the broadband absorption feature exhibited by the chromophore.
Collapse
Affiliation(s)
- Devika Sasikumar
- School of Chemistry, Indian Institute of Science Education and Research Thiruvananthapuram Maruthamala P.O., Vithura Thiruvananthapuram Kerala 695551 India
| | - Kavya Vinod
- School of Chemistry, Indian Institute of Science Education and Research Thiruvananthapuram Maruthamala P.O., Vithura Thiruvananthapuram Kerala 695551 India
| | - Jeswin Sunny
- School of Chemistry, Indian Institute of Science Education and Research Thiruvananthapuram Maruthamala P.O., Vithura Thiruvananthapuram Kerala 695551 India
| | - Mahesh Hariharan
- School of Chemistry, Indian Institute of Science Education and Research Thiruvananthapuram Maruthamala P.O., Vithura Thiruvananthapuram Kerala 695551 India
| |
Collapse
|
3
|
Abstract
One essential prerequisite of any experiment involving a purified protein, such as interaction studies or structural and biophysical characterization, is to work with a "good-quality" sample in order to ensure reproducibility and reliability of the data. Here, we define a "good-quality" sample as a protein preparation that fulfills three criteria: (1) the preparation contains a protein that is pure and soluble and exhibits structural and functional integrity, (2) the protein must be structurally homogeneous, and (3) the preparation must be reproducible. To ensure effective quality control (QC) of all these parameters, we suggest to follow a simple workflow involving the use of gel electrophoresis, light scattering, and spectroscopic experiments. We describe the techniques used in every step of this workflow and provide easy-to-use standard protocols for each step.
Collapse
|
4
|
Acharyya A, Zhang W, Gai F. Tryptophan as a Template for Development of Visible Fluorescent Amino Acids. J Phys Chem B 2021; 125:5458-5465. [PMID: 34029101 DOI: 10.1021/acs.jpcb.1c02321] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Most biological systems, at both molecular and cellular levels, are intrinsically complex, diverse, and nonfluorescent. Therefore, studying their structures, dynamics, and interactions via fluorescence-based methods requires incorporation of one or multiple external fluorophores that would not significantly affect any native property of the system in question. This requirement necessitates the development of a diverse set of fluorescence reporters that differ in chemical, physical, and photophysical properties. Herein, we offer our perspective on the need for, recent progress in, and future directions of developing tryptophan-based fluorescent amino acids.
Collapse
Affiliation(s)
- Arusha Acharyya
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Wenkai Zhang
- Department of Physics and Applied Optics Beijing Area Major Laboratory, Beijing Normal University, Beijing 100875, China
| | - Feng Gai
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| |
Collapse
|
5
|
Micikas RJ, Ahmed IA, Acharyya A, Smith AB, Gai F. Tuning the electronic transition energy of indole via substitution: application to identify tryptophan-based chromophores that absorb and emit visible light. Phys Chem Chem Phys 2021; 23:6433-6437. [PMID: 33710175 DOI: 10.1039/d0cp06710e] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Fluorescent amino acids (FAAs) offer significant advantages over fluorescent proteins in applications where the fluorophore size needs to be limited or minimized. A long-sought goal in biological spectroscopy/microcopy is to develop visible FAAs by modifying the indole ring of tryptophan. Herein, we examine the absorption spectra of a library of 4-substituted indoles and find that the frequency of the absorption maximum correlates linearly with the global electrophilicity index of the substituent. This finding permits us to identify two promising candidates, 4-formyltryptophan (4CHO-Trp) and 4-nitrotryptophan (4NO2-Trp), both of which can be excited by visible light. Further fluorescence measurements indicate that while 4CHO-indole (and 4CHO-Trp) emits cyan fluorescence with a reasonably large quantum yield (ca. 0.22 in ethanol), 4NO2-indole is essentially non-fluorescent, suggesting that 4CHO-Trp (4NO2-Trp) could be useful as a fluorescence reporter (quencher). In addition, we present a simple method for synthesizing 4CHO-Trp.
Collapse
Affiliation(s)
- Robert J Micikas
- Department of Chemistry, University of Pennsylvania, 231 South 34th Street, Philadelphia, Pennsylvania 19104, USA.
| | | | | | | | | |
Collapse
|
6
|
DeRose BT, Kelley RS, Ravi R, Kokona B, Beld J, Spiliotis ET, Padrick SB. Production and analysis of a mammalian septin hetero-octamer complex. Cytoskeleton (Hoboken) 2020; 77:485-499. [PMID: 33185030 DOI: 10.1002/cm.21643] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 10/26/2020] [Accepted: 11/08/2020] [Indexed: 01/19/2023]
Abstract
The septins are filament-forming proteins found in diverse eukaryotes from fungi to vertebrates, with roles in cytokinesis, shaping of membranes and modifying cytoskeletal organization. These GTPases assemble into rod-shaped soluble hetero-hexamers and hetero-octamers in mammals, which polymerize into filaments and higher order structures. While the cell biology and pathobiology of septins are advancing rapidly, mechanistic study of the mammalian septins is limited by a lack of recombinant hetero-octamer materials. We describe here the production and characterization of a recombinant mammalian septin hetero-octamer of defined stoichiometry, the SEPT2/SEPT6/SEPT7/SEPT3 complex. Using a fluorescent protein fusion to the complex, we observed filaments assembled from this complex. In addition, we used this novel tool to resolve recent questions regarding the organization of the soluble septin complex. Biochemical characterization of a SEPT3 truncation that disrupts SEPT3-SEPT3 interactions is consistent with SEPT3 occupying a central position in the complex while the SEPT2 subunits are at the ends of the rod-shaped octameric complexes. Consistent with SEPT2 being on the complex ends, we find that our purified SEPT2/SEPT6/SEPT7/SEPT3 hetero-octamer copolymerizes into mixed filaments with separately purified SEPT2/SEPT6/SEPT7 hetero-hexamer. We expect this new recombinant production approach to lay essential groundwork for future studies into mammalian septin mechanism and function.
Collapse
Affiliation(s)
- Barry T DeRose
- Department of Biochemistry and Molecular Biology, Drexel University, Philadelphia, Pennsylvania, USA
| | - Robert S Kelley
- Department of Biochemistry and Molecular Biology, Drexel University, Philadelphia, Pennsylvania, USA.,VCU Health System, Richmond, Virginia, USA
| | - Roshni Ravi
- Department of Biochemistry and Molecular Biology, Drexel University, Philadelphia, Pennsylvania, USA.,WuXi Advanced Therapies, Philadelphia, Pennsylvania, USA
| | - Bashkim Kokona
- Department of Chemistry, Haverford College, Haverford, Pennsylvania, USA
| | - Joris Beld
- Department of Microbiology and Immunology, Drexel University, Philadelphia, Pennsylvania, USA
| | - Elias T Spiliotis
- Department of Biology, Drexel University, Philadelphia, Pennsylvania, USA
| | - Shae B Padrick
- Department of Biochemistry and Molecular Biology, Drexel University, Philadelphia, Pennsylvania, USA
| |
Collapse
|
7
|
Zhang J, Li X, Ismail F, Xu S, Wang Z, Peng X, Yang C, Chang H, Wang H, Gao Y. Priority Strategy of Intracellular Ca 2+ Homeostasis in Skeletal Muscle Fibers During the Multiple Stresses of Hibernation. Cells 2019; 9:cells9010042. [PMID: 31877883 PMCID: PMC7016685 DOI: 10.3390/cells9010042] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 12/19/2019] [Accepted: 12/19/2019] [Indexed: 01/16/2023] Open
Abstract
: Intracellular calcium (Ca2+) homeostasis plays a vital role in the preservation of skeletal muscle. In view of the well-maintained skeletal muscle found in Daurian ground squirrels (Spermophilus dauricus) during hibernation, we hypothesized that hibernators possess unique strategies of intracellular Ca2+ homeostasis. Here, cytoplasmic, sarcoplasmic reticulum (SR), and mitochondrial Ca2+ levels, as well as the potential Ca2+ regulatory mechanisms, were investigated in skeletal muscle fibers of Daurian ground squirrels at different stages of hibernation. The results showed that cytoplasmic Ca2+ levels increased in the skeletal muscle fibers during late torpor (LT) and inter-bout arousal (IBA), and partially recovered when the animals re-entered torpor (early torpor, ET). Furthermore, compared with levels in the summer active or pre-hibernation state, the activity and protein expression levels of six major Ca2+ channels/proteins were up-regulated during hibernation, including the store-operated Ca2+ entry (SOCE), ryanodine receptor 1 (RyR1), leucine zipper-EF-hand containing transmembrane protein 1 (LETM1), SR Ca2+ ATPase 1 (SERCA1), mitochondrial calcium uniporter complex (MCU complex), and calmodulin (CALM). Among these, the increased extracellular Ca2+ influx mediated by SOCE, SR Ca2+ release mediated by RyR1, and mitochondrial Ca2+ extrusion mediated by LETM1 may be triggers for the periodic elevation in cytoplasmic Ca2+ levels observed during hibernation. Furthermore, the increased SR Ca2+ uptake through SERCA1, mitochondrial Ca2+ uptake induced by MCU, and elevated free Ca2+ binding capacity mediated by CALM may be vital strategies in hibernating ground squirrels to attenuate cytoplasmic Ca2+ levels and restore Ca2+ homeostasis during hibernation. Compared with that in LT or IBA, the decreased extracellular Ca2+ influx mediated by SOCE and elevated mitochondrial Ca2+ uptake induced by MCU may be important mechanisms for the partial cytoplasmic Ca2+ recovery in ET. Overall, under extreme conditions, hibernating ground squirrels still possess the ability to maintain intracellular Ca2+ homeostasis.
Collapse
Affiliation(s)
- Jie Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western China, College of Life Sciences, Northwest University, Ministry of Education, Xi’an 710069, China; (J.Z.); (F.I.); (S.X.); (Z.W.); (X.P.); (H.W.)
- Shaanxi Key Laboratory for Animal Conservation, Northwest University, Xi’an 710069, China
| | - Xiaoyu Li
- Human Functional Genomics Laboratory, Northwest University, Xi’an 710069, China;
| | - Fazeela Ismail
- Key Laboratory of Resource Biology and Biotechnology in Western China, College of Life Sciences, Northwest University, Ministry of Education, Xi’an 710069, China; (J.Z.); (F.I.); (S.X.); (Z.W.); (X.P.); (H.W.)
- Shaanxi Key Laboratory for Animal Conservation, Northwest University, Xi’an 710069, China
| | - Shenhui Xu
- Key Laboratory of Resource Biology and Biotechnology in Western China, College of Life Sciences, Northwest University, Ministry of Education, Xi’an 710069, China; (J.Z.); (F.I.); (S.X.); (Z.W.); (X.P.); (H.W.)
- Shaanxi Key Laboratory for Animal Conservation, Northwest University, Xi’an 710069, China
| | - Zhe Wang
- Key Laboratory of Resource Biology and Biotechnology in Western China, College of Life Sciences, Northwest University, Ministry of Education, Xi’an 710069, China; (J.Z.); (F.I.); (S.X.); (Z.W.); (X.P.); (H.W.)
- Shaanxi Key Laboratory for Animal Conservation, Northwest University, Xi’an 710069, China
| | - Xin Peng
- Key Laboratory of Resource Biology and Biotechnology in Western China, College of Life Sciences, Northwest University, Ministry of Education, Xi’an 710069, China; (J.Z.); (F.I.); (S.X.); (Z.W.); (X.P.); (H.W.)
- Shaanxi Key Laboratory for Animal Conservation, Northwest University, Xi’an 710069, China
| | - Chenxi Yang
- College of Biological Science and Engineering, North Minzu University, Yinchuan 750021, China;
| | - Hui Chang
- Key Laboratory of Resource Biology and Biotechnology in Western China, College of Life Sciences, Northwest University, Ministry of Education, Xi’an 710069, China; (J.Z.); (F.I.); (S.X.); (Z.W.); (X.P.); (H.W.)
- Shaanxi Key Laboratory for Animal Conservation, Northwest University, Xi’an 710069, China
- Correspondence: (H.C.); (Y.G.)
| | - Huiping Wang
- Key Laboratory of Resource Biology and Biotechnology in Western China, College of Life Sciences, Northwest University, Ministry of Education, Xi’an 710069, China; (J.Z.); (F.I.); (S.X.); (Z.W.); (X.P.); (H.W.)
- Shaanxi Key Laboratory for Animal Conservation, Northwest University, Xi’an 710069, China
| | - Yunfang Gao
- Key Laboratory of Resource Biology and Biotechnology in Western China, College of Life Sciences, Northwest University, Ministry of Education, Xi’an 710069, China; (J.Z.); (F.I.); (S.X.); (Z.W.); (X.P.); (H.W.)
- Shaanxi Key Laboratory for Animal Conservation, Northwest University, Xi’an 710069, China
- Correspondence: (H.C.); (Y.G.)
| |
Collapse
|
8
|
Chopra A, Willmore WG, Biggar KK. Protein quantification and visualization via ultraviolet-dependent labeling with 2,2,2-trichloroethanol. Sci Rep 2019; 9:13923. [PMID: 31558752 PMCID: PMC6763483 DOI: 10.1038/s41598-019-50385-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 09/09/2019] [Indexed: 11/09/2022] Open
Abstract
The incorporation of 2,2,2-trichloroethanol in polyacrylamide gels allows for fluorescent visualization of proteins following electrophoresis. Ultraviolet-light exposure, in the presence of this trichlorinated compound, results in a covalent modification of the tryptophan indole ring that shifts the fluorescent emission into the visible range. Based on this principle, we used 2,2,2-trichloroethanol to develop a microplate format protein quantification assay based on the fluorescent signal generated by modified proteins. We also demonstrated a specific fluorescent emission of 2,2,2-trichloroethanol-labeled protein at 450 nm, with a 310 nm excitation, resulting from modification of both tryptophan and tyrosine residues. Following optimization, this protein quantification assay displayed superior sensitivity when compared to UV absorbance at 280 nm (A280), and enabled quantification beyond the linear range permitted by the Bradford method. This 100 μL assay displayed a sensitivity of 10.5 μg in a range up to at least 200 μg. Furthermore, we extended the utility of this method through the development of a 20 μL low-volume assay, with a sensitivity of 8.7 μg tested up to 100 μg, which enabled visualization of proteins following SDS-PAGE. Collectively, these results demonstrate the utility of 2,2,2-trichloroethanol-based protein quantification and demonstrates the protein visualization in polyacrylamide gels based on 2,2,2-trichloroethanol-labeling pre-electrophoresis.
Collapse
Affiliation(s)
- Anand Chopra
- Department of Biology, Carleton University, 1125 Colonel By Dr, Ottawa, ON, K1S 5B6, Canada
| | - William G Willmore
- Department of Biology, Carleton University, 1125 Colonel By Dr, Ottawa, ON, K1S 5B6, Canada. .,Institute of Biochemistry, Carleton University, 1125 Colonel By Dr, Ottawa, ON, K1S 5B6, Canada. .,Department of Chemistry, Carleton University, 1125 Colonel By Dr, Ottawa, ON, K1S 5B6, Canada.
| | - Kyle K Biggar
- Department of Biology, Carleton University, 1125 Colonel By Dr, Ottawa, ON, K1S 5B6, Canada. .,Institute of Biochemistry, Carleton University, 1125 Colonel By Dr, Ottawa, ON, K1S 5B6, Canada.
| |
Collapse
|
9
|
Rojas-Rengifo DF, Ulloa-Guerrero CP, Joppich M, Haas R, Del Pilar Delgado M, Jaramillo C, Jiménez-Soto LF. Tryptophan usage by Helicobacter pylori differs among strains. Sci Rep 2019; 9:873. [PMID: 30696868 PMCID: PMC6351589 DOI: 10.1038/s41598-018-37263-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 11/19/2018] [Indexed: 11/14/2022] Open
Abstract
Because of its association with severe gastric pathologies, including gastric cancer, Helicobacter pylori has been subject of research for more than 30 years. Its capacity to adapt and survive in the human stomach can be attributed to its genetic flexibility. Its natural competence and its capacity to turn genes on and off allows H. pylori to adapt rapidly to the changing conditions of its host. Because of its genetic variability, it is difficult to establish the uniqueness of each strain obtained from a human host. The methods considered to-date to deliver the best result for differentiation of strains are Rapid Amplification of Polymorphic DNA (RAPD), Multilocus Sequence Typing (MLST) and Whole Genome Sequencing (WGS) analysis. While RAPD analysis is cost-effective, it requires a stable genome for its reliability. MLST and WGS are optimal for strain identification, however, they require analysis of data at the bioinformatics level. Using the StainFree method, which modifies tryptophan residues on proteins using 2, 2, 2, - trichloroethanol (TCE), we observed a strain specific pattern of tryptophan in 1D acrylamide gels. In order to establish the effectiveness of tryptophan fingerprinting for strain identification, we compared the graphic analysis of tryptophan-labelled bands in the gel images with MLST results. Based on this, we find that tryptophan banding patterns can be used as an alternative method for the differentiation of H. pylori strains. Furthermore, investigating the origin for these differences, we found that H. pylori strains alters the number and/or position of tryptophan present in several proteins at the genetic code level, with most exchanges taking place in membrane- and cation-binding proteins, which could be part of a novel response of H. pylori to host adaptation.
Collapse
Affiliation(s)
- Diana F Rojas-Rengifo
- Molecular Diagnostic and Bioinformatics Laboratory, Biological Sciences Department, Los Andes University, Carrera 1 Nr.18A-10, Bogotá, Colombia.,Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, Pettenkoferstr. 9a, D-80336, Munich, Germany
| | - Cindy P Ulloa-Guerrero
- Molecular Diagnostic and Bioinformatics Laboratory, Biological Sciences Department, Los Andes University, Carrera 1 Nr.18A-10, Bogotá, Colombia.,Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, Pettenkoferstr. 9a, D-80336, Munich, Germany
| | - Markus Joppich
- Lehr- und Forschungseinheit Bioinformatik. Institut für Informatik, Ludwig-Maximilians-Universität München, Amalienstr. 17, D-80333, Munich, Germany
| | - Rainer Haas
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, Pettenkoferstr. 9a, D-80336, Munich, Germany
| | - Maria Del Pilar Delgado
- Molecular Diagnostic and Bioinformatics Laboratory, Biological Sciences Department, Los Andes University, Carrera 1 Nr.18A-10, Bogotá, Colombia
| | - Carlos Jaramillo
- Molecular Diagnostic and Bioinformatics Laboratory, Biological Sciences Department, Los Andes University, Carrera 1 Nr.18A-10, Bogotá, Colombia
| | - Luisa F Jiménez-Soto
- Max von Pettenkofer Institute of Hygiene and Medical Microbiology, Faculty of Medicine, LMU Munich, Pettenkoferstr. 9a, D-80336, Munich, Germany. .,Ludwig-Maximillians University, Munich, Germany.
| |
Collapse
|
10
|
Wu ZL, Tatge TJ, Grill AE, Zou Y. Detecting and Imaging O-GlcNAc Sites Using Glycosyltransferases: A Systematic Approach to Study O-GlcNAc. Cell Chem Biol 2018; 25:1428-1435.e3. [PMID: 30100348 DOI: 10.1016/j.chembiol.2018.07.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Revised: 05/20/2018] [Accepted: 07/05/2018] [Indexed: 12/17/2022]
Abstract
O-GlcNAcylation is a reversible serine/threonine glycosylation for regulating protein activity and availability inside cells. In a given protein, O-GlcNAcylated and unoccupied O-linked β-N-acetylglucosamine (O-GlcNAc) sites are referred to as closed and open sites, respectively. The balance between open and closed sites is believed to be dynamically regulated. In this report, closed sites are detected using in vitro incorporation of GalNAz by B3GALNT2, and open sites are detected by in vitro incorporation of GlcNAz by O-GlcNAc transferase (OGT), via click chemistry. For assessing total O-GlcNAc sites, a sample is O-GlcNAcylated in vitro by OGT before detecting by B3GALNT2. The methods are demonstrated on purified recombinant proteins including CK2, AKT1, and PFKFB3, and cellular extracts of HEK cells. Through O-GlcNAc imaging, the modification degree of O-GlcNAc in nuclei of Chinese hamster ovary cells was estimated. The detection and imaging of both open and closed O-GlcNAc sites provide a systematic approach to study this important post-translational modification.
Collapse
Affiliation(s)
- Zhengliang L Wu
- Department of Enzyme, Bio-techne, R&D Systems, Inc., 614 McKinley Place N.E., Minneapolis, MN 55413, USA.
| | - Timothy J Tatge
- Department of Enzyme, Bio-techne, R&D Systems, Inc., 614 McKinley Place N.E., Minneapolis, MN 55413, USA
| | - Alex E Grill
- Department of Product Support Process Improvement, Bio-techne, R&D Systems, Inc., 614 McKinley Place N.E., Minneapolis, MN 55413, USA
| | - Yonglong Zou
- Department of Antibody Application Quality Control, Bio-techne, R&D Systems, Inc., 614 McKinley Place N.E., Minneapolis, MN 55413, USA
| |
Collapse
|
11
|
Pichlo C, Toelzer C, Chojnacki K, Öcal S, Uthoff M, Ruegenberg S, Hermanns T, Schacherl M, Denzel MS, Hofmann K, Niefind K, Baumann U. Improved protein-crystal identification by using 2,2,2-trichloroethanol as a fluorescence enhancer. Acta Crystallogr F Struct Biol Commun 2018; 74:307-314. [PMID: 29717999 PMCID: PMC5931144 DOI: 10.1107/s2053230x18005253] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Accepted: 04/03/2018] [Indexed: 11/10/2022] Open
Abstract
The identification of initial lead conditions for successful protein crystallization is crucial for structural studies using X-ray crystallography. In order to reduce the number of false-negative conditions, an emerging number of fluorescence-based methods have been developed which allow more efficient identification of protein crystals and help to distinguish them from salt crystals. Detection of the native tryptophan fluorescence of protein crystals is one of the most widely used methods. However, this method can fail owing to the properties of the crystallized protein or the chemical composition of the crystallization trials. Here, a simple, fast and cost-efficient method employing 2,2,2-trichloroethanol (TCE) has been developed. It can be performed with a standard UV-light microscope and can be applied to cases in which detection of native tryptophan fluorescence fails. In four test cases this method had no effect on the diffraction properties of the crystals and no structural changes were observed. Further evidence is provided that TCE can be added to crystallization trials during their preparation, making this method compatible with high-throughput approaches.
Collapse
Affiliation(s)
- Christian Pichlo
- Institute of Biochemistry, University of Cologne, Zülpicher Strasse 47, 50674 Cologne, Germany
| | - Christine Toelzer
- Institute of Biochemistry, University of Cologne, Zülpicher Strasse 47, 50674 Cologne, Germany
| | - Konrad Chojnacki
- Institute of Biochemistry, University of Cologne, Zülpicher Strasse 47, 50674 Cologne, Germany
- Faculty of Chemistry, Warsaw University of Technology, ul. Noakowskiego 3, 00-664 Warsaw, Poland
| | - Sinan Öcal
- Institute of Biochemistry, University of Cologne, Zülpicher Strasse 47, 50674 Cologne, Germany
| | - Matthias Uthoff
- Institute of Biochemistry, University of Cologne, Zülpicher Strasse 47, 50674 Cologne, Germany
| | - Sabine Ruegenberg
- Max Planck Institute for Biology of Ageing, Research Institute, Joseph-Stelzmann-Strasse 9b, 50931 Cologne, Germany
| | - Thomas Hermanns
- Institute for Genetics, University of Cologne, Zülpicher Strasse 47a, 50674 Cologne, Germany
| | - Magdalena Schacherl
- Structural Dynamics of Proteins, Center of Advanced European Studies and Research, Ludwig-Erhard-Allee 2, 53175 Bonn, Germany
| | - Martin S. Denzel
- Max Planck Institute for Biology of Ageing, Research Institute, Joseph-Stelzmann-Strasse 9b, 50931 Cologne, Germany
| | - Kay Hofmann
- Institute for Genetics, University of Cologne, Zülpicher Strasse 47a, 50674 Cologne, Germany
| | - Karsten Niefind
- Institute of Biochemistry, University of Cologne, Zülpicher Strasse 47, 50674 Cologne, Germany
| | - Ulrich Baumann
- Institute of Biochemistry, University of Cologne, Zülpicher Strasse 47, 50674 Cologne, Germany
| |
Collapse
|
12
|
Fluorescent Protein Visualization Immediately After Gel Electrophoresis Using an In-Gel Trichloroethanol Photoreaction with Tryptophan. Methods Mol Biol 2018; 1853:179-190. [PMID: 30097944 DOI: 10.1007/978-1-4939-8745-0_22] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
SDS-polyacrylamide gel electrophoresis (SDS-PAGE) is one of the essential techniques in molecular biology and biochemistry laboratories and requires rapid visualization methods for efficient sample analysis. Proteins on polyacrylamide gels can be visualized within 5 min via the photoreaction of tryptophan with trichloroethanol. This process does not require protein fixation, staining, or destaining. In this method polyacrylamide gels are prepared by adding trichloroethanol before polymerization. After electrophoresis, the gel is immediately activated on a standard UV transilluminator and the fluorescently labeled proteins are imaged. The reaction is based on the photoreaction of trichloroethanol with tryptophan residues within the protein. This generates a visible blue-green fluorescence (∼500 nm) that is accurately imaged. Here we describe the preparation of Tris-glycine and Tris-tricine SDS-polyacrylamide gels with trichloroethanol and the photoreaction and visualization of tryptophan containing proteins.
Collapse
|
13
|
Raykin J, Snider E, Bheri S, Mulvihill J, Ethier CR. A modified gelatin zymography technique incorporating total protein normalization. Anal Biochem 2017; 521:8-10. [PMID: 28069453 DOI: 10.1016/j.ab.2017.01.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Revised: 12/16/2016] [Accepted: 01/05/2017] [Indexed: 10/20/2022]
Abstract
Gelatinase zymography is a commonly used laboratory procedure; however, variability in sample loading and concentration reduce the accuracy of quantitative results obtained from this technique. To facilitate normalization of gelatinase activity by loaded protein amount, we developed a protocol using the trihalocompound 2,2,2-trichloroethanol to allow for gelatin zymography and total protein labeling within the same gel. We showed that detected protein levels increased linearly with loading, and describe a loading concentration range over which normalized gelatinase activity was constant. We conclude that in-gel total protein detection is feasible in gelatin zymography and greatly improves comparison of gelatinase activity between samples.
Collapse
Affiliation(s)
- Julia Raykin
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, United States
| | - Eric Snider
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, United States
| | - Sruti Bheri
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, United States
| | - John Mulvihill
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, United States; Department of Mechanical and Manufacturing Engineering, School of Engineering, Trinity College Dublin, Dublin, Ireland
| | - C Ross Ethier
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, United States; George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA, United States.
| |
Collapse
|
14
|
Gonzalez-Lozano MA, Klemmer P, Gebuis T, Hassan C, van Nierop P, van Kesteren RE, Smit AB, Li KW. Dynamics of the mouse brain cortical synaptic proteome during postnatal brain development. Sci Rep 2016; 6:35456. [PMID: 27748445 PMCID: PMC5066275 DOI: 10.1038/srep35456] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 09/28/2016] [Indexed: 01/04/2023] Open
Abstract
Development of the brain involves the formation and maturation of numerous synapses. This process requires prominent changes of the synaptic proteome and potentially involves thousands of different proteins at every synapse. To date the proteome analysis of synapse development has been studied sparsely. Here, we analyzed the cortical synaptic membrane proteome of juvenile postnatal days 9 (P9), P15, P21, P27, adolescent (P35) and different adult ages P70, P140 and P280 of C57Bl6/J mice. Using a quantitative proteomics workflow we quantified 1560 proteins of which 696 showed statistically significant differences over time. Synaptic proteins generally showed increased levels during maturation, whereas proteins involved in protein synthesis generally decreased in abundance. In several cases, proteins from a single functional molecular entity, e.g., subunits of the NMDA receptor, showed differences in their temporal regulation, which may reflect specific synaptic development features of connectivity, strength and plasticity. SNARE proteins, Snap 29/47 and Stx 7/8/12, showed higher expression in immature animals. Finally, we evaluated the function of Cxadr that showed high expression levels at P9 and a fast decline in expression during neuronal development. Knock down of the expression of Cxadr in cultured primary mouse neurons revealed a significant decrease in synapse density.
Collapse
Affiliation(s)
- Miguel A Gonzalez-Lozano
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics &Cognitive Research, Neuroscience Campus Amsterdam, VU University, Amsterdam, The Netherlands
| | - Patricia Klemmer
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics &Cognitive Research, Neuroscience Campus Amsterdam, VU University, Amsterdam, The Netherlands
| | - Titia Gebuis
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics &Cognitive Research, Neuroscience Campus Amsterdam, VU University, Amsterdam, The Netherlands
| | - Chopie Hassan
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Pim van Nierop
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics &Cognitive Research, Neuroscience Campus Amsterdam, VU University, Amsterdam, The Netherlands
| | - Ronald E van Kesteren
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics &Cognitive Research, Neuroscience Campus Amsterdam, VU University, Amsterdam, The Netherlands
| | - August B Smit
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics &Cognitive Research, Neuroscience Campus Amsterdam, VU University, Amsterdam, The Netherlands
| | - Ka Wan Li
- Department of Molecular and Cellular Neurobiology, Center for Neurogenomics &Cognitive Research, Neuroscience Campus Amsterdam, VU University, Amsterdam, The Netherlands
| |
Collapse
|
15
|
Holzmüller W, Kulozik U. Quantification of MFGM proteins in buttermilk and butter serum by means of a stain free SDS-PAGE method. J Food Compost Anal 2016. [DOI: 10.1016/j.jfca.2016.04.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
16
|
Holzmüller W, Kulozik U. Protein quantification by means of a stain-free SDS-PAGE technology without the need for analytical standards: Verification and validation of the method. J Food Compost Anal 2016. [DOI: 10.1016/j.jfca.2016.03.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
17
|
Glycoprotein labeling with click chemistry (GLCC) and carbohydrate detection. Carbohydr Res 2015; 412:1-6. [DOI: 10.1016/j.carres.2015.04.018] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2015] [Revised: 04/09/2015] [Accepted: 04/22/2015] [Indexed: 11/20/2022]
|
18
|
Vigelsø A, Dybboe R, Hansen CN, Dela F, Helge JW, Guadalupe Grau A. GAPDH and β-actin protein decreases with aging, making Stain-Free technology a superior loading control in Western blotting of human skeletal muscle. J Appl Physiol (1985) 2014; 118:386-94. [PMID: 25429098 DOI: 10.1152/japplphysiol.00840.2014] [Citation(s) in RCA: 93] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Reference proteins (RP) or the total protein (TP) loaded is used to correct for uneven loading and/or transfer in Western blotting. However, the signal sensitivity and the influence of physiological conditions may question the normalization methods. Therefore, three widely used reference proteins [β-actin, glyceraldehyde 3-phosphate dehydrogenase (GAPDH), and α-tubulin], as well as TP loaded measured by Stain-Free technology (SF) as normalization tool were tested. This was done using skeletal muscle samples from men subjected to physiological conditions often investigated in applied physiology where the intervention has been suggested to impede normalization (ageing, muscle atrophy, and different muscle fiber type composition). The linearity of signal and the methodological variation coefficient was obtained. Furthermore, the inter- and intraindividual variation in signals obtained from SF and RP was measured in relation to ageing, muscle atrophy, and different muscle fiber type composition, respectively. A stronger linearity of SF and β-actin compared with GAPDH and α-tubulin was observed. The methodological variation was relatively low in all four methods (4-11%). Protein level of β-actin and GAPDH was lower in older men compared with young men. In conclusion, β-actin, GAPDH, and α-tubulin may not be used for normalization in studies that include subjects with a large age difference. In contrast, the RPs may not be affected in studies that include muscle wasting and differences in muscle fiber type. The novel SF technology adds lower variation to the results compared with the existing methods for correcting for loading inaccuracy in Western blotting of human skeletal muscle in applied physiology.
Collapse
Affiliation(s)
- Andreas Vigelsø
- Center for Healthy Aging, Department of Biomedical Sciences, Faculty of Health Sciences, University of Copenhagen, Denmark
| | - Rie Dybboe
- Center for Healthy Aging, Department of Biomedical Sciences, Faculty of Health Sciences, University of Copenhagen, Denmark
| | - Christina Neigaard Hansen
- Center for Healthy Aging, Department of Biomedical Sciences, Faculty of Health Sciences, University of Copenhagen, Denmark
| | - Flemming Dela
- Center for Healthy Aging, Department of Biomedical Sciences, Faculty of Health Sciences, University of Copenhagen, Denmark
| | - Jørn W Helge
- Center for Healthy Aging, Department of Biomedical Sciences, Faculty of Health Sciences, University of Copenhagen, Denmark
| | - Amelia Guadalupe Grau
- Center for Healthy Aging, Department of Biomedical Sciences, Faculty of Health Sciences, University of Copenhagen, Denmark
| |
Collapse
|
19
|
Takasuka TE, Walker JA, Bergeman LF, Vander Meulen KA, Makino SI, Elsen NL, Fox BG. Cell-free translation of biofuel enzymes. Methods Mol Biol 2014; 1118:71-95. [PMID: 24395410 DOI: 10.1007/978-1-62703-782-2_5] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
In nature, bacteria and fungi are able to utilize recalcitrant plant materials by secreting a diverse set of enzymes. While genomic sequencing efforts offer exhaustive lists of genes annotated as potential polysaccharide-degrading enzymes, biochemical and functional characterizations of the encoded proteins are still needed to realize the full potential of this natural genomic diversity. This chapter outlines an application of wheat germ cell-free translation to the study of biofuel enzymes using genes from Clostridium thermocellum, a model cellulolytic organism. Since wheat germ extract lacks enzymatic activities that can hydrolyze insoluble polysaccharide substrates and is likewise devoid of enzymes that consume the soluble sugar products, the cell-free translation reactions provide a clean background for production and study of the reactions of biofuel enzymes. Examples of assays performed with individual enzymes or with small sets of enzymes obtained directly from cell-free translation are provided.
Collapse
Affiliation(s)
- Taichi E Takasuka
- Department of Biochemistry, University of Wisconsin, Madison, WI, USA
| | | | | | | | | | | | | |
Collapse
|
20
|
Ladner CL, Tran K, Le M, Turner RJ, Edwards RA. Excited State Photoreaction between the Indole Side Chain of Tryptophan and Halocompounds Generates New Fluorophores and Unique Modifications. Photochem Photobiol 2014; 90:1027-33. [DOI: 10.1111/php.12279] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2014] [Accepted: 03/27/2014] [Indexed: 11/29/2022]
Affiliation(s)
- Carol L. Ladner
- Department of Biological Sciences; Faculty of Science; University of Calgary; Calgary AB Canada
| | - Khai Tran
- Department of Biological Sciences; Faculty of Science; University of Calgary; Calgary AB Canada
| | - Mary Le
- Department of Biological Sciences; Faculty of Science; University of Calgary; Calgary AB Canada
| | - Raymond J. Turner
- Department of Biological Sciences; Faculty of Science; University of Calgary; Calgary AB Canada
| | - Robert A. Edwards
- Department of Biological Sciences; Faculty of Science; University of Calgary; Calgary AB Canada
| |
Collapse
|
21
|
Rivardo F, Leach TGH, Chan CS, Winstone TML, Ladner CL, Sarfo KJ, Turner RJ. Unique Photobleaching Phenomena of the Twin-Arginine Translocase Respiratory Enzyme Chaperone DmsD. Open Biochem J 2014; 8:1-11. [PMID: 24497893 PMCID: PMC3912628 DOI: 10.2174/1874091x01408010001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2013] [Revised: 11/27/2013] [Accepted: 12/01/2013] [Indexed: 11/22/2022] Open
Abstract
DmsD is a chaperone of the redox enzyme maturation protein family specifically required for biogenesis of DMSO reductase in Escherichia coli. It exists in multiple folding forms, all of which are capable of binding its known substrate, the twin-arginine leader sequence of the DmsA catalytic subunit. It is important for maturation of the reductase and targeting to the cytoplasmic membrane for translocation. Here, we demonstrate that DmsD exhibits an irreversible photobleaching phenomenon upon 280 nm excitation irradiation. The phenomenon is due to quenching of the tryptophan residues in DmsD and is dependent on its folding and conformation. We also show that a tryptophan residue involved in DmsA signal peptide binding (W87) is important for photobleaching of DmsD. Mutation of W87, or binding of the DmsA twin-arginine signal peptide to DmsD in the pocket that includes W72, W80, and W91 significantly affects the degree of photobleaching. This study highlights the advantage of a photobleaching phenomenon to study protein folding and conformation changes within a protein that was once considered unusable in fluorescence spectroscopy.
Collapse
Affiliation(s)
- Fabrizio Rivardo
- BI 156, Department of Biological Sciences, University of Calgary, 2500 University Dr NW, Calgary, Alberta, Canada T2N 1N4
| | - Thorin G H Leach
- BI 156, Department of Biological Sciences, University of Calgary, 2500 University Dr NW, Calgary, Alberta, Canada T2N 1N4
| | - Catherine S Chan
- BI 156, Department of Biological Sciences, University of Calgary, 2500 University Dr NW, Calgary, Alberta, Canada T2N 1N4
| | - Tara M L Winstone
- BI 156, Department of Biological Sciences, University of Calgary, 2500 University Dr NW, Calgary, Alberta, Canada T2N 1N4
| | - Carol L Ladner
- BI 156, Department of Biological Sciences, University of Calgary, 2500 University Dr NW, Calgary, Alberta, Canada T2N 1N4
| | - Kwabena J Sarfo
- BI 156, Department of Biological Sciences, University of Calgary, 2500 University Dr NW, Calgary, Alberta, Canada T2N 1N4
| | - Raymond J Turner
- BI 156, Department of Biological Sciences, University of Calgary, 2500 University Dr NW, Calgary, Alberta, Canada T2N 1N4
| |
Collapse
|
22
|
Schweighauser L, Wegner HA. Cyclotetraazocarbazole – a multichromic molecule. Chem Commun (Camb) 2013; 49:4397-9. [DOI: 10.1039/c2cc37956b] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
23
|
Colella AD, Chegenii N, Tea MN, Gibbins IL, Williams KA, Chataway TK. Comparison of Stain-Free gels with traditional immunoblot loading control methodology. Anal Biochem 2012; 430:108-10. [PMID: 22929699 DOI: 10.1016/j.ab.2012.08.015] [Citation(s) in RCA: 111] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2012] [Revised: 08/16/2012] [Accepted: 08/16/2012] [Indexed: 10/27/2022]
Abstract
Loading controls are necessary for semiquantitative Western blotting to compensate for loading errors. Loading control methods include the reprobing of membranes with an antibody against a constitutively expressed protein or staining the membrane with a total protein stain. We compared the loading control performance of recently released Stain-Free (SF) gels with Sypro Ruby (SR) and reprobing using β-actin. SF gels demonstrated superior performance in that they were faster, required fewer steps and consumables, and allowed the quality of electrophoresis and Western transfer to be assessed before committing to costly and time-consuming Western blots.
Collapse
Affiliation(s)
- Alex D Colella
- Department of Ophthalmology, Flinders University, Bedford Park, SA 5042, Australia.
| | | | | | | | | | | |
Collapse
|
24
|
Conformational changes and loose packing promote E. coli Tryptophanase cold lability. BMC STRUCTURAL BIOLOGY 2009; 9:65. [PMID: 19814824 PMCID: PMC2770544 DOI: 10.1186/1472-6807-9-65] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/07/2009] [Accepted: 10/08/2009] [Indexed: 11/25/2022]
Abstract
Background Oligomeric enzymes can undergo a reversible loss of activity at low temperatures. One such enzyme is tryptophanase (Trpase) from Escherichia coli. Trpase is a pyridoxal phosphate (PLP)-dependent tetrameric enzyme with a Mw of 210 kD. PLP is covalently bound through an enamine bond to Lys270 at the active site. The incubation of holo E. coli Trpases at 2°C for 20 h results in breaking this enamine bond and PLP release, as well as a reversible loss of activity and dissociation into dimers. This sequence of events is termed cold lability and its understanding bears relevance to protein stability and shelf life. Results We studied the reversible cold lability of E. coli Trpase and its Y74F, C298S and W330F mutants. In contrast to the holo E. coli Trpase all apo forms of Trpase dissociated into dimers already at 25°C and even further upon cooling to 2°C. The crystal structures of the two mutants, Y74F and C298S in their apo form were determined at 1.9Å resolution. These apo mutants were found in an open conformation compared to the closed conformation found for P. vulgaris in its holo form. This conformational change is further supported by a high pressure study. Conclusion We suggest that cold lability of E. coli Trpases is primarily affected by PLP release. The enhanced loss of activity of the three mutants is presumably due to the reduced size of the side chain of the amino acids. This prevents the tight assembly of the active tetramer, making it more susceptible to the cold driven changes in hydrophobic interactions which facilitate PLP release. The hydrophobic interactions along the non catalytic interface overshadow the effect of point mutations and may account for the differences in the dissociation of E. coli Trpase to dimers and P. vulgaris Trpase to monomers.
Collapse
|
25
|
Ladner CL, Turner RJ, Edwards RA. Development of indole chemistry to label tryptophan residues in protein for determination of tryptophan surface accessibility. Protein Sci 2007; 16:1204-13. [PMID: 17525468 PMCID: PMC2206665 DOI: 10.1110/ps.062728407] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Solvent accessibility can be used to evaluate protein structural models, identify binding sites, and characterize protein conformational changes. The differential modification of amino acids at specific sites enables the accessible surface residues to be identified by mass spectrometry. Tryptophan residues within proteins can be differentially labeled with halocompounds by a photochemical reaction. In this study, tryptophan residues of carbonic anhydrase are reacted with chloroform, 2,2,2-trichloroethanol (TCE), 2,2,2-trichloroacetate (TCA), or 3-bromo-1-propanol (BP) under UV irradiation at 280 nm. The light-driven reactions with chloroform, TCE, TCA, and BP attach a formyl, hydroxyethanone, carboxylic acid, and propanol group, respectively, onto the indole ring of tryptophan. Trypsin and chymotrypsin digests of the modified carbonic anhydrase are used to map accessible tryptophan residues using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS). Tryptophan reactivity is determined by identifying peptides with tryptophan residues modified with the appropriate label. The reactivity is calculated from the frequency that the modification is identified and a semiquantitative measure of the amount of products formed. Both of these measures of tryptophan reactivity correlate significantly with the accessible surface area of tryptophan residues in carbonic anhydrase determined from the X-ray crystal structure. Therefore the photochemical reaction of halocompounds with tryptophan residues in carbonic anhydrase indicates the degree of solvent accessibility of these residues.
Collapse
Affiliation(s)
- Carol L Ladner
- Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
| | | | | |
Collapse
|
26
|
Dvortsov IA, Lunina NA, Chekanovskaya LA, Shedova EN, Gening LV, Velikodvorskaya GA. Ethidium bromide is good not only for staining of nucleic acids but also for staining of proteins after polyacrylamide gel soaking in trichloroacetic acid solution. Anal Biochem 2006; 353:293-5. [PMID: 16597429 DOI: 10.1016/j.ab.2006.03.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2006] [Accepted: 03/01/2006] [Indexed: 12/01/2022]
Affiliation(s)
- I A Dvortsov
- Institute of Molecular Genetics, Moscow, Russia 123182, Russian Federation.
| | | | | | | | | | | |
Collapse
|
27
|
Ladner CL, Yang J, Turner RJ, Edwards RA. Visible fluorescent detection of proteins in polyacrylamide gels without staining. Anal Biochem 2004; 326:13-20. [PMID: 14769330 DOI: 10.1016/j.ab.2003.10.047] [Citation(s) in RCA: 199] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2003] [Indexed: 11/29/2022]
Abstract
2,2,2-Trichloroethanol (TCE) incorporated into polyacrylamide gels before polymerization provides fluorescent visible detection of proteins in less than 5min of total processing time. The tryptophans in proteins undergo an ultraviolet light-induced reaction with trihalocompounds to produce fluorescence in the visible range so that the protein bands can be visualized on a 300-nm transilluminator. In a previous study trichloroacetic acid or chloroform was used to stain polyacrylamide gel electrophoresis (PAGE) gels for protein visualization. This study shows that placing TCE in the gel before electrophoresis can eliminate the staining step. The gel is removed from the electrophoresis apparatus and placed on a transilluminator and then the protein bands develop their fluorescence in less than 5min. In addition to being rapid this visualization method provides detection of 0.2microg of typical globular proteins, which for some proteins is slightly more sensitive than the standard Coomassie brilliant blue (CBB) method. Integral membrane proteins, which do not stain well with CBB, are visualized well with the TCE in-gel method. After TCE in-gel visualization the same gel can then be CBB stained, allowing for complementary detection of proteins. In addition, visualization with TCE in the gel is compatible with two-dimensional PAGE, native PAGE, Western blotting, and autoradiography.
Collapse
Affiliation(s)
- Carol L Ladner
- Structural Biology Research Group, Department of Biological Sciences, University of Calgary, 2500 University Dr. N.W., Calgary, Alta., Canada, T2N 1N4.
| | | | | | | |
Collapse
|