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Das D, Sen V, Chakraborty G, Pillai V, Tambade R, Jonnalagadda PN, Rao AVSSN, Chittela RK. Quinaldine Red as a fluorescent probe for determining the melting temperature ( Tm) of proteins: a simple, rapid and high-throughput assay. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2024; 16:950-956. [PMID: 38291911 DOI: 10.1039/d3ay01941a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Proteins play an important role in biological systems and several proteins are used in diagnosis, therapy, food industry etc. Thus, knowledge about the physical properties of the proteins is of utmost importance, which will aid in understanding their function and subsequent applications. The melting temperature (Tm) of a protein is one of the essential parameters which gives information about the stability of a protein under different conditions. In the present study, we have demonstrated a method for determining the Tm of proteins using the supramolecular interaction between Quinaldine Red (QR) and proteins. Using this method, we have determined the Tm of 5 proteins and compared our results with established protocols. Our results showed good agreement with the other methods and published values. The method developed in this study is inexpensive, quick, and devoid of complex instruments and pre/post-treatment of the samples. In addition, this method can be adopted for high throughput in multi-plate mode. Thus, this study projects a new methodology for Tm determination of various proteins with user friendly operation.
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Affiliation(s)
- Dhruv Das
- Applied Genomics Section, Bhabha Atomic Research Centre, Mumbai-400085, India.
- Homi Bhabha National Institute, Anushaktinagar, Mumbai-400094, India
| | - Vikram Sen
- UM-DAE Centre for Excellence in Basic Sciences, Vidyanagari, Mumbai-400098, India
| | - Goutam Chakraborty
- Laser and Plasma Technology Division, Bhabha Atomic Research Centre, Homi Bhabha National Institute, Mumbai-400085, India
| | - Vinayaki Pillai
- Applied Genomics Section, Bhabha Atomic Research Centre, Mumbai-400085, India.
- Homi Bhabha National Institute, Anushaktinagar, Mumbai-400094, India
| | - Rahul Tambade
- Applied Genomics Section, Bhabha Atomic Research Centre, Mumbai-400085, India.
- Homi Bhabha National Institute, Anushaktinagar, Mumbai-400094, India
| | - Padma Nilaya Jonnalagadda
- Homi Bhabha National Institute, Anushaktinagar, Mumbai-400094, India
- Laser and Plasma Technology Division, Bhabha Atomic Research Centre, Homi Bhabha National Institute, Mumbai-400085, India
| | | | - Rajani Kant Chittela
- Applied Genomics Section, Bhabha Atomic Research Centre, Mumbai-400085, India.
- Homi Bhabha National Institute, Anushaktinagar, Mumbai-400094, India
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Production of the Food Enzyme Acetolactate Decarboxylase (ALDC) from Bacillus subtilis ICA 56 Using Agro-Industrial Residues as Feedstock. FERMENTATION-BASEL 2022. [DOI: 10.3390/fermentation8120675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
During the beer brewing process, some compounds are formed in the primary fermentation step and may affect the final quality of beer. These compounds, called off flavors, such as diacetyl, are produced during fermentation and are related to a buttery taste. The use of acetolactate decarboxylase (ALDC) in the traditional beer brewing process may significantly increase productivity since it allows for a faster decrease in the adverse flavor caused by diacetyl. However, production costs directly impact its application. For this reason, we analyzed the effect of different cultivation media on ALDC production by Bacillus subtilis ICA 56 and process economics. Different carbon and nitrogen sources, including agro-industrial residues, were evaluated. The best result was obtained using sugarcane molasses and corn steep solids (CSS), allowing a 74% reduction in ALDC production cost and an enzyme activity of 4.43 ± 0.12 U·mL−1. The enzymatic extract was then characterized, showing an optimum temperature at 40 °C and stability at different pH levels, being able to maintain more than 80% of its catalytic capacity between pH values of 3.6 and 7.0, with higher enzymatic activity at pH 6.0 (50 mM MES Buffer), reaching an ALDC activity of 5.30 ± 0.06 U·mL−1.
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Dušeková E, Berta M, Sedláková D, Řeha D, Dzurillová V, Shaposhnikova A, Fadaei F, Tomková M, Minofar B, Sedlák E. Specific anion effect on properties of HRV 3C protease. Biophys Chem 2022; 287:106825. [PMID: 35597150 DOI: 10.1016/j.bpc.2022.106825] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 04/19/2022] [Accepted: 05/07/2022] [Indexed: 12/12/2022]
Abstract
Specific salts effect is intensively studied from the prospective of modification of different physico-chemical properties of biomacromolecules. Limited knowledge of the specific salts effect on enzymes led us to address the influence of five sodium anions: sulfate, phosphate, chloride, bromide, and perchlorate, on catalytic and conformational properties of human rhinovirus-14 (HRV) 3C protease. The enzyme conformation was monitored by circular dichroism spectrum (CD) and by tyrosines fluorescence. Stability and flexibility of the enzyme have been analyzed by CD in the far-UV region, differential scanning calorimetry and molecular dynamics simulations, respectively. We showed significant influence of the anions on the enzyme properties in accordance with the Hofmeister effect. The HRV 3C protease in the presence of kosmotropic anions, in contrast with chaotropic anions, exhibits increased stability, rigidity. Correlations of stabilization effect of anions on the enzyme with their charge density and the rate constant of the enzyme with the viscosity B-coefficients of anions suggest direct interaction of the anions with HRV 3C protease. The role of stabilization and decreased fluctuation of the polypeptide chain of HRV 3C protease on its activation in the presence of kosmotropic anions is discussed within the frame of the macromolecular rate theory.
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Affiliation(s)
- Eva Dušeková
- Department of Biophysics, Faculty of Science, P. J. Šafárik University in Košice, Jesenná 5, 04154 Košice, Slovakia
| | - Martin Berta
- Department of Biophysics, Faculty of Science, P. J. Šafárik University in Košice, Jesenná 5, 04154 Košice, Slovakia
| | - Dagmar Sedláková
- Department of Biophysics, Faculty of Science, P. J. Šafárik University in Košice, Jesenná 5, 04154 Košice, Slovakia; Department of Biophysics, Institute of Experimental Physics, Slovak Academy of Sciences, Watsonova 47, 040 01 Košice, Slovakia
| | - David Řeha
- Faculty of Science, University of South Bohemia in České Budějovice, Branišovská 1645/31A, 37005 České Budějovice, Czech Republic
| | - Veronika Dzurillová
- Department of Biophysics, Faculty of Science, P. J. Šafárik University in Košice, Jesenná 5, 04154 Košice, Slovakia
| | - Anastasiia Shaposhnikova
- Faculty of Science, University of South Bohemia in České Budějovice, Branišovská 1645/31A, 37005 České Budějovice, Czech Republic; Laboratory of Structural Biology and Bioinformatics, Institute of Microbiology of the Czech Academy of Sciences, Zámek 136, 37333 Nové Hrady, Czech Republic
| | - Fatemeh Fadaei
- Faculty of Science, University of South Bohemia in České Budějovice, Branišovská 1645/31A, 37005 České Budějovice, Czech Republic; Laboratory of Structural Biology and Bioinformatics, Institute of Microbiology of the Czech Academy of Sciences, Zámek 136, 37333 Nové Hrady, Czech Republic
| | - Mária Tomková
- Centre for Interdisciplinary Biosciences, P. J. Šafárik University in Košice, Jesenná 5, 04154 Košice, Slovakia
| | - Babak Minofar
- Faculty of Science, University of South Bohemia in České Budějovice, Branišovská 1645/31A, 37005 České Budějovice, Czech Republic.
| | - Erik Sedlák
- Centre for Interdisciplinary Biosciences, P. J. Šafárik University in Košice, Jesenná 5, 04154 Košice, Slovakia.
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Imangaliyeva AN, Sela A, Eltzov E, Poverenov E. The polyaminosaccharide-based buffers as a new type of zwitterionic buffering macromolecules for biochemical applications. Carbohydr Polym 2021; 273:118601. [PMID: 34561001 DOI: 10.1016/j.carbpol.2021.118601] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 08/04/2021] [Accepted: 08/19/2021] [Indexed: 11/25/2022]
Abstract
A new type of biocompatible buffers based on zwitterionic polyaminosaccharides is reported. The carboxy- and amino-groups containing carboxymethyl chitosan (CM-CS) was synthesized and reacted with hydrochloric/acetic acid resulting in CM-CS-HCl and CM-CS-HAc buffers with buffering capacity of 20.6 and 15.2 mM/pH. The new buffers were comprehensively characterized for their physicochemical properties and checked on enzymatic reactions of acetylcholinesterase (AChE) and alkaline phosphatase (ALP). Their performance was compared to the phosphate and Tris buffers. The chloride-free, CM-CS-HAc demonstrated excellent buffering activity with Michaelis constants of 0.50 and 1.00 mM and maximum reaction rates of 5.62 and 2.26 μmol/min/mL for AChE and ALP reactions, respectively. Toxicity studies on stress-sensitive bioreporter bacteria verified nontoxicity of CM-CS-HAc. Zwitterionic polyaminosaccharides overcome drawbacks of monomeric buffers, such as interference with enzyme active sites, cell membrane injury and purification difficulties. Therefore, they may become the next generation of effective buffers for biological and biochemical applications.
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Affiliation(s)
- Ainur N Imangaliyeva
- Agro-nanotechnology and Advanced Materials Research Center, Postharvest and Food Sciences Institute, Agricultural Research Organization, The Volcani Institute, Rishon LeZion 7505101, Israel.
| | - Aviad Sela
- Agro-nanotechnology and Advanced Materials Research Center, Postharvest and Food Sciences Institute, Agricultural Research Organization, The Volcani Institute, Rishon LeZion 7505101, Israel; Institute of Biochemistry, Food Science and Nutrition, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 7610001, Israel.
| | - Evgeni Eltzov
- Agro-nanotechnology and Advanced Materials Research Center, Postharvest and Food Sciences Institute, Agricultural Research Organization, The Volcani Institute, Rishon LeZion 7505101, Israel.
| | - Elena Poverenov
- Agro-nanotechnology and Advanced Materials Research Center, Postharvest and Food Sciences Institute, Agricultural Research Organization, The Volcani Institute, Rishon LeZion 7505101, Israel.
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Jordan JH, Ashbaugh HS, Mague JT, Gibb BC. Buffer and Salt Effects in Aqueous Host-Guest Systems: Screening, Competitive Binding, or Both? J Am Chem Soc 2021; 143:18605-18616. [PMID: 34704751 PMCID: PMC8587612 DOI: 10.1021/jacs.1c08457] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
There are many open questions regarding the supramolecular properties of ions in water, a fact that has ramifications within any field of study involving buffered solutions. Indeed, as Pielak has noted (Buffers, Especially the Good Kind, Biochemistry, 2021, in press. DOI:10.1021/acs.biochem.1c00200) buffers were conceived of with little regard to their supramolecular properties. But there is a difficulty here; the mathematical models supramolecular chemists use for affinity determinations do not account for screening. As a result, there is uncertainty as to the magnitude of any screening effect and how this compares to competitive salt/buffer binding. Here we use a tetra-cation cavitand to compare halide affinities obtained using a traditional unscreened model and a screened (Debye-Hückel) model. The rule of thumb that emerges is that if ionic strength is changed by >1 order of magnitude─either during a titration or if a comparison is sought between two different buffered solutions─screening should be considered. We also build a competitive mathematical model showing that binding attenuation in buffer is largely due to competitive binding to the host by said buffer. For the system at hand, we find that the effect of competition is approximately twice that of the effect of screening (∼RT at 25 °C). Thus, for strong binders it is less important to account for screening than it is to account for competitive complexation, but for weaker binders both effects should be considered. We anticipate these results will help supramolecular chemists unravel the properties of buffers and so help guide studies of biomacromolecules.
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Affiliation(s)
- Jacobs H Jordan
- Agricultural Research Service Southern Regional Research Center, U.S. Department of Agriculture, New Orleans, Louisiana 70124, United States
| | - Henry S Ashbaugh
- Department of Chemical and Biomolecular Engineering, Tulane University, New Orleans, Louisiana 70118, United States
| | - Joel T Mague
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118, United States
| | - Bruce C Gibb
- Department of Chemistry, Tulane University, New Orleans, Louisiana 70118, United States
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Fan HF, Su S. The regulation mechanism of the C-terminus of RecA proteins during DNA strand-exchange process. Biophys J 2021; 120:3166-3179. [PMID: 34197804 DOI: 10.1016/j.bpj.2021.06.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 04/21/2021] [Accepted: 06/03/2021] [Indexed: 12/14/2022] Open
Abstract
The C-terminus of Escherichia coli RecA protein can affect the DNA binding affinity, interact with accessory proteins, and regulate the RecA activity. A substantial upward shift in the pH-reaction profile of RecA-mediated DNA strand-exchange reactions was observed for C-terminal-truncated E. coli ΔC17 RecA, Deinococcus radiodurans RecA, and Deinococcus ficus RecA. Here, the process of RecA-mediated strand exchange from the beginning to the end was investigated with florescence resonance energy transfer and tethered particle motion experiments to determine the detailed regulation mechanism. RecA proteins with a shorter C-terminus possess more stable nuclei, higher DNA binding affinities, and lower protonation requirements for the formation of nucleoprotein filaments. Moreover, more stable synaptic complexes in the homologous sequence searching process were also observed for RecA proteins with a shorter C-terminus. Our results suggest that the C-terminus of RecA proteins regulates not only the formation of RecA nucleoprotein filaments but also the entrance of secondary DNA into RecA nucleoprotein filaments.
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Affiliation(s)
- Hsiu-Fang Fan
- Institute of Medical Science and Technology, Kaohsiung, Taiwan; Department of Chemistry, Kaohsiung, Taiwan; Aerosol Science Research Center, National Sun Yat-sen University, Kaohsiung, Taiwan.
| | - Shu Su
- Department of Life Sciences and Institute of Genome Sciences, National Yang-Ming University, Taipei, Taiwan
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Insight into interactions between enzyme and biological buffers: Enhanced thermal stability of stem bromelain. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2020.114526] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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8
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Salis A, Cappai L, Carucci C, Parsons DF, Monduzzi M. Specific Buffer Effects on the Intermolecular Interactions among Protein Molecules at Physiological pH. J Phys Chem Lett 2020; 11:6805-6811. [PMID: 32787211 DOI: 10.1021/acs.jpclett.0c01900] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
BSA and lysozyme molecular motion at pH 7.15 is buffer-specific. Adsorption of buffer ions on protein surfaces modulates the protein surface charge and thus protein-protein interactions. Interactions were estimated by means of the interaction parameter kD obtained from plots of diffusion coefficients at different protein concentrations (Dapp = D0[1 + kDCprotein]) via dynamic light scattering and nuclear magnetic resonance. The obtained results agree with recent findings confirming doubts regarding the validity of the Henderson-Hasselbalch equation, which has traditionally provided a basis for understanding pH buffers of primary importance in solution chemistry, electrochemistry, and biochemistry.
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Affiliation(s)
- Andrea Salis
- Department of Chemical and Geological Sciences, University of Cagliari, and Centro NanoBiotecnologie Sardegna (CNBS), Cittadella Universitaria, SS 554 bivio Sestu, 09042 Monserrato (CA), Italy
- Consorzio Interuniversitario per lo Sviluppo dei Sistemi a Grande Interfase (CSGI), Florence, Italy
- Unità Operativa University of Cagliari, Cagliari, Italy
| | - Luca Cappai
- Department of Chemical and Geological Sciences, University of Cagliari, and Centro NanoBiotecnologie Sardegna (CNBS), Cittadella Universitaria, SS 554 bivio Sestu, 09042 Monserrato (CA), Italy
| | - Cristina Carucci
- Department of Chemical and Geological Sciences, University of Cagliari, and Centro NanoBiotecnologie Sardegna (CNBS), Cittadella Universitaria, SS 554 bivio Sestu, 09042 Monserrato (CA), Italy
- Consorzio Interuniversitario per lo Sviluppo dei Sistemi a Grande Interfase (CSGI), Florence, Italy
- Unità Operativa University of Cagliari, Cagliari, Italy
| | - Drew F Parsons
- Discipline of Chemistry and Physics, College of Science, Health, Engineering & Education, Murdoch University, 90 South Street, Murdoch, WA 6150, Australia
| | - Maura Monduzzi
- Department of Chemical and Geological Sciences, University of Cagliari, and Centro NanoBiotecnologie Sardegna (CNBS), Cittadella Universitaria, SS 554 bivio Sestu, 09042 Monserrato (CA), Italy
- Consorzio Interuniversitario per lo Sviluppo dei Sistemi a Grande Interfase (CSGI), Florence, Italy
- Unità Operativa University of Cagliari, Cagliari, Italy
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Panuszko A, Stangret J, Nowosielski B, Bruździak P. Interactions between hydration spheres of two different solutes in solution: The least squares fitting with constraints as a tool to determine water properties in ternary systems. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.113181] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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10
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MUC4-ErbB2 Oncogenic Complex: Binding studies using Microscale Thermophoresis. Sci Rep 2019; 9:16678. [PMID: 31723153 PMCID: PMC6853952 DOI: 10.1038/s41598-019-53099-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 10/27/2019] [Indexed: 02/06/2023] Open
Abstract
The MUC4 membrane-bound mucin is a large O-glycoprotein involved in epithelial homeostasis. At the cancer cell surface MUC4 interacts with ErbB2 receptor via EGF domains to promote cell proliferation and migration. MUC4 is highly regarded as a therapeutic target in pancreatic cancer as it is not expressed in healthy pancreas, while it is neoexpressed in early preneoplastic stages (PanINs). However, the association/dissociation constant of MUC4-ErbB2 complex is unknown. Protein-protein interactions (PPIs) have become a major area of research in the past years and the characterization of their interactions, especially by biophysical methods, is intensively used in drug discovery. To characterize the MUC4-ErbB2 interaction, we used MicroScale Thermophoresis (MST), a powerful method for quantitative protein interaction analysis under challenging conditions. We worked with CHO cell lysates containing either the transmembrane β subunit of MUC4 (MUC4β) or a truncated mutant encompassing only the EGF domains (MUC4EGF3+1+2). MST studies have led to the characterization of equilibrium dissociation constants (Kd) for MUC4β-ErbB2 (7–25 nM) and MUC4EGF3+1+2/ErbB2 (65–79 nM) complexes. This work provides new information regarding the MUC4-ErbB2 interaction at the biophysical level and also confirms that the presence of the three EGF domains of MUC4 is sufficient to provide efficient interaction. This technological approach will be very useful in the future to validate small molecule binding affinities targeting MUC4-ErbB2 complex for drug discovery development in cancer. It will also be of high interest for the other known membrane mucins forming oncogenic complexes with ErbBs at the cancer cell surface.
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Brudar S, Hribar-Lee B. The Role of Buffers in Wild-Type HEWL Amyloid Fibril Formation Mechanism. Biomolecules 2019; 9:E65. [PMID: 30769878 PMCID: PMC6406783 DOI: 10.3390/biom9020065] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 02/04/2019] [Accepted: 02/05/2019] [Indexed: 01/06/2023] Open
Abstract
Amyloid fibrils, highly ordered protein aggregates, play an important role in the onset of several neurological disorders. Many studies have assessed amyloid fibril formation under specific solution conditions, but they all lack an important phenomena in biological solutions-buffer specific effects. We have focused on the formation of hen egg-white lysozyme (HEWL) fibrils in aqueous solutions of different buffers in both acidic and basic pH range. By means of UV-Vis spectroscopy, fluorescence measurements and CD spectroscopy, we have managed to show that fibrillization of HEWL is affected by buffer identity (glycine, TRIS, phosphate, KCl-HCl, cacodylate, HEPES, acetate), solution pH, sample incubation (agitated vs. static) and added excipients (NaCl and PEG). HEWL only forms amyloid fibrils at pH = 2.0 under agitated conditions in glycine and KCl-HCl buffers of high enough ionic strength. Phosphate buffer on the other hand stabilizes the HEWL molecules. Similar stabilization effect was achieved by addition of PEG12000 molecules to the solution.
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Affiliation(s)
- Sandi Brudar
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, SI-1000 Ljubljana, Slovenia.
| | - Barbara Hribar-Lee
- Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, SI-1000 Ljubljana, Slovenia.
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Gong X, Li C, Zhai R, Xie J, Jiang Y, Fang X. Supercharging of Proteins by Salts during Polarity Reversed Nano-Electrospray Ionization. Anal Chem 2019; 91:1826-1837. [PMID: 30620564 DOI: 10.1021/acs.analchem.8b02759] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Supercharging is beneficial in many ways to the analysis of proteins by mass spectrometry (MS). In this work, a novel supercharging method was developed. It made use of our previously developed ionization technique: namely, polarity reversed nanoelectrospray ionization (PR-nESI) for the ionization of proteins. Supercharging of proteins was achieved by just adding 1-10 mM of a salt to the sample, such as sodium chloride (NaCl). The charge state of proteins obtained by our method was significantly higher than that by nano-ESI with 1% (v/v) acetic acid (HAc). Different kinds of salts were investigated. Salts with strong acid anions were capable of supercharging proteins, including chlorides, bromides, iodides, and nitrates. The signal intensity and signal to noise ratio ( S/ N) of proteins were increased at the same time. Phosphates were also found to have a supercharging effect, due to the fact that phosphoric acid was a medium-strong acid. In comparison, salts with weak acid anions had no supercharging effect, such as carbonates, sulfides, acetates, and formates. The species of the salt anion was critical to the supercharging effect, while the species of the salt cation showed little influence on the supercharging effect. Investigations were made into the mechanism of our method. The supercharging effect was caused by interactions between protein molecules and salt anions, as well as the influence of protons. The present work offered us an alternative way for the supercharging of proteins. The use of common salts for supercharging made the procedure more convenient. The concentration of salts needed for supercharging was much lower than those conventionally used for supercharging reagents. Taking into consideration the fact that many biological samples are buffered with phosphates and chlorides, these samples could be directly supercharged by our method without any additional additives. Furthermore, as many salts are nontoxic and can easily be found in a chemical laboratory, the use of salts for supercharging would be a much more practical and economical choice. In addition, the present work also furthered our understandings about the mechanism of supercharging, as well as electrospray.
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Affiliation(s)
- Xiaoyun Gong
- Mass Spectrometry Engineering Technology Research Center, Center for Advanced Measurement Science , National Institute of Metrology , Beijing 100029 , People's Republic of China
| | - Chang Li
- Mass Spectrometry Engineering Technology Research Center, Center for Advanced Measurement Science , National Institute of Metrology , Beijing 100029 , People's Republic of China
| | - Rui Zhai
- Mass Spectrometry Engineering Technology Research Center, Center for Advanced Measurement Science , National Institute of Metrology , Beijing 100029 , People's Republic of China
| | - Jie Xie
- Mass Spectrometry Engineering Technology Research Center, Center for Advanced Measurement Science , National Institute of Metrology , Beijing 100029 , People's Republic of China
| | - You Jiang
- Mass Spectrometry Engineering Technology Research Center, Center for Advanced Measurement Science , National Institute of Metrology , Beijing 100029 , People's Republic of China
| | - Xiang Fang
- Mass Spectrometry Engineering Technology Research Center, Center for Advanced Measurement Science , National Institute of Metrology , Beijing 100029 , People's Republic of China
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Muinao T, Pal M, Boruah HPD. Cytosolic and Transmembrane Protein Extraction Methods of Breast and Ovarian Cancer Cells: A Comparative Study. J Biomol Tech 2018; 29:71-78. [PMID: 30174558 PMCID: PMC6091320 DOI: 10.7171/jbt.18-2903-002] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Efficient extraction of proteins is a great challenge for numerous downstream proteomic analyses. During the protein extraction procedure, it is critical to maintain the conformational stability, integrity, as well as higher yield of the protein. To do so, 5-different lysis buffers of Tris and HEPES have been used as the primary buffering reagents with variable compositions at different concentrations and pH using human cancer cells. In this study, different protein lysates of human breast cancer cells T47D and MDA-MB-231 and ovarian cancer cell PA-1 were subjected to run SDS-PAGE for separation of proteins based on their molecular size, followed by Coomassie blue, silver staining, and immunoblot assays to compare the extraction yield of total cytoplasmic proteins, glyceraldehyde-3-phosphate dehydrogenase (GAPDH) and the integral membrane protein, integrin β-1. Our results revealed that Tris-based lysis buffer with 50 mM concentration, pH 7.5, is relatively the efficient and reliable protein extraction method for a wide range of MW subcellular markers, cytoplasmic GAPDH and transmembrane integrin β-1 proteins. We anticipate that this simple and cost-effective protein extraction protocol might be extremely useful across a broad range of subcellular proteins in different biologic samples.
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Affiliation(s)
- Thingreila Muinao
- Biological Sciences and Technology Division, Biotechnology Group, Council of Scientific and Industrial Research-North East Institute of Science and Technology, Academy of Scientific and Innovative Research, Jorhat, Assam, India
| | - Mintu Pal
- Biological Sciences and Technology Division, Biotechnology Group, Council of Scientific and Industrial Research-North East Institute of Science and Technology, Academy of Scientific and Innovative Research, Jorhat, Assam, India
| | - Hari Prasanna Deka Boruah
- Biological Sciences and Technology Division, Biotechnology Group, Council of Scientific and Industrial Research-North East Institute of Science and Technology, Academy of Scientific and Innovative Research, Jorhat, Assam, India
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The effects of biological buffers TRIS, TAPS, TES on the stability of lysozyme. Int J Biol Macromol 2018; 112:720-727. [DOI: 10.1016/j.ijbiomac.2018.01.203] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Revised: 01/23/2018] [Accepted: 01/30/2018] [Indexed: 12/20/2022]
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15
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Buffer formulation affects the interaction between lysozyme and polymeric nanoparticles. J Colloid Interface Sci 2017; 504:78-85. [DOI: 10.1016/j.jcis.2017.05.031] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 05/11/2017] [Accepted: 05/11/2017] [Indexed: 11/21/2022]
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16
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Investigating the structural transitions of proteins during dissolution by mass spectrometry. Talanta 2017; 164:418-426. [DOI: 10.1016/j.talanta.2016.11.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Revised: 11/07/2016] [Accepted: 11/09/2016] [Indexed: 11/17/2022]
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17
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Rodrigo AC, Laurini E, Vieira VMP, Pricl S, Smith DK. Effect of buffer at nanoscale molecular recognition interfaces – electrostatic binding of biological polyanions. Chem Commun (Camb) 2017; 53:11580-11583. [DOI: 10.1039/c7cc07413a] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The electrostatic binding of polyanionic heparin by cationic receptors is highly dependent on the buffer in which the binding assay is carried out.
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Affiliation(s)
| | - Erik Laurini
- Simulation Engineering (MOSE) Laboratory
- Department of Engineering and Architectures (DEA)
- University of Trieste
- Trieste
- Italy
| | | | - Sabrina Pricl
- Simulation Engineering (MOSE) Laboratory
- Department of Engineering and Architectures (DEA)
- University of Trieste
- Trieste
- Italy
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18
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Zbacnik TJ, Holcomb RE, Katayama DS, Murphy BM, Payne RW, Coccaro RC, Evans GJ, Matsuura JE, Henry CS, Manning MC. Role of Buffers in Protein Formulations. J Pharm Sci 2016; 106:713-733. [PMID: 27894967 DOI: 10.1016/j.xphs.2016.11.014] [Citation(s) in RCA: 122] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Revised: 10/25/2016] [Accepted: 11/17/2016] [Indexed: 12/19/2022]
Abstract
Buffers comprise an integral component of protein formulations. Not only do they function to regulate shifts in pH, they also can stabilize proteins by a variety of mechanisms. The ability of buffers to stabilize therapeutic proteins whether in liquid formulations, frozen solutions, or the solid state is highlighted in this review. Addition of buffers can result in increased conformational stability of proteins, whether by ligand binding or by an excluded solute mechanism. In addition, they can alter the colloidal stability of proteins and modulate interfacial damage. Buffers can also lead to destabilization of proteins, and the stability of buffers themselves is presented. Furthermore, the potential safety and toxicity issues of buffers are discussed, with a special emphasis on the influence of buffers on the perceived pain upon injection. Finally, the interaction of buffers with other excipients is examined.
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Affiliation(s)
| | - Ryan E Holcomb
- LegacyBioDesign LLC, Johnstown, Colorado 80534; Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523
| | - Derrick S Katayama
- LegacyBioDesign LLC, Johnstown, Colorado 80534; Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523
| | - Brian M Murphy
- LegacyBioDesign LLC, Johnstown, Colorado 80534; Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523
| | - Robert W Payne
- LegacyBioDesign LLC, Johnstown, Colorado 80534; Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523
| | | | | | | | - Charles S Henry
- Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523
| | - Mark Cornell Manning
- LegacyBioDesign LLC, Johnstown, Colorado 80534; Department of Chemistry, Colorado State University, Fort Collins, Colorado 80523.
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19
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Affiliation(s)
- Ching W. Chan
- Department of Chemistry, University of York, York, UK
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20
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Young BH, Caldwell TA, McKenzie AM, Kokhan O, Berndsen CE. Characterization of the structure and catalytic activity of Legionella pneumophila VipF. Proteins 2016; 84:1422-30. [PMID: 27315603 DOI: 10.1002/prot.25087] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2016] [Revised: 05/31/2016] [Accepted: 06/13/2016] [Indexed: 11/05/2022]
Abstract
The pathogenic bacteria Legionella pneumophila is known to cause Legionnaires' Disease, a severe pneumonia that can be fatal to immunocompromised individuals and the elderly. Shohdy et al. identified the L. pneumophila vacuole sorting inhibitory protein VipF as a putative N-acetyltransferase based on sequence homology. We have characterized the basic structural and functional properties of VipF to confirm this original functional assignment. Sequence conservation analysis indicates two putative CoA-binding regions within VipF. Homology modeling and small angle X-ray scattering suggest a monomeric, dual-domain structure joined by a flexible linker. Each domain contains the characteristic beta-splay motif found in many acetyltransferases, suggesting that VipF may contain two active sites. Docking experiments suggest reasonable acetyl-CoA binding locations within each beta-splay motif. Broad substrate screening indicated that VipF is capable of acetylating chloramphenicol and both domains are catalytically active. Given that chloramphenicol is not known to be N-acetylated, this is a surprising finding suggesting that VipF is capable of O-acetyltransferase activity. Proteins 2016; 84:1422-1430. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Byron H Young
- Department of Chemistry and Biochemistry, James Madison University, Harrisonburg, Virginia, 22807
| | - Tracy A Caldwell
- Department of Chemistry and Biochemistry, James Madison University, Harrisonburg, Virginia, 22807
| | - Aidan M McKenzie
- Department of Chemistry and Biochemistry, James Madison University, Harrisonburg, Virginia, 22807
| | - Oleksandr Kokhan
- Department of Chemistry and Biochemistry, James Madison University, Harrisonburg, Virginia, 22807
| | - Christopher E Berndsen
- Department of Chemistry and Biochemistry, James Madison University, Harrisonburg, Virginia, 22807.
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21
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Salis A, Monduzzi M. Not only pH. Specific buffer effects in biological systems. Curr Opin Colloid Interface Sci 2016. [DOI: 10.1016/j.cocis.2016.04.004] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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22
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Light TP, Corbett KM, Metrick MA, MacDonald G. Hofmeister Ion-Induced Changes in Water Structure Correlate with Changes in Solvation of an Aggregated Protein Complex. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:1360-1369. [PMID: 26760222 DOI: 10.1021/acs.langmuir.5b04489] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
RecA is a naturally aggregating Escherichia coli protein that catalyzes the strand exchange reaction utilized in DNA repair. Previous studies have shown that the presence of salts influence RecA activity, aggregation, and stability and that salts stabilize RecA in an inverse-anionic Hofmeister series. Here we utilized attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopy and circular dichroism (CD) to investigate how various Hofmeister salts alter the water structure and RecA solvation and aggregation. Spectroscopic studies performed in water and deuterium oxide suggest that salts alter water O-(1)H and O-(2)H stretch and bend vibrations as well as protein amide I (or I') and amide II (or II') vibrations. Anions have a much larger influence on water vibrations than cations. Water studies also show increased water-water and/or water-ion interactions in the presence of strongly hydrated SO4(2-) salts and evidence for decreased interactions with weakly hydrated Cl(-) and ClO4(-) salts. Salt-water difference infrared spectra show that kosmotropic salts are more hydrated than chaotropic salts. Interestingly, this is the opposite trend to the changes in protein solvation. Infrared spectra of RecA show that vibrations associated with protein desolvation were observed in the presence of SO4(2-) salts. Conversely, vibrations associated with protein solvation were observed in the presence of Cl(-) and ClO4(-) salts. Difference infrared studies on the dehydration of model proteins aided in identifying changes in RecA-solvent interactions. This study provides evidence that salt-induced changes in water vibrations correlate to changes in protein solvent interactions and thermal stability.
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Affiliation(s)
- Taylor P Light
- Department of Chemistry and Biochemistry, James Madison University , Harrisonburg, Virginia 22807, United States
| | - Karen M Corbett
- Department of Chemistry and Biochemistry, James Madison University , Harrisonburg, Virginia 22807, United States
| | - Michael A Metrick
- Department of Chemistry and Biochemistry, James Madison University , Harrisonburg, Virginia 22807, United States
| | - Gina MacDonald
- Department of Chemistry and Biochemistry, James Madison University , Harrisonburg, Virginia 22807, United States
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23
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Du Pont KE, McKenzie AM, Kokhan O, Sumner I, Berndsen CE. The Disulfide Bonds within BST-2 Enhance Tensile Strength during Viral Tethering. Biochemistry 2016; 55:940-7. [DOI: 10.1021/acs.biochem.5b01362] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Kelly E. Du Pont
- Department of Chemistry and
Biochemistry, James Madison University, Harrisonburg, Virginia 22807, United States
| | - Aidan M. McKenzie
- Department of Chemistry and
Biochemistry, James Madison University, Harrisonburg, Virginia 22807, United States
| | - Oleksandr Kokhan
- Department of Chemistry and
Biochemistry, James Madison University, Harrisonburg, Virginia 22807, United States
| | - Isaiah Sumner
- Department of Chemistry and
Biochemistry, James Madison University, Harrisonburg, Virginia 22807, United States
| | - Christopher E. Berndsen
- Department of Chemistry and
Biochemistry, James Madison University, Harrisonburg, Virginia 22807, United States
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24
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Cugia F, Sedda S, Pitzalis F, Parsons DF, Monduzzi M, Salis A. Are specific buffer effects the new frontier of Hofmeister phenomena? Insights from lysozyme adsorption on ordered mesoporous silica. RSC Adv 2016. [DOI: 10.1039/c6ra17356j] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Different 10 mM buffers at the same nominal pH affect specifically the adsorption of lysozyme on ordered mesoporous silica. It emerges that specific buffer effects should be considered within ‘Hofmeister phenomena’.
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Affiliation(s)
- Francesca Cugia
- Department of Chemical and Geological Sciences
- University of Cagliari-CSGI and CNBS
- Cittadella Universitaria
- 09042-Monserrato
- Italy
| | - Silvia Sedda
- Department of Chemical and Geological Sciences
- University of Cagliari-CSGI and CNBS
- Cittadella Universitaria
- 09042-Monserrato
- Italy
| | - Federica Pitzalis
- Department of Chemical and Geological Sciences
- University of Cagliari-CSGI and CNBS
- Cittadella Universitaria
- 09042-Monserrato
- Italy
| | - Drew F. Parsons
- School of Engineering and Information Technology
- Murdoch University
- Australia
| | - Maura Monduzzi
- Department of Chemical and Geological Sciences
- University of Cagliari-CSGI and CNBS
- Cittadella Universitaria
- 09042-Monserrato
- Italy
| | - Andrea Salis
- Department of Chemical and Geological Sciences
- University of Cagliari-CSGI and CNBS
- Cittadella Universitaria
- 09042-Monserrato
- Italy
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25
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Inaba S, Fukada H, Oda M. Folding thermodynamics of c-Myb DNA-binding domain in correlation with its α-helical contents. Int J Biol Macromol 2016; 82:725-32. [DOI: 10.1016/j.ijbiomac.2015.10.035] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Revised: 10/12/2015] [Accepted: 10/12/2015] [Indexed: 11/28/2022]
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26
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Warfel JD, LiCata VJ. Enhanced DNA binding affinity of RecA protein from Deinococcus radiodurans. DNA Repair (Amst) 2015; 31:91-6. [PMID: 26021744 DOI: 10.1016/j.dnarep.2015.05.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Revised: 05/03/2015] [Accepted: 05/04/2015] [Indexed: 11/19/2022]
Abstract
Deinococcus radiodurans (Dr) has a significantly more robust DNA repair response than Escherichia coli (Ec), which helps it survive extremely high doses of ionizing radiation and prolonged periods of desiccation. DrRecA protein plays an essential part in this DNA repair capability. In this study we directly compare the binding of DrRecA and EcRecA to the same set of short, defined single (ss) and double stranded (ds) DNA oligomers. In the absence of cofactors (ATPγS or ADP), DrRecA binds to dsDNA oligomers more than 20 fold tighter than EcRecA, and binds ssDNA up to 9 fold tighter. Binding to dsDNA oligomers in the absence of cofactor presumably predominantly monitors DNA end binding, and thus suggests a significantly higher affinity of DrRecA for ds breaks. Upon addition of ATPγS, this species-specific affinity difference is nearly abolished, as ATPγS significantly decreases the affinity of DrRecA for DNA. Other findings include that: (1) both proteins exhibit a dependence of binding affinity on the length of the ssDNA oligomer, but not the dsDNA oligomer; (2) the salt dependence of binding is modest for both species of RecA, and (3) in the absence of DNA, DrRecA produces significantly shorter and/or fewer free-filaments in solution than does EcRecA. The results suggest intrinsic biothermodynamic properties of DrRecA contribute directly to the more robust DNA repair capabilities of D. radiodurans.
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Affiliation(s)
- Jaycob D Warfel
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA
| | - Vince J LiCata
- Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA.
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27
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Rudloff MW, Woosley AN, Wright NT. Biophysical characterization of naturally occurring titin M10 mutations. Protein Sci 2015; 24:946-55. [PMID: 25739468 DOI: 10.1002/pro.2670] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 02/17/2015] [Accepted: 02/18/2015] [Indexed: 12/15/2022]
Abstract
The giant proteins titin and obscurin are important for sarcomeric organization, stretch response, and sarcomerogenesis in myofibrils. The extreme C-terminus of titin (the M10 domain) binds to the N-terminus of obscurin (the Ig1 domain) in the M-band. The high-resolution structure of human M10 has been solved, along with M10 bound to one of its two known molecular targets, the Ig1 domain of obscurin-like. Multiple M10 mutations are linked to limb-girdle muscular dystrophy type 2J (LGMD2J) and tibial muscular dystrophy (TMD). The effect of the M10 mutations on protein structure and function has not been thoroughly characterized. We have engineered all four of the naturally occurring human M10 missense mutants and biophysically characterized them in vitro. Two of the four mutated constructs are severely misfolded, and cannot bind to the obscurin Ig1 domain. One mutation, H66P, is folded at room temperature but unfolds at 37°C, rendering it binding incompetent. The I57N mutation shows no significant structural, dynamic, or binding differences from the wild-type domain. We suggest that this mutation is not directly responsible for muscle wasting disease, but is instead merely a silent mutation found in symptomatic patients. Understanding the biophysical basis of muscle wasting disease can help streamline potential future treatments.
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Affiliation(s)
- Michael W Rudloff
- Department of Chemistry and Biochemistry, James Madison University, Harrisonburg, Virginia, 22807
| | - Alec N Woosley
- Department of Chemistry and Biochemistry, James Madison University, Harrisonburg, Virginia, 22807
| | - Nathan T Wright
- Department of Chemistry and Biochemistry, James Madison University, Harrisonburg, Virginia, 22807
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28
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Ferreira CMH, Pinto ISS, Soares EV, Soares HMVM. (Un)suitability of the use of pH buffers in biological, biochemical and environmental studies and their interaction with metal ions – a review. RSC Adv 2015. [DOI: 10.1039/c4ra15453c] [Citation(s) in RCA: 189] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The present work reviews, discusses and update the metal complexation characteristics of thirty one buffers commercially available. Additionally, their impact on the biological systems is also presented and discussed.
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Affiliation(s)
- Carlos M. H. Ferreira
- REQUIMTE/LAQV
- Department of Chemical Engineering
- Faculty of Engineering
- University of Porto
- Porto
| | - Isabel S. S. Pinto
- REQUIMTE/LAQV
- Department of Chemical Engineering
- Faculty of Engineering
- University of Porto
- Porto
| | - Eduardo V. Soares
- Bioengineering Laboratory
- Chemical Engineering Department
- ISEP-School of Engineering of Polytechnic Institute of Porto
- Porto
- Portugal
| | - Helena M. V. M. Soares
- REQUIMTE/LAQV
- Department of Chemical Engineering
- Faculty of Engineering
- University of Porto
- Porto
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