1
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Rossi M, Tomaselli F, Hochkoeppler A. The four subunits of rabbit skeletal muscle lactate dehydrogenase do not exert their catalytic action additively. Biochem Biophys Res Commun 2024; 690:149294. [PMID: 38011772 DOI: 10.1016/j.bbrc.2023.149294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Accepted: 11/17/2023] [Indexed: 11/29/2023]
Abstract
Oligomeric enzymes containing multiple active sites are usually considered to perform their catalytic action at higher rates when compared with their monomeric counterparts. This implies, in turn, that the activity performed by different holoenzyme subunits features additivity. Nevertheless, the extent of this additivity occurring in holoenzymes is far from being adequately understood. To tackle this point, we used tetrameric rabbit lactate dehydrogenase (rbLDH) as a model system to assay the reduction of pyruvate catalysed by this enzyme at the expense of β-NADH under pre-steady-state conditions. In particular, we observed the kinetics of reactions triggered by concentrations of β-NADH equimolar to 1, 2, 3, or all 4 subunits of the rbLDH holoenzyme, in the presence of an excess of pyruvate. Surprisingly, when the concentration of the limiting reactant exceeded that of a single holoenzyme subunit, we observed a sharp slowdown of the enzyme conformational rearrangements associated to the generation and the release of l-lactate. Furthermore, using a model to interpret the complex kinetics observed under the highest concentration of the limiting reactant, we estimated the diversity of the rates describing the action of the different rbLDH subunits.
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Affiliation(s)
- Martina Rossi
- Department of Pharmacy and Biotechnology, University of Bologna, Viale Risorgimento 4, 40136, Bologna, Italy
| | - Fabio Tomaselli
- Department of Pharmacy and Biotechnology, University of Bologna, Viale Risorgimento 4, 40136, Bologna, Italy
| | - Alejandro Hochkoeppler
- Department of Pharmacy and Biotechnology, University of Bologna, Viale Risorgimento 4, 40136, Bologna, Italy; CSGI, University of Firenze, Via della Lastruccia 3, 50019, Sesto Fiorentino, FI, Italy.
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2
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Waner MJ, Ellis G, Graeca M, Ieraci N, Morell C, Murphy A, Mascotti DP. Avidin cooperative allosterism upon binding biotin observed by differential changes in intrinsic fluorescence. Biochem Biophys Rep 2023; 36:101554. [PMID: 37854942 PMCID: PMC10579862 DOI: 10.1016/j.bbrep.2023.101554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 10/05/2023] [Accepted: 10/06/2023] [Indexed: 10/20/2023] Open
Abstract
Similar to streptavidin, the binding of biotin by avidin does not appear to be cooperative in the traditional sense of altered binding strength, though it appears to be cooperative in terms of ligand induced structural communication across subunits in the protein as previously shown for streptavidin. In this work we provide data from intrinsic tryptophan fluorescence as evidence of a cooperative structural change. The technique involves examination of the changes in fluorescence emission corresponding to the various tryptophan populations accompanying avidin-biotin binding. We note that the 335 nm emission population (i.e. more hydrophobic local environment) saturates prior to full ligation and the saturation of the 350 nm emission population commonly used in standard binding activity assays. We also note that total integrated fluorescence emission and peak height during the titration of ligand into streptavidin also reach saturation prior to the 4:1 stoichiometric end point. Unique to avidin and distinct from the behavior of streptavidin described in our prior work, the wavelength of maximum emission and full width at half maximum (FWHM) data do not saturate prior to the 4:1 stoichiometric end point. Avidin also exhibited larger FWHM for both apo and holo forms suggesting greater heterogeneity in local tryptophan environments, as compared to streptavidin. Taken together, the data suggests that the binding of the first 3 biotins effect greater structural changes in the protein than the final ligand in a similar way for avidin and streptavidin.
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Affiliation(s)
- Mark J. Waner
- Department of Chemistry, John Carroll University, 1 John Carroll Blvd., University Heights, OH, 44118, USA
| | - Gianna Ellis
- Department of Chemistry, John Carroll University, 1 John Carroll Blvd., University Heights, OH, 44118, USA
| | - Meghan Graeca
- Department of Chemistry, John Carroll University, 1 John Carroll Blvd., University Heights, OH, 44118, USA
| | - Nicholas Ieraci
- Department of Chemistry, John Carroll University, 1 John Carroll Blvd., University Heights, OH, 44118, USA
| | - Cole Morell
- Department of Chemistry, John Carroll University, 1 John Carroll Blvd., University Heights, OH, 44118, USA
| | - Alycia Murphy
- Department of Chemistry, John Carroll University, 1 John Carroll Blvd., University Heights, OH, 44118, USA
| | - David P. Mascotti
- Department of Chemistry, John Carroll University, 1 John Carroll Blvd., University Heights, OH, 44118, USA
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3
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Poboinev VV, Khrustalev VV, Akunevich AA, Shalygo NV, Stojarov AN, Khrustaleva TA, Kordyukova LV. Peptide Models of the Cytoplasmic Tail of Influenza A/H1N1 Virus Hemagglutinin Expand Understanding its pH-Dependent Modes of Interaction with Matrix Protein M1. Protein J 2023:10.1007/s10930-023-10101-z. [PMID: 36952102 PMCID: PMC10034248 DOI: 10.1007/s10930-023-10101-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/27/2023] [Indexed: 03/24/2023]
Abstract
Influenza A virus hemagglutinin (HA) is a major virus antigen. No cryo-electron microscopy or X-ray data can be obtained for the HA intraviral (cytoplasmic) domain (CT) post-translationally modified with long fatty acid residues bound to three highly conserved cysteines. We recently proposed a model of HA CT of Influenza A/H1N1 virus possessing an antiparallel beta structure based on the experimental secondary structure analysis of four 14-15 amino acid long synthetic peptides, corresponding to the HA CT sequence, with free or acetaminomethylated cysteines. To dispel doubts about possible non-specific "amyloid-like" aggregation of those synthetic peptides in phosphate buffer solution, we have determined the order of oligomers based on blue native gel electrophoresis, membrane filtration, fluorescence spectroscopy and molecular modeling approaches. We have found that unmodified peptides form only low molecular weight oligomers, while modified peptides form both oligomers of low order similar to those found for unmodified peptides and high order conglomerates, which however are not of beta-amyloid-like fold. This study confirms that the beta structure previously detected by circular dichroism spectroscopy analysis is more likely the result of intrinsic propensity of the HA CT amino acid sequence than the consequence of aggregation. The structures of low order oligomers of the synthetic peptides were used for in silico experiments on modeling of HA CT interactions with matrix protein M1 at physiological and acidic pH levels and revealed two different areas of binding. Finally, tripeptides capable of blocking interactions between HA CT and M1 were proposed.
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Abstract
Fluorescence spectroscopy is routinely used for the determination of the interaction of a ligand with a protein. The quick detection of the interaction between the ligand and the protein is one of the most significant advantages of fluorescence spectroscopic methods. In this chapter, we have described assays to monitor drug -tubulin interactions using several fluorescence spectroscopic techniques. We have provided detailed protocols for different assays for investigating tubulin-drug interactions with key practical considerations for performing the experiments. We have also discussed how to deduce the binding parameters by fitting the fluorescence change data in different binding isotherms. Further, we have described detailed protocols to monitor the binding site of a ligand on tubulin by competitive inhibition. Though the methods are described for tubulin, these methods can also be used to monitor any drug -protein interactions.
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Affiliation(s)
- Anuradha Kumari
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Dulal Panda
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India.
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5
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Rasheed Z, Alharbi A, Alrakebeh A, Almansour K, Almadi A, Almuzaini A, Salem M, Aloboody B, Alkobair A, Albegami A, Alhomaidan HT, Rasheed N, Alqossayir FM, Musa KH, Hamad EM, Al Abdulmonem W. Thymoquinone provides structural protection of human hemoglobin against oxidative damage: Biochemical studies. Biochimie 2021; 192:102-110. [PMID: 34655671 DOI: 10.1016/j.biochi.2021.10.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 09/03/2021] [Accepted: 10/11/2021] [Indexed: 11/30/2022]
Abstract
Hydroxyl radicals (OH.) are one of the most active reactive oxidants recognized for their deleterious effects to cause protein oxidative damage. Thymoquinone, a monoterpene molecule abundantly present in black cumin and known for its pharmacological activities, but its activity against the OH.-induced protein oxidative damage has never been explored. This study determined the therapeutic potential of thymoquinone against OH.-induced oxidative human hemoglobin damage. Novel data demonstrated that thymoquinone provides structural protection of hemoglobin against oxidative damage. Treatment of hemoglobin with OH. induces hypochromicity at 280 and 405 nm, whereas thymoquinone reversed these hypochromic effects. In addition, OH. cause significant reduction in tryptophan fluorescence, however thymoquinone also reversed these damaging effects. Thymoquinone also reduces OH.-induced hydrophobicity and also reduces OH.-induced carbonylation. Moreover, it also inhibits thermal stabilization of OH.-hemoglobin complex. SDS-PAGE of unmodified hemoglobin showed four bands, which disappeared upon OH. treatment and these changes were also retained by thymoquinone. In conclusion, this is the first study that shows the therapeutic potential of thymoquinone against OH.-induced oxidative damage in human hemoglobin.
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Affiliation(s)
- Zafar Rasheed
- Department of Medical Biochemistry, College of Medicine, Qassim University, Buraidah, Saudi Arabia.
| | - Adel Alharbi
- Department of Family and Community Medicine, College of Medicine, Qassim University, Buraidah, Saudi Arabia
| | - Abdullah Alrakebeh
- Department of Family and Community Medicine, College of Medicine, Qassim University, Buraidah, Saudi Arabia
| | - Khaled Almansour
- Department of Family and Community Medicine, College of Medicine, Qassim University, Buraidah, Saudi Arabia
| | - Abdulaziz Almadi
- Department of Family and Community Medicine, College of Medicine, Qassim University, Buraidah, Saudi Arabia
| | - Ahmed Almuzaini
- Department of Family and Community Medicine, College of Medicine, Qassim University, Buraidah, Saudi Arabia
| | - Mohammed Salem
- Department of Family and Community Medicine, College of Medicine, Qassim University, Buraidah, Saudi Arabia
| | - Bassim Aloboody
- Department of Family and Community Medicine, College of Medicine, Qassim University, Buraidah, Saudi Arabia
| | - Abdulsalam Alkobair
- Department of Family and Community Medicine, College of Medicine, Qassim University, Buraidah, Saudi Arabia
| | - Ahmad Albegami
- Department of Family and Community Medicine, College of Medicine, Qassim University, Buraidah, Saudi Arabia
| | - Homaidan T Alhomaidan
- Department of Family and Community Medicine, College of Medicine, Qassim University, Buraidah, Saudi Arabia
| | - Naila Rasheed
- Department of Medical Biochemistry, College of Medicine, Qassim University, Buraidah, Saudi Arabia
| | - Fuhaid M Alqossayir
- Department of Family and Community Medicine, College of Medicine, Qassim University, Buraidah, Saudi Arabia
| | - Khalid H Musa
- Department of Food Science and Human Nutrition, College of Agriculture and Veterinary Medicine, Qassim University, Buraidah, Saudi Arabia
| | - Essam M Hamad
- Department of Food Science and Human Nutrition, College of Agriculture and Veterinary Medicine, Qassim University, Buraidah, Saudi Arabia
| | - Waleed Al Abdulmonem
- Department of Pathology, College of Medicine, Qassim University, Buraidah, Saudi Arabia
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Dean DN, Lee JC. Purification and characterization of an amyloidogenic repeat domain from the functional amyloid Pmel17. Protein Expr Purif 2021; 187:105944. [PMID: 34293440 DOI: 10.1016/j.pep.2021.105944] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 07/16/2021] [Accepted: 07/17/2021] [Indexed: 01/15/2023]
Abstract
The pre-melanosomal protein (Pmel17) is a human functional amyloid that supports melanin biosynthesis within melanocytes. This occurs in the melanosome, a membrane-bound organelle with an acidic intraluminal pH. The repeat region of Pmel17 (RPT, residues 315-444) has been previously shown to form amyloid aggregates under acidic melanosomal conditions, but not under neutral cytosolic conditions, when expressed and purified using a C-terminal hexa-histidine tag (RPT-His). Given the importance of protonation states in RPT-His aggregation, we questioned whether the histidine tag influenced the pH-dependent behavior. In this report, we generated a tagless RPT by inserting a tobacco etch virus (TEV) protease recognition sequence (ENLYGQ(G/S)) immediately upstream of a native glycine residue at position 312 in Pmel17. After purification of the fusion construct using a histidine tag, cleavage with TEV protease generated a fully native RPT (nRPT) spanning resides 312-444. We characterized the aggregation of nRPT, which formed amyloid fibrils under acidic conditions (pH ≤ 6) but not at neutral pH. Characterizing the morphologies of nRPT aggregates using transmission electron microscopy revealed a pH-dependent maturation from short, curved structures at pH 4 to paired, rod-like fibrils at pH 6. This was accompanied by a secondary structural transition from mixed random coil/β-sheet at pH 4 to canonical β-sheet at pH 6. We also show that pre-formed nRPT fibrils undergo disaggregation upon dilution into pH 7 buffer. More broadly, this strategy can be utilized to generate native amyloidogenic domains from larger proteins by utilizing intrinsic N-terminal glycine or serine residues.
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Affiliation(s)
- Dexter N Dean
- Laboratory of Protein Conformation and Dynamics, Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, United States
| | - Jennifer C Lee
- Laboratory of Protein Conformation and Dynamics, Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, United States.
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Siddiqui GA, Naeem A. Refolding of Hemoglobin Under Macromolecular Confinement: Impersonating In Vivo Volume Exclusion. J Fluoresc 2021; 31:1371-1377. [PMID: 34156613 DOI: 10.1007/s10895-021-02751-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Accepted: 05/20/2021] [Indexed: 11/27/2022]
Abstract
Biomacromolecules evolve and function inside the cell under crowded conditions. The effect of macromolecular crowding and confinement on nature and interactions of biomacromolecules cannot be ruled out. This study demonstrates the effect of volume exclusion due to macromolecular crowding on refolding rate of Gn-HCl induced unfolded hemoglobin. The in vivo like crowding milieu was created using dextran 70. Unfolding of Hb was followed by the absorbance at 280 nm and intrinsic fluorescence intensity along with a bathochromic shift that shows the destabilization of Hb in the presence of the denaturing agent. This was supported by a decrease in soret absorbance, increased hydrodynamic radii and loss in secondary structure, evidenced from dynamic light scattering and circular dichroism experiments respectively. Refolding process of Hb was followed by an increase in soret absorbance, decrease in intrinsic fluorescence intensity with a hypsochromic shift, decreased hydrodynamic radii and gain in secondary structural content. The results revealed that the effect of confinement and volume exclusion is insignificant on the process of Hb refolding.
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Affiliation(s)
- Gufran Ahmed Siddiqui
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, 202002, UP, India
| | - Aabgeena Naeem
- Department of Biochemistry, Faculty of Life Sciences, Aligarh Muslim University, Aligarh, 202002, UP, India.
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8
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Li Y, Valdez NA, Mnatsakanyan N, Weber J. The nucleotide binding affinities of two critical conformations of Escherichia coli ATP synthase. Arch Biochem Biophys 2021; 707:108899. [PMID: 33991499 DOI: 10.1016/j.abb.2021.108899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 04/27/2021] [Accepted: 04/28/2021] [Indexed: 10/21/2022]
Abstract
ATP synthase is essential in aerobic energy metabolism, and the rotary catalytic mechanism is one of the core concepts to understand the energetic functions of ATP synthase. Disulfide bonds formed by oxidizing a pair of cysteine mutations halted the rotation of the γ subunit in two critical conformations, the ATP-waiting dwell (αE284C/γQ274C) and the catalytic dwell (αE284C/γL276C). Tryptophan fluorescence was used to measure the nucleotide binding affinities for MgATP, MgADP and MgADP-AlF4 (a transition state analog) to wild-type and mutant F1 under reducing and oxidizing conditions. In the reduced state, αE284C/γL276C F1 showed a wild-type-like nucleotide binding pattern; after oxidation to lock the enzyme in the catalytic dwell state, the nucleotide binding parameters remained unchanged. In contrast, αE284C/γQ274C F1 showed significant differences in the affinities of the oxidized versus the reduced state. Locking the enzyme in the ATP-waiting dwell reduced nucleotide binding affinities of all three catalytic sites. Most importantly, the affinity of the low affinity site was reduced to such an extent that it could no longer be detected in the binding assay (Kd > 5 mM). The results of the present study allow to present a model for the catalytic mechanism of ATP synthase under consideration of the nucleotide affinity changes during a 360° cycle of the rotor.
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Affiliation(s)
- Yunxiang Li
- Department of Chemistry and Biochemistry, Texas Woman's University, Denton, TX, 76204, USA; Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, 79409, USA.
| | - Neydy A Valdez
- Department of Biology, Texas Woman's University, Denton, TX, 76204, USA
| | - Nelli Mnatsakanyan
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, 79409, USA; School of Medicine, Yale University, New Haven, CT, 06520, USA
| | - Joachim Weber
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, 79409, USA; Center for Membrane Protein Research, Texas Tech University Health Sciences Center, Lubbock, TX, 79430, USA.
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Pletneva NV, Maksimov EG, Protasova EA, Mamontova AV, Simonyan TR, Ziganshin RH, Lukyanov KA, Muslinkina L, Pletnev S, Bogdanov AM, Pletnev VZ. Amino acid residue at the 165th position tunes EYFP chromophore maturation. A structure-based design. Comput Struct Biotechnol J 2021; 19:2950-2959. [PMID: 34136094 PMCID: PMC8163865 DOI: 10.1016/j.csbj.2021.05.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 05/06/2021] [Accepted: 05/09/2021] [Indexed: 01/07/2023] Open
Abstract
For the whole GFP family, a few cases, when a single mutation in the chromophore environment strongly inhibits maturation, were described. Here we study EYFP-F165G - a variant of the enhanced yellow fluorescent protein - obtained by a single F165G replacement, and demonstrated multiple fluorescent states represented by the minor emission peaks in blue and yellow ranges (~470 and ~530 nm), and the major peak at ~330 nm. The latter has been assigned to tryptophan fluorescence, quenched due to excitation energy transfer to the mature chromophore in the parental EYFP protein. EYFP-F165G crystal structure revealed two general independent routes of post-translational chemistry, resulting in two main states of the polypeptide chain with the intact chromophore forming triad (~85%) and mature chromophore (~15%). Our experiments thus highlighted important stereochemical role of the 165th position strongly affecting spectral characteristics of the protein. On the basis of the determined EYFP-F165G three-dimensional structure, new variants with ~ 2-fold improved brightness were engineered.
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Key Words
- Ala (A), alanine
- Arg (R), arginine
- Asn (R), asparagine
- Chromophore maturation
- DTT, dithiothreitol
- EC, extinction coefficient
- EET, excitation energy transfer
- EGFP, enhanced green fluorescent protein
- ESET, excited-state electron transfer
- EYFP
- EYFP, enhanced yellow fluorescent protein
- Excitation energy transfer
- FLIM, fluorescence lifetime imaging microscopy
- FP, fluorescent protein
- FQY, fluorescence quantum yield
- FRET, Förster resonance energy transfer
- FTIR, Fourier-transform infrared (spectroscopy
- Femtosecond spectroscopy
- Fluorescent proteins
- GFP, green fluorescent protein
- GYG, glycine-tyrosine-glycine
- Gln (Q), glutamine
- Glu (E), glutamic acid
- Gly (G), glycine
- His (H), histidine
- IVA-cloning, in vivo assembly cloning
- Leu (L), leucine
- PBS, phosphate buffered saline
- PCR, polymerase chain reaction
- Phe (F), phenylalanine
- REACh, resonance energy-accepting chromoprotein
- Ser (S), serine
- Structure-guided mutagenesis
- Trp (W), tryptophan
- Tryptophan fluorescence
- Tyr (Y), tyrosine
- Val (V), valine
- X-ray structure
- avGFP, Aequorea victoria green fluorescent protein
- sfGFP, superfolder GFP
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Affiliation(s)
- Nadya V. Pletneva
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia
| | - Eugene G. Maksimov
- Faculty of Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
| | - Elena A. Protasova
- Faculty of Biology, Lomonosov Moscow State University, 119992 Moscow, Russia
| | - Anastasia V. Mamontova
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow 121205, Russia
| | - Tatiana R. Simonyan
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow 121205, Russia
| | - Rustam H. Ziganshin
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia
| | - Konstantin A. Lukyanov
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow 121205, Russia
| | - Liya Muslinkina
- Structural Biology Section, Research Technologies Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sergei Pletnev
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Alexey M. Bogdanov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia,Corresponding authors at: Depatment of biophotonics (both), Laboratory of genetically encoded molecular tools ( A.M.B.), Laboratory of of X-ray study ( V.Z.P.).
| | - Vladimir Z. Pletnev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Moscow 117997, Russia,Corresponding authors at: Depatment of biophotonics (both), Laboratory of genetically encoded molecular tools ( A.M.B.), Laboratory of of X-ray study ( V.Z.P.).
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Lapenna A, Stefan A, Hochkoeppler A. ASFV DNA polymerase extends recessed DNAs with catalytic efficiencies outperforming those exerted on gapped DNA substrates. Biochem Biophys Res Commun 2021; 534:526-32. [PMID: 33223051 DOI: 10.1016/j.bbrc.2020.11.049] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2020] [Accepted: 11/12/2020] [Indexed: 01/17/2023]
Abstract
The DNA polymerase from african swine fever virus (ASFV Pol X), lacking both 8 kDa and thumb domains, is the smallest enzyme featuring competence in DNA extension. Here we show that ASFV Pol X features poor filling activity of DNA gaps consisting of 15 bases, and exerts a more efficient action at the expense of DNA substrates containing a recessed end of equal length. We also show that shortening the recessed end of DNA substrates decreases the rate of DNA elongation catalysed by ASFV Pol X. Finally, by means of stopped-flow experiments we were able to determine that DNA binding is a step responsible for restraining the efficiency of ASFV Pol X catalytic action.
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11
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Lara-Popoca J, Thoke HS, Stock RP, Rudino-Pinera E, Bagatolli LA. Inductive effects in amino acids and peptides: Ionization constants and tryptophan fluorescence. Biochem Biophys Rep 2020; 24:100802. [PMID: 32984556 PMCID: PMC7498751 DOI: 10.1016/j.bbrep.2020.100802] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Revised: 07/26/2020] [Accepted: 07/27/2020] [Indexed: 10/26/2022] Open
Abstract
Although inductive effects in organic compounds are known to influence chemical properties such as ionization constants, their specific contribution to the properties/behavior of amino acids and functional groups in peptides remains largely unexplored. In this study we developed a computationally economical algorithm for ab initio calculation of the magnitude of inductive effects for non-aromatic molecules. The value obtained by the algorithm is called the Inductive Index and we observed a high correlation (R2 = 0.9427) between our calculations and the pKa values of the alpha-amino groups of amino acids with non-aromatic side-chains. Using a series of modified amino acids, we also found similarly high correlations (R2 > 0.9600) between Inductive Indexes and two wholly independent chemical properties: i) the pKa values of ionizable side-chains and, ii) the fluorescence response of the indole group of tryptophan. After assessing the applicability of the method of calculation at the amino acid level, we extended our study to tryptophan-containing peptides and established that inductive contributions of neighboring side-chains are transmitted through peptide bonds. We discuss possible contributions to the study of proteins.
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Affiliation(s)
- Jesús Lara-Popoca
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Departamento de Medicina Molecular y Bioprocesos, Av. Universidad #2001, Col. Chamilpa, 62210, Cuernavaca, Morelos, Mexico
| | - Henrik S Thoke
- MEMPHYS - International and Interdisciplinary Research Network, Odense, Denmark
| | - Roberto P Stock
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Departamento de Medicina Molecular y Bioprocesos, Av. Universidad #2001, Col. Chamilpa, 62210, Cuernavaca, Morelos, Mexico
| | - Enrique Rudino-Pinera
- Instituto de Biotecnología, Universidad Nacional Autónoma de México, Departamento de Medicina Molecular y Bioprocesos, Av. Universidad #2001, Col. Chamilpa, 62210, Cuernavaca, Morelos, Mexico
| | - Luis A Bagatolli
- MEMPHYS - International and Interdisciplinary Research Network, Odense, Denmark.,Instituto de Investigación Médica Mercedes y Martín Ferreyra (INIMEC-CONICET-Universidad Nacional de Córdoba), Friuli 2434, 5016, Córdoba, Argentina
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12
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Stefan A, Gentilucci L, Piaz FD, D'Alessio F, Santino F, Hochkoeppler A. Purification from Deinococcus radiodurans of a 66 kDa ABC transporter acting on peptides containing at least 3 amino acids. Biochem Biophys Res Commun 2020; 529:869-875. [PMID: 32819591 DOI: 10.1016/j.bbrc.2020.06.060] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 06/12/2020] [Indexed: 11/24/2022]
Abstract
Deinococcus radiodurans is a Gram positive bacterium the capability of which to withstand high doses of ionizing radiations is well known. Physiologically speaking, D. radiodurans is a proteolytic prokaryote able to express and secrete quite a number of proteases, and to use amino acids as an energy source. When considering this, it is surprising that little information is available on the biochemical components responsible for the uptake of peptides in D. radiodurans. Here we report on the purification and characterization of an ABC peptide transporter, isolated from D. radiodurans cells grown in tryptone-glucose-yeast extract (TGY) medium. In particular, we show here that the action of this transporter (denoted DR1571, SwissProt data bank accession number Q9RU24 UF71_DEIRA) is exerted on peptides containing at least 3 amino acids. Further, using tetra-peptides as model systems, we were able to observe that the DR1571 protein does not bind to peptides containing phenylalanine or valine, but associates with high efficiency to tetra-glycine, and with moderate affinity to tetra-peptides containing arginine or aspartate.
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Affiliation(s)
- Alessandra Stefan
- Department of Pharmacy and Biotechnology, University of Bologna, Viale Risorgimento 4, 40136, Bologna, Italy; CSGI, University of Firenze, Via della Lastruccia 3, 50019, Sesto Fiorentino, (FI), Italy
| | - Luca Gentilucci
- Department of Chemistry "Giacomo Ciamician", Via Selmi 2, 40126, Bologna, Italy
| | - Fabrizio Dal Piaz
- Department of Medicine, University of Salerno, Via Giovanni Paolo II 132, 84084, Fisciano, Salerno, Italy
| | - Federico D'Alessio
- Department of Pharmacy and Biotechnology, University of Bologna, Viale Risorgimento 4, 40136, Bologna, Italy
| | - Federica Santino
- Department of Chemistry "Giacomo Ciamician", Via Selmi 2, 40126, Bologna, Italy
| | - Alejandro Hochkoeppler
- Department of Pharmacy and Biotechnology, University of Bologna, Viale Risorgimento 4, 40136, Bologna, Italy; CSGI, University of Firenze, Via della Lastruccia 3, 50019, Sesto Fiorentino, (FI), Italy.
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13
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Sekhon G, Singh R. Human aldose reductase unfolds through an intermediate. F1000Res 2019; 8:564. [PMID: 31723418 PMCID: PMC6844136 DOI: 10.12688/f1000research.18963.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/22/2019] [Indexed: 11/26/2022] Open
Abstract
Background: Human aldose reductase (hAR) is the first and rate-limiting enzyme of the polyol pathway. For the development of secondary complications of diabetes in chronic hyperglycemic conditions, one of the critical factors is the increased flux of glucose through the polyol pathway. Due to this clinical implication, hAR attracted considerable attention from the drug discovery perspective. In spite of extensive characterization in the context of biochemical and structural aspects, we know very little about the unfolding behavior of hAR. This study reports equilibrium unfolding studies of hAR. Methods: We carried out thermal denaturation and chemical-induced equilibrium unfolding studies of hAR monitored by circular dichroism and fluorescence spectroscopy. Results: Thermal denaturation studies presented a classical picture of two-state unfolding from native to the denatured state. The data was used to derive thermodynamic parameters and study the thermostability of hAR. Chemical induced equilibrium unfolding studies led us to discover an intermediate state, which gets populated at 3.5-4.0 M and 0.7-2.0 M of urea and GuHCl, respectively. Thermodynamic parameters derived from chemical-induced unfolding are in agreement with those obtained from thermal denaturation of hAR. Conclusion: This study revealed that aldose reductase unfolds from native to the unfolded state via an intermediate. Assessment of the thermodynamic stability of native, intermediate, and unfolded states shows that significant energy barriers separate these states, which ensures the cooperativity of unfolding. As hAR functions in cells that are under osmotic and oxidative stress, these
in vitro findings may have implications for its native conformation under the physiological state.
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Affiliation(s)
- Gurprit Sekhon
- Department cum National Center for Human Genome Studies and Research, Panjab University, Chandigarh, 160014, India
| | - Ranvir Singh
- Department cum National Center for Human Genome Studies and Research, Panjab University, Chandigarh, 160014, India
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14
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Vasquez-Montes V, Gerhart J, Thévenin D, Ladokhin AS. Divalent Cations and Lipid Composition Modulate Membrane Insertion and Cancer-Targeting Action of pHLIP. J Mol Biol 2019; 431:5004-5018. [PMID: 31689432 DOI: 10.1016/j.jmb.2019.10.016] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2019] [Revised: 10/24/2019] [Accepted: 10/24/2019] [Indexed: 02/06/2023]
Abstract
The pH-Low Insertion Peptide (pHLIP) has emerged as an important tool for targeting cancer cells; it has been assumed that its targeting mechanism depends solely on the mild acidic environment surrounding tumors. Here, we examine the role of Ca2+ and Mg2+ on pHLIP's insertion, cellular targeting, and drug delivery. We demonstrate that physiologically relevant concentrations of either cation can shift the protonation-dependent transition by up to several pH units toward basic pH and induce substantial protonation-independent transmembrane insertion of pHLIP at pH as high as 10. Consistent with these results, the ability of pHLIP to deliver the cytotoxic compound monomethyl-auristatin-F to HeLa cells is increased several fold in presence of Ca2+. Complementary measurements with model membranes confirmed this Ca2+/Mg2+-dependent membrane-insertion mechanism. The magnitude of this alternative Ca2+/Mg2+-dependent effect is also modulated by lipid composition-specifically by the presence of phosphatidylserine-providing new clues to pHLIP's unique tumor-targeting ability in vivo. These results exemplify the complex coupling between protonation of anionic residues and lipid-selective targeting by divalent cations, which is relevant to the general signaling on membrane interfaces.
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Affiliation(s)
- Victor Vasquez-Montes
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, KS, 66160, USA
| | - Janessa Gerhart
- Department of Chemistry, Lehigh University, 6 East Packer Avenue, Bethlehem, PA, 18015, USA
| | - Damien Thévenin
- Department of Chemistry, Lehigh University, 6 East Packer Avenue, Bethlehem, PA, 18015, USA
| | - Alexey S Ladokhin
- Department of Biochemistry and Molecular Biology, The University of Kansas Medical Center, Kansas City, KS, 66160, USA.
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15
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Mahapatra K, Roy S. An insight into the folding and stability of Arabidopsis thaliana SOG1 transcription factor under salinity stress in vitro. Biochem Biophys Res Commun 2019; 515:531-7. [PMID: 31176488 DOI: 10.1016/j.bbrc.2019.05.183] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2019] [Accepted: 05/30/2019] [Indexed: 11/20/2022]
Abstract
The present study describes the biophysical characterization of Arabidopsis thaliana SOG1 (SUPPRESSOR OF GAMMA RESPONSE 1) protein, a NAC domain transcription factor which plays central role in DNA damage response pathway, under salinity stress in vitro. Tryptophan fluorescence studies using purified recombinant wild type (full length) AtSOG1 and its N-terminal or C-terminal deletion forms (AtSOG1ΔNAC and AtSOG1ΔCT respectively) have revealed high salinity induced conformational change due to removal of the N-terminal NAC domain. Bis-ANS binding assays indicate that removal of the N-terminal NAC domain increases the surface hydrophobic binding sites, while the C-terminal region of SOG1 also plays important role in regulating the surface hydrophobicity aspects following exposure to high salinity. Circular dichroism (CD) spectral studies have indicated that removal of the N-terminal NAC domain affects the structural conformation of the protein under high salt concentration. Urea-induced equilibrium unfolding studies revealed decreased stability of C-terminal region due to removal of the N-terminal NAC domain. In vitro aggregation studies have indicated higher propensity of aggregation of AtSOG1ΔNAC due to salt treatment. Overall, our results provide evidence for the importance of both N-terminal NAC domain and the C-terminal region in regulating the stability of SOG1 protein under salinity stress in vitro.
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16
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Chatterjee S, Das A, Raghuraman H. Biochemical and biophysical characterization of a prokaryotic Mg 2+ ion channel: Implications for cost-effective purification of membrane proteins. Protein Expr Purif 2019; 161:8-16. [PMID: 31028884 DOI: 10.1016/j.pep.2019.04.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 04/19/2019] [Indexed: 10/26/2022]
Abstract
Although magnesium is the second most abundant cation present in the cell, the transport mechanism of Mg2+ across membranes is poorly understood. Importantly, the prokaryotic MgtE Mg2+ channel is related to mammalian SLC41A1 transporters and, therefore, biochemical and biophysical characterization of MgtE and its orthologs assumes significance. To date, the purification and structure determination of MgtE from Thermus thermophilus has been carried out using the widely used nonionic detergent, n-dodecyl-β-d-maltopyranoside (DDM). However, DDM is an expensive detergent and alternative methods to produce high-quality proteins in stable and functional form will be practically advantageous to carry out structural studies in a cost-effective manner. In this work, we have utilized 'dual-detergent strategy' to successfully purify MgtE channel in a stable and functional form by employing relatively inexpensive detergents (Triton X-100 and Anzergent 3-14) for membrane solubilization and subsequently changed to DDM during purification. Our results show that Triton X-100 and Anzergent 3-14 extract MgtE well and the quality of purified protein is comparable to DDM-extracted MgtE. Interestingly, addition of high concentration of salt and glycerol during solubilization does not significantly affect the quantity and quality of MgtE. Importantly, limited proteolysis assay, circular dichroism spectroscopy and ensemble tryptophan fluorescence strongly support the use of Triton X-100, in particular, as an inexpensive, alternative detergent for the purification of MgtE without compromising the structural integrity of the channel and Mg2+-induced gating-related conformational dynamics. Overall, these results are relevant for the cost-effective purification of stable and functional membrane proteins in general, and magnesium channels, in particular.
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Affiliation(s)
- Satyaki Chatterjee
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, Homi Bhabha National Institute, 1/AF Bidhannagar, Kolkata, 700 064, India
| | - Anindita Das
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, Homi Bhabha National Institute, 1/AF Bidhannagar, Kolkata, 700 064, India
| | - H Raghuraman
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, Homi Bhabha National Institute, 1/AF Bidhannagar, Kolkata, 700 064, India.
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17
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Knox PP, Korvatovskiy BN, Gorokhov VV, Goryachev SN, Mamedov MD, Paschenko VZ. Comparison of tryptophan fluorescence lifetimes in cyanobacterial photosystem I frozen in the light and in the dark. Photosynth Res 2019; 139:441-448. [PMID: 30353420 DOI: 10.1007/s11120-018-0595-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Accepted: 10/09/2018] [Indexed: 06/08/2023]
Abstract
The dependence on temperature of tryptophan fluorescence lifetime in trimeric photosystem I (PSI) complexes from cyanobacteria Synechocystis sp. PCC 6803 during the heating of pre-frozen to - 180 °C in the dark or in the light-activated preparations has been studied. Fluorescence lifetime in samples frozen in the light was longer than in samples frozen in the dark. For samples in 65% glycerol at λreg = 335 nm and at 20 °C, the lifetime of components were as follows: τ1 ≈ 1.2 ns, τ2 ≈ 4.9 ns, and τ3 ≈ 20 ns. The contribution of the first component was negligible. To analyze the contribution of components 2 and 3 derived from frozen-thawed samples, two temperature ranges from - 180 to - 90 °C and above - 90 °C are considered. In doing so, the contributions of these components appear antiphase course to each other. The dependence on temperature of these contributions is explained by the influence of the microconformational protein dynamics on the tryptophan fluorescence lifetime. In the present work, a comparative analysis of temperature-dependent conformational dynamics and electron transfer in cyanobacterial PSI (Schlodder et al., in Biochemistry 37:9466-9476, 1998) and Rhodobacter sphaeroides reaction center complexes (Knox et al., in J Photochem Photobiol B 180:140-148, 2018) was also carried out.
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Affiliation(s)
- Peter P Knox
- Department of Biophysics, Biological Faculty of the M.V. Lomonosov Moscow State University, Moscow, Russia, 119991
| | - Boris N Korvatovskiy
- Department of Biophysics, Biological Faculty of the M.V. Lomonosov Moscow State University, Moscow, Russia, 119991
| | - Vladimir V Gorokhov
- Department of Biophysics, Biological Faculty of the M.V. Lomonosov Moscow State University, Moscow, Russia, 119991
| | - Sergey N Goryachev
- Department of Biophysics, Biological Faculty of the M.V. Lomonosov Moscow State University, Moscow, Russia, 119991
| | - Mahir D Mamedov
- A.N. Belozersky Institute of Physical-Chemical Biology, M.V. Lomonosov Moscow State University, Moscow, Russia, 119991
| | - Vladimir Z Paschenko
- Department of Biophysics, Biological Faculty of the M.V. Lomonosov Moscow State University, Moscow, Russia, 119991.
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18
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Waner MJ, Hiznay JM, Mustovich AT, Patton W, Ponyik C, Mascotti DP. Streptavidin cooperative allosterism upon binding biotin observed by differential changes in intrinsic fluorescence. Biochem Biophys Rep 2019; 17:127-131. [PMID: 30805560 PMCID: PMC6372923 DOI: 10.1016/j.bbrep.2018.12.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 11/12/2018] [Accepted: 12/25/2018] [Indexed: 12/02/2022] Open
Abstract
While the binding of biotin by streptavidin does not appear to be cooperative in the traditional sense of altered binding strength, it has been suggested that it may be cooperative in terms of differential structural changes in the protein. In this work we present intrinsic tryptophan fluorescence data as evidence of a cooperative structural change. The technique involves examination of the differences in fluorescence emission corresponding to distinct tryptophan populations accompanying protein-ligand binding. Specifically we note that the 335 nm emission population (i.e. more hydrophobic) saturates prior to the saturation of the 350 nm emission population commonly used in the standard binding activity assay. We also note that the wavelength of maximum emission, total integrated fluorescence emission and full width at half maximum during the titration of ligand into streptavidin also reach saturation before the expected 4:1 stoichiometric end point. This suggests that the binding of the first 3 biotins effect greater structural changes in the protein than the final ligand. Structurally sensitive intrinsic Trp fluorescence changes upon biotin addition. Key features of this fluorescence stops changing prior to full biotin saturation. This suggests that ligand-induced structural changes are allosteric. We introduce use of ‘cooperative allosterism’ to distinguish from traditional usage.
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19
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Noguchi H, Mylemans B, De Zitter E, Van Meervelt L, Tame JRH, Voet A. Design of tryptophan-containing mutants of the symmetrical Pizza protein for biophysical studies. Biochem Biophys Res Commun 2018; 497:1038-1042. [PMID: 29481797 DOI: 10.1016/j.bbrc.2018.02.168] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 02/22/2018] [Indexed: 01/29/2023]
Abstract
β-propeller proteins are highly symmetrical, being composed of a repeated motif with four anti-parallel β-sheets arranged around a central axis. Recently we designed the first completely symmetrical β-propeller protein, Pizza6, consisting of six identical tandem repeats. Pizza6 is expected to prove a useful building block for bionanotechnology, and also a tool to investigate the folding and evolution of β-propeller proteins. Folding studies are made difficult by the high stability and the lack of buried Trp residues to act as monitor fluorophores, so we have designed and characterized several Trp-containing Pizza6 derivatives. In total four proteins were designed, of which three could be purified and characterized. Crystal structures confirm these mutant proteins maintain the expected structure, and a clear redshift of Trp fluorescence emission could be observed upon denaturation. Among the derivative proteins, Pizza6-AYW appears to be the most suitable model protein for future folding/unfolding kinetics studies as it has a comparable stability as natural β-propeller proteins.
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Affiliation(s)
- Hiroki Noguchi
- Laboratory of Biomolecular Modelling and Design, Department of Chemistry, University of Leuven, Celestijnenlaan 200G-bus2403, Heverlee, Belgium
| | - Bram Mylemans
- Laboratory of Biomolecular Modelling and Design, Department of Chemistry, University of Leuven, Celestijnenlaan 200G-bus2403, Heverlee, Belgium
| | - Elke De Zitter
- Laboratory of Biomolecular Architecture, Department of Chemistry, University of Leuven, Celestijnenlaan 200F-bus2404, Heverlee, Belgium
| | - Luc Van Meervelt
- Laboratory of Biomolecular Architecture, Department of Chemistry, University of Leuven, Celestijnenlaan 200F-bus2404, Heverlee, Belgium
| | - Jeremy R H Tame
- Drug Design Laboratory, Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro, Yokohama, Kanagawa, 230-0045, Japan
| | - Arnout Voet
- Laboratory of Biomolecular Modelling and Design, Department of Chemistry, University of Leuven, Celestijnenlaan 200G-bus2403, Heverlee, Belgium.
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20
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Knox PP, Gorokhov VV, Korvatovskiy BN, Lukashev EP, Goryachev SN, Paschenko VZ, Rubin AB. The effect of light and temperature on the dynamic state of Rhodobacter sphaeroides reaction centers proteins determined from changes in tryptophan fluorescence lifetime and P +Q A- recombination kinetics. J Photochem Photobiol B 2018; 180:140-148. [PMID: 29413697 DOI: 10.1016/j.jphotobiol.2018.01.027] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Revised: 01/22/2018] [Accepted: 01/29/2018] [Indexed: 11/26/2022]
Abstract
The temperature dependencies of the rate of dark recombination of separated charges between the photoactive bacteriochlorophyll and the primary quinone acceptor (QA) in photosynthetic reaction centers (RCs) of the purple bacteria Rhodobacter sphaeroides (Rb. sphaeroides) were investigated. Measurements were performed in water-glycerol and trehalose environments after freezing to -180 °C in the dark and under actinic light with subsequent heating. Simultaneously, the RC tryptophanyl fluorescence lifetime in the spectral range between 323 and 348 nm was measured under these conditions. A correlation was found between the temperature dependencies of the functional and dynamic parameters of RCs in different solvent mixtures. For the first time, differences in the average fluorescence lifetime of tryptophanyl residues were measured between RCs frozen in the dark and in the actinic light. The obtained results can be explained by the RC transitions between different conformational states and the dynamic processes in the structure of the hydrogen bonds of RCs. We assumed that RCs exist in two main microconformations - "fast" and "slow", which are characterized by different rates of P+ and QA- recombination reactions. The "fast" conformation is induced in frozen RCs in the dark, while the "slow" conformation of RC occurs when the RC preparation is frozen under actinic light. An explanation of the temperature dependencies of tryptophan fluorescence lifetimes in RC proteins was made under the assumption that temperature changes affect mainly the electron transfer from the indole ring of the tryptophan molecule to the nearest amide or carboxyl groups.
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Affiliation(s)
- Peter P Knox
- Department of Biophysics, Biological Faculty of the M.V. Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Vladimir V Gorokhov
- Department of Biophysics, Biological Faculty of the M.V. Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Boris N Korvatovskiy
- Department of Biophysics, Biological Faculty of the M.V. Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Eugene P Lukashev
- Department of Biophysics, Biological Faculty of the M.V. Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Sergey N Goryachev
- Department of Biophysics, Biological Faculty of the M.V. Lomonosov Moscow State University, 119991 Moscow, Russia
| | - Vladimir Z Paschenko
- Department of Biophysics, Biological Faculty of the M.V. Lomonosov Moscow State University, 119991 Moscow, Russia.
| | - Andrew B Rubin
- Department of Biophysics, Biological Faculty of the M.V. Lomonosov Moscow State University, 119991 Moscow, Russia
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21
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Malarkani K, Sarkar I, Selvam S. Denaturation studies on bovine serum albumin-bile salt system: Bile salt stabilizes bovine serum albumin through hydrophobicity. J Pharm Anal 2018; 8:27-36. [PMID: 29568665 PMCID: PMC5859114 DOI: 10.1016/j.jpha.2017.06.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2016] [Revised: 06/14/2017] [Accepted: 06/21/2017] [Indexed: 11/25/2022] Open
Abstract
Protein denaturation is under intensive research, since it leads to neurological disorders of severe consequences. Avoiding denaturation and stabilizing the proteins in their native state is of great importance, especially when proteins are used as drug molecules or vaccines. It is preferred to add pharmaceutical excipients in protein formulations to avoid denaturation and thereby stabilize them. The present study aimed at using bile salts (BSs), a group of well-known drug delivery systems, for stabilization of proteins. Bovine serum albumin (BSA) was taken as the model protein, whose association with two BSs, namely sodium cholate (NaC) and sodium deoxycholate (NaDC), was studied. Denaturation studies on the pre-formed BSA-BS systems were carried out under chemical and physical denaturation conditions. Urea was used as the chemical denaturant and BSA-BS systems were subjected to various temperature conditions to understand the thermal (physical) denaturation. With the denaturation conditions prescribed here, the data obtained is informative on the association of BSA-BS systems to be hydrophobic and this effect of hydrophobicity plays an important role in stabilizing the serum albumin in its native state under both chemical and thermal denaturation.
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Affiliation(s)
| | - Ivy Sarkar
- Department of Chemistry, Indian Institute of Technology Madras, Chennai 600036, India
| | - Susithra Selvam
- Department of Chemistry, Vel Tech University, Avadi, Chennai 600062, India
- Department of Chemistry, PSG College of Technology, Peelamedu, Coimbatore 641004, India
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22
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Abstract
The Escherichia coli chemotaxis protein CheY is a model receiver domain containing a native tryptophan residue that serves as a fluorescent probe for CheY autophosphorylation with small molecule phosphodonors. Here we describe fluorescence measurement of apparent bimolecular rate constants for reaction of wild type and mutant CheY with phosphodonors acetyl phosphate, phosphoramidate, or monophosphoimidazole. Step-by-step protocols to synthesize phosphoramidate (K+ salt) and monophosphoimidazole (Na+ salt), which are not commercially available, are provided. Key factors to consider in developing autophosphorylation assays for other response regulators are also discussed.
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Affiliation(s)
- Ruth E Silversmith
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC, USA
| | - Robert B Bourret
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC, USA.
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23
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Vasquez-Montes V, Gerhart J, King KE, Thévenin D, Ladokhin AS. Comparison of lipid-dependent bilayer insertion of pHLIP and its P20G variant. Biochim Biophys Acta Biomembr 2017; 1860:534-543. [PMID: 29138065 DOI: 10.1016/j.bbamem.2017.11.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 10/18/2017] [Accepted: 11/10/2017] [Indexed: 02/07/2023]
Abstract
The ability of the pH-Low Insertion Peptide (pHLIP) to insert into lipid membranes in a transbilayer conformation makes it an important tool for targeting acidic diseased tissues. pHLIP can also serve as a model template for thermodynamic studies of membrane insertion. We use intrinsic fluorescence and circular dichroism spectroscopy to examine the effect of replacing pHLIP's central proline on the pH-triggered lipid-dependent conformational switching of the peptide. We find that the P20G variant (pHLIP-P20G) has a higher helical propensity than the native pHLIP (pHLIP-WT), in both water:organic solvent mixtures and in the presence of lipid bilayers. Spectral shifts of tryptophan fluorescence reveal that with both pHLIP-WT and pHLIP-P20G, the deeply penetrating interfacial form (traditionally called State II) is populated only in pure phosphocholine bilayers. The presence of either anionic lipids or phosphatidylethanolamine leads to a much shallower penetration of the peptide (referred to here as State IIS, for "shallow"). This novel state can be differentiated from soluble state by a reduction in accessibility of tryptophans to acrylamide and by FRET to vesicles doped with Dansyl-PE, but not by a spectral shift in fluorescence emission. FRET experiments indicate free energies for interfacial partitioning range from 6.2 to 6.8kcal/mol and are marginally more favorable for pHLIP-P20G. The effective pKa for the insertion of both peptides depends on the lipid composition, but is always higher for pHLIP-P20G than for pHLIP-WT by approximately one pH unit, which corresponds to a difference of 1.3kcal/mol in free energy of protonation favoring insertion of pHLIP-P20G.
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Affiliation(s)
- Victor Vasquez-Montes
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, 66160, United States
| | - Janessa Gerhart
- Department of Chemistry, Lehigh University, Bethlehem, PA, 18015, United States
| | - Kelly E King
- Department of Chemistry, Lehigh University, Bethlehem, PA, 18015, United States
| | - Damien Thévenin
- Department of Chemistry, Lehigh University, Bethlehem, PA, 18015, United States
| | - Alexey S Ladokhin
- Department of Biochemistry and Molecular Biology, University of Kansas Medical Center, Kansas City, KS, 66160, United States.
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24
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Zelent B, Bialas C, Gryczynski I, Chen P, Chib R, Lewerissa K, Corradini MG, Ludescher RD, Vanderkooi JM, Matschinsky FM. Tryptophan Fluorescence Yields and Lifetimes as a Probe of Conformational Changes in Human Glucokinase. J Fluoresc 2017; 27:1621-1631. [PMID: 28432632 PMCID: PMC6025808 DOI: 10.1007/s10895-017-2099-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2017] [Accepted: 04/04/2017] [Indexed: 10/19/2022]
Abstract
Five variants of glucokinase (ATP-D-hexose-6-phosphotransferase, EC 2.7.1.1) including wild type and single Trp mutants with the Trp residue at positions 65, 99, 167 and 257 were prepared. The fluorescence of Trp in all locations studied showed intensity changes when glucose bound, indicating that conformational change occurs globally over the entire protein. While the fluorescence quantum yield changes upon glucose binding, the enzyme's absorption spectra, emission spectra and fluorescence lifetimes change very little. These results are consistent with the existence of a dark complex for excited state Trp. Addition of glycerol, L-glucose, sucrose, or trehalose increases the binding affinity of glucose to the enzyme and increases fluorescence intensity. The effect of these osmolytes is thought to shift the protein conformation to a condensed, high affinity form. Based upon these results, we consider the nature of quenching of the Trp excited state. Amide groups are known to quench indole fluorescence and amides of the polypeptide chain make interact with excited state Trp in the relatively unstructured, glucose-free enzyme. Also, removal of water around the aromatic ring by addition of glucose substrate or osmolyte may reduce the quenching.
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Affiliation(s)
- Bogumil Zelent
- Department of Biochemistry and Biophysics and Diabetes Research Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
- Department of Food Science, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA.
| | - Chris Bialas
- Johnson Research Foundation, Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Ignacy Gryczynski
- Department of Cell Biology and Immunology, Center for Fluorescence Technologies and Nanomedicine, University of North Texas Health Science Center, Fort Worth, TX, USA
| | - Pan Chen
- Department of Biochemistry and Biophysics and Diabetes Research Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Rahul Chib
- Department of Food Science, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
| | - Karina Lewerissa
- Department of Food Science, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
| | - Maria G Corradini
- Department of Food Science, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
- Department of Food Science, University of Massachusetts Amherst, Massachusetts, MA, USA
| | - Richard D Ludescher
- Department of Food Science, Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
| | - Jane M Vanderkooi
- Johnson Research Foundation, Department of Biochemistry and Biophysics, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Franz M Matschinsky
- Department of Biochemistry and Biophysics and Diabetes Research Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.
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Sehanobish E, Dow BA, Davidson VL. Analytical Methods for Assessing the Effects of Site-Directed Mutagenesis on Protein-Cofactor and Protein-Protein Functional Relationships. Methods Mol Biol 2017; 1498:421-438. [PMID: 27709593 DOI: 10.1007/978-1-4939-6472-7_29] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
To completely understand the role of an amino acid residue that is targeted for site-directed mutagenesis a thorough analysis of the impact that the mutation has on the function of the protein is required. General methods for performing site-directed mutagenesis and expressing the recombinant protein variant are described. Protein-cofactor interactions are important because cofactors are often directly involved in facilitating catalysis by enzymes and in electron transfer by redox proteins. Many cofactors also have characteristic spectroscopic properties. As such, general methods are described to analyze the spectroscopic, redox and catalytic properties of protein-bound cofactors. Methods for assessing the effects of a mutation on protein-protein interactions are also described. Lastly, methods for assessing the overall structural integrity of the protein are described, as this is important to ensure that the mutation has not caused a global disruption of protein structure, rather than a specific effect on function.
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Affiliation(s)
- Esha Sehanobish
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, 6900 Lake Nona Blvd., Orlando, FL, 32827, USA
| | - Brian A Dow
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, 6900 Lake Nona Blvd., Orlando, FL, 32827, USA
| | - Victor L Davidson
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, 6900 Lake Nona Blvd., Orlando, FL, 32827, USA.
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26
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Fendley GA, Urbatsch IL, Sutton RB, Zoghbi ME, Altenberg GA. Nucleotide dependence of the dimerization of ATP binding cassette nucleotide binding domains. Biochem Biophys Res Commun 2016; 480:268-272. [PMID: 27765627 DOI: 10.1016/j.bbrc.2016.10.046] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Accepted: 10/16/2016] [Indexed: 10/20/2022]
Abstract
ATP-binding cassette proteins are ubiquitously present throughout all known genomes. Their basic functional unit possesses two transmembrane domains and two nucleotide-binding domains. The nucleotide-binding domains are responsible for ATP binding and hydrolysis, and their 3-dimensional structure is conserved across ATP-binding cassette proteins. Binding of ATP produces nucleotide-binding domain dimerization, a step necessary for hydrolysis. However, the possibility that nucleotide-binding domains bind and/or hydrolyze nucleotide triphosphates different from ATP has not been explored in detail. Here, we studied that possibility using M. jannaschii MJ0796, a prototypical ATP-binding cassette nucleotide-binding domain. We found that nucleotide-binding domain dimerization occurs as a result of binding to the natural nucleotide triphosphates ATP, GTP, CTP and UTP, and also to the analog ATP-γ-S. All the natural nucleotide triphosphates are hydrolyzed at similar rates, whereas ATP-γ-S is not hydrolyzed. We also found that the non-hydrolyzable ATP analog AMP-PNP, frequently assumed to produce the nucleotide-bound conformation, failed to elicit nucleotide-binding domain dimerization. Our results raise the possibility that not all the nucleotide binding sites of nucleotide-binding domains are occupied by ATP under physiological conditions, and that ATP is not always the nucleotide hydrolyzed to dissociate the nucleotide-binding domain dimers.
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Affiliation(s)
- Gregory A Fendley
- Department of Cell Physiology and Molecular Biophysics, Texas Tech University Health Sciences Center, Lubbock, TX 79430-6551, USA
| | - Ina L Urbatsch
- Center for Membrane Protein Research, Texas Tech University Health Sciences Center, Lubbock, TX 79430-6551, USA; Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Center, Lubbock, TX 79430-6540, USA
| | - Roger B Sutton
- Department of Cell Physiology and Molecular Biophysics, Texas Tech University Health Sciences Center, Lubbock, TX 79430-6551, USA; Center for Membrane Protein Research, Texas Tech University Health Sciences Center, Lubbock, TX 79430-6551, USA
| | - Maria E Zoghbi
- School of Natural Sciences, University of California, Merced, 4225 N. Hospital Road, Atwater, CA 95301, USA
| | - Guillermo A Altenberg
- Department of Cell Physiology and Molecular Biophysics, Texas Tech University Health Sciences Center, Lubbock, TX 79430-6551, USA; Center for Membrane Protein Research, Texas Tech University Health Sciences Center, Lubbock, TX 79430-6551, USA.
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27
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Sehgal P, Olesen C, Møller JV. Tryptophan Fluorescence Changes Related to Ca(2+)-ATPase Function. Methods Mol Biol 2016; 1377:227-30. [PMID: 26695036 DOI: 10.1007/978-1-4939-3179-8_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Fluorescence measurements as monitored with either extrinsic or intrinsic probes constitute important ways with which to study the molecular properties of macromolecules. With high-quality spectrofluorimeters, it is, e.g., possible kinetically to follow local conformational changes, induced by ligands and inhibitors, with a sensitivity that is unsurpassed by any other physicochemical technique. We demonstrate here with Ca(2+) and two specific inhibitors of SERCA how this can be done by measurements of the intrinsic fluorescence of the tryptophan residues of SERCA.
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Affiliation(s)
- Pankaj Sehgal
- Department of Biomedicine, Aarhus University, Aarhus C, Denmark.,Centre for Membrane Pumps in Cells and Disease, Danish National Research Foundation, Aarhus C, Denmark
| | - Claus Olesen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, Denmark.,Centre for Membrane Pumps in Cells and Disease, Danish National Research Foundation, Aarhus C, Denmark
| | - Jesper V Møller
- Department of Biomedicine, Aarhus University, Aarhus C, Denmark. .,Centre for Membrane Pumps in Cells and Disease, Danish National Research Foundation, Aarhus C, Denmark.
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28
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Giménez RE, Vargová V, Rey V, Turbay MBE, Abatedaga I, Morán Vieyra FE, Paz Zanini VI, Mecchia Ortiz JH, Katz NE, Ostatná V, Borsarelli CD. Interaction of singlet oxygen with bovine serum albumin and the role of the protein nano-compartmentalization. Free Radic Biol Med 2016; 94:99-109. [PMID: 26898504 DOI: 10.1016/j.freeradbiomed.2016.02.014] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/09/2015] [Revised: 02/13/2016] [Accepted: 02/15/2016] [Indexed: 12/30/2022]
Abstract
Singlet molecular oxygen ((1)O2) contributes to protein damage triggering biophysical and biochemical changes that can be related with aging and oxidative stress. Serum albumins, such as bovine serum albumin (BSA), are abundant proteins in blood plasma with different biological functions. This paper presents a kinetic and spectroscopic study of the (1)O2-mediated oxidation of BSA using the tris(2,2'-bipyridine)ruthenium(II) cation [Ru(bpy)3](2+) as sensitizer. BSA quenches efficiently (1)O2 with a total (chemical+physical interaction) rate constant kt(BSA)=7.3(±0.4)×10(8)M(-1)s(-1), where the chemical pathway represented 37% of the interaction. This efficient quenching by BSA indicates the participation of several reactive residues. MALDI-TOF MS analysis of intact BSA confirmed that after oxidation by (1)O2, the mass protein increased the equivalent of 13 oxygen atoms. Time-resolved emission spectra analysis of BSA established that Trp residues were oxidized to N'-formylkynurenine, being the solvent-accessible W134 preferentially oxidized by (1)O2 as compared with the buried W213. MS confirmed oxidation of at least two Tyr residues to form dihydroxyphenylalanine, with a global reactivity towards (1)O2 six-times lower than for Trp residues. Despite the lack of MS evidences, kinetic and chemical analysis also suggested that residues other than Trp and Tyr, e.g. Met, must react with (1)O2. Modeling of the 3D-structure of BSA indicated that the oxidation pattern involves a random distribution of (1)O2 into BSA; allowing also the interaction of (1)O2 with buried residues by its diffusion from the bulk solvent through interconnected internal hydrophilic and hydrophobic grooves.
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Affiliation(s)
- Rodrigo E Giménez
- Instituto de Bionanotecnología, INBIONATEC-CONICET, Universidad Nacional de Santiago del Estero (UNSE), RN9, Km 1125, G4206XCP Santiago del Estero, Argentina
| | - Veronika Vargová
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, 612 65 Brno, Czech Republic
| | - Valentina Rey
- Instituto de Bionanotecnología, INBIONATEC-CONICET, Universidad Nacional de Santiago del Estero (UNSE), RN9, Km 1125, G4206XCP Santiago del Estero, Argentina
| | - M Beatriz Espeche Turbay
- Instituto de Bionanotecnología, INBIONATEC-CONICET, Universidad Nacional de Santiago del Estero (UNSE), RN9, Km 1125, G4206XCP Santiago del Estero, Argentina
| | - Inés Abatedaga
- Instituto de Bionanotecnología, INBIONATEC-CONICET, Universidad Nacional de Santiago del Estero (UNSE), RN9, Km 1125, G4206XCP Santiago del Estero, Argentina
| | - Faustino E Morán Vieyra
- Instituto de Bionanotecnología, INBIONATEC-CONICET, Universidad Nacional de Santiago del Estero (UNSE), RN9, Km 1125, G4206XCP Santiago del Estero, Argentina
| | - Verónica I Paz Zanini
- Instituto de Bionanotecnología, INBIONATEC-CONICET, Universidad Nacional de Santiago del Estero (UNSE), RN9, Km 1125, G4206XCP Santiago del Estero, Argentina
| | - Juan H Mecchia Ortiz
- INQUINOA-CONICET, Instituto de Química Física, Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán, Ayacucho 471, T4000INI San Miguel de Tucumán, Argentina
| | - Néstor E Katz
- INQUINOA-CONICET, Instituto de Química Física, Facultad de Bioquímica, Química y Farmacia, Universidad Nacional de Tucumán, Ayacucho 471, T4000INI San Miguel de Tucumán, Argentina
| | - Veronika Ostatná
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Královopolská 135, 612 65 Brno, Czech Republic
| | - Claudio D Borsarelli
- Instituto de Bionanotecnología, INBIONATEC-CONICET, Universidad Nacional de Santiago del Estero (UNSE), RN9, Km 1125, G4206XCP Santiago del Estero, Argentina.
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Kameel NIA, Wong YH, Shuib AS, Tayyab S. Conformational analysis of champedak galactose-binding lectin under different urea concentrations. Plant Physiol Biochem 2016; 98:57-63. [PMID: 26642433 DOI: 10.1016/j.plaphy.2015.11.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Revised: 11/02/2015] [Accepted: 11/16/2015] [Indexed: 06/05/2023]
Abstract
Conformational analysis of champedak galactose-binding (CGB) lectin under different urea concentrations was studied in phosphate-buffered saline (pH 7.2) using far-ultraviolet circular dichroism (far-UV CD), tryptophan (Trp) fluorescence and ANS fluorescence. In all cases, CGB lectin displayed a two-step, three-state transition. The first transition (from the native state to the intermediate state) started at ∼2.0 M urea and ended at ∼4.5 M urea, while the second transition (from the intermediate state to the completely denatured state) was characterized by the start- and end-points at ∼5.75 M and ∼7.5 M urea, respectively, when analyzed by the emission maximum of Trp fluorescence. A marked increase in the Trp fluorescence, ANS fluorescence and -CD values at 218 nm (-CD218 nm) represented the first transition, whereas a decrease in these parameters defined the second transition. On the other hand, emission maximum of the Trp fluorescence showed a continuous increase throughout the urea concentration range. Transformation of tetramer into monomer represented the first transition, whereas the second transition reflected the unfolding of monomer. Far-UV CD, Trp fluorescence and ANS fluorescence spectra were used to characterize the native, the intermediate and the completely denatured states of CGB lectin, obtained at 0.0 M, 5.0 M and 9.0 M urea, respectively. The intermediate state was characterized by the presence of higher secondary structures, increased ANS binding as well as increased Trp fluorescence intensity. A gradual decrease in the hemagglutination activity of CGB lectin was observed with increasing urea concentrations, showing complete loss at 4.0 M urea.
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Affiliation(s)
- Nurul Iman Ahamed Kameel
- Biomolecular Research Group, Biochemistry Programme, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia.
| | - Yin How Wong
- Biomolecular Research Group, Biochemistry Programme, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia.
| | - Adawiyah Suriza Shuib
- Biomolecular Research Group, Biochemistry Programme, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia.
| | - Saad Tayyab
- Biomolecular Research Group, Biochemistry Programme, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia.
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30
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Thistle J, Martinon D, Weers PMM. Helix 1 tryptophan variants in Galleria mellonella apolipophorin III. Chem Phys Lipids 2015; 193:18-23. [PMID: 26462904 DOI: 10.1016/j.chemphyslip.2015.10.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Revised: 09/21/2015] [Accepted: 10/05/2015] [Indexed: 01/19/2023]
Abstract
Apolipophorin III (apoLp-III) from Galleria mellonella is a critical apolipoprotein aiding in lipid transport and has gained considerable interest for a role in innate immunity. Both functions are likely related and form the rationale to gain a more detailed understanding of the lipid binding properties of this insect apolipoprotein. Tryptophan residues were introduced at positions 16, 20 or 24, all in helix 1 as it may play a critical role in the initial steps of lipid binding. Steady-state fluorescence analysis showed that each tryptophan displayed unique properties, indicating different environments both in lipid-free as in lipid-bound states, and demonstrating potential for use in lipid binding analysis. While α-helical contents of wild-type and the tryptophan variant proteins were similar, W20- and W24-apoLp-III displayed increased protein stability. These variants were significantly slower in their ability to convert phosphatidylcholine vesicles into discoidal lipoproteins, which was employed as a measure for lipid binding. In contrast, W16-apoLp-III displayed decreased protein stability but an order of magnitude higher rate of discoidal lipoprotein formation. This demonstrates an inverse correlation between protein stability and the ability to convert vesicles in discoidal lipoproteins. The most stable W20-apoLp-III variant displayed comprised LDL binding capabilities, indicating a partial loss of function. Thus, there is a delicate balance between helix bundle stability and the ability to bind lipids, and helix 1 may play a critical role in this process.
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Affiliation(s)
- Jake Thistle
- Department of Chemistry and Biochemistry, California State University Long Beach, CA 90840, USA
| | - Daisy Martinon
- Department of Chemistry and Biochemistry, California State University Long Beach, CA 90840, USA
| | - Paul M M Weers
- Department of Chemistry and Biochemistry, California State University Long Beach, CA 90840, USA.
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31
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Serrán-Aguilera L, Nuti R, López-Cara LC, Mezo MÁG, Macchiarulo A, Entrena A, Hurtado-Guerrero R. Pharmacophore-Based Virtual Screening to Discover New Active Compounds for Human Choline Kinase α1. Mol Inform 2015; 34:458-66. [PMID: 27490389 DOI: 10.1002/minf.201400140] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2014] [Accepted: 03/10/2015] [Indexed: 01/12/2023]
Abstract
Choline kinase (CK) catalyses the transfer of the ATP γ-phosphate to choline to generate phosphocholine and ADP in the presence of magnesium leading to the synthesis of phosphatidylcholine. Of the three isoforms of CK described in humans, only the α isoforms (HsCKα) are strongly associated with cancer and have been validated as drug targets to treat this disease. Over the years, a large number of Hemicholinium-3 (HC-3)-based HsCKα biscationic inhibitors have been developed though the relevant common features important for the biological function have not been defined. Here, selecting a large number of previous HC-3-based inhibitors, we discover through computational studies a pharmacophore model formed by five moieties that are included in the 1-benzyl-4-(N-methylaniline)pyridinium fragment. Using a pharmacophore-guided virtual screening, we then identified 6 molecules that showed binding affinities in the low μM range to HsCKα1. Finally, protein crystallization studies suggested that one of these molecules is bound to the choline and ATP-binding sites. In conclusion, we have developed a pharmacophore model that not only allowed us to dissect the structural important features of the previous HC-3 derivatives, but also enabled the identification of novel chemical tools with good ligand efficiencies to investigate the biological functions of HsCKα1.
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Affiliation(s)
- Lucía Serrán-Aguilera
- Department of Pharmaceutical and Organic Chemistry, Faculty of Pharmacy, University of Granada, Campus Cartuja, Granada 18071, Spain phone: +34 958 243848
| | - Roberto Nuti
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Perugia, Via del Liceo, 1, 06123 Perugia, Italy
| | - Luisa C López-Cara
- Department of Pharmaceutical and Organic Chemistry, Faculty of Pharmacy, University of Granada, Campus Cartuja, Granada 18071, Spain phone: +34 958 243848
| | - Miguel Á Gallo Mezo
- Department of Pharmaceutical and Organic Chemistry, Faculty of Pharmacy, University of Granada, Campus Cartuja, Granada 18071, Spain phone: +34 958 243848
| | - Antonio Macchiarulo
- Dipartimento di Scienze Farmaceutiche, Università degli Studi di Perugia, Via del Liceo, 1, 06123 Perugia, Italy.
| | - Antonio Entrena
- Department of Pharmaceutical and Organic Chemistry, Faculty of Pharmacy, University of Granada, Campus Cartuja, Granada 18071, Spain phone: +34 958 243848.
| | - Ramón Hurtado-Guerrero
- Institute of Biocomputation and Physics of Complex Systems (BIFI) and BIFI-IQFR (CSIC) Joint Unit, University of Zaragoza, Campus Río Ebro, Zaragoza 50018, Spain; Edificio I+D; Fundación ARAID, Edificio Pignatelli 36, Spain phones: +39 075 5855160; +34 976 762997.
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Goovaerts V, Stroobants K, Absillis G, Parac-Vogt TN. Eu(III) luminescence and tryptophan fluorescence spectroscopy as a tool for understanding interactions between hen egg white lysozyme and metal-substituted Keggin type polyoxometalates. J Inorg Biochem 2015; 150:72-80. [PMID: 25870147 DOI: 10.1016/j.jinorgbio.2015.03.015] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Revised: 03/17/2015] [Accepted: 03/26/2015] [Indexed: 01/11/2023]
Abstract
The interaction between the lacunary Keggin K7PW11O39, the Eu(III)-substituted Keggin K4EuPW11O39 (Eu-Keggin) and the Ce(IV)-substituted Keggin [Me2NH2]10[Ce(PW11O39)2] (Ce-Keggin) polyoxometalates (POMs), and the proteins hen egg white lysozyme (HEWL) and the structurally homologous α-lactalbumin (α-LA) was studied by steady state and time-resolved Eu(III) luminescence and tryptophan (Trp) fluorescence spectroscopy. The excitation spectrum of Eu-Keggin at lower concentrations ([Eu-Keggin]<100 μM) is dominated by a ligand-to-metal charge transfer band (291 nm). For higher concentrations ([Eu-Keggin]>250 μM) the (5)L6←(7)F0 transition becomes the most intense peak. In the absence of protein, the number of coordinated water molecules to the Eu(III) centre of Eu-Keggin is 4, indicating a 1:1 Eu(III):POM species. In the presence of phosphate buffer this number linearly decreases from 4 to 2 upon increasing phosphate buffer concentration. Upon addition of HEWL, there are no coordinated water molecules, suggesting interaction between Eu-Keggin and the protein surface. In addition, this interaction results in a more than threefold increase of the hypersensitive (5)D0→(7)F2 transition for the Eu-Keggin/HEWL mixture. The calculated association constant amounted to 2.2×10(2) M(-1) for the Eu-Keggin/HEWL complex. Tryptophan fluorescence quenching studies were performed and the quenching constants were calculated to be 9.1×10(4) M(-1), 4×10(4) M(-1) and 4.1×10(5) M(-1) for the lacunary Keggin/HEWL, the Eu-Keggin/HEWL and the Ce-Keggin/HEWL complexes, respectively. The number of bound POM molecules to HEWL was 1.04 for the lacunary Keggin POM, and 1.0 for Eu-Keggin, indicating the formation of a 1:1 POM/HEWL complex. The value of 1.38 for Ce-Keggin might indicate a transition from 1:1 to 1:2 interaction.
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Affiliation(s)
- Vincent Goovaerts
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Leuven, Belgium
| | - Karen Stroobants
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Leuven, Belgium
| | - Gregory Absillis
- Department of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Leuven, Belgium
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Lo SY, Säbel CE, Mapletoft JP, Siemann S. Influence of chemical denaturants on the activity, fold and zinc status of anthrax lethal factor. Biochem Biophys Rep 2015; 1:68-77. [PMID: 29124135 PMCID: PMC5668564 DOI: 10.1016/j.bbrep.2015.03.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Revised: 03/11/2015] [Accepted: 03/12/2015] [Indexed: 11/17/2022] Open
Abstract
Anthrax lethal factor (LF) is a zinc-dependent endopeptidase which, through a process facilitated by protective antigen, translocates to the host cell cytosol in a partially unfolded state. In the current report, the influence of urea and guanidine hydrochloride (GdnHCl) on LF׳s catalytic function, fold and metal binding was assessed at neutral pH. Both urea and GdnHCl were found to inhibit LF prior to the onset of unfolding, with the inhibition by the latter denaturant being a consequence of its ionic strength. With the exception of demetallated LF (apoLF) in urea, unfolding, as monitored by tryptophan fluorescence spectroscopy, was found to follow a two-state (native to unfolded) mechanism. Analysis of the metal status of LF with 4-(2-pyridylazoresorcinol) (PAR) following urea or GdnHCl exposure suggests the enzyme to be capable of maintaining its metal ion passed the observed unfolding transition in a chelator-inaccessible form. Although an increase in the concentration of the denaturants eventually allowed the chelator access to the protein׳s zinc ion, such process is not correlated with the release of the metal ion. Indeed, significant dissociation of the zinc ion from LF was not observed even at 6 M urea, and only high concentrations of GdnHCl (>3 M) were capable of inducing the release of the metal ion from the protein. Hence, the current study demonstrates not only the propensity of LF to tightly bind its zinc ion beyond the spectroscopically determined unfolding transition, but also the utility of PAR as a structural probe. Lethal factor (LF) is strongly inhibited by guanidine hydrochloride. Except of apoLF in urea, unfolding follows a two-state mechanism. LF shields and retains its zinc ion in an unfolded state. Pyridylazoresorcinol is a useful probe to assess metal accessibility and release.
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Key Words
- 4-(2-pyridylazo)resorcinol
- CD, circular dichroism
- Chemical denaturants
- DPA, dipicolinic acid
- EDTA, ethylenediaminetetraacetic acid
- EF, edema factor
- LF, anthrax lethal factor
- Lethal factor
- MWCO, molecular weight cut-off
- PA, protective antigen
- PAR, 4-(2-pyridylazo)resorcinol
- Protein folding
- S-pNA, lethal factor substrate
- SASA, solvent-accessible surface area
- SOD, superoxide dismutase
- Tryptophan fluorescence
- Zinc
- ZnLF, zinc-containing lethal factor
- cps, counts per second
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Affiliation(s)
- Suet Y. Lo
- Department of Chemistry and Biochemistry, Laurentian University, Sudbury, Ontario, Canada
| | - Crystal E. Säbel
- Bharti School of Engineering, Laurentian University, Sudbury, Ontario, Canada
| | | | - Stefan Siemann
- Department of Chemistry and Biochemistry, Laurentian University, Sudbury, Ontario, Canada
- Correspondence to: Department of Chemistry and Biochemistry, Laurentian University, 935 Ramsey Lake Road, Sudbury, Ontario, Canada P3E 2C6. Tel.: +1 705 675 1151; fax: +1 705 675 4844.
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Thomas S, Bakkes PJ, Smits SHJ, Schmitt L. Equilibrium folding of pro-HlyA from Escherichia coli reveals a stable calcium ion dependent folding intermediate. Biochim Biophys Acta 2014; 1844:1500-10. [PMID: 24865936 DOI: 10.1016/j.bbapap.2014.05.006] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Revised: 05/13/2014] [Accepted: 05/16/2014] [Indexed: 11/17/2022]
Abstract
HlyA from Escherichia coli is a member of the repeats in toxin (RTX) protein family, produced by a wide range of Gram-negative bacteria and secreted by a dedicated Type 1 Secretion System (T1SS). RTX proteins are thought to be secreted in an unfolded conformation and to fold upon secretion by Ca(2+) binding. However, the exact mechanism of secretion, ion binding and folding to the correct native state remains largely unknown. In this study we provide an easy protocol for high-level pro-HlyA purification from E. coli. Equilibrium folding studies, using intrinsic tryptophan fluorescence, revealed the well-known fact that Ca(2+) is essential for stability as well as correct folding of the whole protein. In the absence of Ca(2+), pro-HlyA adopts a non-native conformation. Such molecules could however be rescued by Ca(2+) addition, indicating that these are not dead-end species and that Ca(2+) drives pro-HlyA folding. More importantly, pro-HlyA unfolded via a two-state mechanism, whereas folding was a three-state process. The latter is indicative of the presence of a stable folding intermediate. Analysis of deletion and Trp mutants revealed that the first folding transition, at 6-7M urea, relates to Ca(2+) dependent structural changes at the extreme C-terminus of pro-HlyA, sensed exclusively by Trp914. Since all Trp residues of HlyA are located outside the RTX domain, our results demonstrate that Ca(2+) induced folding is not restricted to the RTX domain. Taken together, Ca(2+) binding to the pro-HlyA RTX domain is required to drive the folding of the entire protein to its native conformation.
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Affiliation(s)
- Sabrina Thomas
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Universitätsstr 1, 40225 Düsseldorf, Germany
| | - Patrick J Bakkes
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Universitätsstr 1, 40225 Düsseldorf, Germany
| | - Sander H J Smits
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Universitätsstr 1, 40225 Düsseldorf, Germany
| | - Lutz Schmitt
- Institute of Biochemistry, Heinrich Heine University Düsseldorf, Universitätsstr 1, 40225 Düsseldorf, Germany.
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Montecinos-Franjola F, James NG, Concha-Marambio L, Brunet JE, Lagos R, Monasterio O, Jameson DM. Single tryptophan mutants of FtsZ: nucleotide binding/exchange and conformational transitions. Biochim Biophys Acta 2014; 1844:1193-200. [PMID: 24704635 DOI: 10.1016/j.bbapap.2014.03.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Revised: 03/24/2014] [Accepted: 03/26/2014] [Indexed: 11/27/2022]
Abstract
Cell division protein FtsZ cooperatively self-assembles into straight filaments when bound to GTP. A set of conformational changes that are linked to FtsZ GTPase activity are involved in the transition from straight to curved filaments that eventually disassemble. In this work, we characterized the fluorescence of single Trp mutants as a reporter of the predicted conformational changes between the GDP- and GTP-states of Escherichia coli FtsZ. Steady-state fluorescence characterization showed the Trp senses different environments and displays low solvent accessibility. Time-resolved fluorescence data indicated that the main conformational changes in FtsZ occur at the interaction surface between the N and C domains, but also minor rearrangements were detected in the bulk of the N domain. Surprisingly, despite its location near the bottom protofilament interface at the C domain, the Trp 275 fluorescence lifetime did not report changes between the GDP and GTP states. The equilibrium unfolding of FtsZ features an intermediate that is stabilized by the nucleotide bound in the N-domain as well as by quaternary protein-protein interactions. In this context, we characterized the unfolding of the Trp mutants using time-resolved fluorescence and phasor plot analysis. A novel picture of the structural transition from the native state in the absence of denaturant, to the solvent-exposed unfolded state is presented. Taken together our results show that conformational changes between the GDP and GTP states of FtsZ, such as those observed in FtsZ unfolding, are restricted to the interaction surface between the N and C domains.
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Affiliation(s)
- Felipe Montecinos-Franjola
- Laboratorio de Biología Estructural y Molecular, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago 7800024, Chile.
| | - Nicholas G James
- Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii, Honolulu 96813, HI, USA.
| | - Luis Concha-Marambio
- Laboratorio de Biología Estructural y Molecular, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago 7800024, Chile.
| | - Juan E Brunet
- Instituto de Química, Facultad de Ciencias, Pontificia Universidad Católica de Valparaíso, Valparaíso 2373223, Chile.
| | - Rosalba Lagos
- Laboratorio de Biología Estructural y Molecular, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago 7800024, Chile.
| | - Octavio Monasterio
- Laboratorio de Biología Estructural y Molecular, Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Santiago 7800024, Chile.
| | - David M Jameson
- Department of Cell and Molecular Biology, John A. Burns School of Medicine, University of Hawaii, Honolulu 96813, HI, USA.
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Tognotti D, Gabellieri E, Morelli E, Cioni P. Temperature and pressure dependence of azurin stability as monitored by tryptophan fluorescence and phosphorescence. The case of F29A mutant. Biophys Chem 2013; 182:44-50. [PMID: 23816248 DOI: 10.1016/j.bpc.2013.06.005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2013] [Revised: 06/07/2013] [Accepted: 06/07/2013] [Indexed: 10/26/2022]
Abstract
The effects of a single-point, F29A, cavity-forming mutation on the unfolding thermodynamic parameters of azurin from Pseudomonas aeruginosa and on the internal dynamics of the protein fold under pressure were probed by the fluorescence and phosphorescence emission of Trp48, deeply buried in the compact hydrophobic core of the macromolecule. Pressure-induced unfolding, monitored by the shift in the fluorescence spectrum, led to a volume change of 70-90mlmol(-1). The difference in the unfolding volume between F29A and wild type azurin was smaller than the volume of the space theoretically created in the mutant, indicating that the cavity is, at least partially, filled with water molecules. The complex temperature dependence of the unfolding volume, for temperatures up to 20°C, suggests the formation of an expanded form of the protein and highlights how the packing efficiency of azurin appears to contribute to the magnitude of internal void volume at any given temperature. Changes in flexibility of the protein matrix around the chromophore were monitored by the intrinsic phosphorescence lifetime. At 40°C the application of pressure in the predenaturation range initially decreases the internal flexibility of azurin, the trend eventually reverting on approaching unfolding. The main difference between wild type and the cavity mutant is the inversion point which happens at 300MPa for wild type and at 150MPa for F29A. This suggests that, for the cavity mutant, pressure-induced internal hydration is more dominant than any compaction of the globular fold at relatively low pressures.
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Affiliation(s)
- Danika Tognotti
- Istituto di Biofisica, CNR, via G. Moruzzi 1, 56124 Pisa, Italy.
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