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Korkola NC, Stillman MJ. Human apo-metallothionein 1a is not a random coil: Evidence from guanidinium chloride, high temperature, and acidic pH unfolding studies. Biochim Biophys Acta Proteins Proteom 2024:141010. [PMID: 38490456 DOI: 10.1016/j.bbapap.2024.141010] [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] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 01/18/2024] [Accepted: 03/11/2024] [Indexed: 03/17/2024]
Abstract
The structures of apo-metallothioneins (apo-MTs) have been relatively elusive due to their fluxional, disordered state which has been difficult to characterize. However, intrinsically disordered protein (IDP) structures are rather diverse, which raises questions about where the structure of apo-MTs fit into the protein structural spectrum. In this paper, the unfolding transitions of apo-MT1a are discussed with respect to the effect of the chemical denaturant GdmCl, temperature conditions, and pH environment. Cysteine modification in combination with electrospray ionization mass spectrometry was used to probe the unfolding transition of apo-MT1a in terms of cysteine exposure. Circular dichroism spectroscopy was also used to monitor the change in secondary structure as a function of GdmCl concentration. For both of these techniques, cooperative unfolding was observed, suggesting that apo-MT1a is not a random coil. More GdmCl was required to unfold the protein backbone than to expose the cysteines, indicating that cysteine exposure is likely an early step in the unfolding of apo-MT1a. MD simulations complement the experimental results, suggesting that apo-MT1a adopts a more compact structure than expected for a random coil. Overall, these results provide further insight into the intrinsically disordered structure of apo-MT.
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Affiliation(s)
- Natalie C Korkola
- Department of Chemistry, The University of Western Ontario, 1151 Richmond St., London, ON N6A5B7, Canada
| | - Martin J Stillman
- Department of Chemistry, The University of Western Ontario, 1151 Richmond St., London, ON N6A5B7, Canada.
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2
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Andersson A, Linse S, Sparr E, Fornasier M, Jönsson P. The density of anionic lipids modulates the adsorption of α-Synuclein onto lipid membranes. Biophys Chem 2024; 305:107143. [PMID: 38100855 DOI: 10.1016/j.bpc.2023.107143] [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: 09/22/2023] [Revised: 11/20/2023] [Accepted: 11/28/2023] [Indexed: 12/17/2023]
Abstract
α-Synuclein is an intrinsically disordered presynaptic protein associated with Parkinson's disease. The physiological role of α-Synuclein is not fully understood, but the protein is known to interact with lipid membranes. We here study how membrane charge affects the adsorption of α-Synuclein to (i) supported lipid bilayers and (ii) small unilamellar vesicles with varying amounts of anionic lipids. The results showed that α-Synuclein adsorbs onto membranes containing ≥5% anionic phosphatidylserine (DOPS) lipids, but not to membranes containing ≤1% DOPS. The density of adsorbed α-Synuclein increased steadily with the DOPS content up to 20% DOPS, after which it leveled off. The vesicles were saturated with α-Synuclein at a 3-5 times higher protein density compared to the supported bilayers, which suggests that a more deformable membrane binds more α-Synuclein. Altogether, the results show that both membrane charge density and flexibility influence the association of α-Synuclein to lipid membranes.
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Affiliation(s)
| | - Sara Linse
- Department of Chemistry, Lund University, Lund, Sweden
| | - Emma Sparr
- Department of Chemistry, Lund University, Lund, Sweden
| | | | - Peter Jönsson
- Department of Chemistry, Lund University, Lund, Sweden.
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3
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Shankar M, Rani MSS, Gopi P, P A, Pandya P. Structure and energetics of serum protein complex of tea adulterant dye Bismarck brown Y using experimental and computational methods. Comput Biol Chem 2024; 108:107976. [PMID: 37956472 DOI: 10.1016/j.compbiolchem.2023.107976] [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: 09/25/2023] [Revised: 10/25/2023] [Accepted: 10/26/2023] [Indexed: 11/15/2023]
Abstract
Tea, a widely consumed aromatic beverage, is often adulterated with dyes such as Bismarck brown Y (C.I. 21000) (BBY), Prussian blue, and Plumbago, which pose potential health risks. The objective of this study is to analyze how the food dye BBY interacts with serum protein, bovine serum albumin (BSA). This study investigated the BBY-BSA interaction at the molecular level. Fluorescence spectroscopy results showed that the quenching of BSA by BBY is carried out by dynamic quenching mechanism. The displacement assay and molecular docking studies revealed that BBY binds at the flavanone binding site of BSA with hydrophobic interactions. Circular Dichroism results indicate the structural stability of the protein upon BBY binding. Molecular dynamics simulations demonstrated the stability of the complex in a dynamic solvent system, and quantum mechanics calculations showed slight conformational changes of the diaminophenyl ring due to increased hydrophobic interaction. The energetics of gas phase optimized and stable MD structures of BBY indicated similar values which further confirmed that the conformational changes were minor, and it also exhibited a moderate binding with BSA as shown by the MM/PBSA results. This study enhances our understanding of the molecular-level interactions between BBY and BSA, emphasizing the critical role of hydrophobic interactions.
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Affiliation(s)
- Manwi Shankar
- Amity Institute of Forensic Sciences, Amity University, Noida, Uttar Pradesh 201303, India.
| | - Majji Sai Sudha Rani
- Amity Institute of Forensic Sciences, Amity University, Noida, Uttar Pradesh 201303, India.
| | - Priyanka Gopi
- Amity Institute of Forensic Sciences, Amity University, Noida, Uttar Pradesh 201303, India.
| | - Arsha P
- Amity Institute of Forensic Sciences, Amity University, Noida, Uttar Pradesh 201303, India.
| | - Prateek Pandya
- Amity Institute of Forensic Sciences, Amity University, Noida, Uttar Pradesh 201303, India.
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4
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Sankar TV, Saharay M, Santhosh D, Menon S, Raran-Kurussi S, Padmasree K. Biomolecular interaction of purified recombinant Arabidopsis thaliana's alternative oxidase 1A with TCA cycle metabolites: Biophysical and molecular docking studies. Int J Biol Macromol 2024; 258:128814. [PMID: 38114006 DOI: 10.1016/j.ijbiomac.2023.128814] [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: 04/14/2023] [Revised: 11/08/2023] [Accepted: 12/13/2023] [Indexed: 12/21/2023]
Abstract
In higher plants, the mitochondrial alternative oxidase (AOX) pathway plays an essential role in maintaining the TCA cycle/cellular carbon and energy balance under various physiological and stress conditions. Though the activation of AOX pathway upon exogenous addition of α-ketoacids/TCA cycle metabolites [pyruvate, α-ketoglutarate (α-KG), oxaloacetic acid (OAA), succinate and malic acid] to isolated mitochondria is known, the molecular mechanism of interaction of these metabolites with AOX protein is limited. The present study is designed to understand the biomolecular interaction of pure recombinant Arabidopsis thaliana AOX1A with TCA cycle metabolites under in vitro conditions using various biophysical and molecular docking studies. The binding of α-KG, fumaric acid and OAA to rAtAOX1A caused conformational change in the microenvironment of tryptophan residues as evidenced by red shift in the synchronous fluorescence spectra (∆λ = 60 nm). Besides, a decrease in conventional fluorescence emission spectra, tyrosine specific synchronous fluorescence spectra (∆λ = 15 nm) and α-helical content of CD spectra revealed the conformation changes in rAtAOX1A structure associated with binding of various TCA cycle metabolites. Further, surface plasmon resonance (SPR) and microscale thermophoresis (MST) studies revealed the binding affinity, while docking studies identified binding pocket residues, respectively, for these metabolites on rAtAOX1A.
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Affiliation(s)
- Tadiboina Veera Sankar
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad 500046, India
| | - Moumita Saharay
- Department of Systems and Computational Biology, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad 500046, India
| | - Dharawath Santhosh
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad 500046, India
| | - Saji Menon
- Senior Field Application Scientist, Nanotemper Technologies GmbH, India
| | - Sreejith Raran-Kurussi
- TIFR Centre for Interdisciplinary Sciences, Tata Institute of Fundamental Research, Hyderabad, 500107, India
| | - Kollipara Padmasree
- Department of Biotechnology and Bioinformatics, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad 500046, India.
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Korkola NC, Stillman MJ. Structural motifs in the early metallation steps of Zn(II) and Cd(II) binding to apo-metallothionein 1a. J Inorg Biochem 2024; 251:112429. [PMID: 38000179 DOI: 10.1016/j.jinorgbio.2023.112429] [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: 09/19/2023] [Revised: 10/26/2023] [Accepted: 11/12/2023] [Indexed: 11/26/2023]
Abstract
Many proteins require a metal cofactor to function and these metals are often involved in the protein folding process. The protein metallothionein (MT) has a dynamic structure capable of binding to a variety of metals with different stoichiometries. The most well-understood structure is the seven-metal, two domain structure formed upon metallation using Zn(II) or Cd(II). However, the partially metallated states and the pathways to form these clusters are less well-understood, although it is known that the pathways are pH dependent. Using stopped flow methods, it is shown that the metallation rates of the less cooperative Zn(II) binding pathway is much more impacted by low pH conditions that that of the more cooperative Cd(II) binding pathway. Electrospray ionization mass spectrometry (ESI-MS) methods reveal specific mixtures of bridging and terminally bound MxSy structures form in the first few metallation steps. Using a combination of methods, the data show that the result of unfolding this intrinsically disordered apo-MT structure using guanidinium chloride is that the formation of preliminary bridging structures that form in the first few metallation steps is impeded. The data show that more terminally bound structures form. Our conclusion is that the compact conformation of the native apo-MT at physiological pH allows for rapid formation of complex metal-thiolate structures with high affinity that provides protection from oxidation, a function that is suppressed upon unfolding. Overall, these results highlight both the importance of the apo-MT structure in the metallation pathway, but also the differences in Zn(II) and Cd(II) binding under different conditions.
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Affiliation(s)
- Natalie C Korkola
- Department of Chemistry, The University of Western Ontario, 1151 Richmond St., London, ON N6A5B7, Canada
| | - Martin J Stillman
- Department of Chemistry, The University of Western Ontario, 1151 Richmond St., London, ON N6A5B7, Canada.
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Kumari N, Singh D, Singh P, Mishra A, Gond C, Ojha H, Tiwari AK. Biological Evaluation and Binding Mechanism of 5-HT 7 Specific Arylpiperazinyl-Alkyl Benzothiazolone: Radiobiology and Photo-physical Studies. J Fluoresc 2024; 34:341-352. [PMID: 37249676 DOI: 10.1007/s10895-023-03266-4] [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: 01/26/2023] [Accepted: 05/09/2023] [Indexed: 05/31/2023]
Abstract
Diversely substituted methoxy derivatives of arylpiperazinyl-alkyl benzothiazolone has been evaluated as specific probe for 5HT7. To determine the best methoxy derivative for 5HT7 receptor affinity, we synthesised a number of 2-benzothiazolone arylalkyl piperazine derivatives. In-vitro/vivo studies with C-2 substituted [11C]ABT showed 5HT7 specific binding. The radiochemical purity of [11C]ABT was found to be more than 99% with radiochemical stability persistence for more than 1.5 hr at 25 °C. The interaction of BSA and ABT has been analysed by photophysical studies for better understanding of properties such as adsortion, distribution, metabolism and elemination (ADME). The interaction between ABT and BSA was analyzed by using the UV-vis and fluorescence spectra. UV-vis spectra analyzed the changes in primary structure of BSA on its interaction with ABT. ABT showed quenched fluorescence emission intensity of tryptophan residues in BSA via static quenching mechanism. This study might help to understand how ABT binds to serum protein or subsequently to know the ADME of this drug candidate.
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Affiliation(s)
- Neelam Kumari
- Department of Chemistry, Babasaheb Bhimrao Ambedkar University, Uttar Pradesh, Lucknow, 226025, India
- CBRN Protection and decontamination research group, Division of Cyclotron and Radiological, Nuclear and Imaging Sciences, Institute of Nuclear Medicine and Allied Sciences, Timarpur, 110054, Delhi, India
- Department of Chemistry, Sri Venkateswara College, University of Delhi, Benito JuarezMarg, New Delhi, 110021, India
| | - Deepika Singh
- Department of Chemistry, Babasaheb Bhimrao Ambedkar University, Uttar Pradesh, Lucknow, 226025, India
| | - Priya Singh
- Department of Chemistry, Babasaheb Bhimrao Ambedkar University, Uttar Pradesh, Lucknow, 226025, India
| | - Akanksha Mishra
- Department of Chemistry, Babasaheb Bhimrao Ambedkar University, Uttar Pradesh, Lucknow, 226025, India
| | - Chandraprakash Gond
- Department of Chemistry, Babasaheb Bhimrao Ambedkar University, Uttar Pradesh, Lucknow, 226025, India
| | - Himanshu Ojha
- CBRN Protection and decontamination research group, Division of Cyclotron and Radiological, Nuclear and Imaging Sciences, Institute of Nuclear Medicine and Allied Sciences, Timarpur, 110054, Delhi, India
| | - Anjani Kumar Tiwari
- Department of Chemistry, Babasaheb Bhimrao Ambedkar University, Uttar Pradesh, Lucknow, 226025, India.
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Fleming AM, Omaga CA, Burrows CJ. NEIL3 promoter G-quadruplex with oxidatively modified bases shows magnesium-dependent folding that stalls polymerase bypass. Biochimie 2023; 214:156-166. [PMID: 37437684 PMCID: PMC10592359 DOI: 10.1016/j.biochi.2023.07.001] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 06/29/2023] [Accepted: 07/03/2023] [Indexed: 07/14/2023]
Abstract
Oxidative stress unleashes reactive species capable of oxidizing 2'-deoxyguanosine (G) nucleotides in G-rich sequences of the genome, such as the potential G-quadruplex forming sequencing (PQS) in the NEIL3 gene promoter. Oxidative modification of G yields 8-oxo-7,8-dihydro-2'-deoxyguanosine (OG) that can be further oxidized to hydantoin products. Herein, OG was synthesized into the NEIL3 PQS that was allowed to fold to a G-quadruplex (G4) in K+ ion solutions with varying amounts of Mg2+ in the physiological range. The Mg2+ dependency in the oxidatively modified NEIL3 G4 to stall a replicative DNA polymerase was evaluated. The polymerase was found to stall at the G4 or OG, as well as continue to full-length extension with dependency on the location of the modification and the concentration of Mg2+. To provide some clarity on these findings, OG or the hydantoins were synthesized in model NEIL3 G4 folding sequences at the positions of the polymerase study. The model G4 sequences were allowed to fold in K+ ion solutions with varying levels of Mg2+ to identify how the presence of the divalent metal impacted G4 folding depending on the location of the modification. The presence of Mg2+ either caused the transition of the NEIL3 G4 folds from an antiparallel to parallel orientation of the strands or had no impact. Structural models are proposed to understand the findings using the literature as a guide. The biological significance of the results is discussed.
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Affiliation(s)
- Aaron M Fleming
- Department of Chemistry, University of Utah, Salt Lake City, UT, 84112-0850, USA
| | - Carla A Omaga
- Department of Chemistry, University of Utah, Salt Lake City, UT, 84112-0850, USA
| | - Cynthia J Burrows
- Department of Chemistry, University of Utah, Salt Lake City, UT, 84112-0850, USA.
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8
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Takeda Y, Ohtsu I, Suzuki T, Nakasone Y, Fushimi K, Ikeuchi M, Terazima M, Dohra H, Narikawa R. Conformational change in an engineered biliverdin-binding cyanobacteriochrome during the photoconversion process. Arch Biochem Biophys 2023; 745:109715. [PMID: 37549803 DOI: 10.1016/j.abb.2023.109715] [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: 03/17/2023] [Revised: 08/02/2023] [Accepted: 08/05/2023] [Indexed: 08/09/2023]
Abstract
Cyanobacteriochromes (CBCRs) derived from cyanobacteria are linear-tetrapyrrole-binding photoreceptors related to the canonical red/far-red reversible phytochrome photoreceptors. CBCRs contain chromophore-binding cGMP-specific phosphodiesterase/adenylate cyclase/FhlA (GAF) domains that are highly diverse in their primary sequences and are categorized into many subfamilies. Among this repertoire, the biliverdin (BV)-binding CBCR GAF domains receive considerable attention for their in vivo optogenetic and bioimaging applications because BV is a mammalian intrinsic chromophore and can absorb far-red light that penetrates deep into the mammalian body. The typical BV-binding CBCR GAF domain exhibits reversible photoconversion between far-red-absorbing dark-adapted and orange-absorbing photoproduct states. Herein, we applied various biochemical and spectral studies to identify the details of the conformational change during this photoconversion process. No oligomeric state change was observed, whereas the surface charge would change with a modification of the α-helix structures during the photoconversion process. Combinatorial analysis using partial protease digestion and mass spectrometry identified the region where the conformational change occurred. These results provide clues for the future development of optogenetic tools.
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Affiliation(s)
- Yuka Takeda
- Graduate School of Science and Technology, Shizuoka University, 836 Ohya, Suruga, Shizuoka, 422-8529, Japan
| | - Itsuki Ohtsu
- Graduate School of Science and Technology, Shizuoka University, 836 Ohya, Suruga, Shizuoka, 422-8529, Japan
| | - Takahisa Suzuki
- Graduate School of Biological Sciences, Faculty of Science, Tokyo Metropolitan University, 1-1 Minami-Ohsawa, Hachioji, Tokyo, 192-0397, Japan
| | - Yusuke Nakasone
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, 606-8502, Japan
| | - Keiji Fushimi
- Graduate School of Science, Technology and Innovation, Kobe University, Hyogo, 657-0013, Japan
| | - Masahiko Ikeuchi
- Graduate School of Biological Sciences, Faculty of Science, Tokyo Metropolitan University, 1-1 Minami-Ohsawa, Hachioji, Tokyo, 192-0397, Japan
| | - Masahide Terazima
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, 606-8502, Japan
| | - Hideo Dohra
- Graduate School of Science and Technology, Shizuoka University, 836 Ohya, Suruga, Shizuoka, 422-8529, Japan; Research Institute of Green Science and Technology, Shizuoka University, 836 Ohya, Suruga, Shizuoka, 422-8529, Japan
| | - Rei Narikawa
- Graduate School of Biological Sciences, Faculty of Science, Tokyo Metropolitan University, 1-1 Minami-Ohsawa, Hachioji, Tokyo, 192-0397, Japan.
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9
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Krokengen OC, Raasakka A, Kursula P. The intrinsically disordered protein glue of the myelin major dense line: Linking AlphaFold2 predictions to experimental data. Biochem Biophys Rep 2023; 34:101474. [PMID: 37153862 PMCID: PMC10160357 DOI: 10.1016/j.bbrep.2023.101474] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 03/31/2023] [Accepted: 04/19/2023] [Indexed: 05/10/2023] Open
Abstract
Numerous human proteins are classified as intrinsically disordered proteins (IDPs). Due to their physicochemical properties, high-resolution structural information about IDPs is generally lacking. On the other hand, IDPs are known to adopt local ordered structures upon interactions with e.g. other proteins or lipid membrane surfaces. While recent developments in protein structure prediction have been revolutionary, their impact on IDP research at high resolution remains limited. We took a specific example of two myelin-specific IDPs, the myelin basic protein (MBP) and the cytoplasmic domain of myelin protein zero (P0ct). Both of these IDPs are crucial for normal nervous system development and function, and while they are disordered in solution, upon membrane binding, they partially fold into helices, being embedded into the lipid membrane. We carried out AlphaFold2 predictions of both proteins and analysed the models in light of experimental data related to protein structure and molecular interactions. We observe that the predicted models have helical segments that closely correspond to the membrane-binding sites on both proteins. We furthermore analyse the fits of the models to synchrotron-based X-ray scattering and circular dichroism data from the same IDPs. The models are likely to represent the membrane-bound state of both MBP and P0ct, rather than the conformation in solution. Artificial intelligence-based models of IDPs appear to provide information on the ligand-bound state of these proteins, instead of the conformers dominating free in solution. We further discuss the implications of the predictions for mammalian nervous system myelination and their relevance to understanding disease aspects of these IDPs.
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Affiliation(s)
| | - Arne Raasakka
- Department of Biomedicine, University of Bergen, Norway
| | - Petri Kursula
- Department of Biomedicine, University of Bergen, Norway
- Faculty of Biochemistry and Molecular Medicine & Biocenter Oulu, Oulu, Finland
- Corresponding author. Department of Biomedicine, University of Bergen, Norway.
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Kerler Y, Sass S, Hille C, Menger MM. Determination of Aptamer Structure Using Circular Dichroism Spectroscopy. Methods Mol Biol 2023; 2570:119-28. [PMID: 36156778 DOI: 10.1007/978-1-0716-2695-5_9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
G-quadruplexes can be important as three-dimensional structures for aptamers as they improve the properties of the nucleic acids like higher nuclease degradation resistance. For the characterization of the quadruplex type and its formation, circular dichroism (CD) spectroscopy is one of the most common used identification methods. It is possible to differentiate the parallel and antiparallel G-quadruplex forms as well as the different number of nucleic acid strands by very specific CD spectral patterns at distinct absorption wavelengths. In this chapter, the protocol describes the model characterization of the anthracycline aptamer DRN-10 by CD spectroscopy, in order to show the usefulness and simple handling of this method for analyzing three-dimensional nucleic acid structures.
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11
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Bhuvanachandra B, Sivaramakrishna D, Alim S, Swamy MJ, Podile AR. Deciphering the thermotolerance of chitinase O from Chitiniphilus shinanonensis by in vitro and in silico studies. Int J Biol Macromol 2022; 210:44-52. [PMID: 35537581 DOI: 10.1016/j.ijbiomac.2022.05.013] [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: 02/22/2022] [Revised: 05/01/2022] [Accepted: 05/02/2022] [Indexed: 11/05/2022]
Abstract
Biochemical and biophysical studies revealed that chitinase O from Chitiniphilus shinanonensis (CsChiO) exhibits considerable thermotolerance, possibly due to the formation of a stable structural conformation. CsChiO is an exochitinase with a temperature optimum of 70 °C. The secondary structures of CsChiO and its catalytic domain (Cat-CsChiO) are only marginally affected upon heating up to 90 °C, as revealed by circular dichroism (CD) spectroscopy. Differential scanning calorimetric (DSC) studies revealed that CsChiO exhibits two endothermic transitions at ca. 51 °C (Tm1) and 59 °C (Tm2), whereas Cat-CsChiO shows a single endothermic transition at 52 °C. Together, the CD and DSC analyses suggested that the catalytic domain of CsChiO undergoes a thermotropic transition at ~52 °C from native state to another stable structural conformation. Results from molecular dynamic simulations corroborated that Cat-CsChiO adopts a stable structural conformation above 50 °C by partial unfolding. Thermotolerant CsChiO would be useful for the conversion of chitin, which is highly abundant, to biologically active COS. This study unveiled the adaptability of enzymes/proteins in nature to perform biological functions at elevated temperatures.
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Affiliation(s)
- Bhoopal Bhuvanachandra
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad 500 046, Telangana, India
| | - Dokku Sivaramakrishna
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad 500 046, Telangana, India
| | - Sk Alim
- School of Chemistry, University of Hyderabad, Gachibowli, Hyderabad 500 046, Telangana, India
| | - Musti J Swamy
- School of Chemistry, University of Hyderabad, Gachibowli, Hyderabad 500 046, Telangana, India
| | - Appa Rao Podile
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Gachibowli, Hyderabad 500 046, Telangana, India.
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12
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Feng X, Liao D, Sun L, Feng S, Wu S, Lan P, Wang Z, Lan X. Exploration of interaction between angiotensin I-converting enzyme (ACE) and the inhibitory peptide from Wakame (Undaria pinnatifida). Int J Biol Macromol 2022; 204:193-203. [PMID: 35090938 DOI: 10.1016/j.ijbiomac.2022.01.114] [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: 10/16/2021] [Revised: 01/04/2022] [Accepted: 01/18/2022] [Indexed: 11/18/2022]
Abstract
The interaction between angiotensin I-converting enzyme (ACE) and the inhibitory peptide KNFL from Wakame was explored using isothermal titration calorimetry, multiple spectroscopic techniques and molecular dynamics simulations, and an inhibition model was established based on free energy binding theory. The experiments revealed that the binding of KNFL to ACE was a spontaneous exothermic process driven by enthalpy and entropy and occurred via multiple binding sites to form stable complexes. The complexes may be formed through multiple steps of inducing fit and conformational selection. The peptide KNFL had a fluorescence quenching effect on ACE and its addition not only affected the microenvironment around the ACE Trp and Tyr residues, but also increased the diameter and altered the conformation of ACE. This study should prove useful for improving our understanding of the mechanism of ACE inhibitory peptides.
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Affiliation(s)
- Xuezhen Feng
- Guangxi Key Laboratory of Petrochemical Resource Processing and Process Intensification Technology, School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, People's Republic of China; Medical College, Guangxi University of Science and Technology, Liuzhou, Guangxi 545006, People's Republic of China
| | - Dankui Liao
- Guangxi Key Laboratory of Petrochemical Resource Processing and Process Intensification Technology, School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, People's Republic of China.
| | - Lixia Sun
- Guangxi Key Laboratory of Petrochemical Resource Processing and Process Intensification Technology, School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, People's Republic of China
| | - Shuzhen Feng
- Guangxi Key Laboratory of Petrochemical Resource Processing and Process Intensification Technology, School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, People's Republic of China
| | - Shanguang Wu
- Medical College, Guangxi University of Science and Technology, Liuzhou, Guangxi 545006, People's Republic of China
| | - Ping Lan
- Guangxi Key Laboratory of Polysaccharide Materials and Modifications, School of Chemistry and Chemical Engineering, Guangxi University for Nationalities, Nanning 530008, People's Republic of China
| | - Zefen Wang
- Guangxi Key Laboratory of Petrochemical Resource Processing and Process Intensification Technology, School of Chemistry and Chemical Engineering, Guangxi University, Nanning 530004, People's Republic of China
| | - Xiongdiao Lan
- Guangxi Key Laboratory of Polysaccharide Materials and Modifications, School of Chemistry and Chemical Engineering, Guangxi University for Nationalities, Nanning 530008, People's Republic of China
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13
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Imamura T, Isozumi N, Higashimura Y, Koga H, Segawa T, Desaka N, Takagi H, Matsumoto K, Ohki S, Mori M. Red-Beet Betalain Pigments Inhibit Amyloid-β Aggregation and Toxicity in Amyloid-β Expressing Caenorhabditis elegans. Plant Foods Hum Nutr 2022; 77:90-97. [PMID: 35088214 DOI: 10.1007/s11130-022-00951-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 01/16/2022] [Indexed: 06/14/2023]
Abstract
Betalain pigments are mainly produced by plants belonging to the order of Caryophyllales. Betalains exhibit strong antioxidant activity and responds to environmental stimuli and stress in plants. Recent reports of antioxidant, anti-inflammatory and anti-cancer properties of betalain pigments have piqued interest in understanding their biological functions. We investigated the effects of betalain pigments (betanin and isobetanin) derived from red-beet on amyloid-β (Aβ) aggregation, which causes Alzheimer's disease. Non-specific inhibition of Aβ aggregation against Aβ40 and Aβ42 by red-beet betalain pigments, in vitro was demonstrated using the thioflavin t fluorescence assay, circular dichroism spectroscopy analysis, transmission electron microscopy and nuclear magnetic resonance (NMR) analysis. Furthermore, we examined the ability of red-beet betalain pigments to interfere with Aβ toxicity by using the transgenic Caenorhabditis elegans model, which expresses the human Aβ42 protein intracellularly within the body wall muscle. It responds to Aβ-toxicity with paralysis and treatment with 50 μM red-beet betalain pigments significantly delayed the paralysis of C. elegans. These results suggest that betalain pigments reduce Aβ-induced toxicity.
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Affiliation(s)
- Tomohiro Imamura
- Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, 308-1 Suematsu, Nonoichi, Ishikawa, 921-8836, Japan.
| | - Noriyoshi Isozumi
- Center for Nano Materials and Technology (CNMT), Japan Advanced Institute of Science and Technology (JAIST), 1-1 Asahidai, Nomi, Ishikawa, 923-1292, Japan
| | - Yasuki Higashimura
- Department of Food Science, Ishikawa Prefectural University, 308-1 Suematsu, Nonoichi, Ishikawa, 921-8836, Japan
| | - Hironori Koga
- Department of Bioproduction Science, Ishikawa Prefectural University, 308-1 Suematsu, Nonoichi, Ishikawa, 921-8836, Japan
| | - Tenta Segawa
- Department of Bioproduction Science, Ishikawa Prefectural University, 308-1 Suematsu, Nonoichi, Ishikawa, 921-8836, Japan
| | - Natsumi Desaka
- Department of Food Science, Ishikawa Prefectural University, 308-1 Suematsu, Nonoichi, Ishikawa, 921-8836, Japan
| | - Hiroki Takagi
- Department of Bioproduction Science, Ishikawa Prefectural University, 308-1 Suematsu, Nonoichi, Ishikawa, 921-8836, Japan
| | - Kenji Matsumoto
- Department of Food Science, Ishikawa Prefectural University, 308-1 Suematsu, Nonoichi, Ishikawa, 921-8836, Japan
| | - Shinya Ohki
- Center for Nano Materials and Technology (CNMT), Japan Advanced Institute of Science and Technology (JAIST), 1-1 Asahidai, Nomi, Ishikawa, 923-1292, Japan
| | - Masashi Mori
- Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, 308-1 Suematsu, Nonoichi, Ishikawa, 921-8836, Japan.
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14
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Gomes Ramalli S, John Miles A, Janes RW, Wallace BA. The PCDDB (Protein Circular Dichroism Data Bank): A Bioinformatics Resource for Protein Characterisations and Methods Development. J Mol Biol 2022; 434:167441. [PMID: 34999124 DOI: 10.1016/j.jmb.2022.167441] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [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: 11/21/2021] [Revised: 12/19/2021] [Accepted: 01/01/2022] [Indexed: 12/20/2022]
Abstract
The Protein Circular Dichroism Data Bank (PCDDB) [https://pcddb.cryst.bbk.ac.uk] is an established resource for the biological, biophysical, chemical, bioinformatics, and molecular biology communities. It is a freely-accessible repository of validated protein circular dichroism (CD) spectra and associated sample and other metadata, with entries having links to other bioinformatics resources including, amongst others, structure (PDB) and sequence (UniProt) databases, as well as to published papers which produced the data and cite the database entries. It includes primary (unprocessed) and final (processed) spectral data, which are available in both text and pictorial formats, as well as detailed sample and validation information produced for each of the entries. Recently the metadata content associated with each of the entries, as well as the number and structural breadth of the protein components included, have been expanded. The PCDDB includes data on both wild-type and mutant proteins, and because CD studies primarily examine proteins in solution, it also contains examples of the effects of different environments on their structures, plus thermal unfolding/folding series. Methods for both sequence and spectral comparisons are included. The data included in the PCDDB complement results from crystal, cryo-electron microscopy, NMR spectroscopy, bioinformatics characterisations and classifications, and other structural information available for the proteins via links to other databases. The entries in the PCDDB have been used for the development of new analytical methodologies, for interpreting spectral and other biophysical data, and for providing insight into structures and functions of individual soluble and membrane proteins and protein complexes.
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Affiliation(s)
- Sergio Gomes Ramalli
- Institute of Structural and Molecular Biology, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK
| | - Andrew John Miles
- Institute of Structural and Molecular Biology, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK
| | - Robert W Janes
- School of Biological and Behavioural Sciences, Queen Mary University of London, London E1 4NS, UK.
| | - B A Wallace
- Institute of Structural and Molecular Biology, Birkbeck, University of London, Malet Street, London WC1E 7HX, UK.
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15
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Abstract
Despite substantial development of production and purification protocols for heterologous recombinant proteins, some proteins are difficult to produce or, when produced, are accumulated in inclusion bodies (IBs). Nondenaturing protocols can be used to recover the entrapped protein from these protein aggregates. In this chapter, we provide a detailed procedure to analyze the physicochemical properties of one of those proteins produced in prokaryotic expression systems. Serum amyloid A3 (SAA3) was recovered from inclusion bodies (IBs) and its secondary structure associated to thermal stability and size was determined by circular dichroism (CD) and dynamic light scattering (DLS), respectively. These techniques were also applied to evaluate the SAA3 interaction with model membranes. These results show the importance of the structural analysis of proteins released from inclusion bodies under nondenaturing procedures, although similar approaches can be extended to any type of recombinant protein preparation.
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Affiliation(s)
- Julieta M Sánchez
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain.
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain.
- Facultad de Ciencias Exactas, Físicas y Naturales, ICTA and Departamento de Química, Cátedra de Química Biológica, Universidad Nacional de Córdoba, Córdoba, Argentina.
- CONICET, Instituto de Investigaciones Biológicas y Tecnológicas (IIBYT), Córdoba, Argentina.
| | - Jose Vicente Carratalá
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain
- Networking Research Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Barcelona, Spain
| | - Laia Gifre-Renom
- Department of Ruminant Production, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Caldes de Montbui, Spain
- Department of Cardiovascular Sciences, Center for Molecular and Vascular Biology, Leuven, Belgium
| | - Anna Arís
- Department of Ruminant Production, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Caldes de Montbui, Spain
| | - Elena Garcia-Fruitós
- Department of Ruminant Production, Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Caldes de Montbui, Spain
| | - Neus Ferrer-Miralles
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain.
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain.
- Networking Research Center on Bioengineering, Biomaterials and Nanomedicine (CIBER-BBN), Barcelona, Spain.
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16
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Mukherjee D, Ahmed IA, Gai F. Site-Specific Interrogation of Protein Structure and Stability. Methods Mol Biol 2022; 2376:65-87. [PMID: 34845603 DOI: 10.1007/978-1-0716-1716-8_3] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
To execute their function or activity, proteins need to possess variability in local electrostatic environment, solvent accessibility, structure, and stability. However, assessing any protein property in a site-specific manner is not easy since native spectroscopic signals often lack the needed specificity. One strategy that overcomes this limitation is to use unnatural amino acids that exhibit distinct spectroscopic features. In this chapter, we describe several such unnatural amino acids (UAAs) and their respective applications in site-specific interrogation of protein structure and stability using standard biophysical methods, including circular dichroism (CD), infrared (IR), and fluorescence spectroscopies.
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Affiliation(s)
| | - Ismail A Ahmed
- Department of Biochemistry and Molecular Biophysics, University of Pennsylvania, Philadelphia, PA, USA
| | - Feng Gai
- Department of Chemistry, University of Pennsylvania, Philadelphia, PA, USA.
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17
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Lennartz F, Higgins MK. Surface Plasmon Resonance Analysis of PfEMP1 Interaction with Receptors. Methods Mol Biol 2022; 2470:467-482. [PMID: 35881367 DOI: 10.1007/978-1-0716-2189-9_35] [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] [Indexed: 06/15/2023]
Abstract
A detailed understanding of the interaction between the highly variant Plasmodium falciparum erythrocyte membrane proteins 1 (PfEMP1) and their human binding partners is essential to explain their roles in disease development in malaria, as well as to understand how antibodies can inhibit these interactions and how the parasite manages to evade such an immune response. This chapter focuses on using surface plasmon resonance (SPR) as a reproducible, high-throughput method to quantitatively characterize these interactions. We describe how to utilize protein A or A/G and streptavidin for protein immobilization on SPR sensor chips and provide instructions on how to biotinylate proteins for this purpose and how to use SPR for binding competition assays. Since these experiments rely on recombinant proteins, we also present a method to verify their structural integrity using circular dichroism spectroscopy.
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Affiliation(s)
- Frank Lennartz
- Department of Biochemistry, University of Oxford, Oxford, UK.
- Helmholtz-Zentrum Berlin für Materialien und Energie, Macromolecular Crystallography, Berlin, Germany.
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18
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Julien JA, Fernandez MG, Brandmier KM, Del Mundo JT, Bator CM, Loftus LA, Gomez EW, Gomez ED, Glover KJ. Rapid preparation of nanodiscs for biophysical studies. Arch Biochem Biophys 2021; 712:109051. [PMID: 34610337 DOI: 10.1016/j.abb.2021.109051] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 09/22/2021] [Accepted: 09/30/2021] [Indexed: 11/15/2022]
Abstract
Nanodiscs, which are disc-shaped entities that contain a central lipid bilayer encased by an annulus of amphipathic helices, have emerged as a leading native-like membrane mimic. The current approach for the formation of nanodiscs involves the creation of a mixed-micellar solution containing membrane scaffold protein, lipid, and detergent followed by a time consuming process (3-12 h) of dialysis and/or incubation with sorptive beads to remove the detergent molecules from the sample. In contrast, the methodology described herein provides a facile and rapid procedure for the preparation of nanodiscs in a matter of minutes (<15 min) using Sephadex® G-25 resin to remove the detergent from the sample. A panoply of biophysical techniques including analytical ultracentrifugation, dynamic light scattering, gel filtration chromatography, circular dichroism spectroscopy, and cryogenic electron microscopy were employed to unequivocally confirm that aggregates formed by this method are indeed nanodiscs. We believe that this method will be attractive for time-sensitive and high-throughput experiments.
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Affiliation(s)
- Jeffrey A Julien
- Department of Chemistry, Lehigh University, 6 E. Packer Ave. Bethlehem, Pennsylvania, 18015, USA
| | - Martin G Fernandez
- Department of Chemistry, Lehigh University, 6 E. Packer Ave. Bethlehem, Pennsylvania, 18015, USA
| | - Katrina M Brandmier
- Department of Chemistry, Lehigh University, 6 E. Packer Ave. Bethlehem, Pennsylvania, 18015, USA
| | - Joshua T Del Mundo
- Department of Chemical Engineering, The Pennsylvania State University, 121 Chemical and Biomedical Engineering Building, University Park, PA, 16802, USA
| | - Carol M Bator
- Huck Institutes of Life Sciences, Cryo-EM Facility, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Lucie A Loftus
- Department of Chemistry, Lehigh University, 6 E. Packer Ave. Bethlehem, Pennsylvania, 18015, USA
| | - Esther W Gomez
- Department of Chemical Engineering, The Pennsylvania State University, 121 Chemical and Biomedical Engineering Building, University Park, PA, 16802, USA
| | - Enrique D Gomez
- Department of Chemical Engineering, The Pennsylvania State University, 121 Chemical and Biomedical Engineering Building, University Park, PA, 16802, USA; Department of Materials Science and Engineering, The Pennsylvania State University, 404 Steidle Building, University Park, PA, 16802, USA
| | - Kerney Jebrell Glover
- Department of Chemistry, Lehigh University, 6 E. Packer Ave. Bethlehem, Pennsylvania, 18015, USA.
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19
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Sousa VK, Pedro JAF, Kumagai PS, Lopes JLS. Effect of setting data collection parameters on the reliability of a circular dichroism spectrum. Eur Biophys J 2021; 50:687-97. [PMID: 33538870 DOI: 10.1007/s00249-021-01499-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 11/12/2020] [Accepted: 01/13/2021] [Indexed: 10/22/2022]
Abstract
Circular dichroism (CD) spectroscopy is a well-established biophysical technique used to investigate the structure of molecules. The analysis of a protein CD spectrum depends on the quality of the original CD data, which can be affected by the sample purity, background absorption of the additives/solvent/buffer, the choice of the parameters used for data collection, etc. In this paper, the CD spectrum of myoglobin was used as a model to exploit how variations on each data collection parameter could affect the final protein CD spectrum and, the subsequent effect of them on the quantitative analysis of protein secondary structure. Bioinformatics analysis carried out with SESCA package and PDBMD2CD server predicted a theoretical myoglobin CD spectrum, and a Monte Carlo-like model was implemented to estimate the uncertainty in secondary structure predictions performed with CDSSTR, Selcon 3 and ContinLL algorithms. An inappropriate choice of data collection parameters can lead to a misinterpretation of the CD data in terms of the protein structural content.
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20
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Abstract
Recent years have seen a growing number of examples of designed oligomeric molecules with artificial backbone connectivity that are capable of adopting complex folded tertiary structures analogous to those seen in natural proteins. A range of experimental techniques from structural biology and biophysics have been brought to bear in the study of these proteomimetic agents. Here, we discuss some considerations encountered in the characterization of high-resolution folded structure as well as folding thermodynamics of protein-like artificial backbones. We provide an overview of the use of X-ray crystallography and NMR spectroscopy in such systems and review example applications of these methods in the primary literature. Further, we provide detailed protocols for two experiments that have proved useful in our prior and ongoing efforts to compare folding thermodynamics between natural protein domains and heterogeneous-backbone counterparts.
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Affiliation(s)
| | - Shilpa R Rao
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, United States
| | - W Seth Horne
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA, United States.
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21
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Wang J, Wang J, Kranthi Vanga S, Raghavan V. Influence of high-intensity ultrasound on the IgE binding capacity of Act d 2 allergen, secondary structure, and In-vitro digestibility of kiwifruit proteins. Ultrason Sonochem 2021; 71:105409. [PMID: 33341536 PMCID: PMC8187882 DOI: 10.1016/j.ultsonch.2020.105409] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [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: 04/01/2020] [Revised: 11/08/2020] [Accepted: 11/09/2020] [Indexed: 05/02/2023]
Abstract
Kiwifruit can trigger allergic reactions that can lead to death, causing public health concerns worldwide. In the present study, we treated kiwifruit samples with high-intensity ultrasound (20 kHz, 400 W, 50% duty cycle) for 0 to 16 min to evaluate its effect on the IgE binding capacity of kiwifruit allergen Act d 2, secondary structure and in-vitro digestibility of kiwifruit proteins. The changes in the protein solubility and microstructures of kiwifruit were also analyzed. The results showed that treatment with powerful ultrasound caused a significant disruption in the microstructure of kiwifruit tissues, leading to the changes in the secondary structures of proteins, including a loss of alpha-helixes and an increase in beta-sheet structures. These structural changes were due to the ultrasound treatment, especially 16 min of treatment, resulted in a 50% reduction in Act d 2 allergen content and significantly improved in-vitro digestibility up to 62% from the initial level of 35%. Furthermore, the solubility of the total proteins present in kiwifruit samples was significantly decreased by 20% after 16-min ultrasound processing. The results of this work showed that high-intensity ultrasound treatment has a potential application in reducing the allergenicity of kiwifruit or related products.
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Affiliation(s)
- Jin Wang
- School of Advanced Agricultural Sciences, Peking University, Beijing 100871, China; Department of Bioresource Engineering, Faculty of Agricultural and Environmental Sciences, McGill University, Sainte-Anne-de-Bellevue, QC H9X 3V9, Canada.
| | - Jun Wang
- College of Food Science and Engineering, Northwest A&F University, Yangling, Shaanxi 712100, China.
| | - Sai Kranthi Vanga
- Department of Bioresource Engineering, Faculty of Agricultural and Environmental Sciences, McGill University, Sainte-Anne-de-Bellevue, QC H9X 3V9, Canada
| | - Vijaya Raghavan
- Department of Bioresource Engineering, Faculty of Agricultural and Environmental Sciences, McGill University, Sainte-Anne-de-Bellevue, QC H9X 3V9, Canada
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22
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Chauhan JV, Mathukiya RP, Singh SP, Gohel SD. Two steps purification, biochemical characterization, thermodynamics and structure elucidation of thermostable alkaline serine protease from Nocardiopsis alba strain OM-5. Int J Biol Macromol 2020; 169:39-50. [PMID: 33316342 DOI: 10.1016/j.ijbiomac.2020.12.061] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 11/26/2020] [Accepted: 12/07/2020] [Indexed: 10/22/2022]
Abstract
The Nocardiopsis alba strain OM-5 showed maximum protease production in submerged culture. The OM-5 protease was purified by hydrophobic interaction chromatography. The purified protease of 68 kDa showed maximum activity (3312 ± 1.64 U/mL) at 70 °C and was quite stable at 80 °C up to 4 M NaCl (w/v) at pH 9. The purified protease showed significant activity and stability in different cations, denaturing agents, metal ions, and osmolytes. The thermodynamic parameters including deactivation rate constant (Kd) and half lives (t1/2) at 50-80 °C were in the range of 2.50 × 10-3 to 5.50 × 10-3 and 277.25-111.25 min respectively at 0-4 M NaCl. The structural stability of the OM-5 protease under various harsh conditions was elucidated by circular dichroism (CD) spectroscopy followed by K2D3 analysis revealed that the native structure of OM-5 protease was stable even in sodium dodecyl sulfate and Tween 20 indicated by increased α-helices content assisted with decreased β-sheets content.
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Affiliation(s)
- Jagruti V Chauhan
- UGC-CAS Department of Biosciences, Saurashtra University, Rajkot 360005, Gujarat, India
| | - Riddhi P Mathukiya
- UGC-CAS Department of Biosciences, Saurashtra University, Rajkot 360005, Gujarat, India
| | - Satya P Singh
- UGC-CAS Department of Biosciences, Saurashtra University, Rajkot 360005, Gujarat, India
| | - Sangeeta D Gohel
- UGC-CAS Department of Biosciences, Saurashtra University, Rajkot 360005, Gujarat, India.
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23
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Murata T, Unno Y, Fukuda M, Utsunomiya-Tate N. The dynamic structure of Rab35 is stabilized in the presence of GTP under physiological conditions. Biochem Biophys Rep 2020; 23:100776. [PMID: 32613087 PMCID: PMC7322127 DOI: 10.1016/j.bbrep.2020.100776] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 05/18/2020] [Accepted: 05/20/2020] [Indexed: 12/11/2022] Open
Abstract
Rab proteins, a family of small guanosine triphosphatases, play key roles in intracellular membrane trafficking and the regulation of various cellular processes. As a Rab isoform, Rab35 is crucial for recycling endosome trafficking, cytokinesis and neurite outgrowth. In this report, we analyzed dynamic structural changes and physicochemical features of Rab35 in response to different external conditions, including temperature, pH, salt concentration and guanosine triphosphate (GTP), by circular dichroism (CD) spectroscopy. CD spectra revealed that the α-helix content of Rab35 varies under different conditions considerably. The addition of GTP increases the α-helix content of Rab35 when the temperature, pH and salt concentration match physiological conditions. The results suggest that the external environment affects the secondary structure of Rab35. In particular, the presence of GTP stabilized the α-helices of Rab35 under physiological conditions. These structural changes may translate to changes in Rab35 function and relate to its role in membrane trafficking.
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Affiliation(s)
- Takuya Murata
- Faculty of Pharma-Science, Teikyo University, 2-11-1, Kaga, Itabashi-ku, Tokyo, 173-8605, Japan
| | - Yuka Unno
- Faculty of Pharma-Science, Teikyo University, 2-11-1, Kaga, Itabashi-ku, Tokyo, 173-8605, Japan
| | - Mitsunori Fukuda
- Laboratory of Membrane Trafficking Mechanisms, Department of Integrative Life Sciences, Graduate School of Life Sciences, Tohoku University, Aobayama, Aoba-ku, Sendai, Miyagi, 980-8578, Japan
| | - Naoko Utsunomiya-Tate
- Faculty of Pharma-Science, Teikyo University, 2-11-1, Kaga, Itabashi-ku, Tokyo, 173-8605, Japan
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24
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Ko MS, Biswas T, Mulero MC, Bobkov AA, Ghosh G, Huxford T. Structurally plastic NEMO and oligomerization prone IKK2 subunits define the behavior of human IKK2:NEMO complexes in solution. Biochim Biophys Acta Proteins Proteom 2020; 1868:140526. [PMID: 32853772 DOI: 10.1016/j.bbapap.2020.140526] [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] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Revised: 07/30/2020] [Accepted: 08/08/2020] [Indexed: 10/23/2022]
Abstract
The human IκB Kinase (IKK) is a multisubunit protein complex of two kinases and one scaffolding subunit that controls induction of transcription factor NF-κB activity. IKK behaves as an entity of aberrantly high apparent molecular weight in solution. Recent X-ray crystallographic and cryo-electron microscopy structures of individual catalytic subunits (IKK1/IKKα and IKK2/IKKβ) reveal that they are both stably folded dimeric proteins that engage in extensive homo-oligomerization through unique surfaces that are required for activation of their respective catalytic activities. The NEMO/IKKγ subunit is a predominantly coiled coil protein that is required for activation of IKK through the canonical NF-κB signaling pathway. Here we report size-exclusion chromatography, multi-angle light scattering, analytical centrifugation, and thermal denaturation analyses of full-length human recombinant NEMO as well as deletion and disease-linked variants. We observe that NEMO is predominantly a dimer in solution, although by virtue of its modular coiled coil regions NEMO exhibits complicated solution dynamics involving portions that are mutually antagonistic toward homodimerization. This behavior causes NEMO to behave as a significantly larger sized particle in solution. Analyses of NEMO in complex with IKK2 indicate that NEMO preserves this structurally dynamic character within the multisubuit complex and provides the complex-bound IKK2 further propensity toward homo-oligomerization. These observations provide critical information on the structural plasticity of NEMO subunit dimers which helps clarify its role in diseases and in IKK regulation through oligomerization-dependent phosphorylation of catalytic IKK2 subunit dimers.
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Affiliation(s)
- Myung Soo Ko
- Structural Biochemistry Laboratory, Department of Chemistry & Biochemistry, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182-1030, United States; Department of Chemistry & Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0357, United States
| | - Tapan Biswas
- Department of Chemistry & Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0357, United States
| | | | - Andrey A Bobkov
- Sanford Burnham Prebys Medical Discovery Institute, United States
| | - Gourisankar Ghosh
- Department of Chemistry & Biochemistry, University of California, San Diego, 9500 Gilman Drive, La Jolla, CA 92093-0357, United States.
| | - Tom Huxford
- Structural Biochemistry Laboratory, Department of Chemistry & Biochemistry, San Diego State University, 5500 Campanile Drive, San Diego, CA 92182-1030, United States.
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25
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Bendre AD, Shukla E, Ramasamy S. Functional Stability and Structural Transitions of a Kunitz trypsin Inhibitor from Chickpea (CaTI2). Protein J 2020; 39:350-357. [PMID: 32671517 DOI: 10.1007/s10930-020-09911-2] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Enzymes are important tools for various applications. We have studied structural transitions and functional stability of a Kunitz trypsin inhibitor from Chickpea (CaTI2), a potent insect gut-protease inhibitor, under different stress conditions like non-neutral pH, elevated temperature and co-solvent concentrations. CaTI2 was cloned and expressed in an eukaryotic system P. pastoris and was investigated for conformational transitions using circular dichroism spectroscopy, differential scanning fluorimetry and activity assay. Native CaTI2 has a sheet dominant structure with 40% β sheets and possess a single tryptophan residue situated in the hydrophobic core of the enzyme. The recombinant inhibitor maintained its maximum activity under alkaline pH with its secondary structure intact between pH 6-10. CaTI2 was observed to be thermally stable up to 55 °C with a Tm of 61.3 °C above which the protein unfolds. On treating with chemical denaturant (urea), the CaTI2 lost its inhibitory potential and native conformation beyond 2 M urea concentration. Moreover, the protein unfolded at lower temperatures as the concentration of denaturant increased, suggesting more complex structural changes. Further, the stability of the inhibitor was found to be directly proportional to the solvent polarity. The data, herein offers significant information of inhibitor stability and activity which could be exploited for its further development into an effective pesticide.
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Affiliation(s)
- Ameya D Bendre
- Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Pune, 411008, India. .,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India. .,National Centre for Cell Science, Ganeshkhind, Pune, 411007, India.
| | - Ekta Shukla
- Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Pune, 411008, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.,National Centre for Cell Science, Ganeshkhind, Pune, 411007, India
| | - Sureshkumar Ramasamy
- Division of Biochemical Sciences, CSIR-National Chemical Laboratory, Pune, 411008, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
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Chuan J, He S, Xie T, Wang G, Yang Z. Characterization of guanine nucleotide exchange activity of DH domain of human FGD2. Protein Expr Purif 2020; 176:105693. [PMID: 32681954 DOI: 10.1016/j.pep.2020.105693] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Revised: 05/10/2020] [Accepted: 06/24/2020] [Indexed: 11/21/2022]
Abstract
FGD2, a member of FGD family, contains a Dbl homology domain (DH) and two pleckstrin homology domains segregated by a FYVE domain. The DH domain has been deduced to be responsible for guanine nucleotide exchange of CDC42 to activate downstream factors. Our aim was to build a prokaryotic expression system for the DH domain and to examine its guanine nucleotide exchange activity toward CDC42 in vitro. A recombinant vector, which was successfully constructed based on pGEX-6P-1, was employed to express the DH domain of human FGD2 (FGD2-DH) in E. coli BL21 (DE3). Purified FGD2-DH behaved as a homogeneous monomer with an estimated molecular weight that corresponded to the theoretical molecular weight and was predicted to be an α-helix protein by circular dichroism spectroscopy. FGD2-DH displayed weak guanine nucleotide exchange activity in vitro and very weak interactions with CDC42 following glutaraldehyde cross-linking.
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Yin L, Fu S, Wu R, Wei S, Yi J, Zhang LM, Yang L. A neutral polysaccharide from green tea: Structure, effect on α-amylase activity and hydrolysis property. Arch Biochem Biophys 2020; 687:108369. [PMID: 32335047 DOI: 10.1016/j.abb.2020.108369] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [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: 10/29/2019] [Revised: 04/05/2020] [Accepted: 04/08/2020] [Indexed: 12/27/2022]
Abstract
A neutral tea polysaccharide (TPSN) was isolated from green tea. Gas chromatography analysis showed that TPSN was composed of d-glucose, l-arabinose and d-galactose residues at a molar ratio of 90.0: 9.1: 0.9. The weight-averaged molecular weight of TPSN was determined as about 2.0 × 105 g mol-1 using static light scattering analysis. The result of nuclear magnetic resonance (NMR) spectroscopy indicated that TPSN and water-soluble starch had similar structures. TPSN exhibited inhibitory activity towards α-amylase through the noncompetitive inhibition mechanism, but the tertiary structure of α-amylase related to enzymatic activity, analyzed using circular dichroism spectroscopy, was not affected by TPSN. Meanwhile, TPSN exhibited hydrolysis properties catalyzed by α-amylase. Molecular docking analysis revealed that the various behaviors of TPSN to α-amylase could be attributed to that the different chain segments of TPSN combined with different amino acid residues of α-amylase.
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Affiliation(s)
- Lin Yin
- Department of Polymer and Material Science, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Shanshan Fu
- Department of Polymer and Material Science, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Roujun Wu
- Department of Polymer and Material Science, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Shuyue Wei
- Department of Polymer and Material Science, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Juzhen Yi
- Department of Polymer and Material Science, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China; Key Laboratory for Polymeric Composite and Functional Materials of Ministry of Education, Guangdong Provincial Key Laboratory for High Performance Polymer-based Composites, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Li-Ming Zhang
- School of Materials Science and Engineering, Sun Yat-sen University, Guangzhou, 510275, China; Key Laboratory for Polymeric Composite and Functional Materials of Ministry of Education, Guangdong Provincial Key Laboratory for High Performance Polymer-based Composites, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Liqun Yang
- Department of Polymer and Material Science, School of Chemistry, Sun Yat-Sen University, Guangzhou, 510275, China; Key Laboratory for Polymeric Composite and Functional Materials of Ministry of Education, Guangdong Provincial Key Laboratory for High Performance Polymer-based Composites, Sun Yat-Sen University, Guangzhou, 510275, China.
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Almutairi FM, Ajmal MR, Siddiqi MK, Majid N, Al-Alawy AIA, Abdelhameed AS, Khan RH. Biophysical insight into the interaction of levocabastine with human serum albumin: spectroscopy and molecular docking approach. J Biomol Struct Dyn 2020; 39:1525-1534. [PMID: 32308140 DOI: 10.1080/07391102.2020.1750486] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Interaction of levocabastine with human serum albumin (HSA) is investigated by applying fluorescence spectroscopy, circular dichroism spectroscopy and molecular docking methods. Levocabastine is an important drug in treatment of allergy and currently a target drug for drug repurposing to treat other diseases like vernal keratoconjuctivitis. Fluorescence quenching data revealed that levocabastine bind weakly to protein with binding constant in the order of 103 M-1. Förster resonance energy transfer results indicated the binding distance of 2.28 nm for levocabastine. Synchronous fluorescence result suggest slight blue shift for tryptophan upon levocabastine binding, binding of levocabastine impelled rise in α-helical structure in protein, while there are minimal changes in tertiary structure in protein. Moreover, docking results indicate levocabastine binds to pocket near to the drug site-I in HSA via hydrogen bonding and hydrophobic interactions. Understanding the interaction of levocabastine with HSA is significant for the advancement of therapeutic and diagnostic strategies for optimal treatment results.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Fahad M Almutairi
- Biochemistry Department, Faculty of Science, Physical Biochemistry Research Laboratory, University of Tabuk, Tabuk, Saudi Arabia
| | - Mohammad Rehan Ajmal
- Biochemistry Department, Faculty of Science, Physical Biochemistry Research Laboratory, University of Tabuk, Tabuk, Saudi Arabia
| | | | - Nabeela Majid
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, India
| | - Adel Ibrahim Ahmad Al-Alawy
- Biochemistry Department, Faculty of Science, Physical Biochemistry Research Laboratory, University of Tabuk, Tabuk, Saudi Arabia
| | - Ali Saber Abdelhameed
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Rizwan Hasan Khan
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, India
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Ponomarenko NS, Kokhan O, Pokkuluri PR, Mulfort KL, Tiede DM. Examination of abiotic cofactor assembly in photosynthetic biomimetics: site-specific stereoselectivity in the conjugation of a ruthenium(II) tris(bipyridine) photosensitizer to a multi-heme protein. Photosynth Res 2020; 143:99-113. [PMID: 31925630 PMCID: PMC6989566 DOI: 10.1007/s11120-019-00697-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [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: 10/01/2019] [Accepted: 12/02/2019] [Indexed: 05/18/2023]
Abstract
To understand design principles for assembling photosynthetic biohybrids that incorporate precisely-controlled sites for electron injection into redox enzyme cofactor arrays, we investigated the influence of chirality in assembly of the photosensitizer ruthenium(II)bis(2,2'-bipyridine)(4-bromomethyl-4'-methyl-2,2'-bipyridine), Ru(bpy)2(Br-bpy), when covalently conjugated to cysteine residues introduced by site-directed mutagenesis in the triheme periplasmic cytochrome A (PpcA) as a model biohybrid system. For two investigated conjugates that show ultrafast electron transfer, A23C-Ru and K29C-Ru, analysis by circular dichroism spectroscopy, CD, demonstrated site-specific chiral discrimination as a factor emerging from the close association between [Ru(bpy)3]2+ and heme cofactors. CD analysis showed the A23C-Ru and K29C-Ru conjugates to have distinct, but opposite, stereoselectivity for the Λ and Δ-Ru(bpy)2(Br-bpy) enantiomers, with enantiomeric excesses of 33.1% and 65.6%, respectively. In contrast, Ru(bpy)2(Br-bpy) conjugation to a protein site with high flexibility, represented by the E39C-Ru construct, exhibited a nearly negligible chiral selectivity, measured by an enantiomeric excess of 4.2% for the Λ enantiomer. Molecular dynamics simulations showed that site-specific stereoselectivity reflects steric constraints at the conjugating sites and that a high degree of chiral selectivity correlates to reduced structural disorder for [Ru(bpy)3]2+ in the linked assembly. This work identifies chiral discrimination as means to achieve site-specific, precise geometric positioning of introduced photosensitizers relative to the heme cofactors in manner that mimics the tuning of cofactors in photosynthesis.
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Affiliation(s)
- Nina S Ponomarenko
- Chemical Sciences and Engineering Division, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL, 60439, USA.
| | - Oleksandr Kokhan
- Department of Chemistry and Biochemistry, James Madison University, 901 Carrier Drive, Harrisonburg, VA, 22807, USA
| | - Phani R Pokkuluri
- Biosciences Division, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL, 60439, USA
| | - Karen L Mulfort
- Chemical Sciences and Engineering Division, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL, 60439, USA
| | - David M Tiede
- Chemical Sciences and Engineering Division, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL, 60439, USA.
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Méndez AAE, Pena LB, Curto LM, Sciorra MD, Ulloa RM, Garza Aguilar SM, Vázquez Ramos JM, Gallego SM. Optimization of recombinant maize CDKA;1 and CycD6;1 production in Escherichia coli by response surface methodology. Protein Expr Purif 2020; 165:105483. [PMID: 31479737 DOI: 10.1016/j.pep.2019.105483] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 08/30/2019] [Accepted: 08/30/2019] [Indexed: 11/24/2022]
Abstract
The complex formed by the cyclin-dependent kinase A (CDKA) and cyclin D is responsible for the G1-S transition in the plant cell cycle. Maize (Zea mays L) CDKA; 1 and CycD6; 1 were cloned and expressed in E. coli. The present study describes the optimization of both proteins production using a statistical approach known as response surface methodology (RSM). The experimental design took into account the effects of four variables: optical density of the culture (OD600) before induction, isopropyl β-d-1-thiogalactopyranoside (IPTG) concentration, post-induction temperature, and post-induction time. For each protein, a 24 full factorial central composite rotary design for these four independent variables (at five levels each) was employed to fit a polynomial model; which indicated that 30 experiments were required for this procedure. An optimization of CDKA; 1 and CycD6; 1 production levels in the soluble fraction was achieved. Protein conformation and stability were studied by circular dichroism and fluorescence spectroscopy. Finally, in vitro Cyc-CDK complex formation and its kinase activity were confirmed.
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31
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Nelea V, Reinhardt DP. Biophysical Techniques to Analyze Elastic Tissue Extracellular Matrix Proteins Interacting with ADAMTS Proteins. Methods Mol Biol 2020; 2043:213-35. [PMID: 31463915 DOI: 10.1007/978-1-4939-9698-8_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Multidomain matrix-associated zinc extracellular proteases ADAMTS and ADAMTS-like proteins have important biological activities in cells and tissues. Beyond their traditional role in procollagen and von Willebrand factor processing and proteoglycan cleavage, ADAMTS/ADAMTSL likely participate in or at least have some role in ECM assembly as some of these proteins bind ECM proteins including fibrillins, fibronectin, and LTBPs. In this chapter, we present four biophysical techniques largely used for the characterization, multimerization, and interaction of proteins: surface plasmon resonance spectroscopy, dynamic light scattering, atomic force microscopy, and circular dichroism spectroscopy.
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Ngamdee K, Chaiendoo K, Saiyasombat C, Busayaporn W, Ittisanronnachai S, Promarak V, Ngeontae W. Highly selective circular dichroism sensor based on d-penicillamine/cysteamine‑cadmium sulfide quantum dots for copper (II) ion detection. Spectrochim Acta A Mol Biomol Spectrosc 2019; 211:313-321. [PMID: 30579214 DOI: 10.1016/j.saa.2018.12.027] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [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: 09/21/2018] [Revised: 12/10/2018] [Accepted: 12/12/2018] [Indexed: 06/09/2023]
Abstract
A highly selective circular dichroism sensor based on cysteamine-capped cadmium sulfide quantum dots (Cys-CdS QDs) was successfully developed for the determination of Cu2+. Basically, the Cys-CdS QDs are not active in circular dichroism spectroscopy. However, the circular dichroism probe (DPA@Cys-CdS QDs) can be simply generated in situ by mixing achiral Cys-CdS QDs with D-penicillamine. The detection principle was based on measuring the circular dichroism signal change upon the addition of Cu2+. The strong CD signal of the DPA@Cys-CdS QDs dramatically decreased in the presence of Cu2+, while other cations did not result in any spectral changes. In addition, the degree of the CD signal decrease was linearly proportional to the concentration of Cu2+ in the range of 0.50-2.25 μM (r2 = 0.9919) with a detection limit of 0.34 μM. Furthermore, the proposed sensor was applied to detect Cu2+ in drinking water samples with %recovery values of 102-114% and %RSD less than 6%.
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Affiliation(s)
- Kessarin Ngamdee
- Materials Chemistry Research Center, Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Kanokwan Chaiendoo
- Materials Chemistry Research Center, Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Khon Kaen University, Khon Kaen 40002, Thailand
| | | | | | - Somlak Ittisanronnachai
- Frontier Research Center (FRC), Vidyasirimedhi Institute of Science and Technology, Wang Chan, Rayong 21210, Thailand
| | - Vinich Promarak
- School of Molecular Science and Engineering, Vidyasirimedhi Institute of Science and Technology, Wang Chan, Rayong 21210, Thailand
| | - Wittaya Ngeontae
- Materials Chemistry Research Center, Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Khon Kaen University, Khon Kaen 40002, Thailand; Research Center for Environmental and Hazardous Substance Management, Khon Kaen University, Khon Kaen 40002, Thailand; Center of Excellence for Environmental and Hazardous Waste Management (EHWM), Bangkok 10330, Thailand.
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Abstract
Circular Dichroic (CD) spectroscopy is one of the most frequently used methods for guanine quadruplex studies and in general for studies of conformational properties of nucleic acids. The reason is its high sensitivity to even slight changes in mutual orientation of absorbing bases of DNA. CD can reveal formation of particular structural DNA arrangements and can be used to search for the conditions stabilizing the structures, to follow the transitions between various structural states, to explore kinetics of their appearance, to determine thermodynamic parameters, and also to detect formation of higher order structures. CD spectroscopy is an important complementary technique to NMR spectroscopy and X-ray diffraction in quadruplex studies due to its sensitivity, easy manipulation of studied samples, and relative inexpensiveness. In this part, we present the protocol for the use of CD spectroscopy in the study of guanine quadruplexes, together with practical advice and cautions about various, particularly interpretation, difficulties.
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Affiliation(s)
- Iva Kejnovská
- The Czech Academy of Sciences, Institute of Biophysics, Brno, Czech Republic
| | - Daniel Renčiuk
- The Czech Academy of Sciences, Institute of Biophysics, Brno, Czech Republic
| | - Jan Palacký
- The Czech Academy of Sciences, Institute of Biophysics, Brno, Czech Republic
| | - Michaela Vorlíčková
- The Czech Academy of Sciences, Institute of Biophysics, Brno, Czech Republic.
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34
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Webby MN, Sullivan MP, Yegambaram KM, Radjainia M, Keown JR, Kingston RL. A method for analyzing the composition of viral nucleoprotein complexes, produced by heterologous expression in bacteria. Virology 2018; 527:159-168. [PMID: 30529564 DOI: 10.1016/j.virol.2018.11.013] [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: 08/04/2018] [Revised: 10/23/2018] [Accepted: 11/22/2018] [Indexed: 12/27/2022]
Abstract
Viral genomes are protected and organized by virally encoded packaging proteins. Heterologous production of these proteins often results in formation of particles resembling the authentic viral capsid or nucleocapsid, with cellular nucleic acids packaged in place of the viral genome. Quantifying the total protein and nucleic acid content of particle preparations is a recurrent biochemical problem. We describe a method for resolving this problem, developed when characterizing particles resembling the Menangle Virus nucleocapsid. The protein content was quantified using the biuret assay, which is largely independent of amino acid composition. Bound nucleic acids were quantified by determining the phosphorus content, using inductively coupled plasma mass spectrometry. Estimates for the amount of RNA packaged within the particles were consistent with the structurally-characterized packaging mechanism. For a bacterially-produced nucleoprotein complex, phosphorus usually provides a unique elemental marker of bound nucleic acids, hence this method of analysis should be routinely applicable.
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Affiliation(s)
- Melissa N Webby
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Matthew P Sullivan
- School of Chemical Sciences, University of Auckland, Auckland, New Zealand
| | | | - Mazdak Radjainia
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Jeremy R Keown
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Richard L Kingston
- School of Biological Sciences, University of Auckland, Auckland, New Zealand.
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Jäger S, Büchel C. Cation-dependent changes in the thylakoid membrane appression of the diatom Thalassiosira pseudonana. Biochim Biophys Acta Bioenerg 2018; 1860:41-51. [PMID: 30447184 DOI: 10.1016/j.bbabio.2018.11.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Revised: 09/21/2018] [Accepted: 11/04/2018] [Indexed: 11/16/2022]
Abstract
Diatoms show a special organisation of their plastid membranes, such that their thylakoids span the entire plastid in bands of three. While in higher plants the interaction of the light harvesting complex II and photosystem II with divalent cations (especially Mg2+) was found to take part in the interplay of electrostatic attraction and repulsion in grana membrane appression, for diatoms the key players in maintaining proper membrane distances were not identified so far. In this work, we investigated the changes in the thylakoid architecture of Thalassiosira pseudonana in reaction to different salts by using circular dichroism and fluorescence spectroscopy in combination with other techniques. We show that divalent cations have an important influence on optimal pigment organisation and thus also on maintaining membrane appression. Thereby, monovalent cations are far less effective. The concentration needed is in a physiological range and fits well with the values obtained for higher plant grana stacking, despite the fact that strict protein segregation as seen in higher plant grana is missing.
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Affiliation(s)
- Stefanie Jäger
- Institute of Molecular Biosciences, Goethe University Frankfurt, Max-von-Laue Straße 9, 60438 Frankfurt, Germany
| | - Claudia Büchel
- Institute of Molecular Biosciences, Goethe University Frankfurt, Max-von-Laue Straße 9, 60438 Frankfurt, Germany.
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Hariharan P, Tikhonova E, Medeiros-Silva J, Jeucken A, Bogdanov MV, Dowhan W, Brouwers JF, Weingarth M, Guan L. Structural and functional characterization of protein-lipid interactions of the Salmonella typhimurium melibiose transporter MelB. BMC Biol 2018; 16:85. [PMID: 30075778 PMCID: PMC6091025 DOI: 10.1186/s12915-018-0553-0] [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: 06/06/2018] [Accepted: 07/23/2018] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Membrane lipids play critical roles in the structure and function of membrane-embedded transporters. Salmonella typhimurium MelB (MelBSt) is a symporter coupling melibiose translocation with a cation (Na+, Li+, or H+). We present an extensive study on the effects of specific phospholipids on the structure of MelBSt and the melibiose transport catalyzed by this protein. RESULTS Lipidomic analysis and thin-layer chromatography (TLC) experiments reveal that at least one phosphatidylethanolamine (PE) and one phosphatidylglycerol (PG) molecule associate with MelBSt at high affinities. Solid-state nuclear magnetic resonance (ssNMR) spectroscopy experiments confirmed the presence of lipid tails and glycerol backbones that co-purified with MelBSt; headgroups of PG were also observed. Studies with lipid-engineered strains, including PE-deficient, cardiolipin (CL)- and PG-deficient, or CL-deficient strains, show that lack of PE or PG, however not CL, largely inhibits both H+- and Na+-coupled melibiose active transport to different extents. Interestingly, neither the co-substrate binding (melibiose or Na+) nor MelBSt folding and stability are affected by changing lipid compositions. Remarkably, the delipidated MelBSt with only 2-3 bound lipids, regardless of the headgroup species, also exhibits unchanged melting temperature values as shown by circular dichroism spectroscopy. CONCLUSIONS (1) Lipid tails and glycerol backbones of interacting PE and PG may contribute to the stability of the structure of MelBSt. (2) The headgroups of PE and PG, but not of CL, play important roles in melibiose transport; however, lipid headgroups do not modulate the folding and stability of MelBSt.
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Affiliation(s)
- Parameswaran Hariharan
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, 79430, USA
| | - Elena Tikhonova
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, 79430, USA
| | - João Medeiros-Silva
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Aike Jeucken
- Department of Biochemistry & Cell Biology, Lipidomics Facility, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 2, 3584 CM, Utrecht, The Netherlands
| | - Mikhail V Bogdanov
- Department of Biochemistry and Molecular Biology, the University of Texas Health Science, Center McGovern Medical School, Houston, TX, 77030, USA
| | - William Dowhan
- Department of Biochemistry and Molecular Biology, the University of Texas Health Science, Center McGovern Medical School, Houston, TX, 77030, USA
| | - Jos F Brouwers
- Department of Biochemistry & Cell Biology, Lipidomics Facility, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 2, 3584 CM, Utrecht, The Netherlands
| | - Markus Weingarth
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Department of Chemistry, Faculty of Science, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands.
| | - Lan Guan
- Department of Cell Physiology and Molecular Biophysics, Center for Membrane Protein Research, School of Medicine, Texas Tech University Health Sciences Center, Lubbock, TX, 79430, USA.
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Azam AA, Kinder JM, Khan GN, Alase A, Ma P, Liu Y, Ault JR, Henderson PJF, Chowdhry BZ, Alexander BD, Harding SE, Phillips-Jones MK. Production of membrane proteins for characterisation of their pheromone-sensing and antimicrobial resistance functions. Eur Biophys J 2018; 47:723-37. [PMID: 30066130 DOI: 10.1007/s00249-018-1325-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 06/08/2018] [Accepted: 07/21/2018] [Indexed: 12/15/2022]
Abstract
Despite the importance of membrane proteins in cellular processes, studies of these hydrophobic proteins present major technical challenges, including expression and purification for structural and biophysical studies. A modified strategy of that proposed previously by Saidijam et al. (2005) and others, for the routine expression of bacterial membrane proteins involved in environmental sensing and antimicrobial resistance (AMR), is proposed which results in purification of sufficient proteins for biophysical experiments. We report expression successes amongst a collection of enterococcal vancomycin resistance membrane proteins: VanTG, VanTG-M transporter domain, VanZ and the previously characterised VanS (A-type) histidine protein kinase (HPK). Using the same strategy, we report on the successful amplification and purification of intact BlpH and ComD2 HPKs of Streptococcus pneumoniae. Near-UV circular dichroism revealed both recombinant proteins bound their pheromone ligands BlpC and CSP2. Interestingly, CSP1 also interacted with ComD. Finally, we evaluate the alternative strategy for studying sensory HPKs involving isolated soluble sensory domain fragments, exemplified by successful production of VicKESD of Enterococcus faecalis VicK. Purified VicKESD possessed secondary structure post-purification. Thermal denaturation experiments using far-UV CD, a technique which can be revealing regarding ligand binding, revealed that: (a) VicKESD denaturation occurs between 15 and 50 °C; and (b) reducing conditions did not detectably affect denaturation profiles suggesting reducing conditions per se are not directly sensed by VicKESD. Our findings provide information on a modified strategy for the successful expression, production and/or storage of bacterial membrane HPKs, AMR proteins and sensory domains for their future crystallisation, and ligand binding studies.
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38
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Salas RL, Garcia JKDL, Miranda ACR, Rivera WL, Nellas RB, Sabido PMG. Effects of truncation of the peptide chain on the secondary structure and bioactivities of palmitoylated anoplin. Peptides 2018; 104:7-14. [PMID: 29614317 DOI: 10.1016/j.peptides.2018.03.019] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [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: 08/08/2017] [Revised: 03/28/2018] [Accepted: 03/30/2018] [Indexed: 12/29/2022]
Abstract
Anoplin (GLLKRIKTLL-NH2) is of current interest due to its short sequence and specificity towards bacteria. Recent studies on anoplin have shown that truncation and acylation compromises its antimicrobial activity and specificity, respectively. In this study, truncated analogues (pal-ano-9 to pal-ano-5) of palmitoylated anoplin (pal-anoplin) were synthesized to determine the effects of C-truncation on its bioactivities. Moreover, secondary structure of each analogue using circular dichroism (CD) spectroscopy was determined to correlate with bioactivities. Interestingly, pal-anoplin, pal-ano-9 and pal-ano-6 were helical in water, unlike anoplin. In contrast, pal-ano-8, pal-ano-7 and pal-ano-5, with polar amino acid residues at the C-terminus, were random coil in water. Nevertheless, all the peptides folded into helical structures in 30% trifluoroethanol/water (TFE/H2O) except for the shortest analogue pal-ano-5. Hydrophobicity played a significant role in the enhancement of activity against bacteria E. coli and S. aureus as all lipopeptides including the random coil pal-ano-5 were more active than the parent anoplin. Meanwhile, the greatest improvement in activity against the fungus C. albicans was observed for pal-anoplin analogues (pal-ano-9 and pal-ano-6) that were helical in water. Although, hydrophobicity is a major factor in the secondary structure and antimicrobial activity, it appears that the nature of amino acids at the C-terminus also influence folding of lipopeptides in water and its antifungal activity. Moreover, the hemolytic activity of the analogues was found to correlate with hydrophobicity, except for the least hemolytic, pal-ano-5. Since most of the analogues are more potent and shorter than anoplin, they are promising drug candidates for further development.
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Affiliation(s)
- Remmer L Salas
- Institute of Chemistry, College of Science, University of the Philippines, Diliman, Quezon City, 1101, Philippines
| | - Jan Kathryne D L Garcia
- Institute of Chemistry, College of Science, University of the Philippines, Diliman, Quezon City, 1101, Philippines; Natural Sciences Research Institute, University of the Philippines, Diliman, Quezon City, 1101, Philippines
| | - Ana Carmela R Miranda
- Institute of Chemistry, College of Science, University of the Philippines, Diliman, Quezon City, 1101, Philippines
| | - Windell L Rivera
- Natural Sciences Research Institute, University of the Philippines, Diliman, Quezon City, 1101, Philippines; Institute of Biology, College of Science, University of the Philippines, Diliman, Quezon City, 1101, Philippines
| | - Ricky B Nellas
- Institute of Chemistry, College of Science, University of the Philippines, Diliman, Quezon City, 1101, Philippines; Natural Sciences Research Institute, University of the Philippines, Diliman, Quezon City, 1101, Philippines
| | - Portia Mahal G Sabido
- Institute of Chemistry, College of Science, University of the Philippines, Diliman, Quezon City, 1101, Philippines; Natural Sciences Research Institute, University of the Philippines, Diliman, Quezon City, 1101, Philippines.
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Phillips-Jones MK, Harding SE. Antimicrobial resistance (AMR) nanomachines-mechanisms for fluoroquinolone and glycopeptide recognition, efflux and/or deactivation. Biophys Rev 2018; 10:347-362. [PMID: 29525835 PMCID: PMC5899746 DOI: 10.1007/s12551-018-0404-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 02/05/2018] [Indexed: 12/11/2022] Open
Abstract
In this review, we discuss mechanisms of resistance identified in bacterial agents Staphylococcus aureus and the enterococci towards two priority classes of antibiotics-the fluoroquinolones and the glycopeptides. Members of both classes interact with a number of components in the cells of these bacteria, so the cellular targets are also considered. Fluoroquinolone resistance mechanisms include efflux pumps (MepA, NorA, NorB, NorC, MdeA, LmrS or SdrM in S. aureus and EfmA or EfrAB in the enterococci) for removal of fluoroquinolone from the intracellular environment of bacterial cells and/or protection of the gyrase and topoisomerase IV target sites in Enterococcus faecalis by Qnr-like proteins. Expression of efflux systems is regulated by GntR-like (S. aureus NorG), MarR-like (MgrA, MepR) regulators or a two-component signal transduction system (TCS) (S. aureus ArlSR). Resistance to the glycopeptide antibiotic teicoplanin occurs via efflux regulated by the TcaR regulator in S. aureus. Resistance to vancomycin occurs through modification of the D-Ala-D-Ala target in the cell wall peptidoglycan and removal of high affinity precursors, or by target protection via cell wall thickening. Of the six Van resistance types (VanA-E, VanG), the VanA resistance type is considered in this review, including its regulation by the VanSR TCS. We describe the recent application of biophysical approaches such as the hydrodynamic technique of analytical ultracentrifugation and circular dichroism spectroscopy to identify the possible molecular effector of the VanS receptor that activates expression of the Van resistance genes; both approaches demonstrated that vancomycin interacts with VanS, suggesting that vancomycin itself (or vancomycin with an accessory factor) may be an effector of vancomycin resistance. With 16 and 19 proteins or protein complexes involved in fluoroquinolone and glycopeptide resistances, respectively, and the complexities of bacterial sensing mechanisms that trigger and regulate a wide variety of possible resistance mechanisms, we propose that these antimicrobial resistance mechanisms might be considered complex 'nanomachines' that drive survival of bacterial cells in antibiotic environments.
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Affiliation(s)
- Mary K Phillips-Jones
- National Centre for Macromolecular Hydrodynamics, School of Biosciences, University of Nottingham, Sutton Bonington, LE12 5RD, Loughborough, Leicestershire, UK.
| | - Stephen E Harding
- National Centre for Macromolecular Hydrodynamics, School of Biosciences, University of Nottingham, Sutton Bonington, LE12 5RD, Loughborough, Leicestershire, UK
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Stojković MR, Gonzalez-Garcia J, Šupljika F, Galiana-Rosello C, Guijarro L, Gazze SA, Francis LW, Piantanida I, Garcia-Espana E. Specific and highly efficient condensation of GC and IC DNA by polyaza pyridinophane derivatives. Int J Biol Macromol 2018; 109:143-51. [PMID: 29247733 DOI: 10.1016/j.ijbiomac.2017.11.156] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 11/24/2017] [Accepted: 11/25/2017] [Indexed: 11/23/2022]
Abstract
Two bis-polyaza pyridinophane derivatives and their monomeric reference compounds revealed strong interactions with ds-DNA and RNA. The bis-derivatives show a specific condensation of GC- and IC-DNA, which is almost two orders of magnitude more efficient than the well-known condensation agent spermine. The type of condensed DNA was identified as ψ-DNA, characterized by the exceptionally strong CD signals. At variance to the almost silent AT(U) polynucleotides, these strong CD signals allow the determination of GC-condensates at nanomolar nucleobase concentrations. Detailed thermodynamic characterisation by ITC reveals significant differences between the DNA binding of the bis-derivative compounds (enthalpy driven) and that of spermine and of their monomeric counterparts (entropy driven). Atomic force microscopy confirmed GC-DNA compaction by the bis-derivatives and the formation of toroid- and rod-like structures responsible for the ψ-type pattern in the CD spectra.
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Zamiri B, Mirceta M, Abu-Ghazalah R, Wold MS, Pearson CE, Macgregor RB. Stress-induced acidification may contribute to formation of unusual structures in C9orf72-repeats. Biochim Biophys Acta Gen Subj 2018; 1862:1482-1491. [PMID: 29550431 DOI: 10.1016/j.bbagen.2018.03.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [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: 10/18/2017] [Revised: 02/22/2018] [Accepted: 03/04/2018] [Indexed: 12/12/2022]
Abstract
BACKGROUND Expansion of the C9orf72 hexanucleotide repeat (GGGGCC)n·(GGCCCC)n is the most common cause of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD). Both strands of the C9orf72 repeat have been shown to form unusual DNA and RNA structures that are thought to be involved in mutagenesis and/or pathogenesis. We previously showed that the C-rich DNA strands from the C9orf72 repeat can form four-stranded quadruplexes at neutral pH. The cytosine residues become protonated under slightly acidic pH (pH 4.5-6.2), facilitating the formation of intercalated i-motif structures. METHODS Using CD spectroscopy, UV melting, and gel electrophoresis, we demonstrate a pH-induced structural transition of the C-rich DNA strand of the C9orf72 repeat at pHs reported to exist in living cells under stress, including during neurodegeneration and cancer. RESULTS We show that the repeats with lengths of 4, 6, and 8 units, form intercalated quadruplex i-motifs at low pH (pH < 5) and monomolecular hairpins and monomolecular quadruplexes under neutral-basic conditions (pH ≥ 8). Furthermore, we show that the human replication protein A (RPA) binds to the G-rich and C-rich DNA strands under acidic conditions, suggesting that it can bind to i-motif structures. CONCLUSIONS In the proper sequence context, i-motif structures can form at pH values found in some cells in vivo. GENERAL SIGNIFICANCE DNA conformational plasticity exists over broad range of solution conditions.
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Affiliation(s)
- Bita Zamiri
- Graduate Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario M5S 3M2, Canada
| | - Mila Mirceta
- Program of Genetics & Genome Biology, The Hospital for Sick Children, Toronto, Ontario M5G 1L7, Canada; Program of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A1, Canada
| | - Rashid Abu-Ghazalah
- W. Booth School of Engineering Technology Practice and Technology, McMaster University, Hamilton, Ontario L8S 0A3, Canada
| | - Marc S Wold
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA 52242, USA
| | - Christopher E Pearson
- Program of Genetics & Genome Biology, The Hospital for Sick Children, Toronto, Ontario M5G 1L7, Canada; Program of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A1, Canada
| | - Robert B Macgregor
- Graduate Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, Toronto, Ontario M5S 3M2, Canada.
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Krishnamoorthy A, Witkowski A, Tran JJ, Weers PMM, Ryan RO. Characterization of secondary structure and lipid binding behavior of N-terminal saposin like subdomain of human Wnt3a. Arch Biochem Biophys 2017; 630:38-46. [PMID: 28754322 DOI: 10.1016/j.abb.2017.07.015] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [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: 05/11/2017] [Revised: 07/14/2017] [Accepted: 07/24/2017] [Indexed: 02/06/2023]
Abstract
Wnt signaling is essential for embryonic development and adult homeostasis in multicellular organisms. A conserved feature among Wnt family proteins is the presence of two structural domains. Within the N-terminal (NT) domain there exists a motif that is superimposable upon saposin-like protein (SAPLIP) family members. SAPLIPs are found in plants, microbes and animals and possess lipid surface seeking activity. To investigate the function of the Wnt3a saposin-like subdomain (SLD), recombinant SLD was studied in isolation. Bacterial expression of this Wnt fragment was achieved only when the core SLD included 82 NT residues of Wnt3a (NT-SLD). Unlike SAPLIPs, NT-SLD required the presence of detergent to achieve solubility at neutral pH. Deletion of two hairpin loop extensions present in NT-SLD, but not other SAPLIPs, had no effect on the solubility properties of NT-SLD. Far UV circular dichroism spectroscopy of NT-SLD yielded 50-60% α-helix secondary structure. Limited proteolysis of isolated NT-SLD in buffer and detergent micelles showed no differences in cleavage kinetics. Unlike prototypical saposins, NT-SLD exhibited weak membrane-binding affinity and lacked cell lytic activity. In cell-based canonical Wnt signaling assays, NT-SLD was unable to induce stabilization of β-catenin or modulate the extent of β-catenin stabilization induced by full-length Wnt3a. Taken together, the results indicate neighboring structural elements within full-length Wnt3a affect SLD conformational stability. Moreover, SLD function(s) in Wnt proteins appear to have evolved away from those commonly attributed to SAPLIP family members.
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Affiliation(s)
- Aparna Krishnamoorthy
- Department of Nutritional Sciences and Toxicology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Andrzej Witkowski
- Children's Hospital Oakland Research Institute, 5700 Martin Luther King Jr. Way, Oakland, CA 94609, USA
| | - Jesse J Tran
- 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
| | - Robert O Ryan
- Department of Nutritional Sciences and Toxicology, University of California Berkeley, Berkeley, CA 94720, USA; Children's Hospital Oakland Research Institute, 5700 Martin Luther King Jr. Way, Oakland, CA 94609, USA.
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Qiao Y, Song L, Zhu C, Wang Q, Guo T, Yan Y, Li Q. Development of a phosphorylated Momordica charantia protein system for inhibiting susceptible dose-dependent C. albicans to available antimycotics: An allosteric regulation of protein. Eur J Pharm Sci 2017; 109:262-268. [PMID: 28834733 DOI: 10.1016/j.ejps.2017.08.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [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: 03/21/2017] [Revised: 08/14/2017] [Accepted: 08/18/2017] [Indexed: 02/01/2023]
Abstract
A regulatory Momordica charantia protein system was constructed allosterically by in vitro protein phosphorylation, in an attempt to evaluate antimycological pluripotency against dose-dependent susceptibilities in C. albicans. Fungal strain lineages susceptible to ketoconazole, econazole, miconazole, 5-flucytosine, nystatin and amphotericin B were prepared in laboratory, followed by identification via antifungal susceptibility testing. Protein phosphorylation was carried out in reactions with 5'-adenylic, guanidylic, cytidylic and uridylic acids and cyclic adenosine triphosphate, through catalysis of cyclin-dependent kinase 1, protein kinase A and protein kinase C respectively. Biochemical analysis of enzymatic reactions indicated the apparent Michaelis-Menten constants and maximal velocity values of 16.57-91.97mM and 55.56-208.33μM·min-1, together with an approximate 1:1 reactant stoichiometric ratio. Three major protein phosphorylation sites were theoretically predicted at Thr255, Thr102 and Thr24 by a KinasePhos tool. Additionally, circular dichroism spectroscopy demonstrated that upon phosphorylation, protein folding structures were decreased in random coil, β6-sheet and α1-helix partial regions. McFarland equivalence standard testing yielded the concentration-dependent inhibition patterns, while fungus was grown in Sabouraud's dextrose agar. The minimal inhibitory concentrations of 0.16-0.51μM (at 50% response) were obtained for free protein and phosphorylated counterparts. With respect to the 3-cycling susceptibility testing regimen, individuals of total protein forms were administrated in-turn at 0.14μM/cycle. Relative inhibition ratios were retained to 66.13-81.04% of initial ones regarding the ketoconazole-susceptible C. albicans growth. An inhibitory protein system, with an advantage of decreasing antifungal susceptibilities to diverse antimycotics, was proposed because of regulatory pluripotency whereas little contribution to susceptibility in itself.
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Affiliation(s)
- Yuanbiao Qiao
- Graduate Institute of Pharmaceutical Chemistry, Luliang University, Shanxi 033001, PR China.
| | - Li Song
- Department of Bioscience, Luliang University, Shanxi 033001, PR China
| | - Chenchen Zhu
- Department of Bioscience, Luliang University, Shanxi 033001, PR China
| | - Qian Wang
- Department of Bioscience, Luliang University, Shanxi 033001, PR China
| | - Tianyan Guo
- Department of Bioscience, Luliang University, Shanxi 033001, PR China
| | - Yanhua Yan
- Department of Bioscience, Luliang University, Shanxi 033001, PR China
| | - Qingshan Li
- College of Traditional Chinese Pharmacology, Shanxi University of Traditional Chinese Medicine, Shanxi 030619, PR China; School of Pharmaceutical Sciences, Shanxi Medical University, Shanxi 030001, PR China.
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O'Reilly AO, Lattrell A, Miles AJ, Klinger AB, Nau C, Wallace BA, Lampert A. Mutagenesis of the NaChBac sodium channel discloses a functional role for a conserved S6 asparagine. Eur Biophys J 2017; 46:665-74. [PMID: 28825121 DOI: 10.1007/s00249-017-1246-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2017] [Revised: 07/21/2017] [Accepted: 07/29/2017] [Indexed: 12/11/2022]
Abstract
Asparagine is conserved in the S6 transmembrane segments of all voltage-gated sodium, calcium, and TRP channels identified to date. A broad spectrum of channelopathies including cardiac arrhythmias, epilepsy, muscle diseases, and pain disorders is associated with its mutation. To investigate its effects on sodium channel functional properties, we mutated the simple prokaryotic sodium channel NaChBac. Electrophysiological characterization of the N225D mutant reveals that this conservative substitution shifts the voltage-dependence of inactivation by 25 mV to more hyperpolarized potentials. The mutant also displays greater thermostability, as determined by synchrotron radiation circular dichroism spectroscopy studies of purified channels. Based on our analyses of high-resolution structures of NaChBac homologues, we suggest that the side-chain amine group of asparagine 225 forms one or more hydrogen bonds with different channel elements and that these interactions are important for normal channel function. The N225D mutation eliminates these hydrogen bonds and the structural consequences involve an enhanced channel inactivation.
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Kumagai PS, Araujo APU, Lopes JLS. Going deep into protein secondary structure with synchrotron radiation circular dichroism spectroscopy. Biophys Rev 2017; 9:517-527. [PMID: 28825203 DOI: 10.1007/s12551-017-0314-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [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: 06/27/2017] [Accepted: 08/03/2017] [Indexed: 10/25/2022] Open
Abstract
Circular dichroism (CD) spectroscopy is a fast, powerful, well-established, and widely used analytical technique in the biophysical and structural biology community to study protein secondary structure and to track changes in protein conformation in different environments. The use of the intense light of a synchrotron beam as the light source for collecting CD measurements has emerged as an enhanced method, known as synchrotron radiation circular dichroism (SRCD) spectroscopy, that has several advantages over the conventional CD method, including a significant spectral range extension for data collection, deeper access to the lower limit (cut-off) of conventional CD spectroscopy, an improved signal-to-noise ratio to increase accuracy in the measurements, and the possibility to collect measurements in highly absorbing solutions. In this review, we discuss different applications of the SRCD technique by researchers from Latin America. In this context, we specifically look at the use of this method for examining the secondary structure and conformational behavior of proteins belonging to the four main classes of the hierarchical protein domain classification CATH (Class, Architecture, Topology, Homology) database, focusing on the advantages and improvements associated with SRCD spectroscopy in terms of characterizing proteins composed of different structural elements.
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Affiliation(s)
- Patricia S Kumagai
- Instituto de Física de São Carlos, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Ana P U Araujo
- Instituto de Física de São Carlos, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Jose L S Lopes
- Departamento Física Aplicada, Instituto de Física,, Universidade de São Paulo, Rua do Matão 1371, Cidade Universitária, São Paulo, SP, 05508-090, Brazil.
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Nowicka AM, Matysiak-Brynda E, Hepel M. Charge-transfer interactions of Cr species with DNA. J Inorg Biochem 2017; 175:148-53. [PMID: 28753493 DOI: 10.1016/j.jinorgbio.2017.07.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 06/28/2017] [Accepted: 07/17/2017] [Indexed: 11/20/2022]
Abstract
Interactions of Cr species with nucleic acids in living organisms depend strongly on Cr oxidation state and the environmental conditions. As the effects of these interactions range from benign to pre-mutagenic to carcinogenic, careful assessment of the hazard they pose to human health is necessary. We have investigated methods that would enable quantifying the DNA damage caused by Cr species under varying environmental conditions, including UV, O2, and redox potential, using simple instrumental techniques which could be in future combined into a field-deployable instrumentation. We have employed electrochemical quartz crystal nanogravimetry (EQCN), cyclic voltammetry (CV), and electrochemical impedance spectroscopy (EIS) to evaluate the extent of DNA damage expressed in terms of guanine oxidation yield (η) and changes in specific characteristics provided by these techniques. The effects of the interactions of Cr species with DNA were analyzed using a model calf thymus DNA (ctDNA) film on a gold electrode (Au@ctDNA) in different media, including: (i) Cr(VI), (ii) Cr(VI) reduced at -0.2V, (iii) Cr(III)+UV radiation+O2, and Cr(III), obtaining the η values: 7.4±1.4, 1.5±0.4, 1.1±0.31%, and 0%, respectively, thus quantifying the hazard posed. The EIS measurements have enabled utilizing the decrease in charge-transfer resistance (Rct) for ferri/ferrocyanide redox probe at an Au@ctDNA electrode to assess the oxidative ctDNA damage by Cr(VI) species. In this case, circular dichroism indicates an extensive damage to the ctDNA hydrogen bonding. On the other hand, Cr(III) species have not induced any damage to ctDNA, although the EQCN measurements show an electrostatic binding to DNA.
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Janes RW. PDB2CD visualises dynamics within protein structures. Eur Biophys J 2017; 46:607-16. [PMID: 28374045 DOI: 10.1007/s00249-017-1203-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Revised: 02/13/2017] [Accepted: 02/17/2017] [Indexed: 11/23/2022]
Abstract
Proteins tend to have defined conformations, a key factor in enabling their function. Atomic resolution structures of proteins are predominantly obtained by either solution nuclear magnetic resonance (NMR) or crystal structure methods. However, when considering a protein whose structure has been determined by both these approaches, on many occasions, the resultant conformations are subtly different, as illustrated by the examples in this study. The solution NMR approach invariably results in a cluster of structures whose conformations satisfy the distance boundaries imposed by the data collected; it might be argued that this is evidence of the dynamics of proteins when in solution. In crystal structures, the proteins are often in an energy minimum state which can result in an increase in the extent of regular secondary structure present relative to the solution state depicted by NMR, because the more dynamic ends of alpha helices and beta strands can become ordered at the lower temperatures. This study examines a novel way to display the differences in conformations within an NMR ensemble and between these and a crystal structure of a protein. Circular dichroism (CD) spectroscopy can be used to characterise protein structures in solution. Using the new bioinformatics tool, PDB2CD, which generates CD spectra from atomic resolution protein structures, the differences between, and possible dynamic range of, conformations adopted by a protein can be visualised.
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Pattanayak R, Basak P, Sen S, Bhattacharyya M. An insight to the binding of ellagic acid with human serum albumin using spectroscopic and isothermal calorimetry studies. Biochem Biophys Rep 2017; 10:88-93. [PMID: 29114572 PMCID: PMC5637241 DOI: 10.1016/j.bbrep.2017.03.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [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: 02/27/2017] [Accepted: 03/01/2017] [Indexed: 11/27/2022] Open
Abstract
Ellagic acid (EA), a natural polyphenol evidence several pharmacological benefits. The binding profile of EA with human serum albumin (HSA) has been explored and investigated by Isothermal titration calorimetry (ITC), circular dichroism (CD) spectroscopy, time-correlated single-photon counting (TCSPC), absorbance spectroscopy, steady-state fluorescence spectroscopy, and modelling studies. The ITC data analysis revealed the binding Constant (Ka), ΔH, ΔS and ΔG values to be 15.5×104M−1, −116.2±18.1 Kcal mol−1, −366 cal mol−1K−1 and −7.13 Kcal mol−1 respectively with a unique binding site at HSA. EA effectively quenched the intrinsic fluorescence of HSA by static quenching, whereas TCSPC data also revealed association of dynamic quenching also. Thermodynamic analysis confirmed that hydrophobic and mainly hydrogen bonding interaction played important role in stabilizing the HSA-EA complex. It further dictates the binding reaction to be enthalpy driven. The secondary structure of HSA was altered upon binding with EA. CD spectroscopic data indicated the fraction of alpha helicity to be decreased from 52% to 40% upon binding to EA. This study will provide an insight on evaluation of this bioactive interaction during transport and releasing efficiency at the target site in human physiological system since HSA is the most important carrier protein in blood serum. A single state binding mode of Human Serum Albumin with Ellagic Acid is proposed. Fluoresence quenching of HSA with Ellagic acid is validated in this study. Number of binding sites of HSA is characterized using Molecular Docking and ITC study.
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Affiliation(s)
- Rudradip Pattanayak
- Department of Biochemistry, University of Calcutta, 35, Ballygunge Circular Road, Kolkata 700019, West Bengal, India
| | - Pijush Basak
- Jagadis Bose National Science Talent Search, 1300, Rajdanga Main Road, Sector C, East Kolkata Township, Kolkata 700107, West Bengal, India
| | - Srikanta Sen
- 229A/230, Mira Tower, Lake Town, Block-A, Kolkata 700089, India
| | - Maitree Bhattacharyya
- Department of Biochemistry, University of Calcutta, 35, Ballygunge Circular Road, Kolkata 700019, West Bengal, India.,Jagadis Bose National Science Talent Search, 1300, Rajdanga Main Road, Sector C, East Kolkata Township, Kolkata 700107, West Bengal, India
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Cristiglio V, Grillo I, Fomina M, Wien F, Shalaev E, Novikov A, Brassamin S, Réfrégiers M, Pérez J, Hennet L. Combination of acoustic levitation with small angle scattering techniques and synchrotron radiation circular dichroism. Application to the study of protein solutions. Biochim Biophys Acta Gen Subj 2016; 1861:3693-3699. [PMID: 27155578 DOI: 10.1016/j.bbagen.2016.04.026] [Citation(s) in RCA: 11] [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: 01/22/2016] [Revised: 04/25/2016] [Accepted: 04/27/2016] [Indexed: 10/21/2022]
Abstract
BACKGROUND The acoustic levitation technique is a useful sample handling method for small solid and liquids samples, suspended in air by means of an ultrasonic field. This method was previously used at synchrotron sources for studying pharmaceutical liquids and protein solutions using x-ray diffraction and small angle x-ray scattering (SAXS). METHODS In this work we combined for the first time this containerless method with small angle neutron scattering (SANS) and synchrotron radiation circular dichroism (SRCD) to study the structural behavior of proteins in solutions during the water evaporation. SANS results are also compared with SAXS experiments. RESULTS The aggregation behavior of 45μl droplets of lysozyme protein diluted in water was followed during the continuous increase of the sample concentration by evaporating the solvent. The evaporation kinetics was followed at different drying stage by SANS and SAXS with a good data quality. In a prospective work using SRCD, we also studied the evolution of the secondary structure of the myoglobin protein in water solution in the same evaporation conditions. CONCLUSIONS Acoustic levitation was applied for the first time with SANS and the high performances of the used neutron instruments made it possible to monitor fast container-less reactions in situ. A preliminary work using SRCD shows the potentiality of its combination with acoustic levitation for studying the evolution of the protein structure with time. GENERAL SIGNIFICANCE This multi-techniques approach could give novel insights into crystallization and self-assembly phenomena of biological compound with promising potential applications in pharmaceutical, food and cosmetics industry. This article is part of a Special Issue entitled "Science for Life" Guest Editor: Dr. Austen Angell, Dr. Salvatore Magazù and Dr. Federica Migliardo.
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Affiliation(s)
- Viviana Cristiglio
- Institut Laue Langevin, 71 avenue des Martyrs, 38000 Grenoble cedex 2, France
| | - Isabelle Grillo
- Institut Laue Langevin, 71 avenue des Martyrs, 38000 Grenoble cedex 2, France
| | - Margarita Fomina
- Department of Physics and Chemistry, University of Palermo, via Archirafi 36, 90123 Palermo, Italy
| | - Frank Wien
- Synchrotron Soleil, L'Orme des Merisiers, BP 48, 91192 Gif sur Yvette Cedex, France
| | | | - Alexey Novikov
- CNRS-CEMHTI, University of Orléans, 1D avenue de la Recherche Scientifique, 45071, Orléans cedex 2, France
| | - Séverine Brassamin
- CNRS-CEMHTI, University of Orléans, 1D avenue de la Recherche Scientifique, 45071, Orléans cedex 2, France
| | - Matthieu Réfrégiers
- Synchrotron Soleil, L'Orme des Merisiers, BP 48, 91192 Gif sur Yvette Cedex, France
| | - Javier Pérez
- Synchrotron Soleil, L'Orme des Merisiers, BP 48, 91192 Gif sur Yvette Cedex, France
| | - Louis Hennet
- CNRS-CEMHTI, University of Orléans, 1D avenue de la Recherche Scientifique, 45071, Orléans cedex 2, France.
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Ajmal MR, Abdelhameed AS, Alam P, Khan RH. Interaction of new kinase inhibitors cabozantinib and tofacitinib with human serum alpha-1 acid glycoprotein. A comprehensive spectroscopic and molecular Docking approach. Spectrochim Acta A Mol Biomol Spectrosc 2016; 159:199-208. [PMID: 26851488 DOI: 10.1016/j.saa.2016.01.049] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [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: 10/14/2015] [Revised: 01/15/2016] [Accepted: 01/23/2016] [Indexed: 06/05/2023]
Abstract
In the current study we have investigated the interaction of newly approved kinase inhibitors namely Cabozantinib (CBZ) and Tofacitinib (TFB) with human Alpha-1 acid glycoprotein (AAG) under simulated physiological conditions using fluorescence quenching measurements, circular dichroism, dynamic light scattering and molecular docking methods. CBZ and TFB binds to AAG with significant affinity and the calculated binding constant for the drugs lie in the order of 10(4). With the increase in temperature the binding constant values decreased for both CBZ and TFB. The fluorescence resonance energy transfer (FRET) from AAG to CBZ and TFB suggested the fluorescence intensity of AAG was quenched by the two studied drugs via the formation of a non-fluorescent complex in the static manner. The molecular distance r value calculated from FRET is around 2 nm for both drugs, fluorescence spectroscopy data was employed for the study of thermodynamic parameters, standard Gibbs free energy change at 300 K was calculated as -5.234 kcal mol(-1) for CBZ-AAG interaction and -6.237 kcal mol(-1) for TFB-AAG interaction, standard enthalpy change and standard entropy change for CBZ-AAG interaction are -9.553 kcal mol(-1) and -14.618 cal mol(-1) K(-1) respectively while for AAG-TFB interaction, standard enthalpy and standard entropy change was calculated as 4.019 kcal mol(-1) and 7.206 cal mol(-1) K(-1) respectively. Protein binding of the two drugs caused the tertiary structure alterations. Dynamic light scattering measurements demonstrated the reduction in the hydrodynamic radii of the protein. Furthermore molecular docking results suggested the Hydrophobic interaction and hydrogen bonding were the interactive forces in the binding process of CBZ to AAG while in case of TFB only hydrophobic interactions were found to be involved, overlap of the binding site for two studied drugs on the AAG molecule was revealed by docking results.
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Affiliation(s)
- Mohammad Rehan Ajmal
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
| | - Ali Saber Abdelhameed
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, P.O. Box 2457, Riyadh 11451, Saudi Arabia
| | - Parvez Alam
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
| | - Rizwan Hasan Khan
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India.
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