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Morales JJD, Téllez Monzón LA, Nieto RL, Jorge-Montalvo P, Visitación-Figueroa L. Valorization of treated wastewater from the soaking of baby alpaca skin fur. Heliyon 2024; 10:e38247. [PMID: 39364233 PMCID: PMC11447450 DOI: 10.1016/j.heliyon.2024.e38247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2024] [Revised: 09/08/2024] [Accepted: 09/20/2024] [Indexed: 10/05/2024] Open
Abstract
Baby alpaca fur industry generates considerable wastewater during the soaking process, which contains high levels of total suspended solids (TSSs), proteins, and salts, among other components. The valorization of wastewater after precipitation, coagulation-flocculation, and aeration treatments was evaluated for use in irrigation water, fertigation, groundwater recharge, concrete construction, and disposal. The precipitation treatment sludge and the coagulation-flocculation treatment were evaluated as a protein source, soil quality improvement, and disposal. The treatment system included evaluations of nine pH levels, seven coagulant doses, and seven aeration times. The contents of TSSs, chemical oxygen demand (COD), total Kjeldalh nitrogen (TKN), ammonia nitrogen (N-NH3), and oils and fats (O&G), among other parameters, were determined in the treated and untreated wastewater. Before entering the treatment system, the physicochemical characterization of the wastewater showed a high concentration of parameters related to organic matter and dust, such as O&G, five-day biological oxygen demand (BOD5), COD, TSSs, TKN, and N-NH3. The optimal removal parameters were pH 12 for the chemical precipitation of proteins, a dose of 480 mg/L FeCl3 as a coagulant for TSSs removal, and 150 min of aeration; removal efficiencies of 99.02 %, 77.49 %, 79.93 %, and 64.62 % for TSSs, Cod, TKN, and N-NH3, respectively, were obtained. The wastewater after treatment can be used for groundwater recharge and concrete construction, and the wastewater with 2 % dilution can be used for irrigation water and fertigation. The sludge after precipitation is rich in protein and can be used as a protein source or soil quality improver.
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Affiliation(s)
- Jacqueline Jannet Dioses Morales
- Center for Research in Chemistry, Toxicology, and Environmental Biotechnology, Department of Chemistry, Faculty of Science, Universidad Nacional Agraria La Molina, 15024, Lima, Peru
| | - Lena Asunción Téllez Monzón
- Center for Research in Chemistry, Toxicology, and Environmental Biotechnology, Department of Chemistry, Faculty of Science, Universidad Nacional Agraria La Molina, 15024, Lima, Peru
| | | | - Paola Jorge-Montalvo
- Center for Research in Chemistry, Toxicology, and Environmental Biotechnology, Department of Chemistry, Faculty of Science, Universidad Nacional Agraria La Molina, 15024, Lima, Peru
| | - Lizardo Visitación-Figueroa
- Center for Research in Chemistry, Toxicology, and Environmental Biotechnology, Department of Chemistry, Faculty of Science, Universidad Nacional Agraria La Molina, 15024, Lima, Peru
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2
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Chota A, Abrahamse H, George BP. Green synthesis and characterization of AgNPs, liposomal loaded AgNPs and ZnPcS 4 photosensitizer for enhanced photodynamic therapy effects in MCF-7 breast cancer cells. Photodiagnosis Photodyn Ther 2024; 48:104252. [PMID: 38901719 DOI: 10.1016/j.pdpdt.2024.104252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Revised: 06/13/2024] [Accepted: 06/17/2024] [Indexed: 06/22/2024]
Abstract
Breast cancer remains a formidable challenge in oncology despite significant advancements in treatment modalities. Conventional therapies such as surgery, chemotherapy, radiation therapy, and hormonal therapy have been the mainstay in managing breast cancer for decades. However, a subset of patient's experiences treatment failure, leading to disease recurrence and progression. Therefore, this study investigates the therapeutic potential of green-synthesized silver nanoparticles (AgNPs) using an African medicinal plant (Dicoma anomala methanol root extract) as a reducing agent for combating breast cancer. AgNPs were synthesized using the bottom-up approach and later modified with liposomes (Lip) loaded with photosensitizer (PS) zinc phthalocyanine tetrasulfonate (Lip@ZnPcS4) using thin film hydration method. The successful formation and Lip modification of AgNPs, alongside ZnPcS4, were confirmed through various analytical techniques including UV-Vis spectroscopy, Fourier-transform infrared spectroscopy (FT-IR), high-resolution transmission electron microscopy (HR-TEM), scanning electron microscopy (SEM) and energy dispersive X-ray spectroscopy (EDS). Following a 24 h treatment period, MCF-7 cells were assessed for viability using 3-[4,5-dimethylthiazol-2-yl]-2,5 diphenyl tetrazolium bromide (MTT viability assay), cell death analysis using mitochondrial membrane potential (MMP) (ΔΨm), Annexin V-fluorescein isothiocyanate (FITC)-propidium iodide (PI) kit, and caspase- 3, 8 and 9 activities. The experiments were repeated four times (n = 4), and the results were analyzed using SPSS statistical software version 27, with a confidence interval set at 0.95. The synthesized nanoparticles and nanocomplex, including AgNPs, AgNPs-Lip, Lip@ZnPcS4, and AgNPs-Lip@ZnPcS4, exhibited notable cytotoxicity and therapeutic efficacy against MCF-7 breast cancer cells. Notably, the induction of apoptosis, governed by the upregulation of apoptotic proteins i.e., caspase 8 and 9 activities. In addition, caspase 3 was not expressed by MCF-7 cells in both control and experimental groups. Given the challenging prognosis associated with breast cancer, the findings underscore the promise of liposomal nanoformulations in cancer photodynamic therapy (PDT), thus warranting further exploration in clinical settings.
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Affiliation(s)
- Alexander Chota
- Laser Research Centre, Faculty of Health Sciences, University of Johannesburg, P.O. Box 17011, Doornfontein 2028, South Africa
| | - Heidi Abrahamse
- Laser Research Centre, Faculty of Health Sciences, University of Johannesburg, P.O. Box 17011, Doornfontein 2028, South Africa
| | - Blassan P George
- Laser Research Centre, Faculty of Health Sciences, University of Johannesburg, P.O. Box 17011, Doornfontein 2028, South Africa.
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Bhatt P, Garad PS, Rayala VVSPK, Radhakrishnanand P, Sankaranarayanan K. Non-thermal plasma modulated l-tyrosine self-assemblies: a potential avenue for fabrication of supramolecular self-assembled biomaterials. RSC Adv 2024; 14:13984-13996. [PMID: 38686299 PMCID: PMC11056826 DOI: 10.1039/d4ra01891e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Accepted: 04/22/2024] [Indexed: 05/02/2024] Open
Abstract
Aromatic amino acids (AAs) have garnered particular interest due to their pivotal roles in numerous biological processes and disorders. Variations in AA self-assembly not only affect protein structures and functions, but their non-covalent interactions such as hydrogen bonding, van der Waals forces, and π-π stacking, yield versatile assemblies vital in bio-inspired material fabrication. Tyrosine (Tyr), a non-essential aromatic amino acid, holds multifaceted significance in the body as a protein building block, neurotransmitter precursor, thyroid hormone contributor, and melanin synthesis regulator. The proficiency of Cold Atmospheric Plasma (CAP) in generating a spectrum of reactive oxygen and nitrogen species has spurred innovative research avenues in the studies of biomolecular components, including its potential for targeted cancer cell ablation and biomolecule modification. In this work, we have assessed the chemical as well as the structural changes in Tyrosine-derived self-assembled structures arising from the CAP-induced reactive species. For a comprehensive understanding of the mechanism, different treatment times, feed gases, and the role of solvent acidification are compared using various spectroscopic and microscopic techniques. LC-ESI-QQQ mass spectra unveiled the emergence of oxygenated and nitro derivatives of l-tyrosine following its interaction with CAP-derived ROS/RNS. SEM and TEM images demonstrated an enhanced surface size of self-assembled structures and the formation of novel nanomaterial-shaped assemblies following CAP treatment. Overall, this study aims to explore CAP's interaction with a single-amino acid, hypothesizing the creation of novel supramolecular structures and scrutinizing CAP-instigated transformations in l-tyrosine self-assembled structures, potentially advancing biomimetic-attributed nanomaterial fabrication which might present a novel frontier in the field of designing functional biomaterials.
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Affiliation(s)
- Priya Bhatt
- Physical Sciences Division, Institute of Advanced Study in Science and Technology, (An Autonomous Institute Under DST, Govt. of India) Vigyan Path, Paschim Boragaon, Garchuk Guwahati Assam 781035 India
- Academy of Scientific and Innovative Research (AcSIR), Campus Postal Staff College Area Sector 19, Kamla Nehru Nagar Ghaziabad 201002 Uttar Pradesh India
| | - Prajakta Sharad Garad
- Department of Medical Device, National Institute of Pharmaceutical Education and Research SilaKatamur (Halugurisuk), P.O.: Changsari, Dist: Kamrup Guwahati Assam-781101 India
| | - V V S Prasanna Kumari Rayala
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research SilaKatamur (Halugurisuk), P.O.: Changsari, Dist: Kamrup Guwahati Assam-781101 India
| | - P Radhakrishnanand
- Department of Pharmaceutical Analysis, National Institute of Pharmaceutical Education and Research SilaKatamur (Halugurisuk), P.O.: Changsari, Dist: Kamrup Guwahati Assam-781101 India
| | - Kamatchi Sankaranarayanan
- Physical Sciences Division, Institute of Advanced Study in Science and Technology, (An Autonomous Institute Under DST, Govt. of India) Vigyan Path, Paschim Boragaon, Garchuk Guwahati Assam 781035 India
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4
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Karkisaval AG, Hassan R, Nguyen A, Balster B, Abedin F, Lal R, Tatulian SA. The structure of tyrosine-10 favors ionic conductance of Alzheimer's disease-associated full-length amyloid-β channels. Nat Commun 2024; 15:1296. [PMID: 38351257 PMCID: PMC10864385 DOI: 10.1038/s41467-023-43821-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Accepted: 11/21/2023] [Indexed: 02/16/2024] Open
Abstract
Amyloid β (Aβ) ion channels destabilize cellular ionic homeostasis, which contributes to neurotoxicity in Alzheimer's disease. The relative roles of various Aβ isoforms are poorly understood. We use bilayer electrophysiology, AFM imaging, circular dichroism, FTIR and fluorescence spectroscopy to characterize channel activities of four most prevalent Aβ peptides, Aβ1-42, Aβ1-40, and their pyroglutamylated forms (AβpE3-42, AβpE3-40) and correlate them with the peptides' structural features. Solvent-induced fluorescence splitting of tyrosine-10 is discovered and used to assess the sequestration from the solvent and membrane insertion. Aβ1-42 effectively embeds in lipid membranes, contains large fraction of β-sheet in a β-barrel-like structure, forms multi-subunit pores in membranes, and displays well-defined ion channel features. In contrast, the other peptides are partially solvent-exposed, contain minimal β-sheet structure, form less-ordered assemblies, and produce irregular ionic currents. These findings illuminate the structural basis of Aβ neurotoxicity through membrane permeabilization and may help develop therapies that target Aβ-membrane interactions.
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Affiliation(s)
- Abhijith G Karkisaval
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, CA, USA
| | - Rowan Hassan
- Department of Physics, University of Central Florida, Orlando, FL, USA
| | - Andrew Nguyen
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Benjamin Balster
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA
| | - Faisal Abedin
- Department of Physics, University of Central Florida, Orlando, FL, USA
- Department of Biology, Xavier University of Louisiana, New Orleans, LA, USA
| | - Ratnesh Lal
- Department of Mechanical and Aerospace Engineering, University of California San Diego, La Jolla, CA, USA.
- Department of Bioengineering, University of California San Diego, La Jolla, CA, USA.
| | - Suren A Tatulian
- Department of Physics, University of Central Florida, Orlando, FL, USA.
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5
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Wiethorn ZR, Hunter KE, Zuehlsdorff TJ, Montoya-Castillo A. Beyond the Condon limit: Condensed phase optical spectra from atomistic simulations. J Chem Phys 2023; 159:244114. [PMID: 38153146 DOI: 10.1063/5.0180405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Accepted: 12/06/2023] [Indexed: 12/29/2023] Open
Abstract
While dark transitions made bright by molecular motions determine the optoelectronic properties of many materials, simulating such non-Condon effects in condensed phase spectroscopy remains a fundamental challenge. We derive a Gaussian theory to predict and analyze condensed phase optical spectra beyond the Condon limit. Our theory introduces novel quantities that encode how nuclear motions modulate the energy gap and transition dipole of electronic transitions in the form of spectral densities. By formulating the theory through a statistical framework of thermal averages and fluctuations, we circumvent the limitations of widely used microscopically harmonic theories, allowing us to tackle systems with generally anharmonic atomistic interactions and non-Condon fluctuations of arbitrary strength. We show how to calculate these spectral densities using first-principles simulations, capturing realistic molecular interactions and incorporating finite-temperature, disorder, and dynamical effects. Our theory accurately predicts the spectra of systems known to exhibit strong non-Condon effects (phenolate in various solvents) and reveals distinct mechanisms for electronic peak splitting: timescale separation of modes that tune non-Condon effects and spectral interference from correlated energy gap and transition dipole fluctuations. We further introduce analysis tools to identify how intramolecular vibrations, solute-solvent interactions, and environmental polarization effects impact dark transitions. Moreover, we prove an upper bound on the strength of cross correlated energy gap and transition dipole fluctuations, thereby elucidating a simple condition that a system must follow for our theory to accurately predict its spectrum.
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Affiliation(s)
- Zachary R Wiethorn
- Department of Chemistry, University of Colorado Boulder, Boulder, Colorado 80309, USA
| | - Kye E Hunter
- Department of Chemistry, Oregon State University, Corvallis, Oregon 97331, USA
| | - Tim J Zuehlsdorff
- Department of Chemistry, Oregon State University, Corvallis, Oregon 97331, USA
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6
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Sandau KC, Arrigali EM, Serban BA, Serban MA. Colorimetric Properties of Bombyx mori Silk Fibroin. ACS Biomater Sci Eng 2023; 9:6623-6631. [PMID: 37931249 DOI: 10.1021/acsbiomaterials.3c00794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2023]
Abstract
Recent reports highlighted several novel applications for the Bombyx mori silk fibroin (SF), as edible coatings for the preservation of food freshness, smart labels, or packaging materials. This study complements these reports and additionally describes the colorimetric sensing properties of the natural protein that could be explored to enhance the practical value of such applications. Our data show that in response to pH changes, reconstituted SF is able to undergo visible color changes that correlate with the intensity of the stimuli, regardless of its physical format or physical cross-linking state. The intensity of the developed color was proportional to the extent of the protein's hydrolytic degradation. We also found that these pH-driven color changes were reversible and interchangeable, with colorless samples at neutral pH, purple in acidic environments, and yellow under basic conditions. Our mechanistic studies identified tryptophan as being responsible for these colorimetric responses, which could be further intensified by the presence of ionized tyrosine functionalities. In addition, we determined that SF's sensing properties also applied to ultraviolet light exposure. Finally, we showed that the innate sensing capabilities of activated SF can be enhanced via the covalent incorporation of additional tryptophan into the protein. Overall, our results further support the utility of SF for sensing applications.
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Affiliation(s)
- Kolton C Sandau
- Department of Biomedical and Pharmaceutical Sciences, University of Montana, Missoula, Montana 59812, United States
- Montana Biotechnology Center (BIOTECH), University of Montana, Missoula, Montana 59812, United States
| | - Elizabeth M Arrigali
- Department of Biomedical and Pharmaceutical Sciences, University of Montana, Missoula, Montana 59812, United States
- Montana Biotechnology Center (BIOTECH), University of Montana, Missoula, Montana 59812, United States
| | - Bogdan A Serban
- Department of Biomedical and Pharmaceutical Sciences, University of Montana, Missoula, Montana 59812, United States
- Montana Biotechnology Center (BIOTECH), University of Montana, Missoula, Montana 59812, United States
| | - Monica A Serban
- Department of Biomedical and Pharmaceutical Sciences, University of Montana, Missoula, Montana 59812, United States
- Montana Biotechnology Center (BIOTECH), University of Montana, Missoula, Montana 59812, United States
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7
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O’Sullivan JJ, Uyeda KS, Stevenson MJ, Heffern MC. Investigation of metal modulation of oxytocin structure receptor-mediated signaling. RSC Chem Biol 2023; 4:165-172. [PMID: 36794023 PMCID: PMC9906307 DOI: 10.1039/d2cb00225f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2022] [Accepted: 12/16/2022] [Indexed: 01/06/2023] Open
Abstract
Oxytocin is a 9-amino acid peptide hormone. Since its discovery in 1954, it has most commonly been studied in relation to its role in stimulating parturition and lactation. However, it is now known that oxytocin has a widely diverse set of functions throughout the body including neuromodulation, bone growth, and inflammation. Previous research has suggested that divalent metal ions may be required for oxytocin activity, but the exact metal species and specific pathways have yet to be fully elucidated. In this work, we focus on characterizing copper and zinc bound forms of oxytocin and related analogs through far-UV circular dichroism. We report that Cu(ii) and Zn(ii) bind uniquely to oxytocin and all analogs investigated. Furthermore, we investigate how these metal bound forms may affect downstream signaling of MAPK activation upon receptor binding. We find that both Cu(ii) and Zn(ii) bound oxytocin attenuates the activation of the MAPK pathway upon receptor binding relative to oxytocin alone. Interestingly, we observed that Zn(ii) bound forms of linear oxytocin facilitate increased MAPK signaling. This study lays the foundation for future work on elucidating the metal effects on oxytocin's diverse bioactivity.
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Affiliation(s)
| | - Kylie S. Uyeda
- Department of Chemistry, University of California, DavisDavisCA95616USA
| | | | - Marie C. Heffern
- Department of Chemistry, University of California, DavisDavisCA95616USA
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8
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Insight into binding mechanism between three whey proteins and mogroside V by multi-spectroscopic and silico methods: Impacts on structure and foaming properties. Food Hydrocoll 2023. [DOI: 10.1016/j.foodhyd.2022.108207] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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9
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Smith E, Condict L, Ashton J, Kasapis S. Molecular interactions between soybean glycinin (11S) and genistein using spectroscopic and in silico analyses. Food Hydrocoll 2023. [DOI: 10.1016/j.foodhyd.2023.108523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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10
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Espina A, Cañamares MV, Jurašeková Z, Sanchez-Cortes S. Analysis of Iron Complexes of Tannic Acid and Other Related Polyphenols as Revealed by Spectroscopic Techniques: Implications in the Identification and Characterization of Iron Gall Inks in Historical Manuscripts. ACS OMEGA 2022; 7:27937-27949. [PMID: 35990485 PMCID: PMC9386834 DOI: 10.1021/acsomega.2c01679] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Accepted: 07/22/2022] [Indexed: 06/15/2023]
Abstract
In this work, a structural analysis of the polyphenol complexes with iron and copper at several conditions is reported. The investigated polyphenols were tannic acid, gallic acid, pyrogallol, and syringic acid, being components and molecular models of the gallnuts usually employed in the past in fabrication of iron gall inks (IGIs). Commercial tannic acid extracted from gallnuts, which is a complex mixture of different gallotannins and simpler galloylglucoses, was also employed in this analysis. This analysis comprised the use of Raman, Fourier-transform infrared (FTIR), UV-vis absorption, and fluorescence spectroscopy. The complexation of iron with these molecules leads to a strong change in color due to the deep restructuring of the polyphenol that can be clearly seen by Raman and FTIR spectra. Three main Raman bands appeared at 1450-1490 cm-1 (ν1), 1320-1345 cm-1 (ν2), and 400-650 cm-1 (ν3), which are characteristic of the metal complexes. The structural changes of the polyphenol complexes with iron were also investigated at different pHs and different polyphenol/iron stoichiometries. Other effects of the interaction of polyphenols with iron are the pH decrease of the mixture upon metal complexation and fluorescence quenching induced by the interaction of iron. This quenching is important since it facilitates the Raman inspection of manuscripts since polyphenols show a strong fluorescence emission that overlaps the Raman spectrum. Furthermore, DFT calculations were performed for the first time on the gallic acid complex with iron in order to elaborate a detailed assignment of the vibrational modes of polyphenols and their metal complexes, something that was missed in previous applications of Raman to IGIs.
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Affiliation(s)
- Alba Espina
- Department of Biophysics, Faculty of Science, P. J. Safarik University, Kosice 04154, Slovakia
| | | | - Zuzana Jurašeková
- Department of Biophysics, Faculty of Science, P. J. Safarik University, Kosice 04154, Slovakia
| | - Santiago Sanchez-Cortes
- Instituto de Estructura de la Materia (CSIC), Serrano, 121. Madrid 28006, Spain
- Center for Interdisciplinary Biosciences, Technology and Innovation Park, P. J. Safarik University, Kosice 04154, Slovakia
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11
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O-GlcNAc modification of leucyl-tRNA synthetase 1 integrates leucine and glucose availability to regulate mTORC1 and the metabolic fate of leucine. Nat Commun 2022; 13:2904. [PMID: 35614056 PMCID: PMC9133088 DOI: 10.1038/s41467-022-30696-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 05/12/2022] [Indexed: 12/11/2022] Open
Abstract
All living organisms have the ability to sense nutrient levels to coordinate cellular metabolism. Despite the importance of nutrient-sensing pathways that detect the levels of amino acids and glucose, how the availability of these two types of nutrients is integrated is unclear. Here, we show that glucose availability regulates the central nutrient effector mTORC1 through intracellular leucine sensor leucyl-tRNA synthetase 1 (LARS1). Glucose starvation results in O-GlcNAcylation of LARS1 on residue S1042. This modification inhibits the interaction of LARS1 with RagD GTPase and reduces the affinity of LARS1 for leucine by promoting phosphorylation of its leucine-binding site by the autophagy-activating kinase ULK1, decreasing mTORC1 activity. The lack of LARS1 O-GlcNAcylation constitutively activates mTORC1, supporting its ability to sense leucine, and deregulates protein synthesis and leucine catabolism under glucose starvation. This work demonstrates that LARS1 integrates leucine and glucose availability to regulate mTORC1 and the metabolic fate of leucine. Leucyl-tRNA synthetase 1 (LARS1) is a leucine sensor for mTORC1 signaling and regulates leucine utilization depending on glucose availability. Here, the author show that O-GlcNAcylation of LARS1 is crucial for its ability to regulate mTORC1 activity and leucine metabolism upon glucose starvation.
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12
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Parray ZA, Ahmad F, Chaudhary AA, Rudayni HA, Al-Zharani M, Hassan MI, Islam A. Size-Dependent Interplay of Volume Exclusion Versus Soft Interactions: Cytochrome c in Macromolecular Crowded Environment. Front Mol Biosci 2022; 9:849683. [PMID: 35693552 PMCID: PMC9174945 DOI: 10.3389/fmolb.2022.849683] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 02/28/2022] [Indexed: 12/03/2022] Open
Abstract
Even though there are a great number of possible conformational states, how a protein generated as a linear unfolded polypeptide efficiently folds into its physiologically active form remained a fascinating and unanswered enigma inside crowded conditions of cells. In this study, various spectroscopic techniques have been exploited to know and understand the effect and mechanism of action of two different sizes of polyethylene glycols, or PEGs (molecular mass ∼10 and ∼20 kilo Daltons, kDa), on cytochrome c (cyt c). The outcomes showed that small size of the PEG leads to perturbation of the protein structure, and conversely, large size of the PEG has stabilizing effect on cyt c. Moreover, binding measurements showed that small size of PEG interacts strongly via soft interactions compared to the larger size of PEG, the latter being governed more by excluded volume effect or preferential exclusion from the protein. Overall, this finding suggests that conformations of protein may be influenced in cellular crowded conditions via interactions which depend upon the size of molecule in the environment. This study proposes that both volume exclusion and soft (chemical) interactions governs the protein’s conformation and functional activities. The cellular environment’s internal architecture as evident from crowder size and shape in this study has a significant role.
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Affiliation(s)
- Zahoor Ahmad Parray
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
- Department of Chemistry, Indian Institute of Technology Delhi, New Delhi, India
| | - Faizan Ahmad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
- Department of Biochemistry, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi, India
| | - Anis Ahmad Chaudhary
- Department of Biology, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia
| | - Hassan Ahmad Rudayni
- Department of Biology, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia
| | - Mohammed Al-Zharani
- Department of Biology, College of Science, Imam Mohammad Ibn Saud Islamic University (IMSIU), Riyadh, Saudi Arabia
| | - Md. Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
- *Correspondence: Asimul Islam,
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13
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Anant A, Saha M, Dhiman S, Singh P, Kurmi BD, Gupta GD, Asati V. An analytical review for the estimation of montelukast sodium. SEPARATION SCIENCE PLUS 2022. [DOI: 10.1002/sscp.202100069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Arjun Anant
- Department of Pharmaceutical Analysis ISF College of Pharmacy Moga Punjab India
| | - Moumita Saha
- Department of Pharmaceutical Analysis ISF College of Pharmacy Moga Punjab India
| | - Shubham Dhiman
- Department of Pharmaceutical Analysis ISF College of Pharmacy Moga Punjab India
| | - Priti Singh
- Department of Pharmaceutical Analysis ISF College of Pharmacy Moga Punjab India
| | - Balak Das Kurmi
- Department of Pharmaceutics ISF College of Pharmacy Moga Punjab India
| | | | - Vivek Asati
- Department of Pharmaceutical Chemistry ISF College of Pharmacy Moga Punjab India
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14
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Impact of high-pressure homogenization on physico-chemical, structural, and rheological properties of quinoa protein isolates. FOOD STRUCTURE 2022. [DOI: 10.1016/j.foostr.2022.100265] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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15
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Espina A, Sanchez-Cortes S, Jurašeková Z. Vibrational Study (Raman, SERS, and IR) of Plant Gallnut Polyphenols Related to the Fabrication of Iron Gall Inks. Molecules 2022; 27:279. [PMID: 35011511 PMCID: PMC8746386 DOI: 10.3390/molecules27010279] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Revised: 12/29/2021] [Accepted: 12/29/2021] [Indexed: 11/29/2022] Open
Abstract
FT-Raman, FTIR, and SERS spectra of the structurally related gallnut polyphenols tannic acid, gallic acid, pyrogallol, and syringic acid are reported in this work aiming at performing a comparative assignation of the bands and finding specific marker features that can identify these compounds in complex polyphenol mixtures. Tannic and gallic acids are the principal components in oak gallnuts, and they can be found in iron gall inks. The different functional groups existing in these molecules and their spatial distribution lead to slight changes of the vibrations. The Raman spectra are dominated by bands corresponding to the ring vibrations, but the substituents in the ring strongly affect these vibrations. In contrast, the FTIR spectra of these molecules are dominated by the peripheral oxygen-containing substituents of the aromatic ring and afford complementary information. SERS spectroscopy can be used to analyze trace amounts of these compounds, but the spectra of these polyphenols show strong changes in comparison with the Raman spectra, indicating a strong interaction with the metal. The most significant modification observed in the SERS spectra of these compounds is the weakening of the benzene 8a ring vibration and the subsequent intensification of the 19a mode of the benzene ring. This mode is also more intense in the FTIR spectra, and its intensification in the SERS spectra could be related to a drastic change in the molecular polarizability associated with the interaction of the polyphenol with the metal in Ag NPs.
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Affiliation(s)
- Alba Espina
- Department of Biophysics, Faculty of Science, Pavol Jozef Safarik University, 040 01 Kosice, Slovakia;
| | - Santiago Sanchez-Cortes
- Instituto de Estructura de la Materia (CSIC), Serrano, 121, 280 06 Madrid, Spain;
- Center for Interdisciplinary Biosciences, Technology and Innovation Park, Pavol Jozef Safarik University, 040 01 Kosice, Slovakia
| | - Zuzana Jurašeková
- Department of Biophysics, Faculty of Science, Pavol Jozef Safarik University, 040 01 Kosice, Slovakia;
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16
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Biocompatible Osmium Telluride-Polypyrrole Nanocomposite Material: Application in Prostate Specific Antigen Immunosensing. Processes (Basel) 2021. [DOI: 10.3390/pr9122203] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Prostate cancer is a dominant global threat to society. It affects nearly 4000 men in South Africa annually, making it the second most threatening cancerous disease after lung cancer. A potential serological biomarker to monitor early diagnosis of prostate cancer is prostate specific antigen (PSA). We used the PSA biomarker in our work to develop an extremely sensitive electrochemical immunosensor to achieve low detection limits. The fabrication steps followed with the combination of thioglycolic acid capped osmium telluride quantum dots (TGA-OsTe2QD)-polypyrrole (PPy) nanocomposite and prostate specific antigen modified on a glassy carbon electrode. The UV-Vis signatures of TGA-OsTe2QD-PPy showed an absorption band at 262 nm which is attributed to the PPy and TGA-OsTe2QD composite. This band corresponds to the energy band gap of 4.4 and 5.4 eV. The CV responses of BSA|Ab|TGA-OsTe2QD|PPy|GCE modified electrode to prostate specific antigen (PSA) was studied within a range of 0–16 ng/mL PSA that was linear, herein referred to as liner range (LR), which produced a limit of detection (LOD) value of 0.36 ng/mL PSA. The values of the immunosensor’s calibration parameters (LR and LOD) make them suitable for real sample application, due to their coverage of the PSA concentration range (0–14 ng/mL) that is of clinical importance.
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17
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Natumi R, Dieziger C, Janssen EML. Cyanobacterial Toxins and Cyanopeptide Transformation Kinetics by Singlet Oxygen and pH-Dependence in Sunlit Surface Waters. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2021; 55:15196-15205. [PMID: 34714625 DOI: 10.1021/acs.est.1c04194] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
To assess the risks associated with cyanobacterial blooms, the persistence and fate processes of cyanotoxins and other bioactive cyanobacterial metabolites need to be evaluated. Here, we investigated the reaction with photochemically produced singlet oxygen (1O2) for 30 cyanopeptides synthesized by Dolichospermum flos aquae, including 9 anabaenopeptins, 18 microcystins, 2 cyanopeptolins, and 1 cyclamide. All compounds were stable in UVA light alone but in the presence of a photosensitizer we observed compound-specific degradation. A strong pH effect on the decay was observed for 18 cyanopeptides that all contained tyrosine or structurally related moieties. We can attribute this effect to the reaction with 1O2 and triplet sensitizer that preferentially react with the deprotonated form of tyrosine moieties. The contribution of 1O2 to indirect phototransformation ranged from 12 to 39% and second-order rate constants for 9 tyrosine-containing cyanopeptides were assessed. Including the pH dependence of the reaction and system-independent second-order rate constants with 1O2 will improve the estimation of half-lives for multiclass cyanopeptide in surface waters. Our data further indicates that naturally occurring triplet sensitizers are likely to oxidize deprotonated tyrosine moieties of cyanopeptides and the specific reactivity and its pH dependence needs to be investigated in future studies.
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Affiliation(s)
- Regiane Natumi
- Department of Environmental Chemistry, Swiss Federal Institute of Aquatic Science and Technology (Eawag), 8600 Dübendorf, Switzerland
| | - Christoph Dieziger
- Department of Environmental Chemistry, Swiss Federal Institute of Aquatic Science and Technology (Eawag), 8600 Dübendorf, Switzerland
| | - Elisabeth M-L Janssen
- Department of Environmental Chemistry, Swiss Federal Institute of Aquatic Science and Technology (Eawag), 8600 Dübendorf, Switzerland
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18
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Adsorption kinetics and dilatational rheological properties of recombinant Pea Albumin-2 at the oil-water interface. Food Hydrocoll 2021. [DOI: 10.1016/j.foodhyd.2021.106866] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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19
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Menard LM, Wood NB, Vigoreaux JO. Secondary Structure of the Novel Myosin Binding Domain WYR and Implications within Myosin Structure. BIOLOGY 2021; 10:603. [PMID: 34209926 PMCID: PMC8301185 DOI: 10.3390/biology10070603] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2021] [Revised: 06/25/2021] [Accepted: 06/27/2021] [Indexed: 01/05/2023]
Abstract
Structural changes in the myosin II light meromyosin (LMM) that influence thick filament mechanical properties and muscle function are modulated by LMM-binding proteins. Flightin is an LMM-binding protein indispensable for the function of Drosophila indirect flight muscle (IFM). Flightin has a three-domain structure that includes WYR, a novel 52 aa domain conserved throughout Pancrustacea. In this study, we (i) test the hypothesis that WYR binds the LMM, (ii) characterize the secondary structure of WYR, and (iii) examine the structural impact WYR has on the LMM. Circular dichroism at 260-190 nm reveals a structural profile for WYR and supports an interaction between WYR and LMM. A WYR-LMM interaction is supported by co-sedimentation with a stoichiometry of ~2.4:1. The WYR-LMM interaction results in an overall increased coiled-coil content, while curtailing ɑ helical content. WYR is found to be composed of 15% turns, 31% antiparallel β, and 48% 'other' content. We propose a structural model of WYR consisting of an antiparallel β hairpin between Q92-K114 centered on an ASX or β turn around N102, with a G1 bulge at G117. The Drosophila LMM segment used, V1346-I1941, encompassing conserved skip residues 2-4, is found to possess a traditional helical profile but is interpreted as having <30% helical content by multiple methods of deconvolution. This low helicity may be affiliated with the dynamic behavior of the structure in solution or the inclusion of a known non-helical region in the C-terminus. Our results support the hypothesis that WYR binds the LMM and that this interaction brings about structural changes in the coiled-coil. These studies implicate flightin, via the WYR domain, for distinct shifts in LMM secondary structure that could influence the structural properties and stabilization of the thick filament, scaling to modulation of whole muscle function.
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Affiliation(s)
| | | | - Jim O. Vigoreaux
- Department of Biology, University of Vermont, Burlington, VT 05405, USA; (L.M.M.); (N.B.W.)
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20
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Application of Fundamental Techniques for Physicochemical Characterizations to Understand Post-Formulation Performance of Pharmaceutical Nanocrystalline Materials. CRYSTALS 2021. [DOI: 10.3390/cryst11030310] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Nanocrystalline materials (NCM, i.e., crystalline nanoparticles) have become an important class of materials with great potential for applications ranging from drug delivery and electronics to optics. Drug nanocrystals (NC) and nano co-crystals (NCC) are examples of NCM with fascinating physicochemical properties and have attracted significant attention in drug delivery. NCM are categorized by advantageous properties, such as high drug-loading efficiency, good long-term physical stability, steady and predictable drug release, and long systemic circulation time. These properties make them excellent formulations for the efficient delivery of a variety of active pharmaceutical ingredients (API). In this review, we summarize the recent advances in drug NCM-based therapy options. Currently, there are three main methods to synthesize drug NCM, including top-down, bottom-up, and combination methods. The fundamental characterization methods of drug NCM are elaborated. Furthermore, the applications of these characterizations and their implications on the post-formulation performance of NCM are introduced.
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21
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Parray ZA, Ahmad F, Alajmi MF, Hussain A, Hassan MI, Islam A. Interaction of polyethylene glycol with cytochrome c investigated via in vitro and in silico approaches. Sci Rep 2021; 11:6475. [PMID: 33742055 PMCID: PMC7979836 DOI: 10.1038/s41598-021-85792-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2020] [Accepted: 02/12/2021] [Indexed: 12/11/2022] Open
Abstract
One of the significant proteins that have attracted research groups due to virtue of being a potent selective anticancer drug target and property of triggering apoptosis upon release in cytoplasm is cytochrome c (cyt c). The mechanical transformations due to the macromolecular crowding in membrane in the mammalian cell are proposed to be useful inductors of changes in volume. It is very interesting to know that mitochondrial function were observed to be improved by polyethylene glycol (PEG) interaction, which in turn inhibits the cyt c (a pro-apoptotic cell death factor). In this work, the effect of polyethylene glycol of molecular weight 4 kilo Dalton (PEG 4 kDa) was investigated to highlight the structural transformations (tertiary and secondary structure) in cyt c using a choice of spectroscopic techniques (including UV-Vis absorption, near-UV, far-UV and Soret circular dichroism and fluorescence spectroscopy), which shows noteworthy shifts in the secondary and tertiary structures at higher concentrations of PEG 4 kDa with small changes in the heme-globular interactions. The size distribution changes of native protein treated with various concentrations of the crowder were observed and analyzed by dynamic light scattering (DLS). The interaction studies of the crowder with the protein was observed and analyzed by FTIR, isothermal titration calorimetry, time resolved fluorescence and molecular docking. The investigations suggested that the structural changes in the protein occurred due to soft interactions of PEG 4 kDa, which usually destabilizes proteins. The experimental evidence in this study proposed that crowding could be another approach to mechanical super-competition and free of certain markers that could aid in the identification and control of various diseases. This study suggests that crowders at specific concentrations, which softly interact with proteins, can be exploited as remedy for various diseases.
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Affiliation(s)
- Zahoor Ahmad Parray
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Faizan Ahmad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Mohamed F Alajmi
- Department of Pharmacognosy College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Afzal Hussain
- Department of Pharmacognosy College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Md Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India
| | - Asimul Islam
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, Jamia Nagar, New Delhi, 110025, India.
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22
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Kim H, Bang KM, Ha H, Cho NH, Namgung SD, Im SW, Cho KH, Kim RM, Choi WI, Lim YC, Shin JY, Song HK, Kim NK, Nam KT. Tyrosyltyrosylcysteine-Directed Synthesis of Chiral Cobalt Oxide Nanoparticles and Peptide Conformation Analysis. ACS NANO 2021; 15:979-988. [PMID: 33332089 DOI: 10.1021/acsnano.0c07655] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Chiral inorganic nanomaterials have revealed opportunities in various fields owing to their strong light-matter interactions. In particular, chiral metal oxide nanomaterials that can control light and biochemical reactions have been highlighted due to their catalytic activity and biocompatibility. In this study, we present the synthesis of chiral cobalt oxide nanoparticles with a g-factor of 0.01 in the UV-visible region using l- and d-Tyr-Tyr-Cys ligands. The conformation of the Tyr-Tyr-Cys peptide on the nanoparticle surfaces was identified by 2D NMR spectroscopy analysis. In addition, the sequence effect of Tyr-Tyr-Cys developing chiral nanoparticles was analyzed. The revealed peptide structure, along with the experimental results, demonstrate the important role of the thiol group and carboxyl group of the Tyr-Tyr-Cys ligand in chirality evolution. Importantly, due to the magnetic properties of chiral cobalt oxide nanoparticles and their strong absorption in the UV region, the circular dichroism (CD) responses can be dramatically modulated under an external magnetic field.
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Affiliation(s)
- Hyeohn Kim
- Department of Materials Science and Engineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Kyeong-Mi Bang
- Department of Life Sciences, Korea University, Seoul 02841, Republic of Korea
- Advanced Analysis Center, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea
| | - Heonjin Ha
- Department of Materials Science and Engineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Nam Heon Cho
- Department of Materials Science and Engineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Seok Daniel Namgung
- Department of Materials Science and Engineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Sang Won Im
- Department of Materials Science and Engineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Kang Hee Cho
- Department of Materials Science and Engineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Ryeong Myeong Kim
- Department of Materials Science and Engineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Won Il Choi
- Department of Materials Science and Engineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Yae-Chan Lim
- Department of Materials Science and Engineering, Seoul National University, Seoul 08826, Republic of Korea
| | - Ji-Yeon Shin
- Department of Life Sciences, Korea University, Seoul 02841, Republic of Korea
- Advanced Analysis Center, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea
| | - Hyun Kyu Song
- Department of Life Sciences, Korea University, Seoul 02841, Republic of Korea
| | - Nak-Kyoon Kim
- Advanced Analysis Center, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea
| | - Ki Tae Nam
- Department of Materials Science and Engineering, Seoul National University, Seoul 08826, Republic of Korea
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23
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Huamani-Palomino RG, Córdova BM, Pichilingue L. ER, Venâncio T, Valderrama AC. Functionalization of an Alginate-Based Material by Oxidation and Reductive Amination. Polymers (Basel) 2021; 13:polym13020255. [PMID: 33466684 PMCID: PMC7828833 DOI: 10.3390/polym13020255] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 01/03/2021] [Accepted: 01/05/2021] [Indexed: 01/28/2023] Open
Abstract
This research focused on the synthesis of a functional alginate-based material via chemical modification processes with two steps: oxidation and reductive amination. In previous alginate functionalization with a target molecule such as cysteine, the starting material was purified and characterized by UV-Vis, 1H-NMR and HSQC. Additionally, the application of FT-IR techniques during each step of alginate functionalization was very useful, since new bands and spiked signals around the pyranose ring (1200–1000 cm−1) and anomeric region (1000–750 cm−1) region were identified by a second derivative. Additionally, the presence of C1-H1 of β-D-mannuronic acid residue as well as C1-H1 of α-L-guluronic acid residue was observed in the FT-IR spectra, including a band at 858 cm−1 with characteristics of the N-H moiety from cysteine. The possibility of attaching cysteine molecules to an alginate backbone by oxidation and post-reductive amination processes was confirmed through 13C-NMR in solid state; a new peak at 99.2 ppm was observed, owing to a hemiacetal group formed in oxidation alginate. Further, the peak at 31.2 ppm demonstrates the presence of carbon -CH2-SH in functionalized alginate—clear evidence that cysteine was successfully attached to the alginate backbone, with 185 μmol of thiol groups per gram polymer estimated in alginate-based material by UV-Visible. Finally, it was observed that guluronic acid residue of alginate are preferentially more affected than mannuronic acid residue in the functionalization.
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Affiliation(s)
- Ronny G. Huamani-Palomino
- Laboratorio de Investigación en Biopolímeros y Metalofármacos, Facultad de Ciencias, Escuela Profesional de Química, Universidad Nacional de Ingeniería, Av. Túpac Amaru 210, Lima 15333, Peru;
- Correspondence: (R.G.H.-P.); (A.C.V.)
| | - Bryan M. Córdova
- Laboratorio de Investigación en Biopolímeros y Metalofármacos, Facultad de Ciencias, Escuela Profesional de Química, Universidad Nacional de Ingeniería, Av. Túpac Amaru 210, Lima 15333, Peru;
| | - Elvis Renzo Pichilingue L.
- Facultad de Ciencias, Escuela de Química, Universidad Nacional de Ingeniería. Av. Túpac Amaru 210, Lima 15333, Peru;
| | - Tiago Venâncio
- Laboratório de Ressonância Magnética Nuclear, Departamento de Química, Universidade Federal de Sao Carlos, São Carlos 13565-905, São Paulo, Brazil;
| | - Ana C. Valderrama
- Laboratorio de Investigación en Biopolímeros y Metalofármacos, Facultad de Ciencias, Escuela Profesional de Química, Universidad Nacional de Ingeniería, Av. Túpac Amaru 210, Lima 15333, Peru;
- Correspondence: (R.G.H.-P.); (A.C.V.)
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24
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Ramohlola KE, Iwuoha EI, Hato MJ, Modibane KD. Instrumental Techniques for Characterization of Molybdenum Disulphide Nanostructures. JOURNAL OF ANALYTICAL METHODS IN CHEMISTRY 2020; 2020:8896698. [PMID: 33381353 PMCID: PMC7758135 DOI: 10.1155/2020/8896698] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 11/10/2020] [Accepted: 11/27/2020] [Indexed: 06/12/2023]
Abstract
The excellent chemical and physical properties of materials (nanomaterials) with dimensions of less than 100 nm (nanometers) resulted in researchers and industrialists to have great interest in their discovery and applications in various systems/applications. As their sizes are reduced to nanoscale, these nanomaterials tend to possess exceptional properties differing from those of their bulk counterparts; hence, they have found applications in electronics and medicines. In order to apply them in those applications, there is a need to synthesise these nanomaterials and study their structural, optical, and electrochemical properties. Among several nanomaterials, molybdenum disulphide (MoS2) has received a great interest in energy applications due to its exceptional properties such as stability, conductivity, and catalytic activities. Hence, the great challenge lies in finding the state-of-the-art characterization techniques to reveal the different properties of MoS2 nanostructures with great accuracy. In this regard, there is a need to study and employ several techniques to accurately study the surface chemistry and physics of the MoS2 nanostructures. Hence, this review will comprehensively discuss a detailed literature survey on analytical techniques that can be used to study the chemical, physical, and surface properties of MoS2 nanostructures, namely, ultraviolet-visible spectroscopy (UV-vis), photoluminescence spectroscopy (PL), Fourier transform infrared spectroscopy (FTIR), Raman spectroscopy, time-of-flight secondary ion mass spectroscopy (TOF-SIMS), X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), scanning and transmission electron microscopies (SEM and TEM), atomic force microscopy (AFM), energy dispersive X-ray spectroscopy (EDS/X), thermogravimetric analysis (TGA), differential scanning calorimetry (DSC), and electroanalytical methods which include linear sweep (LSV) and cyclic (CV) voltammetry and electrochemical impedance spectroscopy (EIS).
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Affiliation(s)
- Kabelo E. Ramohlola
- Nanotechnology Research Lab, Department of Chemistry, School of Physical and Mineral Sciences, University of Limpopo (Turfloop), Sovenga 0727, Polokwane, South Africa
| | - Emmanuel I. Iwuoha
- SensorLab, Chemistry Department, University of the Western Cape, Bellville, 7535 Cape Town, South Africa
| | - Mpitloane J. Hato
- Nanotechnology Research Lab, Department of Chemistry, School of Physical and Mineral Sciences, University of Limpopo (Turfloop), Sovenga 0727, Polokwane, South Africa
| | - Kwena D. Modibane
- Nanotechnology Research Lab, Department of Chemistry, School of Physical and Mineral Sciences, University of Limpopo (Turfloop), Sovenga 0727, Polokwane, South Africa
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25
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Lo SY, Goulet DL, Fraaz U, Siemann S. Effect of pH and denaturants on the fold and metal status of anthrax lethal factor. Arch Biochem Biophys 2020; 692:108547. [PMID: 32828796 DOI: 10.1016/j.abb.2020.108547] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 08/02/2020] [Accepted: 08/17/2020] [Indexed: 01/26/2023]
Abstract
Anthrax lethal factor (LF) is a critical component of the anthrax toxin, and functions intracellularly as a zinc-dependent endopeptidase targeting proteins involved in maintaining critical host signaling pathways. To reach the cytoplasm, LF requires to be unfolded and guided through the narrow protective antigen pore in a pH-dependent process. The current study sought to address the question as to whether LF is capable of retaining its metal ion when exposed to a low-pH environment (similar to that found in late endosomes) and an unfolding stress (induced by urea). Using a combination of tryptophan fluorescence spectroscopy and chelation studies, we show that a decrease in the pH value (from 7.0 to 5.0) leads to a pronounced shift in the onset of structural alterations in LF to lower urea concentrations. More importantly, the enzyme was found to retain its Zn2+ ion beyond the unfolding transitions monitored by Trp fluorescence, a finding indicative of tight metal binding to LF in a non-native state. In addition, an analysis of red-edge excitation shift (REES) spectra suggests the protein to maintain residual structure (a feature necessary for metal binding) even at very high denaturant concentrations. Furthermore, studies using the chromophoric chelator 4-(2-pyridylazo)resorcinol (PAR) revealed LF's Zn2+ ion to become accessible to complexation at urea concentrations in between those required to cause structural changes and metal dissociation. This phenomenon likely originates from the conversion of a PAR-inaccessible (closed) to a PAR-accessible (open) state of LF at intermediate denaturant concentrations.
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Affiliation(s)
- Suet Y Lo
- Department of Chemistry and Biochemistry, Laurentian University, Sudbury, Ontario, P3E 2C6, Canada
| | - Danica L Goulet
- Department of Chemistry and Biochemistry, Laurentian University, Sudbury, Ontario, P3E 2C6, Canada
| | - Usama Fraaz
- Department of Chemistry and Biochemistry, Laurentian University, Sudbury, Ontario, P3E 2C6, Canada
| | - Stefan Siemann
- Department of Chemistry and Biochemistry, Laurentian University, Sudbury, Ontario, P3E 2C6, Canada.
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26
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Mancini G, Del Galdo S, Chandramouli B, Pagliai M, Barone V. Computational Spectroscopy in Solution by Integration of Variational and Perturbative Approaches on Top of Clusterized Molecular Dynamics. J Chem Theory Comput 2020; 16:5747-5761. [PMID: 32697580 PMCID: PMC8009517 DOI: 10.1021/acs.jctc.0c00454] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
![]()
Multiscale QM/MM approaches have
become the most suitable and effective
methods for the investigation of spectroscopic properties of medium-
or large-size chromophores in condensed phases. On these grounds,
we are developing a novel workflow aimed at improving the generality,
reliability, and ease of use of the available tools. In the present
paper, we report the latest developments of such an approach with
specific reference to a general workplan starting with the addition
of acetonitrile to the panel of solvents already available in the
General Liquid Optimized Boundary (GLOB) model enforcing nonperiodic
boundary conditions (NPBC). Next, the solvatochromic shifts induced
by acetonitrile on both rigid (uracil and thymine) and flexible (thyrosine)
chromophores have been studied introducing in our software a number
of new features ranging from rigid-geometry NPBC molecular dynamics
based on the quaternion formalism to a full integration of variational
(ONIOM) and perturbative (perturbed matrix method (PMM)) approaches
for describing different solute–solvent topologies and local
fluctuations, respectively. Finally, thymine and uracil have been
studied also in methanol to point out the generality of the computational
strategy. While further developments are surely needed, the strengths
of our integrated approach even in its present version are demonstrated
by the accuracy of the results obtained by an unsupervised approach
and coupled to a computational cost strongly reduced with respect
to that of conventional QM/MM models without any appreciable accuracy
deterioration.
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Affiliation(s)
- Giordano Mancini
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.,Istituto Nazionale di Fisica Nucleare (INFN) sezione di Pisa, Largo Bruno Pontecorvo 3, 56127 Pisa, Italy
| | - Sara Del Galdo
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
| | | | - Marco Pagliai
- Dipartimento di Chimica "Ugo Schiff", Università degli Studi di Firenze, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7, I-56126 Pisa, Italy.,Istituto Nazionale di Fisica Nucleare (INFN) sezione di Pisa, Largo Bruno Pontecorvo 3, 56127 Pisa, Italy
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27
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Karadi K, Kapetanaki SM, Raics K, Pecsi I, Kapronczai R, Fekete Z, Iuliano JN, Collado JT, Gil AA, Orban J, Nyitrai M, Greetham GM, Vos MH, Tonge PJ, Meech SR, Lukacs A. Functional dynamics of a single tryptophan residue in a BLUF protein revealed by fluorescence spectroscopy. Sci Rep 2020; 10:2061. [PMID: 32029866 PMCID: PMC7005313 DOI: 10.1038/s41598-020-59073-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 01/23/2020] [Indexed: 11/17/2022] Open
Abstract
Blue Light Using Flavin (BLUF) domains are increasingly being adopted for use in optogenetic constructs. Despite this, much remains to be resolved on the mechanism of their activation. The advent of unnatural amino acid mutagenesis opens up a new toolbox for the study of protein structural dynamics. The tryptophan analogue, 7-aza-Trp (7AW) was incorporated in the BLUF domain of the Activation of Photopigment and pucA (AppA) photoreceptor in order to investigate the functional dynamics of the crucial W104 residue during photoactivation of the protein. The 7-aza modification to Trp makes selective excitation possible using 310 nm excitation and 380 nm emission, separating the signals of interest from other Trp and Tyr residues. We used Förster energy transfer (FRET) between 7AW and the flavin to estimate the distance between Trp and flavin in both the light- and dark-adapted states in solution. Nanosecond fluorescence anisotropy decay and picosecond fluorescence lifetime measurements for the flavin revealed a rather dynamic picture for the tryptophan residue. In the dark-adapted state, the major population of W104 is pointing away from the flavin and can move freely, in contrast to previous results reported in the literature. Upon blue-light excitation, the dominant tryptophan population is reorganized, moves closer to the flavin occupying a rigidly bound state participating in the hydrogen-bond network around the flavin molecule.
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Affiliation(s)
- Kristof Karadi
- Department of Biophysics, Medical School, University of Pécs, 7624, Pécs, Hungary.,Szentagothai Research Center, University of Pécs, 7624, Pécs, Hungary
| | - Sofia M Kapetanaki
- Department of Biophysics, Medical School, University of Pécs, 7624, Pécs, Hungary.,Szentagothai Research Center, University of Pécs, 7624, Pécs, Hungary
| | - Katalin Raics
- Department of Biophysics, Medical School, University of Pécs, 7624, Pécs, Hungary
| | - Ildiko Pecsi
- Department of Biophysics, Medical School, University of Pécs, 7624, Pécs, Hungary
| | - Robert Kapronczai
- Department of Biophysics, Medical School, University of Pécs, 7624, Pécs, Hungary
| | - Zsuzsanna Fekete
- Department of Biophysics, Medical School, University of Pécs, 7624, Pécs, Hungary
| | - James N Iuliano
- Department of Chemistry, Stony Brook University, Stony Brook, NY, 11794-3400, USA
| | | | - Agnieszka A Gil
- Department of Chemistry, Stony Brook University, Stony Brook, NY, 11794-3400, USA
| | - Jozsef Orban
- Department of Biophysics, Medical School, University of Pécs, 7624, Pécs, Hungary
| | - Miklos Nyitrai
- Department of Biophysics, Medical School, University of Pécs, 7624, Pécs, Hungary.,Szentagothai Research Center, University of Pécs, 7624, Pécs, Hungary
| | - Greg M Greetham
- Central Laser Facility, Harwell Science and Innovation Campus, Didcot, Oxfordshire, UK
| | - Marten H Vos
- LOB, CNRS, INSERM, Ecole Polytechnique, Institut Polytechnique de Paris, 91128, Palaiseau, Cedex, France
| | - Peter J Tonge
- Department of Chemistry, Stony Brook University, Stony Brook, NY, 11794-3400, USA
| | - Stephen R Meech
- School of Chemistry, University of East Anglia, Norwich, NR4 7TJ, UK
| | - Andras Lukacs
- Department of Biophysics, Medical School, University of Pécs, 7624, Pécs, Hungary. .,Szentagothai Research Center, University of Pécs, 7624, Pécs, Hungary.
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28
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Wang G, Platas-Iglesias C, Angelovski G. Europium(III) Macrocyclic Chelates Appended with Tyrosine-based Chromophores and Di-(2-picolyl)amine-based Receptors: Turn-On Luminescent Chemosensors Selective to Zinc(II) Ions. Chempluschem 2020; 85:806-814. [PMID: 31967740 DOI: 10.1002/cplu.201900731] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Revised: 01/08/2020] [Indexed: 11/06/2022]
Abstract
Zinc ions play an important role in many biological processes in the human body. To selectively detect Zn2+ , two EuDO3A-based complexes (DO3A=1,4,7,10-tetraazacyclododecane-1,4,7-tricarboxylic acid) appended with tyrosine as a chromophore and di-(2-picolyl)amine (DPA) as the Zn2+ recognition moiety were developed as suitable luminescent sensors. Their luminescence intensity is affected by the photoinduced electron transfer mechanism. Upon addition of Zn2+ , both probes display an up to sevenfold enhancement in Eu3+ emission. Competition experiments demonstrated their specificity toward Zn2+ over other metal ions, while also revealing the nonspecificity of the derivatives lacking the DPA-moiety, thus confirming the essential role of the DPA for the recognition of Zn2+ . The induced emission changes of Eu3+ allow for precise quantitative analysis of Zn2+ , establishing these lanthanide-based complexes as viable chemosensors for biological applications.
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Affiliation(s)
- Gaoji Wang
- MR Neuroimaging Agents, Max Planck Institute for Biological Cybernetics, Max-Planck-Ring 11, 72076, Tübingen, Germany
| | - Carlos Platas-Iglesias
- Centro de Investigacións Científicas Avanzadas (CICA) and Departamento de Química Facultade de Ciencias, Universidade da Coruña, A Coruña, Galicia, Spain
| | - Goran Angelovski
- MR Neuroimaging Agents, Max Planck Institute for Biological Cybernetics, Max-Planck-Ring 11, 72076, Tübingen, Germany
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29
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Honegger P, Steinhauser O. The protein-water nuclear Overhauser effect (NOE) as an indirect microscope for molecular surface mapping of interaction patterns. Phys Chem Chem Phys 2019; 22:212-222. [PMID: 31799520 DOI: 10.1039/c9cp04752b] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
In this computational study, the intermolecular solute-solvent Nuclear Overhauser Effect (NOE) of the model protein ubiquitin in different chemical environments (free, bound to a partner protein and encapsulated) is investigated. Short-ranged NOE observables such as the NOE/ROE ratio reveal hydration phenomena on absolute timescales such as fast hydration sites and slow water clefts. We demonstrate the ability of solute-solvent NOE differences measured of the same protein in different chemical environments to reveal hydration changes on the relative timescale. The resulting NOE/ROE-surface maps are shown to be a central key for analyzing biologically relevant chemical influences such as complexation and confinement: the presence of a complexing macromolecule or a confining surface wall modulates the water mobility in the vicinity of the probe protein, hence revealing which residues of said protein are proximate to the foreign interface and which are chemically unaffected. This way, hydration phenomena can serve to indirectly map the precise influence (position) of other molecules or interfaces onto the protein surface. This proposed one-protein many-solvents approach may offer experimental benefits over classical one-protein other-protein pseudo-intermolecular transient NOEs. Furthermore, combined influences such as complexation and confinement may exert non-additive influences on the protein compared to a reference state. We offer a mathematical method to disentangle the influence of these two different chemical environments.
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Affiliation(s)
- Philipp Honegger
- University of Vienna, Faculty of Chemistry, Department of Computational Biological Chemistry, Währingerstr. 17, A-1090 Vienna, Austria.
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30
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Szekeres LI, Bálint S, Galbács G, Kálomista I, Kiss T, Larsen FH, Hemmingsen L, Jancsó A. Hg 2+ and Cd 2+ binding of a bioinspired hexapeptide with two cysteine units constructed as a minimalistic metal ion sensing fluorescent probe. Dalton Trans 2019; 48:8327-8339. [PMID: 31111849 DOI: 10.1039/c9dt01141b] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Hg2+ and Cd2+ complexation of a short hexapeptide, Ac-DCSSCY-NH2 (DY), was studied by pH-potentiometry, UV and NMR spectroscopy and fluorimetry in aqueous solutions and the Hg2+-binding ability of the ligand was also described in an immobilized form, where the peptides were anchored to a hydrophilic resin. Hg2+ was demonstrated to form a 1 : 1 complex with the ligand even at pH = 2.0 while Cd2+ coordination by the peptide takes place only above pH ∼ 3.5. Both metal ions form bis-ligand complexes by the coordination of four Cys-thiolates at ligand excess above pH ∼ 5.5 (Cd2+) and 7.0 (Hg2+). Fluorescence studies demonstrated a Hg2+ induced concentration-dependent quenching of the Tyr fluorescence until a 1 : 1 Hg2+ : DY ratio. The fluorescence emission intensity decreases linearly with the increasing Hg2+ concentration in a range of over two orders of magnitude. The fact that this occurs even in the presence of 1.0 eq. of Cd2+ per ligand reflects a complete displacement of the latter metal ion by Hg2+ from its peptide-bound form. The immobilized peptide was also shown to bind Hg2+ very efficiently even from samples at pH = 2.0. However, the existence of lower affinity binding sites was also demonstrated by binding of more than 1.0 eq. of Hg2+ per immobilized DY molecule under Hg2+-excess conditions. Experiments performed with a mixture of four metal ions, Hg2+, Cd2+, Zn2+ and Ni2+, indicate that this molecular probe may potentially be used in Hg2+-sensing systems under acidic conditions for the measurement of μM range concentrations.
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Affiliation(s)
- Levente I Szekeres
- Department of Inorganic and Analytical Chemistry, University of Szeged, Dóm tér 7, Szeged, H-6720, Hungary.
| | - Sára Bálint
- Department of Inorganic and Analytical Chemistry, University of Szeged, Dóm tér 7, Szeged, H-6720, Hungary.
| | - Gábor Galbács
- Department of Inorganic and Analytical Chemistry, University of Szeged, Dóm tér 7, Szeged, H-6720, Hungary.
| | - Ildikó Kálomista
- Department of Inorganic and Analytical Chemistry, University of Szeged, Dóm tér 7, Szeged, H-6720, Hungary.
| | - Tamás Kiss
- Department of Inorganic and Analytical Chemistry, University of Szeged, Dóm tér 7, Szeged, H-6720, Hungary.
| | - Flemming H Larsen
- Department of Food Science, University of Copenhagen, Rolighedsvej 30, 1958 Frederiksberg C, Denmark
| | - Lars Hemmingsen
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark
| | - Attila Jancsó
- Department of Inorganic and Analytical Chemistry, University of Szeged, Dóm tér 7, Szeged, H-6720, Hungary.
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31
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Sauer DG, Melcher M, Mosor M, Walch N, Berkemeyer M, Scharl-Hirsch T, Leisch F, Jungbauer A, Dürauer A. Real-time monitoring and model-based prediction of purity and quantity during a chromatographic capture of fibroblast growth factor 2. Biotechnol Bioeng 2019; 116:1999-2009. [PMID: 30934111 PMCID: PMC6618329 DOI: 10.1002/bit.26984] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 03/15/2019] [Accepted: 03/28/2019] [Indexed: 12/14/2022]
Abstract
Process analytical technology combines understanding and control of the process with real‐time monitoring of critical quality and performance attributes. The goal is to ensure the quality of the final product. Currently, chromatographic processes in biopharmaceutical production are predominantly monitored with UV/Vis absorbance and a direct correlation with purity and quantity is limited. In this study, a chromatographic workstation was equipped with additional online sensors, such as multi‐angle light scattering, refractive index, attenuated total reflection Fourier‐transform infrared, and fluorescence spectroscopy. Models to predict quantity, host cell proteins (HCP), and double‐stranded DNA (dsDNA) content simultaneously were developed and exemplified by a cation exchange capture step for fibroblast growth factor 2 expressed in Escherichia coliOnline data and corresponding offline data for product quantity and co‐eluting impurities, such as dsDNA and HCP, were analyzed using boosted structured additive regression. Different sensor combinations were used to achieve the best prediction performance for each quality attribute. Quantity can be adequately predicted by applying a small predictor set of the typical chromatographic workstation sensor signals with a test error of 0.85 mg/ml (range in training data: 0.1–28 mg/ml). For HCP and dsDNA additional fluorescence and/or attenuated total reflection Fourier‐transform infrared spectral information was important to achieve prediction errors of 200 (2–6579 ppm) and 340 ppm (8–3773 ppm), respectively.
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Affiliation(s)
| | - Michael Melcher
- Austrian Centre of Industrial Biotechnology, Vienna, Austria.,Institute of Applied Statistics and Computing, University of Natural Resources and Life Sciences Vienna, Vienna, Austria
| | - Magdalena Mosor
- Austrian Centre of Industrial Biotechnology, Vienna, Austria
| | - Nicole Walch
- Biopharmaceuticals Operations Austria, Manufacturing Science, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, Vienna, Austria
| | - Matthias Berkemeyer
- Biopharma Process Science Austria, Boehringer Ingelheim Regional Center Vienna GmbH & Co KG, Vienna, Austria
| | - Theresa Scharl-Hirsch
- Austrian Centre of Industrial Biotechnology, Vienna, Austria.,Institute of Applied Statistics and Computing, University of Natural Resources and Life Sciences Vienna, Vienna, Austria
| | - Friedrich Leisch
- Austrian Centre of Industrial Biotechnology, Vienna, Austria.,Institute of Applied Statistics and Computing, University of Natural Resources and Life Sciences Vienna, Vienna, Austria
| | - Alois Jungbauer
- Austrian Centre of Industrial Biotechnology, Vienna, Austria.,Department of Biotechnology, University of Natural Resources and Life Sciences Vienna, Vienna, Austria
| | - Astrid Dürauer
- Austrian Centre of Industrial Biotechnology, Vienna, Austria.,Department of Biotechnology, University of Natural Resources and Life Sciences Vienna, Vienna, Austria
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32
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Del Galdo S, Chandramouli B, Mancini G, Barone V. Assessment of Multi-Scale Approaches for Computing UV–Vis Spectra in Condensed Phases: Toward an Effective yet Reliable Integration of Variational and Perturbative QM/MM Approaches. J Chem Theory Comput 2019; 15:3170-3184. [DOI: 10.1021/acs.jctc.9b00120] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Sara Del Galdo
- Istituto di Chimica dei Composti OrganoMetallici (ICCOMCNR), UOS di Pisa, Area della Ricerca CNR, Consiglio Nazionale delle Ricerche, Via G. Moruzzi 1, I-56124 Pisa, Italy
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
| | - Balasubramanian Chandramouli
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
- Compunet, Istituto Italiano di Tecnologia (IIT), Via Morego 30, I-16163 Genova, Italy
| | - Giordano Mancini
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
- Istituto Nazionale di Fisica Nucleare (INFN) sezione di Pisa, Largo Bruno Pontecorvo 3, I-56127 Pisa, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7, I-56126 Pisa, Italy
- Istituto Nazionale di Fisica Nucleare (INFN) sezione di Pisa, Largo Bruno Pontecorvo 3, I-56127 Pisa, Italy
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33
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Vignali V, S. Miranda B, Lodoso-Torrecilla I, van Nisselroy CAJ, Hoogenberg BJ, Dantuma S, Hollmann F, de Vries JW, Warszawik EM, Fischer R, Commandeur U, van Rijn P. Biocatalytically induced surface modification of the tobacco mosaic virus and the bacteriophage M13. Chem Commun (Camb) 2019; 55:51-54. [DOI: 10.1039/c8cc08042a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A one-step laccase induced free radical oxidation of the tobacco mosaic virus and bacteriophage M13 led to acrylate-functionalized viruses with customizable properties.
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34
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Rocha FS, Gomes AJ, Lunardi CN, Kaliaguine S, Patience GS. Experimental methods in chemical engineering: Ultraviolet visible spectroscopy-UV-Vis. CAN J CHEM ENG 2018. [DOI: 10.1002/cjce.23344] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Fellipy S. Rocha
- Nanoscience and Nanobiotechnology Program; University of Brasília; Brasília Brazil
- Laboratory of Photochemistry and Nanobiotechnology; University of Brasília; Brasília Brazil
| | - Anderson J. Gomes
- Laboratory of Photochemistry and Nanobiotechnology; University of Brasília; Brasília Brazil
| | - Claure N. Lunardi
- Laboratory of Photochemistry and Nanobiotechnology; University of Brasília; Brasília Brazil
| | - Serge Kaliaguine
- Department of Chemical Engineering; Laval University; Québec City, QC Canada
| | - Gregory S. Patience
- Department of Chemical Engineering; Polytechnique Montréal; Montréal, QC Canada
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35
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Blaffert J, Haeri HH, Blech M, Hinderberger D, Garidel P. Spectroscopic methods for assessing the molecular origins of macroscopic solution properties of highly concentrated liquid protein solutions. Anal Biochem 2018; 561-562:70-88. [PMID: 30243977 DOI: 10.1016/j.ab.2018.09.013] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2018] [Revised: 09/08/2018] [Accepted: 09/17/2018] [Indexed: 01/14/2023]
Abstract
In cases of subcutaneous injection of therapeutic monoclonal antibodies, high protein concentrations (>50 mg/ml) are often required. During the development of these high concentration liquid formulations (HCLF), challenges such as aggregation, gelation, opalescence, phase separation, and high solution viscosities are more prone compared to low concentrated protein formulations. These properties can impair manufacturing processes, as well as protein stability and shelf life. To avoid such unfavourable solution properties, a detailed understanding about the nature of these properties and their driving forces are required. However, the fundamental mechanisms that lead to macroscopic solution properties, as above mentioned, are complex and not fully understood, yet. Established analytical methods for assessing the colloidal stability, i.e. the ability of a native protein to remain dispersed in solution, are restricted to dilute conditions and provide parameters such as the second osmotic virial coefficient, B22, and the diffusion interaction coefficient, kD. These parameters are routinely applied for qualitative estimations and identifications of proteins with challenging solution behaviours, such as high viscosities and aggregation, although the assays are prepared for low protein concentration conditions, typically between 0.1 and 20 mg/ml ("ideal" solution conditions). Quantitative analysis of samples of high protein concentration is difficult and it is hard to obtain information about the driving forces of such solution properties and corresponding protein-protein self-interactions. An advantage of using specific spectroscopic methods is the potential of directly analysing highly concentrated protein solutions at different solution conditions. This allows for collecting/gaining valuable information about the fundamental mechanisms of solution properties of the high protein concentration regime. In addition, the derived parameters might be more predictive as compared to the parameters originating from assays which are optimized for the low protein concentration range. The provided information includes structural data, molecular dynamics at various timescales and protein-solvent interactions, which can be obtained at molecular resolution. Herein, we provide an overview about spectroscopic techniques for analysing the origins of macroscopic solution behaviours in general, with a specific focus on pharmaceutically relevant high protein concentration and formulation conditions.
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Affiliation(s)
- Jacob Blaffert
- Institute of Chemistry, Martin Luther University Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120, Halle/Saale, Germany
| | - Haleh Hashemi Haeri
- Institute of Chemistry, Martin Luther University Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120, Halle/Saale, Germany
| | - Michaela Blech
- Boehringer Ingelheim Pharma GmbH & Co. KG, Protein Science, Birkerndorfer Str. 65, 88397, Biberach/Riß, Germany
| | - Dariush Hinderberger
- Institute of Chemistry, Martin Luther University Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120, Halle/Saale, Germany
| | - Patrick Garidel
- Institute of Chemistry, Martin Luther University Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120, Halle/Saale, Germany; Boehringer Ingelheim Pharma GmbH & Co. KG, Protein Science, Birkerndorfer Str. 65, 88397, Biberach/Riß, Germany.
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36
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Del Galdo S, Mancini G, Daidone I, Zanetti Polzi L, Amadei A, Barone V. Tyrosine absorption spectroscopy: Backbone protonation effects on the side chain electronic properties. J Comput Chem 2018; 39:1747-1756. [DOI: 10.1002/jcc.25351] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 04/17/2018] [Accepted: 04/18/2018] [Indexed: 01/12/2023]
Affiliation(s)
- Sara Del Galdo
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7 I-56126; Pisa Italy
| | - Giordano Mancini
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7 I-56126; Pisa Italy
- Istituto Nazionale di Fisica Nucleare (INFN) sezione di Pisa, Largo Bruno Pontecorvo 3; Pisa 56127 Italy
| | - Isabella Daidone
- Dipartimento di Scienze Fisiche e Chimiche; Università di L'Aquila, Via Vetoio s.n.c.67100; L'Aquila Italy
| | - Laura Zanetti Polzi
- Dipartimento di Scienze Fisiche e Chimiche; Università di L'Aquila, Via Vetoio s.n.c.67100; L'Aquila Italy
| | - Andrea Amadei
- Dipartimento di Scienze e Tecnologie Chimiche; Università di Roma Tor Vergata, Via Della Ricerca Scientifica; Roma 00100 Italy
| | - Vincenzo Barone
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7 I-56126; Pisa Italy
- Istituto Nazionale di Fisica Nucleare (INFN) sezione di Pisa, Largo Bruno Pontecorvo 3; Pisa 56127 Italy
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37
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Kiratitanavit W, Bruno FF, Kumar J, Nagarajan R. Facile enzymatic preparation of fluorescent conjugated polymers of phenols and their application in sensing. J Appl Polym Sci 2018. [DOI: 10.1002/app.46496] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
| | - Ferdinando F. Bruno
- US Army Natick Soldier Research Development and Engineering Center, RDECOM; Natick Massachusetts 01760
| | - Jayant Kumar
- Center for Advanced Materials and HEROES Initiative, University of Massachusetts; Lowell Massachusetts 01854
- Department of Physics; University of Massachusetts; Lowell Massachusetts 01854
| | - Ramaswamy Nagarajan
- Department of Plastics Engineering; University of Massachusetts; Lowell Massachusetts 01854
- Center for Advanced Materials and HEROES Initiative, University of Massachusetts; Lowell Massachusetts 01854
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38
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Honegger P, Steinhauser O. Revival of collective water structure and dynamics in reverse micelles brought about by protein encapsulation. Phys Chem Chem Phys 2018; 20:22932-22945. [DOI: 10.1039/c8cp03422b] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A novel mechanism of depolarization in reverse micelles with zwitterionic surfactants and containing polar species but lacking ions is reported.
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Affiliation(s)
- Philipp Honegger
- Faculty of Chemistry
- Department of Computational Biological Chemistry
- University of Vienna
- A-1090 Vienna
- Austria
| | - Othmar Steinhauser
- Faculty of Chemistry
- Department of Computational Biological Chemistry
- University of Vienna
- A-1090 Vienna
- Austria
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39
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Ansari MZ, Kumar A, Ahari D, Priyadarshi A, Lolla P, Bhandari R, Swaminathan R. Protein charge transfer absorption spectra: an intrinsic probe to monitor structural and oligomeric transitions in proteins. Faraday Discuss 2018; 207:91-113. [DOI: 10.1039/c7fd00194k] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The utility of ProCharTS as an intrinsic spectral probe to track protein aggregation and monitor conformational changes is reported.
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Affiliation(s)
- Mohd. Ziauddin Ansari
- Department of Biosciences & Bioengineering
- Indian Institute of Technology Guwahati
- Guwahati 781039
- India
| | - Amrendra Kumar
- Department of Biosciences & Bioengineering
- Indian Institute of Technology Guwahati
- Guwahati 781039
- India
| | - Dileep Ahari
- Department of Biosciences & Bioengineering
- Indian Institute of Technology Guwahati
- Guwahati 781039
- India
| | - Anurag Priyadarshi
- Department of Biosciences & Bioengineering
- Indian Institute of Technology Guwahati
- Guwahati 781039
- India
| | - Padmavathi Lolla
- Laboratory of Cell Signalling
- Centre for DNA Fingerprinting and Diagnostics (CDFD)
- Hyderabad 500001
- India
| | - Rashna Bhandari
- Laboratory of Cell Signalling
- Centre for DNA Fingerprinting and Diagnostics (CDFD)
- Hyderabad 500001
- India
| | - Rajaram Swaminathan
- Department of Biosciences & Bioengineering
- Indian Institute of Technology Guwahati
- Guwahati 781039
- India
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40
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Honegger P, Schmollngruber M, Steinhauser O. Macromolecular crowding and the importance of proper hydration for the structure and dynamics of protein solutions. Phys Chem Chem Phys 2018; 20:19581-19594. [DOI: 10.1039/c8cp02360c] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Extensive computational studies of ubiquitin crowding with a special focus on protein hydration directly visible in dielectric spectra.
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Affiliation(s)
- Philipp Honegger
- University of Vienna
- Faculty of Chemistry
- Department of Computational Biological Chemistry
- A-1090 Vienna
- Austria
| | - Michael Schmollngruber
- University of Vienna
- Faculty of Chemistry
- Department of Computational Biological Chemistry
- A-1090 Vienna
- Austria
| | - Othmar Steinhauser
- University of Vienna
- Faculty of Chemistry
- Department of Computational Biological Chemistry
- A-1090 Vienna
- Austria
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41
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Carrillo-Parramon O, Del Galdo S, Aschi M, Mancini G, Amadei A, Barone V. Flexible and Comprehensive Implementation of MD-PMM Approach in a General and Robust Code. J Chem Theory Comput 2017; 13:5506-5514. [DOI: 10.1021/acs.jctc.7b00341] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
| | - Sara Del Galdo
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7 I-56126, Pisa, Italy
| | - Massimiliano Aschi
- Dipartimento
di Scienze Fisiche e Chimiche, Universitá di L’Aquila, Via
Vetoio s.n.c.67100, L’Aquila, Italy
| | - Giordano Mancini
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7 I-56126, Pisa, Italy
- Istituto Nazionale di Fisica Nucleare (INFN) sezione di Pisa, Largo Bruno Pontecorvo 3, 56127 Pisa, Italy
| | - Andrea Amadei
- Dipartimento
di Scienze e Tecnologie Chimiche, Universitá di Roma ’Tor Vergata’, Via Della Ricerca Scientifica, 00100 Roma, Italy
| | - Vincenzo Barone
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7 I-56126, Pisa, Italy
- Istituto Nazionale di Fisica Nucleare (INFN) sezione di Pisa, Largo Bruno Pontecorvo 3, 56127 Pisa, Italy
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Prokopowicz M, Greń B, Cieśla J, Kierdaszuk B. Towards understanding the E. coli PNP binding mechanism and FRET absence between E. coli PNP and formycin A. Biophys Chem 2017; 230:99-108. [PMID: 28947300 DOI: 10.1016/j.bpc.2017.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 08/25/2017] [Accepted: 09/07/2017] [Indexed: 10/18/2022]
Abstract
The aim of this study is threefold: (1) augmentation of the knowledge of the E. coli PNP binding mechanism; (2) explanation of the previously observed 'lack of FRET' phenomenon and (3) an introduction of the correction (modified method) for FRET efficiency calculation in the PNP-FA complexes. We present fluorescence studies of the two E. coli PNP mutants (F159Y and F159A) with formycin A (FA), that indicate that the aromatic amino acid is indispensable in the nucleotide binding, additional hydroxyl group at position 159 probably enhances the strength of binding and that the amino acids pair 159-160 has a great impact on the spectroscopic properties of the enzyme. The experiments were carried out in hepes and phosphate buffers, at pH7 and 8.3. Two methods, a conventional and a modified one, that utilizes the dissociation constant, for calculations of the energy transfer efficiency (E) and the acceptor-to-donor distance (r) between FA and the Tyr (energy donor) were employed. Total difference spectra were calculated for emission spectra (λex 280nm, 295nm, 305nm and 313nm) for all studied systems. Time-resolved techniques allowed to conclude the existence of a specific structure formed by amino acids at positions 159 and 160. The results showed an unexpected pattern change of FRET in the mutants, when compared to the wild type enzyme and a probable presence of a structure created between 159 and 160 residue, that might influence the binding efficiency. Additionally, we confirmed the indispensable role of the modification of the FRET efficiency (E) calculation on the fraction of enzyme saturation in PNP-FA systems.
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Affiliation(s)
- Małgorzata Prokopowicz
- Inter-Faculty Interdisciplinary Doctoral Studies in Natural Sciences and Mathematics, University of Warsaw, Stefana Banacha 2C, Warsaw 02-097, Poland; Department of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Żwirki i Wigury 93, Warsaw 02-089, Poland.
| | - Bartosz Greń
- Department of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Żwirki i Wigury 93, Warsaw 02-089, Poland
| | - Joanna Cieśla
- Department of Drug Technology and Biotechnology, Institute of Biotechnology Faculty of Chemistry, Warsaw University of Technology, Koszykowa 75, Warsaw 00-664, Poland
| | - Borys Kierdaszuk
- Department of Biophysics, Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Żwirki i Wigury 93, Warsaw 02-089, Poland
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43
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Dos Remedios C. A review and summary of the contents of biophysical reviews volume 8, 2016. Biophys Rev 2017; 9:1-4. [PMID: 28510044 DOI: 10.1007/s12551-017-0249-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 01/16/2017] [Indexed: 12/12/2022] Open
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