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Kuril AK, Saravanan K, Subbappa PK. Analytical considerations for characterization of generic peptide product: A regulatory insight. Anal Biochem 2024; 694:115633. [PMID: 39089363 DOI: 10.1016/j.ab.2024.115633] [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: 05/11/2024] [Revised: 07/23/2024] [Accepted: 07/29/2024] [Indexed: 08/03/2024]
Abstract
The Peptide therapeutics market was evaluated to be around USD 45.67 BN in 2023 and is projected to witness massive growth at a CAGR of around 5.63 % from 2024 to 2032 (USD 80.4 BN). Generic peptides are expected to reach USD 27.1 billion by 2032 after the patent monopoly of the pioneer peptides expires, and generic peptides become accessible. The generic manufacturers are venturing into peptide-based therapeutics for the aforementioned reasons. There is an abundance of material accessible regarding the characterization of peptides, which can be quite confusing for researchers. The FDA believes that an ANDA applicant may now demonstrate that the active component in a proposed generic synthetic peptide drug product is the "same" as the active ingredient in a peptide of rDNA origin that has previously been approved. To ensure the efficacy, safety, and quality of peptide therapies during development, regulatory bodies demand comprehensive characterization utilizing several orthogonal methodologies. This article elaborates the peptide characterization by segmenting into different segments as per the critical quality attribute from identification of the peptide to the physicochemical property of the peptide therapeutics which will be required to demonstrate the sameness with reference product based on the size of the peptide chain and molecular weight of the peptides. Article insights briefly on each individual technique and the orthogonal techniques for each test were explained. The impurities requirements in the generic peptides as per the regulatory requirement were also discussed.
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Affiliation(s)
| | - K Saravanan
- Bhagwant University, Sikar Road, Ajmer, Rajasthan, India
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2
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Ray D, Chamlagai D, Kumar S, Mukhopadhyay S, Chakrabarty S, Aswal VK, Mitra S. Molecular Insights into the Conformational and Binding Behaviors of Human Serum Albumin Induced by Surface-Active Ionic Liquids. J Phys Chem B 2024; 128:6622-6637. [PMID: 38937939 DOI: 10.1021/acs.jpcb.4c01915] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/29/2024]
Abstract
Extensive research has been carried out to investigate the stability and function of human serum albumin (HSA) when exposed to surface-active ionic liquids (SAILs) with different head groups (imidazolium, morpholinium, and pyridinium) and alkyl chain lengths (ranging from decyl to tetradecyl). Analysis of the protein fluorescence spectra indicates noticeable changes in the secondary structure of HSA with varying concentrations of all SAILs tested. Helicity calculations based on the Fourier transform infrared (FTIR) data show that HSA becomes more organized at the micellar concentration of SAILs, leading to an increased protein activity at this level. Small-angle neutron scattering (SANS) data confirm the formation of a bead-necklace structure between the SAILs and HSA. Atomistic molecular dynamics (MD) simulation results identify several hotspots on the protein surface for interaction with SAIL, which results in the modulation of protein conformational fluctuation and stability. Furthermore, fluorescence resonance energy transfer (FRET) experiments with the intramolecular charge transfer (ICT) probe trans-ethyl p-(dimethylamino) cinnamate (EDAC) demonstrate that higher alkyl chain lengths and SAIL concentrations result in a significantly increased energy transfer efficiency. The findings of this study provide a detailed molecular-level understanding of how the protein structure and function are affected by the presence of SAILs, with potential implications for a wide range of applications involving protein-SAIL composite systems.
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Affiliation(s)
- Dhiman Ray
- Department of Chemistry, North-Eastern Hill University, Shillong 793 022, India
| | - Dipak Chamlagai
- Department of Chemistry, North-Eastern Hill University, Shillong 793 022, India
| | - Sugam Kumar
- Solid State Physics Division, Bhabha Atomic Research Centre, Mumbai 400085, India
| | - Sutanu Mukhopadhyay
- Department of Chemical and Biological Sciences, S. N. Bose National Centre for Basic Sciences, Kolkata 700106, India
| | - Suman Chakrabarty
- Department of Chemical and Biological Sciences, S. N. Bose National Centre for Basic Sciences, Kolkata 700106, India
| | - Vinod K Aswal
- Solid State Physics Division, Bhabha Atomic Research Centre, Mumbai 400085, India
| | - Sivaprasad Mitra
- Department of Chemistry, North-Eastern Hill University, Shillong 793 022, India
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Chen Y, Wei S, Li R, Xie W, Yang H. Bioclay Enzyme with Bimetal Synergistic Sterilization and Infectious Wound Regeneration. NANO LETTERS 2024; 24:8046-8054. [PMID: 38912748 DOI: 10.1021/acs.nanolett.4c01671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/25/2024]
Abstract
Bacteria invasion is the main factor hindering the wound-healing process. However, current antibacterial therapies inevitably face complex challenges, such as the abuse of antibiotics or severe inflammation during treatment. Here, a drug-free bioclay enzyme (Bio-Clayzyme) consisting of Fe2+-tannic acid (TA) network-coated kaolinite nanoclay and glucose oxidase (GOx) was reported to destroy harmful bacteria via bimetal antibacterial therapy. At the wound site, Bio-Clayzyme was found to enhance the generation of toxic hydroxyl radicals for sterilization via cascade catalysis of GOx and Fe2+-mediated peroxidase mimetic activity. Specifically, the acidic characteristics of the infection microenvironment accelerated the release of Al3+ from kaolinite, which further led to bacterial membrane damage and amplified the antibacterial toxicity of Fe2+. Besides, Bio-Clayzyme also performed hemostasis and anti-inflammatory functions inherited from Kaol and TA. By the combination of hemostasis and anti-inflammatory and bimetal synergistic sterilization, Bio-Clayzyme achieves efficient healing of infected wounds, providing a revolutionary approach for infectious wound regeneration.
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Affiliation(s)
- Ying Chen
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, China University of Geosciences, Wuhan 430074, China
- Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
- Laboratory of Advanced Mineral Materials, China University of Geosciences, Wuhan 430074, China
| | - Shiqi Wei
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, China University of Geosciences, Wuhan 430074, China
- Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
- Laboratory of Advanced Mineral Materials, China University of Geosciences, Wuhan 430074, China
| | - Rui Li
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, China University of Geosciences, Wuhan 430074, China
- Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
- Laboratory of Advanced Mineral Materials, China University of Geosciences, Wuhan 430074, China
| | - Weimin Xie
- Hunan Key Laboratory of Mineral Materials and Application, School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China
| | - Huaming Yang
- Engineering Research Center of Nano-Geomaterials of Ministry of Education, China University of Geosciences, Wuhan 430074, China
- Faculty of Materials Science and Chemistry, China University of Geosciences, Wuhan 430074, China
- Laboratory of Advanced Mineral Materials, China University of Geosciences, Wuhan 430074, China
- Hunan Key Laboratory of Mineral Materials and Application, School of Minerals Processing and Bioengineering, Central South University, Changsha 410083, China
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Di Gregorio E, Staelens M, Hosseinkhah N, Karimpoor M, Liburd J, Lim L, Shankar K, Tuszyński JA. Raman Spectroscopy Reveals Photobiomodulation-Induced α-Helix to β-Sheet Transition in Tubulins: Potential Implications for Alzheimer's and Other Neurodegenerative Diseases. NANOMATERIALS (BASEL, SWITZERLAND) 2024; 14:1093. [PMID: 38998698 PMCID: PMC11243591 DOI: 10.3390/nano14131093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 06/03/2024] [Accepted: 06/12/2024] [Indexed: 07/14/2024]
Abstract
In small clinical studies, the application of transcranial photobiomodulation (PBM), which typically delivers low-intensity near-infrared (NIR) to treat the brain, has led to some remarkable results in the treatment of dementia and several neurodegenerative diseases. However, despite the extensive literature detailing the mechanisms of action underlying PBM outcomes, the specific mechanisms affecting neurodegenerative diseases are not entirely clear. While large clinical trials are warranted to validate these findings, evidence of the mechanisms can explain and thus provide credible support for PBM as a potential treatment for these diseases. Tubulin and its polymerized state of microtubules have been known to play important roles in the pathology of Alzheimer's and other neurodegenerative diseases. Thus, we investigated the effects of PBM on these cellular structures in the quest for insights into the underlying therapeutic mechanisms. In this study, we employed a Raman spectroscopic analysis of the amide I band of polymerized samples of tubulin exposed to pulsed low-intensity NIR radiation (810 nm, 10 Hz, 22.5 J/cm2 dose). Peaks in the Raman fingerprint region (300-1900 cm-1)-in particular, in the amide I band (1600-1700 cm-1)-were used to quantify the percentage of protein secondary structures. Under this band, hidden signals of C=O stretching, belonging to different structures, are superimposed, producing a complex signal as a result. An accurate decomposition of the amide I band is therefore required for the reliable analysis of the conformation of proteins, which we achieved through a straightforward method employing a Voigt profile. This approach was validated through secondary structure analyses of unexposed control samples, for which comparisons with other values available in the literature could be conducted. Subsequently, using this validated method, we present novel findings of statistically significant alterations in the secondary structures of polymerized NIR-exposed tubulin, characterized by a notable decrease in α-helix content and a concurrent increase in β-sheets compared to the control samples. This PBM-induced α-helix to β-sheet transition connects to reduced microtubule stability and the introduction of dynamism to allow for the remodeling and, consequently, refreshing of microtubule structures. This newly discovered mechanism could have implications for reducing the risks associated with brain aging, including neurodegenerative diseases like Alzheimer's disease, through the introduction of an intervention following this transition.
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Affiliation(s)
- Elisabetta Di Gregorio
- Department of Physics, Faculty of Science, University of Alberta, Edmonton, AB T6G 2E1, Canada
- Department of Mechanical and Aerospace Engineering (DIMEAS), Faculty of Biomedical Engineering, Polytechnic University of Turin, 10129 Turin, Italy
- Department of Physics, Freie Universität Berlin, 14195 Berlin, Germany
| | - Michael Staelens
- Department of Physics, Faculty of Science, University of Alberta, Edmonton, AB T6G 2E1, Canada
- Instituto de Física Corpuscular, CSIC–Universitat de València, Carrer Catedràtic José Beltrán 2, 46980 Paterna, Spain
| | | | | | | | - Lew Lim
- Vielight Inc., Toronto, ON M4Y 2G8, Canada
| | - Karthik Shankar
- Department of Electrical and Computer Engineering, Faculty of Engineering, University of Alberta, Edmonton, AB T6G 1H9, Canada
| | - Jack A. Tuszyński
- Department of Physics, Faculty of Science, University of Alberta, Edmonton, AB T6G 2E1, Canada
- Department of Mechanical and Aerospace Engineering (DIMEAS), Faculty of Biomedical Engineering, Polytechnic University of Turin, 10129 Turin, Italy
- Department of Data Science and Engineering, Silesian University of Technology, 44-100 Gliwice, Poland
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Sleiman L, Lazăr (Popa) AD, Albu-Kaya M, Marin MM, Kaya DA, Vasile OR, Dinescu S. Development and Investigation of an Innovative 3D Biohybrid Based on Collagen and Silk Sericin Enriched with Flavonoids for Potential Wound Healing Applications. Polymers (Basel) 2024; 16:1627. [PMID: 38931977 PMCID: PMC11207284 DOI: 10.3390/polym16121627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2024] [Revised: 05/27/2024] [Accepted: 06/05/2024] [Indexed: 06/28/2024] Open
Abstract
Skin tissue injuries necessitate particular care due to associated complex healing mechanisms. Current investigations in the domain of tissue engineering and regenerative medicine are focused on obtaining novel scaffolds adapted as potential delivery systems to restore lost tissue functions and properties. In this study, we describe the fabrication and evaluation of a novel 3D scaffold structure based on collagen and silk sericin (CollSS) enriched with microcapsules containing natural compounds, curcumin (C), and/or quercetin (Q). These 3D composites were characterized by FT-IR spectroscopy, water uptake, in vitro collagenase degradation, and SEM microscopy. Furthermore, they were biologically evaluated in terms of biocompatibility, cell adhesion, anti-inflammatory, and antioxidant properties. All tested materials indicated an overall suitable biocompatibility, with the best results obtained for the one containing both flavonoids. This study suggests the cumulative beneficial effect of C and Q, encapsulated in the same composite, as a potential non-invasive therapeutic strategy for skin tissue regeneration in patients suffering from chronic wounds.
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Affiliation(s)
- Lea Sleiman
- Department of Biochemistry and Molecular Biology, University of Bucharest, 050095 Bucharest, Romania; (L.S.); (A.-D.L.)
| | - Andreea-Daniela Lazăr (Popa)
- Department of Biochemistry and Molecular Biology, University of Bucharest, 050095 Bucharest, Romania; (L.S.); (A.-D.L.)
| | - Mădălina Albu-Kaya
- The National Research and Development Institute for Textiles and Leather (INCDTP)-Division Leather and Footwear Research Institute, 93 Ion Minulescu Str., 031215 Bucharest, Romania;
| | - Minodora Maria Marin
- Advanced Polymer Materials Group, Faculty of Applied Chemistry and Materials Science, Politehnica University of Bucharest, 1-7 Polizu Street, 01106 Bucharest, Romania;
| | - Durmuș Alpaslan Kaya
- Department of Field Crops, Faculty of Agriculture, Hatay Mustafa Kemal University, Antakya-Hatay 31034, Turkey;
| | - Otilia-Ruxandra Vasile
- Science and Engineering of Oxide Materials and Nanomaterials Department, Faculty of Chemical Engineering and Biotechnologies, Politehnica University of Bucharest, 1-7 Polizu Street, 01106 Bucharest, Romania;
| | - Sorina Dinescu
- Department of Biochemistry and Molecular Biology, University of Bucharest, 050095 Bucharest, Romania; (L.S.); (A.-D.L.)
- Research Institute of the University of Bucharest (ICUB), 050663 Bucharest, Romania
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6
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El Fawal G, Sobhy SE, Hafez EE. Biological activities of fig latex -loaded cellulose acetate/poly(ethylene oxide) nanofiber for potential therapeutics: Anticancer and antioxidant material. Int J Biol Macromol 2024; 270:132176. [PMID: 38750845 DOI: 10.1016/j.ijbiomac.2024.132176] [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: 02/20/2024] [Revised: 04/14/2024] [Accepted: 05/05/2024] [Indexed: 05/19/2024]
Abstract
Cancer is a fatal disease, and unfortunately, the anticancer drugs harm normal cells. Plant's extracts are the golden key to solving this issue. In this research, fig latex - from Ficus carica- was encapsulated using cellulose acetate (CA) and poly (ethylene oxide) (PEO) polymers via electrospinning method (Fig@CA/PEO). Fig@CA/PEO nanofiber scaffold was characterized by thermogravimetric analysis (TGA), Fourier-transform infrared spectroscopy (FT-IR), and scanning electron microscopy (SEM). The average fiber diameter was decreased with an increase in latex concentration from 715 nm to 583 nm. FT-IR spectroscopy indicated the presence of fig latex in Fig@CA/PEO nanofibers. Compared to 5-fluorouracil, Fig@CA/PEO nanofiber scaffold considered safe towards normal cells (WI-38). Moreover, the nanofiber scaffold was efficient against colon cancer cells (Caco) and liver cancer cells (HepG2) as it demonstrated IC50 values for cells by 23.97 μg/mL and 23.96 μg/mL, respectively. Besides, the nanofiber scaffold revealed mechanistic variations in apoptotic oncogenes; described by the upregulation of BCL2 and P21, combined by downregulation of p53 and TNF. Moreover, the nanofiber scaffold showed antioxidant activity counting 33.4, 36 and 41 % of DPPH scavenging as the fig latex concentration increased. The results demonstrate that the Fig@CA/PEO nanofiber scaffold is a promising substitute to traditional chemotherapy.
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Affiliation(s)
- Gomaa El Fawal
- Polymer Materials Research Department, Advanced Technology and New Materials Research Institute (ATNMRI), City of Scientific Research and Technological Applications (SRTA-City), New Borg El-Arab City, 21934, Alexandria, Egypt.
| | - Sherien E Sobhy
- Plant Protection and Bimolecular Diagnosis Department, Arid Lands Cultivation Research Institute, City of Scientific Research and Technological Applications (SRTA-City), New Borg EL-Arab City, 21934, Alexandria, Egypt
| | - Elsayed E Hafez
- Plant Protection and Bimolecular Diagnosis Department, Arid Lands Cultivation Research Institute, City of Scientific Research and Technological Applications (SRTA-City), New Borg EL-Arab City, 21934, Alexandria, Egypt
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Tan V, Berg F, Maleki H. Diatom-inspired silicification process for development of green flexible silica composite aerogels. Sci Rep 2024; 14:6973. [PMID: 38521812 PMCID: PMC10960801 DOI: 10.1038/s41598-024-57257-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2023] [Accepted: 03/15/2024] [Indexed: 03/25/2024] Open
Abstract
In this study, we have developed novel biomimetic silica composite aerogels and cryogels for the first time, drawing inspiration from the natural diatom's silicification process. Our biomimetic approach involved the modification of tyrosinase-mediated oxidized silk fibroin (SFO) surfaces with polyethyleneimine (PEI). This modification introduced ample amine groups onto the SF polymer, which catalyzed the silicification of the SFO-PEI gel surface with silicic acid. This process emulates the catalytic function of long-chain polyamines and silaffin proteins found in diatoms, resulting in a silica network structure on the primary SFO-PEI network gel's surface. The SFO-PEI gel matrix played a dual role in this process: (1) It provided numerous amine functional groups that directly catalyzed the silicification of silicic acid on the porous structure's exterior surface, without encapsulating the created silica network in the gel. (2) It served as a flexible mechanical support facilitating the creation of the silica network. As a result, the final ceramic composite exhibits a mechanically flexible nature (e.g., cyclic compressibility up to 80% strain), distinguishing it from conventional composite aerogels. By mimicking the diatom's silicification process, we were able to simplify the development of silica-polymer composite aerogels. It eliminates the need for surfactants, multi-step procedures involving solvent exchange, and gel washing. Instead, the reaction occurs under mild conditions, streamlining the composite aerogels fabrication process.
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Affiliation(s)
- Valerie Tan
- Department of Chemistry, Institute of Inorganic Chemistry, University of Cologne, Greinstresse 6, 50939, Cologne, Germany
| | - Florian Berg
- Department of Chemistry, Institute of Inorganic Chemistry, University of Cologne, Greinstresse 6, 50939, Cologne, Germany
| | - Hajar Maleki
- Department of Chemistry, Institute of Inorganic Chemistry, University of Cologne, Greinstresse 6, 50939, Cologne, Germany.
- Center for Molecular Medicine Cologne, CMMC Research Center, Robert-Koch-Str. 21, 50931, Cologne, Germany.
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Ye S, Zhong K, Huang Y, Zhang G, Sun C, Jiang J. Artificial Intelligence-based Amide-II Infrared Spectroscopy Simulation for Monitoring Protein Hydrogen Bonding Dynamics. J Am Chem Soc 2024; 146:2663-2672. [PMID: 38240637 DOI: 10.1021/jacs.3c12258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
The structurally sensitive amide II infrared (IR) bands of proteins provide valuable information about the hydrogen bonding of protein secondary structures, which is crucial for understanding protein dynamics and associated functions. However, deciphering protein structures from experimental amide II spectra relies on time-consuming quantum chemical calculations on tens of thousands of representative configurations in solvent water. Currently, the accurate simulation of amide II spectra for whole proteins remains a challenge. Here, we present a machine learning (ML)-based protocol designed to efficiently simulate the amide II IR spectra of various proteins with an accuracy comparable to experimental results. This protocol stands out as a cost-effective and efficient alternative for studying protein dynamics, including the identification of secondary structures and monitoring the dynamics of protein hydrogen bonding under different pH conditions and during protein folding process. Our method provides a valuable tool in the field of protein research, focusing on the study of dynamic properties of proteins, especially those related to hydrogen bonding, using amide II IR spectroscopy.
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Affiliation(s)
- Sheng Ye
- School of Artificial Intelligence, Anhui University, Hefei, Anhui 230601, People's Republic of China
| | - Kai Zhong
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, Groningen 9747AG, Netherlands
| | - Yan Huang
- Key Laboratory of Precision and Intelligent Chemistry, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Guozhen Zhang
- Hefei National Research Center of Physical Sciences at the Microscale, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui 230026, China
- Hefei National Laboratory, University of Science and Technology of China, Hefei 230088, China
| | - Changyin Sun
- School of Artificial Intelligence, Anhui University, Hefei, Anhui 230601, People's Republic of China
| | - Jun Jiang
- Key Laboratory of Precision and Intelligent Chemistry, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui 230026, China
- Hefei National Laboratory, University of Science and Technology of China, Hefei 230088, China
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9
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Maleš P, Brkljača Z, Crnolatac I, Petrov D, Bakarić D. Phase-Dependent Adsorption of Myelin Basic Protein to Phosphatidylcholine Lipid Bilayers. MEMBRANES 2024; 14:15. [PMID: 38248705 PMCID: PMC10819005 DOI: 10.3390/membranes14010015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 12/23/2023] [Accepted: 01/02/2024] [Indexed: 01/23/2024]
Abstract
The dense packing of opposite cytoplasmic surfaces of the lipid-enriched myelin membrane, responsible for the proper saltatory conduction of nerve impulses through axons, is ensured by the adhesive properties of myelin basic protein (MBP). Although preferentially interacting with negatively charged phosphatidylserine (PS) lipids, as an intrinsically disordered protein, it can easily adapt its shape to its immediate environment and thus adsorb to domains made of zwitterionic phosphatidylcholine (PC) lipids. As the molecular-level interaction pattern between MBP and PC lipid membranes suffers from scarce characterization, an experimental and computational study of multilamellar liposomes (MLVs) composed of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) in the presence of bovine MBP is presented here. Calorimetric and temperature-dependent UV-Vis measurements identified DPPC pretransition temperature (Tp) and calorimetric enthalpy (ΔHcal) as the physicochemical parameters most responsive to the presence of MBP. Besides suggesting an increase in β-sheet fractions of structured MBP segments as DPPC lipids undergo from the gel (20 °C) to the fluid (50 °C) phase, FTIR spectra unraveled the significant contribution of lysine (Lys) residues in the adsorption pattern, especially when DPPC is in the fluid (50 °C) phase. In addition to highlighting the importance of Lys residues in the MBP adsorption on DPPC lipid bilayer, employing salt bridges (SBs) and hydrogen bonds (HBs), MD data suggest the crucial importance of the orientation of MBP with respect to the surface of the DPPC lipid bilayer.
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Affiliation(s)
- Petra Maleš
- Division for Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia; (P.M.); (Z.B.); (I.C.)
| | - Zlatko Brkljača
- Division for Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia; (P.M.); (Z.B.); (I.C.)
| | - Ivo Crnolatac
- Division for Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia; (P.M.); (Z.B.); (I.C.)
| | - Dražen Petrov
- Institute of Molecular Modeling and Simulation, University of Natural Resources and Life Sciences, 1180 Vienna, Austria;
| | - Danijela Bakarić
- Division for Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička 54, 10000 Zagreb, Croatia; (P.M.); (Z.B.); (I.C.)
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Schmid SY, Lachowski K, Chiang HT, Pozzo L, De Yoreo J, Zhang S. Mechanisms of Biomolecular Self-Assembly Investigated Through In Situ Observations of Structures and Dynamics. Angew Chem Int Ed Engl 2023; 62:e202309725. [PMID: 37702227 DOI: 10.1002/anie.202309725] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Indexed: 09/14/2023]
Abstract
Biomolecular self-assembly of hierarchical materials is a precise and adaptable bottom-up approach to synthesizing across scales with considerable energy, health, environment, sustainability, and information technology applications. To achieve desired functions in biomaterials, it is essential to directly observe assembly dynamics and structural evolutions that reflect the underlying energy landscape and the assembly mechanism. This review will summarize the current understanding of biomolecular assembly mechanisms based on in situ characterization and discuss the broader significance and achievements of newly gained insights. In addition, we will also introduce how emerging deep learning/machine learning-based approaches, multiparametric characterization, and high-throughput methods can boost the development of biomolecular self-assembly. The objective of this review is to accelerate the development of in situ characterization approaches for biomolecular self-assembly and to inspire the next generation of biomimetic materials.
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Affiliation(s)
- Sakshi Yadav Schmid
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
| | - Kacper Lachowski
- Chemical Engineering, University of Washington, Seattle, WA 98105, USA
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA 98105, USA
| | - Huat Thart Chiang
- Chemical Engineering, University of Washington, Seattle, WA 98105, USA
| | - Lilo Pozzo
- Chemical Engineering, University of Washington, Seattle, WA 98105, USA
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA 98105, USA
- Materials Science and Engineering, University of Washington, Seattle, WA 98105, USA
| | - Jim De Yoreo
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
- Materials Science and Engineering, University of Washington, Seattle, WA 98105, USA
| | - Shuai Zhang
- Physical Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99354, USA
- Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA 98105, USA
- Materials Science and Engineering, University of Washington, Seattle, WA 98105, USA
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11
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Seredin P, Goloshchapov D, Kashkarov V, Lukin A, Peshkov Y, Ippolitov I, Ippolitov Y, Litvinova T, Vongsvivut J, Chae B, Freitas RO. Changes in Dental Biofilm Proteins' Secondary Structure in Groups of People with Different Cariogenic Situations in the Oral Cavity and Using Medications by Means of Synchrotron FTIR-Microspectroscopy. Int J Mol Sci 2023; 24:15324. [PMID: 37895003 PMCID: PMC10607285 DOI: 10.3390/ijms242015324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 10/13/2023] [Accepted: 10/17/2023] [Indexed: 10/29/2023] Open
Abstract
This work unveils the idea that the cariogenic status of the oral cavity (the presence of active caries lesions) can be predicted via a lineshape analysis of the infrared spectral signatures of the secondary structure of proteins in dental biofilms. These spectral signatures that work as natural markers also show strong sensitivity to the application in patients of a so-called modulator-a medicinal agent (a pelleted mineral complex with calcium glycerophosphate). For the first time, according to our knowledge, in terms of deconvolution of the complete spectral profile of the amide I and amide II bands, significant intra- and intergroup differences were determined in the secondary structure of proteins in the dental biofilm of patients with a healthy oral cavity and with a carious pathology. This allowed to conduct a mathematical assessment of the spectral shifts in proteins' secondary structure in connection with the cariogenic situation in the oral cavity and with an external modulation. It was shown that only for the component parallel β-strands in the amide profile of the biofilm, a statistically significant (p < 0.05) change in its percentage weight (composition) was registered in a cariogenic situation (presence of active caries lesions). Note that no significant differences were detected in a normal situation (control) and in the presence of a carious pathology before and after the application of the modulator. The change in the frequency and percentage weight of parallel β-strands in the spectra of dental biofilms proved to be the result of the presence of cariogenic mutans streptococci in the film as well as of the products of their metabolism-glucan polymers. We foresee that the results presented here can inherently provide the basis for the infrared spectral diagnosis of changes (shifts) in the oral microbiome driven by the development of the carious process in the oral cavity as well as for the choice of optimal therapeutic treatments of caries based on microbiome-directed prevention measures.
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Affiliation(s)
- Pavel Seredin
- Department of Solid-State Physics and Nanostructures, Voronezh State University, 394018 Voronezh, Russia
| | - Dmitry Goloshchapov
- Department of Solid-State Physics and Nanostructures, Voronezh State University, 394018 Voronezh, Russia
| | - Vladimir Kashkarov
- Department of Solid-State Physics and Nanostructures, Voronezh State University, 394018 Voronezh, Russia
| | - Anatoly Lukin
- Department of Solid-State Physics and Nanostructures, Voronezh State University, 394018 Voronezh, Russia
| | - Yaroslav Peshkov
- Department of Solid-State Physics and Nanostructures, Voronezh State University, 394018 Voronezh, Russia
| | - Ivan Ippolitov
- Department of Pediatric Dentistry with Orthodontia, Voronezh State Medical University, 394006 Voronezh, Russia
| | - Yuri Ippolitov
- Department of Pediatric Dentistry with Orthodontia, Voronezh State Medical University, 394006 Voronezh, Russia
| | - Tatiana Litvinova
- Computational Semasiology Laboratory, Voronezh State Pedagogical University, 394043 Voronezh, Russia
| | - Jitraporn Vongsvivut
- Australian Synchrotron (Synchrotron Light Source Australia Pty LTD), Clayton, VIC 3168, Australia;
| | - Boknam Chae
- Pohang Accelerator Laboratory, Beamline Research Division, Pohang 37673, Republic of Korea
| | - Raul O. Freitas
- Brazilian Synchrotron Light Laboratory (LNLS), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas 13083-970, Brazil
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12
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Barra M, Tomaiuolo G, Villella VR, Esposito S, Liboà A, D'Angelo P, Marasso SL, Cocuzza M, Bertana V, Camilli E, Preziosi V. Organic Electrochemical Transistor Immuno-Sensors for Spike Protein Early Detection. BIOSENSORS 2023; 13:739. [PMID: 37504137 PMCID: PMC10377135 DOI: 10.3390/bios13070739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 07/03/2023] [Accepted: 07/05/2023] [Indexed: 07/29/2023]
Abstract
The global COVID-19 pandemic has had severe consequences from the social and economic perspectives, compelling the scientific community to focus on the development of effective diagnostics that can combine a fast response and accurate sensitivity/specificity performance. Presently available commercial antigen-detecting rapid diagnostic tests (Ag-RDTs) are very fast, but still face significant criticisms, mainly related to their inability to amplify the protein signal. This translates to a limited sensitive outcome and, hence, a reduced ability to hamper the spread of SARS-CoV-2 infection. To answer the urgent need for novel platforms for the early, specific and highly sensitive detection of the virus, this paper deals with the use of organic electrochemical transistors (OECTs) as very efficient ion-electron converters and amplifiers for the detection of spike proteins and their femtomolar concentration. The electrical response of the investigated OECTs was carefully analyzed, and the changes in the parameters associated with the transconductance (i.e., the slope of the transfer curves) in the gate voltage range between 0 and 0.3 V were found to be more clearly correlated with the spike protein concentration. Moreover, the functionalization of OECT-based biosensors with anti-spike and anti-nucleocapside proteins, the major proteins involved in the disease, demonstrated the specificity of these devices, whose potentialities should also be considered in light of the recent upsurge of the so-called "long COVID" syndrome.
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Affiliation(s)
- Mario Barra
- CNR-SPIN, c/o Department of Physics ''Ettore Pancini'', P.le Tecchio, 80, 80125 Napoli, Italy
| | - Giovanna Tomaiuolo
- Department of Chemical, Materials and Production Engineering-University Federico II, P.le Tecchio 80, 80125 Napoli, Italy
- CEINGE, Advanced Biotechnologies, 80145 Napoli, Italy
| | - Valeria Rachela Villella
- Department of Chemical, Materials and Production Engineering-University Federico II, P.le Tecchio 80, 80125 Napoli, Italy
- CEINGE, Advanced Biotechnologies, 80145 Napoli, Italy
| | - Speranza Esposito
- Department of Chemical, Materials and Production Engineering-University Federico II, P.le Tecchio 80, 80125 Napoli, Italy
- CEINGE, Advanced Biotechnologies, 80145 Napoli, Italy
| | - Aris Liboà
- IMEM-CNR, Parco Area delle Scienze 37/A, 43124 Parma, Italy
- Graduate School in Science and Technologies of Materials and Department of Physics, University of Parma, Parco Area delle Scienze, 7/A, 43121 Parma, Italy
| | | | - Simone Luigi Marasso
- IMEM-CNR, Parco Area delle Scienze 37/A, 43124 Parma, Italy
- ChiLab, Department of Applied Science and Technology, Politecnico di Torino, 10129 Torino, Italy
| | - Matteo Cocuzza
- IMEM-CNR, Parco Area delle Scienze 37/A, 43124 Parma, Italy
- ChiLab, Department of Applied Science and Technology, Politecnico di Torino, 10129 Torino, Italy
| | - Valentina Bertana
- ChiLab, Department of Applied Science and Technology, Politecnico di Torino, 10129 Torino, Italy
| | - Elena Camilli
- ChiLab, Department of Applied Science and Technology, Politecnico di Torino, 10129 Torino, Italy
| | - Valentina Preziosi
- Department of Chemical, Materials and Production Engineering-University Federico II, P.le Tecchio 80, 80125 Napoli, Italy
- CEINGE, Advanced Biotechnologies, 80145 Napoli, Italy
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13
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Santhosh PB, Tenev T, Šturm L, Ulrih NP, Genova J. Effects of Hydrophobic Gold Nanoparticles on Structure and Fluidity of SOPC Lipid Membranes. Int J Mol Sci 2023; 24:10226. [PMID: 37373371 DOI: 10.3390/ijms241210226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 05/31/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023] Open
Abstract
Gold nanoparticles (AuNPs) are promising candidates in various biomedical applications such as sensors, imaging, and cancer therapy. Understanding the influence of AuNPs on lipid membranes is important to assure their safety in the biological environment and to improve their scope in nanomedicine. In this regard, the present study aimed to analyze the effects of different concentrations (0.5, 1, and 2 wt.%) of dodecanethiol functionalized hydrophobic AuNPs on the structure and fluidity of zwitterionic 1-stearoyl-2-oleoyl-sn-glycerol-3-phosphocholine (SOPC) lipid bilayer membranes using Fourier-transform infrared (FTIR) spectroscopy and fluorescent spectroscopy. The size of AuNPs was found to be 2.2 ± 1.1 nm using transmission electron microscopy. FTIR results have shown that the AuNPs induced a slight shift in methylene stretching bands, while the band positions of carbonyl and phosphate group stretching were unaffected. Temperature-dependent fluorescent anisotropy measurements showed that the incorporation of AuNPs up to 2 wt.% did not affect the lipid order in membranes. Overall, these results indicate that the hydrophobic AuNPs in the studied concentration did not cause any significant alterations in the structure and membrane fluidity, which suggests the suitability of these particles to form liposome-AuNP hybrids for diverse biomedical applications including drug delivery and therapy.
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Affiliation(s)
- Poornima Budime Santhosh
- Institute of Solid State Physics, Bulgarian Academy of Sciences, Tzarigradsko Chaussee 72, 1784 Sofia, Bulgaria
| | - Tihomir Tenev
- Institute of Solid State Physics, Bulgarian Academy of Sciences, Tzarigradsko Chaussee 72, 1784 Sofia, Bulgaria
| | - Luka Šturm
- Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Nataša Poklar Ulrih
- Department of Food Science and Technology, Biotechnical Faculty, University of Ljubljana, 1000 Ljubljana, Slovenia
| | - Julia Genova
- Institute of Solid State Physics, Bulgarian Academy of Sciences, Tzarigradsko Chaussee 72, 1784 Sofia, Bulgaria
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14
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Tempra C, Chamorro VC, Jungwirth P. Effects of Water Deuteration on Thermodynamic and Structural Properties of Proteins and Biomembranes. J Phys Chem B 2023; 127:1138-1143. [PMID: 36722049 PMCID: PMC10017026 DOI: 10.1021/acs.jpcb.2c08270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Light and heavy water are often used interchangeably in spectroscopic experiments with the tacit assumption that the structure of the investigated biomolecule does not depend too much on employing one or the other solvent. While this may often be a good approximation, we demonstrate here using molecular dynamics simulations incorporating nuclear quantum effects via modification of the interaction potential that there are small but significant differences. Namely, as quantified and discussed in the present study, both proteins and biomembranes tend to be slightly more compact and rigid in D2O than in H2O, which reflects the stronger hydrogen bonding in the former solvent.
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Affiliation(s)
- Carmelo Tempra
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, 160 00 Prague 6, Czech Republic
| | - Victor Cruces Chamorro
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, 160 00 Prague 6, Czech Republic
| | - Pavel Jungwirth
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, 160 00 Prague 6, Czech Republic
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15
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Waeytens J, De Meutter J, Goormaghtigh E, Dazzi A, Raussens V. Determination of Secondary Structure of Proteins by Nanoinfrared Spectroscopy. Anal Chem 2023; 95:621-627. [PMID: 36598929 PMCID: PMC9851152 DOI: 10.1021/acs.analchem.2c01431] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 10/21/2022] [Indexed: 01/05/2023]
Abstract
Nanoscale infrared spectroscopy (AFMIR) is becoming an important tool for the analysis of biological sample, in particular protein assemblies, at the nanoscale level. While the amide I band is usually used to determine the secondary structure of proteins in Fourier transform infrared spectroscopy, no tool has been developed so far for AFMIR. The paper introduces a method for the study of secondary structure of protein based on a protein library of 38 well-characterized proteins. Ascending stepwise linear regression (ASLR) and partial least square (PLS) regression were used to correlate spectrum characteristic bands with the major secondary structures (α-helixes and β-sheets). ASLR appears to provide better results than PLS. The secondary structure predictions are characterized by a root mean square standard error in a cross validation of 6.39% for α-helixes and 6.23% for β-sheets.
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Affiliation(s)
- Jehan Waeytens
- Center
for Structural Biology and Bioinformatics, Laboratory for the Structure
and Function of Biological Membranes, Université
libre de Bruxelles, 1050Brussels, Belgium
- Institut
de Chimie Physique d’Orsay, CNRS
UMR8000, Université Paris-Saclay, 91400Orsay, France
| | - Joëlle De Meutter
- Center
for Structural Biology and Bioinformatics, Laboratory for the Structure
and Function of Biological Membranes, Université
libre de Bruxelles, 1050Brussels, Belgium
| | - Erik Goormaghtigh
- Center
for Structural Biology and Bioinformatics, Laboratory for the Structure
and Function of Biological Membranes, Université
libre de Bruxelles, 1050Brussels, Belgium
| | - Alexandre Dazzi
- Institut
de Chimie Physique d’Orsay, CNRS
UMR8000, Université Paris-Saclay, 91400Orsay, France
| | - Vincent Raussens
- Center
for Structural Biology and Bioinformatics, Laboratory for the Structure
and Function of Biological Membranes, Université
libre de Bruxelles, 1050Brussels, Belgium
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16
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ATR-FTIR Biosensors for Antibody Detection and Analysis. Int J Mol Sci 2022; 23:ijms231911895. [PMID: 36233197 PMCID: PMC9570191 DOI: 10.3390/ijms231911895] [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: 09/04/2022] [Revised: 09/29/2022] [Accepted: 10/04/2022] [Indexed: 11/17/2022] Open
Abstract
Quality control of drug products is of paramount importance in the pharmaceutical world. It ensures product safety, efficiency, and consistency. In the case of complex biomolecules such as therapeutic proteins, small variations in bioprocess parameters can induce substantial variations in terms of structure, impacting the drug product quality. Conditions for obtaining highly reproducible grafting of 11-mercaptoundecanoic acid were determined. On that basis, we developed an easy-to-use, cost effective, and timesaving biosensor based on ATR-FTIR spectroscopy able to detect immunoglobulins during their production. A germanium crystal, used as an internal reflection element (IRE) for FTIR spectroscopy, was covalently coated with immunoglobulin-binding proteins. This thereby functionalized surface could bind only immunoglobulins present in complex media such as culture media or biopharmaceutical products. The potential subsequent analysis of their structure by ATR-FTIR spectroscopy makes this biosensor a powerful tool to monitor the production of biotherapeutics and assess important critical quality attributes (CQAs) such as high-order structure and aggregation level.
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17
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Barrera FN. On 'Fourier transform infrared study of proteins with parallel β-chains' by Heino Susi, D. Michael Byler. Arch Biochem Biophys 2022; 726:109114. [PMID: 34973205 DOI: 10.1016/j.abb.2021.109114] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 12/23/2021] [Accepted: 12/27/2021] [Indexed: 11/24/2022]
Abstract
In 1987, Susi & Byler published a groundbreaking paper for the determination of the secondary structure of proteins. Notably, they determined the characteristic signature of the β-strand in the infrared spectrum. As a result, Fourier-transform infrared spectroscopy became a general method to determine protein structure.
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Affiliation(s)
- Francisco N Barrera
- Department of Biochemistry & Cellular and Molecular Biology, The University of Tennessee Knoxville, USA.
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18
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A mid-infrared lab-on-a-chip for dynamic reaction monitoring. Nat Commun 2022; 13:4753. [PMID: 35963870 PMCID: PMC9376098 DOI: 10.1038/s41467-022-32417-7] [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: 02/14/2022] [Accepted: 07/29/2022] [Indexed: 11/08/2022] Open
Abstract
Mid-infrared spectroscopy is a sensitive and selective technique for probing molecules in the gas or liquid phase. Investigating chemical reactions in bio-medical applications such as drug production is recently gaining particular interest. However, monitoring dynamic processes in liquids is commonly limited to bulky systems and thus requires time-consuming offline analytics. In this work, we show a next-generation, fully-integrated and robust chip-scale sensor for online measurements of molecule dynamics in a liquid solution. Our fingertip-sized device utilizes quantum cascade technology, combining the emitter, sensing section and detector on a single chip. This enables real-time measurements probing only microliter amounts of analyte in an in situ configuration. We demonstrate time-resolved device operation by analyzing temperature-induced conformational changes of the model protein bovine serum albumin in heavy water. Quantitative measurements reveal excellent performance characteristics in terms of sensor linearity, wide coverage of concentrations, extending from 0.075 mg ml-1 to 92 mg ml-1 and a 55-times higher absorbance than state-of-the-art bulky and offline reference systems.
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19
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Andoh V, Chen L, Zhu F, Ge Q, Ma L, Wang Q, Chen K. The Evaluation of the Biological Effects of Melanin by Using Silkworm as a Model Animal. Toxins (Basel) 2022; 14:421. [PMID: 35878159 PMCID: PMC9317675 DOI: 10.3390/toxins14070421] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Revised: 06/14/2022] [Accepted: 06/19/2022] [Indexed: 02/04/2023] Open
Abstract
Melanin has been reported to have potential applications in industries such as cosmetics and food due to its anti-UV and antioxidative qualities. However, the corresponding data on its safety evaluation or biological consequences are fairly limited; such data are critical given its widespread use. The effect of different concentrations (1, 2, 3, and 4%) of melanin on growth status (larvae length and weight, cocoon weight, and morphology), the microstructure of the various tissues (fat body, silk gland, and midgut), and silk properties was studied by using the silkworm (bombyx mori) as the model organism. The weight and length of silkworm larvae fed with melanin were lower than the control, indicating that melanin appears to have a negative effect on the growth status of silkworms; however, the histophysiology analysis indicates that the cell morphologies are not changed, the XRD and FTIR spectra indicate that the secondary and crystalline structures of silks are also well preserved, and the thermogravimetric analysis and tensile test indicate that the thermal stability and mechanical properties are well maintained and even improved to some extent. Generally, it indicates that melanin has a certain inhibitory effect on the growth of silkworm larva but causes no harm to the cell microstructures or silk properties; this demonstrates that the safety of melanin as a food addictive should be considered seriously. The increase of thermal stability and mechanical properties shows that melanin may be a good chemical modifier in textile industries.
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Affiliation(s)
- Vivian Andoh
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China;
- School of Life Sciences, Jiangsu University, Zhenjiang 212013, China; (L.C.); (F.Z.); (Q.G.)
| | - Liang Chen
- School of Life Sciences, Jiangsu University, Zhenjiang 212013, China; (L.C.); (F.Z.); (Q.G.)
| | - Feifei Zhu
- School of Life Sciences, Jiangsu University, Zhenjiang 212013, China; (L.C.); (F.Z.); (Q.G.)
| | - Qi Ge
- School of Life Sciences, Jiangsu University, Zhenjiang 212013, China; (L.C.); (F.Z.); (Q.G.)
- School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Lin Ma
- College of Biotechnology, Jiangsu University of Science and Technology, Zhenjiang 212100, China
| | - Qiang Wang
- School of Life Sciences, Jiangsu University, Zhenjiang 212013, China; (L.C.); (F.Z.); (Q.G.)
| | - Keping Chen
- School of Food and Biological Engineering, Jiangsu University, Zhenjiang 212013, China;
- School of Life Sciences, Jiangsu University, Zhenjiang 212013, China; (L.C.); (F.Z.); (Q.G.)
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20
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Dissection of the amyloid formation pathway in AL amyloidosis. Nat Commun 2021; 12:6516. [PMID: 34764275 PMCID: PMC8585945 DOI: 10.1038/s41467-021-26845-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 10/25/2021] [Indexed: 11/18/2022] Open
Abstract
In antibody light chain (AL) amyloidosis, overproduced light chain (LC) fragments accumulate as fibrils in organs and tissues of patients. In vitro, AL fibril formation is a slow process, characterized by a pronounced lag phase. The events occurring during this lag phase are largely unknown. We have dissected the lag phase of a patient-derived LC truncation and identified structural transitions that precede fibril formation. The process starts with partial unfolding of the VL domain and the formation of small amounts of dimers. This is a prerequisite for the formation of an ensemble of oligomers, which are the precursors of fibrils. During oligomerization, the hydrophobic core of the LC domain rearranges which leads to changes in solvent accessibility and rigidity. Structural transitions from an anti-parallel to a parallel β-sheet secondary structure occur in the oligomers prior to amyloid formation. Together, our results reveal a rate-limiting multi-step mechanism of structural transitions prior to fibril formation in AL amyloidosis, which offers, in the long run, opportunities for therapeutic intervention. AL amyloidosis is caused by the accumulation of overproduced light chain (LC) fragments as fibrils in patient organs and it is the most prevalent systemic amyloidosis. Here, the authors combine biochemical and biophysical experiments to characterise the lag phase of a patient-derived truncated LC and they identify structural transitions that precede fibril formation.
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21
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De Meutter J, Goormaghtigh E. Protein Structural Denaturation Evaluated by MCR-ALS of Protein Microarray FTIR Spectra. Anal Chem 2021; 93:13441-13449. [PMID: 34592098 DOI: 10.1021/acs.analchem.1c01416] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The loss of native structure is common in proteins. Among others, aggregation is one structural modification of particular importance as it is a major concern for the efficiency and safety of biotherapeutic proteins. Yet, recognizing the structural features associated with intermolecular bridging in a high-throughput manner remains a challenge. We combined here the use of protein microarrays spotted at a density of ca 2500 samples per cm2 and Fourier transform infrared (FTIR) imaging to analyze structural modifications in a set of 85 proteins characterized by widely different secondary structure contents, submitted or not to mild denaturing conditions. Multivariate curve resolution alternating least squares (MCR-ALS) was used to model a new spectral component appearing in the protein set subject to denaturing conditions. In the native protein set, 6 components were found to be sufficient to obtain good modeling of the spectra. Furthermore, their shape allowed them to be assigned to α-helix, β-sheet, and other structures. Their content in each protein was correlated with the known secondary structure, confirming these assignments. In the denatured proteins, a new component was necessary and modeled by MCR-ALS. This new component could be assigned to the intermolecular β-sheet, bridging protein molecules. MCR-ALS, therefore, unveiled a potential spectroscopic marker of protein aggregation and allowed a semiquantitative evaluation of its content. Insight into other structural rearrangements was also obtained.
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Affiliation(s)
- Joëlle De Meutter
- Center for Structural Biology and Bioinformatics, Laboratory for the Structure and Function of Biological Membranes, Campus Plaine, Université Libre de Bruxelles CP206/2, B1050 Brussels, Belgium
| | - Erik Goormaghtigh
- Center for Structural Biology and Bioinformatics, Laboratory for the Structure and Function of Biological Membranes, Campus Plaine, Université Libre de Bruxelles CP206/2, B1050 Brussels, Belgium
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22
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England P, Jowitt TA. Community-building and promotion of technological excellence in molecular biophysics: the ARBRE-MOBIEU network. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2021; 50:307-311. [PMID: 34057541 DOI: 10.1007/s00249-021-01550-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Patrick England
- Molecular Biophysics Facility, Institut Pasteur, 25-28 rue du Docteur Roux, 75724, Paris cedex 15, France.
| | - Thomas A Jowitt
- Biomolecular Analysis Core Facility, Faculty of Biology Medicine and Health, University of Manchester, Oxford Road, Manchester, M13 9PT, UK.
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