1
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Matinong AME, Pickering KL, Waterland MR, Chisti Y, Haverkamp RG. Gelatin and Collagen from Sheepskin. Polymers (Basel) 2024; 16:1563. [PMID: 38891509 PMCID: PMC11174695 DOI: 10.3390/polym16111563] [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: 04/03/2024] [Revised: 05/08/2024] [Accepted: 05/28/2024] [Indexed: 06/21/2024] Open
Abstract
Abattoirs dispose of sheepskins as solid waste due to low price and poor demand for sheepskin leather. In principle, as an alternative to being disposed of in landfill, sheepskins can serve as a source of the protein collagen or the hydrolysis product, gelatin. In this research, sheepskins collected from abattoirs were used as a source of collagen. Three extraction methods were compared: acid extraction, acid with enzymes, and alkali extraction. The extracted material was characterized using scanning electron microscopy (SEM) and Fourier-transform infrared spectroscopy (FTIR), small angle X-ray scattering (SAXS), and sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE). The collagen and gelatin extraction yield ranged from 3.1% to 4.8% with the product purity determined by hydroxyproline, ranging from 7.8% for the alkali process to 59% and 68% for the acid and acid-enzyme processes. SDS PAGE showed that the acid process produced fragments with molecular weights in the range 100 to >250 kDa, while acid-enzyme resulted in smaller fragments, below 30 kDa. The FTIR region of the amide I band at 1800-1550 cm-1, which was used as an indicator of the collagen and gelatin content, showed that the gelatin dominated in the acid extracts, and the alkaline extract contained a large portion of keratin. SAXS was found to be a sensitive method for showing the presence of intact collagen fibrils in materials from all of the extraction methods, albeit at low concentrations. Herein, sheepskin is shown to be a useful source for collagen-gelatin material of varying molecular weights.
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Affiliation(s)
- Andrea Marie E. Matinong
- School of Food and Natural Sciences, Massey University, Palmerston North 4442, New Zealand; (A.M.E.M.); (M.R.W.)
| | - Kim L. Pickering
- School of Engineering, University of Waikato, Hamilton 3240, New Zealand;
| | - Mark R. Waterland
- School of Food and Natural Sciences, Massey University, Palmerston North 4442, New Zealand; (A.M.E.M.); (M.R.W.)
| | - Yusuf Chisti
- Institute of Tropical Aquaculture and Fisheries, Universiti Malaysia Terengganu, Kuala Nerus 21030, Malaysia;
| | - Richard G. Haverkamp
- School of Food and Natural Sciences, Massey University, Palmerston North 4442, New Zealand; (A.M.E.M.); (M.R.W.)
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2
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Varga V, Smeller L, Várdai R, Kocsis B, Zsoldos I, Cruciani S, Pala R, Hornyák I. Water-Insoluble, Thermostable, Crosslinked Gelatin Matrix for Soft Tissue Implant Development. Int J Mol Sci 2024; 25:4336. [PMID: 38673921 PMCID: PMC11050114 DOI: 10.3390/ijms25084336] [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: 02/26/2024] [Revised: 04/09/2024] [Accepted: 04/11/2024] [Indexed: 04/28/2024] Open
Abstract
In this present study, the material science background of crosslinked gelatin (GEL) was investigated. The aim was to assess the optimal reaction parameters for the production of a water-insoluble crosslinked gelatin matrix suitable for heat sterilization. Matrices were subjected to enzymatic degradation assessments, and their ability to withstand heat sterilization was evaluated. The impact of different crosslinkers on matrix properties was analyzed. It was found that matrices crosslinked with butanediol diglycidyl ether (BDDE) and poly(ethylene glycol) diglycidyl ether (PEGDE) were resistant to enzymatic degradation and heat sterilization. Additionally, at 1 v/v % crosslinker concentration, the crosslinked weight was lower than the starting weight, suggesting simultaneous degradation and crosslinking. The crosslinked weight and swelling ratio were optimal in the case of the matrices that were crosslinked with 3% and 5% v/v BDDE and PEGDE. FTIR analysis confirmed crosslinking, and the reduction of free primary amino groups indicated effective crosslinking even at a 1% v/v crosslinker concentration. Moreover, stress-strain and compression characteristics of the 5% v/v BDDE crosslinked matrix were comparable to native gelatin. Based on material science measurements, the crosslinked matrices may be promising candidates for scaffold development, including properties such as resistance to enzymatic degradation and heat sterilization.
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Affiliation(s)
- Viktória Varga
- Institute of Translational Medicine, Semmelweis University, 1094 Budapest, Hungary;
- Department of Materials Science and Technology, University of Győr, 9026 Győr, Hungary; (B.K.); (I.Z.)
| | - László Smeller
- Department of Biophysics and Radiation Biology, Semmelweis University, 1094 Budapest, Hungary;
| | - Róbert Várdai
- Laboratory of Plastics and Rubber Technology, Department of Physical Chemistry and Materials Science, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, 1111 Budapest, Hungary;
- Research Centre for Natural Sciences, Institute of Materials and Environmental Chemistry, 1111 Budapest, Hungary
| | - Bence Kocsis
- Department of Materials Science and Technology, University of Győr, 9026 Győr, Hungary; (B.K.); (I.Z.)
| | - Ibolya Zsoldos
- Department of Materials Science and Technology, University of Győr, 9026 Győr, Hungary; (B.K.); (I.Z.)
| | - Sara Cruciani
- Department of Biomedical Sciences, University of Sassari, Viale San Pietro 43/B, 07100 Sassari, Italy; (S.C.); (R.P.)
| | - Renzo Pala
- Department of Biomedical Sciences, University of Sassari, Viale San Pietro 43/B, 07100 Sassari, Italy; (S.C.); (R.P.)
| | - István Hornyák
- Institute of Translational Medicine, Semmelweis University, 1094 Budapest, Hungary;
- Department of Materials Science and Technology, University of Győr, 9026 Győr, Hungary; (B.K.); (I.Z.)
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3
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Zhao J, Yu P, Dong T, Wu Y, Yang F, Wang J. Chasing weakly-bound biological water in aqueous environment near the peptide backbone by ultrafast 2D infrared spectroscopy. Commun Chem 2024; 7:82. [PMID: 38605209 PMCID: PMC11009226 DOI: 10.1038/s42004-024-01170-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Accepted: 04/05/2024] [Indexed: 04/13/2024] Open
Abstract
There has been a long-standing debate as to how many hydrogen bonds a peptide backbone amide can form in aqueous solution. Hydrogen-bonding structural dynamics of N-ethylpropionamide (a β-peptide model) in water was examined using infrared (IR) spectroscopy. Two amide-I sub bands arise mainly from amide C=O group that forms strong H-bonds with solvent water molecules (SHB state), and minorly from that involving one weak H-bond with water (WHB state). This picture is supported by molecular dynamics simulations and ab-initio calculations. Further, thermodynamics and kinetics of the SHB and WHB species were examined mainly by chemical-exchange two-dimensional IR spectroscopy, yielding an activation energy for the SHB-to-WHB exchange of 13.25 ± 0.52 kJ mol‒1, which occurs in half picosecond at room temperature. Our results provided experimental evidence of an unstable water molecule near peptide backbone, allowing us to gain more insights into the dynamics of the protein backbone hydration.
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Affiliation(s)
- Juan Zhao
- Molecular Reaction Dynamics Laboratory, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Pengyun Yu
- Molecular Reaction Dynamics Laboratory, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Tiantian Dong
- Molecular Reaction Dynamics Laboratory, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yanzhou Wu
- Molecular Reaction Dynamics Laboratory, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Fan Yang
- Molecular Reaction Dynamics Laboratory, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jianping Wang
- Molecular Reaction Dynamics Laboratory, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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4
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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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5
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Scaggion C, Marinato M, Dal Sasso G, Nodari L, Saupe T, Aneli S, Pagani L, Scheib CL, Rigo M, Artioli G. A fresh perspective on infrared spectroscopy as a prescreening method for molecular and stable isotopes analyses on ancient human bones. Sci Rep 2024; 14:1028. [PMID: 38200208 PMCID: PMC10781948 DOI: 10.1038/s41598-024-51518-5] [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: 06/08/2023] [Accepted: 01/06/2024] [Indexed: 01/12/2024] Open
Abstract
Following the development of modern genome sequencing technologies, the investigation of museum osteological finds is increasingly informative and popular. Viable protocols to help preserve these collections from exceedingly invasive analyses, would allow greater access to the specimens for scientific research. The main aim of this work is to survey skeletal tissues, specifically petrous bones and roots of teeth, using infrared spectroscopy as a prescreening method to assess the bone quality for molecular analyses. This approach could overcome the major problem of identifying useful genetic material in archaeological bone collections without resorting to demanding, time consuming and expensive laboratory studies. A minimally invasive sampling of archaeological bones was developed and bone structural and compositional changes were examined, linking isotopic and genetic data to infrared spectra. The predictive model based on Infrared parameters is effective in determining the occurrence of ancient DNA (aDNA); however, the quality/quantity of aDNA cannot be determined because of the influence of environmental and local factors experienced by the examined bones during the burial period.
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Affiliation(s)
- Cinzia Scaggion
- Department of Geosciences, University of Padova, 35131, Padova, Italy.
- INSTM, National Interuniversity Consortium of Materials Science and Technology, 50121, Firenze, Italy.
| | - Maurizio Marinato
- Department of Cultural Heritage: Archaeology and History of Art, Cinema and Music, University of Padova, 35139, Padova, Italy
| | - Gregorio Dal Sasso
- Institute of Geosciences and Earth Resources, Italian National Research Council-CNR, 35131, Padova, Italy
| | - Luca Nodari
- Institute of Condensed Matter Chemistry and Technologies for Energy, Italian National Research Council-CNR, 35127, Padova, Italy
| | - Tina Saupe
- Estonian Biocentre, Institute of Genomics, University of Tartu, 51010, Tartu, Estonia
| | - Serena Aneli
- Department of Biology, University of Padova, 35122, Padova, Italy
- Department of Public Health Sciences and Pediatrics, University of Torino, 10126, Torino, Italy
| | - Luca Pagani
- Estonian Biocentre, Institute of Genomics, University of Tartu, 51010, Tartu, Estonia
- Department of Biology, University of Padova, 35122, Padova, Italy
| | - Christiana L Scheib
- Estonian Biocentre, Institute of Genomics, University of Tartu, 51010, Tartu, Estonia
| | - Manuel Rigo
- Department of Geosciences, University of Padova, 35131, Padova, Italy
- Institute of Geosciences and Earth Resources, Italian National Research Council-CNR, 35131, Padova, Italy
| | - Gilberto Artioli
- Department of Geosciences, University of Padova, 35131, Padova, Italy
- INSTM, National Interuniversity Consortium of Materials Science and Technology, 50121, Firenze, Italy
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6
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Krevert C, Chavez D, Chatterjee S, Stelzl LS, Pütz S, Roeters SJ, Rudzinski JF, Fawzi NL, Girard M, Parekh SH, Hunger J. Liquid-Liquid Phase Separation of the Intrinsically Disordered Domain of the Fused in Sarcoma Protein Results in Substantial Slowing of Hydration Dynamics. J Phys Chem Lett 2023; 14:11224-11234. [PMID: 38056002 PMCID: PMC10726384 DOI: 10.1021/acs.jpclett.3c02790] [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: 10/06/2023] [Revised: 11/30/2023] [Accepted: 12/01/2023] [Indexed: 12/08/2023]
Abstract
Formation of liquid condensates plays a critical role in biology via localization of different components or via altered hydrodynamic transport, yet the hydrogen-bonding environment within condensates, pivotal for solvation, has remained elusive. We explore the hydrogen-bond dynamics within condensates formed by the low-complexity domain of the fused in sarcoma protein. Probing the hydrogen-bond dynamics sensed by condensate proteins using two-dimensional infrared spectroscopy of the protein amide I vibrations, we find that frequency-frequency correlations of the amide I vibration decay on a picosecond time scale. Interestingly, these dynamics are markedly slower for proteins in the condensate than in a homogeneous protein solution, indicative of different hydration dynamics. All-atom molecular dynamics simulations confirm that lifetimes of hydrogen-bonds between water and the protein are longer in the condensates than in the protein in solution. Altered hydrogen-bonding dynamics may contribute to unique solvation and reaction dynamics in such condensates.
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Affiliation(s)
- Carola
S. Krevert
- Department
of Molecular Spectroscopy, Max Planck Institute
for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Daniel Chavez
- Department
of Polymer Theory, Max Planck Institute
for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Sayantan Chatterjee
- Department
of Molecular Spectroscopy, Max Planck Institute
for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
- Department
of Biomedical Engineering, The University
of Texas at Austin, 107
West Dean Keeton Street, Stop C0800, Austin, Texas 78712, United States
| | - Lukas S. Stelzl
- KOMET 1,
Institute of Physics, Johannes Gutenberg
University, Staudingerweg 7, 55099 Mainz, Germany
- Faculty of
Biology, Johannes Gutenberg University Mainz, Gresemundweg 2, 55128 Mainz, Germany
- Institute
of Molecular Biology (IMB), Ackermannweg 2, 55128 Mainz, Germany
| | - Sabine Pütz
- Department
of Molecular Spectroscopy, Max Planck Institute
for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Steven J. Roeters
- Department
of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
- Department
of Anatomy and Neurosciences, Amsterdam
UMC, Vrije Universiteit, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands
| | - Joseph F. Rudzinski
- Department
of Polymer Theory, Max Planck Institute
for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
- IRIS
Adlershof, Humboldt-Universität zu
Berlin, Zum Großen
Windkanal 2, 12489 Berlin, Germany
| | - Nicolas L. Fawzi
- Department
of Molecular Biology, Cell Biology, and Biochemistry, Brown University, 70 Ship Street, Providence, Rhode Island 02912, United States
| | - Martin Girard
- Department
of Polymer Theory, Max Planck Institute
for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Sapun H. Parekh
- Department
of Molecular Spectroscopy, Max Planck Institute
for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
- Department
of Biomedical Engineering, The University
of Texas at Austin, 107
West Dean Keeton Street, Stop C0800, Austin, Texas 78712, United States
| | - Johannes Hunger
- Department
of Molecular Spectroscopy, Max Planck Institute
for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
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7
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Maia RN, Mitra S, Baiz CR. Extracting accurate infrared lineshapes from weak vibrational probes at low concentrations. MethodsX 2023; 11:102309. [PMID: 37577166 PMCID: PMC10416016 DOI: 10.1016/j.mex.2023.102309] [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: 05/01/2023] [Accepted: 07/31/2023] [Indexed: 08/15/2023] Open
Abstract
Fourier-transform infrared (FTIR) spectroscopy using vibrational probes is an ideal tool to detect changes in structure and local environments within biological molecules. However, challenges arise when dealing with weak infrared probes, such as thiocyanates, due to their inherent low signal strengths and overlap with solvent bands. In this protocol we demonstrate:•A streamlined approach for the precise extraction of weak infrared absorption lineshapes from a strong solvent background.•A protocol combining a spectral filter, background modeling, and subtraction.•Our methodology successfully extracts the CN stretching mode peak from methyl thiocyanate at remarkably low concentrations (0.25 mM) in water, previously a challenge for FTIR spectroscopy.This approach offers valuable insights and tools for more accurate FTIR measurements using weak vibrational probes. This enhanced precision can potentially enable new approaches to enhance our understanding of protein structure and dynamics in solution.
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Affiliation(s)
- Raiza N.A. Maia
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712-1224, USA
| | - Sunayana Mitra
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712-1224, USA
| | - Carlos R. Baiz
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712-1224, USA
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8
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Ma Z, Chen L, Xu C, Fournier JA. Two-Dimensional Infrared Spectroscopy of Isolated Molecular Ions. J Phys Chem Lett 2023; 14:9683-9689. [PMID: 37871134 DOI: 10.1021/acs.jpclett.3c02661] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Two-dimensional infrared (2D IR) spectroscopy of mass-selected, cryogenically cooled molecular ions is presented. Nonlinear response pathways, encoded in the time-domain photodissociation action response of weakly bound N2 messenger tags, were isolated using pulse shaping techniques following excitation with four collinear ultrafast IR pulses. 2D IR spectra of Re(CO)3(CH3CN)3+ ions capture off-diagonal cross-peak bleach signals between the asymmetric and symmetric carbonyl stretching transitions. These cross peaks display intensity variations as a function of pump-probe delay time due to coherent coupling between the vibrational modes. Well-resolved 2D IR features in the congested fingerprint region of protonated caffeine (C8H10N4O2H+) are also reported. Importantly, intense cross-peak signals were observed at 3 ps waiting time, indicating that tag-loss dynamics are not competing with the measured nonlinear signals. These demonstrations pave the way for more precise studies of molecular interactions and dynamics that are not easily obtainable with current condensed-phase methodologies.
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Affiliation(s)
- Zifan Ma
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Liangyi Chen
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Chuzhi Xu
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Joseph A Fournier
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri 63130, United States
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9
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Brüggemann J, Chekmeneva M, Wolter M, Jacob CR. Structural Dependence of Extended Amide III Vibrations in Two-Dimensional Infrared Spectra. J Phys Chem Lett 2023; 14:9257-9264. [PMID: 37812580 PMCID: PMC10591501 DOI: 10.1021/acs.jpclett.3c02662] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 10/05/2023] [Indexed: 10/11/2023]
Abstract
Two-dimensional infrared (2D-IR) spectroscopy is a powerful experimental method for probing the structure and dynamics of proteins in aqueous solution. So far, most experimental studies have focused on the amide I vibrations, for which empirical vibrational exciton models provide a means of interpreting such experiments. However, such models are largely lacking for other regions of the vibrational spectrum. To close this gap, we employ an efficient quantum-chemical methodology for the calculation of 2D-IR spectra, which is based on anharmonic theoretical vibrational spectroscopy with localized modes. We apply this approach to explore the potential of 2D-IR spectroscopy in the extended amide III region. Using calculations for a dipeptide model as well as alanine polypeptides, we show that distinct 2D-IR cross-peaks in the extended amide III region can potentially be used to distinguish α-helix and β-strand structures. We propose that the extended amide III region could be a promising target for future 2D-IR experiments.
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Affiliation(s)
- Julia Brüggemann
- Technische Universität Braunschweig, Institute of Physical and Theoretical Chemistry, Gaußstraße 17, 38106 Braunschweig, Germany
| | - Maria Chekmeneva
- Technische Universität Braunschweig, Institute of Physical and Theoretical Chemistry, Gaußstraße 17, 38106 Braunschweig, Germany
| | - Mario Wolter
- Technische Universität Braunschweig, Institute of Physical and Theoretical Chemistry, Gaußstraße 17, 38106 Braunschweig, Germany
| | - Christoph R. Jacob
- Technische Universität Braunschweig, Institute of Physical and Theoretical Chemistry, Gaußstraße 17, 38106 Braunschweig, Germany
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10
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Xu C, Fracassi A, Baryiames CP, Bhattacharya A, Devaraj NK, Baiz CR. Sponge-phase Lipid Droplets as Synthetic Organelles: An Ultrafast Study of Hydrogen Bonding and Interfacial Environments. Chemphyschem 2023; 24:e202300404. [PMID: 37486881 DOI: 10.1002/cphc.202300404] [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: 06/19/2023] [Revised: 07/12/2023] [Accepted: 07/18/2023] [Indexed: 07/26/2023]
Abstract
Bottom-up design of biomimetic organelles has gained recent attention as a route towards understanding the transition between non-living matter and life. Despite various artificial lipid membranes being developed, the specific relations between lipid structure, composition, interfacial properties, and morphology are not currently understood. Sponge-phase droplets contain dense, nonlamellar lipid bilayer networks that capture the complexities of the endoplasmic reticulum (ER), making them ideal artificial models of such organelles. Here, we combine ultrafast two-dimensional infrared (2D IR) spectroscopy and molecular dynamics simulations to investigate the interfacial H-bond networks in sponge-phase droplets composed of glycolipid and nonionic detergents. In the sponge phase, the interfacial environments are more hydrated and water molecules confined to the nanometer-scale aqueous channels in the sponge phase exhibit dynamics that are significantly slower compared to bulk water. Surfactant configurations and microscopic phase separation play a dominant role in determining membrane curvature and slow dynamics observed in the sponge phase. The studies suggest that H-bond networks within the nanometer-scale channels are disrupted not only by confinement but also by the interactions of surfactants, which extend 1-2 nm from the bilayer surface. The results provide a molecular-level description for controlling phase and morphology in the design of synthetic lipid organelles.
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Affiliation(s)
- Cong Xu
- Department of Chemistry, The University of Texas at Austin, 105 E. 24th St. Stop A5300, 78712-1224, Austin, TX, USA
| | - Alessandro Fracassi
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, Natural Sciences Building 3328, 92093, La Jolla, CA, USA
| | - Christopher P Baryiames
- Department of Chemistry, The University of Texas at Austin, 105 E. 24th St. Stop A5300, 78712-1224, Austin, TX, USA
| | - Ahanjit Bhattacharya
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, Natural Sciences Building 3328, 92093, La Jolla, CA, USA
| | - Neal K Devaraj
- Department of Chemistry and Biochemistry, University of California, San Diego, 9500 Gilman Drive, Natural Sciences Building 3328, 92093, La Jolla, CA, USA
| | - Carlos R Baiz
- Department of Chemistry, The University of Texas at Austin, 105 E. 24th St. Stop A5300, 78712-1224, Austin, TX, USA
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11
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Chen X, Roeters SJ, Cavanna F, Alvarado J, Baiz CR. Crowding alters F-actin secondary structure and hydration. Commun Biol 2023; 6:900. [PMID: 37660224 PMCID: PMC10475093 DOI: 10.1038/s42003-023-05274-3] [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: 04/28/2023] [Accepted: 08/22/2023] [Indexed: 09/04/2023] Open
Abstract
Actin, an important component of eukaryotic cell cytoskeleton, regulates cell shape and transport. The morphology and biochemical properties of actin filaments are determined by their structure and protein-protein contacts. Crowded environments can organize filaments into bundles, but less is known about how they affect F-actin structure. This study used 2D IR spectroscopy and spectral calculations to examine how crowding and bundling impact the secondary structure and local environments in filaments and weakly or strongly bundled networks. The results reveal that bundling induces changes in actin's secondary structure, leading to a decrease in β-sheet and an increase in loop conformations. Strongly bundled networks exhibit a decrease in backbone solvent exposure, with less perturbed α-helices and nearly "locked" β-sheets. Similarly, the loops become less hydrated but maintain a dynamic environment. These findings highlight the role of loop structure in actin network morphology and stability under morphology control by PEG.
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Affiliation(s)
- Xiaobing Chen
- Department of Chemistry, University of Texas at Austin, Austin, TX, USA
| | - Steven J Roeters
- Department of Chemistry, Aarhus University, Aarhus, Denmark
- Department of Anatomy and Neurosciences, Vrije Universiteit, Amsterdam UMC, Amsterdam, Netherlands
| | - Francis Cavanna
- Department of Physics, University of Texas at Austin, Center for Nonlinear Dynamics, Austin, TX, USA
| | - José Alvarado
- Department of Physics, University of Texas at Austin, Center for Nonlinear Dynamics, Austin, TX, USA
| | - Carlos R Baiz
- Department of Chemistry, University of Texas at Austin, Austin, TX, USA.
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12
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Guleken Z, Ceylan Z, Aday A, Bayrak AG, Hindilerden İY, Nalçacı M, Jakubczyk P, Jakubczyk D, Depciuch J. FTIR- based serum structure analysis in molecular diagnostics of essential thrombocythemia disease. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 2023; 245:112734. [PMID: 37295134 DOI: 10.1016/j.jphotobiol.2023.112734] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 04/18/2023] [Accepted: 05/30/2023] [Indexed: 06/12/2023]
Abstract
Essential thrombocythemia (ET) reflects the transformation of a multipotent hematopoietic stem cell, but its molecular pathogenesis remains obscure. Nevertheless, tyrosine kinase, especially Janus kinase 2 (JAK2), has been implicated in myeloproliferative disorders other than chronic myeloid leukaemia. FTIR analysis was performed on the blood serum of 86 patients and 45 healthy volunteers as control with FTIR spectra-based machine learning methods and chemometrics. Thus, the study aimed to determine biomolecular changes and separation of ET and healthy control groups illustration by applying chemometrics and ML techniques to spectral data. The FTIR-based results showed that in ET disease with JAK2 mutation, there are alterations in functional groups associated with lipids, proteins and nucleic acids significantly. Moreover, in ET patients the lower amount of proteins with simultaneously higher amount of lipids was noted in comparison with the control one. Furthermore, the SVM-DA model showed 100% accuracy in calibration sets in both spectral regions and 100.0% and 96.43% accuracy in prediction sets for the 800-1800 cm-1 and 2700-3000 cm-1 spectral regions, respectively. While changes in the dynamic spectra showed that CH2 bending, amide II and CO vibrations could be used as a spectroscopy marker of ET. Finally, it was found a positive correlation between FTIR peaks and first bone marrow fibrosis degree, as well as the absence of JAK2 V617F mutation. The findings of this study contribute to a better understanding of the molecular pathogenesis of ET and identifying biomolecular changes and may have implications for early diagnosis and treatment of this disease.
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Affiliation(s)
- Zozan Guleken
- Department of Physiology, Faculty of Medicine, Gaziantep, Islam, Science and Technology University, 27220, Gaziantep, Turkey.
| | - Zeynep Ceylan
- Samsun University, Faculty of Engineering, Department of Industrial Engineering, Turkey
| | - Aynur Aday
- Istanbul University, Faculty of Medicine, Department of Internal Medicine, Division of Medical Genetics, Turkey
| | - Ayşe Gül Bayrak
- Istanbul University, Faculty of Medicine, Department of Internal Medicine, Division of Medical Genetics, Turkey
| | - İpek Yönal Hindilerden
- Istanbul University Istanbul Faculty of Medicine, Department of Internal Medicine, Division of Hematology, Turkey
| | - Meliha Nalçacı
- Istanbul University Istanbul Faculty of Medicine, Department of Internal Medicine, Division of Hematology, Turkey
| | | | - Dorota Jakubczyk
- Faculty of Mathematics and Applied Physics, Rzeszow University of Technology, Powstancow Warszawy 12, PL-35959 Rzeszow, Poland
| | - Joanna Depciuch
- Institute of Nuclear Physics, PAS, 31342 Krakow, Poland; Department of Biochemistry and Molecular Biology, Medical University of Lublin, 20-093 Lublin, Poland
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13
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Jiang Y, Xu X, Wang M, Zhou Y, Wang Z. Comparative study of the hydrogen bonding interactions between ester-functionalized/non-functionalized imidazolium-based ionic liquids and DMSO. Phys Chem Chem Phys 2023; 25:8789-8798. [PMID: 36912196 DOI: 10.1039/d2cp05048j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
There have been some studies on the microscopic properties of ester-functionalized ionic liquids (ILs), but the microscopic properties of their mixtures with co-solvents have seldom been reported. In practical applications, ILs are usually used together with co-solvents. Therefore, it is very important to study the microstructure of ester-functionalized ILs and co-solvents. In this work, the hydrogen bonding interactions between ester-functionalized IL 1-acetoxyethyl-3-methylimidazolium tetrafluoroborate (AOEMIMBF4) and DMSO were studied using spectroscopic methods and quantum chemical calculations. Non-functionalized IL 1-butyl-3-methylimidazolium tetrafluoroborate (BMIMBF4) and DMSO were used for comparison. The results indicate that (1) by adding DMSO, the hydrogen bonding interactions of ν(C2-H) were enhanced, and DMSO could form hydrogen bonds with anions and cations simultaneously. (2) The incorporation of an ester group could enhance the hydrogen bonding interactions. (3) Both the stretching vibration of C2-H and CO indicated changes in the microscopic structure: AOEMIMBF4 ion clusters first interacted with DMSO, then broke into AOEMIMBF4-DMSO complexes and finally existed as [AOEMIM]+/[BF4]--DMSO complexes.
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Affiliation(s)
- Yuxin Jiang
- Shandong Sino-Japanese Center for Collaborative Research of Carbon Nanomaterials, College of Chemistry and Chemical Engineering, Instrumental Analysis Center of Qingdao University, Qingdao University, Qingdao 266071, China.
| | - Xianzhen Xu
- Shandong Sino-Japanese Center for Collaborative Research of Carbon Nanomaterials, College of Chemistry and Chemical Engineering, Instrumental Analysis Center of Qingdao University, Qingdao University, Qingdao 266071, China.
| | - Mingzhu Wang
- Shandong Sino-Japanese Center for Collaborative Research of Carbon Nanomaterials, College of Chemistry and Chemical Engineering, Instrumental Analysis Center of Qingdao University, Qingdao University, Qingdao 266071, China.
| | - Yu Zhou
- Shandong Sino-Japanese Center for Collaborative Research of Carbon Nanomaterials, College of Chemistry and Chemical Engineering, Instrumental Analysis Center of Qingdao University, Qingdao University, Qingdao 266071, China.
| | - Zonghua Wang
- Shandong Sino-Japanese Center for Collaborative Research of Carbon Nanomaterials, College of Chemistry and Chemical Engineering, Instrumental Analysis Center of Qingdao University, Qingdao University, Qingdao 266071, China.
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14
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van Hengel CDN, van Adrichem KE, Jansen TLC. Simulation of two-dimensional infrared Raman spectroscopy with application to proteins. J Chem Phys 2023; 158:064106. [PMID: 36792507 DOI: 10.1063/5.0138958] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Two-dimensional infrared Raman spectroscopy is a powerful technique for studying the structure and interaction in molecular and biological systems. Here, we present a new implementation of the simulation of the two-dimensional infrared Raman signals. The implementation builds on the numerical integration of the Schrödinger equation approach. It combines the prediction of dynamics from molecular dynamics with a map-based approach for obtaining Hamiltonian trajectories and response function calculations. The new implementation is tested on the amide-I region for two proteins, where one is dominated by α-helices and the other by β-sheets. We find that the predicted spectra agree well with experimental observations. We further find that the two-dimensional infrared Raman spectra at least of the studied proteins are much less sensitive to the laser polarization used compared to conventional two-dimensional infrared experiments. The present implementation and findings pave the way for future applications for the interpretation of two-dimensional infrared Raman spectra.
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Affiliation(s)
- Carleen D N van Hengel
- University of Groningen, Zernike Institute for Advanced Materials, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Kim E van Adrichem
- University of Groningen, Zernike Institute for Advanced Materials, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Thomas L C Jansen
- University of Groningen, Zernike Institute for Advanced Materials, Nijenborgh 4, 9747 AG Groningen, The Netherlands
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15
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Rutherford SH, Baker MJ, Hunt NT. 2D-IR spectroscopy of proteins in H 2O-A Perspective. J Chem Phys 2023; 158:030901. [PMID: 36681646 DOI: 10.1063/5.0129480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The form of the amide I infrared absorption band provides a sensitive probe of the secondary structure and dynamics of proteins in the solution phase. However, the frequency coincidence of the amide I band with the bending vibrational mode of H2O has necessitated the widespread use of deuterated solvents. Recently, it has been demonstrated that ultrafast 2D-IR spectroscopy allows the detection of the protein amide I band in H2O-based fluids, meaning that IR methods can now be applied to study proteins in physiologically relevant solvents. In this perspective, we describe the basis of the 2D-IR method for observing the protein amide I band in H2O and show how this development has the potential to impact areas ranging from our fundamental appreciation of protein structural dynamics to new applications for 2D-IR spectroscopy in the analytical and biomedical sciences. In addition, we discuss how the spectral response of water, rather than being a hindrance, now provides a basis for new approaches to data pre-processing, standardization of 2D-IR data collection, and signal quantification. Ultimately, we visualize a direction of travel toward the creation of 2D-IR spectral libraries that can be linked to advanced computational methods for use in high-throughput protein screening and disease diagnosis.
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Affiliation(s)
- Samantha H Rutherford
- WestCHEM, Department of Pure and Applied Chemistry, University of Strathclyde, Technology and Innovation Centre, 99 George Street, Glasgow G1 1RD, United Kingdom
| | - Matthew J Baker
- School of Medicine, Faculty of Clinical Biomedical Sciences, University of Central Lancashire, Preston PR1 2HE, United Kingdom
| | - Neil T Hunt
- Department of Chemistry and York Biomedical Research Institute, University of York, York YO10 5DD, United Kingdom
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16
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Zakutauskaitė K, Mačernis M, Nguyen HH, Ogilvie JP, Abramavičius D. Extracting the excitonic Hamiltonian of a chlorophyll dimer from broadband two-dimensional electronic spectroscopy. J Chem Phys 2023; 158:015103. [PMID: 36610982 DOI: 10.1063/5.0108166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
We apply Frenkel exciton theory to model the entire Q-band of a tightly bound chlorophyll dimer inspired by the photosynthetic reaction center of photosystem II. The potential of broadband two-dimensional electronic spectroscopy experiment spanning the Qx and Qy regions to extract the parameters of the model dimer Hamiltonian is examined through theoretical simulations of the experiment. We find that the local nature of Qx excitation enables identification of molecular properties of the delocalized Qy excitons. Specifically, we demonstrate that the cross-peak region, where excitation energy is resonant with Qy while detection is at Qx, contains specific spectral signatures that can reveal the full real-space molecular Hamiltonian, a task that is impossible by considering the Qy transitions alone. System-bath coupling and site energy disorder in realistic systems may limit the resolution of these spectral signatures due to spectral congestion.
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Affiliation(s)
- Kristina Zakutauskaitė
- Institute of Chemical Physics, Vilnius University, Sauletekio al. 9-III, Vilnius, Lithuania
| | - Mindaugas Mačernis
- Institute of Chemical Physics, Vilnius University, Sauletekio al. 9-III, Vilnius, Lithuania
| | - Hoang H Nguyen
- Department of Physics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Jennifer P Ogilvie
- Department of Physics, University of Michigan, Ann Arbor, Michigan 48109, USA
| | - Darius Abramavičius
- Institute of Chemical Physics, Vilnius University, Sauletekio al. 9-III, Vilnius, Lithuania
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17
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Brüggemann J, Wolter M, Jacob CR. Quantum-chemical calculation of two-dimensional infrared spectra using localized-mode VSCF/VCI. J Chem Phys 2022; 157:244107. [PMID: 36586972 DOI: 10.1063/5.0135273] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Computational protocols for the simulation of two-dimensional infrared (2D IR) spectroscopy usually rely on vibrational exciton models which require an empirical parameterization. Here, we present an efficient quantum-chemical protocol for predicting static 2D IR spectra that does not require any empirical parameters. For the calculation of anharmonic vibrational energy levels and transition dipole moments, we employ the localized-mode vibrational self-consistent field (L-VSCF)/vibrational configuration interaction (L-VCI) approach previously established for (linear) anharmonic theoretical vibrational spectroscopy [P. T. Panek and C. R. Jacob, ChemPhysChem 15, 3365-3377 (2014)]. We demonstrate that with an efficient expansion of the potential energy surface using anharmonic one-mode potentials and harmonic two-mode potentials, 2D IR spectra of metal carbonyl complexes and dipeptides can be predicted reliably. We further show how the close connection between L-VCI and vibrational exciton models can be exploited to extract the parameters of such models from those calculations. This provides a novel route to the fully quantum-chemical parameterization of vibrational exciton models for predicting 2D IR spectra.
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Affiliation(s)
- Julia Brüggemann
- Institute of Physical and Theoretical Chemistry, Technische Universität Braunschweig, Gaußstraße 17, 38106 Braunschweig, Germany
| | - Mario Wolter
- Institute of Physical and Theoretical Chemistry, Technische Universität Braunschweig, Gaußstraße 17, 38106 Braunschweig, Germany
| | - Christoph R Jacob
- Institute of Physical and Theoretical Chemistry, Technische Universität Braunschweig, Gaußstraße 17, 38106 Braunschweig, Germany
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18
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Krevert CS, Gunkel L, Haese C, Hunger J. Ion-specific binding of cations to the carboxylate and of anions to the amide of alanylalanine. Commun Chem 2022; 5:173. [PMID: 36697920 PMCID: PMC9814750 DOI: 10.1038/s42004-022-00789-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 11/30/2022] [Indexed: 12/24/2022] Open
Abstract
Studies of ion-specific effects on oligopeptides have aided our understanding of Hofmeister effects on proteins, yet the use of different model peptides and different experimental sensitivities have led to conflicting conclusions. To resolve these controversies, we study a small model peptide, L-Alanyl-L-alanine (2Ala), carrying all fundamental chemical protein motifs: C-terminus, amide bond, and N-terminus. We elucidate the effect of GdmCl, LiCl, KCl, KI, and KSCN by combining dielectric relaxation, nuclear magnetic resonance (1H-NMR), and (two-dimensional) infrared spectroscopy. Our dielectric results show that all ions reduce the rotational mobility of 2Ala, yet the magnitude of the reduction is larger for denaturing cations than for anions. The NMR chemical shifts of the amide group are particularly sensitive to denaturing anions, indicative of anion-amide interactions. Infrared experiments reveal that LiCl alters the spectral homogeneity and dynamics of the carboxylate, but not the amide group. Interaction of LiCl with the negatively charged pole of 2Ala, the COO- group, can explain the marked cationic effect on dipolar rotation, while interaction of anions between the poles, at the amide, only weakly perturbs dipolar dynamics. As such, our results provide a unifying view on ions' preferential interaction sites at 2Ala and help rationalize Hofmeister effects on proteins.
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Affiliation(s)
- Carola Sophie Krevert
- grid.419547.a0000 0001 1010 1663Department of Molecular Spectroscopy, Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Lucas Gunkel
- grid.419547.a0000 0001 1010 1663Department of Molecular Spectroscopy, Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Constantin Haese
- grid.419547.a0000 0001 1010 1663Department of Molecular Electronics, Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Johannes Hunger
- grid.419547.a0000 0001 1010 1663Department of Molecular Spectroscopy, Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
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19
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Muindi MP, Lee JH, Kweon H, Kasina M. Effect of Extraction Ingredients on the Conformation and Stability of Silk Sericin (SS). Polymers (Basel) 2022; 14:polym14194118. [PMID: 36236065 PMCID: PMC9572401 DOI: 10.3390/polym14194118] [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: 08/25/2022] [Revised: 09/27/2022] [Accepted: 09/28/2022] [Indexed: 11/07/2022] Open
Abstract
Silk sericin (SS) has different physicochemical properties depending on the extraction technique. In this study, SS was isolated in the presence of ingredients, including 5 to 10% ethanol (EtOH) and 5 to 10% glycine. Furthermore, temperature conditions of 80 °C, 100 °C, and 120 °C were used for 1, 3, and 5 h to evaluate the extraction rates. The extraction, gelation, structural, and cytotoxicity properties of SS extracted under different conditions were investigated. Extraction at 100 °C and 120 °C were found to have the highest SS yield, with 80 °C being the lowest. SS isolated at 100 °C and 120 °C for 1 and 3 h in water, and EtOH gelled at 4 °C in 2 to 3 days and 37 °C in 40 min. Glycine SS extracts were obtained at 100 °C and 120 °C for 1 h, gelled at 4 °C for 20 days and 37 °C for 16 h. SS was observed at 80 °C, with no gelation occurring. Glycine SS extracts obtained for 3, and 5 h at 120 °C showed no gelation. Circular dichroism (CD) results show glycine in SS induces α-helix and random coil structure. SDS-polyacrylamide gel electrophoresis (SDS-PAGE) and fast performance liquid chromatography (FPLC) were used to quantify the molecular weight distribution at 63 and 70 kDa, respectively. The MMT assay (3-(4,5-dimethylthiazol-2-yl)-2, 5-diphenyltetrazolium bromide) revealed no cytotoxicity in macrophage RAW 264.7 cells treated with this method SS; these findings present the significance and possibility of using selected extraction ingredients in SS that allow for the application of native SS at an initial extraction viscosity.
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Affiliation(s)
- Munguti Peter Muindi
- National Sericulture Research Center, Kenya Agricultural and Livestock Research Organization, Thika 7816-01000, Kenya
| | - Ji Hae Lee
- National Institute of Agricultural Sciences, Rural Development Administration, Wanju 55365, Korea
- Correspondence: (J.H.L.); (H.K.)
| | - HaeYong Kweon
- National Institute of Agricultural Sciences, Rural Development Administration, Wanju 55365, Korea
- Correspondence: (J.H.L.); (H.K.)
| | - Muo Kasina
- National Sericulture Research Center, Kenya Agricultural and Livestock Research Organization, Thika 7816-01000, Kenya
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20
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Chatterley AS, Laity P, Holland C, Weidner T, Woutersen S, Giubertoni G. Broadband Multidimensional Spectroscopy Identifies the Amide II Vibrations in Silkworm Films. Molecules 2022; 27:molecules27196275. [PMID: 36234809 PMCID: PMC9571984 DOI: 10.3390/molecules27196275] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 09/19/2022] [Accepted: 09/21/2022] [Indexed: 11/16/2022] Open
Abstract
We used two-dimensional infrared spectroscopy to disentangle the broad infrared band in the amide II vibrational regions of Bombyx mori native silk films, identifying the single amide II modes and correlating them to specific secondary structure. Amide I and amide II modes have a strong vibrational coupling, which manifests as cross-peaks in 2D infrared spectra with frequencies determined by both the amide I and amide II frequencies of the same secondary structure. By cross referencing with well-known amide I assignments, we determined that the amide II (N-H) absorbs at around 1552 and at 1530 cm–1 for helical and β-sheet structures, respectively. We also observed a peak at 1517 cm−1 that could not be easily assigned to an amide II mode, and instead we tentatively assigned it to a Tyrosine sidechain. These results stand in contrast with previous findings from linear infrared spectroscopy, highlighting the ability of multidimensional spectroscopy for untangling convoluted spectra, and suggesting the need for caution when assigning silk amide II spectra.
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Affiliation(s)
| | - Peter Laity
- Department of Materials Science and Engineering, University of Sheffield, Sheffield S1 3JD, UK
| | - Chris Holland
- Department of Materials Science and Engineering, University of Sheffield, Sheffield S1 3JD, UK
| | - Tobias Weidner
- Department of Chemistry, Aarhus University, 8000 Aarhus C, Denmark
| | - Sander Woutersen
- Van ‘t Hoff Institute for Molecular Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - Giulia Giubertoni
- Van ‘t Hoff Institute for Molecular Sciences, University of Amsterdam, 1098 XH Amsterdam, The Netherlands
- Correspondence:
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21
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High-sensitivity hyperspectral vibrational imaging of heart tissues by mid-infrared photothermal microscopy. ANAL SCI 2022; 38:1497-1503. [PMID: 36070070 DOI: 10.1007/s44211-022-00182-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Accepted: 08/20/2022] [Indexed: 11/01/2022]
Abstract
Visualizing the spatial distribution of chemical compositions in biological tissues is of great importance to study fundamental biological processes and origin of diseases. Raman microscopy, one of the label-free vibrational imaging techniques, has been employed for chemical characterization of tissues. However, the low sensitivity of Raman spectroscopy often requires a long acquisition time of Raman measurement or a high laser power, or both, which prevents one from investigating large-area tissues in a nondestructive manner. In this work, we demonstrated chemical imaging of heart tissues using mid-infrared photothermal (MIP) microscopy that simultaneously achieves the high sensitivity benefited from IR absorption of molecules and the high spatial resolution down to a few micrometers. We successfully visualized the distributions of different biomolecules, including proteins, phosphate-including proteins, and lipids/carbohydrates/amino acids. Further, we experimentally compared MIP microscopy with Raman microscopy to evaluate the sensitivity and photodamage to tissues. We proved that MIP microscopy is a highly sensitive technique for obtaining vibrational information of molecules in a broad fingerprint region, thereby it could be employed for biological and diagnostic applications, such as live-tissue imaging.
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22
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Gong Q, Chen L, Wang J, Yuan F, Ma Z, Chen G, Huang Y, Miao Y, Liu T, Zhang XX, Yang Q, Yu J. Coassembly of a New Insect Cuticular Protein and Chitosan via Liquid-Liquid Phase Separation. Biomacromolecules 2022; 23:2562-2571. [PMID: 35561014 DOI: 10.1021/acs.biomac.2c00261] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Insect cuticle is a fiber-reinforced composite material that consists of polysaccharide chitin fibers and a protein matrix. The molecular interactions between insect cuticle proteins and chitin that govern the assembly and evolution of cuticles are still not well understood. Herein, we report that Ostrinia furnacalis cuticular protein hypothetical-1 (OfCPH-1), a newly discovered and most abundant cuticular protein from Asian corn borer O. furnacalis, can form coacervates in the presence of chitosan. The OfCPH-1-chitosan coacervate microdroplets are initially liquid-like but become gel-like with increasing time or salt concentration. The liquid-to-gel transition is driven by hydrogen-bonding interactions, during which an induced β-sheet structure of OfCPH-1 is observed. Given the abundance of OfCPH-1 in the cuticle of O. furnacalis, this liquid-liquid phase separation process and its aging behavior could play critical roles in the formation of the cuticle.
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Affiliation(s)
- Qiuyu Gong
- School of Materials Science and Engineering, Nanyang Technological University, Singapore 639798, Singapore
| | - Lei Chen
- Guangdong Laboratory for Lingnan Modern Agriculture, (Shenzhen Branch), Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 440307, P. R. China.,State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection and Shenzhen Agricultural Genome Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100193, P. R. China.,School of Bioengineering, Dalian University of Technology, Dalian 116024, P. R. China
| | - Jining Wang
- School of Materials Science and Engineering, Nanyang Technological University, Singapore 639798, Singapore.,Singapore Membrane Technology Centre, Nanyang Environment and Water Research Institute, Nanyang Technological University, Singapore 637141, Singapore
| | - Fenghou Yuan
- School of Bioengineering, Dalian University of Technology, Dalian 116024, P. R. China
| | - Zhiming Ma
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Guoxin Chen
- Ningbo Institute of Materials Technology & Engineering, Chinese Academy of Sciences, Ningbo 315201, P. R. China
| | - Yinjuan Huang
- School of Materials Science and Engineering, Nanyang Technological University, Singapore 639798, Singapore
| | - Yansong Miao
- School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore
| | - Tian Liu
- School of Bioengineering, Dalian University of Technology, Dalian 116024, P. R. China
| | - Xin-Xing Zhang
- School of Physics, Dalian University of Technology, Dalian 116024, P. R. China
| | - Qing Yang
- Guangdong Laboratory for Lingnan Modern Agriculture, (Shenzhen Branch), Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 440307, P. R. China.,State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection and Shenzhen Agricultural Genome Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100193, P. R. China
| | - Jing Yu
- School of Materials Science and Engineering, Nanyang Technological University, Singapore 639798, Singapore
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23
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Yamada Y, Obuchi K, Kikuchi N, Almarasy AA, Fujimori A. Immobilization of Trypsin from the Subphase to the Langmuir Monolayer of Fluorocarbon-Modified Single-Walled Carbon Nanotube and Its Activity Maintenance. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2022; 38:5692-5701. [PMID: 35465664 DOI: 10.1021/acs.langmuir.2c00283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Single-walled carbon nanotubes (SWCNTs) synthesized by the improved arc discharge method were modified with a fluorocarbon chain, and the maintenance of trypsin activity upon adsorption from the subphase to the interfacial monolayer of SWCNTs was evaluated. The adsorption of trypsin on the fluorocarbon-modified SWCNT monolayer was confirmed by morphological and spectroscopic evaluations. Fiber morphology studies revealed that the fluorocarbon-modified SWCNT monolayer was covered by trypsin, and a trypsin-derived amide band was detected in the infrared spectra of the multilayers. After adsorption onto the fluorocarbon-modified SWCNT film, the ability of trypsin to cleave the fluorescent casein chain was maintained even at 160 °C. Furthermore, circular dichroism (CD) spectra showed that the second-order structure of the activity of trypsin adsorbed on the fluorocarbon-modified SWCNT was maintained up to nearly 200 °C. At 200 °C, the enhancement of emission intensity by casein chain cleavage was negligible, and the CD signal resulting from the negative Cotton effect was completely altered at 250 °C.
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Affiliation(s)
- Yuna Yamada
- Faculty of Engineering, Saitama University, 255 Shimo-okubo, Sakura-ku, Saitama 338-8570, Japan
| | - Kei Obuchi
- Faculty of Engineering, Saitama University, 255 Shimo-okubo, Sakura-ku, Saitama 338-8570, Japan
| | - Nanata Kikuchi
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-okubo, Sakura-ku, Saitama 338-8570, Japan
| | - Ahmed A Almarasy
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-okubo, Sakura-ku, Saitama 338-8570, Japan
| | - Atsuhiro Fujimori
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-okubo, Sakura-ku, Saitama 338-8570, Japan
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24
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Sanchez Ramirez DO, Tonetti C, Cruz-Maya I, Guarino V, Peila R, Carletto RA, Varesano A, Vineis C. Design of cysteine-S-sulfonated keratin via pH driven processes: Micro-Structural Properties, biocidal activity and in vitro validation. Eur Polym J 2022. [DOI: 10.1016/j.eurpolymj.2022.111169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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25
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van Adrichem KE, Jansen TLC. AIM: A Mapping Program for Infrared Spectroscopy of Proteins. J Chem Theory Comput 2022; 18:3089-3098. [PMID: 35387451 PMCID: PMC9097285 DOI: 10.1021/acs.jctc.2c00113] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
![]()
Here, we present
a new analysis program, AIM, that allows extracting
the vibrational amide-I Hamiltonian using molecular dynamics trajectories
for protein infrared spectroscopy modeling. The constructed Hamiltonians
can be used as input for spectral calculations allowing the calculation
of infrared absorption spectra, vibrational circular dichroism, and
two-dimensional infrared spectra. These spectroscopies allow the study
of the structure and dynamics of proteins. We will explain the essence
of how AIM works and give examples of the information and spectra
that can be obtained with the program using the Trypsin Inhibitor
as an example. AIM is freely available from GitHub, and the package
contains a demonstration allowing easy introduction to the use of
the program.
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Affiliation(s)
- Kim E van Adrichem
- Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, The Netherlands
| | - Thomas L C Jansen
- Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, The Netherlands
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26
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Yang S, Zhang Q, Yang H, Shi H, Dong A, Wang L, Yu S. Progress in infrared spectroscopy as an efficient tool for predicting protein secondary structure. Int J Biol Macromol 2022; 206:175-187. [PMID: 35217087 DOI: 10.1016/j.ijbiomac.2022.02.104] [Citation(s) in RCA: 52] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 02/14/2022] [Accepted: 02/17/2022] [Indexed: 12/21/2022]
Abstract
Infrared (IR) spectroscopy is a highly sensitive technique that provides complete information on chemical compositions. The IR spectra of proteins or peptides give rise to nine characteristic IR absorption bands. The amide I bands are the most prominent and sensitive vibrational bands and widely used to predict protein secondary structures. The interference of H2O absorbance is the greatest challenge for IR protein secondary structure prediction. Much effort has been made to reduce/eliminate the interference of H2O, simplify operation steps, and increase prediction accuracy. Progress in sampling and equipment has rendered the Fourier transform infrared (FTIR) technique suitable for determining the protein secondary structure in broader concentration ranges, greatly simplifying the operating steps. This review highlights the recent progress in sample preparation, data analysis, and equipment development of FTIR in A/T mode, with a focus on recent applications of FTIR spectroscopy in the prediction of protein secondary structure. This review also provides a brief introduction of the progress in ATR-FTIR for predicting protein secondary structure and discusses some combined IR methods, such as AFM-based IR spectroscopy, that are used to analyze protein structural dynamics and protein aggregation.
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Affiliation(s)
- Shouning Yang
- Zhejiang Provincial Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China
| | | | - Huayan Yang
- Zhejiang Provincial Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Haimei Shi
- Zhejiang Provincial Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China
| | - Aichun Dong
- Department of Chemistry and Biochemistry, University of Northern Colorado, Greeley, CO, USA.
| | - Li Wang
- Kweichow Moutai Group, Renhuai, Guizhou 564501, China.
| | - Shaoning Yu
- Zhejiang Provincial Key Laboratory of Advanced Mass Spectrometry and Molecular Analysis, Institute of Mass Spectrometry, School of Material Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, China.
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27
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Abstract
Phenol soluble modulins (PSMs) are an important class of peptides secreted by Staphylococcus aureus bacteria. The toxicity to human cells and unique ability of one such peptide, PSMα3, to aggregate into an α-helical amyloid-like structure may hold a key to a better understanding of the virulence of dangerous pathogens such as methicillin resistant S. aureus. In reporting a detailed two-dimensional infrared (2DIR) analysis of PSMα3, we found direct evidence of multiple aggregate architectures existing in equilibrium with one another. We also discovered a unique and characteristic 2DIR spectroscopic signature that unambiguously reports on the presence of the unusual and highly cytotoxic cross-α amyloid structure. The formation of ordered cross-β amyloid protein aggregates is associated with a variety of human disorders. While conventional infrared methods serve as sensitive reporters of the presence of these amyloids, the recently discovered amyloid secondary structure of cross-α fibrils presents new questions and challenges. Herein, we report results using Fourier transform infrared spectroscopy and two-dimensional infrared spectroscopy to monitor the aggregation of one such cross-α–forming peptide, phenol soluble modulin alpha 3 (PSMα3). Phenol soluble modulins (PSMs) are involved in the formation and stabilization of Staphylococcus aureus biofilms, making sensitive methods of detecting and characterizing these fibrils a pressing need. Our experimental data coupled with spectroscopic simulations reveals the simultaneous presence of cross-α and cross-β polymorphs within samples of PSMα3 fibrils. We also report a new spectroscopic feature indicative of cross-α fibrils.
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28
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Chun SY, Son MK, Park CR, Lim C, Kim HI, Kwak K, Cho M. Direct observation of protein structural transitions through entire amyloid aggregation processes in water using 2D-IR spectroscopy. Chem Sci 2022; 13:4482-4489. [PMID: 35656138 PMCID: PMC9020176 DOI: 10.1039/d1sc06047c] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 03/18/2022] [Indexed: 12/02/2022] Open
Abstract
Amyloid proteins that undergo self-assembly to form insoluble fibrillar aggregates have attracted much attention due to their role in biological and pathological significance in amyloidosis. This study aims to understand the amyloid aggregation dynamics of insulin (INS) in H2O using two-dimensional infrared (2D-IR) spectroscopy. Conventional IR studies have been performed in D2O to avoid spectral congestion despite distinct H–D isotope effects. We observed a slowdown of the INS fibrillation process in D2O compared to that in H2O. The 2D-IR results reveal that different quaternary structures of INS at the onset of the nucleation phase caused the distinct fibrillation pathways of INS in H2O and D2O. A few different biophysical analysis, including solution-phase small-angle X-ray scattering combined with molecular dynamics simulations and other spectroscopic techniques, support our 2D-IR investigation results, providing insight into mechanistic details of distinct structural transition dynamics of INS in water. We found the delayed structural transition in D2O is due to the kinetic isotope effect at an early stage of fibrillation of INS in D2O, i.e., enhanced dimer formation of INS in D2O. Our 2D-IR and biophysical analysis provide insight into mechanistic details of structural transition dynamics of INS in water. This study demonstrates an innovative 2D-IR approach for studying protein dynamics in H2O, which will open the way for observing protein dynamics under biological conditions without IR spectroscopic interference by water vibrations. This study aims to understand the structural transition dynamics of INS during amyloid aggregation in H2O using 2D-IR spectroscopy. The results show that distinct fibrillations in D2O and H2O originated from different quaternary structures of INS.![]()
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Affiliation(s)
- So Yeon Chun
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS) Seoul 02841 Republic of Korea
- Department of Chemistry, Korea University Seoul 02841 Republic of Korea
| | - Myung Kook Son
- Department of Chemistry, Korea University Seoul 02841 Republic of Korea
- Center for Proteogenome Research, Korea University Seoul 02841 Republic of Korea
- Single Cell Analysis Laboratory, Korea University Seoul 02841 Republic of Korea
| | - Chae Ri Park
- Department of Chemistry, Korea University Seoul 02841 Republic of Korea
- Center for Proteogenome Research, Korea University Seoul 02841 Republic of Korea
- Single Cell Analysis Laboratory, Korea University Seoul 02841 Republic of Korea
| | - Chaiho Lim
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS) Seoul 02841 Republic of Korea
- Department of Chemistry, Korea University Seoul 02841 Republic of Korea
| | - Hugh I Kim
- Department of Chemistry, Korea University Seoul 02841 Republic of Korea
- Center for Proteogenome Research, Korea University Seoul 02841 Republic of Korea
- Single Cell Analysis Laboratory, Korea University Seoul 02841 Republic of Korea
| | - Kyungwon Kwak
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS) Seoul 02841 Republic of Korea
- Department of Chemistry, Korea University Seoul 02841 Republic of Korea
| | - Minhaeng Cho
- Center for Molecular Spectroscopy and Dynamics, Institute for Basic Science (IBS) Seoul 02841 Republic of Korea
- Department of Chemistry, Korea University Seoul 02841 Republic of Korea
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29
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Design of Asymmetric Nanofibers-Membranes Based on Polyvinyl Alcohol and Wool-Keratin for Wound Healing Applications. J Funct Biomater 2021; 12:jfb12040076. [PMID: 34940555 PMCID: PMC8706361 DOI: 10.3390/jfb12040076] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Revised: 12/13/2021] [Accepted: 12/14/2021] [Indexed: 02/07/2023] Open
Abstract
The development of asymmetric membranes—i.e., matching two fibrous layers with selected composition and morphological properties to mimic both the epidermis and dermis—currently represents one of the most promising strategies to support skin regeneration during the wound healing process. Herein, a new asymmetric platform fabricated by a sequential electrospinning process was investigated. The top layer comprises cross-linked polyvinylalcohol (PVA) nanofibers (NFs)—from water solution—to replicate the epidermis’s chemical stability and wettability features. Otherwise, the bottom layer is fabricated by integrating PVA with wool-keratin extracted via sulfitolysis. This protein is a biocompatibility polymer with excellent properties for dermis-like structures. Morphological characterization via SEM supported by image analysis showed that the asymmetric membrane exhibited average fiber size—max frequency diameter 450 nm, range 1.40 μm—and porosity suitable for the healing process. FTIR-spectrums confirmed the presence of keratin in the bottom layer and variations of keratin-secondary structures. Compared with pure PVA-NFs, keratin/PVA-NFs showed a significant improvement in cell adhesion in in vitro tests. In perspective, these asymmetric membranes could be promisingly used to confine active species (i.e., antioxidants, antimicrobials) to the bottom layer to support specific cell activities (i.e., proliferation, differentiation) in wound healing applications.
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30
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Sanchez Ramirez DO, Cruz-Maya I, Vineis C, Guarino V, Tonetti C, Varesano A. Wool Keratin-Based Nanofibres-In Vitro Validation. Bioengineering (Basel) 2021; 8:224. [PMID: 34940377 PMCID: PMC8698655 DOI: 10.3390/bioengineering8120224] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 12/13/2021] [Accepted: 12/14/2021] [Indexed: 11/17/2022] Open
Abstract
Protein-based nanofibres are commonly used in the biomedical field to support cell growth. For this study, the cell viability of wool keratin-based nanofibres was tested. Membranes were obtained by electrospinning using formic acid, hexafluoroisopropanol, and water as solvents. For aqueous solutions, polyethylene oxide blended with keratin was employed, and their use to support in vitro cell interactions was also validated. Morphological characterization and secondary structure quantification were carried out by SEM and FTIR analyses. Although formic acid produced the best nanofibres from a morphological point of view, the results showed a better response to cell proliferation after 14 days in the case of fibres from hexafluoroisopropanol solution. Polyethylene oxide in keratin nanofibres was demonstrated, over time, to influence in vitro cell interactions, modifying membranes-wettability and reducing the contact between keratin chains and water molecules, respectively.
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Affiliation(s)
- Diego Omar Sanchez Ramirez
- National Research Council-Institute of Intelligent Industrial Technologies and Systems for Advanced Manufacturing (CNR-STIIMA), Corso Giuseppe Pella 16, 13900 Biella, Italy; (C.V.); (C.T.); (A.V.)
| | - Iriczalli Cruz-Maya
- National Research Council-Institute for Polymers, Composites and Biomaterials (CNR-IPCB), Mostra d’Oltremare, Pad. 20, V.le J.F. Kennedy 54, 80125 Napoli, Italy;
| | - Claudia Vineis
- National Research Council-Institute of Intelligent Industrial Technologies and Systems for Advanced Manufacturing (CNR-STIIMA), Corso Giuseppe Pella 16, 13900 Biella, Italy; (C.V.); (C.T.); (A.V.)
| | - Vincenzo Guarino
- National Research Council-Institute for Polymers, Composites and Biomaterials (CNR-IPCB), Mostra d’Oltremare, Pad. 20, V.le J.F. Kennedy 54, 80125 Napoli, Italy;
| | - Cinzia Tonetti
- National Research Council-Institute of Intelligent Industrial Technologies and Systems for Advanced Manufacturing (CNR-STIIMA), Corso Giuseppe Pella 16, 13900 Biella, Italy; (C.V.); (C.T.); (A.V.)
| | - Alessio Varesano
- National Research Council-Institute of Intelligent Industrial Technologies and Systems for Advanced Manufacturing (CNR-STIIMA), Corso Giuseppe Pella 16, 13900 Biella, Italy; (C.V.); (C.T.); (A.V.)
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31
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Maiti KS. Two-dimensional Infrared Spectroscopy Reveals Better Insights of Structure and Dynamics of Protein. Molecules 2021; 26:molecules26226893. [PMID: 34833985 PMCID: PMC8618531 DOI: 10.3390/molecules26226893] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 11/07/2021] [Accepted: 11/10/2021] [Indexed: 11/25/2022] Open
Abstract
Proteins play an important role in biological and biochemical processes taking place in the living system. To uncover these fundamental processes of the living system, it is an absolutely necessary task to understand the structure and dynamics of the protein. Vibrational spectroscopy is an established tool to explore protein structure and dynamics. In particular, two-dimensional infrared (2DIR) spectroscopy has already proven its versatility to explore the protein structure and its ultrafast dynamics, and it has essentially unprecedented time resolutions to observe the vibrational dynamics of the protein. Providing several examples from our theoretical and experimental efforts, it is established here that two-dimensional vibrational spectroscopy provides exceptionally more information than one-dimensional vibrational spectroscopy. The structural information of the protein is encoded in the position, shape, and strength of the peak in 2DIR spectra. The time evolution of the 2DIR spectra allows for the visualisation of molecular motions.
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Affiliation(s)
- Kiran Sankar Maiti
- Max-Planck-Institut für Quantenoptik, Hans-Kopfermann-Straße 1, 85748 Garching, Germany; ; Tel.: +49-89-289-54056
- Lehrstuhl für Experimental Physik, Ludwig-Maximilians-Universität München, Am Coulombwall 1, 85748 Garching, Germany
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32
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Tumbic GW, Hossan MY, Thielges MC. Protein Dynamics by Two-Dimensional Infrared Spectroscopy. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2021; 14:299-321. [PMID: 34314221 PMCID: PMC8713465 DOI: 10.1146/annurev-anchem-091520-091009] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Proteins function as ensembles of interconverting structures. The motions span from picosecond bond rotations to millisecond and longer subunit displacements. Characterization of functional dynamics on all spatial and temporal scales remains challenging experimentally. Two-dimensional infrared spectroscopy (2D IR) is maturing as a powerful approach for investigating proteins and their dynamics. We outline the advantages of IR spectroscopy, describe 2D IR and the information it provides, and introduce vibrational groups for protein analysis. We highlight example studies that illustrate the power and versatility of 2D IR for characterizing protein dynamics and conclude with a brief discussion of the outlook for biomolecular 2D IR.
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Affiliation(s)
- Goran W Tumbic
- Department of Chemistry, Indiana University, Bloomington, Indiana 47401, USA;
| | - Md Yeathad Hossan
- Department of Chemistry, Indiana University, Bloomington, Indiana 47401, USA;
| | - Megan C Thielges
- Department of Chemistry, Indiana University, Bloomington, Indiana 47401, USA;
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33
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Ripanti F, Luchetti N, Nucara A, Minicozzi V, Venere AD, Filabozzi A, Carbonaro M. Normal mode calculation and infrared spectroscopy of proteins in water solution: Relationship between amide I transition dipole strength and secondary structure. Int J Biol Macromol 2021; 185:369-376. [PMID: 34157332 DOI: 10.1016/j.ijbiomac.2021.06.092] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Revised: 06/11/2021] [Accepted: 06/13/2021] [Indexed: 11/28/2022]
Abstract
Dipole Strength (DS) of the amides has gained a renewed interest in chemical physics since it provides an important tool to disclose the on-site vibrational energy distributions. Apart from earlier experimental efforts on polypeptides, little is still known about DS in complex proteins. We accurately measured the Fourier Transform Infrared absorption spectra of nine proteins in water solution obtaining their Molar Extinction Coefficient in the amide I and II spectral region. Our results show that the amide I DS value depends on the protein secondary structure, being that of the α-rich and unstructured proteins lower by a factor of 2 than that of the β-rich proteins. The average DS for amino acids in α and β secondary structures confirms this finding. Normal Mode calculation and Molecular Dynamics were performed and used as tools for data analysis and interpretation. The present outcomes corroborate the hypothesis that antiparallel β-sheet environment is more prone to delocalize the on-site CO stretching vibration through coupling mechanisms between carbonyl groups, whereas α-helix structures are energetically less stable to permit vibrational mode delocalization.
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Affiliation(s)
- Francesca Ripanti
- Department of Physics, Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy
| | - Nicole Luchetti
- Department of Physics and INFN, Tor Vergata University of Rome, Via della Ricerca Scientifica 1, 00133 Rome, Italy
| | - Alessandro Nucara
- Department of Physics, Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy.
| | - Velia Minicozzi
- Department of Physics and INFN, Tor Vergata University of Rome, Via della Ricerca Scientifica 1, 00133 Rome, Italy
| | - Almerinda Di Venere
- Department of Experimental Medicine, Tor Vergata University of Rome, Via Montpellier 1, 00133 Rome, Italy
| | - Alessandra Filabozzi
- Department of Physics and INFN, Tor Vergata University of Rome, Via della Ricerca Scientifica 1, 00133 Rome, Italy
| | - Marina Carbonaro
- Council for Agricultural Research and Economics (CREA), Research Centre for Food and Nutrition, Via Ardeatina 546, 00178 Rome, Italy
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34
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Gaynor JD, Weakly RB, Khalil M. Multimode two-dimensional vibronic spectroscopy. I. Orientational response and polarization-selectivity. J Chem Phys 2021; 154:184201. [PMID: 34241026 DOI: 10.1063/5.0047724] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Two-dimensional Electronic-Vibrational (2D EV) spectroscopy and two-dimensional Vibrational-Electronic (2D VE) spectroscopy are among the newest additions to the coherent multidimensional spectroscopy toolbox, and they are directly sensitive to vibronic couplings. In this first of two papers, the complete orientational response functions are developed for a model system consisting of two coupled anharmonic oscillators and two electronic states in order to simulate polarization-selective 2D EV and 2D VE spectra with arbitrary combinations of linearly polarized electric fields. Here, we propose analytical methods to isolate desired signals within complicated spectra and to extract the relative orientation between vibrational and vibronic dipole moments of the model system using combinations of polarization-selective 2D EV and 2D VE spectral features. Time-dependent peak amplitudes of coherence peaks are also discussed as means for isolating desired signals within the time-domain. This paper serves as a field guide for using polarization-selective 2D EV and 2D VE spectroscopies to map coupled vibronic coordinates on the molecular frame.
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Affiliation(s)
- James D Gaynor
- Department of Chemistry, University of Washington, P.O. Box 351700, Seattle, Washington 98195, USA
| | - Robert B Weakly
- Department of Chemistry, University of Washington, P.O. Box 351700, Seattle, Washington 98195, USA
| | - Munira Khalil
- Department of Chemistry, University of Washington, P.O. Box 351700, Seattle, Washington 98195, USA
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35
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Sun Y, Giubertoni G, Bakker HJ, Liu J, Wagner M, Ng DYW, Devries AL, Meister K. Disaccharide Residues are Required for Native Antifreeze Glycoprotein Activity. Biomacromolecules 2021; 22:2595-2603. [PMID: 33957041 PMCID: PMC8207503 DOI: 10.1021/acs.biomac.1c00313] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Antifreeze glycoproteins
(AFGPs) are able to bind to ice, halt
its growth, and are the most potent inhibitors of ice recrystallization
known. The structural basis for AFGP’s unique properties remains
largely elusive. Here we determined the antifreeze activities of AFGP
variants that we constructed by chemically modifying the hydroxyl
groups of the disaccharide of natural AFGPs. Using nuclear magnetic
resonance, two-dimensional infrared spectroscopy, and circular dichroism,
the expected modifications were confirmed as well as their effect
on AFGPs solution structure. We find that the presence of all the
hydroxyls on the disaccharides is a requirement for the native AFGP
hysteresis as well as the maximal inhibition of ice recrystallization.
The saccharide hydroxyls are apparently as important as the acetyl
group on the galactosamine, the α-linkage between the disaccharide
and threonine, and the methyl groups on the threonine and alanine.
We conclude that the use of hydrogen-bonding through the hydroxyl
groups of the disaccharide and hydrophobic interactions through the
polypeptide backbone are equally important in promoting the antifreeze
activities observed in the native AFGPs. These important criteria
should be considered when designing synthetic mimics.
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Affiliation(s)
- Yuling Sun
- Max Planck Institute for Polymer Research, 55128 Mainz, Germany
| | - Giulia Giubertoni
- NWO Institute AMOLF, 1098 XG Amsterdam, The Netherlands.,University of Amsterdam, 1098 XH Amsterdam, The Netherlands
| | - Huib J Bakker
- NWO Institute AMOLF, 1098 XG Amsterdam, The Netherlands
| | - Jie Liu
- Max Planck Institute for Polymer Research, 55128 Mainz, Germany
| | - Manfred Wagner
- Max Planck Institute for Polymer Research, 55128 Mainz, Germany
| | - David Y W Ng
- Max Planck Institute for Polymer Research, 55128 Mainz, Germany
| | - Arthur L Devries
- University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Konrad Meister
- Max Planck Institute for Polymer Research, 55128 Mainz, Germany.,University of Alaska Southeast, Juneau, Alaska 99801, United States
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36
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El Khoury Y, Le Breton G, Cunha AV, Jansen TLC, van Wilderen LJGW, Bredenbeck J. Lessons from combined experimental and theoretical examination of the FTIR and 2D-IR spectroelectrochemistry of the amide I region of cytochrome c. J Chem Phys 2021; 154:124201. [PMID: 33810651 DOI: 10.1063/5.0039969] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Amide I difference spectroscopy is widely used to investigate protein function and structure changes. In this article, we show that the common approach of assigning features in amide I difference signals to distinct secondary structure elements in many cases may not be justified. Evidence comes from Fourier transform infrared (FTIR) and 2D-IR spectroelectrochemistry of the protein cytochrome c in the amide I range, in combination with computational spectroscopy based on molecular dynamics (MD) simulations. This combination reveals that each secondary structure unit, such as an alpha-helix or a beta-sheet, exhibits broad overlapping contributions, usually spanning a large part of the amide I region, which in the case of difference absorption experiments (such as in FTIR spectroelectrochemistry) may lead to intensity-compensating and even sign-changing contributions. We use cytochrome c as the test case, as this small electron-transferring redox-active protein contains different kinds of secondary structure units. Upon switching its redox-state, the protein exhibits a different charge distribution while largely retaining its structural scaffold. Our theoretical analysis suggests that the change in charge distribution contributes to the spectral changes and that structural changes are small. However, in order to confidently interpret FTIR amide I difference signals in cytochrome c and proteins in general, MD simulations in combination with additional experimental approaches such as isotope labeling, the insertion of infrared labels to selectively probe local structural elements will be required. In case these data are not available, a critical assessment of previous interpretations of protein amide I 1D- and 2D-IR difference spectroscopy data is warranted.
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Affiliation(s)
- Youssef El Khoury
- Institut für Biophysik, Johann-Wolfgang-Goethe-Universität, Max-von-Laue-Strasse. 1, 60438 Frankfurt am Main, Germany
| | - Guillaume Le Breton
- University of Groningen, Zernike Institute for Advanced Materials, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Ana V Cunha
- University of Groningen, Zernike Institute for Advanced Materials, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Thomas L C Jansen
- University of Groningen, Zernike Institute for Advanced Materials, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Luuk J G W van Wilderen
- Institut für Biophysik, Johann-Wolfgang-Goethe-Universität, Max-von-Laue-Strasse. 1, 60438 Frankfurt am Main, Germany
| | - Jens Bredenbeck
- Institut für Biophysik, Johann-Wolfgang-Goethe-Universität, Max-von-Laue-Strasse. 1, 60438 Frankfurt am Main, Germany
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37
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Paulus A, Engdahl A, Yang Y, Boza-Serrano A, Bachiller S, Torres-Garcia L, Svanbergsson A, Garcia MG, Gouras GK, Li JY, Deierborg T, Klementieva O. Amyloid Structural Changes Studied by Infrared Microspectroscopy in Bigenic Cellular Models of Alzheimer's Disease. Int J Mol Sci 2021; 22:3430. [PMID: 33810433 PMCID: PMC8037084 DOI: 10.3390/ijms22073430] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/19/2021] [Accepted: 03/22/2021] [Indexed: 12/27/2022] Open
Abstract
Alzheimer's disease affects millions of lives worldwide. This terminal disease is characterized by the formation of amyloid aggregates, so-called amyloid oligomers. These oligomers are composed of β-sheet structures, which are believed to be neurotoxic. However, the actual secondary structure that contributes most to neurotoxicity remains unknown. This lack of knowledge is due to the challenging nature of characterizing the secondary structure of amyloids in cells. To overcome this and investigate the molecular changes in proteins directly in cells, we used synchrotron-based infrared microspectroscopy, a label-free and non-destructive technique available for in situ molecular imaging, to detect structural changes in proteins and lipids. Specifically, we evaluated the formation of β-sheet structures in different monogenic and bigenic cellular models of Alzheimer's disease that we generated for this study. We report on the possibility to discern different amyloid signatures directly in cells using infrared microspectroscopy and demonstrate that bigenic (amyloid-β, α-synuclein) and (amyloid-β, Tau) neuron-like cells display changes in β-sheet load. Altogether, our findings support the notion that different molecular mechanisms of amyloid aggregation, as opposed to a common mechanism, are triggered by the specific cellular environment and, therefore, that various mechanisms lead to the development of Alzheimer's disease.
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Affiliation(s)
- Agnes Paulus
- Medical Microspectroscopy Laboratory, Department of Experimental Medical Science, Lund University, 22184 Lund, Sweden; (A.P.); (A.E.)
- Experimental Neuroinflammation Laboratory, Department of Experimental Medical Science, Lund University, 22184 Lund, Sweden; (Y.Y.); (A.B.-S.); (S.B.); (M.G.G.)
| | - Anders Engdahl
- Medical Microspectroscopy Laboratory, Department of Experimental Medical Science, Lund University, 22184 Lund, Sweden; (A.P.); (A.E.)
| | - Yiyi Yang
- Experimental Neuroinflammation Laboratory, Department of Experimental Medical Science, Lund University, 22184 Lund, Sweden; (Y.Y.); (A.B.-S.); (S.B.); (M.G.G.)
| | - Antonio Boza-Serrano
- Experimental Neuroinflammation Laboratory, Department of Experimental Medical Science, Lund University, 22184 Lund, Sweden; (Y.Y.); (A.B.-S.); (S.B.); (M.G.G.)
| | - Sara Bachiller
- Experimental Neuroinflammation Laboratory, Department of Experimental Medical Science, Lund University, 22184 Lund, Sweden; (Y.Y.); (A.B.-S.); (S.B.); (M.G.G.)
| | - Laura Torres-Garcia
- Experimental Dementia Research Unit, Department of Experimental Medical Science, Lund University, 22184 Lund, Sweden; (L.T.-G.); (G.K.G.)
- Neural Plasticity and Repair Unit, Department of Experimental Medical Science, Lund University, 22184 Lund, Sweden; (A.S.); (J.-Y.L.)
| | - Alexander Svanbergsson
- Neural Plasticity and Repair Unit, Department of Experimental Medical Science, Lund University, 22184 Lund, Sweden; (A.S.); (J.-Y.L.)
| | - Megg G. Garcia
- Experimental Neuroinflammation Laboratory, Department of Experimental Medical Science, Lund University, 22184 Lund, Sweden; (Y.Y.); (A.B.-S.); (S.B.); (M.G.G.)
- Experimental Dementia Research Unit, Department of Experimental Medical Science, Lund University, 22184 Lund, Sweden; (L.T.-G.); (G.K.G.)
| | - Gunnar K. Gouras
- Experimental Dementia Research Unit, Department of Experimental Medical Science, Lund University, 22184 Lund, Sweden; (L.T.-G.); (G.K.G.)
| | - Jia-Yi Li
- Neural Plasticity and Repair Unit, Department of Experimental Medical Science, Lund University, 22184 Lund, Sweden; (A.S.); (J.-Y.L.)
| | - Tomas Deierborg
- Experimental Neuroinflammation Laboratory, Department of Experimental Medical Science, Lund University, 22184 Lund, Sweden; (Y.Y.); (A.B.-S.); (S.B.); (M.G.G.)
| | - Oxana Klementieva
- Medical Microspectroscopy Laboratory, Department of Experimental Medical Science, Lund University, 22184 Lund, Sweden; (A.P.); (A.E.)
- Lund Institute for Advanced Neutron and X-ray Science (LINXS), 22370 Lund, Sweden
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38
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Procacci B, Rutherford SH, Greetham GM, Towrie M, Parker AW, Robinson CV, Howle CR, Hunt NT. Differentiation of bacterial spores via 2D-IR spectroscopy. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 249:119319. [PMID: 33360210 DOI: 10.1016/j.saa.2020.119319] [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] [Received: 10/29/2020] [Revised: 11/26/2020] [Accepted: 12/05/2020] [Indexed: 06/12/2023]
Abstract
Ultrafast 2D-IR spectroscopy is a powerful tool for understanding the spectroscopy and dynamics of biological molecules in the solution phase. A number of recent studies have begun to explore the utility of the information-rich 2D-IR spectra for analytical applications. Here, we report the application of ultrafast 2D-IR spectroscopy for the detection and classification of bacterial spores. 2D-IR spectra of Bacillus atrophaeus and Bacillus thuringiensis spores as dry films on CaF2 windows were obtained. The sporulated nature of the bacteria was confirmed using 2D-IR diagonal and off-diagonal peaks arising from the calcium dipicolinate CaDP·3H2O biomarker for sporulation. Distinctive peaks, in the protein amide I region of the spectrum were used to differentiate the two types of spore. The identified marker modes demonstrate the potential for the use of 2D-IR methods as a direct means of spore classification. We discuss these new results in perspective with the current state of analytical 2D-IR measurements, showing that the potential exists to apply 2D-IR spectroscopy to detect the spores on surfaces and in suspensions as well as in dry films. The results demonstrate how applying 2D-IR screening methodologies to spores would enable the creation of a library of spectra for classification purposes.
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Affiliation(s)
- Barbara Procacci
- Department of Chemistry and York Biomedical Research Institute, University of York, Heslington, York YO10 5DD, UK
| | - Samantha H Rutherford
- Department of Physics, University of Strathclyde, SUPA, 107 Rottenrow East, Glasgow G4 0NG, UK
| | - Gregory M Greetham
- STFC Central Laser Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Campus, Didcot OX11 0QX, UK
| | - Michael Towrie
- STFC Central Laser Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Campus, Didcot OX11 0QX, UK
| | - Anthony W Parker
- STFC Central Laser Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Campus, Didcot OX11 0QX, UK
| | - Camilla V Robinson
- Defence Science and Technology Laboratory, Porton Down, Salisbury SP4 0JQ, UK
| | - Christopher R Howle
- Defence Science and Technology Laboratory, Porton Down, Salisbury SP4 0JQ, UK
| | - Neil T Hunt
- Department of Chemistry and York Biomedical Research Institute, University of York, Heslington, York YO10 5DD, UK
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Rutherford SH, Greetham GM, Donaldson PM, Towrie M, Parker AW, Baker MJ, Hunt NT. Detection of Glycine as a Model Protein in Blood Serum Using 2D-IR Spectroscopy. Anal Chem 2021; 93:920-927. [PMID: 33295755 DOI: 10.1021/acs.analchem.0c03567] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Glycine (Gly) is used as a model system to evaluate the ability of ultrafast two-dimensional infrared (2D-IR) spectroscopy to detect and quantify the low-molecular-weight proteinaceous components of blood serum. Combining data acquisition schemes to suppress absorption bands of H2O that overlap with the protein amide I band with analysis of peak patterns appearing in the off-diagonal region of the 2D-IR spectrum allows separation of the Gly spectral signature from that of the dominant protein fraction of serum in a transmission-mode 2D-IR measurement without any sample manipulation, e.g., filtration or drying. 2D-IR spectra of blood serum samples supplemented with varying concentrations of Gly were obtained, and a range of data analysis methods compared, leading to a detection limit of ∼3 mg/mL for Gly. The reported methodology provides a platform for a critical assessment of the sensitivity of 2D-IR for measuring the concentrations of amino acids, peptides, and low-molecular-weight proteins present in serum samples. We conclude that, in the case of several clinically relevant diagnostic molecules and their combinations, the potential exists for 2D-IR to complement IR absorption methods as the benefits of the second frequency dimension offered by 2D-IR spectroscopy outweigh the added technical complexity of the measurement.
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Affiliation(s)
- Samantha H Rutherford
- Department of Physics, University of Strathclyde, SUPA, 107 Rottenrow East, Glasgow G4 0NG, U.K
| | - Gregory M Greetham
- STFC Central Laser Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Campus, Didcot OX11 0QX, U.K
| | - Paul M Donaldson
- STFC Central Laser Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Campus, Didcot OX11 0QX, U.K
| | - Michael Towrie
- STFC Central Laser Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Campus, Didcot OX11 0QX, U.K
| | - Anthony W Parker
- STFC Central Laser Facility, Research Complex at Harwell, Rutherford Appleton Laboratory, Harwell Campus, Didcot OX11 0QX, U.K
| | - Matthew J Baker
- WestCHEM, Department of Pure and Applied Chemistry, University of Strathclyde, Technology and Innovation Centre, 99 George Street, Glasgow G1 1RD, U.K
| | - Neil T Hunt
- Department of Chemistry and York Biomedical Research Institute, University of York, Heslington, York YO10 5DD, U.K
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40
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Zhao J, Wang J. Specific and non-specific interactions between metal cations and zwitterionic alanine tripeptide in saline solutions reported by the symmetric carboxylate stretching and amide-II vibrations. Phys Chem Chem Phys 2020; 22:25042-25053. [PMID: 33112337 DOI: 10.1039/d0cp04247a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The "specific" interaction between metal cations (Na+, Ca2+, Mg2+, and Zn2+) and the charged COO- group, and the "non-specific" interaction between these cations and the peptide backbone of a zwitterionic trialanine (Ala3) in aqueous solutions were examined in detail, using linear infrared (IR) absorptions of the COO- symmetric stretching and the amide-II (mainly the C-N stretching) modes as IR probes. Different IR spectral changes in peak positions and intensities of the two IR probes clearly demonstrate their sensitivities to nearby cation distributions in distance and population. Quantum chemistry calculations and molecular dynamics simulations were used to describe the cation-peptide interaction picture. These combined results suggest that Na+ and Ca2+ tend to bind to the COO- group in the bidentate form, while Mg2+ and Zn2+ tend to bind to the COO- group in the pseudo-bridging form. The results also show that while all three divalent cations indirectly interact with the peptide backbone with large population, Ca2+ and Mg2+ can be sometimes distributed very close to the backbone. Such a non-specific cation interaction can be moderately sensed by the C-N stretching of the amide-II mode when cations approach the polar amide C[double bond, length as m-dash]O group, and is also influenced by the NH3+ charge group located at the N-terminus. The results suggest that the experimentally observed complication of the Hofmeister cation series shall be understood as a combined specific and non-specific cation-peptide interactions.
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Affiliation(s)
- Juan Zhao
- Molecular Reaction Dynamics Laboratory, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing, 100190, P. R. China.
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41
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Ye S, Zhong K, Zhang J, Hu W, Hirst JD, Zhang G, Mukamel S, Jiang J. A Machine Learning Protocol for Predicting Protein Infrared Spectra. J Am Chem Soc 2020; 142:19071-19077. [PMID: 33126795 DOI: 10.1021/jacs.0c06530] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Infrared (IR) absorption provides important chemical fingerprints of biomolecules. Protein secondary structure determination from IR spectra is tedious since its theoretical interpretation requires repeated expensive quantum-mechanical calculations in a fluctuating environment. Herein we present a novel machine learning protocol that uses a few key structural descriptors to rapidly predict amide I IR spectra of various proteins and agrees well with experiment. Its transferability enabled us to distinguish protein secondary structures, probe atomic structure variations with temperature, and monitor protein folding. This approach offers a cost-effective tool to model the relationship between protein spectra and their biological/chemical properties.
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Affiliation(s)
- Sheng Ye
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Center for Excellence in Nanoscience, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
| | - Kai Zhong
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Center for Excellence in Nanoscience, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
| | - Jinxiao Zhang
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Center for Excellence in Nanoscience, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
| | - Wei Hu
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Center for Excellence in Nanoscience, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
| | - Jonathan D Hirst
- School of Chemistry, University of Nottingham, Nottingham, NG7 2RD, United Kingdom
| | - Guozhen Zhang
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Center for Excellence in Nanoscience, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
| | - Shaul Mukamel
- Departments of Chemistry, and Physics & Astronomy, University of California, Irvine, California 92697, United States
| | - Jun Jiang
- Hefei National Laboratory for Physical Sciences at the Microscale, CAS Center for Excellence in Nanoscience, School of Chemistry and Materials Science, University of Science and Technology of China, Hefei, Anhui 230026, People's Republic of China
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42
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Proietti N, Di Tullio V, Carsote C, Badea E. 13 C solid-state NMR complemented by ATR-FTIR and micro-DSC to study modern collagen-based material and historical leather. MAGNETIC RESONANCE IN CHEMISTRY : MRC 2020; 58:840-859. [PMID: 32250473 DOI: 10.1002/mrc.5024] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 03/11/2020] [Accepted: 03/25/2020] [Indexed: 06/11/2023]
Abstract
Ancient vegetable tanned leathers and parchments are very complex materials in which both different manufacturing and deterioration processes make their study and chemical characterisation difficult. In this research, solid-state nuclear magnetic resonance (NMR) spectroscopy was applied to identify different tannin families (condensed and hydrolysable) in historical leather objects such as bookbindings, wall upholsters, footwear and accessories, and military apparel. Furthermore, leather deterioration with special focus on collagen gelatinisation was investigated. A comparison with Fourier transform infrared (FTIR) spectroscopy and micro-differential scanning calorimetry (micro-DSC) was also performed to support the 13 C CP-MAS NMR findings and to point out the advantages and limitations of solid-state NMR in analysing historical and archaeological leathers. A wide database of NMR and FTIR spectra of commercial tannins compounds was also collected in order to characterise historical and archaeological leathers.
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Affiliation(s)
- Noemi Proietti
- "Segre-Capitani" NMR Laboratory, Institute for Biological Systems (ISB-CNR), National Research Council of Italy, Rome, Italy
| | - Valeria Di Tullio
- "Segre-Capitani" NMR Laboratory, Institute for Biological Systems (ISB-CNR), National Research Council of Italy, Rome, Italy
| | - Cristina Carsote
- Center for Research and Physical-Chemical and Biological Investigations, National Museum of Romanian History, Bucharest, Romania
| | - Elena Badea
- Advanced Research for Cultural Heritage Group (ARCH Lab), National Research and Development Institute for Textiles and Leather, ICPI Division, Bucharest, Romania
- Department of Chemistry, Faculty of Sciences, University of Craiova, Craiova, Romania
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43
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Modification of polystyrene maleic anhydride for efficient energy storage applications. J Solid State Electrochem 2020. [DOI: 10.1007/s10008-020-04797-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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44
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Simon R, Chakraborty S, Konikkara N, Mary NL. Functionalized polystyrene maleic anhydride copolymer/ZnO nanocomposites for enhanced electrochemical performance. J Appl Polym Sci 2020. [DOI: 10.1002/app.48945] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Remya Simon
- Department of Chemistry, Stella Maris College (Autonomous)University of Madras Chennai 600086 Tamil Nadu India
| | - Sohini Chakraborty
- Department of Chemistry, Stella Maris College (Autonomous)University of Madras Chennai 600086 Tamil Nadu India
| | - Niketha Konikkara
- Department of Physics, Stella Maris College (Autonomous)University of Madras Chennai 600086 Tamil Nadu India
| | - N. L. Mary
- Department of Chemistry, Stella Maris College (Autonomous)University of Madras Chennai 600086 Tamil Nadu India
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45
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Baiz CR, Błasiak B, Bredenbeck J, Cho M, Choi JH, Corcelli SA, Dijkstra AG, Feng CJ, Garrett-Roe S, Ge NH, Hanson-Heine MWD, Hirst JD, Jansen TLC, Kwac K, Kubarych KJ, Londergan CH, Maekawa H, Reppert M, Saito S, Roy S, Skinner JL, Stock G, Straub JE, Thielges MC, Tominaga K, Tokmakoff A, Torii H, Wang L, Webb LJ, Zanni MT. Vibrational Spectroscopic Map, Vibrational Spectroscopy, and Intermolecular Interaction. Chem Rev 2020; 120:7152-7218. [PMID: 32598850 PMCID: PMC7710120 DOI: 10.1021/acs.chemrev.9b00813] [Citation(s) in RCA: 173] [Impact Index Per Article: 43.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Vibrational spectroscopy is an essential tool in chemical analyses, biological assays, and studies of functional materials. Over the past decade, various coherent nonlinear vibrational spectroscopic techniques have been developed and enabled researchers to study time-correlations of the fluctuating frequencies that are directly related to solute-solvent dynamics, dynamical changes in molecular conformations and local electrostatic environments, chemical and biochemical reactions, protein structural dynamics and functions, characteristic processes of functional materials, and so on. In order to gain incisive and quantitative information on the local electrostatic environment, molecular conformation, protein structure and interprotein contacts, ligand binding kinetics, and electric and optical properties of functional materials, a variety of vibrational probes have been developed and site-specifically incorporated into molecular, biological, and material systems for time-resolved vibrational spectroscopic investigation. However, still, an all-encompassing theory that describes the vibrational solvatochromism, electrochromism, and dynamic fluctuation of vibrational frequencies has not been completely established mainly due to the intrinsic complexity of intermolecular interactions in condensed phases. In particular, the amount of data obtained from the linear and nonlinear vibrational spectroscopic experiments has been rapidly increasing, but the lack of a quantitative method to interpret these measurements has been one major obstacle in broadening the applications of these methods. Among various theoretical models, one of the most successful approaches is a semiempirical model generally referred to as the vibrational spectroscopic map that is based on a rigorous theory of intermolecular interactions. Recently, genetic algorithm, neural network, and machine learning approaches have been applied to the development of vibrational solvatochromism theory. In this review, we provide comprehensive descriptions of the theoretical foundation and various examples showing its extraordinary successes in the interpretations of experimental observations. In addition, a brief introduction to a newly created repository Web site (http://frequencymap.org) for vibrational spectroscopic maps is presented. We anticipate that a combination of the vibrational frequency map approach and state-of-the-art multidimensional vibrational spectroscopy will be one of the most fruitful ways to study the structure and dynamics of chemical, biological, and functional molecular systems in the future.
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Affiliation(s)
- Carlos R. Baiz
- Department of Chemistry, University of Texas at Austin, Austin, TX 78712, U.S.A
| | - Bartosz Błasiak
- Department of Physical and Quantum Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland
| | - Jens Bredenbeck
- Johann Wolfgang Goethe-University, Institute of Biophysics, Max-von-Laue-Str. 1, 60438, Frankfurt am Main, Germany
| | - Minhaeng Cho
- Center for Molecular Spectroscopy and Dynamics, Seoul 02841, Republic of Korea
- Department of Chemistry, Korea University, Seoul 02841, Republic of Korea
| | - Jun-Ho Choi
- Department of Chemistry, Gwangju Institute of Science and Technology, Gwangju 61005, Republic of Korea
| | - Steven A. Corcelli
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, U.S.A
| | - Arend G. Dijkstra
- School of Chemistry and School of Physics and Astronomy, University of Leeds, Leeds LS2 9JT, U.K
| | - Chi-Jui Feng
- Department of Chemistry, James Franck Institute and Institute for Biophysical Dynamics, University of Chicago, Chicago, IL 60637, U.S.A
| | - Sean Garrett-Roe
- Department of Chemistry, University of Pittsburgh, Pittsburgh, PA 15260, U.S.A
| | - Nien-Hui Ge
- Department of Chemistry, University of California at Irvine, Irvine, CA 92697-2025, U.S.A
| | - Magnus W. D. Hanson-Heine
- School of Chemistry, University of Nottingham, Nottingham, University Park, Nottingham, NG7 2RD, U.K
| | - Jonathan D. Hirst
- School of Chemistry, University of Nottingham, Nottingham, University Park, Nottingham, NG7 2RD, U.K
| | - Thomas L. C. Jansen
- University of Groningen, Zernike Institute for Advanced Materials, Nijenborgh 4, 9747 AG Groningen, The Netherlands
| | - Kijeong Kwac
- Center for Molecular Spectroscopy and Dynamics, Seoul 02841, Republic of Korea
| | - Kevin J. Kubarych
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, MI 48109, U.S.A
| | - Casey H. Londergan
- Department of Chemistry, Haverford College, Haverford, Pennsylvania 19041, U.S.A
| | - Hiroaki Maekawa
- Department of Chemistry, University of California at Irvine, Irvine, CA 92697-2025, U.S.A
| | - Mike Reppert
- Chemical Physics Theory Group, Department of Chemistry, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Shinji Saito
- Department of Theoretical and Computational Molecular Science, Institute for Molecular Science, Myodaiji, Okazaki, 444-8585, Japan
| | - Santanu Roy
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831-6110, U.S.A
| | - James L. Skinner
- Institute for Molecular Engineering, University of Chicago, Chicago, IL 60637, U.S.A
| | - Gerhard Stock
- Biomolecular Dynamics, Institute of Physics, Albert Ludwigs University, 79104 Freiburg, Germany
| | - John E. Straub
- Department of Chemistry, Boston University, Boston, MA 02215, U.S.A
| | - Megan C. Thielges
- Department of Chemistry, Indiana University, 800 East Kirkwood, Bloomington, Indiana 47405, U.S.A
| | - Keisuke Tominaga
- Molecular Photoscience Research Center, Kobe University, Nada, Kobe 657-0013, Japan
| | - Andrei Tokmakoff
- Department of Chemistry, James Franck Institute and Institute for Biophysical Dynamics, University of Chicago, Chicago, IL 60637, U.S.A
| | - Hajime Torii
- Department of Applied Chemistry and Biochemical Engineering, Faculty of Engineering, and Department of Optoelectronics and Nanostructure Science, Graduate School of Science and Technology, Shizuoka University, 3-5-1 Johoku, Naka-Ku, Hamamatsu 432-8561, Japan
| | - Lu Wang
- Department of Chemistry and Chemical Biology, Institute for Quantitative Biomedicine, Rutgers University, 174 Frelinghuysen Road, Piscataway, NJ 08854, U.S.A
| | - Lauren J. Webb
- Department of Chemistry, The University of Texas at Austin, 105 E. 24th Street, STOP A5300, Austin, Texas 78712, U.S.A
| | - Martin T. Zanni
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706-1396, U.S.A
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46
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Gautam RP, Pan H, Chalyavi F, Tucker MJ, Barile CJ. Nanostructured Ni-Cu Electrocatalysts for the Oxygen Evolution Reaction. Catal Sci Technol 2020; 10:4960-4967. [PMID: 33796262 PMCID: PMC8009306 DOI: 10.1039/d0cy00427h] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Ni-based materials are promising electrocatalysts for the oxygen evolution reaction (OER) for water splitting in alkaline media. We report the synthesis and OER electrocatalysis of both Ni-Cu nanoparticles (20-50 nm in diameter) and Ni-Cu nanoclusters (<20 metal atoms). Analysis of mass spectral data from matrix-assisted laser desorption/ionization and electrospray ionization techniques demonstrates that discrete heterobimetallic Ni-Cu nanoclusters capped with glutathione ligands were successfully synthesized. Ni-Cu nanoclusters with a 52:48 mol % Ni:Cu metal composition display an OER onset overpotential of 50 mV and an overpotential of 150 mV at 10 mA cm-2, which makes this catalyst one of the most efficient nonprecious metal OER catalysts. The durability of the nanocluster catalysts on carbon electrodes can be extended by appending them to electrodes modified with TiO2 nanoparticles. Infrared spectroscopy results indicate that the aggregation dynamics of the glutathione ligands change during catalysis. Taken together, these results help explain the reactivity of a novel class of nanostructured Ni-Cu OER catalysts, which are underexplored alternatives to more commonly studied Ni-Fe, Ni-Co, and Ni-Mn materials.
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Affiliation(s)
| | - Hanqing Pan
- Department of Chemistry, University of Nevada, Reno, Nevada 89557, USA
| | - Farzaneh Chalyavi
- Department of Chemistry, University of Nevada, Reno, Nevada 89557, USA
| | - Matthew J. Tucker
- Department of Chemistry, University of Nevada, Reno, Nevada 89557, USA
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47
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Ye M, Crozier KB. Metasurface with metallic nanoantennas and graphene nanoslits for sensing of protein monolayers and sub-monolayers. OPTICS EXPRESS 2020; 28:18479-18492. [PMID: 32680046 DOI: 10.1364/oe.394564] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 05/28/2020] [Indexed: 06/11/2023]
Abstract
Biomolecule sensing plays an important role in both fundamental biological studies and medical diagnostic applications. Infrared (IR) spectroscopy presents opportunities for sensing biomolecules as it allows their fingerprints to be determined by directly measuring their absorption spectra. However, the detection of biomolecules at low concentrations is difficult with conventional IR spectroscopy due to signal-to-noise considerations. This has led to recent interest on the use of nanostructured surfaces to boost the signals from biomolecules in a method termed surface enhanced infrared spectroscopy. So far, efforts have largely involved the use of metallic nanoantennas (which produce large field enhancement) or graphene nanostructures (which produce strong field confinement and provide electrical tunability). Here, we propose a nanostructured surface that combines the large field enhancement of metallic nanoantennas with the strong field confinement and electrical tunability of graphene plasmons. Our device consists of an array of plasmonic nanoantennas and graphene nanoslits on a resonant substrate. We perform systematic electromagnetic simulations to quantify the sensing performance of the proposed device and show that it outperforms designs in which only plasmons from metallic nanoantennas or plasmons from graphene are utilized. These investigations consider the model system of a representative protein-goat anti-mouse immunoglobulin G (IgG) - in monolayer or sub-monolayer form. Our findings provide guidance for future biosensors for the sensitive quantification and identification of biomolecules.
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48
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Roberson MG, Duncan JM, Flieth KJ, Geary LM, Tucker MJ. Photo-initiated rupture of azobenzene micelles to enable the spectroscopic analysis of antimicrobial peptide dynamics. RSC Adv 2020; 10:21464-21472. [PMID: 32879729 PMCID: PMC7449587 DOI: 10.1039/d0ra01920h] [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] [Received: 02/28/2020] [Accepted: 05/27/2020] [Indexed: 01/03/2023] Open
Abstract
Antimicrobial peptides (AMPs) show promise for the treatment of bacterial infections, but many have undesired hemolytic activities. The AMP MP1 not only has broad spectrum bactericidal activity, but has been shown to have antitumor activity. The interaction between AMPs and cellular membranes gives rise to a peptide's cell-specificity and activity. However, direct analysis of the biophysical interactions between peptides and membrane is complex, in part due to the nature of membrane environments as well as structural changes in the peptide that occurs upon binding to the membrane. In order to investigate the interplay between cell selectivity, activity, and secondary structural changes involved in antimicrobial peptide activity, we sought to implement photolizable membrane mimics to assess the types of information available from infrared spectroscopic measurements that follow from photoinitiated peptide dynamics. Azo-surfactants (APEG) form micelles containing a photolizable azobenzene core, which upon irradiation can induce membrane deformation resulting in breakdown of micelles. Spectroscopic analysis of membrane deformation may provide insights into the physical behavior associated with unfolding and dissociation of antimicrobial peptides within a membrane environment. Herein, we synthesized and characterized two new azo-surfactants, APEGTMG and APEGNEt2MeI. Furthermore, we demonstrate the viability of azosurfactants as membrane mimics by examining both the membrane binding and dissociation induced secondary structural changes of the antimicrobial peptide, MP1.
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Affiliation(s)
- Matthew G Roberson
- Department of Chemistry, University of Nevada, Reno, Reno, Nevada 89501, USA. ;
| | - Julia M Duncan
- Department of Chemistry, University of Nevada, Reno, Reno, Nevada 89501, USA. ;
| | - Keveen J Flieth
- Department of Chemistry, University of Nevada, Reno, Reno, Nevada 89501, USA. ;
| | - Laina M Geary
- Department of Chemistry, University of Nevada, Reno, Reno, Nevada 89501, USA. ;
| | - Matthew J Tucker
- Department of Chemistry, University of Nevada, Reno, Reno, Nevada 89501, USA. ;
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49
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Smith JW, Chen Q. Liquid-phase electron microscopy imaging of cellular and biomolecular systems. J Mater Chem B 2020; 8:8490-8506. [DOI: 10.1039/d0tb01300e] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Liquid-phase electron microscopy, a new method for real-time nanoscopic imaging in liquid, makes it possible to study cells or biomolecules with a singular combination of spatial and temporal resolution. We review the state of the art in biological research in this growing and promising field.
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Affiliation(s)
- John W. Smith
- Department of Materials Science and Engineering, University of Illinois at Urbana–Champaign
- Urbana
- USA
| | - Qian Chen
- Department of Materials Science and Engineering, University of Illinois at Urbana–Champaign
- Urbana
- USA
- Department of Chemistry
- University of Illinois at Urbana–Champaign
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Kaewpirom S, Boonsang S. Influence of alcohol treatments on properties of silk-fibroin-based films for highly optically transparent coating applications. RSC Adv 2020; 10:15913-15923. [PMID: 35493649 PMCID: PMC9052366 DOI: 10.1039/d0ra02634d] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Accepted: 04/15/2020] [Indexed: 01/01/2023] Open
Abstract
Thin films of silk fibroin were prepared by solvent evaporation from calcium chloride/ethanol aqueous solution. The influence of alcohol treatments on thermal, mechanical and optical properties of silk-fibroin-based film is presented. To understand the conformal structure of the alcohol-treated silk fibroin film, the IR spectral decomposition method is employed. The optical properties especially the optical transparency, haze and fluorescence emission of alcohol-treated silk fibroin film is systematically investigated together with the conformal structure to understand the effect of the fibril such as the beta-sheet influencing the optical properties. Monohydric alcohol treatment increased beta-turn content in the regenerated silk fibroin structure. These affected the amount of light diffusion and scattering within silk-fibroin films. With alcohol-treatment, all the silk-fibroin films exhibit exceptional optical transparency (>90%) with different levels of optical haze (2.56–14.17%). In particular, ethanol-treated silk-fibroin films contain the highest content of beta-turns (22.8%). The ethanol-treated silk-fibroin films displayed a distinct interference of oscillating crests and troughs in the UV-Vis transmittance spectra, thereby showing the lowest optical haze of 2.56%. In contrast, the silk-fibroin films treated with methanol and propanol exhibit the highest (14.17%) and second-highest (10.29%) optical transmittance haze, respectively. The beta-turn content of the silk-fibroin films treated with methanol is the lowest (20.5%). These results show the relationship between the beta-turn content and optical haze properties. The results manifestly provide a method to manufacture exceptional optically transparent silk-fibroin films with adjustable light diffusion and scattering which can be designed to meet specific applications with the potential to provide UV-shielding protection via monohydric alcohol treatment. This research presents a method to manufacture optically transparent silk-fibroin films with adjustable light diffusion and scattering via alcohol treatment.![]()
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Affiliation(s)
- Supranee Kaewpirom
- Department of Chemistry
- Faculty of Science
- Burapha University
- Chonburi 20131
- Thailand
| | - Siridech Boonsang
- Department of Electrical Engineering
- Faculty of Engineering
- King Mongkut's Institute of Technology Ladkrabang
- Bangkok 10520
- Thailand
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