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Kakkanattu A, Eerqing N, Ghamari S, Vollmer F. Review of optical sensing and manipulation of chiral molecules and nanostructures with the focus on plasmonic enhancements [Invited]. OPTICS EXPRESS 2021; 29:12543-12579. [PMID: 33985011 DOI: 10.1364/oe.421839] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 03/23/2021] [Indexed: 06/12/2023]
Abstract
Chiral molecules are ubiquitous in nature; many important synthetic chemicals and drugs are chiral. Detecting chiral molecules and separating the enantiomers is difficult because their physiochemical properties can be very similar. Here we review the optical approaches that are emerging for detecting and manipulating chiral molecules and chiral nanostructures. Our review focuses on the methods that have used plasmonics to enhance the chiroptical response. We also review the fabrication and assembly of (dynamic) chiral plasmonic nanosystems in this context.
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2
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Zheng RH, Wei WM, Liu YY. Theoretical study on spectral differences of polypeptides constituted by L- and D-amino acids. Mol Phys 2021. [DOI: 10.1080/00268976.2020.1812747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Ren-Hui Zheng
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, Beijing, People’s Republic of China
| | - Wen-Mei Wei
- School of Basic Medical Science, Anhui Medical University, Hefei, People’s Republic of China
| | - Yan-Ying Liu
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, Beijing, People’s Republic of China
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Keiderling TA. Structure of Condensed Phase Peptides: Insights from Vibrational Circular Dichroism and Raman Optical Activity Techniques. Chem Rev 2020; 120:3381-3419. [DOI: 10.1021/acs.chemrev.9b00636] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Timothy A. Keiderling
- Department of Chemistry, University of Illinois at Chicago 845 West Taylor Street m/c 111, Chicago, Illinois 60607-7061, United States
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Hope M, Šebestík J, Kapitán J, Bouř P. Understanding CH-Stretching Raman Optical Activity in Ala–Ala Dipeptides. J Phys Chem A 2020; 124:674-683. [DOI: 10.1021/acs.jpca.9b10557] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Marius Hope
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí 2, 16610 Prague, Czech Republic
- Norwegian University of Science and Technology NO-7491 Trondheim, Norway
| | - Jaroslav Šebestík
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí 2, 16610 Prague, Czech Republic
| | - Josef Kapitán
- Department of Optics, Palacký University, 17. listopadu 12, 77146 Olomouc, Czech Republic
| | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences, Flemingovo náměstí 2, 16610 Prague, Czech Republic
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Van de Vondel E, Herrebout W, Johannessen C. Tracking Conformational Changes in Phosvitin throughout a Crowding-Agent-Based Titration. Chembiochem 2019; 20:770-777. [PMID: 30451361 DOI: 10.1002/cbic.201800581] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Indexed: 11/11/2022]
Abstract
The sensitivity of Raman optical activity (ROA) towards small conformational changes is explored by tracking the structural changes in an intrinsically disordered protein-phosvitin-induced by different concentrations of crowding agent. It is shown that ROA is capable of tracking small conformational changes involving β-sheet and α-helical secondary structural properties of the protein. Furthermore, it is indicated that the influences of the crowding agents employed, Ficoll 70 and dextran 70, on the structural properties of phosvitin differ significantly, with the structural changes induced by the presence of Ficoll 70 being more pronounced and already being visible at a lower concentration. The data also suggest that some spectral changes do not arise from a change in the secondary structure of the protein, but are related to differences in interaction between the phosphorylated residues of the protein and the sugar-based crowding agent.
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Affiliation(s)
- Evelien Van de Vondel
- Molecular Spectroscopy Group, Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, 2020, Antwerp, Belgium
| | - Wouter Herrebout
- Molecular Spectroscopy Group, Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, 2020, Antwerp, Belgium
| | - Christian Johannessen
- Molecular Spectroscopy Group, Department of Chemistry, University of Antwerp, Groenenborgerlaan 171, 2020, Antwerp, Belgium
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Mensch C, Bultinck P, Johannessen C. Conformational Disorder and Dynamics of Proteins Sensed by Raman Optical Activity. ACS OMEGA 2018; 3:12944-12955. [PMID: 31458018 PMCID: PMC6644472 DOI: 10.1021/acsomega.8b01955] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 10/03/2018] [Indexed: 06/10/2023]
Abstract
Raman optical activity (ROA) spectra of proteins hold a lot of information about their structure in solution. To create a better understanding of the ROA spectra of, among others, the intrinsically disordered proteins (IDPs), involved in neurodegenerative diseases, the effect of conformational disorder and dynamics on the ROA spectra was studied. Density functional theory (DFT) calculations of small ensembles of model peptides with increasing disorder show that the ROA patterns of α-helical and polyproline II (PPII) structure reflect the average backbone angles in the ensemble. The amide III region in the ROA spectra of the α-helical peptides is shown to retain its typical -/+/+ pattern, while the amide III region of PPII secondary structure diminishes in intensity with increasing structural disorder. The results show that the ROA spectra of IDPs hence more likely stem from short stretches of well-defined PPII helices rather than a very flexible chain. Further DFT calculations support that mixing of PPII with helical secondary structure is consistent with experimental spectra of IDPs, while mixing with β-strand results in spectral patterns that are not observed experimentally. The detailed information obtained from these results contributes to a better understanding of the spectrum-structure relation.
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Affiliation(s)
- Carl Mensch
- Department
of Chemistry, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp, Belgium
- Department
of Chemistry, Ghent University, Krijgslaan 281 (S3), B-9000 Ghent, Belgium
| | - Patrick Bultinck
- Department
of Chemistry, Ghent University, Krijgslaan 281 (S3), B-9000 Ghent, Belgium
| | - Christian Johannessen
- Department
of Chemistry, University of Antwerp, Groenenborgerlaan 171, B-2020 Antwerp, Belgium
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SERS Investigation of Cancer Cells Treated with PDT: Quantification of Cell Survival and Follow-up. Sci Rep 2017; 7:7175. [PMID: 28775257 PMCID: PMC5543153 DOI: 10.1038/s41598-017-07469-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2017] [Accepted: 06/26/2017] [Indexed: 12/04/2022] Open
Abstract
In this study Surface Enhanced Raman Spectroscopy (SERS) data recorded from mouse mammary glands cancer cells (4T1 cell line) was used to assess information regarding differences between control, death and viable cells after Photodynamic Therapy (PDT) treatment. The treatment used nanoemulsions (NE/PS) loaded with different chloroaluminumphthalocyanine (ClAlP) photosensitizer (PS) contents (5 and 10 µmol × L−1) and illumination (660 nm wavelength) at 10 J × cm−2 (10 minutes). The SERS data revealed significant molecular alterations in proteins and lipids due to the PDT treatment. Principal Component Analysis (PCA) was applied to analyze the data recorded. Three-dimensional and well reproductive PCA scatter plots were obtained, revealing that two clusters of dead cells were well separated from one another and from control cluster. Overlap between two clusters of viable cells was observed, though well separated from control cluster. Moreover, the data analysis also pointed out necrosis as the main cell death mechanism induced by the PDT, in agreement with the literature. Finally, Raman modes peaking at 608 cm−1 (proteins) and 1231 cm−1 (lipids) can be selected for follow up of survival rate of neoplastic cells after PDT. We envisage that this finding is key to contribute to a quick development of quantitative infrared thermography imaging.
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Buckley K, Ryder AG. Applications of Raman Spectroscopy in Biopharmaceutical Manufacturing: A Short Review. APPLIED SPECTROSCOPY 2017; 71:1085-1116. [PMID: 28534676 DOI: 10.1177/0003702817703270] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The production of active pharmaceutical ingredients (APIs) is currently undergoing its biggest transformation in a century. The changes are based on the rapid and dramatic introduction of protein- and macromolecule-based drugs (collectively known as biopharmaceuticals) and can be traced back to the huge investment in biomedical science (in particular in genomics and proteomics) that has been ongoing since the 1970s. Biopharmaceuticals (or biologics) are manufactured using biological-expression systems (such as mammalian, bacterial, insect cells, etc.) and have spawned a large (>€35 billion sales annually in Europe) and growing biopharmaceutical industry (BioPharma). The structural and chemical complexity of biologics, combined with the intricacy of cell-based manufacturing, imposes a huge analytical burden to correctly characterize and quantify both processes (upstream) and products (downstream). In small molecule manufacturing, advances in analytical and computational methods have been extensively exploited to generate process analytical technologies (PAT) that are now used for routine process control, leading to more efficient processes and safer medicines. In the analytical domain, biologic manufacturing is considerably behind and there is both a huge scope and need to produce relevant PAT tools with which to better control processes, and better characterize product macromolecules. Raman spectroscopy, a vibrational spectroscopy with a number of useful properties (nondestructive, non-contact, robustness) has significant potential advantages in BioPharma. Key among them are intrinsically high molecular specificity, the ability to measure in water, the requirement for minimal (or no) sample pre-treatment, the flexibility of sampling configurations, and suitability for automation. Here, we review and discuss a representative selection of the more important Raman applications in BioPharma (with particular emphasis on mammalian cell culture). The review shows that the properties of Raman have been successfully exploited to deliver unique and useful analytical solutions, particularly for online process monitoring. However, it also shows that its inherent susceptibility to fluorescence interference and the weakness of the Raman effect mean that it can never be a panacea. In particular, Raman-based methods are intrinsically limited by the chemical complexity and wide analyte-concentration-profiles of cell culture media/bioprocessing broths which limit their use for quantitative analysis. Nevertheless, with appropriate foreknowledge of these limitations and good experimental design, robust analytical methods can be produced. In addition, new technological developments such as time-resolved detectors, advanced lasers, and plasmonics offer potential of new Raman-based methods to resolve existing limitations and/or provide new analytical insights.
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Affiliation(s)
- Kevin Buckley
- Nanoscale Biophotonics Laboratory, School of Chemistry, National University of Ireland - Galway, Galway, Ireland
| | - Alan G Ryder
- Nanoscale Biophotonics Laboratory, School of Chemistry, National University of Ireland - Galway, Galway, Ireland
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Balu R, Mata JP, Knott R, Elvin CM, Hill AJ, Choudhury NR, Dutta NK. Effects of Crowding and Environment on the Evolution of Conformational Ensembles of the Multi-Stimuli-Responsive Intrinsically Disordered Protein, Rec1-Resilin: A Small-Angle Scattering Investigation. J Phys Chem B 2016; 120:6490-503. [PMID: 27281267 DOI: 10.1021/acs.jpcb.6b02475] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
In this study, we explore the overall structural ensembles and transitions of a biomimetic, multi-stimuli-responsive, intrinsically disordered protein (IDP), Rec1-resilin. The structural transition of Rec1-resilin with change in molecular crowding and environment is evaluated using small-angle neutron scattering and small-angle X-ray scattering. The quantitative analyses of the experimental scattering data using a combination of computational models allowed comprehensive description of the structural evolution, organization, and conformational ensembles of Rec1-resilin in response to the changes in concentration, pH, and temperature. Rec1-resilin in uncrowded solutions demonstrates the equilibrium intrinsic structure quality of an IDP with radius of gyration Rg ∼ 5 nm, and a scattering function for the triaxial ellipsoidal model best fit the experimental dataset. On crowding (increase in concentration >10 wt %), Rec1-resilin molecules exert intermolecular repulsive force of interaction, the Rg value reduces with a progressive increase in concentration, and molecular chains transform from a Gaussian coil to a fully swollen coil. It is also revealed that the structural organization of Rec1-resilin dynamically transforms from a rod (pH 2) to coil (pH 4.8) and to globular (pH 12) as a function of pH. The findings further support the temperature-triggered dual-phase-transition behavior of Rec1-resilin, exhibiting rod-shaped structural organization below the upper critical solution temperature (∼4 °C) and a large but compact structure above the lower critical solution temperature (∼75 °C). This work attempted to correlate unusual responsiveness of Rec1-resilin to the evolution of conformational ensembles.
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Affiliation(s)
- Rajkamal Balu
- Future Industries Institute, University of South Australia , Mawson Lakes, SA 5095, Australia
| | - Jitendra P Mata
- Bragg Institute, ANSTO , Private Mail Bag, Kirrawee, NSW 2232, Australia
| | - Robert Knott
- Bragg Institute, ANSTO , Private Mail Bag, Kirrawee, NSW 2232, Australia
| | - Christopher M Elvin
- CSIRO Agriculture, Level 6, Queensland Bioscience Precinct , St Lucia, QLD 4067, Australia
| | - Anita J Hill
- CSIRO Manufacturing , Bayview Avenue, Clayton, VIC 3168, Australia
| | - Namita R Choudhury
- School of Chemical Engineering, The University of Adelaide , Adelaide, SA 5005, Australia.,Future Industries Institute, University of South Australia , Mawson Lakes, SA 5095, Australia
| | - Naba K Dutta
- School of Chemical Engineering, The University of Adelaide , Adelaide, SA 5005, Australia.,Future Industries Institute, University of South Australia , Mawson Lakes, SA 5095, Australia
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