1
|
Ramos S, Lee JC. Raman spectroscopy in the study of amyloid formation and phase separation. Biochem Soc Trans 2024; 52:1121-1130. [PMID: 38666616 PMCID: PMC11346453 DOI: 10.1042/bst20230599] [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: 02/14/2024] [Revised: 04/11/2024] [Accepted: 04/15/2024] [Indexed: 06/27/2024]
Abstract
Neurodegenerative diseases, such as Alzheimer's and Parkinson's, share a common pathological feature of amyloid structure accumulation. However, the structure-function relationship between these well-ordered, β-sheet-rich, filamentous protein deposits and disease etiology remains to be defined. Recently, an emerging hypothesis has linked phase separation, a process involved in the formation of protein condensates, to amyloid formation, suggesting that liquid protein droplets serve as loci for amyloid initiation. To elucidate how these processes contribute to disease progression, tools that can directly report on protein secondary structural changes are needed. Here, we review recent studies that have demonstrated Raman spectroscopy as a powerful vibrational technique for interrogating amyloid structures; one that offers sensitivity from the global secondary structural level to specific residues. This probe-free technique is further enhanced via coupling to a microscope, which affords structural data with spatial resolution, known as Raman spectral imaging (RSI). In vitro and in cellulo applications of RSI are discussed, highlighting studies of protein droplet aging, cellular internalization of fibrils, and Raman imaging of intracellular water. Collectively, utilization of the myriad Raman spectroscopic methods will contribute to a deeper understanding of protein conformational dynamics in the complex cellular milieu and offer potential clinical diagnostic capabilities for protein misfolding and aggregation processes in disease states.
Collapse
Affiliation(s)
- Sashary Ramos
- Laboratory of Protein Conformation and Dynamics, Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, U.S.A
| | - Jennifer C. Lee
- Laboratory of Protein Conformation and Dynamics, Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD, U.S.A
| |
Collapse
|
2
|
Crago M, Lee A, Hoang TP, Talebian S, Naficy S. Protein adsorption on blood-contacting surfaces: A thermodynamic perspective to guide the design of antithrombogenic polymer coatings. Acta Biomater 2024; 180:46-60. [PMID: 38615811 DOI: 10.1016/j.actbio.2024.04.018] [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: 02/04/2024] [Revised: 04/08/2024] [Accepted: 04/09/2024] [Indexed: 04/16/2024]
Abstract
Blood-contacting medical devices often succumb to thrombosis, limiting their durability and safety in clinical applications. Thrombosis is fundamentally initiated by the nonspecific adsorption of proteins to the material surface, which is strongly governed by thermodynamic factors established by the nature of the interaction between the material surface, surrounding water molecules, and the protein itself. Along these lines, different surface materials (such as polymeric, metallic, ceramic, or composite) induce different entropic and enthalpic changes at the surface-protein interface, with material wettability significantly impacting this behavior. Consequently, protein adsorption on medical devices can be modulated by altering their wettability and surface energy. A plethora of polymeric coating modifications have been utilized for this purpose; hydrophobic modifications may promote or inhibit protein adsorption determined by van der Waals forces, while hydrophilic materials achieve this by mainly relying on hydrogen bonding, or unbalanced/balanced electrostatic interactions. This review offers a cohesive understanding of the thermodynamics governing these phenomena, to specifically aid in the design and selection of hemocompatible polymeric coatings for biomedical applications. STATEMENT OF SIGNIFICANCE: Blood-contacting medical devices often succumb to thrombosis, limiting their durability and safety in clinical applications. A plethora of polymeric coating modifications have been utilized for addressing this issue. This review offers a cohesive understanding of the thermodynamics governing these phenomena, to specifically aid in the design and selection of hemocompatible polymeric coatings for biomedical applications.
Collapse
Affiliation(s)
- Matthew Crago
- School of Chemical and Biomolecular Engineering, The University of Sydney, Darlington, NSW 2008, Australia
| | - Aeryne Lee
- School of Chemical and Biomolecular Engineering, The University of Sydney, Darlington, NSW 2008, Australia
| | - Thanh Phuong Hoang
- School of Chemical and Biomolecular Engineering, The University of Sydney, Darlington, NSW 2008, Australia
| | - Sepehr Talebian
- School of Chemical and Biomolecular Engineering, The University of Sydney, Darlington, NSW 2008, Australia.
| | - Sina Naficy
- School of Chemical and Biomolecular Engineering, The University of Sydney, Darlington, NSW 2008, Australia.
| |
Collapse
|
3
|
Ramos S, Lee JC. Water bend-libration as a cellular Raman imaging probe of hydration. Proc Natl Acad Sci U S A 2023; 120:e2313133120. [PMID: 37812697 PMCID: PMC10589711 DOI: 10.1073/pnas.2313133120] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Accepted: 09/06/2023] [Indexed: 10/11/2023] Open
Abstract
Water is a ubiquitous and vital component of living systems. Hydration, which is the interaction between water and intracellular biomolecules, plays an important role in cellular processes. However, it is technically challenging to study water structure within cells directly. Here, we demonstrate the utility and power of the water bend-libration combination band as a unique Raman spectral imaging probe of cellular hydration. Hydration maps reveal distinct water environments within subcellular compartments (e.g., nucleolus and lipid droplet) due to the spectral sensitivity of this coupled vibrational band. Spectroscopic studies using the water bend-libration are broadly applicable, offering the potential to capture the chemical complexity of hydration in numerous systems.
Collapse
Affiliation(s)
- Sashary Ramos
- Laboratory of Protein Conformation and Dynamics, Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD20892
| | - Jennifer C. Lee
- Laboratory of Protein Conformation and Dynamics, Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, NIH, Bethesda, MD20892
| |
Collapse
|
4
|
Ando M, Sugiyama K, Kubo K, Horii S, Hano T, Tomaru Y, Takeyama H. Single-Cell Level Raman Molecular Profiling Reveals the Classification of Growth Phases of Chaetoceros tenuissimus. J Phys Chem B 2023. [PMID: 37243612 DOI: 10.1021/acs.jpcb.3c02152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Harmful algal blooms (HABs) are a natural phenomenon caused by outbreaks of algae, resulting in serious problems for aquatic ecosystems and the coastal environment. Chaetoceros tenuissimus (C. tenuissimus) is one of the diatoms responsible for HABs. The growth curve of C. tenuissimus can be observed from beginning to end of HABs: therefore, detailed analysis is necessary to characterize each growth phase of C. tenuissimus. It is important to examine the phenotype of each diatom cell individually, as they display heterogeneity even in the same growth phase. Raman spectroscopy is a label-free technique to elucidate biomolecular profiles and spatial information at the cellular level. Multivariate data analysis (MVA) is an efficient method for the analysis of complicated Raman spectra, to identify molecular features. Here, we utilized Raman microspectroscopy to identify the molecular information of each diatom cell, at the single-cell level. The MVA, together with a support vector machine, which is a machine learning technique, allowed the classification of proliferating and nonproliferating cells. The classification includes polyunsaturated fatty acids such as linoleic acid, eicosapentaenoic acid, and docosahexaenoic acid. This study indicated that Raman spectroscopy is an appropriate technique to examine C. tenuissimus at the single-cell level, providing relevant data to assess the correlation between the molecular details obtained from the Raman analysis, at each growth phase.
Collapse
Affiliation(s)
- Masahiro Ando
- Research Organization for Nano and Life Innovation, Waseda University, 513 Wasedatsurumaki-Cho, Shinjuku-Ku,Tokyo 169-0041, Japan
| | - Kaori Sugiyama
- Institute for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-Ku, Tokyo 169-8555, Japan
| | - Koya Kubo
- Department of Advanced Science Engineering, Graduate School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-Ku, Tokyo 169-8555, Japan
- Computational Bio Big-Data Open Innovation Laboratory, AIST-Waseda University, 3-4-1 Okubo, Shinjuku-Ku, Tokyo 169-8555, Japan
| | - Shumpei Horii
- Department of Advanced Science Engineering, Graduate School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-Ku, Tokyo 169-8555, Japan
- Computational Bio Big-Data Open Innovation Laboratory, AIST-Waseda University, 3-4-1 Okubo, Shinjuku-Ku, Tokyo 169-8555, Japan
| | - Takeshi Hano
- Environment Conservation Division, National Research and Development Agency, Fisheries Technology Institute, Japan Fisheries Research and Education Agency, 2-17-5 Maruishi, Hatsukaichi, Hiroshima 739-0452, Japan
| | - Yuji Tomaru
- Environment Conservation Division, National Research and Development Agency, Fisheries Technology Institute, Japan Fisheries Research and Education Agency, 2-17-5 Maruishi, Hatsukaichi, Hiroshima 739-0452, Japan
| | - Haruko Takeyama
- Research Organization for Nano and Life Innovation, Waseda University, 513 Wasedatsurumaki-Cho, Shinjuku-Ku,Tokyo 169-0041, Japan
- Institute for Advanced Research of Biosystem Dynamics, Waseda Research Institute for Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-Ku, Tokyo 169-8555, Japan
- Department of Advanced Science Engineering, Graduate School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-Ku, Tokyo 169-8555, Japan
- Computational Bio Big-Data Open Innovation Laboratory, AIST-Waseda University, 3-4-1 Okubo, Shinjuku-Ku, Tokyo 169-8555, Japan
- Department of Life Science and Medical Bioscience, Waseda University, 2-2 Wakamatsu-cho, Shinjuku-ku, Tokyo 162-8480, Japan
| |
Collapse
|
5
|
Sardaru MC, Marangoci NL, Palumbo R, Roviello GN, Rotaru A. Nucleic Acid Probes in Bio-Imaging and Diagnostics: Recent Advances in ODN-Based Fluorescent and Surface-Enhanced Raman Scattering Nanoparticle and Nanostructured Systems. Molecules 2023; 28:molecules28083561. [PMID: 37110795 PMCID: PMC10141977 DOI: 10.3390/molecules28083561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 04/12/2023] [Accepted: 04/13/2023] [Indexed: 04/29/2023] Open
Abstract
Raman nanoparticle probes are a potent class of optical labels for the interrogation of pathological and physiological processes in cells, bioassays, and tissues. Herein, we review the recent advancements in fluorescent and Raman imaging using oligodeoxyribonucleotide (ODN)-based nanoparticles and nanostructures, which show promise as effective tools for live-cell analysis. These nanodevices can be used to investigate a vast number of biological processes occurring at various levels, starting from those involving organelles, cells, tissues, and whole living organisms. ODN-based fluorescent and Raman probes have contributed to the achievement of significant advancements in the comprehension of the role played by specific analytes in pathological processes and have inaugurated new possibilities for diagnosing health conditions. The technological implications that have emerged from the studies herein described could open new avenues for innovative diagnostics aimed at identifying socially relevant diseases like cancer through the utilization of intracellular markers and/or guide surgical procedures based on fluorescent or Raman imaging. Particularly complex probe structures have been developed within the past five years, creating a versatile toolbox for live-cell analysis, with each tool possessing its own strengths and limitations for specific studies. Analyzing the literature reports in the field, we predict that the development of ODN-based fluorescent and Raman probes will continue in the near future, disclosing novel ideas on their application in therapeutic and diagnostic strategies.
Collapse
Affiliation(s)
- Monica-Cornelia Sardaru
- "Petru Poni" Institute of Macromolecular Chemistry, Romanian Academy, Centre of Advanced Research in Bionanoconjugates and Biopolymers, Grigore Ghica Voda Alley 41 A, 700487 Iasi, Romania
- The Research Institute of the University of Bucharest (ICUB), 90 Sos. Panduri, 050663 Bucharest, Romania
| | - Narcisa-Laura Marangoci
- "Petru Poni" Institute of Macromolecular Chemistry, Romanian Academy, Centre of Advanced Research in Bionanoconjugates and Biopolymers, Grigore Ghica Voda Alley 41 A, 700487 Iasi, Romania
| | - Rosanna Palumbo
- Institute of Biostructures and Bioimaging, Italian National Council for Research (IBB-CNR), Area di Ricerca Site and Headquarters, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Giovanni N Roviello
- Institute of Biostructures and Bioimaging, Italian National Council for Research (IBB-CNR), Area di Ricerca Site and Headquarters, Via Pietro Castellino 111, 80131 Naples, Italy
| | - Alexandru Rotaru
- "Petru Poni" Institute of Macromolecular Chemistry, Romanian Academy, Centre of Advanced Research in Bionanoconjugates and Biopolymers, Grigore Ghica Voda Alley 41 A, 700487 Iasi, Romania
- Institute for Research, Innovation and Technology Transfer, UPS "Ion Creanga", Ion Creanga Str. 1, MD2069 Chisinau, Moldova
| |
Collapse
|