Vibrational Spectroscopy in Protein Research: From Purified Proteins to Aggregates and Assemblies

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Vibrational Spectroscopy in Protein Research: From Purified Proteins to Aggregates
and Assemblies
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Contents
List of contributors
Preface
1 ATR-FTIR spectroscopy and spectroscopic imaging of proteins
	1.1 Introduction
		1.1.1 Study of protein behavior—protein in solution, film, and tissue
		1.1.2 Interaction of proteins with infrared—understanding amide bands
			1.1.2.1 Interpreting secondary structures from amide bands
			1.1.2.2 Qualitative and quantitative analysis
			1.1.2.3 Challenges—interference of water spectral bands
			1.1.2.4 Comparison between transmission and ATR spectroscopic analysis of proteins
		1.1.3 The significance of study of protein crystallization and aggregation with new vibrational spectroscopic methods
	1.2 ATR-FTIR spectroscopic imaging of proteins
		1.2.1 Macro-ATR spectroscopic imaging
			1.2.1.1 High-throughput measurements: protein crystallization growth, aggregation, study of protein adsorption by functiona...
			1.2.1.2 Eliminating anomalous dispersion with varying angle-macro-ATR
			1.2.1.3 High-throughput analysis of aggregation of a monoclonal antibody by macro-ATR-FTIR spectroscopic imaging
			1.2.1.4 Protein purification: cleaning-in-place for immunoaffinity resin and in-column ATR-FTIR spectroscopy
		1.2.2 Micro-FTIR spectroscopic imaging
			1.2.2.1 Association with disease: time-resolved imaging of protein aggregation in living cells
	1.3 Further applications
		1.3.1 Monitoring low-concentration protein conformational change with QCL spectroscopy; potential of micro-ATR-FTIR imaging...
	1.4 Conclusions
	Acknowledgments
	References
2 Light-induced difference Fourier-transform infrared spectroscopy of photoreceptive proteins
	2.1 Introduction
	2.2 Methods: light-induced difference Fourier-transform infrared spectroscopy
		2.2.1 Sample preparation
		2.2.2 Experimental measurements
	2.3 Microbial rhodopsins
		2.3.1 Bacteriorhodopsin
		2.3.2 Other microbial rhodopsins
	2.4 Animal rhodopsins
		2.4.1 Bovine rhodopsin
		2.4.2 Primate color visual pigments
	2.5 Flavoproteins
		2.5.1 LOV domain
		2.5.2 BLUF domain
		2.5.3 Photolyase/cryptochrome
	2.6 Concluding remarks
	Acknowledgment
	References
3 Quantum cascade laser-based infrared transmission spectroscopy of proteins in solution
	3.1 Quantum cascade lasers and their advantages for mid-infrared transmission measurements
	3.2 Steady-state broadband infrared transmission spectroscopy of the protein amide bands
		3.2.1 External cavity-quantum cascade laser-based infrared transmission spectroscopy of proteins recorded in sweep mode
		3.2.2 QCL-based infrared transmission spectroscopy of proteins recorded in step-and-measure mode with microfluidic modulation
	3.3 Time-resolved laser-based infrared spectroscopy to monitor protein dynamics
	3.4 Time-resolved infrared spectroscopy of protein dynamics by dual-comb spectroscopy
	3.5 Conclusions and future developments
	References
4 Theoretical simulation of protein two-dimensional infrared spectroscopy
	4.1 Introduction
	4.2 Theoretical simulation
		4.2.1 Hamiltonian construction
			4.2.1.1 Vibrational frequency εm
			4.2.1.2 Couplings between the local vibrational transitions Jmn
		4.2.2 Calculation of third-order optical response functions
		4.2.3 Cumulant expansion of Gaussian fluctuation of third-order response functions
		4.2.4 The numerical integration of the Schrödinger equation
		4.2.5 The stochastic Liouville equations
		4.2.6 Applications of the statistical mechanic methods for longer dynamics or more comprehensive configuration ensembles
			4.2.6.1 Simulating the peptide thermal unfolding 2DIR spectra using the integrated tempering sampling technique
			4.2.6.2 Simulating the temperature jump peptide two-dimensional infrared using the Markov state models
	4.3 Future perspective
	Acknowledgments
	References
5 Infrared spectroscopy and imaging for understanding neurodegenerative protein-misfolding diseases
	5.1 Introduction to Fourier transform infrared spectroscopy and protein misfolding
		5.1.1 In vitro studies
		5.1.2 Isotopic labeling
		5.1.3 Infrared microspectroscopy
		5.1.4 Infrared nanospectroscopy
	5.2 Applications of Fourier transform infrared spectroscopy to neurodegenerative diseases
		5.2.1 Alzheimer’s disease
			5.2.1.1 Amyloid precursor protein
			5.2.1.2 Tau and neurofibrillary tangles
		5.2.2 Cerebral amyloid angiopathy
		5.2.3 Parkinson’s disease
		5.2.4 Amyotrophic lateral sclerosis
		5.2.5 Prion diseases
	5.3 Clinical imaging and diagnosis
	References
6 Near-infrared spectroscopy and imaging in protein research
	6.1 Introduction
	6.2 Applications of near-infrared spectroscopy to protein science
		6.2.1 How to apply near-infrared spectroscopy to protein science
		6.2.2 Near-infrared spectral analysis
		6.2.3 Near-infrared bands due to amide groups
		6.2.4 Thermal denaturation
		6.2.5 Protein hydration study of human serum albumin by near-infrared spectroscopy
		6.2.6 Near-infrared studies of protein secondary structure
	6.3 Near-infrared imaging
		6.3.1 Advantages of near-infrared imaging
		6.3.2 Instruments for near-infrared imaging
	6.4 Application of near-infrared imaging to embryogenesis of fish eggs
		6.4.1 Nonstaining visualization of embryogenesis in Japanese medaka (Oryzias latipes) fish egg by near-infrared imaging
		6.4.2 Near-infrared images of the influence of bioactivity on water molecular structure
		6.4.3 High-speed near-infrared imaging of the embryonic development in fertilized fish eggs
		6.4.4 Near-infrared in vivo imaging of blood flow and molecular distribution in a developing fish egg using an imaging-type...
	6.5 Future prospects
	References
7 Vibrational imaging of proteins: changes in the tissues and cells in the lifestyle disease studies
	7.1 Introduction
	7.2 Raman in vitro studies of the cell apoptosis
	7.3 An effect of fixation on endothelial cells
	7.4 Blood plasma proteins and their diagnostic perspectives
	7.5 Protoporphyrin proteins in leukocytes
	7.6 Resonance Raman spectroscopy in iron-containing proteins in tissues and cells
	7.7 Characterization of lung proteins altered by cancer cell infiltration
	7.8 Proteins of endothelium studied ex vivo
	7.9 Fourier-transform infrared microscopy of proteins
	7.10 Conclusions and perspectives
	Acknowledgments
	References
8 Interpretation of vibrational optical activity spectra of proteins
	8.1 Introduction
	8.2 Theory and calculations
	8.3 Small molecules
		8.3.1 Flexible molecules, Boltzmann averaging
		8.3.2 Solvent models, clusters
	8.4 Large molecules
	8.5 Semiempirical approaches
		8.5.1 Transition dipole coupling
		8.5.2 Cartesian coordinate tensor transfer
		8.5.3 Molecules in molecules
	8.6 Conclusions
	Acknowledgment
	References
9 Nanoscale analysis of protein self-assemblies
	9.1 Introduction
	9.2 Analysis of microscopic steps of abnormal protein aggregation at the nanoscale—a comparison of various experimental app...
		9.2.1 Thioflavin-T–based kinetic measurements
		9.2.2 Scanning probe microscopy
		9.2.3 Superresolving fluorescence microscopy
		9.2.4 Cryoelectron microscopy
		9.2.5 Nanoscale nuclear magnetic resonance
		9.2.6 X-ray spectroscopy
			9.2.6.1 Infrared nanospectroscopy
		9.2.7 Nano-Fourier-transform infrared spectroscopy
		9.2.8 Atomic force microscopy–infrared
			9.2.8.1 TERS
		9.2.9 Hyperspectral nanospectroscopic mapping
	9.3 Conclusions
	References
	Further Reading
10 Vibrational spectroscopic analysis and quantification of proteins in human blood plasma and serum
	10.1 Introduction
		10.1.1 Analysis of biofluids
		10.1.2 Blood sample: preparation of plasma versus serum
		10.1.3 Composition of plasma and serum
			10.1.3.1 Nonprotein constituents
			10.1.3.2 Proteins
				Fibrinogen
				Albumin
				Globulins
				Immunoglobulins
		10.1.4 Pathology of plasma proteins
			10.1.4.1 Abundant proteins
			10.1.4.2 Low-abundance proteins
			10.1.4.3 Cytochrome c
		10.1.5 Vibrational spectroscopic analysis of bodily fluids
		10.1.6 Vibrational spectroscopy
		10.1.7 Experimental approaches
			10.1.7.1 Fourier-transform infrared spectroscopy
			10.1.7.2 Instrumentation for Raman spectroscopy
	10.2 Biospectroscopy
		10.2.1 Vibrational spectroscopy of proteins
		10.2.2 Spectroscopic signature of serum
		10.2.3 Quantitative analysis
	10.3 Clinical translation
	References
11 Vibrational spectroscopy in protein research toward virus identification: challenges, new research, and future perspectives
	11.1 Introduction
	11.2 General structure of viruses
	11.3 A brief overview of vibrational biospectroscopy
		11.3.1 Infrared spectroscopy
			11.3.1.1 Mid-infrared
			11.3.1.2 Near-infrared
		11.3.2 Raman spectroscopy
	11.4 Computational analysis
		11.4.1 Preprocessing
		11.4.2 Multivariate analysis techniques
		11.4.3 Performance evaluation
	11.5 Applications
	11.6 Challenges
	11.7 Future perspectives
	References
12 Two-dimensional correlation spectroscopy of proteins
	12.1 Introduction
	12.2 Background
		12.2.1 Generalized two-dimensional correlation spectroscopy
		12.2.2 Basic concept of two-dimensional correlation spectroscopy
		12.2.3 Interpretation of two-dimensional correlation spectra
		12.2.4 Hetero two-dimensional correlation analysis
	12.3 Applications of two-dimensional correlation spectroscopy to protein study
		12.3.1 Two-dimensional infrared correlation spectroscopy in protein study
		12.3.2 Two-dimensional Raman correlation spectroscopy in protein study
		12.3.3 Two-dimensional vibrational circular dichroism and two-dimensional Raman optical activity correlation spectroscopy i...
		12.3.4 Combination of two-dimensional correlation spectroscopy and principal component analysis in protein study
		12.3.5 Two-dimensional heterocorrelation analysis in protein study
	12.4 Future aspect
	References
13 Resonance Raman spectroscopy of hemoglobin in red blood cells
	13.1 Introduction
	13.2 Molecular structure of oxygenated and deoxygenated hemoglobin
	13.3 Electronic structure of hemoglobin
	13.4 Methods of recording hemes in cells
	13.5 Resonant Raman spectroscopy of hemoglobin in red blood cells
		13.5.1 Raman band assignments of hemoglobin in red blood cells
		13.5.2 Polarized resonance Raman spectra reveal highly ordered heme groups in red blood cell
		13.5.3 Hemoglobin ligand modes in red blood cells revealed with near-infrared excitation
		13.5.4 Enhanced overtone and combination modes observed in hemes using 514-nm excitation
	13.6 Applications of Raman spectroscopy in red blood cell research
		13.6.1 Resonance Raman spectroscopy in malaria research
		13.6.2 Application of Raman spectroscopy to blood storage
		13.6.3 Application to thalassemia and sickle cell anemia
		13.6.4 Optical laser tweezer studies on red blood cells
		13.6.5 Detection, differentiation, and visualization of the dysfunctional Hb adducts and its metabolites
	13.7 Conclusion
	Acknowledgments
	References
14 Ultraviolet Raman spectroscopy for understanding structure and formation mechanism of amyloid fibrils*
	14.1 Introduction
	14.2 Two-dimensional correlation deep ultraviolet resonance Raman spectroscopy
		14.2.1 Fibril nucleus formation
		14.2.2 Apparent inverse order
		14.2.3 Extraction of characteristic times for structural changes
	14.3 Elucidating the kinetic mechanism of early events of hen egg white lysozyme fibrillation
	14.4 Structural characterization of fibrillar proteins
		14.4.1 Hydrogen deuterium exchange
		14.4.2 Bayesian source separation
		14.4.3 Structure determination of the lysozyme fibril core
		14.4.4 Structural variations in the cross-β core
			14.4.4.1 genetically engineered polypeptides
			14.4.4.2 Amyloid β
		14.4.5 Aromatic side chain as a reporter of local environment
	14.5 Conformation changes of amyloid fibrils
		14.5.1 Spontaneous refolding of amyloid fibrils from one polymorph to another
		14.5.2 Purple fibrils and a new protein chromophore
	14.6 Conclusions
	References
15 Recent advances in Raman spectroscopy of proteins for disease diagnosis
	15.1 Introduction
	15.2 Data analysis
		15.2.1 Preprocessing
		15.2.2 Spectral analysis
			15.2.2.1 Univariate analysis
			15.2.2.2 Multivariate analysis
			15.2.2.3 Multivariate curve resolution analysis
	15.3 Raman spectroscopy for disease diagnosis
		15.3.1 Cancer
			15.3.1.1 Breast cancer
			15.3.1.2 Lung cancer
			15.3.1.3 Oral cancer
			15.3.1.4 Ovarian cancer
			15.3.1.5 Prostate cancer
			15.3.1.6 Other cancers
		15.3.2 Diabetes
		15.3.3 Cardiovascular diseases
		15.3.4 Other diseases
	15.4 Conclusions
	References
16 Dynamics and allostery of human hemoglobin as elucidated by time-resolved resonance Raman spectroscopy
	16.1 Introduction
	16.2 Time-resolved resonance Raman spectrometers
	16.3 Primary structural dynamics of hemoglobin A following the ligand dissociation
		16.3.1 Ligand photodissociation in hemoglobin A
		16.3.2 Structural dynamics of heme in hemoglobin A upon the photodissociation
		16.3.3 Comparison of the primary structural dynamics in hemoglobin A to those in relating proteins
		16.3.4 Structural response of heme pocket in HbA upon the photodissociation
	16.4 Intersubunit communication: direct observation for the Perutz mechanism
		16.4.1 Propagation of structural changes between subunits
		16.4.2 Structural dynamics of subunits with ligated heme in half-ligated hemoglobin
		16.4.3 Structural dynamics of subunits with unligated heme in half-ligated hemoglobin
		16.4.4 Perutz’s strain model
	16.5 Dynamical coupling of tertiary and quaternary structures in hemoglobin A
		16.5.1 Hemoglobin mutants of fixed quaternary structure
		16.5.2 Tertiary structural changes dependent on R and T quaternary structures
	16.6 Differences between protein dynamics upon the dissociation of O2 and CO
	16.7 Summary and perspectives
	Acknowledgments
	References
17 Immuno-SERS: from nanotag design to assays and microscopy
	17.1 Introduction
	17.2 Surface-enhanced Raman scattering nanotags
		17.2.1 Surface-enhanced Raman scattering nanotags: plasmonic nanostructures
			17.2.1.1 Quasispherical metallic nanoparticles
			17.2.1.2 Anisotropic nanoparticles
			17.2.1.3 Plasmonic nanoassemblies
			17.2.1.4 Comparison of the surface-enhanced Raman scattering activity on single nanoparticle
		17.2.2 Surface-enhanced Raman scattering nanotags: Raman reporter molecules
			17.2.2.1 Fluorescent chromophores as Raman reporter molecules for SERRS and multiplex capacity
			17.2.2.2 Self-assembled monolayer of Raman reporters and multiplex capacity
		17.2.3 Surface-enhanced Raman scattering nanotags: protection and stabilization
			17.2.3.1 Hydrophilic self-assembled monolayers for stabilizing surface-enhanced Raman scattering nanotags
			17.2.3.2 Polymer and biopolymer-stabilized surface-enhanced Raman scattering nanotags
			17.2.3.3 Silica-encapsulation of surface-enhanced Raman scattering nanotags
		17.2.4 Surface-enhanced Raman scattering nanotags: bioconjugation to surface-enhanced Raman scattering nanotags
			17.2.4.1 Direct conjugation of biomolecules in the absence of a protective shell
			17.2.4.2 Conjugation of biomolecules to surface-enhanced Raman scattering nanotags with a protective shell
	17.3 Immuno-SERS assay
		17.3.1 Sandwich immuno-SERS assay on solid substrates
		17.3.2 Protein immuno-SERS microarray
		17.3.3 Dot-blot semisandwich immuno-SERS assay
		17.3.4 Microfluidic immuno-SERS assay
	17.4 Immuno-SERS microscopy
		17.4.1 Immuno-SERS microscopy for protein localization on cells
			17.4.1.1 Localization of a single target protein on cells
			17.4.1.2 Localization of multiple target proteins on cells
		17.4.2 Immuno-SERS microscopy for protein localization on tissue specimens
			17.4.2.1 Immuno-SERS microscopy for protein localization on frozen or formalin-fixed and paraffin-embedded tissue sections
			17.4.2.2 Immuno-SERS microscopy for protein localization on fresh tissue specimens
	17.5 Summary and perspective
	References
18 Highly localized characterization of protein structure and interaction by surface-enhanced Raman scattering
	18.1 Introduction
	18.2 Local probing gives detailed information on the interaction of proteins
		18.2.1 The protein corona of plasmonic nanoparticles inside living cells
		18.2.2 Binding sites of serum albumins in the protein corona of nanoparticles
		18.2.3 Concentration dependence: implications in live cells
	18.3 Interaction of protein side chains from surface-enhanced hyper Raman scattering
		18.3.1 Surface-enhanced hyper Raman scattering provides complementary information
		18.3.2 Toward surface-enhanced Raman scattering spectra of protein side chains
	18.4 Studies of individual protein molecules in the hot spots of nanolenses
		18.4.1 Plasmonic nanolenses for highly localized surface-enhanced Raman scattering probing
		18.4.2 Detection of single protein molecules in individual gold nanolenses
	Acknowledgments
	References
19 Surface-enhanced Raman scattering chemosensing of proteins
	19.1 Introduction
	19.2 Peptide-based chemosensing
	19.3 Antibody-based chemosensing
	19.4 Bioreceptor-free chemosensing
	19.5 Conclusions
	Acknowledgments
	References
Index
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