Note: Front Cover -- Vibrational Spectroscopy in Protein Research -- Copyright Page -- 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.