Infrared spectroscopy of proteins.

Publisher Summary The vibrational spectrum of a molecule is determined by its three-dimensional structure and its vibrational force field. An analysis of this (usually infrared (IR) and Raman) spectrum can therefore provide information on the structure and on intramolecular and intermolecular interactions. The more probing the analysis, the more detailed is the information that can be obtained. Detailed analyses of the vibrational spectra of macromolecules, however, have provided a deeper understanding of structure and interactions in these systems. An important advance in this direction for proteins came with the determination of the normal modes of vibration of the peptide group in N-methylacetamide, and the characterization of several specific amide vibrations in polypeptide systems. Extensive use has been made of spectra-structure correlations based on some of these amide modes, including attempts to determine secondary structure composition in proteins. Polypeptide molecules exhibit many more vibrational frequencies than the amide modes. Over the years, some normal-mode calculations have provided greater insight into the spectra of particular molecules. However, these have often been based on approximate structures or have employed limited force fields. These force fields can now serve as a basis for detailed analyses of spectral and structural questions in other polypeptide molecules. The aim of this chapter is to present these recent developments in the vibrational spectroscopy of peptides, polypeptides, and proteins.

Vibrational spectroscopy and conformation of peptides, polypeptides, and proteins.

1. Introduction 46372. Theoretical Methodologies and Simulation Tools 46402.1. Ab Initio Quantum Chemistry 46412.2. Molecular Dynamics 46422.2.1. Classical Molecular Dynamics and MonteCarlo Simulations46432.2.2. Empirical Valence Bond Models 46442.2.3. Ab Initio Molecular Dynamics (AIMD) 46452.3. Poisson−Boltzmann Theory 46452.4. Nonequilibrium Statistical Mechanical IonTransport Modeling46462.5. Dielectric Saturation 46473. Transport Mechanisms 46483.1. Proton Conduction Mechanisms 46483.1.1. Homogeneous Media 46483.1.2. Heterogeneous Systems (ConfinementEffects)46553.2. Mechanisms of Parasitic Transport 46613.2.1. Solvated Acidic Polymers 46613.2.2. Oxides 46654. Phenomenology of Transport inProton-Conducting Materials for Fuel-CellApplications46664.1. Hydrated Acidic Polymers 46664.2. PBI−H

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Transport in proton conductors for fuel-cell applications: simulations, elementary reactions, and phenomenology.

This review deals with current concepts of vibrational spectroscopy for the investigation of protein structure and function. While the focus is on infrared (IR) spectroscopy, some of the general aspects also apply to Raman spectroscopy. Special emphasis is on the amide I vibration of the polypeptide backbone that is used for secondary-structure analysis. Theoretical as well as experimental aspects are covered including transition dipole coupling. Further topics are discussed, namely the absorption of amino-acid side-chains, 1H/2H exchange to study the conformational flexibility and reaction-induced difference spectroscopy for the investigation of reaction mechanisms with a focus on interpretation tools.

https://www.cambridge.org/core/services/aop-cambridge-core/content/view/S0033583502003815

What vibrations tell us about proteins

New insight into protein secondary structure from resolution-enhanced infrared spectra.

Recent years have witnessed burgeoning interest in plant flavonoids as novel therapeutic drugs targeting cellular membranes and proteins. Motivated by this scenario, we explored the binding of robinetin (3,7,3′,4′,5′-pentahydroxyflavone, a bioflavonoid with remarkable ‘two color’ intrinsic fluorescence properties), with egg yolk phosphatidylcholine (EYPC) liposomes and normal human hemoglobin (HbA), using steady state and time resolved fluorescence spectroscopy. Distinctive fluorescence signatures obtained for robinetin indicate its partitioning ( K p  =  8.65 × 10 4 ) into the hydrophobic core of the membrane lipid bilayer. HbA–robinetin interaction was examined using both robinetin fluorescence and flavonoid-induced quenching of the protein tryptophan fluorescence. Specific interaction with HbA was confirmed from three lines of evidence: (a) bimolecular quenching constant K q  ≫ diffusion controlled limit; (b) closely matched values of Stern–Volmer quenching constant and binding constant; (c) τ 0 / τ  = 1 (where τ 0 and τ are the unquenched and quenched tryptophan fluorescence lifetimes, respectively). Absorption spectrophotometric assays reveal that robinetin inhibits EYPC membrane lipid peroxidation and HbA glycosylation with high efficiency.

Binding of the bioflavonoid robinetin with model membranes and hemoglobin: Inhibition of lipid peroxidation and protein glycosylation.

Excited-state proton-transfer and dual fluorescence of robinetin in different environments

Influence of reverse micellar environments on the fluorescence emission properties of tryptophan octyl ester.

The fluorescence emission properties of 7-hydroxyflavone (7HF) are examined in reverse micelles of aerosol-OT (AOT) in n-heptane. Excited-state proton transfer (ESPT) leading to dual-emission behaviour (λmax ≈ 396–417 nm and 545–550 nm which can be assigned to the normal and ESPT tautomer emission respectively) as well as red edge excitation shift (REES) of the normal fluorescence band are observed. Upon gradual addition of water to the 7HF-AOT-n-heptane solution, conspicuous enhancement of the ESPT tautomer emission intensity takes place together with a progressive red shift of the normal emission, that continues up to ([H2O]/[AOT]) = W0 ≈ 8–10, beyond which no significant changes occur. Interestingly, with increasing value of W0, the changes observed in the magnitude of the REES effect, Δλ (Δ λ is the difference in λmax of the normal fluorescence as λexc is shifted from midband (λ = 310 nm) to red edge (λ = 350 nm) of the absorption band) parallel to changes in the λmax of normal emission, as well as that of the relative intensity I T l N of the tautomer vs. normal emission bands. Even at high W0 (e.g. W0 = 36), these parameters do not reach the limiting values found in bulk water, indicating that 7HF is predominantly localized near the head groups of AOT, mostly in the bound water phase.

Luminescence behaviour of 7-hydroxyflavone in aerosol OT reverse micelles: excited-state proton transfer and red-edge excitation effects

A brilliant scientist and an outstanding personality who was one of the founders of modern photochemistry-Michael Kasha-is the subject of this Essay. Kasha's rule and the Kasha effect both bear his name, and he also discovered the chemical production of singlet molecular oxygen, and was a pioneer of excited-state proton transfer systems. Kasha combined his passion for chemistry and physics with that for music, photography, and botany.

Pradeep K. Sengupta

Papers

Binding of the bioflavonoid robinetin with model membranes and hemoglobin: Inhibition of lipid peroxidation and protein glycosylation.

Excited-state proton-transfer and dual fluorescence of robinetin in different environments

Influence of reverse micellar environments on the fluorescence emission properties of tryptophan octyl ester.

Luminescence behaviour of 7-hydroxyflavone in aerosol OT reverse micelles: excited-state proton transfer and red-edge excitation effects

Michael Kasha: from photochemistry and flowers to spectroscopy and music.