Singular value decomposition analysis of the secondary structure features contributing to the circular dichroism spectra of model proteins

Abstract

Amyloid fibril formation occurs in restricted environment, such as the interface between intercellular fluids and bio-membranes. Conformational interconversion from α-helix to β-structure does not progress in fluids; however, it can occur after sedimentary aggregation during amyloid fibril formation induced by heat treatment of hen egg white lysozyme (HEWL). Secondary structures of various proteins and denatured proteins titrated with 2,2,2-trifluoroethanol (TFE) were examined using their CD spectra. Gaussian peak/trough and singular value decompositions (SVD) showed that the spectral pattern of the α-helix comprised a sharp trough at wavelength 207 nm and a broad trough at 220 nm. Conversely, we distinguished two patterns for β-sheet—a spread barrel type, corresponding to ConA, and a tightly weaved type, corresponding to the soybean trypsin inhibitor. Herein, we confirmed that the spectral/conformational interconversion of the heat-treated HEWL was not observed in the dissolved fluid.

Hyper Thermostability and Liquid-Crystal-Like Properties of Designed α-Helical Peptide Nanofibers

“…In the curve fitting of the thermal denaturation curve, three- or four-state equilibrium reactions were assumed with no heat capacity change based on eqs –, as follows: d ln .25em K d T = Δ H VH R T 2 normalΔ G o = Δ H VH T m × ( T m − T ) f i = exp ( − Δ G normalo R T ) true{ 1 + exp ( − Δ G normalo R T ) true} [ θ 222 ] = ∑ i false[ θ 222 false] i × f i where K is the equilibrium constant, T is the absolute temperature (K), Δ H VH is the change in van ’t Hoff enthalpy upon thermal transition, R is the gas constant (8.31 JK –1 mol –1 ), Δ G o is the standard free energy change upon thermal transition, T m is the transition temperature (K), f i is the fraction of the i -th state, and [θ 222 ] i is the average residue molar ellipticity of each state. The 20 spectra obtained in the temperature change experiment (wavelength range: 190–250 nm) were subjected to singular value decomposition (SVD) analysis to obtain a detailed picture of the pathway of the structural change induced by the temperature increase . The set of 20 spectra obtained at each 5 °C increment was decomposed according to…”

“…In the curve fitting of the thermal denaturation curve, three- or four-state equilibrium reactions were assumed with no heat capacity change based on eqs –, as follows: where K is the equilibrium constant, T is the absolute temperature (K), Δ H VH is the change in van ’t Hoff enthalpy upon thermal transition, R is the gas constant (8.31 JK –1 mol –1 ), Δ G o is the standard free energy change upon thermal transition, T m is the transition temperature (K), f i is the fraction of the i -th state, and [θ 222 ] i is the average residue molar ellipticity of each state. The 20 spectra obtained in the temperature change experiment (wavelength range: 190–250 nm) were subjected to singular value decomposition (SVD) analysis to obtain a detailed picture of the pathway of the structural change induced by the temperature increase . The set of 20 spectra obtained at each 5 °C increment was decomposed according to eq , as follows: where M , U , W , and V T are assumed to be an m × n matrix, m × m unitary matrix, m × n diagonal matrix, and n × n unitary matrix, respectively; U is the left singular matrix; W is the singular matrix; and V T is the right singular matrix.…”

Effects of Local Anesthetics on Liposomal Membranes Determined by Their Inhibitory Activity of Lipid Peroxidation

“…The matrices describing M are transformed into the following formula, The diagonal matrix E represents the diagonal elements { |1 ≤ i ≤ r } of the positive real values in descending order. These elements are singular values, indicating dispersion . The i th column of the orthogonal matrix V is the coefficient vector corresponding to the singular value s i , and vector is known as a singular vector.…”

“…These elements are singular values, indicating dispersion. 27 The ith column of the orthogonal matrix V is the coefficient vector corresponding to the singular value s i , and vector…”

The pH-responsive precipitation–redissolution of the CspB fusion protein, CspB50TEV-Teriparatide, triggered by changes in secondary structure

“…The aggregation of proteins often changes their secondary structure, for example in amyloid formation [ 15 , 16 ]. Circular dichroism (CD) and Fourier transform infrared (FTIR) spectrometry are effective tools for the analysis of protein secondary structures to examine the mechanisms of protein aggregation and the change of protein activity [ [17] , [18] , [19] , [20] , [21] , [22] ]. For example, the secondary structure of amyloid-β 1-42 changes from a soluble monomer with a random coil form to an insoluble aggregate with a β-sheet structure, which can be monitored by the CD spectra [ 23 ].…”