Content Of Secondary Structure Elements Research Articles

Turbulence in protein folding: Vorticity, scaling and diffusion of probability flows.

Recently, when studying folding of a SH3 domain, we discovered that the flows of transitions between protein states can be surprisingly similar to turbulent fluid flows. This similarity was not restricted by a vortex pattern of the flow fields but extended to a spatial correlation of flow fluctuations, resulting, in particular, in the structure functions such as in the Kolmogorov theory of homogeneous and isotropic turbulence. Here, we undertake a detailed analysis of spatial distribution of folding flows and their similarity to turbulent fluid flows. Using molecular dynamics simulations, we study folding of another benchmark system—Trp-cage miniprotein, which has different content of secondary structure elements and mechanism of folding. Calculating the probability fluxes of transitions in a three-dimensional space of collective variables, we have found that similar to the SH3 domain, the structure functions of the second and third orders correspond to the Kolmogorov functions. The spatial distributions of the probability fluxes are self-similar with a fractal dimension, and the fractal index decreases toward the native state, indicating that the flow becomes more turbulent as the native state is approached. We also show that the process of folding can be viewed as Brownian diffusion in the space of probability fluxes. The diffusion coefficient plays a role of the key parameter that defines the structures functions, similar to the rate of dissipation of kinetic energy in hydrodynamic turbulence. The obtained results, first, show that the very complex dynamics of protein folding allows a simple characterization in terms of scaling and diffusion of probability fluxes, and, secondly, they suggest that the turbulence phenomena similar to hydrodynamic turbulence are not specific of folding of a particular protein but are common to protein folding.

Low-frequency vibrational spectroscopy of proteins with different secondary structures.

Fourier transform infrared (FTIR) and Raman spectra of proteins with significantly different structures are measured in a spectral interval of 50 to 500 ?? cm ? 1 and noticeable spectral differences are revealed. Intensities of several spectral bands correlate with contents of secondary structure elements. FTIR spectra of superhelical proteins exhibit developed spectral features that are absent in the spectra of globular proteins. Significant differences of the Raman spectra of proteins that are not directly related to the difference of the secondary structures can be due to differences of tertiary and/or quaternary structure of protein molecules.

Specific Structural-Functional Role of the Pronounced Negative Molecular Charge of the Sturgeon Gonadotropin β-Subunit

Free negatively charged carboxyl groups (COOH) were selectively modified (neutralised) in sturgeon (Acipenser güldenstädti Br) gonadotropic hormone (GTH) β-subunit (βGTH). Eight COOH groups were neutralised by reaction with glycine ethyl ester. Investigation of modified βGTH showed that specific immunoactivity with antiserum raised against standard βGTH was completely lost. Analysis of CD spectra and the content of secondary structure elements of standard and modified βGTH did not indicate any considerable differences. Investigation of reassociated α-β dimer comprising standard αGTH and modified βGTH showed that hormonal activity was completely lost while immunoreactivity was lowered by about 30% in comparison with that of the standard subunit α-β dimer. It was concluded that eight free COOH groups located on the surface of βGTH are the main structural components of the species-specific antigenic determinant groups of the subunit, but are not directly involved in either maintaining the conformation of the subunit nor in its ability to interact with the native counterpart subunit. COOH groups, as bearers of the negative charge located on the surface of βGTH, play a decisive role in the specific hormonal activity of GTH determined by oocyte maturation tests. Free COOH groups are included in the effector zones (active sites) of GTH dimer molecule responsible for the stereospecific interaction with the test-oocyte membrane hormone-sensitive binding (receptor) sites to induce the biological effects.

New Insights into the Behavior of Bovine Serum Albumin Adsorbed onto Carbon Nanotubes: Comprehensive Spectroscopic Studies

Bovine serum albumin (BSA) nonspecifically binds to well-dispersed multiwalled carbon nanotubes (MWCNTs), forming a stable bioconjugate. After accounting for the inner filter effect, we found the fluorescence intensity of BSA was quenched by MWCNTs in static mode, which was authenticated by lifetime measurements and Stern-Volmer calculations. The thermodynamic parameters DeltaG(o), DeltaS(o), and DeltaH(o) were -9.67 x 10(3) + 2.48 x 10(3) ln lambda J x mol(-1), 41.0 - 0.828 ln lambda J x mol(-1) x K(-1), and 7.30 x 10(3) + 2.23 x 10(3) ln lambda J x mol(-1) (lambda < 1 x 10(-4)), respectively, which shows a spontaneous and electrostatic interaction. Scatchard analysis and UV-visible results provide statistical data concerning changes in the microenvironment of amide moieties in response to different doses of MWCNTs, revealing different behavior of the BSA molecules. The absorption spectra also show that the tertiary structure of the protein was partially destroyed. The content of secondary structure elements of BSA was changed by the tubes. This work elucidates the interaction mechanism of BSA and MWCNTs from a spectroscopic angle.

Studies on the conformational change of adsorbed BSA onto a moderately hydrophobic surface at different denaturant concentrations and surface coverages

This paper is aimed at investigating the conformational change of denatured bovine serum albumin (BSA) in combination with thermodynamic functions and their fractions, adsorption isotherms, Fourier transform infrared (FTIR) spectroscopy, and differential scanning calorimetry (DSC). Microcalorimetric measurements of displacement adsorption enthalpies Δ H of denatured BSA (by guanidine hydrochloride (GuHCl)) adsorbed onto a moderately hydrophobic surface (PEG-600) from solutions were carried out. The contents of secondary structure elements of BSA in solutions and in the adsorbed state were determined by FTIR and the thermal stability of adsorbed BSA was measured by DSC. The adsorption thermodynamic functions Δ H, Δ S, Δ G, and their fractions were calculated based on the thermodynamics of the stoichiometric displacement theory for adsorption (SDT-A) and adsorption isotherms. The results showed that the surface can provide energy to denatured BSA and make it gain a more ordered conformation with GuHCl concentration increment. At a given GuHCl concentration, although the ordered secondary structure of adsorbed BSA molecules decreased, their tertiary structure may be more perfect with surface coverage increment. The thermodynamic analysis of four subprocesses associated with adsorption also confirmed the increment of conformational gain.

Large-scale atomistic simulation of a nanosized fibril formed by thiophene–peptide “molecular chimeras”

We present the results of an extensive molecular dynamics simulation aimed at investigating the structural organization of a nanosized fibrillar aggregate formed by bioinspired diblock copolymers consisting of oligothiophene and β-sheet-forming peptide parts. The main motivation of our study is that those supramolecular structures can be promising for nanoelectronic and other advanced technological applications. In order to construct the initial fibril configuration, a rational approach based on predicting the likely polymorphic structures that are favorable to the formation of fibrils is used. We demonstrate that the system simulated in this work is very stable, at least on the nanosecond timescale, and can be viewed globally as a linear “super-polymer” that exhibits a large length-to-thickness ratio (∼20). The average content of secondary structure elements (β-sheets, bridges, turns, and coils) in the peptide-containing domains as well as the fraction of the thiophene rings participating in π–π-stacking interactions is also analyzed.

Prediction of Folding Rates of Small Proteins: Empirical Relations Based on Length, Secondary Structure Content, Residue Type, and Stability

Delineating the determinants of folding of small proteins is essential for decoding the folding code. By considering the literature data for the folding of 45 two-state proteins that differ widely in sequence, structure, and function, this work suggests two empirical relations for the prediction of the folding rate. One relation is based on the content of secondary structure elements, and the other uses the number of residues of each of the following types: hydrophobic, positively charged, and negatively charged. Both relations incorporate the chain length as an indirect descriptor. The correlation between experimental values for folding rates and free energy is poor, providing little support to the "stability gap" hypothesis based on the folding of simple lattice and off-lattice polymers. The average rate-determining barrier height for these two-state proteins is much larger than the small barriers for the transition-state ensemble envisaged by theoretical models.

Conformation of a synthetic antigenic peptide from HIV-1 p24 protein induced by ionic micelles

We studied the interaction of the peptide AAMQMLKETINEEAAEWDRVHPVHAGPIA from the HIV-1 p24 protein in the presence of SDS (anionic) and CTABr (cationic) micelles at pH 7.0 by circular dichroism, fluorescence, and electron spin resonance (ESR). The micelles induced secondary structure as well as a blue shift in the tryptophan fluorescence emission, indicating an interaction between the peptide and the micelles. However, different contents of secondary structure elements were found when the peptide interacts with SDS or CTABr micelles. Steady-state anisotropy indicates a constraint on the rotational mobility of the tryptophan residue of the peptide upon interaction with micelles. ESR studies pointed to different locations for the peptide in either micelle. Our results suggested that at least part of the peptide might be located at the hydrophobic core of the CTABr micelles, probably at the C-terminal region, while it is more inserted into the SDS micelles.

Native-like secondary structure of molten globules

The most common evidence for the existence of secondary structure in a globular protein is the presence of a strongly pronounced far-UV circular dichroism (CD) spectrum. Although CD spectra of native proteins are well described and their quantitative analysis is widely used, similar studies for denatured proteins have still to be done. Far-UV CD spectra of nine proteins in the native and the pH-induced molten globule states were acquired and analyzed. Singular value decomposition showed that the spectra of molten globules could be described as a superposition of at least three independent components (most likely α-, β- and irregular structure). A self-consistent procedure of CD spectra analysis revealed the existence of a clear correlation between the shape of the molten globule spectra and the content of secondary structure elements in the corresponding native proteins, as determined from X-ray data. A mathematical expression of this correlation in terms of the Pierson coefficient amounts to the value of 0.9 for both the α-helix and the β-structure. Thus, the secondary structure of proteins in the molten globule state is close to that in the native state.

Disordered C-terminal Domain of Tyrosyl Transfer-RNA Synthetase: Evidence for a Folded State

The C-terminal domain (residues 320 to 419) of tyrosyl-tRNA synthetase from Bacillus stearothermophilus(Bst-TyrRS) is necessary for the binding of tRNA Tyrbut disordered in the crystal structure. Four different criteria showed that the isolated C-terminal domain of Bst-TyrRS was at least partially folded in solution. Its spectrum of circular dichroism was compatible with a high content of secondary structure elements (56% of its residues) and these structural elements disappeared in 7.5 M urea. It was unfolded by urea along a unique transition, around 6.0 M, according to the variations in the fluorescence of its tyrosine residues and in its electrophoretic mobility through transverse gradient gels. It was denatured by heat with a temperature of half-precipitation in 30 minutes that was equal to 67.9°C and close to the Bst-TyrRS one, 68.7°C. Its transitions of denaturation by urea or temperature were weakly cooperative. The C-terminal domains of the TyrRSs from Escherichia coli(Eco-TyrRS) and B. stearothermophiluscould be genetically exchanged without a significant loss of aminoacylation activity. A hybrid between the N-terminal domain of Bst-TyrRS and the C-terminal domain of Eco-TyrRS was precipitated by heat in 30 minutes following two transitions: 83% of the molecules were precipitated with a temperature of half-transition (51.6°C) close to the Eco-TyrRS one (48.6°C). The remainder was precipitated with a temperature of half-transition (65.5°C) close to the Bst-TyrRS one (67.2°C) or that of its N-terminal domain (68.0°C). These results showed that the C-terminal domain of Eco-TyrRS could undergo a transition from a soluble active conformation to an insoluble one. The denaturations of Bst-TyrRS and of its N-terminal domain by urea occurred with two successive transitions, around 4 M and 6 M, and thus according to a complex mechanism.

Conformational properties of streptokinase—secondary structure and localization of aromatic amino acids

The conformational properties of streptokinase (Sk) have been assessed by several spectroscopic techniques. A solvent accessibility of about 70% of the 22 Tyr residues was found by u.v. perturbation spectroscopy. Fluorescence spectroscopy indicates also the surface localization of the single Trp 6 residue. Circular dichroism (c.d.), infrared (i.r.), and Raman spectra were analysed in order to estimate the contents of secondary structure elements of Sk. Values in the range of 14-23% alpha-helices, 38-46% beta-structures, 10-30% turns and 12-23% residual structures were found. The characteristics of the c.d. spectrum support the classification of Sk as an alpha + beta protein. Effects of temperature, pH, and denaturants were studied by c.d. spectroscopy, and on spin-labelled Sk, by e.p.r. spectroscopy. Structural effects were induced at temperatures above 40 degrees C, pH values below 3.0 and urea concentrations above 2 M. At temperatures above 70 degrees C, at pH 2.1, and at urea and Gu.HCl concentrations of 7 M and 5 M, respectively, no further structural changes are revealed in the spectra. At temperatures around 50 degrees C, at pH 3.0, and denaturant concentrations of about 1 M Gu.HCl and 1 M to 2 M urea, c.d. effects were observed in the near-u.v. region indicating an increase in the asymmetry for aromatic amino acids in comparison with the structure of Sk in low ionic strength buffers at neutral pH, 20 degrees C and in the absence of denaturants. These effects were most pronounced for the temperature dependence of the c.d. spectra. E.p.r. spectroscopy has shown that loosening of the protein surrounding of the spin label already begins at 1 M urea and that the mobility of the spin label points to a structural change in Sk at 46 degrees C.