Protein structural segments and their interconnections derived from optical spectra. Thermal unfolding of ribonuclease T1 as an example

Broadband terahertz circular polarizers with single- and double-helical array metamaterials

A new broadband terahertz circular polarizer with a double-helix structure is proposed in this paper. Furthermore, we systematically simulated the performance of single- and double-helix circular polarizers. Our numerical simulation results show that the function regions of double-helical metamaterials are about 50% broader than those of the single-helical metamaterials in terahertz. We also analyzed the dependence of the performance of the single- and double-helix metamaterials on different structure parameters. Following the antenna theory and the metal wire grating theory, proper explanations were given to interpret the changes of performance with various structure parameters and the difference between the single and double helix.

Osmolyte-induced protein folding free energy changes

Upon addition of protecting osmolyte to an aqueous solution of an intrinsically unstructured protein, spectral observables are often seen to change in a sigmoid fashion as a function of increasing osmolyte concentration. Commonly, such data are analyzed using the linear extrapolation model (LEM), a method that defines a scale from 0%-100% folded species at each osmolyte concentration by means of extending pre- and post-folding baselines into the transition region. Defining the 0%-100% folding scale correctly for each osmolyte is an important part of the analysis, leading to evaluation of the fraction of folded protein existing in the absence of osmolytes. In this study, we used reduced and carboxyamidated RNase T1 (RCAM-T1) as an intrinsically unstructured protein, and determined the thermodynamic stability of RCAM-T1 induced by naturally occurring osmolytes. Because the folded fraction of the protein population determined by experiments of thermal and urea-induced denaturation is nonzero in the absence of osmolytes at 15 degrees C, the commonly used LEM can lead to false values of DeltaG[stackD-->N0] for protein folding due to the arbitrary assumption that the protein is 100% unfolded in the presence of buffer alone. To correct this problem, titration of the protein solution with urea and extrapolating back to zero urea concentration gives the spectral value for 100% denatured protein. With fluorescence as the observable we redefine F/F0 to F/F0extrap = 1.0 and require that the denatured-state baseline have this value as its intercept. By so doing, the 0%-100% scale-corrected DeltaG[D-->N0] values of RCAM-T1 folding in the presence of various osmolytes are then found to be identical, with small error, demonstrating that DeltaG[D-->N0] is independent of the osmolytes used. Such a finding is an important step in validating this quantity derived from the LEM as having the properties expected of an authentic thermodynamic parameter. The rank order of osmolyte efficacies in stabilizing RCAM-T1 is sarcosine > sucrose > sorbitol > proline > betaine > glycerol.

The optimization of protein secondary structure determination with infrared and circular dichroism spectra

We have used the circular dichroism and infrared spectra of a specially designed 50 protein database [Oberg, K.A., Ruysschaert, J.M. & Goormaghtigh, E. (2003) Protein Sci. 12, 2015-2031] in order to optimize the accuracy of spectroscopic protein secondary structure determination using multivariate statistical analysis methods. The results demonstrate that when the proteins are carefully selected for the diversity in their structure, no smaller subset of the database contains the necessary information to describe the entire set. One conclusion of the paper is therefore that large protein databases, observing stringent selection criteria, are necessary for the prediction of unknown proteins. A second important conclusion is that only the comparison of analyses run on circular dichroism and infrared spectra independently is able to identify failed solutions in the absence of known structure. Interestingly, it was also found in the course of this study that the amide II band has high information content and could be used alone for secondary structure prediction in place of amide I.

Rationally selected basis proteins: a new approach to selecting proteins for spectroscopic secondary structure analysis

Protein basis sets have been extensively used as reference data for the determination of protein structure with optical methods such as circular dichroism and infrared spectroscopies. We have taken a new approach to basis protein selection by utilizing three crystal structure classification databases: CATH, SCOP, and PDB_SELECT. Through the use of the information available in these and other online resources, we identified 115 commercially available proteins as potential basis set candidates. By carefully screening the quality of the crystal structures and commercial protein preparations, we obtained a final set of 50 rationally selected proteins (RaSP50) that has been optimized for use in spectroscopic protein structure determination studies. These proteins span the full range of known protein folds as well as alpha-helix and beta-sheet contents, and they represent a more comprehensive variety of fold types than any previous reference set. This report includes a detailed presentation of the reasoning behind the rational protein selection process, a description of the properties of the RaSP50 set, and a discussion of the types of structural and spectral variations that are represented in the set.

Protein and peptide secondary structure and conformational determination with vibrational circular dichroism

Vibrational circular dichroism (VCD) provides alternative views of protein and peptide conformation with advantages over electronic (UV) CD (ECD) or IR spectroscopy. VCD is sensitive to short-range order, allowing it to discriminate beta-sheet and various helices as well as disordered structure. Quantitative secondary structure analyses use protein VCD bandshapes, but are best combined with ECD and IR for balance. Much recent work has focused on empirical and theoretical VCD analyses of peptides, with detailed prediction of helix, sheet and hairpin spectra and site-specific application of isotopic substitution for structure and folding.

Plasticity of secondary structure in the N-terminal region of beta-dystroglycan

The secondary structure content of the N-terminal extracellular domain of beta-dystroglycan (a recombinant fragment extending from positions 654 to 750) has been quantitatively determined by means of CD and FTIR spectroscopies. The elements of secondary structure, namely an 8-10 residue long alpha-helix (10%) and two beta-strands (24%) have been assigned to specific amino acid sequences by means of a GOR constrained prediction method. The remaining 66% of the whole sequence is classified as turns or unordered. The temperature dependence of CD and FTIR spectra has been investigated in detail. A reversible, non-cooperative thermal transition is observed with both CD and FTIR spectroscopies up to 95 degrees C. The profile of the transition is typical of the unfolding of isolated peptides and corresponds to the progressive loss of the secondary structure elements of the protein with no evidence for collapsing phenomena, typical of globular proteins, upon heating.

Estimation of protein secondary structure from circular dichroism spectra: inclusion of denatured proteins with native proteins in the analysis

We have expanded our reference set of proteins used in the estimation of protein secondary structure by CD spectroscopy from 29 to 37 proteins by including 3 additional globular proteins with known X-ray structure and 5 denatured proteins. We have also modified the self-consistent method for analyzing protein CD spectra, SELCON3, by including a new selection criterion developed by W. C. Johnson, Jr. (Proteins Struct. Funct. Genet. 35, 307-312, 1999). The secondary structure corresponding to the denatured proteins was approximated to be 90% unordered, owing to the spectral similarity of the denatured proteins and unordered structures. We examined the thermal denaturation of ribonuclease T1 by CD using both the original and expanded sets of reference proteins and obtained more consistent results with the expanded set. The expanded set of reference proteins will be helpful for the determination of protein secondary structure from protein CD spectra with higher reliability, especially of proteins with significant unordered structure content and/or in the course of denaturation.

Simulations of oligopeptide vibrational CD: effects of isotopic labeling

Simulated ir absorption and vibrational CD (VCD) spectra of four alanine-based octapeptides, each having its main chain constrained to a different secondary structure conformation, were analyzed and compared with experimental results for several different peptides. The octapeptide simulations were based on transfer of property tensors from a series of ab initio calculations for a short L-alanine based segment containing 3 peptide bonds with relative straight phi, psi angles fixed to those appropriate for alpha-helix, 3(10)-helix, ProII-like helix, and beta-sheet-like strand. The tripeptide force field (FF) and atomic polar tensors were obtained with density functional theory techniques at the BPW91/6-31G** level and the atomic axial tensor at the mixed BPW91/6-31G**/HF/6-31G level. Allowing for frequency correction due to the FF limitations, the octapeptide results obtained are qualitatively consistent with experimental observations for ir and VCD spectra of polypeptides and oligopeptides in established conformations. In all cases, the correct VCD sign patterns for the amide I and II bands were predicted, but the intensities did have some variation from the experimental patterns. Predicted VCD changes upon deuteration of either the peptide or side-chains as well as for (13)C isotopic labeling of the amide C=O at specific sites in the peptide chain were computed for analysis of experimental observations. A combination of theoretical modeling with experimental data for labeled compounds leads both to enhanced resolution of component transitions and added conformational applicability of the VCD spectra.

Instability, stabilization, and formulation of liquid protein pharmaceuticals

One of the most challenging tasks in the development of protein pharmaceuticals is to deal with physical and chemical instabilities of proteins. Protein instability is one of the major reasons why protein pharmaceuticals are administered traditionally through injection rather than taken orally like most small chemical drugs. Protein pharmaceuticals usually have to be stored under cold conditions or freeze-dried to achieve an acceptable shelf life. To understand and maximize the stability of protein pharmaceuticals or any other usable proteins such as catalytic enzymes, many studies have been conducted, especially in the past two decades. These studies have covered many areas such as protein folding and unfolding/denaturation, mechanisms of chemical and physical instabilities of proteins, and various means of stabilizing proteins in aqueous or solid state and under various processing conditions such as freeze-thawing and drying. This article reviews these investigations and achievements in recent years and discusses the basic behavior of proteins, their instabilities, and stabilization in aqueous state in relation to the development of liquid protein pharmaceuticals.

Novel matrix descriptor for secondary structure segments in proteins: demonstration of predictability from circular dichroism spectra

An extension to standard protein secondary structure predictions using optical spectra that encompasses the number and average lengths of segments of uniform secondary structure in the sequence is demonstrated. The connectivity and numbers of segments can be described by a matrix descriptor [sij] (i, j representing segment types such as helix and beta-sheet strands). Independent knowledge of the fractional concentration of each secondary structure type and of the total number of residues in the protein then with [sij] yields the average segment length of each type. The physical background for prediction of this extended structural descriptor from spectral data is summarized, rules for its generation from reference X-ray structures are defined, and formal variants of its form are discussed. Using a novel neural network approach to analyze a training set of electronic circular dichroism (ECD) and vibrational circular dichroism (VCD) spectra for 23 proteins, matrix descriptors encompassing helix, sheet, and other forms are predicted. The results show that the matrix descriptor can be predicted to an accuracy comparable to that of conventionally predicted average fractional secondary structures. In this respect the ECD predictions of [sij] were significantly more accurate than the VCD ones, which may result from the longer range length dependence of the ECD bandshape and intensity. Summary results for a parallel analysis using Fourier transform infrared spectra indicate somewhat lower reliability than those for VCD.

Estimation of the number of alpha-helical and beta-strand segments in proteins using circular dichroism spectroscopy

A simple approach to estimate the number of alpha-helical and beta-strand segments from protein circular dichroism spectra is described. The alpha-helix and beta-sheet conformations in globular protein structures, assigned by DSSP and STRIDE algorithms, were divided into regular and distorted fractions by considering a certain number of terminal residues in a given alpha-helix or beta-strand segment to be distorted. The resulting secondary structure fractions for 29 reference proteins were used in the analyses of circular dichroism spectra by the SELCON method. From the performance indices of the analyses, we determined that, on an average, four residues per alpha-helix and two residues per beta-strand may be considered distorted in proteins. The number of alpha-helical and beta-strand segments and their average length in a given protein were estimated from the fraction of distorted alpha-helix and beta-strand conformations determined from the analysis of circular dichroism spectra. The statistical test for the reference protein set shows the high reliability of such a classification of protein secondary structure. The method was used to analyze the circular dichroism spectra of four additional proteins and the predicted structural characteristics agree with the crystal structure data.

Vibrational circular dichroism spectroscopy of selected oligopeptide conformations

Vibrational circular dichroism (VCD) has been shown to be a useful technique for characterization of the qualitative secondary structure type for linear polypeptides and oligopeptides. A brief review of characteristic spectral responses and applications is given. Since VCD is dependent on relatively short range interactions, it detects residual structure in such oligomers even if long range order is lost. VCD studies presented here for Lys oligomers as well as Lys and Glu polymers as a function of length, salt added and temperature, confirm residual local order in these 'random coils'. Comparison to results with Pro oligomers, supports an interpretation that these extended structures have a left handed twist conformation. The 'coil' VCD is shown to be significantly reduced in intensity by temperature increase and by decrease in peptide length. By contrast, for partially alpha-helical Ac-(AAKAA)3GY-NH2 oligomers, the spectrum changes to the high temperature Lys(n) shape on heating, first losing then gaining intensity, indicating an equilibrium shift between structured states, from helix to coil (locally ordered) forms. VCD is shown to be a useful technique for monitoring local order in otherwise random coil structures.

Infrared and Raman vibrational optical activity: theoretical and experimental aspects

Advances in the field of vibrational optical activity (VOA) are reviewed over the past decade. Topics are surveyed with an emphasis on the theoretical and instrumental progress in both vibrational circular dichroism (VCD) and Raman optical activity (ROA). Applications of VOA to stereochemical and biological problems are reviewed, with a bias toward new kinds of experiments made possible by theoretical and instrumental advances. In the field of VCD, the most notable advances have taken place in the quality and size of ab initio calculations of VOA intensities and in the quality of step-scan Fourier transform instrumentation. For ROA, the most dramatic progress has occurred in the areas of theoretical formulation and high-throughput instrumentation. Applications of VOA now include all major classes of biological and pharmaceutical molecules. VOA's importance as a diagnostic tool will likely grow as the control of molecular chirality increases in research and industrial areas.

Vibrational circular dichroism spectra of proteins in the amide III region: measurement and correlation of bandshape to secondary structure

Vibrational circular dichroism (VCD) spectra have been measured for 23 globular proteins dissolved in H2O/phosphate buffer over the 1400 to 1100 cm(-1) region which encompasses the amide III mode. Spectral responses characteristic of the dominant secondary structure type were found as broad features at approximately 1300 cm(-1), with the extreme forms having positive VCD for highly helical proteins and negative VCD for highly sheet-containing proteins. Quantitative correlation with secondary structure was carried out using previously developed factor analysis and restricted multiple regression (FA/RMR) techniques. Since the absorbance intensity of the amide III mode is difficult to determine due to overlap with other transitions, an alternative, absolute intensity-independent, simple structural analysis method was used. A linear regression was developed between the fractional components of secondary structure for the protein set and the overlap integrals of the normalized spectra from the set with that of a selected protein. The results of this simple method are quite comparable to those of the FA/ RMR approach for analysis with amide III VCD. On the other hand, test calculations with the new method when used with electronic CD spectra are not as good as FA/RMR due to its more intensity-dependent relationship with secondary structure.

Secondary structures comparison of aquaporin-1 and bacteriorhodopsin: a Fourier transform infrared spectroscopy study of two-dimensional membrane crystals

Aquaporins are integral membrane proteins found in diverse animal and plant tissues that mediate the permeability of plasma membranes to water molecules. Projection maps of two-dimensional crystals of aquaporin-1 (AQP1) reconstituted in lipid membranes suggested the presence of six to eight transmembrane helices in the protein. However, data from other sequence and spectroscopic analyses indicate that this protein may adopt a porin-like beta-barrel fold. In this paper, we use Fourier transform infrared spectroscopy to characterize the secondary structure of highly purified native and proteolyzed AQP1 reconstituted in membrane crystalline arrays and compare it to bacteriorhodopsin. For this analysis the fractional secondary structure contents have been determined by using several different algorithms. In addition, a neural network-based evaluation of the Fourier transform infrared spectra in terms of numbers of secondary structure segments and their interconnections [sij] has been performed. The following conclusions were reached: 1) AQP1 is a highly helical protein (42-48% alpha-helix) with little or no beta-sheet content. 2) The alpha-helices have a transmembrane orientation, but are more tilted (21 degrees or 27 degrees, depending on the considered refractive index) than the bacteriorhodopsin helices. 3) The helices in AQP1 undergo limited hydrogen/deuterium exchange and thus are not readily accessible to solvent. Our data support the AQP1 structural model derived from sequence prediction and epitope insertion experiments: AQP1 is a protein with at least six closely associated alpha-helices that span the lipid membrane.