Secondary Structure Of Globular Proteins Research Articles

A simple method for predicting the secondary structure of globular proteins: implications and accuracy.

A method is presented for predicting the secondary structure of globular proteins from their amino acid sequence. It is based on a rigorous statistical exploitation of the well-known biological fact that the amino acid compositions of each secondary structure are different. We also propose an evaluation process that allows us to estimate the capacity of a method to predict the secondary structure of a new protein which does not have any homologous proteins whose structure is already known. This evaluation process shows that our method has a prediction accuracy of 58.7% over three states for the 62 proteins of the Kabsch and Sander (1983a) data bank. This result is better than that obtained by the most widely used methods--Lim (1974), Chou and Fasman (1978) and Garnier et al. (1978)--and also than that obtained by a recent method based on local homologies (Levin et al., 1986). Our prediction method is very simple and may be implemented on any microcomputer and even on programmable pocket calculators. A simple Pascal implementation of the method prediction algorithm is given. The interpretation of our results in terms of protein folding and directions for further work are discussed.

Are secondary structures secondary?

Crystallographically observed secondary structures in globular proteins are divided into two categories based on calculated potential values for these structures. Type I secondary structures are those which have maximum potential in observed structural state. These type I structures consist of those amino acids which intrinsically prefer that structural state. On the other hand type II secondary structures have a calculated potential value which is not maximum for the observed state. Type II structures are composed of those amino acid residues which do not intrinsically prefer the observed state and thus seem to have been formed due to tertiary interactions. All the observed secondary structures have been identified as type I or type II in 31 different globular proteins considered. It is suggested that type II structures are formed at a latter stage of protein folding mainly due to favourable tertiary interactions.

The consistency principle in protein structure and pathways of folding.

It is pointed out that various energy terms contributing to stabilize the native state of globular proteins are consistent in the first approximation with each other in the native state. This means that each energy term is individually minimized at the minimum point of the total energy. I proposed (1) to call this fact "the consistency principle in protein structure." The fair success of various methods of prediction of the secondary structures in globular proteins from their amino acid sequence is often interpreted as indicating the dominance of the short-range interactions in determining the local structures of the polypeptide chains. Partly from such a point of view, the hierarchic condensation model has been popular for the process of protein folding. However the consistency principle indicates that the short-range interactions are just one type of intramolecular interaction which contributes to stabilization of the native structure together with other mutually consistent types of intramolecular interactions. Therefore the hierarchic condensation model is not necessarily a unique model of protein folding. Roles of a possible nonspecific globular state, stabilized by nonspecific long-range intramolecular interactions, in the folding process are discussed. It is expected that this nonspecific globular state is observed either as an equilibrium or a kinetic intermediate state between the unfolded and the folded native states. Observation as a kinetic intermediate state is expected to occur in experiments done under strongly refolding conditions. In this case the polypeptide chain in the unfolded state collapses into a nonspecific globule by the action of nonspecific long-range intramolecular interactions. Two possible mechanisms of the transition from the nonspecific globular state to the specific native folded state are discussed. In an experiment done under weakly refolding conditions, folding is expected to occur according to the embryo-nucleus model. This model is a refined version of the hierarchic condensation model. Refinement is done by taking into account the fact that the intermediate structures assumed in the hierarchic condensation model are unstable against both the native folded state and the unfolded state. A nucleus is an ordered structure of a certain size. Ordered structures of a size larger than a nucleus tend to fold further to become the native specific globule. Ordered structures of a size smaller than a nucleus tend to unfold. Embryos are intrinsically unstable ordered structures smaller than a nucleus. Folding occurs when embryos grow in size to become a nucleus.(ABSTRACT TRUNCATED AT 400 WORDS)

Occurence of a single helix of the collagen type in globular proteins

The occurrence of an eight-residue long segment of polypeptide chain in collagen helical conformation has been detected in bacteriochlorophyll a-protein by the application of an algorithm for identifying secondary structures in globular proteins from their alpha-carbon positions. This segment spans residues 277 to 284 of the protein and is the longest known stretch of collagen helix to be observed in globular proteins.

A study of the occurrence of regulator secondary structures in globular proteins

The distribution of regular secondary structures, viz. α-helices and β-strands, along the length of over 70 properties whose secondary structural details have been reported, has been analysed. The occurrence of these regular structures tends to be a maximum at the N- and C-termini. Our analysis suggests that both these free ends could possibly serve as nucleating centers for secondary structures and could play an important role in the folding of proteins.

Identification of secondary structures in globular proteins--a new algorithm.

A new algorithm has been developed for identifying helices, extended structures, and bends from the positions of the alpha-carbon atoms using the virtual bond approach. The parameters used are two virtual bond angles (delta 1 and delta 2), the virtual dihedral angle (theta), and the distance (D) between the terminal alpha-carbon atoms of the tripeptide. The criteria for classification have been worked out by model building as well as from proteins whose complete secondary structures are known. These criteria are as follows: (i) magnitude of theta less than or equal to 60 degrees and (delta 1 + delta 2) less than or equal to 230 degrees for a bend, (ii) for a helix, successive thetas should not differ by more than 30 degrees, and (iii) for an extended structure, the cumulative deviation of the above parameters should not vary by more than 20% from the ideal extended chain. The method developed has been applied successfully to three proteins wherein the coordinates of alpha-carbon atoms alone are known and a complete mapping of the secondary structures has now been obtained. One interesting observation is that the percentage of residues not taking part in helices, extended structures, and bends is very small--of the order of 4%.

Determination of protein secondary structure in solution by vacuum ultraviolet circular dichroism

A new approach is presented for evaluating the secondary structure of globular proteins in solution by analysis of circular dichroism spectra. Two major improvements are introduced. First, extension of the ultraviolet region down to 165 nm. Extension of the spectral region to the vacuum ultraviolet allows observation of new characteristic bands, which improves substantially the analysis of protein conformation. Secondly, new reference spectra that contain all main protein conformations, including two sets of (β-turns, are taken into account. One set of β-turns representative of all main types of turns, contains the sequences (Ala 2-Gly 2) n, l-Pro- d-Ala, N-acetyl- l-Pro-Gly- l-Leu-OH. A comparison of the results of the analysis with one β-turn and with a set of turns indicates that there is essentially no major improvement; thus one β-turn can be taken as the basis spectrum. In addition, the reference spectra include the β-form represented by polypeptide chains composed of alternating hydrophobic and hydrophilic amino acids, which is more closely related to anti-parallel β-pleated sheet structures in proteins. It appears possible to determine the content of antiparallel and of parallel β-pleated sheets with the present basic β-spectrum. The circular dichroism of aromatic side-chain chromophores was measured in the vacuum ultraviolet in order to take their contribution into account. It appears that for proteins with higher aromatic amino acid content and with weak circular dichroism amide bands, it is necessary to take into account a correction for the aromatic side-chain contribution. The conformation of 13 proteins representative of all main classes of globular proteins was determined from circular dichroism data between 165 nm and 250 nm at 0.2 nm intervals. In particular, the secondary structure of the β-rich class of proteins (concanavalin A, Bence-Jones protein V REI, prealbumin, superoxide dismutase), the α/β class of proteins (lactate dehydrogenase, triose phosphate isomerase, subtilisin, glyceraldehyde-3-phosphate dehydrogenase, flavodoxin and pyruvate kinase) and the (α + β) class of proteins (lysozyme and cytochrome c) were quantitatively characterized in solution. The reliability of the method was also assessed by comparing the data obtained with those available from X-ray crystallography. In general, a good agreement was found between the present circular dichroism data and published X-ray data, except for rubredoxin. By including all types of secondary structure and by enlarging substantially the spectral region, our method permits analysis of the conformation of a variety of proteins, such as nucleic acid-binding proteins, immunoglobulins and β-pleated sheet-rich proteins. It offers new possibilities for investigating the dynamics of protein conformation in solution.

Comparison of protein secondary structure in solution and in crystals

A new approach is presented to estimate secondary structures in globular proteins in solution from vacuum ultraviolet circular dichroism.Two new important Improvements are introduced compared to previous methods. Circular dichroism measurements are extended to vacuum ultraviolet down to 165 nm, the limit imposed by water transmittance. The second improvement concerns the contribution of reverse turns (β-turns) to the secondary structure and the addition of new reference spectra.Estimates of secondary structures from analyses of circular dichroism spectra in solution of the different classes of proteins are in close agreement with X-ray diffraction of the crystals. However for Rubredoxin, a small molecular weight protein (6000 Daltons), a conformational change in secondary structure is found to occur in going from cristalline state to aqueous solution.

Hydrophobic character of amino acid residues in globular proteins.

PREDICTIVE studies on the secondary structure of globular proteins aimed at locating ordered structural segments have provided little information about spatial orientations or even as to whether residues are exposed or buried. However, the physico-chemical properties1 of residues can be used to obtain such information. In particular the hydrophobic character2, is a useful parameter in these studies. The hydrophobic character as defined by the indices given by Tanford3 and Jones4 does not reflect hydrophobic environment within protein structures, but we introduce here a new parameter, the ‘bulk hydrophobic character’ obtained from an analysis of the surrounding hydrophobic environment of amino acid residues in protein crystals. This is a better index of protein hydrophobicity, showing very good correlation with the extent to which residues are buried5 (correlation coefficient r = 0.9) compared with the hydrophobic indices used previously, and it could be used to characterise tertiary structures.

Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins

1. (1) Co-operation between a laboratory interested in developing the theory for protein secondary structure prediction methods and a laboratory interested in applying and comparing such methods has led to the development of a simple predictive algorithm. 2. (2) Four-state predictions, in which each residue is unambiguously assigned one conformational state of α-helix, extended chain, reverse turn or coil, predict 49% of residue states correctly (in a sample of 26 proteins) when the overall helix and extended-chain content is not taken into account. 3. (3) When the relative abundances of helix, extended chain, reverse turn and coil observed by X-ray crystallography are taken into account, a single constant for each protein and type of conformation can be used to bias the prediction. When predictions are optimized in this way, 63% of all residue states are unambiguously and correctly assigned. 4. (4) By analysing the nature of the bias required, proteins can be classified into helix-rich types, pleated-sheet-rich types, and so on. It is shown that, if the type of protein can be determined even approximately by circular dichroism, 57% of residue states can be correctly predicted without taking into account the X-ray structure. Further, comparable predictions can be obtained if, instead of circular dichroism, preliminary predictions are made to assess the protein type. 5. (5) It is emphasized that the numbers quoted here depend on the method used to assess accuracy, and the algorithm is shown to be at least as good as, and usually superior to, the reported prediction methods assessed in the same way. 6. (6) Ways of further enhancing predictions by the use of additional information from hydrophobic triplets and homologous sequences are also explored. Hydro-phobic triplet information does not significantly improve predictive power and it is concluded that this information is used by proteins in the next stage of folding. On the other hand, the use of homologous sequences appears to be very promising. 7. (7) The implication of these results in protein folding is discussed.

Application of the one-dimensional Ising model to the secondary structures in globular proteins. Prediction of beta-regions.

An attempt has been made to predict the beta-regions in 16 globular proteins by applying the one-dimensional Ising model theory of Lifson & Roig (8). The parameters for the theory have been derived from the statistical data on globular proteins given by Chou & Fasman (5). Comparison of our results with the data available from the X-ray crystallographic studies indicates a prediction accuracy which is comparable to those of several other methods, especially in view of the limitations in our method for considering the other secondary structures. It is pointed out that not considering the long-range interactions in our and other methods based on short-range interactions would make these methods incomplete and incapable of being uniformly applicable to all proteins.

A new approach to the calculation of secondary structures of globular proteins by optical rotatory dispersion and circular dichroism

Summary The rotatory contributions can be written as X = ΣfiXi, where the subscripts i = H, β and R represent the fractions of the helix, β-form and unordered form. X can be the bo of the Moffitt equation, [m]233, [θ]222 or other parameters at any chosen wavelength. With fi's from the X-ray diffraction studies, the reference values, X′s, are solved by a least-square method. The helical content of a protein can be determined by: (1) bo = −580fH, (2) [m]233 = −12700fH −2520, and (3) [θ]222 = −30300fH − 2340. The estimation of the β-form is still uncertain.

Effect of the secondary structure of globular proteins in solution on the indicatrix of x-ray diffusion scattering

Effect of the secondary structure of globular proteins in solution on the indicatrix of x-ray diffusion scattering