Triplet information in helix prediction applied to the analysis of super-secondary structures

Secondary structure characterization based on amino acid composition and availability in proteins

The importance of thorough analyses of the secondary structures in proteins as basic structural units cannot be overemphasized. Although recent computational methods have achieved reasonably high accuracy for predicting secondary structures from amino acid sequences, a simple and fundamental empirical approach to characterize the amino acid composition of secondary structures was performed mainly in 1970s, with a small number of analyzed structures. To extend this classical approach using a large number of analyzed structures, here we characterized the amino acid sequences of secondary structures (12 154 alpha-helix units, 4592 3(10)-helix units, 16 787 beta-strand units, and 30 811 "other" units), using the representative three-dimensional protein structure records (1641 protein chains) from the Protein Data Bank. We first examined the length and the amino acid compositions of secondary structures, including rank order differences and assignment relationships among amino acids. These compositional results were largely, but not entirely, consistent with the previous studies. In addition, we examined the frequency of 400 amino acid doublets and 8000 triplets in secondary structures based on their relative counts, termed the availability. We identified not only some triplets that were specific to a certain secondary structure but also so-called zero-count triplets, which did not occur in a given secondary structure at all, even though they were probabilistically predicted to occur several times. Taken together, the present study revealed essential features of secondary structures and suggests potential applications in the secondary structure prediction and the functional design of protein sequences.

Application of expert networks for predicting proteins secondary structure

The present study utilizes expert neural networks for the prediction of proteins secondary structure. We use three independent networks, one for each structure (alpha, beta and coil) as the first-level processing unit; decision upon the chosen structure for each residue is carried out by a second-level, post-processing unit, which utilizes the Chou and Fasman frequency values Falpha and Fbeta in order to strengthen and/or deplete the probability of the specific structure under investigation. The highest prediction case was 76%. Our method requires primitive computational means and a relatively small training set, while still been comparable to previous work. It is not meant to be an alternative to the determination of secondary structure by means of free energy minimization, integration of dynamic equations of motion or crystallography, which are expensive, time-consuming and complicated, but to provide additional constrains, which might be considered and incorporated into larger computing setups in order to reduce the initial search space for the above methods.

A graphic approach to evaluate algorithms of secondary structure prediction

Algorithms of secondary structure prediction have undergone the developments of nearly 30 years. However, the problem of how to appropriately evaluate and compare algorithms has not yet completely solved. A graphic method to evaluate algorithms of secondary structure prediction has been proposed here. Traditionally, the performance of an algorithm is evaluated by a number, i.e., accuracy of various definitions. Instead of a number, we use a graph to completely evaluate an algorithm, in which the mapping points are distributed in a three-dimensional space. Each point represents the predictive result of the secondary structure of a protein. Because the distribution of mapping points in the 3D space generally contains more information than a number or a set of numbers, it is expected that algorithms may be evaluated and compared by the proposed graphic method more objectively. Based on the point distribution, six evaluation parameters are proposed, which describe the overall performance of the algorithm evaluated. Furthermore, the graphic method is simple and intuitive. As an example of application, two advanced algorithms, i.e., the PHD and NNpredict methods, are evaluated and compared. It is shown that there is still much room for further improvement for both algorithms. It is pointed out that the accuracy for predicting either the alpha-helix or beta-strand in proteins with higher alpha-helix or beta-strand content, respectively, should be greatly improved for both algorithms.

Generation of deviation parameters for amino acid singlets, doublets and triplets from three-dimentional structures of proteins and its implications for secondary structure prediction from amino acid sequences

We present a new method, secondary structure prediction by deviation parameter (SSPDP) for predicting the secondary structure of proteins from amino acid sequence. Deviation parameters (DP) for amino acid singlets, doublets and triplets were computed with respect to secondary structural elements of proteins based on the dictionary of secondary structure prediction (DSSP)-generated secondary structure for 408 selected non-homologous proteins. To the amino acid triplets which are not found in the selected dataset, a DP value of zero is assigned with respect to the secondary structural elements of proteins. The total number of parameters generated is 15,432, in the possible parameters of 25,260. Deviation parameter is complete with respect to amino acid singlets, doublets, and partially complete with respect to amino acid triplets. These generated parameters were used to predict secondary structural elements from amino acid sequence. The secondary structure predicted by our method (SSPDP) was compared with that of single sequence (NNPREDICT) and multiple sequence (PHD) methods. The average value of the percentage of prediction accuracy for a helix by SSPDP, NNPREDICT and PHD methods was found to be 57%, 44% and 69% respectively for the proteins in the selected dataset. For b-strand the prediction accuracy is found to be 69%, 21% and 53% respectively by SSPDP, NNPREDICT and PHD methods. This clearly indicates that the secondary structure prediction by our method is as good as PHD method but much better than NNPREDICT method.

What is the minimum number of residues to determine the secondary structural state?

The failure of protein secondary structural prediction is commonly attributed to the neglect of long-range interactions. The question is, what is the minimum length of subsequence required to determine the central secondary structural state, stabilized only by local interactions? In the present work, the 20 amino acids were classified into eight groups to analyze systematically the relationship between the length and secondary structural state of subsequences in the PDB database. It was found that the fraction of subsequences with a unique central secondary structural state increases with increasing length, and the minimum length of subsequence required to determine the central secondary structural state is about 14-17 residues. The low accuracy of secondary structure prediction does not result from the neglect of long-range interactions, but may result from the limitation of the available protein database size or prediction algorithm.

Is beta-pleated sheet the molecular conformation which dictates formation of helicoidal cuticle?

Over 100 sequences for cuticular proteins are now available, but there have been no formal analyses of how these sequences might contribute to the helicoidal architecture of cuticle or to the interaction of these proteins with chitin. A secondary structure prediction scheme (Hamodrakas, S.J., 1988. A protein secondary structure prediction scheme for the IBM PC and compatibles. CABIOS 4, 473-477) that combines six different algorithms predicting alpha-helix, beta-strands and beta-turn/loops/coil has been used to predict the secondary structure of chorion proteins and experimental confirmation has established its utility (Hamodrakas, S.J., 1992. Molecular architecture of helicoidal proteinaceous eggshells. In: Case, S.T. (Ed.), Results and Problems in Cell Differentiation, Vol. 19, Berlin-Heidelberg, Springer Verlag, pp. 116-186 and references therein). We have used this same scheme with eight cuticular protein sequences associated with hard cuticles and nineteen from soft cuticles. Secondary structure predictions were restricted to a conserved 68 amino acid region that begins with a preponderance of hydrophilic residues and ends with a 33 amino acid consensus region, first identified by Rebers and Riddiford (Rebers, J.F., Riddiford, L.M., 1988. Structure and expression of a Manduca sexta larval cuticle gene homologous to Drosophila cuticle genes. J. Mol. Biol. 203, 411-423). Both classes of sequences showed a preponderance of beta-pleated sheet, with four distinct strands in the proteins from 'hard' cuticles and three from 'soft'. In both cases, tyrosine and phenylalanine were found on one face within a sheet, an optimal location for interaction with chitin. We propose that this beta-sheet dictates formation of helicoidal cuticle.

Improvement of protein secondary structure prediction using binary word encoding

We propose a binary word encoding to improve the protein secondary structure prediction. A binary word encoding encodes a local amino acid sequence to a binary word, which consists of 0 or 1. We use an encoding function to map an amino acid to 0 or 1. Using the binary word encoding, we can statistically extract the multiresidue information, which depends on more than one residue. We combine the binary word encoding with the GOR method, its modified version, which shows better accuracy, and the neural network method. The binary word encoding improves the accuracy of GOR by 2.8%. We obtain similar improvement when we combine this with the modified GOR method and the neural network method. When we use multiple sequence alignment data, the binary word encoding similarly improves the accuracy. The accuracy of our best combined method is 68.2%. In this paper, we only show improvement of the GOR and neural network method, we cannot say that the encoding improves the other methods. But the improvement by the encoding suggests that the multiresidue interaction affects the formation of secondary structure. In addition, we find that the optimal encoding function obtained by the simulated annealing method relates to nonpolarity. This means that nonpolarity is important to the multiresidue interaction.

Prediction of protein secondary structures from their hydrophobic characteristics

Deciphering the native conformation of proteins from their amino acid sequences is one of the greatest challenges in the field of molecular biology. The successful prediction of structural class may help to improve the accuracy levels of structure (secondary and tertiary) predictive schemes in globular proteins. In our earlier works we developed a new surrounding hydrophobicity scale for the 20 amino acid residues applicable for both globular and membrane proteins and used it successfully to predict the transmembrane helical and strand segments in membrane proteins. In this article we propose (i) rules to predict the structural class of proteins and (ii) a new predictive scheme for forecasting secondary structures of globular proteins, with the use of the new hydrophobicity scale. This scheme predicts the structural class and secondary structures of globular proteins to 92 and 82% levels of accuracy, respectively, far better than the levels from other existing methods.

De novo design and creation of a stable artificial protein

Protein de novo design has been performed, as an exercise of the inverse folding problem. A beta/alpha-barrel protein was designed and synthesized using the Escherichia coli expression system for the structural characterization. A tertiary model with a two-fold symmetry was built, based upon the geometrical parameters extracted from X-ray crystal structures of several beta/alpha-barrel proteins. Amino acid frequencies at each position on the alpha- and beta-structures were investigated, and an amino acid sequence with 201 residues was designed. The associated gene was chemically synthesized and the fusion protein with human growth hormone was expressed in Escherichia coli. The purified protein after being cleaved and refolded was found to be stable and globular with the large amount of secondary structures. However, it has similar characteristics to the molten globules of natural proteins, with loose packing of side-chains. The approach for the tight packing is discussed.

Redefining the goals of protein secondary structure prediction

Secondary structure prediction recently has surpassed the 70% level of average accuracy, evaluated on the single residue states helix, strand and loop (Q3). But the ultimate goal is reliable prediction of tertiary (three-dimensional, 3D) structure, not 100% single residue accuracy for secondary structure. A comparison of pairs of structurally homologous proteins with divergent sequences reveals that considerable variation in the position and length of secondary structure segments can be accommodated within the same 3D fold. It is therefore sufficient to predict the approximate location of helix, strand, turn and loop segments, provided they are compatible with the formation of 3D structure. Accordingly, we define here a measure of segment overlap (Sov) that is somewhat insensitive to small variations in secondary structure assignments. The new segment overlap measure ranges from an ignorance level of 37% (random protein pairs) via a current level of 72% for a prediction method based on sequence profile input to neural networks (PHD) to an average 90% level for homologous protein pairs. We conclude that the highest scores one can reasonably expect for secondary structure prediction are a single residue accuracy of Q3 > 85% and a fractional segment overlap of Sov > 90%.

The amino acid sequence of a protein from wheat kernel closely related to proteins involved in the mechanisms of plant defence

The amino acid sequence of wheatwin1, a monomeric protein of 125 residues isolated from wheat kernel (variety S. Pastore), is reported. Wheatwin1 is highly homologous (95%) to barwin, a protein from barley seed, which was shown to be related to the C-terminal domain of two proteins encoded by the wound-induced genes win1 and win2 in potato and to a protein encoded by the same domain of the hevein gene (hev1) in rubber tree. Similarly to barwin, wheatwin1 contains six cysteine residues all linked in disulfide bridges and the N-terminal residue is pyroglutamate. Moreover, structural studies performed on wheatwin1 and win1 protein by predictive methods demonstrated that these proteins and barwin are closely related in the secondary structure also. The high level of homology found with the product of win1, win2, and hev1 genes strongly suggests that barwin and wheatwin1 play a common role in the mechanism of plant defence.

Protein fold recognition

An important, yet seemingly unattainable, goal in structural molecular biology is to be able to predict the native three-dimensional structure of a protein entirely from its amino acid sequence. Prediction methods based on rigorous energy calculations have not yet been successful, and best results have been obtained from homology modelling and statistical secondary structure prediction. Homology modelling is limited to cases where significant sequence similarity is shared between a protein of known structure and the unknown. Secondary structure prediction methods are not only unreliable, but also do not offer any obvious route to the full tertiary structure. Recently, methods have been developed whereby entire protein folds are recognized from sequence, even where little or no sequence similarity is shared between the proteins under consideration. In this paper we review the current methods, including our own, and in particular offer a historical background to their development. In addition, we also discuss the future of these methods and outline the developments under investigation in our laboratory.

Use of conditional probabilities for determining relationships between amino acid sequence and protein secondary structure

The conditional probability, P(sigma/x), is a statement of the probability that the value of sigma will be found given the prior information that a value of x has been observed. Here sigma represents any one of the secondary structure types, alpha, beta, tau, and rho for helix, sheet, turn, and random, respectively, and x represents a sequence attribute, including, but not limited to: (1) hydropathy; (2) hydrophobic moments assuming helix and sheet; (3) Richardson and Richardson helical N-cap and C-cap values; (4) Chou-Fasman conformational parameters for helix, P alpha, for sheet, P beta, and for turn, P tau; and (5) Garnier, Osguthorpe, and Robson (GOR) information values for helix, I alpha, for sheet, I beta, for turn, I tau, and for random structure, I rho. Plots of P(sigma/x) vs. x are demonstrated to provide information about the correlation between structure and attribute, sigma and x. The separations between different P(sigma/x) vs. x curves indicate the capacity of a given attribute to discriminate between different secondary structural types and permit comparison of different attributes. P(alpha/x), P(beta/x), P(tau/x) and P(rho/x) vs. x plots show that the most useful attributes for discriminating helix are, in order: hydrophobic moment assuming helix greater than P alpha much greater than N-cap greater than C-cap approximately I alpha approximately I tau. The information value for turns, I tau, was found to discriminate helix better than turns. Discrimination for sheet was found to be in the following order: I beta much greater than P beta approximately hydropathy greater than I rho approximately hydrophobic moment assuming sheet. Three attributes, at their low values, were found to give significant discrimination for the absence of helix: I alpha approximately P alpha approximately hydrophobic moment assuming helix. Also, three other attributes were found to indicate the absence of sheet: P beta much greater than I rho approximately hydropathy. Indications of the absence of sigma could be as useful for some applications as the indication of the presence of sigma.

Characteristics of the principal neutralizing determinant of HIV-1 prevalent in Japan

The principal neutralizing determinants (PNDs) of 29 human immunodeficiency virus type 1 (HIV-1) isolates in Japan were analyzed using polymerase chain reactions. The viruses were isolated from 16 hemophiliacs, 11 individuals infected by their sexual transmission and 1 patient infected by blood transfusion (total 28 patients). Two virus isolates which were obtained from the same individual at different periods were also analyzed. All individuals were Japanese except one. The results produced 32 different PND sequences. A highly conserved central core sequence (GPG) was present in 27 of 32 patients, similar to the number reported in the United States, despite the marked heterogeneity in flanking regions of PNDs. The PNDs of all the 16 HIV-1 isolates obtained from patients with coagulation disorders had GPG sequences. Secondary structure prediction of PNDs by a joint method suggested that they were composed of coil-beta strand-coil-beta strand-alpha helix. It is suggested that the conserved core sequence has a type I turn. These findings may be useful in planning further clinical trials for passive vaccination.

Three trans-acting regulatory functions control hydrogenase synthesis in Alcaligenes eutrophus

Random Tn5 mutagenesis of the regulatory region of megaplasmid pHG1 of Alcaligenes eutrophus led to the identification of three distinct loci designated hoxA, hoxD, and hoxE. Sequencing of the hoxA locus revealed an open reading frame which could code for a polypeptide of 482 amino acids with a molecular mass of 53.5 kDa. A protein of comparable apparent molecular mass was detected in heterologous expression studies with a plasmid-borne copy of the hoxA gene. Amino acid alignments revealed striking homologies between HoxA and the transcriptional activators NifA and NtrC of Klebsiella pneumoniae and HydG of Escherichia coli. HoxA- mutants of A. eutrophus lacked both NAD-reducing soluble hydrogenase and membrane-bound hydrogenase. In HoxA- mutants, the synthesis of beta-galactosidase from a hoxS'-'lacZ operon fusion was drastically reduced, indicating that HoxA is essential for the transcription of hydrogenase genes. Mutants defective in hoxD and hoxE also lacked the catalytic activities of the two hydrogenases; however, in contrast to HoxA- mutants, they contained immunologically detectable NAD-reducing soluble hydrogenase and membrane-bound hydrogenase proteins, although at a reduced level. The low hydrogenase content in the HoxD- and HoxE- mutants correlated with a decrease in beta-galactosidase synthesized under the direction of a hoxS'-'lacZ operon fusion. Thus, hoxD and hoxE apparently intervene both in the regulation of hydrogenase synthesis and in subsequent steps leading to the formation of catalytically active enzymes.

Chloroplast transit peptides. The perfect random coil?

Structural analysis of chloroplast transit peptides (cTPs), including secondary structure prediction and analysis of 'cTP-like' peptides of known 3D structure, suggests that cTPs are essentially flexible peptides devoid of regular secondary or tertiary structure. It is proposed that cTPs may be designed to interact with a succession of different chaperones on the chloroplast protein-import pathway.

Secondary structure of human interleukin-3

1. The secondary structure of human interleuken-3 in solution was determined by circular dichroism spectroscopy. 2. The results were then compared with empirical secondary structure predictions based on primary sequence structure of the protein. 3. The two approaches are in extremently close agreement showing the protein to have 40% alpha-helix, 12% total beta-structure and 48% random coil content.

Sequence similarity between protein B and human apolipoprotein A-IV

Sequence comparison of protein B (CAMP-factor) with human apolipoprotein A-IV (apo A-IV) revealed 32% similarity between the N-terminal part of protein B and a part of the putative lipid-binding domain of apo A-IV. The significance of this similarity is discussed with respect to the structure/function relationship of protein B.

Secondary structure predictions for rat osteopontin

Five computerized methods were used to predict the secondary structure of osteopontin - a bone-derived cell attachment protein. The amino terminal one-fifth and the carboxy terminal one-third of the 301 amino acid protein contain eight alpha helices (41% of the total residues). The middle of the molecule contains a very acidic region of no predicted structure followed by two segments of beta structure which flank the cell attachment site of osteopontin. Examination of the amino acid sequence also revealed a potential calcium binding loop and two potential heparin binding sites.

Protein secondary structure prediction with a neural network

A method is presented for protein secondary structure prediction based on a neural network. A training phase was used to teach the network to recognize the relation between secondary structure and amino acid sequences on a sample set of 48 proteins of known structure. On a separate test set of 14 proteins of known structure, the method achieved a maximum overall predictive accuracy of 63% for three states: helix, sheet, and coil. A numerical measure of helix and sheet tendency for each residue was obtained from the calculations. When predictions were filtered to include only the strongest 31% of predictions, the predictive accuracy rose to 79%.

Prediction of three-dimensional structure of Escherichia coli ribosomal RNA

A model for the tertiary structure of 23S, 16S and 5S ribosomal RNA molecules interacting with three tRNA molecules is presented using the secondary structure models common to E. coli, Z. mays chloroplast, and mammalian mitochondria. This ribosomal RNA model is represented by phosphorus atoms which are separated by 5.9 A in the standard A-form double helix conformation. The accumulated proximity data summarized in Table 1 were used to deduce the most reasonable assembly of helices separated from each other by at least 6.2 A. Straight-line approximation for single strands was adopted to describe the maximum allowed distance between helices. The model of a ribosome binding three tRNA molecules by Nierhaus (1984), the stereochemical model of codon-anticodon interaction by Sundaralingam et al. (1975) and the ribosomal transpeptidation model, forming an alpha-helical nascent polypeptide, by Lim & Spirin (1986), were incorporated in this model. The distribution of chemically modified nucleotides, cross-linked sites, invariant and missing regions in mammalian mitochondrial rRNAs are indicated on the model.

Cloning of a full-length complementary DNA for fatty-acid-binding protein from bovine heart

A full-length cDNA for bovine heart fatty-acid-binding protein (H-FABP) was cloned from a lambda gt11 cDNA library established from bovine heart muscle. The cDNA sequence shows an open reading frame coding for a protein with 133 amino acids. Colinearity with the amino acid sequences of four tryptic peptides was asserted. H-FABP isolated from bovine heart begins with an N-acetylated valine residue, however, as derived from analysis of the tryptic, amino-terminal-blocked peptide and the molecular mass of the peptide obtained via secondary-ion mass spectrometry. The molecular mass of the total protein is 14673 Da. Bovine H-FABP is 89% homologous to rat H-FABP and 97% homologous to the bovine mammary-derived growth-inhibition factor described recently by Böhmer et al. [J. Biol. Chem. 262, 15137-15143 (1987)]. Significant homologies were also found with bovine myelin protein P2 and murine adipocyte protein p422. Secondary-structure predictions were proposed for these proteins, based on computer analysis, which reveal striking similarities.

Isolation, characterization and microsequence analysis of a small basic methylated DNA-binding protein from the Archaebacterium, Sulfolobus solfataricus

DNA-binding proteins have been extracted from the thermoacidophilic archaebacterium Sulfolobus solfataricus strain P1, grown at 86 degrees C and pH 4.5. These proteins, which may have a histone-like function, were isolated and purified under standard, non-denaturing conditions, and can be grouped into three molecular mass classes of 7, 8 and 10 kDa. We have purified to homogenity the main 7 kDa protein and determined its DNA-binding affinity by filter binding assays and electron microscopy. The Stokes radius of gyration indicates that the protein occurs as a monomer. The complete amino-acid sequence of this protein contains 14 lysine residues out of 63 amino acids and the calculated Mr is 7149. Five of the lysine residues are partially monomethylated to varying extents and the methylated residues are located exclusively in the N-terminal (positions 4 and 6) and the C-terminal (positions 60, 62 and 63) regions only. The protein is strongly homologous to the 7 kDa proteins of Sulfolobus acidocaldarius with the highest homology to protein 7d. Accordingly, the name of this protein from S. solfataricus was assigned as DNA-binding protein Sso7d.

Secondary structure and thermostability of the phage P22 tailspike. XX. Analysis by Raman spectroscopy of the wild-type protein and a temperature-sensitive folding mutant

The thermostable tailspike endorhamnosidase of bacteriophage P22 has been investigated by laser Raman spectroscopy to determine the protein's secondary structure and the basis of its thermostability. The conformation of the native tailspike, determined by Raman amide I and amide III band analyses, is 52 to 61% beta-sheet, 24 to 27% alpha-helix, 15 to 21% beta-turn and 0 to 10% other structure types. The secondary structure of the wild-type tailspike, as monitored by the conformation-sensitive Raman amide bands, was stable to 80 degrees C, denatured reversibly between 80 and 90 degrees C, and irreversibly above 90 degrees C. The purified native form of a temperature-sensitive folding mutant (tsU38) contains secondary structures virtually identical to those in the wild-type in aqueous solution at physiological conditions (0.05 M-Na+ (pH 7.5], at both permissive (20 degrees C) and restrictive (40 degrees C) temperatures. This supports previous results showing that the mutational defect at 40 degrees C affects intermediates in the folding pathway rather than the native structure. At temperatures above 60 degrees C the wild-type and mutant forms were distinguishable: the reversible and irreversible denaturation thresholds were approximately 15 to 20 degrees C lower in the mutant than in the wild-type protein. The irreversible denaturation of the mutant tailspikes led to different aggregation/polymerization products from the wild-type, indicating that the mutation altered the unfolding pathway. In both cases only a small percentage of the native secondary structure was altered by irreversible thermal denaturation, indicating that the aggregated states retain considerable native structure.

Further developments of protein secondary structure prediction using information theory. New parameters and consideration of residue pairs

We have re-evaluated the information used in the Garnier-Osguthorpe-Robson (GOR) method of secondary structure prediction with the currently available database. The framework of information theory provides a means to formulate the influence of local sequence upon the conformation of a given residue, in a rigorous manner. However, the existing database does not allow the evaluation of parameters required for an exact treatment of the problem. The validity of the approximations drawn from the theory is examined. It is shown that the first-level approximation, involving single-residue parameters, is only marginally improved by an increase in the database. The second-level approximation, involving pairs of residues, provides a better model. However, in this case the database is not big enough and this method might lead to parameters with deficiencies. Attention is therefore given to overcoming this lack of data. We have determined the significant pairs and the number of dummy observations necessary to obtain the best result for the prediction. This new version of the GOR method increases the accuracy of prediction by 7%, bringing the amount of residues correctly predicted to 63% for three states and 68 proteins, each protein to be predicted being removed from the database and the parameters derived from the other proteins. If the protein to be predicted is kept in the database the accuracy goes up to 69.7%.

Relationship between hydropathic variability and functional properties of alpha-lactalbumins and type c lysozymes

Hydropathic profiles obtained from the amino acid sequences of 8 alpha-lactalbumins were averaged and compared to the average profile deduced from the primary structure of 21 type c lysozymes. This analysis was performed in order to detect differences between both types of molecules, since it could explain their different functional properties. The application of the method herein described reveals the existence of very significative differences (P less than 0.001) between the amino acid residues located at positions 31-32, 34-35, 37-45, 47-48, 80-85 and 108-113 of alpha-lactalbumins and their homologous in type c lysozymes. These differences are in agreement with the chemical data about the interaction sites of both galactosyltransferase and calcium ions with alpha-lactalbumin, which are not required for the lysozyme function.

T4-induced alpha- and beta-glucosyltransferase: cloning of the genes and a comparison of their products based on sequencing data

Bacteriophage T4 alpha- and beta-glucosyltransferases link glucosyl units to the 5-HMdC residues of its DNA. The monoglucosyl group in alpha-linkage predominates over the one in beta linkage. Having recently reported on the nucleotide sequence of gene alpha gt (1) we now determined the nucleotide sequence of gene beta gt. The genes were each cloned on a high expression vector under the control of the lambda pL promoter. After thermo-induction the proteins were isolated and purified to homogeneity. To verify that the translational starting sites and the proposed reading frames are effective in vivo the sequence of the first 31 amino acid residues from gp alpha gt and the first 30 amino acid residues from gp beta gt were determined by Edman degradation. The primary structures of the two proteins seem to have only limited structural similarities. The results are discussed comparing secondary structure predictions and homologies with other proteins from the protein sequence database of the Protein Identification Resource.

Plant peroxidases. Their primary, secondary and tertiary structures, and relation to cytochrome c peroxidase

The amino acid sequences of the 51% different horseradish peroxidase HRP C and turnip peroxidase TP 7 have previously been completed by us, but the three-dimensional structures are unknown. Recently the amino acid sequence and the crystal structure of yeast cytochrome c peroxidase have appeared. The three known apoperoxidases consist of 300 +/- 8 amino acid residues. The sequences have now been aligned and show 18% and 16% identity only, between the yeast peroxidase and plant peroxidase HRP C and TP 7, respectively. We show that different structural tests all support similar protein folds in plant peroxidases and yeast peroxidase and, therefore, a common evolutionary origin. The following tests support this thesis: (a) predicted helices in the plant peroxidases follow the complex pattern observed in the crystal structure of cytochrome c peroxidase; (b) their hydropathic profiles are similar and agree with observed buried and exposed peptide chain in cytochrome c peroxidase; (c) half-cystines which are distant in the amino acid sequence of plant peroxidases become spatial neighbours when fitted into the cytochrome c peroxidase model; (d) the two-domain structure proposed from limited proteolysis of apoperoxidase HRP C is observed in the crystal structure of cytochrome c peroxidase. The similarities and differences of the plant and yeast peroxidases and the reactive side chains of a plant peroxidase active site are described. The characteristics of Ca2+-binding sequences, derived from several superfamilies, are applied to predict the Ca2+-binding sequences in plant peroxidases.

The complete primary structure of ribosomal proteins L1, L14, L15, L23, L24 and L29 from Bacillus stearothermophilus

The amino acid sequences of ribosomal proteins L1, L14, L15, L23, L24 and L29 from Bacillus stearothermophilus have been completely determined. This has been achieved by sequence analyses of peptides derived from enzymatic digestions of the proteins with trypsin, chymotrypsin, pepsin, Staphylococcus aureus protease, and Armillaria mellea protease as well as by chemical cleavage with hydroxylamine and cyanogen bromide. Based on the primary structures of the six proteins, their secondary structures were predicted using four different computer prediction programs. A comparison of the amino acid sequences of the studied proteins from B. stearothermophilus with the homologous proteins from Escherichia coli revealed that in four proteins (L1, L15, L24 and L29) between 40-50% of the residue in the sequences are identical, whereas this value is significantly higher (69%) for L14 and lower (28%) for L23. The distribution of those amino acid residues which are identical in the corresponding proteins from the two bacteria is not random along the protein chain: some regions are highly conserved whereas others are not. This finding indicates that the regions which are conserved during evolution are important for the spatial structure and/or function of the protein.

Colicin E3 and its immunity genes

A DNA segment of plasmid ColE3-CA38 was cloned into pBR328 and its nucleotide sequence was determined. This segment contains the putative promoter-operator region, the structural genes of protein A (gene A) and protein B (gene B) of colicin E3, and a part of gene H. Just behind the promoter region, there is an inverted repeat structure of two 'SOS boxes', the specific binding site of the lexA protein. This suggests that the expression of colicin E3 is regulated directly by the lexA protein. Genes A and B face the same direction, with an intergenic space of nine nucleotides between them. ColE3-CA38 and ColE1-K30 are homologous in their promoter-operator regions, but hardly any homology was found in their structural genes. On the other hand, ColE3-CA38 is fairly homologous to CloDF13 throughout the regions sequenced, with some exceptions including putative receptor-binding regions. By deletion mapping of the immunity gene and recloning of gene B, it was shown genetically that protein B itself is the actual immunity substance of colicin E3. It was also found that the expression of E3 immunity partially depends on the recA function. Thus, we propose two modes of expression of E3 immunity: in the uninduced state, only a slight amount of protein B is produced constitutively to protect the cell from being attacked by the exogenous colicin; and in the SOS-induced state, a large amount of protein B is produced to protect the protein synthesis system of the host cell from ribosome inactivation by endogenously produced colicin E3.

Structural implications of primary sequences from a family of Balbiani ring-encoded proteins in Chironomus

DNA sequencing has revealed an internal, tandemly repetitive structure in the family of giant polypeptides encoded by three types of Balbiani ring (BR) genes, in three different species of Chironomus. Each major BR repeat can be subdivided into two halves: a region consisting of short subrepeats and a more constant region that lacks obvious subrepeats. Comparative predictions of secondary structure indicate that an alpha-helical segment is consistently present in the amino-terminal half of the constant region in all known BR proteins. Comparative predictions, coupled with consideration of the known phosphorylation of serine and threonine residues in BR proteins, suggest that the alpha-helical structure may also extend into the carboxy-terminal half of the constant region, possibly interrupted by beta-turn(s). However, it is also possible that the structure is variable, and that a beta-strand is present in that half in some cases. All of the constant regions conserve one methionine and one phenylalanine residue, as well as all four cysteines; these residues presumably play roles in the packing or cross-linking of aligned constant regions. The structure of the subrepeat region is not clear, but the prevalence of a tripeptide pattern (basic-proline-acidic) suggests some type of structural regularity, possibly an extended helix. The possible significance of these conserved molecular features is discussed in the context of how they may serve the elasticity, insolubility, and hydrophilicity of the fibrils and threads formed by the BR polypeptides.

The complete amino acid sequences of ribosomal proteins L17, L27, and S9 from Bacillus stearothermophilus

The complete primary structures of proteins L17, L27 and S9 extracted from the Bacillus stearothermophilus ribosomes with 1 M NaCl and purified to homogeneity by column chromatography have been determined. The amino acid sequences of these proteins are compared to those of the homologous ribosomal proteins from Escherichia coli. The number of identical amino acid residues between the homologous proteins lies between 33-55%.

Cystatin. Amino acid sequence and possible secondary structure

The amino acid sequence of cystatin, the protein from chicken egg-white that is a tight-binding inhibitor of many cysteine proteinases, is reported. Cystatin is composed of 116 amino acid residues, and the Mr is calculated to be 13 143. No striking similarity to any other known sequence has been detected. The results of computer analysis of the sequence and c.d. spectrometry indicate that the secondary structure includes relatively little alpha-helix (about 20%) and that the remainder is mainly beta-structure.