Detection of unrelated proteins in sequences multiple alignments by using predicted secondary structures

MOTIVATION: Multiple sequence alignments are essential tools for establishing the homology relations between proteins. Essential amino acids for the function and/or the structure are generally conserved, thus providing key arguments to help in protein characterization. However for distant proteins, it is more difficult to establish, in a reliable way, the homology relations that may exist between them. In this article, we show that secondary structure prediction is a valuable way to validate protein families at low identity rate. RESULTS: We show that the analysis of the secondary structures compatibility is a reliable way to discard non-related proteins in low identity multiple alignment. AVAILABILITY: This validation is possible through our NPS@ server (http://npsa-pbil.ibcp.fr)     

Dihedral angle and secondary structure database of short amino acid fragments

Dihedral angles of amino acids are of considerable importance in protein tertiary structure prediction as they define the backbone of a protein and hence almost define the protein's entire conformation. Most ab initio protein structure prediction methods predict the secondary structure of a protein before predicting the tertiary structure because three-dimensional fold consists of repeating units of secondary structures. Hence, both dihedral angles and secondary structures are important in tertiary structure prediction of proteins. Here we describe a database called DASSD (Dihedral Angle and Secondary Structure Database of Short Amino acid Fragments) that contains dihedral angle values and secondary structure details of short amino acid fragments of lengths 1, 3 and 5. Information stored in this database was extracted from a set of 5,227 non-redundant high resolution (less than 2-angstroms) protein structures. In total, DASSD stores details for about 733,000 fragments. This database finds application in the development of ab initio protein structure prediction methods using fragment libraries and fragment assembly techniques. It is also useful in protein secondary structure prediction.

Availability     

Prediction of the occurrence of the ADP-binding beta alpha beta-fold in proteins, using an amino acid sequence fingerprint

An amino acid sequence "fingerprint" has been derived that can be used to test if a particular sequence will fold into a beta alpha beta-unit with ADP-binding properties. It was deduced from a careful analysis of the known three-dimensional structures of ADP-binding beta alpha beta-folds. This fingerprint is in fact a set of 11 rules describing the type of amino acid that should occur at a specific position in a peptide fragment. The total length of this fingerprint varies between 29 and 31 residues. By checking against all possible sequences in a database, it appeared that every peptide, which exactly follows this fingerprint, does indeed fold into an ADP-binding beta alpha beta-unit.     

The amino acid sequence of human chorionic gonadotropin. The alpha subunit and beta subunit.

The amino acid sequences of both the alpha and beta subunits of human chorionic gonadotropin have been determined. The amino acid sequence of the alpha subunit is: Ala - Asp - Val - Gln - Asp - Cys - Pro - Glu - Cys-10 - Thr - Leu - Gln - Asp - Pro - Phe - Ser - Gln-20 - Pro - Gly - Ala - Pro - Ile - Leu - Gln - Cys - Met - Gly-30 - Cys - Cys - Phe - Ser - Arg - Ala - Tyr - Pro - Thr - Pro-40 - Leu - Arg - Ser - Lys - Lys - Thr - Met - Leu - Val - Gln-50 - Lys - Asn - Val - Thr - Ser - Glu - Ser - Thr - Cys - Cys-60 - Val - Ala - Lys - Ser - Thr - Asn - Arg - Val - Thr - Val-70 - Met - Gly - Gly - Phe - Lys - Val - Glu - Asn - His - Thr-80 - Ala - Cys - His - Cys - Ser - Thr - Cys - Tyr - Tyr - His-90 - Lys - Ser. Oligosaccharide side chains are attached at residues 52 and 78. In the preparations studied approximately 10 and 30% of the chains lack the initial 2 and 3 NH2-terminal residues, respectively. This sequence is almost identical with that of human luteinizing hormone (Sairam, M. R., Papkoff, H., and Li, C. H. (1972) Biochem. Biophys. Res. Commun. 48, 530-537). The amino acid sequence of the beta subunit is: Ser - Lys - Glu - Pro - Leu - Arg - Pro - Arg - Cys - Arg-10 - Pro - Ile - Asn - Ala - Thr - Leu - Ala - Val - Glu - Lys-20 - Glu - Gly - Cys - Pro - Val - Cys - Ile - Thr - Val - Asn-30 - Thr - Thr - Ile - Cys - Ala - Gly - Tyr - Cys - Pro - Thr-40 - Met - Thr - Arg - Val - Leu - Gln - Gly - Val - Leu - Pro-50 - Ala - Leu - Pro - Gin - Val - Val - Cys - Asn - Tyr - Arg-60 - Asp - Val - Arg - Phe - Glu - Ser - Ile - Arg - Leu - Pro-70 - Gly - Cys - Pro - Arg - Gly - Val - Asn - Pro - Val - Val-80 - Ser - Tyr - Ala - Val - Ala - Leu - Ser - Cys - Gln - Cys-90 - Ala - Leu - Cys - Arg - Arg - Ser - Thr - Thr - Asp - Cys-100 - Gly - Gly - Pro - Lys - Asp - His - Pro - Leu - Thr - Cys-110 - Asp - Asp - Pro - Arg - Phe - Gln - Asp - Ser - Ser - Ser - Ser - Lys - Ala - Pro - Pro - Pro - Ser - Leu - Pro - Ser-130 - Pro - Ser - Arg - Leu - Pro - Gly - Pro - Ser - Asp - Thr-140 - Pro - Ile - Leu - Pro - Gln. Oligosaccharide side chains are found at residues 13, 30, 121, 127, 132, and 138. The proteolytic enzyme, thrombin, which appears to cleave a limited number of arginyl bonds, proved helpful in the determination of the beta sequence.     

Critical amino acid residues of the alpha4 subunit for alpha4beta7 integrin function

A characteristic feature of integrin-ligand interactions is the requirement for divalent cations. Putative cation binding sites have been identified in the alpha and beta subunit of the alpha4 integrins, alpha4beta1 and alpha4beta7, and within their ligands which display the tripeptide LDV in fibronectin and homologous motifs in VCAM-1 and MAdCAM-1. The extracellular domain of the murine and human alpha4-subunit contains three conserved LDV motifs, designated LDV-1 to -3. Using site directed mutagenesis and transfection studies, we now examined the functional relevance of the LDV motifs for alpha4beta7 integrins. We present evidence that LDV-1 mutants (D489N) behave like alpha4 wt cells, but LDV-3 mutants (D811N) are impaired in alpha4beta7 integrin-triggered homotypic cell aggregation and in adhesion and spreading on alpha4 specific ligands. Further characterization of LDV-3 mutants revealed a defect in mAb-induced alpha4beta7-cell surface cluster formation. Mutation of the LDV-2 motif (D698N) caused loss of alpha4beta7 integrin cell surface expression. Our results indicate: (i) that LDV-3, located proximal to the cell membrane, is important for alpha4beta7 integrin-triggered functions and for lateral clustering and (ii) that LDV-2 affects alpha4beta7 heterodimer stability.     

The amino acid sequences of the alpha and beta chains of hemoglobin from the snake, Liophis miliaris

The hemoglobin of Liophis miliaris has unusual properties. The hemoglobin is dimeric in the oxy form, and the cooperativity of O2 binding is very low, but both the Bohr effect and cooperativity are greatly enhanced in the presence of ATP (Matsuura, M. S. A., Ogo, S. H., and Focesi, A., Jr. (1987) Comp. Biochem. Physiol. 86A, 683-687). Four unique chains (2 alpha, 2 beta) can be isolated from the hemolysate. The amino acid sequences of one alpha and one beta chain have been determined in an effort to understand the functional properties. Comparison of the sequences with those of the alpha and beta chains of human Hb shows the following. (i) All 7 of the residues in the beta chain normally conserved in globins are identical to those of the human chain: Gly(B6), Phe(CD1), His(E7), Leu(F4), His(F8), Lys(H10), and Tyr(HC2), except that the distal His(E7) has been replaced by Gln in the alpha chain. (ii) All heme contact residues in the beta chain are identical with those in the human chain, but two differences are present in the alpha chain: the distal His(E7) is replaced by Gln and Met(B13) by Leu. (iii) All residues that form the binding site for organic phosphates are identical to those in human Hb. (iv) The major residues that contribute to the normal Bohr effect in human Hb, Asp-beta 94, His-beta 146, and Val-alpha 1 are conserved. (v) All beta chain residues at the alpha 1 beta 2 interface are identical with those in the human chain except two: Glu(G3)----Val and Glu(CD2)----Thr; these differences in charged residues may explain the dissociation to dimers. (vi) The 23 residues of the alpha chain in the alpha 1 beta 2 contact region are identical with those of the human chain except three: Phe(B14)----Leu, Thr(C3)----Gln and Pro(CD2)----Ser. (vii) A total of 17 differences occur at the alpha 1 beta 1 interface, 11 in the alpha chain and 6 in the beta chain.     

Families of membranous proteins can be characterized by the amino acid composition of their transmembrane domains

SUMMARY: In eukaryotes, membranous proteins account for 20-30% of the proteome. Most of these proteins contain one or more transmembrane (TM) domains. These are short segments that transverse the bilayer lipid membrane. Various properties of the TM domains, such as their number, their topology and their arrangement within the membrane, are closely related to the protein's cellular functions. The properties of the TM domains also determine the cellular targeting and localization of these proteins. It is not known, however, whether the information encoded by TM domains suffices for the purpose of classifying proteins into their functional families. This is the question we address here. We introduce an algorithm that creates a profile of each functional family of membranous proteins based only on the amino acid composition of their TM domains. This is complemented by a classifier program for each such family (to determine whether a given protein belongs to it or not). We find that in most instances TM domains contain enough information to allow an accurate discrimination of approximately 80% sensitivity and approximately 90% specificity among unrelated polytopic functional families with the same number of TM domains. SUPPLEMENTARY INFORMATION: Available at www.protonet.cs.huji.ac.il/TM/     

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.     

Generation of deviation parameters for amino acid singlets, doublets and triplets from three-dimensional 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 nonhomologous 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 αhelix by SSPDP, NNPREDICT and PHD methods was found to be 57%, 44% and 69% respectively for the proteins in the selected dataset. For Β-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.     

Relation of amino acid composition and the Moffitt parameters to the secondary structure of proteins

A statistical analysis of the relation between the amino acid composition of proteins and the amount of helical secondary structure as characterized by the Moffitt b₀ parameter has shown a high degree of correlation of the b₀ parameter with those amino acids whose homopolymers can form helical structures. Using the data for 107 proteins, a linear relation was found between b₀ and the sum of the residue percentages of alanine, arginine, aspartic acid, cysteine, glutamic acid, leucine, andlysine. A statistical analysis of the Moffitt a₀ parameter, on the other hand, showed no statistically significant grouping of amino acids in relation to the amount of secondary β structure in a protein. A plot of b₀ versus a₀–a, where a represents the a⁰ parameter for a fully denatured protein, for 55 proteins showed distinct nonlinearity. This nonlinearity was postulated to be due to presence of β structure, and a nomagram was constructed which allowed a semiquantitative estimate of the amount of helical and β-type secondary structures from the b₀ versus a₀–a plot.     

Variation of amino acid properties in protein secondary structures, alpha-helices and beta-strands

A study was made on the physical, chemical, energetic, conformational, geometric, and dynamic property potentials of amino acid residues in protein secondary structures: alpha-helix and beta-strand. Property patterns were obtained by computing the average property values for specified residue units partitioned longitudinally and transversely about the chain. It was found that in alpha-helices with not more than 15 residues, there exist longitudinally opposing portions, one characteristically higher in average property potentials than the other. The helical chain, in general, acquires either an increasing or decreasing average potential in the N-terminal to C-terminal direction. The sequence-wise and surface-wise variations of property potentials in the elements of beta-structure also revealed such general patterns. Possible wrong predictions in statistical methods of one secondary structural class over the other are pointed out.     

Prediction of the secondary and tertiary structures of interferon from four homologous amino acid sequences

The secondary and tertiary structures of interferon were predicted from four homologous amino acid sequences. Three methods of secondary structure prediction gave differing results that were interpreted to suggest that there might be four α-helices that are important in the tertiary fold. The validity of this interpretation was assessed by the application of the methods to predict the secondary structures of two proteins known to consist of four α-helices. A possible tertiary model for interferon is then proposed in which the four α-helices pack into a right-handed bundle similar to that observed in several known protein structures. This model was shown to be stereochemically feasible by an α-helix docking algorithm. One of the resultant structures is shown to be compatible with the known disulphide linkages in interferon. Certain residues that are conserved between the different sequences lie near each other in our model and these residues might form a functional site. In the absence of a crystal structure for interferon, a predicted tertiary model will help further structural and functional studies.     

The amino acid sequence of the beta subunit of allophycocyanin

The complete amino acid sequence of the beta subunit of Anabaena variabilis allophycocyanin is: H2N-Ala-Gln-Asp-Ala-Ile-Thr-Ala-Val-Ile-Asn-Ser-Ala-Asp-Val-Gln-Gly-Lys-Tyr-Leu-Asp-Thr-Ala-Ala-Leu-Glu-Lys-Leu-Lys-Ala-Tyr-Phe-Ser-Thr-Gly-Glu-Leu-Arg-Val-Arg-Ala-Ala-Thr-Thr-Ile-Ser-Ala-Asn-Ala-Ala-Ala-Ile-Val-Lys-Glu-Ala-Val-Ala-Lys-Ser-Leu-Leu-Tyr-Ser-Asp-Ile-Thr-Arg-Pro-Gly-Gly-Asn-Met-Tyr-Thr-Thr-Arg-Arg-Tyr-Ala-Ala-Cys-Ile-Arg-Asp-Leu-Asp-Tyr-Tyr-Leu-Arg-Tyr-Ala-Thr-Tyr-Ala-Met-Leu-Ala-Gly-Asp-Pro-Ser-Ile-Leu-Asp-Glu-Arg-Val-Leu-Asn-Gly-Leu-Lys-Glu-Thr-Tyr-Asn-Ser-Leu-Gly-Val-Pro-Val-Gly-Ala-Thr-Val-Gln-Ala-Ile-Gln-Ala-Ile-Lys-Glu-Val-Thr-Ala-Ser-Leu-Val-Gly-Ala-Asp-Ala-Gly-Lys-Glu-Met-Gly-Ile-Tyr-Leu-Asp-Tyr-Ile-Ser-Ser-Gly-Leu-Ser-COOH Phycocyanobilin is attached though a thioether linkage to cysteinyl residue 81, indicated by an asterisk. Comparison of this sequence with those of C-phycocyanins shows that there are 60 identities between corresponding subunits of these two biliproteins. Of the region between residues 79 and 120, 29 residues are identical in the beta subunits of allophycocyanin and phycocyanin. The character of all 10 charged residues in this region of the beta subunit sequences is completely conserved.     

The amino acid sequence of the rabbit lutropin beta subunit

The amino acid sequence of the beta subunit of rabbit lutropin (lLH) has been determined. The amino terminus of about 97% of the beta subunit has a two amino acid extension (pyro-Glu-Pro) compared to other lutropin beta sequences. Overlapping peptides from trypsin and chymotrypsin digestions of the performic acid-oxidized beta subunit and trypsin digestion of the S-aminoethylated cysteine beta subunit were isolated by chromatography on TSK Fractogel 40F and high-pressure liquid chromatography (HPLC). Sequencing was by a combination of the dansyl-Edman method and the direct Edman method. Amide placements were established by HPLC analysis of the PTH amino acid derivatives. The proposed sequence of lLH subunit is: This sequence is highly homologous to the other known lutropin beta subunits, especially rat and pig lutropin beta (91%). Partial cleavage of the peptide bond between Asp-79 and Pro-80 was observed during cyanogen bromide treatment. Rabbit thyrotropin and thyrotropin beta subunit copurified with lLH and lLH except at a final chromatography on Sephadex G-100.