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Currently, the main α-amylase family GH13 has been divided into 47 subfamilies in CAZy, with new subfamilies regularly emerging. The present in silico study was performed to highlight the groups, represented by the maltogenic amylase from Thermotoga neapolitana and the α-amylase from Haloarcula japonica, which are worth of creating their own new GH13 subfamilies. This enlarges functional annotation and thus allows more precise prediction of the function of putative proteins. Interestingly, those two share certain sequence features, e.g. the highly conserved cysteine in the second conserved sequence region (CSR-II) directly preceding the catalytic nucleophile, or the well-preserved GQ character of the end of CSR-VII. On the other hand, the two groups bear also specific and highly conserved positions that distinguish them not only from each other but also from representatives of remaining GH13 subfamilies established so far. For the T. neapolitana maltogenic amylase group, it is the stretch of residues at the end of CSR-V highly conserved as L-[DN]. The H. japonica α-amylase group can be characterized by a highly conserved [WY]-[GA] sequence at the end of CSR-II. Other specific sequence features include an almost fully conserved aspartic acid located directly preceding the general acid/base in CSR-III or well-preserved glutamic acid in CSR-IV. The assumption that these two groups represent two mutually related, but simultaneously independent GH13 subfamilies has been supported by phylogenetic analysis as well as by comparison of tertiary structures. The main α-amylase family GH13 has thus been expanded by two novel subfamilies GH13_48 and GH13_49. Key points: • In silico analysis of two groups of family GH13 members with characterized representatives • Identification of certain common, but also some specific sequence features in seven CSRs • Creation of two novel subfamilies—GH13_48 and GH13_49 within the CAZy database [ABSTRACT FROM AUTHOR]

In the sequence-based classification of glycoside hydrolases (GHs) of the CAZy database, the family GH119 represents one of the four α-amylase GH families. The family GH119 was established based on a study describing the α-amylase from Bacillus circulans (currently re-classified as Niallia circulans), a product of the igtZ gene. This family with ~ 40 members belongs to the smallest GH families. In addition to a partial biochemical characterization of the α-amylase from N. circulans, nothing has been found in GH119 until now. There was only a single in silico study predicting the catalytic domain structure, catalytic machinery and conserved sequence regions (CSRs) as shared with those well-established in the second α-amylase family GH57. The present bioinformatics study was undertaken in an effort to deliver a detailed analysis of all family GH119 members with regard to their domain arrangement, exact location of all five CSRs and potentially unique sequence features. In order to perform a relevant comparison, the studied set of actual GH119 members was completed by all characterized family GH57 members, i.e. 80 sequences were compared in total. Taking into account the experimentally determined tertiary structure of the GH57 Thermococcus litoralis 4-α-glucanotransferase and the AlphaFold database model of the GH119 N. circulans α-amylase, the position of the CSR-5 in the family GH119 has been precisely re-defined. Phylogenetic trees constructed separately for the N-terminal and C-terminal parts of sequences demonstrated that taxonomy was most probably the main driving factor governing the evolution of the family GH119. [ABSTRACT FROM AUTHOR]

The seismic capacity of a structure is determined by the performance index that reaches its ultimate bearing or deformation capacity first. This paper presents a multi-index seismic capacity evaluation method for accurately evaluating the seismic capacity of a structure. The normalized response curves of several indices are concurrently plotted to form a multi-index seismic capacity evaluation figure, in which the seismic capacity and demand values that correspond to various indices can be determined by vertical and horizontal threshold lines. Based on an incremental dynamic analysis (IDA), a 6-story buckling-restrained braced frame (BRBF) and a series of comparable 6-story steel frames are analyzed using the proposed method to verify the method and investigate the seismic behavior of BRBFs. The results show that the seismic performance of buckling-restrained braces is not the only factor that determines the seismic capacity of BRBFs and indicate that the multi-index seismic capacity evaluation method can effectively identify the critical index of a structure and the weakest links that restrict the structural seismic capacity. [ABSTRACT FROM AUTHOR]

In this study, we have made homology models of mouse, rat, and monkey vascular adhesion protein-1 (VAP-1) to reveal basis for the species-specific ligand recognition of VAP-1. Based on the structural comparisons, rodent VAP-1s have a narrower active site channel than primate VAP-1s. The variable residues in mouse and rat VAP-1, Phe447 from arm I and the polar residues from the first α-helix of the D3 domain together with C-terminal residues are likely to affect ligand recognition and binding. [ABSTRACT FROM AUTHOR]

Several studies based on the known three-dimensional (3-D) structures of proteins show that two homologous proteins with insignificant sequence similarity could adopt a common fold and may perform same or similar biochemical functions. Hence, it is appropriate to use similarities in 3-D structure of proteins rather than the amino acid sequence similarities in modelling evolution of distantly related proteins. Here we present an assessment of using 3-D structures in modelling evolution of homologous proteins. Using a dataset of 108 protein domain families of known structures with at least 10 members per family we present a comparison of extent of structural and sequence dissimilarities among pairs of proteins which are inputs into the construction of phylogenetic trees. We find that correlation between the structure-based dissimilarity measures and the sequence-based dissimilarity measures is usually good if the sequence similarity among the homologues is about 30% or more. For protein families with low sequence similarity among the members, the correlation coefficient between the sequence-based and the structure-based dissimilarities are poor. In these cases the structure-based dendrogram clusters proteins with most similar biochemical functional properties better than the sequence-similarity based dendrogram. In multi-domain protein families and disulphide-rich protein families the correlation coefficient for the match of sequence-based and structure-based dissimilarity (SDM) measures can be poor though the sequence identity could be higher than 30%. Hence it is suggested that protein evolution is best modelled using 3-D structures if the sequence similarities (SSM) of the homologues are very low. [ABSTRACT FROM AUTHOR]

Structural comparison (i.e., the simultaneous analysis of multiple structures) is a problem which arises frequently in such diverse arenas as the study of organizational forms, social network analysis, and automated text analysis. Prior work has demonstrated the applicability of a range of standard multivariate analysis procedures to the structural comparison problem. Here, some simple algorithms are provided which elucidate several of these methods in an easily implemented form. [ABSTRACT FROM AUTHOR]

We describe a graph theoretic method designed to perform efficient searches for substructural patterns in nucleic acid structural coordinate databases using a simplified vectorial representation. Two vectors represent each nucleic acid base and the relative positions of bases with respect to one another are described in terms of distances between the defined start and end points of the vectors on each base. These points comprise the nodes and the distances the edges of a graph, and a pattern search can then be performed using a subgraph isomorphism algorithm. The minimal representation was designed to facilitate searches for complex patterns but was first tested on simple, well-characterised arrangements of bases such as base pairs and GNRA-tetraloop receptor interactions. The method performed very well for these interaction types. A survey of side-by-side base interactions, of which the adenosine platform is the best known example, also locates examples of similar base rearrangements that we consider to be important in structural regulation. A number of examples were found, with GU platforms being particularly prevalent. A GC platform in the RNA of the Thermus thermophilus small ribosomal subunit is in an analogous position to an adenosine platform in other species. An unusual GG platform is also observed close to one of the substrate binding sites in Haloarcula marismortui large ribosomal subunit RNA. [ABSTRACT FROM AUTHOR]