Repetitive Structural Elements Research Articles

A 3D Parameterized BIM-Modeling Method for Complex Engineering Structures in Building Construction Projects

The structural components of large-scale public construction projects are more complex than those of ordinary residential buildings, with irregular and diverse components, as well as a large number of repetitive structural elements, which increase the difficulty of BIM-modeling operations. Additionally, there is a significant amount of inherent parameter information in the construction process, which puts forward higher requirements for the application and management capabilities of BIM technology. However, the current BIM software still has deficiencies in the parameterization of complex and irregular structural components, fine modeling, and project management information. To address these issues, this paper takes Grasshopper as the core parametric tool and Revit as the carrier of component attribute information. It investigates the parametric modeling logic of Grasshopper and combines the concepts of parameterization, modularization, standardization, and engineering practicality to create a series of parametric programs for complex structural components in building projects. This approach mainly addresses intricate challenges pertaining to the parametric structural shapes (including batch processing) and parametric structural attributes (including the batch processing of diverse attribute parameters), thereby ensuring the efficiency in BIM modeling throughout the design and construction phases of complex building projects.

Orphan gene in Littorina: An unexpected role of symbionts in the host evolution

Mechanisms of reproductive isolation between closely related sympatric species are of high evolutionary significance as they may function as initial drivers of speciation and protect species integrity afterwards. Proteins involved in the establishment of reproductive barriers often evolve fast and may be key players in cessation of gene flow between the incipient species. The five Atlantic Littorina (Neritrema) species represent a notable example of recent radiation. The geographic ranges of these young species largely overlap and the mechanisms of reproductive isolation are poorly understood. In this study, we performed a detailed analysis of the reproductive protein LOSP, previously identified in Littorina. We showed that this protein is evolutionary young and taxonomically restricted to the genus Littorina. It has high sequence variation both within and between Littorina species, which is compatible with its presumable role in the reproductive isolation. The strongest differences in the LOSP structure were detected between Littorina subgenera with distinctive repetitive motifs present exclusively in the Neritrema species, but not in L. littorea. Moreover, the sequence of these repetitive structural elements demonstrates a high homology with genetic elements of bacteria, identified as components of Littorina associated microbiomes. We suggest that these elements were acquired from a symbiotic bacterial donor via horizontal genetic transfer (HGT), which is indirectly confirmed by the presence of multiple transposable elements in the LOSP flanking and intronic regions. Furthermore, we hypothesize that this HGT-driven evolutionary innovation promoted LOSP function in reproductive isolation, which might be one of the factors determining the intensive cladogenesis in the Littorina (Neritrema) lineage in contrast to the anagenesis in the L. littorea clade.

Философский анализ проблемы усовершенствования человека в свете расширения возможностей биотехнологий

The paper examines the transformation of ethical norms governing the activities of “eugenicists” in the context of increasing opportunities for biotechnology. The main question is formulated as follows: whether the successes of science bring novelty to the “humanitarian” sphere of eugenics. Eugenic discourse since its formation in ancient times is characterized by repetitive structural elements, such as the thesis of the degeneration of man in the course of civilizational de­velopment, a reference to “scientific” knowledge and an appeal to power struc­tures as the force that should carry out eugenic transformations in society. It is also noted that at all times eugenic programs have represented a certain chal­lenge to public morality, since the improvement of the “human breed” reduces man to the position of an agricultural animal. The development of biotechnology has made it really possible to adjust the genome (for the first time since the birth of the eugenic idea). However, ethical standards have not changed significantly since the criticism of racial hygiene programs. The progress of biotechnology gives the impression that significant progress is taking place in the “humanitar­ian” part of eugenics. However, a balanced analysis shows that completely dif­ferent processes are taking place in this area. Thus, the turn towards the liberal project marks the abandonment of the central task of classical eugenics, namely the improvement of the species homo sapiens. Whereas the goal of liberal eugen­ics is to correct individual genomes, which cannot significantly affect the ge­nome of mankind. The use of digital technologies, in addition to the direct pur­pose of processing large amounts of data, also serves to blur responsibility for interfering with the human genome, since part of the decisions (for example, di­agnosis and determination of the treatment strategy) are transferred to machine intelligence. This circumstance shows that the search for new arguments in favor of (or against) eugenic policy will be appropriate and in demand.

Protein folding - seeing is deceiving.

This Perspective is intended to raise questions about the conventional interpretation of protein folding. According to the conventional interpretation, developed over many decades, a protein population can visit a vast number of conformations under unfolding conditions, but a single dominant native population emerges under folding conditions. Accordingly, folding comes with a substantial loss of conformational entropy. How is this price paid? The conventional answer is that favorable interactions between and among the side chains can compensate for entropy loss, and moreover, these interactions are responsible for the structural particulars of the native conformation. Challenging this interpretation, the Perspective introduces a proposal that high energy (i.e., unfavorable) excluding interactions winnow the accessible population substantially under physical–chemical conditions that favor folding. Both steric clash and unsatisfied hydrogen bond donors and acceptors are classified as excluding interactions, so called because conformers with such disfavored interactions will be largely excluded from the thermodynamic population. Both excluding interactions and solvent factors that induce compactness are somewhat nonspecific, yet together they promote substantial chain organization. Moreover, proteins are built on a backbone scaffold consisting of α‐helices and strands of β‐sheet, where the number of hydrogen bond donors and acceptors is exactly balanced. These repetitive secondary structural elements are the only two conformers that can be both completely hydrogen‐bond satisfied and extended indefinitely without encountering a steric clash. Consequently, the number of fundamental folds is limited to no more than ~10,000 for a protein domain. Once excluding interactions are taken into account, the issue of “frustration” is largely eliminated and the Levinthal paradox is resolved. Putting the “bottom line” at the top: it is likely that hydrogen‐bond satisfaction represents a largely under‐appreciated parameter in protein folding models.

Phage tail fibre assembly proteins employ a modular structure to drive the correct folding of diverse fibres

Phage tail fibres are elongated protein assemblies capable of specific recognition of bacterial surfaces during the first step of viral infection1-4. The folding of these complex trimeric structures often requires a phage-encoded tail fibre assembly (Tfa) protein5-7. Despite the wide occurrence of Tfa proteins, their functional mechanism has not been elucidated. Here, we investigate the tail fibre and Tfa of Escherichia coli phage Mu. We demonstrate that Tfa forms a stable complex with the tail fibre, and present a 2.1 Å resolution X-ray crystal structure of this complex. We find that Tfa proteins are comprised of two domains: a non-conserved N-terminal domain that binds to the C-terminal region of the fibre and a conserved C-terminal domain that probably mediates fibre oligomerization and assembly. Tfa forms rapidly exchanging multimers on its own, but not a stable trimer, implying that Tfa does not specify the trimeric state of the fibre. We propose that the key conserved role of Tfa is to ensure that fibre assembly and multimerization initiates at the C terminus, ensuring that the intertwined and repetitive structural elements of fibres come together in the correct sequence. The universal importance of correctly aligning the C termini of phage fibres is highlighted by our work.

RepeatsDB-lite: a web server for unit annotation of tandem repeat proteins.

RepeatsDB-lite (http://protein.bio.unipd.it/repeatsdb-lite) is a web server for the prediction of repetitive structural elements and units in tandem repeat (TR) proteins. TRs are a widespread but poorly annotated class of non-globular proteins carrying heterogeneous functions. RepeatsDB-lite extends the prediction to all TR types and strongly improves the performance both in terms of computational time and accuracy over previous methods, with precision above 95% for solenoid structures. The algorithm exploits an improved TR unit library derived from the RepeatsDB database to perform an iterative structural search and assignment. The web interface provides tools for analyzing the evolutionary relationships between units and manually refine the prediction by changing unit positions and protein classification. An all-against-all structure-based sequence similarity matrix is calculated and visualized in real-time for every user edit. Reviewed predictions can be submitted to RepeatsDB for review and inclusion.

Alpha-helix to beta-sheet transition in long-chain poly-l-lysine: Formation of alpha-helical fibrils by poly-l-lysine

The temperature-induced α-helix to β-sheet transition in long-chain poly-l-lysine (PLL), accompanied by the gauche-to-trans isomerization of CH2 groups in the hydrocarbon side chains of Lys amino acid residues, and formation of β-sheet as well as α-helix fibrillar aggregates of PLL have been studied using Fourier-transform infrared (FT-IR) and vibrational circular dichroism (VCD) spectroscopy, and transmission electron microscopy (TEM). In a low-temperature alkaline water solution or in a methanol-rich water mixture, the secondary structure of PLL is represented by α-helical conformations with unordered and gauche-rich hydrocarbon side chains. Under these conditions, PLL molecules aggregate into α-helical fibrils. PLLs dominated by extended antiparallel β-sheet structures with highly ordered trans-rich hydrocarbon side chains are formed in a high-temperature range at alkaline pD and aggregate into fibrillar, protofibrillar, and spherical forms. Presented data support the idea that fibrillar aggregation is a varied phenomenon possible in repetitive structural elements with not only a β-sheet-rich conformation, but also an α-helical-rich conformation.

Three-dimensional reconstruction method of Tang Dynasty building based on point clouds

We present a method to reconstruct the three-dimensional (3-D) Tang Dynasty building model from raw point clouds. Different from previous building modeling techniques, our method is developed for the Tang Dynasty building which does not exhibit planar primitives, facades, and repetitive structural elements as residential low- or high-rise buildings. The proposed method utilizes the structural property of the Tang Dynasty building to process the original point clouds. First, the raw point clouds are sliced into many parallel layers to generate a top-bottom hierarchical structure, and each layer is resampled to achieve a subset purification of 3-D point clouds. In addition, a series of different building components of the building are recognized by clustering these purifications of 3-D point clouds. In particular, we get the tree-structured topology of these different building components during slicing and clustering. Second, different solutions are explored to reconstruct its 3-D model for different building components. The overall model of building can be gotten based on the building components and tree-structured topology. Experimental results demonstrate that the proposed method is more efficient for generating a high realistic 3-D model of the Tang Dynasty building.

The Long and the Short of Bacterial Adhesion Regulation

The Long and the Short of Bacterial Adhesion Regulation

RNA Tetraloop Folding Reveals Tension between Backbone Restraints and Molecular Interactions

In RNA, A-form helices are commonly terminated by tetraloops or 3' dangling ends. Aside from helices themselves, these helix-breaking motifs appear to be among the most frequent and repetitive structural elements of large folded RNAs. We show here that within a frequent type of tetraloop, cGNRAg (G is guanine, N is any base, R is purine, A is adenine), a tension exists between the backbone torsional energy of the loop and the energy contributed by molecular interactions (stacking and pairing). A model in which favorable bond rotamers are opposed by favorable stacking and pairing interactions is consistent with our observation that release of torsional restraints upon conversion of one or more loop riboses to more flexible trimethylene phosphate(s) contributes favorably to the enthalpy of folding. This effect presumably results from improved stacking and hydrogen-bonding interactions upon release of torsional restraints. The most obvious possibility for improving molecular interactions is a repositioning of A, which is proximal to the unfavorable torsion angles in native cGNRAg tetraloops, and which is unstacked on the 3' side and unpaired (it forms a single hydrogen bond with the opposing G). This tension between favorable bond rotamers and favorable molecular interactions may be representative of a general evolutionary strategy to prevent achievement of deep and irreversible thermodynamic wells in folded RNAs. Finally, we observe a simple stacking substructure with conserved geometry and sequence that forms a scaffold for both tetraloops and 3' dangling ends. It seems that simple substructures can build RNA motifs, which combine to establish the fundamental architecture of RNA.

Invivo folding efficiencies for mutants of the P22 tailspike β-helix protein correlate with predicted stability changes

Parallel β-helices are among the simplest repetitive structural elements in proteins. The folding behavior of β-helix proteins has been studied intensively, also to gain insight on the formation of amyloid fibrils, which share the parallel β-helix as a central structural motif. An important system for investigating β-helix folding is the tailspike protein from the Salmonella bacteriophage P22. The central domain of this protein is a right-handed parallel β-helix with 13 windings. Extensive mutational analyses of the P22 tailspike protein have revealed two main phenotypes: temperature-sensitive-folding (tsf) mutations that reduce the folding efficiency at elevated temperatures, and global suppressor (su) mutations that increase the tailspike folding efficiency. A central question is whether these phenotypes can be understood from changes in the protein stability induced by the mutations. Experimental determination of the protein stability is complicated by the nearly irreversible trimerization of the folded tailspike protein. Here, we present calculations of stability changes with the program FoldX, focusing on a recently published extensive data set of 145 singe-residue alanine mutants. We find that the calculated stability changes are correlated with the experimentally measured in vivo folding efficiencies. In addition, we determine the free-energy landscape of the P22 tailspike protein in a nucleation–propagation model to explore the folding mechanism of this protein, and obtain a processive folding route on which the protein nucleates in the N-terminal region of the helix.

Weighing in on a timeless controversy

Timeless (Tim) and Period (Per) are coordinately synthesized interacting proteins that in response to positional/environmental cues comigrate to the nucleus as obligate heterodimers where they act to suppress their own gene expression as part of the circadian rhythm network in Drosophila. There has been considerable controversy about the structural nature of Tim because of somewhat conflicting results generated by the automated threading algorithm 3D-PSSM. With use of a computer-assisted but largely manual approach, it is shown here that Tim is composed of repetitive structural elements and that those elements comprise two ARM repeat domains, validating the essence of the original 3D-PSSM prediction. Eleven individual ARM structural units are assigned, and a phylogenetic analysis showing their relatedness to one another is performed. In addition, there appears to be a small domain of prenyltransferase-like repeats C-terminal to the second ARM domain, which went undetected in previous analyses. Although we cannot know the precise conformation it adopts until a structure is solved, Tim emerges here as clearly a member of the helical repeat protein superfamily. Given its role in periodic nuclear translocation, Tim may, therefore, have a functional analogy with the photoperiod-responsive protein Phor1 and other karyopherin-like molecules.

The role of complement in innate and adaptive immunity.

The complement system is an ancient element of innate immunity present at progressively more evolved forms in the blood or lymph of all vertebrates studied and in at least some invertebrate species (Nonaka 1998). It provides one of the best examples of an effective first line of host defense system. Complement can recognize conserved repetitive structural elements important for the survival of pathogens and therefore shared by large groups of them. Recognition leads to the activation of the system and elimination of the pathogens either by direct killing or by opsonophagocytosis and intracellular killing. In parallel, complement also provides signals to adaptive immunity instructing it to respond vigorously against pathogens (Carroll 1998; Fearon 1998). Furthermore, through its ability to discriminate between free and antigen-bound immunoglobulins, complement serves as an effector arm of adaptive humoral immunity leading to elimination of pathogens recognized by specific antibodies. Finally, complement appears to have a special relationship with natural antibodies depending on them for recognition of important pathogens and in turn providing signals for clonal selection and expansion of CD5+ B-1 cells that produce natural antibodies (Carroll and Prodeus 1998).

Folding and Function of Repetitive Structure in the Homotrimeric Phage P22 Tailspike Protein

TheSalmonellabacteriophage P22 recognizes its host cell receptor, lipopolysaccharide, by means of six tailspikes, thermostable homotrimers of 72-kDa polypeptides. Biophysical results on the binding reaction, together with high-resolution structural information from X-ray crystallography, have shed light on the interactions determining the viral host range. Folding and assembly of the tailspike proteinin vitrohave been analyzed in detail, and the data have been compared with observations on thein vivoassembly pathway. Repetitive structural elements in the tailspike protein, like a side-by-side trimer of parallel beta-helices, a parallel alpha-helical bundle, a triangular prism made up from antiparallel beta-sheets, and a short segment of a triple beta-helix can be considered building blocks for larger structural proteins, and thus, the results on P22 tailspike may have implications for fibrous protein structure and folding.

Topography of the histone octamer surface: repeating structural motifs utilized in the docking of nucleosomal DNA.

The histone octamer core of the nucleosome is a protein superhelix of four spirally arrayed histone dimers. The cylindrical face of this superhelix is marked by intradimer and interdimer pseudodyad axes, which derive from the nature of the histone fold. The histone fold appears as the result of a tandem, parallel duplication of the "helix-strand-helix" motif. This motif, by its occurrence in the four dimers, gives rise to repetitive structural elements--i.e., the "parallel beta bridges" and the "paired ends of helix I" motifs. A preponderance of positive charges on the surface of the octamer appears as a left-handed spiral situated at the expected path of the DNA. We have matched a subset of DNA pseudodyads with the octamer pseudodyads and thus have built a model of the nucleosome. In it, the two DNA strands coincide with the path of the histone-positive charges, and the central 12 turns of the double helix contact the surface of the octamer at the repetitive structural motifs. The properties of these complementary contacts appear to explain the preference of histones for double-helical DNA and to suggest a possible basis for allosteric regulation of nucleosome function.

Primary structure of the 170-kDa surface lectin of pathogenic Entamoeba histolytica.

The adherence of Entamoeba histolytica to colonic mucins and to host cells appears to be predominantly mediated by a 170-kDa surface lectin of the amoebae. By using an antiserum to the purified lectin, the corresponding cDNA was isolated from an expression library of the pathogenic E. histolytica isolate HM-1:IMSS. Northern blot analysis indicated a transcript of approximately 4 kilobases, and Southern blot analyses suggested that multiple genes may encode the lectin or closely related proteins in HM-1:IMSS trophozoites. The cDNA-deduced amino acid sequence revealed an N-terminal signal peptide and a mature protein of 1270 amino acids corresponding to a molecular mass of 143 kDa, which comprises a short C-terminal cytoplasmic domain with potential phosphorylation sites, a transmembrane region, and a large extracellular portion with nine potential asparagine-linked glycosylation sites. The extracellular portion may be separated into a cysteine-poor domain and a cysteine-rich domain, the latter of which shows in part repetitive structural elements with a low degree of sequence homology to wheat germ agglutinin and to pDd63, a developmentally expressed protein of Dictyostelium discoideum.

Transcription of mouse rDNA terminates downstream of the 3' end of 28S RNA and involves interaction of factors with repeated sequences in the 3' spacer.

RNA polymerase I terminates transcription of mouse rDNA 565 bp downstream of the 3' end of mature 28S rRNA. This specific termination event can be duplicated in a nuclear extract system. RNA molecules with authentic 3' ends are transcribed from ribosomal minigene constructs provided the templates retain a minimal length of downstream spacer sequences. The nucleotide sequence of the region of transcription termination contains a set of repetitive structural elements consisting of 18 bp conserved nucleotides surrounded by stretches of pyrimidines. Termination in vivo occurs within the first element. This site is preferentially used in vitro at low template concentrations. At increasing DNA concentrations a termination site within the second repetitive element is used. Competition experiments with defined 3'-terminal fragments suggest that transcription termination by RNA polymerase I requires interaction of some factor (or factors) with the repetitive structural elements in the 3' nontranscribed spacer.

Structural characteristics of a major seed albumin of Pisum sativum.

The major pea seed albumin from Pisum sativum was carboxymethylated, cleaved with CNBr, and submitted to sequence analysis of the fragments in order to characterize the structural organization of the protein chains. Four major pools of largely homogeneous CNBr fragments were obtained, and likely N- and C-terminal fragments were identified. Structural analysis suggested the presence of single positions with microheterogeneities. It also revealed structures with long segments of distinct homology (52% structural identity), indicating the presence of different but related protein chains, or less likely, of repetitive structural elements within a chain. However, preparations appear largely homogeneous in protein class, and contain similar polypeptide chains of about 200 residues in mainly hydrophilic structures, with few methionine and cysteine/half-cystine residues.

Internal structure of the chromatin subunit.

The digestion of chromatin insitu with DNase I reveals, after denaturation, a regular series of single stranded DNA fragments the lengths of which represent multiples of 10 bases. These experiments are compatible with the DNA being on the outside of the chromatin subunit and suggest that the subunit structure itself contains repetitive structural elements. Possible models are discussed.