Journal articles: 'Sequence-Structure relationship'

1

Dosztanyi, Z. "Servers for sequence-structure relationship analysis and prediction." Nucleic Acids Research 31, no. 13 (July 1, 2003): 3359–63. http://dx.doi.org/10.1093/nar/gkg589.

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Morris, Kyle L., Alison Rodger, Matthew R. Hicks, Maya Debulpaep, Joost Schymkowitz, Frederic Rousseau, and Louise C. Serpell. "Exploring the sequence–structure relationship for amyloid peptides." Biochemical Journal 450, no. 2 (February 15, 2013): 275–83. http://dx.doi.org/10.1042/bj20121773.

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Amyloid fibril formation is associated with misfolding diseases, as well as fulfilling a functional role. The cross-β molecular architecture has been reported in increasing numbers of amyloid-like fibrillar systems. The Waltz algorithm is able to predict ordered self-assembly of amyloidogenic peptides by taking into account the residue type and position. This algorithm has expanded the amyloid sequence space, and in the present study we characterize the structures of amyloid-like fibrils formed by three peptides identified by Waltz that form fibrils but not crystals. The structural challenge is met by combining electron microscopy, linear dichroism, CD and X-ray fibre diffraction. We propose structures that reveal a cross-β conformation with ‘steric-zipper’ features, giving insights into the role for side chains in peptide packing and stability within fibrils. The amenity of these peptides to structural characterization makes them compelling model systems to use for understanding the relationship between sequence, self-assembly, stability and structure of amyloid fibrils.

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Sadowski, M. I., and D. T. Jones. "The sequence–structure relationship and protein function prediction." Current Opinion in Structural Biology 19, no. 3 (June 2009): 357–62. http://dx.doi.org/10.1016/j.sbi.2009.03.008.

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Nekrasov, Alexei N., Yuri P. Kozmin, Sergey V. Kozyrev, Rustam H. Ziganshin, Alexandre G. de Brevern, and Anastasia A. Anashkina. "Hierarchical Structure of Protein Sequence." International Journal of Molecular Sciences 22, no. 15 (August 3, 2021): 8339. http://dx.doi.org/10.3390/ijms22158339.

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Most non-communicable diseases are associated with dysfunction of proteins or protein complexes. The relationship between sequence and structure has been analyzed for a long time, and the analysis of the sequences organization in domains and motifs remains an actual research area. Here, we propose a mathematical method for revealing the hierarchical organization of protein sequences. The method is based on the pentapeptide as a unit of protein sequences. Employing the frequency of occurrence of pentapeptides in sequences of natural proteins and a special mathematical approach, this method revealed a hierarchical structure in the protein sequence. The method was applied to 24,647 non-homologous protein sequences with sizes ranging from 50 to 400 residues from the NRDB90 database. Statistical analysis of the branching points of the graphs revealed 11 characteristic values of y (the width of the inscribed function), showing the relationship of these multiple fragments of the sequences. Several examples illustrate how fragments of the protein spatial structure correspond to the elements of the hierarchical structure of the protein sequence. This methodology provides a promising basis for a mathematically-based classification of the elements of the spatial organization of proteins. Elements of the hierarchical structure of different levels of the hierarchy can be used to solve biotechnological and medical problems.

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Nakamura, Shugo, and Kentaro Shimizu. "2P004 Analysis of sequence-structure relationship of protein loop regions(Proteins-structure and structure-function relationship,Poster Presentations)." Seibutsu Butsuri 47, supplement (2007): S114. http://dx.doi.org/10.2142/biophys.47.s114_1.

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Kuroda, D., H. Shirai, M. Kobori, and H. Nakamura. "Relationship between sequence and structure of CDR-H3 in antibodies." Acta Crystallographica Section A Foundations of Crystallography 64, a1 (August 23, 2008): C228. http://dx.doi.org/10.1107/s0108767308092684.

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Krissinel, E. "On the relationship between sequence and structure similarities in proteomics." Bioinformatics 23, no. 6 (January 22, 2007): 717–23. http://dx.doi.org/10.1093/bioinformatics/btm006.

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Song, Jianxing. "Environment-transformable sequence–structure relationship: a general mechanism for proteotoxicity." Biophysical Reviews 10, no. 2 (December 4, 2017): 503–16. http://dx.doi.org/10.1007/s12551-017-0369-0.

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Mansiaux, Yohann, Agnel Praveen Joseph, Jean-Christophe Gelly, and Alexandre G. de Brevern. "Assignment of PolyProline II Conformation and Analysis of Sequence – Structure Relationship." PLoS ONE 6, no. 3 (March 31, 2011): e18401. http://dx.doi.org/10.1371/journal.pone.0018401.

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Leopold, P. E., M. Montal, and J. N. Onuchic. "Protein folding funnels: a kinetic approach to the sequence-structure relationship." Proceedings of the National Academy of Sciences 89, no. 18 (September 15, 1992): 8721–25. http://dx.doi.org/10.1073/pnas.89.18.8721.

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Su, Ying Ying, Di Liang, and Hai Dong. "Connector Structure-Based Modeling of Assembly Sequence Planning." Applied Mechanics and Materials 496-500 (January 2014): 2729–32. http://dx.doi.org/10.4028/www.scientific.net/amm.496-500.2729.

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Assembly Sequence planning is one of the important stages during the product manufacturing process. For the purpose of effectively reducing the degree of complexity and improving the efficiency, the modeling method of assembly sequence planning based on connector structures is proposed. The concept of connector structure is presented, which is regarded as basic assembly units to cover features of assembly parts and package functional parts and connectors. The model of assembly sequence planning is built, which represents the precedence constraint relationship among connector structures. Finally, an example is studied and the model of assembly sequence planning based on connector structure is built to illustrate the effectiveness of the modeling method.

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Sun, S., and R. Parthasarathy. "Protein sequence and structure relationship ARMA spectral analysis: application to membrane proteins." Biophysical Journal 66, no. 6 (June 1994): 2092–106. http://dx.doi.org/10.1016/s0006-3495(94)81004-5.

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Benros, Cristina, Alexandre G. de Brevern, and Serge Hazout. "Analyzing the sequence–structure relationship of a library of local structural prototypes." Journal of Theoretical Biology 256, no. 2 (January 2009): 215–26. http://dx.doi.org/10.1016/j.jtbi.2008.08.032.

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Abiko, T., and H. Sekino. "Relationship of amino acid sequence to immunological activity ? syntheses and structure-activity relationships of thymosin? 4 family." Amino Acids 1, no. 2 (1991): 215–23. http://dx.doi.org/10.1007/bf00806919.

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Hockenberry, Adam J., Adam R. Pah, Michael C. Jewett, and Luís A. N. Amaral. "Leveraging genome-wide datasets to quantify the functional role of the anti-Shine–Dalgarno sequence in regulating translation efficiency." Open Biology 7, no. 1 (January 2017): 160239. http://dx.doi.org/10.1098/rsob.160239.

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Studies dating back to the 1970s established that sequence complementarity between the anti-Shine–Dalgarno (aSD) sequence on prokaryotic ribosomes and the 5′ untranslated region of mRNAs helps to facilitate translation initiation. The optimal location of aSD sequence binding relative to the start codon, the full extents of the aSD sequence and the functional form of the relationship between aSD sequence complementarity and translation efficiency have not been fully resolved. Here, we investigate these relationships by leveraging the sequence diversity of endogenous genes and recently available genome-wide estimates of translation efficiency. We show that—after accounting for predicted mRNA structure—aSD sequence complementarity increases the translation of endogenous mRNAs by roughly 50%. Further, we observe that this relationship is nonlinear, with translation efficiency maximized for mRNAs with intermediate levels of aSD sequence complementarity. The mechanistic insights that we observe are highly robust: we find nearly identical results in multiple datasets spanning three distantly related bacteria. Further, we verify our main conclusions by re-analysing a controlled experimental dataset.

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Li, Chuan, and Fei Hu Chen. "Analysis of Spatial and Temporal Sequence Structure of the Environment Modality for Chinese Meishan Cultural Park." Applied Mechanics and Materials 357-360 (August 2013): 228–32. http://dx.doi.org/10.4028/www.scientific.net/amm.357-360.228.

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this thesis analyzes the spatial and temporal sequence structure of environment modality for Meishan Cultural Park, discussing its spatial sequence from the four aspects of point, line, surface, and body, and elaborating synchronic and diachronic structure characteristics of its time sequence. This thesis for the first time discusses the dialectical unity of the relationship between the two, thus forming a complete basic framework of space-time sequence structure theory, and proposing its revelation role of Meishan Cultural Park environmental and morphological designs on the designs of other cultures and environments.

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Toyota, Hitoshi, Toshihiro Nakashima, Itaru Urabe, and Tetsuya Yomo. "1P028 Evolution of functionality and structure from a random-sequence protein(Proteins-structure and structure-function relationship,Oral Presentations)." Seibutsu Butsuri 47, supplement (2007): S30. http://dx.doi.org/10.2142/biophys.47.s30_3.

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Tong, Jing, Ruslan I. Sadreyev, Jimin Pei, Lisa N. Kinch, and Nick V. Grishin. "Using homology relations within a database markedly boosts protein sequence similarity search." Proceedings of the National Academy of Sciences 112, no. 22 (May 18, 2015): 7003–8. http://dx.doi.org/10.1073/pnas.1424324112.

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Inference of homology from protein sequences provides an essential tool for analyzing protein structure, function, and evolution. Current sequence-based homology search methods are still unable to detect many similarities evident from protein spatial structures. In computer science a search engine can be improved by considering networks of known relationships within the search database. Here, we apply this idea to protein-sequence–based homology search and show that it dramatically enhances the search accuracy. Our new method, COMPADRE (COmparison of Multiple Protein sequence Alignments using Database RElationships) assesses the relationship between the query sequence and a hit in the database by considering the similarity between the query and hit’s known homologs. This approach increases detection quality, boosting the precision rate from 18% to 83% at half-coverage of all database homologs. The increased precision rate allows detection of a large fraction of protein structural relationships, thus providing structure and function predictions for previously uncharacterized proteins. Our results suggest that this general approach is applicable to a wide variety of methods for detection of biological similarities. The web server is available at prodata.swmed.edu/compadre.

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Liu, Tong-Jian, Cai-Yun Zhang, Hai-Fei Yan, Lu Zhang, Xue-Jun Ge, and Gang Hao. "Complete plastid genome sequence ofPrimula sinensis(Primulaceae): structure comparison, sequence variation and evidence foraccDtransfer to nucleus." PeerJ 4 (June 28, 2016): e2101. http://dx.doi.org/10.7717/peerj.2101.

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Species-rich genusPrimulaL. is a typical plant group with which to understand genetic variance between species in different levels of relationships. Chloroplast genome sequences are used to be the information resource for quantifying this difference and reconstructing evolutionary history. In this study, we reported the complete chloroplast genome sequence ofPrimula sinensisand compared it with other related species. This genome of chloroplast showed a typical circular quadripartite structure with 150,859 bp in sequence length consisting of 37.2% GC base. Two inverted repeated regions (25,535 bp) were separated by a large single-copy region (82,064 bp) and a small single-copy region (17,725 bp). The genome consists of 112 genes, including 78 protein-coding genes, 30 tRNA genes and four rRNA genes. Among them, seven coding genes, seven tRNA genes and four rRNA genes have two copies due to their locations in the IR regions. TheaccDandinfAgenes lacking intact open reading frames (ORF) were identified as pseudogenes. SSR and sequence variation analyses were also performed on the plastome ofPrimula sinensis, comparing with another available plastome ofP. poissonii. The four most variable regions,rpl36–rps8,rps16–trnQ,trnH–psbAandndhC–trnV, were identified. Phylogenetic relationship estimates using three sub-datasets extracted from a matrix of 57 protein-coding gene sequences showed the identical result that was consistent with previous studies. A transcript found fromP. sinensistranscriptome showed a high similarity to plastidaccDfunctional region and was identified as a putative plastid transit peptide at the N-terminal region. The result strongly suggested that plastidaccDhas been functionally transferred to the nucleus inP. sinensis.

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Mu, Xiaodong, Zhaoju Zeng, Danyao Shen, and Bo Zhang. "Multi-Feature Behavior Relationship for Multi-Behavior Recommendation." Applied Sciences 12, no. 24 (December 15, 2022): 12909. http://dx.doi.org/10.3390/app122412909.

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Multi-behavior recommendation aims to model the interaction information of multiple behaviors to enhance the target behavior’s recommendation performance. Despite progress in recent research, it is challenging to represent users’ preferences using the multi-feature behavior information of user interactions. In this paper, we propose a Multi-Feature Behavior Relationship for Multi-Behavior Recommendation (MFBR) framework, which models the multi-behavior recommendation problem from both sequence structure and graph structure perspectives for user preference prediction of target behaviors. Specifically, the MFBR model is designed with a sequence encoder and a graph encoder to construct behavioral representations of different aspects of the user; the correlations between behaviors are modeled by a behavioral relationship encoding layer, and the importance of different behaviors is finally learned in order to construct the final representation of user preferences. Experimental validation conducted on two real-world recommendation datasets shows that our MFBR consistently outperforms state-of-the-art methods.

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Pons, Benoît J., Julien Vignard, and Gladys Mirey. "Cytolethal Distending Toxin Subunit B: A Review of Structure–Function Relationship." Toxins 11, no. 10 (October 12, 2019): 595. http://dx.doi.org/10.3390/toxins11100595.

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The Cytolethal Distending Toxin (CDT) is a bacterial virulence factor produced by several Gram-negative pathogenic bacteria. These bacteria, found in distinct niches, cause diverse infectious diseases and produce CDTs differing in sequence and structure. CDTs have been involved in the pathogenicity of the associated bacteria by promoting persistent infection. At the host-cell level, CDTs cause cell distension, cell cycle block and DNA damage, eventually leading to cell death. All these effects are attributable to the catalytic CdtB subunit, but its exact mode of action is only beginning to be unraveled. Sequence and 3D structure analyses revealed similarities with better characterized proteins, such as nucleases or phosphatases, and it has been hypothesized that CdtB exerts a biochemical activity close to those enzymes. Here, we review the relationships that have been established between CdtB structure and function, particularly by mutation experiments on predicted key residues in different experimental systems. We discuss the relevance of these approaches and underline the importance of further study in the molecular mechanisms of CDT toxicity, particularly in the context of different pathological conditions.

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Gao, Meng, Fei Yang, Lei Zhang, Zhengding Su, and Yongqi Huang. "Exploring the sequence–structure–function relationship for the intrinsically disordered βγ-crystallin Hahellin." Journal of Biomolecular Structure and Dynamics 36, no. 5 (April 13, 2017): 1171–81. http://dx.doi.org/10.1080/07391102.2017.1316519.

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Tejera, E., J. Nieto-Villar, and I. Rebelo. "Protein sequence complexity revisited. Relationship with fractal 3D structure, topological and kinetic parameters." Physica A: Statistical Mechanics and its Applications 410 (September 2014): 287–301. http://dx.doi.org/10.1016/j.physa.2014.05.019.

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van Belkum, Alex, Willem van Leeuwen, Stewart Scherer, and Henri Verbrugh. "Occurrence and structure-function relationship of pentameric short sequence repeats in microbial genomes." Research in Microbiology 150, no. 9-10 (November 1999): 617–26. http://dx.doi.org/10.1016/s0923-2508(99)00129-1.

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Giles, I., A. Lambrianides, and A. Rahman. "Examining the non-linear relationship between monoclonal antiphospholipid antibody sequence, structure and function." Lupus 17, no. 10 (October 2008): 895–903. http://dx.doi.org/10.1177/0961203308091541.

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Nyembe, Priscilla L., Thandokuhle Ntombela, and Maya M. Makatini. "Review: Structure-Activity Relationship of Antimicrobial Peptoids." Pharmaceutics 15, no. 5 (May 15, 2023): 1506. http://dx.doi.org/10.3390/pharmaceutics15051506.

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Due to their broad-spectrum activity against Gram-negative and Gram-positive bacteria, natural antimicrobial peptides (AMPs) and their synthetic analogs have emerged as prospective therapies for treating illnesses brought on by multi-drug resistant pathogens. To overcome the limitations of AMPs, such as protease degradation, oligo-N-substituted glycines (peptoids) are a promising alternative. Despite having the same backbone atom sequence as natural peptides, peptoid structures are more stable because, unlike AMP, their functional side chains are attached to the backbone nitrogen (N)-atom rather than the alpha carbon atom. As a result, peptoid structures are less susceptible to proteolysis and enzymatic degradation. The advantages of AMPs, such as hydrophobicity, cationic character, and amphipathicity, are mimicked by peptoids. Furthermore, structure-activity relationship studies (SAR) have shown that tuning the structure of peptoids is a crucial step in developing effective antimicrobials.

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Kusano, A., M. Iwama, A. Sanda, K. Suwa, E. Nakaizumi, Y. Nakatani, H. Ohkawa, K. Ohgi, and M. Irie. "Primary structure of porcine spleen ribonuclease: sequence homology." Acta Biochimica Polonica 44, no. 4 (December 31, 1997): 689–99. http://dx.doi.org/10.18388/abp.1997_4371.

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The primary structure of porcine spleen RNase (RNase Psp1) was investigated as a mean of assessing the structure-function relationship of base non-specific ribonucleases of animal origin. N-terminal analysis of RNase Psp1 yielded three N-terminal sequences. These peptides were separated by gel-filtration on Superdex 75HR, after reduction and S-carboxymethylation of RNase Psp1. Determination of the amino-acid sequence of these peptides indicated that the RNase Psp1 preparation consisted of three peptides having 20 (RCM RNase Psp1 pep1), 15 (RCM RNase Psp1 pep2), and 164 (RCM RNase Psp1 pro) amino-acid residues, respectively. It possessed two unique segments containing most of the active site amino-acid residues of the RNases of the RNase T2 family. The alignment of these three peptides in RNase Psp1 was determined by comparison with the other enzymes in the RNase T2 family. The overall results showed that RCM RNase Psp1 pep1 and RCM RNase Psp1 pep2 are derived from the N-terminal and C-terminal regions of RNase Psp1, respectively, probably by processing by some protease. The molecular mass of the protein moiety of RNase Psp1 was 23235 Da.

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Zou, Chen, Cheng Long Song, Wen Ke Wang, and Si Kun Li. "The Research on Synthesized Visualization Metadata Model of Molecular Structure and Gene Sequence." Advanced Materials Research 846-847 (November 2013): 1578–81. http://dx.doi.org/10.4028/www.scientific.net/amr.846-847.1578.

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With the rise and rapid development of the systems biology, in order to explore the relationship between different levels of Bioinformatics relevance, the need of integrated visualization of biological scientific computing data at different levels is increasingly urgent. This paper propses a molecular structure and genome sequence synthesized visualization metadata model, and then implements the integration management of the visualization data of molecular structure and genome sequence. This method can effectively support the development of visualization capabilities of molecular structure and gene sequence. Based on the XML technology, by deep researching in the field of visualization data format and applying this synthesized visualization metadata model, this paper designs and introduces the conversion method for visualization data of molecular structure and genome sequence. Ultimately, based on this synthesized visualization metadata model, a synthesized visualization prototype system for molecular structure and gene sequence (VMG) has been developed.

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Choi, Yushin. "Educational implication through comparison of Korean beginner textbook reading text structure: With a focus on rhetorical structure characteristics." Korean Association for Literacy 14, no. 6 (December 31, 2023): 429–60. http://dx.doi.org/10.37736/kjlr.2023.12.14.6.15.

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This study compared and analyzed rhetorical structure to solidify text hierarchization according to the Rhetorical Structure theory in Korean elementary textbooks. Therefore, 70% of Korean beginner reading text suggests that it needs to be composed with a center of joint, sequence, elaboration, and cause and effect relationship. Likewise, schematic relationship appearing with semantic relationship, needs to be composed to appear incomplete three-stage composition and complex deformation structure, and an educational effect may exist in various language functions. Based on this result, this study helps set the foundation for Korean beginner reading text hierarchization.

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Lambrianides, A., and IP Giles. "Use of monoclonal antibodies to dissect specificity and pathogenesis of antiphospholipid antibodies." Lupus 19, no. 4 (March 30, 2010): 359–64. http://dx.doi.org/10.1177/0961203309360809.

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Monoclonal antiphospholipid antibodies (aPL) have been utilized to dissect the relationship between their sequence, structure, binding and biological properties relevant to the pathogenesis of the antiphospholipid syndrome. In particular, sequence analysis of aPL has highlighted the clustering of certain amino acid residues in the antigen contact sites of their heavy and light chains. Therefore, these sequence motifs are likely to be important in determining aPL binding properties and their pathogenic effects. Experiments, however, using monoclonal aPL engineered to contain specific point mutations in their sequence which alter their ability to bind relevant antigens have shown that these alterations in binding are not directly mirrored by their pathogenic effects. In this review we focus on work carried out by others and ourselves using monoclonal antibodies with specific binding properties to extend our knowledge of the non-linear structure—binding—function relationship of aPL.

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Shen, Libing, Chao Chen, Hongxiang Zheng, and Li Jin. "The Evolutionary Relationship between Microbial Rhodopsins and Metazoan Rhodopsins." Scientific World Journal 2013 (2013): 1–10. http://dx.doi.org/10.1155/2013/435651.

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Rhodopsins are photoreceptive proteins with seven-transmembrane alpha-helices and a covalently bound retinal. Based on their protein sequences, rhodopsins can be classified into microbial rhodopsins and metazoan rhodopsins. Because there is no clearly detectable sequence identity between these two groups, their evolutionary relationship was difficult to decide. Through ancestral state inference, we found that microbial rhodopsins and metazoan rhodopsins are divergently related in their seven-transmembrane domains. Our result proposes that they are homologous proteins and metazoan rhodopsins originated from microbial rhodopsins. Structure alignment shows that microbial rhodopsins and metazoan rhodopsins share a remarkable structural homology while the position of retinal-binding lysine is different between them. It suggests that the function of photoreception was once lost during the evolution of rhodopsin genes. This result explains why there is no clearly detectable sequence similarity between the two rhodopsin groups: after losing the photoreception function, rhodopsin gene was freed from the functional constraint and the process of divergence could quickly change its original sequence beyond recognition.

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Hall, Branwen M., Sue A. Roberts, and Matthew H. J. Cordes. "Extreme divergence between one-to-one orthologs: the structure of N15 Cro bound to operator DNA and its relationship to the λ Cro complex." Nucleic Acids Research 47, no. 13 (June 10, 2019): 7118–29. http://dx.doi.org/10.1093/nar/gkz507.

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Abstract The gene cro promotes lytic growth of phages through binding of Cro protein dimers to regulatory DNA sites. Most Cro proteins are one-to-one orthologs, yet their sequence, structure and binding site sequences are quite divergent across lambdoid phages. We report the cocrystal structure of bacteriophage N15 Cro with a symmetric consensus site. We contrast this complex with an orthologous structure from phage λ, which has a dissimilar binding site sequence and a Cro protein that is highly divergent in sequence, dimerization interface and protein fold. The N15 Cro complex has less DNA bending and smaller DNA-induced changes in protein structure. N15 Cro makes fewer direct contacts and hydrogen bonds to bases, relying mostly on water-mediated and Van der Waals contacts to recognize the sequence. The recognition helices of N15 Cro and λ Cro make mostly nonhomologous and nonanalogous contacts. Interface alignment scores show that half-site binding geometries of N15 Cro and λ Cro are less similar to each other than to distantly related CI repressors. Despite this divergence, the Cro family shows several code-like protein–DNA sequence covariations. In some cases, orthologous genes can achieve a similar biological function using very different specific molecular interactions.

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Zarina, S., A. Abbasi, and Z. H. Zaidi. "Primary structure of βs-crystallin from human lens." Biochemical Journal 287, no. 2 (October 15, 1992): 375–81. http://dx.doi.org/10.1042/bj2870375.

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The complete primary structure of beta s-crystallin from human lens is reported. The sequence was elucidated by automatic Edman degradation of tryptic and CNBr peptides. The blocked N-terminal dipeptide was identified by fast-atom-bombardment mass spectroscopy. The sequence comparison with other members of crystallin family reveals a closer relationship to human gamma-crystallin (53% identity) than with beta A3/A1 crystallin (37% identity). The structure, evolutionary characteristics and role of beta s-crystallin in lens are discussed.

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Osorio, Manuel I., and Dino G. Salinas. "Exploring the structure–function relationship in a hypothetical membrane protein from a nucleotide sequence." Biochemistry and Molecular Biology Education 49, no. 4 (April 29, 2021): 652–57. http://dx.doi.org/10.1002/bmb.21524.

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Ohshima, Keiichic, Sachiyo Takeda, Mariko Hirose, Yasuto Akiyama, Kazuaki Iguchi, Minoru Hoshino, Ken Yamaguchi, and Tohru Mochizuki. "Structure-function relationship of the nuclear localization signal sequence of parathyroid hormone-related protein." Biomedical Research 33, no. 3 (2012): 191–99. http://dx.doi.org/10.2220/biomedres.33.191.

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Cinti, F. R., L. Cucci, F. Marra, and P. Montone. "The 1997 Umbria-Marche (Italy) earthquake sequence: Relationship between ground deformation and seismogenic structure." Geophysical Research Letters 26, no. 7 (April 1, 1999): 895–98. http://dx.doi.org/10.1029/1999gl900142.

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Aina, A., and S. Wallin. "Multisequence algorithm for coarse-grained biomolecular simulations: Exploring the sequence-structure relationship of proteins." Journal of Chemical Physics 147, no. 9 (September 7, 2017): 095102. http://dx.doi.org/10.1063/1.4986933.

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PETERSON, M. Gregory, Frances HANNAN, and Julian F. B. MERCER. "The sheep metallothionein gene family. Structure, sequence and evolutionary relationship of five linked genes." European Journal of Biochemistry 174, no. 2 (June 1988): 417–24. http://dx.doi.org/10.1111/j.1432-1033.1988.tb14114.x.

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Toogood, C. I. A., R. Murali, R. M. Burnett, and R. T. Hay. "The Adenovirus Type 40 Hexon: Sequence, Predicted Structure and Relationship to Other Adenovirus Hexons." Journal of General Virology 70, no. 12 (December 1, 1989): 3203–14. http://dx.doi.org/10.1099/0022-1317-70-12-3203.

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Kumar, Shiv, Puja Bhagabati, Reena Sachan, Aman Chandra Kaushik, and Vivek Dhar Dwivedi. "In Silico Analysis of Sequence–Structure–Function Relationship of the Escherichia coli Methionine Synthase." Interdisciplinary Sciences: Computational Life Sciences 7, no. 4 (July 30, 2015): 382–90. http://dx.doi.org/10.1007/s12539-015-0271-z.

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Zelezetsky, Igor, and Alessandro Tossi. "Alpha-helical antimicrobial peptides—Using a sequence template to guide structure–activity relationship studies." Biochimica et Biophysica Acta (BBA) - Biomembranes 1758, no. 9 (September 2006): 1436–49. http://dx.doi.org/10.1016/j.bbamem.2006.03.021.

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MacGregor, E. Ann, Štefan Janeček, and Birte Svensson. "Relationship of sequence and structure to specificity in the α-amylase family of enzymes." Biochimica et Biophysica Acta (BBA) - Protein Structure and Molecular Enzymology 1546, no. 1 (March 2001): 1–20. http://dx.doi.org/10.1016/s0167-4838(00)00302-2.

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Wang, Zhiyong, and Jinbo Xu. "A conditional random fields method for RNA sequence–structure relationship modeling and conformation sampling." Bioinformatics 27, no. 13 (June 14, 2011): i102—i110. http://dx.doi.org/10.1093/bioinformatics/btr232.

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Esque, Jérémy, Aurélie Urbain, Catherine Etchebest, and Alexandre G. de Brevern. "Sequence–structure relationship study in all-α transmembrane proteins using an unsupervised learning approach." Amino Acids 47, no. 11 (June 5, 2015): 2303–22. http://dx.doi.org/10.1007/s00726-015-2010-5.

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LIU, XIN, and WEI-MOU ZHENG. "AN AMINO ACID SUBSTITUTION MATRIX FOR PROTEIN CONFORMATION IDENTIFICATION." Journal of Bioinformatics and Computational Biology 04, no. 03 (June 2006): 769–82. http://dx.doi.org/10.1142/s0219720006002156.

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Amino acid substitution matrices play an essential role in protein sequence alignment, a fundamental task in bioinformatics. Most widely used matrices, such as PAM matrices derived from homologous sequences and BLOSUM matrices derived from aligned segments of PROSITE, did not integrate conformation information in their construction. There are a few structure-based matrices, which are derived from limited data of structure alignment. Using databases PDB_SELECT and DSSP, we create a database of sequence-conformation blocks which explicitly represent sequence-structure relationship. Members in a block are identical in conformation and are highly similar in sequence. From this block database, we derive a conformation-specific amino acid substitution matrix CBSM60. The matrix shows an improved performance in conformational segment search and homolog detection.

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Wool, Ira G., Yuen-Ling Chan, and Anton Glück. "Structure and evolution of mammalian ribosomal proteins." Biochemistry and Cell Biology 73, no. 11-12 (December 1, 1995): 933–47. http://dx.doi.org/10.1139/o95-101.

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Mammalian (rat) ribosomes have 80 proteins; the sequence of amino acids in 75 have been determined. What has been learned of the structure of the rat ribosomal proteins is reviewed with particular attention to their evolution and to amino acid sequence motifs. The latter include: clusters of basic or acidic residues; sequence repeats or shared sequences; zinc finger domains; bZIP elements; and nuclear localization signals. The occurrence and the possible significance of phosphorylated residues and of ubiquitin extensions is noted. The characteristics of the mRNAs that encode the proteins are summarized. The relationship of the rat ribosomal proteins to the proteins in ribosomes from humans, yeast, archaebacteria, and Escherichia coli is collated.Key words: ribosomes, ribosomal proteins, amino acid sequence, evolution.

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Raethong, Nachon, Jirasak Wong-ekkabut, Kobkul Laoteng, and Wanwipa Vongsangnak. "Sequence- and Structure-Based Functional Annotation and Assessment of Metabolic Transporters inAspergillus oryzae: A Representative Case Study." BioMed Research International 2016 (2016): 1–13. http://dx.doi.org/10.1155/2016/8124636.

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Aspergillus oryzaeis widely used for the industrial production of enzymes. InA. oryzaemetabolism, transporters appear to play crucial roles in controlling the flux of molecules for energy generation, nutrients delivery, and waste elimination in the cell. While theA. oryzaegenome sequence is available, transporter annotation remains limited and thus the connectivity of metabolic networks is incomplete. In this study, we developed a metabolic annotation strategy to understand the relationship between the sequence, structure, and function for annotation ofA. oryzaemetabolic transporters. Sequence-based analysis with manual curation showed that 58 genes of 12,096 total genes in theA. oryzaegenome encoded metabolic transporters. Under consensus integrative databases, 55 unambiguous metabolic transporter genes were distributed into channels and pores (7 genes), electrochemical potential-driven transporters (33 genes), and primary active transporters (15 genes). To reveal the transporter functional role, a combination of homology modeling and molecular dynamics simulation was implemented to assess the relationship between sequence to structure and structure to function. As in the energy metabolism ofA. oryzae, the H+-ATPase encoded by the AO090005000842 gene was selected as a representative case study of multilevel linkage annotation. Our developed strategy can be used for enhancing metabolic network reconstruction.

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Wetzel, Katharina S., and Michael A. R. Meier. "Monodisperse, sequence-defined macromolecules as a tool to evaluate the limits of ring-closing metathesis." Polymer Chemistry 10, no. 21 (2019): 2716–22. http://dx.doi.org/10.1039/c9py00438f.

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Sequence-defined macromolecules of uniform size unlock the door to many new applications in polymer chemistry, such as structure/property or structure/activity relationship investigations, which cannot be conducted accurately, if the investigated macromolecules exhibit dispersity.

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Su, Ying Ying, Hai Dong, and Di Liang. "Assembly Sequence Planning Based on Connector Structure and Ant Colony Algorithm." Advanced Materials Research 712-715 (June 2013): 2482–86. http://dx.doi.org/10.4028/www.scientific.net/amr.712-715.2482.

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For the purpose of effectively reducing the degree of complexity and improving the efficiency, the method of assembly sequence planning based on connector structure and ant algorithm was proposed. The concept of connector structure was presented, which was regarded as basic assembly unit to cover features of assembly parts. Then, a model of assembly sequence planning was built, which represented the precedence constraint relationship among connector structures. Additionally, the combination of the connector structure concept and characteristics of ant colony algorithm was developed for generating optimal assembly sequences under the guidance of precedence relations in the model. Finally, an example was studied to illustrate the effectiveness of the strategy.

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Fridmanis, Jēkabs, Zigmantas Toleikis, Tomas Sneideris, Mantas Ziaunys, Raitis Bobrovs, Vytautas Smirnovas, and Kristaps Jaudzems. "Aggregation Condition–Structure Relationship of Mouse Prion Protein Fibrils." International Journal of Molecular Sciences 22, no. 17 (September 6, 2021): 9635. http://dx.doi.org/10.3390/ijms22179635.

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Prion diseases are associated with conformational conversion of cellular prion protein into a misfolded pathogenic form, which resembles many properties of amyloid fibrils. The same prion protein sequence can misfold into different conformations, which are responsible for variations in prion disease phenotypes (prion strains). In this work, we use atomic force microscopy, FTIR spectroscopy and magic-angle spinning NMR to devise structural models of mouse prion protein fibrils prepared in three different denaturing conditions. We find that the fibril core region as well as the structure of its N- and C-terminal parts is almost identical between the three fibrils. In contrast, the central part differs in length of β-strands and the arrangement of charged residues. We propose that the denaturant ionic strength plays a major role in determining the structure of fibrils obtained in a particular condition by stabilizing fibril core interior-facing glutamic acid residues.

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Journal articles on the topic 'Sequence-Structure relationship'

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