scholarly journals Finding Aquaporins in Annelids: An Evolutionary Analysis and a Case Study

Cells ◽  
2021 ◽  
Vol 10 (12) ◽  
pp. 3562
Author(s):  
Serena Mucciolo ◽  
Andrea Desiderato ◽  
Marika Salonna ◽  
Tomasz Mamos ◽  
Viviane Prodocimo ◽  
...  
Keyword(s):  
High Salinity ◽  
Phylogenetic Analyses ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Evolutionary Analysis ◽  
Gene Duplications ◽  
Rt Pcr ◽  
Conserved Residues ◽  
Physiological Relevance

Aquaporins (AQPs) are a family of membrane channels facilitating diffusion of water and small solutes into and out of cells. Despite their biological relevance in osmoregulation and ubiquitous distribution throughout metazoans, the presence of AQPs in annelids has been poorly investigated. Here, we searched and annotated Aqp sequences in public genomes and transcriptomes of annelids, inferred their evolutionary relationships through phylogenetic analyses and discussed their putative physiological relevance. We identified a total of 401 Aqp sequences in 27 annelid species, including 367 sequences previously unrecognized as Aqps. Similar to vertebrates, phylogenetic tree reconstructions clustered these annelid Aqps in four clades: AQP1-like, AQP3-like, AQP8-like and AQP11-like. We found no clear indication of the existence of paralogs exclusive to annelids; however, several gene duplications seem to have occurred in the ancestors of some Sedentaria annelid families, mainly in the AQP1-like clade. Three of the six Aqps annotated in Alitta succinea, an estuarine annelid showing high salinity tolerance, were validated by RT-PCR sequencing, and their similarity to human AQPs was investigated at the level of “key” conserved residues and predicted three-dimensional structure. Our results suggest a diversification of the structures and functions of AQPs in Annelida comparable to that observed in other taxa.

scholarly journals Generative Models for Relief Perspective Architectures

2021 ◽  
Author(s):  
Leonardo Baglioni ◽  
Federico Fallavollita
Keyword(s):  
Research Methodology ◽  
Affine Space ◽  
Three Dimensional ◽  
Generative Models ◽  
Linear Perspective ◽  
Dimensional Structure ◽  
Three Dimensional Structure ◽  
Present Essay ◽  
Santa Maria

AbstractThe present essay investigates the potential of generative representation applied to the study of relief perspective architectures realized in Italy between the sixteenth and seventeenth centuries. In arts, and architecture in particular, relief perspective is a three-dimensional structure able to create the illusion of great depths in small spaces. A method of investigation applied to the case study of the Avila Chapel in Santa Maria in Trastevere in Rome (Antonio Gherardi 1678) is proposed. The research methodology can be extended to other cases and is based on the use of a Relief Perspective Camera, which can create both a linear perspective and a relief perspective. Experimenting mechanically and automatically the perspective transformations from the affine space to the illusory space and vice versa has allowed us to see the case study in a different light.

scholarly journals Computational Protein Stabilization Can Affect Folding Energy Landscapes and Lead to Domain-Swapped Dimers

2021 ◽  
Author(s):  
Klara Markova ◽  
Antonin Kunka ◽  
Klaudia Chmelova ◽  
Martin Havlasek ◽  
Petra Babkova ◽  
...  
Keyword(s):  
Protein Folding ◽  
Protein Design ◽  
Energy Landscape ◽  
Single Point ◽  
Three Dimensional ◽  
Protein Stabilization ◽  
Dimensional Structure ◽  
Evolutionary Analysis ◽  
Folding Energy

<p>The functionality of a protein depends on its unique three-dimensional structure, which is a result of the folding process when the nascent polypeptide follows a funnel-like energy landscape to reach a global energy minimum. Computer-encoded algorithms are increasingly employed to stabilize native proteins for use in research and biotechnology applications. Here, we reveal a unique example where the computational stabilization of a monomeric α/β-hydrolase enzyme (<i>T</i><sub>m</sub> = 73.5°C; Δ<i>T</i><sub>m</sub> > 23°C) affected the protein folding energy landscape. Introduction of eleven single-point stabilizing mutations based on force field calculations and evolutionary analysis yielded catalytically active domain-swapped intermediates trapped in local energy minima. Crystallographic structures revealed that these stabilizing mutations target cryptic hinge regions and newly introduced secondary interfaces, where they make extensive non-covalent interactions between the intertwined misfolded protomers. The existence of domain-swapped dimers in a solution is further confirmed experimentally by data obtained from SAXS and crosslinking mass spectrometry. Unfolding experiments showed that the domain-swapped dimers can be irreversibly converted into native-like monomers, suggesting that the domain-swapping occurs exclusively <i>in vivo</i>. Our findings uncovered hidden protein-folding consequences of computational protein design, which need to be taken into account when applying a rational stabilization to proteins of biological and pharmaceutical interest.</p>

scholarly journals Computational Protein Stabilization Can Affect Folding Energy Landscapes and Lead to Domain-Swapped Dimers

2021 ◽  
Author(s):  
Klara Markova ◽  
Antonin Kunka ◽  
Klaudia Chmelova ◽  
Martin Havlasek ◽  
Petra Babkova ◽  
...  
Keyword(s):  
Protein Folding ◽  
Protein Design ◽  
Energy Landscape ◽  
Single Point ◽  
Three Dimensional ◽  
Protein Stabilization ◽  
Dimensional Structure ◽  
Evolutionary Analysis ◽  
Folding Energy

<p>The functionality of a protein depends on its unique three-dimensional structure, which is a result of the folding process when the nascent polypeptide follows a funnel-like energy landscape to reach a global energy minimum. Computer-encoded algorithms are increasingly employed to stabilize native proteins for use in research and biotechnology applications. Here, we reveal a unique example where the computational stabilization of a monomeric α/β-hydrolase enzyme (<i>T</i><sub>m</sub> = 73.5°C; Δ<i>T</i><sub>m</sub> > 23°C) affected the protein folding energy landscape. Introduction of eleven single-point stabilizing mutations based on force field calculations and evolutionary analysis yielded catalytically active domain-swapped intermediates trapped in local energy minima. Crystallographic structures revealed that these stabilizing mutations target cryptic hinge regions and newly introduced secondary interfaces, where they make extensive non-covalent interactions between the intertwined misfolded protomers. The existence of domain-swapped dimers in a solution is further confirmed experimentally by data obtained from SAXS and crosslinking mass spectrometry. Unfolding experiments showed that the domain-swapped dimers can be irreversibly converted into native-like monomers, suggesting that the domain-swapping occurs exclusively <i>in vivo</i>. Our findings uncovered hidden protein-folding consequences of computational protein design, which need to be taken into account when applying a rational stabilization to proteins of biological and pharmaceutical interest.</p>

scholarly journals Patterns of Diversity of Floral Symmetry in Angiosperms: A Case Study of the Order Apiales

Symmetry ◽  
2019 ◽  
Vol 11 (4) ◽  
pp. 473
Author(s):  
Maxim Nuraliev ◽  
Dmitry Sokoloff ◽  
Polina Karpunina ◽  
Alexei Oskolski
Keyword(s):  
Three Dimensional ◽  
Ecological Factors ◽  
Morphological Characters ◽  
Reproductive Organs ◽  
Dimensional Structure ◽  
Geometrical Approach ◽  
Floral Symmetry ◽  
Developmental Significance ◽  
General Appearance

Floral symmetry is widely known as one of the most important structural traits of reproductive organs in angiosperms. It is tightly related to the shape and arrangement of floral parts, and at the same time, it plays a key role in general appearance (visual gestalt) of a flower, which is especially important for the interactions of zoophilous flowers with their pollinators. The traditional classification of floral symmetry divides nearly all the diversity of angiosperm flowers into actinomorphic and zygomorphic ones. Within this system, which is useful for ecological studies, many variations of symmetry appear to be disregarded. At the same time, the diversity of floral symmetry is underpinned not only by ecological factors, but also by morphogenetic mechanisms and constraints. Sometimes it is not an easy task to uncover the adaptive or developmental significance of a change of the floral symmetry in a particular lineage. Using the asterid order Apiales as a model group, we demonstrate that such changes can correlate with the merism of the entire flower or of its particular whorl, with the relative orientation of gynoecium to the rest of the flower, with the presence of sterile floral elements and other morphological characters. Besides, in some taxa, the shape and symmetry of the flower change in the course of its development, which should be taken in consideration in morphological comparisons and evaluations of synapomorphies in a particular clade. Finally, we show that different results can be obtained due to employment of different approaches: for instance, many flowers that are traditionally described as actinomorphic turn out to be disymmetric, monosymmetric, or asymmetric from a more detailed look. The traditional method of division into actinomorphy and zygomorphy deals with the general appearance of a flower, and mainly considers the shape of the corolla, while the geometrical approach handles the entire three-dimensional structure of the flower, and provides an exact number of its symmetry planes.

scholarly journals Modelling the 2-kinase domain of 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase on adenylate kinase

1997 ◽  
Vol 321 (3) ◽  
pp. 615-621 ◽  
Author(s):  
Luc BERTRAND ◽  
Didier VERTOMMEN ◽  
Eric DEPIEREUX ◽  
Louis HUE ◽  
Mark H. RIDER ◽  
...  
Keyword(s):  
Adenylate Kinase ◽  
Structural Model ◽  
Three Dimensional ◽  
Kinase Domain ◽  
Multiple Alignment ◽  
Site Directed Mutagenesis ◽  
Dimensional Structure ◽  
Conserved Residues ◽  
Nucleotide Binding Proteins ◽  
Sequence Similarities

Simultaneous multiple alignment of available sequences of the bifunctional enzyme 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase revealed several segments of conserved residues in the 2-kinase domain. The sequence of the kinase domain was also compared with proteins of known three-dimensional structure. No similarity was found between the kinase domain of 6-phosphofructo-2-kinase and 6-phosphofructo-1-kinase. This questions the modelling of the 2-kinase domain on bacterial 6-phosphofructo-1-kinase that has previously been proposed [Bazan, Fletterick and Pilkis (1989) Proc. Natl. Acad. Sci. U.S.A. 86, 9642Ő9646]. However, sequence similarities were found between the 2-kinase domain and several nucleotide-binding proteins, the most similar being adenylate kinase. A structural model of the 2-kinase domain based on adenylate kinase is proposed. It accommodates all the results of site-directed mutagenesis studies carried out to date on residues in the 2-kinase domain. It also allows residues potentially involved in catalysis and/or substrate binding to be predicted.

scholarly journals Mechanistic insights into molecular evolution of species-specific differential glycosaminoglycan binding surfaces in growth-related oncogene chemokines

2017 ◽  
Vol 4 (9) ◽  
pp. 171059 ◽  
Author(s):  
Khushboo Gulati ◽  
Minal Jamsandekar ◽  
Krishna Mohan Poluri
Keyword(s):  
Mammalian Species ◽  
Three Dimensional ◽  
Purifying Selection ◽  
Tissue Growth ◽  
Binding Domain ◽  
Dimensional Structure ◽  
Evolutionary Analysis ◽  
Evolutionary Mechanisms ◽  
Species Specific ◽  
Positively Selected Sites

Chemokines are chemotactic cytokines involved in leucocyte trafficking to infected tissue. Growth-related oncogene (GRO) chemokines namely CXCL1, CXCL2 and CXCL3 are neutrophil activating chemokines sharing a conserved three-dimensional structure, but encompassing functional diversity due to gene duplication and evolutionary events. However, the evolutionary mechanisms including selection pressures involved in diversification of GRO genes have not yet been characterized. Here, we performed comprehensive evolutionary analysis of GRO genes among different mammalian species. Phylogenetic analysis illustrated a species-specific evolution pattern. Selection analysis evidenced that these genes have undergone concerted evolution. Seventeen positively selected sites were obtained, although the majority of the protein is under purifying selection. Interestingly, these positively selected sites are more concentrated on the C-terminal/glycosaminoglycan (GAG) binding and dimerization segment compared to receptor binding domain. Substitution rate analysis confirmed the C-terminal domain of GRO genes as the highest substituted segment. Further, structural analysis established that the nucleotide alterations in the GAG binding domain are the source of surface charge modulation, thus generating the differential GAG binding surfaces and multiple binding sites as per evolutionary pressure, although the helical surface is primordial for GAG binding. Indeed, such variable electrostatic surfaces are crucial to regulate chemokine gradient formation during a host's defence against pathogens and also explain the significance of chemokine promiscuity.

scholarly journals Structural organization and evolution of the marsupial zona pellucida

Reproduction ◽  
2002 ◽  
pp. 13-21 ◽  
Author(s):  
WG Breed ◽  
RM Hope ◽  
OW Wiebkin ◽  
SC Spargo ◽  
JA Chapman
Keyword(s):  
Zona Pellucida ◽  
Structural Organization ◽  
Sequence Similarity ◽  
Phylogenetic Analyses ◽  
Three Dimensional ◽  
Reducing Agents ◽  
Molecular Organization ◽  
Dimensional Structure ◽  
High Sequence Similarity ◽  
Lectin Staining

In this review, the biochemical composition and structural organization of the marsupial and eutherian zonae pellucidae are compared. Differences between the zonae from these two groups of mammals are observed in their response to dilute proteases and reducing agents, in their potential glycosylation patterns, and in some of their functions. However, studies on the glycoconjugates and polypeptides of the three zona pellucida genes have not explained these different responses to the proteases and reducing agents. There is high sequence similarity between the zona polypeptides of marsupials and eutherians, as well as a similarity in the oligosaccharides present, as demonstrated by lectin staining. As the marsupial and eutherian lineages diverged from a common ancestor over 100 million years ago, these observations indicate that the three-dimensional structure of these glycoproteins is highly conserved throughout all mammals, although the complexity of its molecular organization has yet to be resolved. Phylogenetic analyses indicate that there are at least four groups of paralogous zona pellucida genes in vertebrates. The marsupial ZPA and ZPB genes have been named in accordance with their orthologues but the phylogenetic relationships of the marsupial ZPC gene require further investigation.

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