scholarly journals Exploring the binding properties and structural stability of an opsin in the chytrid Spizellomyces punctatus using comparative and molecular modeling

2016 ◽  
Author(s):  
Steven R Ahrendt ◽  
Edgar Mauricio Medina ◽  
Chia-en A Chang ◽  
Jason E Stajich
Keyword(s):  
Molecular Modeling ◽  
Structural Characteristics ◽  
Sequence Similarity ◽  
Ligand Docking ◽  
Binding Properties ◽  
Function Relationship ◽  
Relationship Of ◽  
Future Work

Background. Opsin proteins are seven transmembrane receptor proteins which detect light. Opsins can be classified into two types and share little sequence identity: type 1, typically found in bacteria, and type 2, primarily characterized in metazoa. The type 2 opsins (Rhodopsins) are a subfamily of G-protein coupled receptors (GPCRs), a large and diverse class of seven transmembrane proteins and are generally restricted to metazoan lineages. Fungi use light receptors including opsins to sense the environment and transduce signals for developmental or metabolic changes. Opsins characterized in the Dikarya (Ascomycetes and Basidiomycetes) are of the type 1 bacteriorhodopsin family but the early diverging fungal lineages have not been as well surveyed. We identified by sequence similarity a rhodopsin-like GPCR in genomes of early diverging chytrids and examined the structural characteristics of this protein to assess its likelihood to be homologous to animal rhodopsins and bind similar chromophores. Methods. We used template-based structure modeling, automated ligand docking, and molecular modeling to assess the structural and binding properties of an identified opsin-like protein found in Spizellomyces punctatus, a unicellular, flagellated species belonging to Chytridiomycota, one of the earliest diverging fungal lineages. We tested if sequence and inferred structure were consistent with a solved crystal structure of a type 2 rhodopsin from the squid Todarodes pacificus. Results. Our results indicate that the Spizellomyces opsin has structural characteristics consistent with functional animal type 2 rhodopsins and is capable of maintaining a stable structure when associated with the retinaldehyde chromophore, specifically the 9-cis­-retinal isomer. Together, these results support further the homology of Spizellomyces opsins to animal type 2 rhodopsins. Discussion. This represents the first test of structure/function relationship of a type 2 rhodopsin identified in early branching fungal lineages, and provides a foundation for future work exploring pathways and components of photoreception in early fungi.

scholarly journals Exploring the binding properties and structural stability of an opsin in the chytrid Spizellomyces punctatus using comparative and molecular modeling

2017 ◽  
Author(s):  
Steven R Ahrendt ◽  
Edgar Mauricio Medina ◽  
Chia-en A Chang ◽  
Jason E Stajich
Keyword(s):  
Molecular Modeling ◽  
Structural Characteristics ◽  
Sequence Similarity ◽  
Ligand Docking ◽  
Binding Properties ◽  
Function Relationship ◽  
Relationship Of ◽  
Future Work

Background. Opsin proteins are seven transmembrane receptor proteins which detect light. Opsins can be classified into two types and share little sequence identity: type 1, typically found in bacteria, and type 2, primarily characterized in metazoa. The type 2 opsins (Rhodopsins) are a subfamily of G-protein coupled receptors (GPCRs), a large and diverse class of seven transmembrane proteins and are generally restricted to metazoan lineages. Fungi use light receptors including opsins to sense the environment and transduce signals for developmental or metabolic changes. Opsins characterized in the Dikarya (Ascomycetes and Basidiomycetes) are of the type 1 bacteriorhodopsin family but the early diverging fungal lineages have not been as well surveyed. We identified by sequence similarity a rhodopsin-like GPCR in genomes of early diverging chytrids and examined the structural characteristics of this protein to assess its likelihood to be homologous to animal rhodopsins and bind similar chromophores. Methods. We used template-based structure modeling, automated ligand docking, and molecular modeling to assess the structural and binding properties of an identified opsin-like protein found in Spizellomyces punctatus, a unicellular, flagellated species belonging to Chytridiomycota, one of the earliest diverging fungal lineages. We tested if sequence and inferred structure were consistent with a solved crystal structure of a type 2 rhodopsin from the squid Todarodes pacificus. Results. Our results indicate that the Spizellomyces opsin has structural characteristics consistent with functional animal type 2 rhodopsins and is capable of maintaining a stable structure when associated with the retinaldehyde chromophore, specifically the 9-cis­-retinal isomer. Together, these results support further the homology of Spizellomyces opsins to animal type 2 rhodopsins. Discussion. This represents the first test of structure/function relationship of a type 2 rhodopsin identified in early branching fungal lineages, and provides a foundation for future work exploring pathways and components of photoreception in early fungi.

scholarly journals Exploring the binding properties and structural stability of an opsin in the chytridSpizellomyces punctatususing comparative and molecular modeling

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3206 ◽  
Author(s):  
Steven R. Ahrendt ◽  
Edgar Mauricio Medina ◽  
Chia-en A. Chang ◽  
Jason E. Stajich
Keyword(s):  
Molecular Modeling ◽  
Structural Characteristics ◽  
Sequence Similarity ◽  
Ligand Docking ◽  
Binding Properties ◽  
Function Relationship ◽  
Relationship Of ◽  
Future Work

BackgroundOpsin proteins are seven transmembrane receptor proteins which detect light. Opsins can be classified into two types and share little sequence identity: type 1, typically found in bacteria, and type 2, primarily characterized in metazoa. The type 2 opsins (Rhodopsins) are a subfamily of G-protein coupled receptors (GPCRs), a large and diverse class of seven transmembrane proteins and are generally restricted to metazoan lineages. Fungi use light receptors including opsins to sense the environment and transduce signals for developmental or metabolic changes. Opsins characterized in the Dikarya (Ascomycetes and Basidiomycetes) are of the type 1 bacteriorhodopsin family but the early diverging fungal lineages have not been as well surveyed. We identified by sequence similarity a rhodopsin-like GPCR in genomes of early diverging chytrids and examined the structural characteristics of this protein to assess its likelihood to be homologous to animal rhodopsins and bind similar chromophores.MethodsWe used template-based structure modeling, automated ligand docking, and molecular modeling to assess the structural and binding properties of an identified opsin-like protein found inSpizellomyces punctatus, a unicellular, flagellated species belonging to Chytridiomycota, one of the earliest diverging fungal lineages. We tested if the sequence and inferred structure were consistent with a solved crystal structure of a type 2 rhodopsin from the squidTodarodes pacificus.ResultsOur results indicate that theSpizellomycesopsin has structural characteristics consistent with functional animal type 2 rhodopsins and is capable of maintaining a stable structure when associated with the retinaldehyde chromophore, specifically the 9-cis-retinal isomer. Together, these results support further the homology ofSpizellomycesopsins to animal type 2 rhodopsins.DiscussionThis represents the first test of structure/function relationship of a type 2 rhodopsin identified in early branching fungal lineages, and provides a foundation for future work exploring pathways and components of photoreception in early fungi.

scholarly journals Exploring the binding properties and structural stability of an opsin in the chytrid Spizellomyces punctatus using comparative and molecular modeling

2017 ◽  
Author(s):  
Steven R Ahrendt ◽  
Edgar Mauricio Medina ◽  
Chia-en A Chang ◽  
Jason E Stajich
Keyword(s):  
Molecular Modeling ◽  
Structural Characteristics ◽  
Sequence Similarity ◽  
Ligand Docking ◽  
Binding Properties ◽  
Function Relationship ◽  
Relationship Of ◽  
Future Work

Background. Opsin proteins are seven transmembrane receptor proteins which detect light. Opsins can be classified into two types and share little sequence identity: type 1, typically found in bacteria, and type 2, primarily characterized in metazoa. The type 2 opsins (Rhodopsins) are a subfamily of G-protein coupled receptors (GPCRs), a large and diverse class of seven transmembrane proteins and are generally restricted to metazoan lineages. Fungi use light receptors including opsins to sense the environment and transduce signals for developmental or metabolic changes. Opsins characterized in the Dikarya (Ascomycetes and Basidiomycetes) are of the type 1 bacteriorhodopsin family but the early diverging fungal lineages have not been as well surveyed. We identified by sequence similarity a rhodopsin-like GPCR in genomes of early diverging chytrids and examined the structural characteristics of this protein to assess its likelihood to be homologous to animal rhodopsins and bind similar chromophores. Methods. We used template-based structure modeling, automated ligand docking, and molecular modeling to assess the structural and binding properties of an identified opsin-like protein found in Spizellomyces punctatus, a unicellular, flagellated species belonging to Chytridiomycota, one of the earliest diverging fungal lineages. We tested if sequence and inferred structure were consistent with a solved crystal structure of a type 2 rhodopsin from the squid Todarodes pacificus. Results. Our results indicate that the Spizellomyces opsin has structural characteristics consistent with functional animal type 2 rhodopsins and is capable of maintaining a stable structure when associated with the retinaldehyde chromophore, specifically the 9-cis­-retinal isomer. Together, these results support further the homology of Spizellomyces opsins to animal type 2 rhodopsins. Discussion. This represents the first test of structure/function relationship of a type 2 rhodopsin identified in early branching fungal lineages, and provides a foundation for future work exploring pathways and components of photoreception in early fungi.

Comparing the Arrangements of Governance and Sustainable Development in OECD Countries: Coupled or Decoupled?

2019 ◽  
Vol 34 (1) ◽  
pp. 99-117
Author(s):  
Huh Taewook
Keyword(s):  
Sustainable Development ◽  
Oecd Countries ◽  
The Other ◽  
Type Analysis ◽  
Ideal Types ◽  
Type 3 ◽  
Relationship Of ◽  
The Relationship

This study attempts to analyze to what extent governance and sustainable development (SD) empirically appear compatible in the thirtyfive OECD countries through the fuzzy-set ideal type analysis, and identify which ideal types appear coupled or decoupled, and then reveal which countries belong to the coupled types or to the decoupled types. In short, twenty-two countries (including Sweden (fuzzy score, 0.953), Denmark (0.920), Finland (0.914), Norway (0.911) in Type 1 (G*S, ‘strong G-S coupled countries’); and Turkey (0.906), Greece (0.833), Mexico (0.828) in Type 4 (g*s, ‘lite g-s coupled countries’) are in line with the accepted conventions regarding the compatible relationship between governance and SD. On the other hand, the rest of thirteen countries (including USA (fuzzy score, 0.815), Luxembourg (0.721), Australia (0.660) in Type 2 (G*s, ‘G-s decoupled countries’); and Slovenia (0.728), France (0.644), Czech Rep. (0.625) in Type 3 (g*S, ‘g-S decoupled countries’) may indicate that the relationship of governance and SD is in fact experiencing tensions in the national contexts. These findings are characterized by the substance (of SD) and procedure (of governance) divide. Considering the results, this study focuses on the idea of reflexivity or reflexive capacity.

scholarly journals The Role of the Fibronectin IGD Motif in Stimulating Fibroblast Migration

2007 ◽  
Vol 282 (49) ◽  
pp. 35530-35535 ◽  
Author(s):  
Christopher J. Millard ◽  
Ian R. Ellis ◽  
Andrew R. Pickford ◽  
Ana M. Schor ◽  
Seth L. Schor ◽  
...  
Keyword(s):  
Fibroblast Migration ◽  
Wide Range ◽  
Migration Stimulating Factor ◽  
Function Relationship ◽  
Relationship Of ◽  
Stimulating Factor ◽  
Insight Into ◽  
Stimulation Of

The motogenic activity of migration-stimulating factor, a truncated isoform of fibronectin (FN), has been attributed to the IGD motifs present in its FN type 1 modules. The structure-function relationship of various recombinant IGD-containing FN fragments is now investigated. Their structure is assessed by solution state NMR and their motogenic ability tested on fibroblasts. Even conservative mutations in the IGD motif are inactive or have severely reduced potency, while the structure remains essentially the same. A fragment with two IGD motifs is 100 times more active than a fragment with one and up to 106 times more than synthetic tetrapeptides. The wide range of potency in different contexts is discussed in terms of cryptic FN sites and cooperativity. These results give new insight into the stimulation of fibroblast migration by IGD motifs in FN.

The Neutralization Relationship of HIV Type 1, HIV Type 2, and SIVcpz Is Reflected in the Genetic Diversity that Distinguishes Them

1997 ◽  
Vol 13 (1) ◽  
pp. 7-17 ◽  
Author(s):  
PHILLIPE N. NYAMBI ◽  
BETTY WILLEMS ◽  
WOUTER JANSSENS ◽  
KATRIEN FRANSEN ◽  
JOHN NKENGASONG ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Hiv Type 1 ◽  
Relationship Of

Depression and the Reporting of Diabetes Symptoms

1989 ◽  
Vol 18 (4) ◽  
pp. 295-303 ◽  
Author(s):  
Patrick J. Lustman ◽  
Ray E. Clouse ◽  
Robert M. Carney
Keyword(s):  
Metabolic Control ◽  
Glycosylated Hemoglobin ◽  
Blood Glucose Control ◽  
Depressive Mood ◽  
Diabetes Mellitus Type 1 ◽  
Patients With Diabetes ◽  
Relationship Of ◽  
The Relationship

The relationship of diabetes symptoms to current mood and general metabolic control was studied. Symptoms commonly associated with poorly controlled diabetes (e.g., thirst, polyuria, weight loss) were measured in 114 patients with diabetes mellitus (type 1 = 57, type 2 = 57). Scores for these individual symptoms were correlated with glycosylated hemoglobin (HbA1) and depression as measured by the Beck Depression Inventory (BDI). HbA1 was poorly correlated ( r < 0.2) with nine of the eleven symptoms and made a significant independent contribution only to the reporting of polyuria ( p = 0.04). In contrast, depression was moderately correlated with nine symptoms and had a significant effect on the reporting of two of three hyperglycemic symptoms, five of six hypoglycemic symptoms, and both nonspecific symptoms of poor control ( p < 0.05 for each). We conclude that many reported symptoms often attributed to diabetes are more related to depressive mood than to a conventional clinical measure of blood glucose control. Diabetes symptoms may be unreliable indicators of poor metabolic control when features suggestive of depression are present.

scholarly journals Investigation of Action Pattern of a Novel Chondroitin Sulfate/Dermatan Sulfate 4-O-Endosulfatase

2020 ◽  
Author(s):  
Wenshuang Wang ◽  
Cédric Przybylski ◽  
Xiaojuan Cai ◽  
Chrystel Lopin-Bon ◽  
Runmiao Jiao ◽  
...  
Keyword(s):  
Chondroitin Sulfate ◽  
Marine Bacterium ◽  
Catalytic Mechanism ◽  
Dermatan Sulfate ◽  
Structural Characteristics ◽  
Action Pattern ◽  
Substrate Specificities ◽  
Substrate Size ◽  
Function Relationship ◽  
Relationship Of

Recently, a novel CS/DS 4-O-endosulfatase was identified from a marine bacterium and its catalytic mechanism was investigated further (Wang, W., et.al (2015) J. Biol. Chem. 290, 7823-7832; Wang, S., et.al (2019) Front. Microbiol. 10:1309). In the study herein, we provide new insight about the structural characteristics of substrate which determine the activity of this enzyme. The substrate specificities of the 4-O-endosulfatase were probed by using libraries of structure-defined CS/DS oligosacccharides issued from synthetic and enzymatic sources. We found that this 4-O-endosulfatase effectively remove the 4-O-sulfate of disaccharide sequences GlcUAβ1-3GalNAc(4S) or GlcUAβ1-3GalNAc(4S,6S) in all tested hexasaccharides. The sulfated GalNac residue is resistant to the enzyme when adjacent uronic residues are sulfated as shown by the lack of enzymatic desulfation of GlcUAβ1-3GalNAc(4S) connected to a disaccharide GlcUA(2S)β1-3GalNAc(6S) in an octasaccharide. The 3-O-sulfation of GlcUA was also shown to hinder the action of this enzyme. The 4-O-endosulfatase exhibited an oriented action from the reducing to the non-reducing whatever the saturation or not of the non-reducing end. Finally, the activity of the 4-O-endosulfatase decreases with the increase of substrate size. With the deeper understanding of this novel 4-O-endosulfatase, such chondroitin sulfate (CS)/dermatan sulfate (DS) sulfatase is a useful tool for exploring the structure-function relationship of CS/DS.

Characterization of the pits in parenchyma cells of the moso bamboo [Phyllostachys edulis (Carr.) J. Houz.] culm

Holzforschung ◽  
2019 ◽  
Vol 73 (7) ◽  
pp. 629-636 ◽  
Author(s):  
Caiping Lian ◽  
Rong Liu ◽  
Cheng Xiufang ◽  
Shuqing Zhang ◽  
Junji Luo ◽  
...  
Keyword(s):  
Structural Characteristics ◽  
Parenchyma Cell ◽  
Environmental Scanning Electron Microscopy ◽  
Environmental Scanning ◽  
Bordered Pits ◽  
Parenchyma Cells ◽  
Vascular Parenchyma ◽  
Function Relationship ◽  
Relationship Of ◽  
First Time

Abstract The pits on parenchyma cell walls facilitate transfer of liquids between adjacent cells in the bamboo. To better understand the structure-function relationship of the pits, the structural characteristics of the pits in bamboo parenchyma cells need to be investigated. In this study, the pit structures were studied by field-emission environmental scanning electron microscopy (SEM). The samples included the native structure and the replica structure via resin castings. The results showed that the parenchyma cells possessed various shapes and the pits were diverse. Parenchyma cells exposed both simple and bordered pits. Pitting between vascular parenchyma cells (VPCs) was similar to that of the metaxylem vessel. In particular, a branched pit structure was found for the first time in the parenchyma cell.

scholarly journals Botanical, Pharmacological, Phytochemical, and Toxicological Aspects of the Antidiabetic PlantBidens pilosaL.

2014 ◽  
Vol 2014 ◽  
pp. 1-14 ◽  
Author(s):  
Wen-Chin Yang
Keyword(s):  
Present Review ◽  
Bidens Pilosa ◽  
Traditional Use ◽  
The Past ◽  
Preliminary Information ◽  
Structure Activity ◽  
Biological Studies ◽  
Relationship Of

Bidens pilosaL. is an easy-to-grow, widespread, and palatable perennial on earth. Hence, it has traditionally been used as foods and medicines without noticeable adverse effects. Despite significant advancement in chemical and biological studies ofB. pilosaover the past few years, comprehensive and critical reviews on its anti-diabetic properties are missing. The present review is to summarize up-to-date information on the pharmacology, phytochemistry, and toxicology ofB. pilosa, in regard to type 1 diabetes and type 2 diabetes from the literature. In addition to botanical studies and records of the traditional use ofB. pilosain diabetes, scientific studies investigating antidiabetic action of this species and its active phytochemicals are presented and discussed. The structure and biosynthesis ofB. pilosaand its polyynes in relation to their anti-diabetic action and mechanism are emphasized. Although some progress has been made, rigorous efforts are further required to unlock the molecular basis and structure-activity relationship of the polyynes isolated fromB. pilosabefore their clinical applications. The present review provides preliminary information and gives guidance for further anti-diabetic research and development of this plant.

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