Structural and phylogenetic analysis of α-glucosidase protein in insects

Biologia ◽  
2015 ◽  
Vol 70 (6) ◽  
Author(s):  
Samin Seddigh ◽  
Maryam Darabi
Keyword(s):  
Phylogenetic Analysis ◽  
Tertiary Structure ◽  
Transmembrane Domain ◽  
Data Bank ◽  
Protein Data Bank Code ◽  
Protein Structure Analysis ◽  
Thale Cress ◽  
Wide Range ◽  
Protein Properties ◽  
Close Relationship

Abstractα-Glucosidases (αglus) (EC 3.2.1.20) have been detected in a wide range of plants, animals and microorganisms and are described by their ability to catalyze the hydrolysis of 1,4-α-glucosidic linkages, releasing α-glucose. In this study, 96 αglu protein sequences from 33 organisms species including different insects species, plants (including thale cress and rice), mammals (including human and mouse) and Mycobacterium tuberculosis as a bacterium were aligned. Sequences were analyzed by computational tools to predict the protein properties, such as molecular mass, isoelectric point, signal peptide, conserved motifs, transmembrane domain and secondary structure. Drosophila melanogaster (GenBank Accession No.: NP 610382) was chosen as one of the representatives of insects for further analyses. The tertiary structure of representative samples were acquired using the tertiary structure of oligo-1,6-glucosidase from Bacillus cereus (Protein Data Bank code: 1UOK) as a template by Phyre2 server. Protein structure analysis revealed there is a high identity among insects and other organisms. There were some similar functional domains between D. melanogaster and M. tuberculosis. The modeled αglu has a typical spatial structure in insects and exhibits a high similarity with other organisms, especially Arabidopsis thaliana. Phylogenetic analysis indicated that D. melanogaster αglu has a close relationship with other αglus from different insect families. According to these results, αglu in insects should be evolved from a common ancestor.

scholarly journals Molecular Dynamics Simulations of Mite Aquaporin DerfAQP1 from the Dust Mite Dermatophagoides farinae (Acariformes: Pyroglyphidae)

2020 ◽  
Vol 2020 ◽  
pp. 1-7
Author(s):  
Li-lei Wang ◽  
Li-li Yu ◽  
Ying Zhou ◽  
Mei-li Wu ◽  
Fei-xiang Teng ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Tertiary Structure ◽  
Large Family ◽  
Data Bank ◽  
Mite Species ◽  
Dynamics Simulation ◽  
Protein Data Bank Code ◽  
Dermatophagoides Farinae ◽  
Dust Mite ◽  
Dynamics Simulations

Aquaporins are a large family of transmembrane channel proteins that facilitate the passive but highly selective transport of water and other small solutes across biological membranes. House dust mite (Dermatophagoides farinae) is the major source of household immunogens, and we have recently reported six cDNA sequence encoding aquaporins from this mite species. To better understand the structure and role of mite aquaporin, we constructed a tertiary structure for DerfAQP1 by homology modeling from the X-ray structure of malaria aquaporin PfAQP (Protein Data Bank code No. 3C02) and conducted molecular dynamics simulation. The simulation arranged seven water molecules in a single file through the pores of the DerfAQP1. Further, two conserved Asn-Pro-Ala motifs were located on Asn203 and Asn77; residues Arg206, Trp57, Met190, Gly200, and Asp207 constituted an extracellular vestibule of the pore; and residues His75, Val80, Ile65, and Ile182 constituted the cytoplasmic portions. The overall free energy profile for water transport through DerfAQP1 revealed an energy barrier of ~2.5 kcal/mol. These results contribute to the understanding of mite physiology and pathology.

Constant pH Molecular Dynamics Reveals How Proton Release Drives the Conformational Transition of a Transmembrane Efflux Pump

2017 ◽  
Author(s):  
Jana Shen ◽  
Zhi Yue ◽  
Helen Zgurskaya ◽  
Wei Chen
Keyword(s):  
Molecular Dynamics ◽  
Conformational Changes ◽  
Transmembrane Domain ◽  
Conformational Transition ◽  
Conformational Dynamics ◽  
Proton Release ◽  
Intrinsic Resistance ◽  
Constant Ph ◽  
Wide Range ◽  
Constant Ph Molecular Dynamics

AcrB is the inner-membrane transporter of E. coli AcrAB-TolC tripartite efflux complex, which plays a major role in the intrinsic resistance to clinically important antibiotics. AcrB pumps a wide range of toxic substrates by utilizing the proton gradient between periplasm and cytoplasm. Crystal structures of AcrB revealed three distinct conformational states of the transport cycle, substrate access, binding and extrusion, or loose (L), tight (T) and open (O) states. However, the specific residue(s) responsible for proton binding/release and the mechanism of proton-coupled conformational cycling remain controversial. Here we use the newly developed membrane hybrid-solvent continuous constant pH molecular dynamics technique to explore the protonation states and conformational dynamics of the transmembrane domain of AcrB. Simulations show that both Asp407 and Asp408 are deprotonated in the L/T states, while only Asp408 is protonated in the O state. Remarkably, release of a proton from Asp408 in the O state results in large conformational changes, such as the lateral and vertical movement of transmembrane helices as well as the salt-bridge formation between Asp408 and Lys940 and other sidechain rearrangements among essential residues.Consistent with the crystallographic differences between the O and L protomers, simulations offer dynamic details of how proton release drives the O-to-L transition in AcrB and address the controversy regarding the proton/drug stoichiometry. This work offers a significant step towards characterizing the complete cycle of proton-coupled drug transport in AcrB and further validates the membrane hybrid-solvent CpHMD technique for studies of proton-coupled transmembrane proteins which are currently poorly understood. <p><br></p>

scholarly journals Re-Evaluation of the Podosphaera tridactyla Species Complex in Australia

2021 ◽  
Vol 7 (3) ◽  
pp. 171
Author(s):  
Reannon L. Smith ◽  
Tom W. May ◽  
Jatinder Kaur ◽  
Tim I. Sawbridge ◽  
Ross C. Mann ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Powdery Mildew ◽  
Species Complex ◽  
Taxonomic Revision ◽  
Stone Fruit ◽  
Prunus Species ◽  
Wide Range ◽  
Unidentified Species ◽  
The Rose ◽  
Generation Sequencing

The Podosphaera tridactyla species complex is highly variable morphologically and causes powdery mildew on a wide range of Prunus species, including stone fruit. A taxonomic revision of the Po. tridactyla species complex in 2020 identified 12 species, seven of which were newly characterised. In order to clarify which species of this complex are present in Australia, next generation sequencing was used to isolate the fungal ITS+28S and host matK chloroplast gene regions from 56 powdery mildew specimens of stone fruit and ornamental Prunus species accessioned as Po. tridactyla or Oidium sp. in Australian reference collections. The specimens were collected in Australia, Switzerland, Italy and Korea and were collected from 1953 to 2018. Host species were confirmed using matK phylogenetic analysis, which identified that four had been misidentified as Prunus but were actually Malusprunifolia. Podosphaera species were identified using ITS+28S phylogenetic analysis, recognising three Podosphaera species on stone fruit and related ornamental Prunus hosts in Australia. These were Po.pannosa, the rose powdery mildew, and two species in the Po. tridactyla species complex: Po. ampla, which was the predominant species, and a previously unidentified species from peach, which we describe here as Po. cunningtonii.

scholarly journals High Prevalence of Three Potyviruses Infecting Cucurbits in Oklahoma and Phylogenetic Analysis of Cucurbit Aphid-Borne Yellows Virus Isolated from Pumpkins

Pathogens ◽  
2021 ◽  
Vol 10 (1) ◽  
pp. 53
Author(s):  
Vivek Khanal ◽  
Harrington Wells ◽  
Akhtar Ali
Keyword(s):  
Phylogenetic Analysis ◽  
Mosaic Virus ◽  
Zucchini Yellow Mosaic Virus ◽  
Yellow Mosaic Virus ◽  
Watermelon Mosaic Virus ◽  
High Prevalence ◽  
The Us ◽  
Close Relationship ◽  
The Status ◽  
Low Incidence

Field information about viruses infecting crops is fundamental for understanding the severity of the effects they cause in plants. To determine the status of cucurbit viruses, surveys were conducted for three consecutive years (2016–2018) in different agricultural districts of Oklahoma. A total of 1331 leaf samples from >90 fields were randomly collected from both symptomatic and asymptomatic cucurbit plants across 11 counties. All samples were tested with the dot-immunobinding assay (DIBA) against the antisera of 10 known viruses. Samples infected with papaya ringspot virus (PRSV-W), watermelon mosaic virus (WMV), zucchini yellow mosaic virus (ZYMV), and cucurbit aphid-borne-yellows virus (CABYV) were also tested by RT-PCR. Of the 10 viruses, PRSV-W was the most widespread, with an overall prevalence of 59.1%, present in all 11 counties, followed by ZYMV (27.6%), in 10 counties, and WMV (20.7%), in seven counties, while the remaining viruses were present sporadically with low incidence. Approximately 42% of the infected samples were positive, with more than one virus indicating a high proportion of mixed infections. CABYV was detected for the first time in Oklahoma, and the phylogenetic analysis of the first complete genome sequence of a CABYV isolate (BL-4) from the US showed a close relationship with Asian isolates.

Use of tall fescue EST-SSR markers in phylogenetic analysis of cool-season forage grasses

Genome ◽  
2005 ◽  
Vol 48 (4) ◽  
pp. 637-647 ◽  
Author(s):  
M A. Rouf Mian ◽  
Malay C Saha ◽  
Andrew A Hopkins ◽  
Zeng-Yu Wang
Keyword(s):  
Phylogenetic Analysis ◽  
Ssr Markers ◽  
Tall Fescue ◽  
Related Species ◽  
Grass Species ◽  
Forage Grass ◽  
Forage Grasses ◽  
Cool Season ◽  
Phylogenetic Relations ◽  
Wide Range

Microsatellites or simple sequence repeats (SSRs) are highly useful molecular markers for plant improvement. Expressed sequence tag (EST)-SSR markers have a higher rate of transferability across species than genomic SSR markers and are thus well suited for application in cross-species phylogenetic studies. Our objectives were to examine the amplification of tall fescue EST-SSR markers in 12 grass species representing 8 genera of 4 tribes from 2 subfamilies of Poaceae and the applicability of these markers for phylogenetic analysis of grass species. About 43% of the 145 EST-SSR primer pairs produced PCR bands in all 12 grass species and had high levels of polymorphism in all forage grasses studied. Thus, these markers will be useful in a variety of forage grass species, including the ones tested in this study. SSR marker data were useful in grouping genotypes within each species. Lolium temulentum, a potential model species for cool-season forage grasses, showed a close relation with the major Festuca–Lolium species in the study. Tall wheatgrass was found to be closely related to hexaploid wheat, thereby confirming the known taxonomic relations between these species. While clustering of closely related species was found, the effectiveness of such data in evaluating distantly related species needs further investigations. The phylogenetic trees based on DNA sequences of selected SSR bands were in agreement with the phylogenetic relations based on length polymorphism of SSRs markers. Tall fescue EST-SSR markers depicted phylogenetic relations among a wide range of cool-season forage grass species and thus are an important resource for researchers working with such grass species.Key words: phylogeny, EST-SSR, forage grasses, tall fescue.

scholarly journals Quantifying seed production by volunteer canola (Brassica napus) and Sinapis arvensis

2011 ◽  
Vol 29 (3) ◽  
pp. 489-497
Author(s):  
E Soltani ◽  
A Soltani ◽  
S Galeshi ◽  
F Ghaderi-far ◽  
E Zeinali
Keyword(s):  
Brassica Napus ◽  
Seed Production ◽  
Cropping Systems ◽  
Plant Size ◽  
Quantitative Information ◽  
Sinapis Arvensis ◽  
Soil Seed Banks ◽  
Sowing Dates ◽  
Wide Range ◽  
Close Relationship

Volunteer canola (Brassica napus) and Sinapis arvensis are well identified weeds of different cropping systems. Quantitative information on regarding seed production by them is limited. Such information is necessary to model dynamics of soil seed banks. The aim of this work was to quantify seed production as a function of the size of those weeds. A wide range of plant size was produced by using a fan seeding system performed at two sowing dates (environments). Plant size varied from 3 to 167 g per plant for canola and from 6 to 104 g per plant for S. arvensis. Seed production ranged from 543 to14,773 seeds per plant for canola, and from 264 to 10,336 seeds per plant for S. arvensis. There was a close relationship between seed production per plant and plant size which was well-described by a power function (y = 130.6x0.94; R² = 0.93 for canola and y = 28x1.27; R² = 0.95 for S. arvensis). There was also strong relationships among the number of pods produced in individual plants and the quantity of seeds produced (g per plant) with the size of the plant. The relationships found in this study can be used in dynamic seed bank models of volunteer canola and S. arvensis.

scholarly journals Protein dynamics revealed by NMR relaxation methods

2018 ◽  
Vol 2 (1) ◽  
pp. 93-105 ◽  
Author(s):  
Fa-An Chao ◽  
R. Andrew Byrd
Keyword(s):  
Protein Dynamics ◽  
Structural Biology ◽  
Dynamic Models ◽  
Dimensional Space ◽  
Three Dimensional ◽  
Data Bank ◽  
Biological Macromolecules ◽  
Relaxation Methods ◽  
Genomic Databases ◽  
Wide Range

Structural biology often focuses primarily on three-dimensional structures of biological macromolecules, deposited in the Protein Data Bank (PDB). This resource is a remarkable entity for the worldwide scientific and medical communities, as well as the general public, as it is a growing translation into three-dimensional space of the vast information in genomic databases, e.g. GENBANK. There is, however, significantly more to understanding biological function than the three-dimensional co-ordinate space for ground-state structures of biomolecules. The vast array of biomolecules experiences natural dynamics, interconversion between multiple conformational states, and molecular recognition and allosteric events that play out on timescales ranging from picoseconds to seconds. This wide range of timescales demands ingenious and sophisticated experimental tools to sample and interpret these motions, thus enabling clearer insights into functional annotation of the PDB. NMR spectroscopy is unique in its ability to sample this range of timescales at atomic resolution and in physiologically relevant conditions using spin relaxation methods. The field is constantly expanding to provide new creative experiments, to yield more detailed coverage of timescales, and to broaden the power of interpretation and analysis methods. This review highlights the current state of the methodology and examines the extension of analysis tools for more complex experiments and dynamic models. The future for understanding protein dynamics is bright, and these extended tools bring greater compatibility with developments in computational molecular dynamics, all of which will further our understanding of biological molecular functions. These facets place NMR as a key component in integrated structural biology.

A new species of Scrophularia (Scrophulariaceae) from Hubei, China

Phytotaxa ◽  
2018 ◽  
Vol 350 (1) ◽  
pp. 1
Author(s):  
RUI-HONG WANG ◽  
MAO-QIN XIA ◽  
JIN-BO TAN ◽  
CHUAN CHEN ◽  
XIN-JIE JIN ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
New Species ◽  
Species Delimitation ◽  
Morphological Characters ◽  
Central China ◽  
Molecular Phylogenetic Analysis ◽  
Leaf Margin ◽  
Close Relationship ◽  
Molecular Phylogenetic ◽  
A New Species

A new species, Scrophularia jinii (Scrophulariaceae), from Central China is described and illustrated. This new species was formerly misidentified as S. fargesii, from which it differs in many morphological characters. Moreover, it is distinct with all known Scrophularia species in its unique deeply double serrate leaf margin with 3–7 big teeth on each side. Molecular phylogenetic analysis further supports its species delimitation and suggests a close relationship with several Japanese and North American species.

scholarly journals Anchoring a secreted plasmodium antigen on the surface of recombinant vaccinia virus-infected cells increases its immunogenicity.

1986 ◽  
Vol 6 (9) ◽  
pp. 3191-3199 ◽  
Author(s):  
C J Langford ◽  
S J Edwards ◽  
G L Smith ◽  
G F Mitchell ◽  
B Moss ◽  
...  
Keyword(s):  
Transmembrane Domain ◽  
Poor Response ◽  
Subcellular Location ◽  
Epidemiological Data ◽  
Recombinant Vaccinia Virus ◽  
Live Virus ◽  
Recombinant Vaccinia ◽  
Wide Range ◽  
Vaccinia Viruses ◽  
Infected Cells

We show that the subcellular location of foreign antigens expressed in recombinant vaccinia viruses influences their effectiveness as immunogens. Live recombinant viruses induced very poor antibody responses to a secreted repetitive plasmodial antigen (the S-antigen) in rabbits and mice. The poor response accords with epidemiological data suggesting that S-antigens are poorly immunogenic. Appending the transmembrane domain of a membrane immunoglobulin (immunoglobulin G1) to its carboxy terminus produced a hybrid S-antigen that was no longer secreted but was located on the surface of virus-infected cells. This recombinant virus elicited high antibody titers to the S-antigen. This approach will facilitate the use of live virus delivery systems to immunize against a wide range of foreign nonsurface antigens.

scholarly journals The evolution of the metazoan Toll receptor family and its expression during protostome development

2021 ◽  
Author(s):  
Andrea Orús-Alcalde ◽  
Tsai-Ming Lu ◽  
Andreas Hejnol
Keyword(s):  
Phylogenetic Analysis ◽  
Transmembrane Domain ◽  
Leucine Rich Repeat ◽  
Animal Development ◽  
Phylogenetic Studies ◽  
Repeat Domain ◽  
Toll Receptor ◽  
P Type

Abstract Background: Toll-like receptors (TLRs) play a crucial role in immunity and development. They contain leucine-rich repeat domains, one transmembrane domain, and one Toll/IL-1 receptor domain. TLRs have been classified into V-type/scc and P-type/mcc TLRs, based on differences in the leucine-rich repeat domain region. Although TLRs are widespread in animals, detailed phylogenetic studies of this gene family are lacking. Here we aim to uncover TLR evolution by conducting a survey and a phylogenetic analysis in species across Bilateria. To discriminate between their role in development and immunity we furthermore analyzed stage-specific transcriptomes of the ecdysozoans Priapulus caudatus and Hypsibius exemplaris, and the spiralians Crassostrea gigas and Terebratalia transversa.Results: We detected a low number of TLRs in ecdysozoan species, and multiple independent radiations within the Spiralia. V-type/scc and P-type/mcc type-receptors are present in cnidarians, protostomes and deuterostomes, and therefore they emerged early in TLR evolution, followed by a loss in xenacoelomorphs. Our phylogenetic analysis shows that TLRs cluster into three major clades: clade α is present in cnidarians, ecdysozoans, and spiralians; clade β in deuterostomes, ecdysozoans, and spiralians; and clade γ is only found in spiralians. Our stage-specific transcriptome and in situ hybridization analyses show that TLRs are expressed during development in all species analyzed, which indicates a broad role of TLRs during animal development.Conclusions: Our findings suggest that the bilaterian TLRs likely emerged by duplication from a single TLR encoding gene (proto-TLR) present in the last common cnidarian-bilaterian ancestor. This proto-TLR gene duplicated before the split of protostomes and deuterostomes; a second duplication occurred in the lineage to the Trochozoa. While all three clades further radiated in several spiralian lineages, specific TLRs clades have been presumably lost in others. Furthermore, the expression of the majority of these genes during protostome ontogeny suggests their involvement in immunity and development.

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