scholarly journals Sequence analysis and structure prediction of ABHD16A and the roles of the ABHD family members in human disease

Open Biology ◽  
2018 ◽  
Vol 8 (5) ◽  
pp. 180017 ◽  
Author(s):  
Jun Xu ◽  
Weizhen Gu ◽  
Kai Ji ◽  
Zhao Xu ◽  
Haihua Zhu ◽  
...  
Keyword(s):  
Amino Acid ◽  
Structure Prediction ◽  
Active Sites ◽  
Metabolic Regulation ◽  
Acid Sites ◽  
Amino Acid Sequences ◽  
The Body ◽  
Gene Location ◽  
Future Research ◽  
Animal Cells

Abhydrolase domain containing 16A (ABHD16A) is a member of the α/β hydrolase domain-containing (ABHD) protein family and is expressed in a variety of animal cells. Studies have shown that ABHD16A has acylglycerol lipase and phosphatidylserine lipase activities. Its gene location in the main histocompatibility complex (MHC) III gene cluster suggests that this protein may participate in the immunomodulation of the body. The results of studies investigating nearly 20 species of ABHDs reveal that the ABHD proteins are key factors in metabolic regulation and disease occurrence and development. In this paper, we summarize the related progress regarding the function of ABHD16A and other ABHD proteins. A prediction of the active sites and structural domains of ABHD16A and an analysis of the amino acid sites are included. Moreover, we analysed the amino acid sequences of the ABHD16A molecules in different species and provide an overview of the related functions and diseases associated with these proteins. The functions and diseases related to ABHD are systematically summarized and highlighted. Future research directions for studies investigating the functions and mechanisms of these proteins are also suggested. Further studies investigating the function of ABHD proteins may further confirm their positions as important determinants of lipid metabolism and related diseases.

scholarly journals In-silicoprediction and modeling of theEntamoeba histolyticaproteins: Serine-richEntamoeba histolyticaprotein and 29 kDa Cysteine-rich protease

PeerJ ◽  
2017 ◽  
Vol 5 ◽  
pp. e3160 ◽  
Author(s):  
Kumar Manochitra ◽  
Subhash Chandra Parija
Keyword(s):  
Amino Acid ◽  
Structure Prediction ◽  
Tertiary Structure ◽  
Protein Structures ◽  
Amino Acid Sequences ◽  
Treatment Modalities ◽  
Bioinformatic Tools ◽  
Complex Protein ◽  
A Cell ◽  
Quaternary Structures

BackgroundAmoebiasis is the third most common parasitic cause of morbidity and mortality, particularly in countries with poor hygienic settings. There exists an ambiguity in the diagnosis of amoebiasis, and hence there arises a necessity for a better diagnostic approach. Serine-richEntamoeba histolyticaprotein (SREHP), peroxiredoxin and Gal/GalNAc lectin are pivotal inE. histolyticavirulence and are extensively studied as diagnostic and vaccine targets. For elucidating the cellular function of these proteins, details regarding their respective quaternary structures are essential. However, studies in this aspect are scant. Hence, this study was carried out to predict the structure of these target proteins and characterize them structurally as well as functionally using appropriatein-silicomethods.MethodsThe amino acid sequences of the proteins were retrieved from National Centre for Biotechnology Information database and aligned using ClustalW. Bioinformatic tools were employed in the secondary structure and tertiary structure prediction. The predicted structure was validated, and final refinement was carried out.ResultsThe protein structures predicted by i-TASSER were found to be more accurate than Phyre2 based on the validation using SAVES server. The prediction suggests SREHP to be an extracellular protein, peroxiredoxin a peripheral membrane protein while Gal/GalNAc lectin was found to be a cell-wall protein. Signal peptides were found in the amino-acid sequences of SREHP and Gal/GalNAc lectin, whereas they were not present in the peroxiredoxin sequence. Gal/GalNAc lectin showed better antigenicity than the other two proteins studied. All the three proteins exhibited similarity in their structures and were mostly composed of loops.DiscussionThe structures of SREHP and peroxiredoxin were predicted successfully, while the structure of Gal/GalNAc lectin could not be predicted as it was a complex protein composed of sub-units. Also, this protein showed less similarity with the available structural homologs. The quaternary structures of SREHP and peroxiredoxin predicted from this study would provide better structural and functional insights into these proteins and may aid in development of newer diagnostic assays or enhancement of the available treatment modalities.

scholarly journals Insights into the Selective Pressures Restricting Pelargonium Flower Break Virus Genome Variability: Evidence for Host Adaptation

2006 ◽  
Vol 80 (16) ◽  
pp. 8124-8132 ◽  
Author(s):  
Patricia Rico ◽  
Pilar Ivars ◽  
Santiago F. Elena ◽  
Carmen Hernández
Keyword(s):  
Amino Acid ◽  
Leucine Zipper ◽  
Critical Role ◽  
Chenopodium Quinoa ◽  
Virus Genome ◽  
Acid Sites ◽  
Genomic Region ◽  
Amino Acid Sequences ◽  
Nucleotide Substitutions ◽  
Selective Pressures

ABSTRACT The molecular diversity of Pelargonium flower break virus (PFBV) was assessed using a collection of isolates from different geographical origins, hosts, and collecting times. The genomic region examined was 1,828 nucleotides (nt) long and comprised the coding sequences for the movement (p7 and p12) and the coat (CP) proteins, as well as flanking segments including the entire 3′ untranslated region (3′ UTR). Some constraints limiting viral heterogeneity could be inferred from sequence analyses, such as the conservation of the amino acid sequences of p7 and of the shell domain of the CP, the maintenance of a leucine zipper motif in p12, and the preservation of a particular folding in the 3′ UTR. A remarkable covariation, involving five specific amino acid sites, was found in the CP of isolates largely propagated in the local lesion host Chenopodium quinoa and in the progeny of a PFBV variant subjected to serial passages in this host. Concomitant with this covariation, up to 30 nucleotide substitutions in a 1,428-nt region of the viral RNA could be attributable to C. quinoa-specific adaptation, representing one of the most outstanding cases of host-driven genome variation for a plant virus. Globally, the results indicate that the selective pressures exerted by the host play a critical role in shaping PFBV populations and that these populations are likely being selected for at both protein and RNA levels.

scholarly journals Characterization of human and mouse granulocyte-macrophage-colony-stimulating factors derived from Escherichia coli

1987 ◽  
Vol 247 (1) ◽  
pp. 195-199 ◽  
Author(s):  
J L Schrimsher ◽  
K Rose ◽  
M G Simona ◽  
P Wingfield
Keyword(s):  
Escherichia Coli ◽  
Amino Acid ◽  
Amino Acid Sequences ◽  
Natural Material ◽  
Animal Cells ◽  
Colony Stimulating Factors ◽  
E Coli ◽  
Macrophage Colony ◽  
The One ◽  
Human And Mouse

Human and mouse granulocyte-macrophage-colony-stimulating factors (hGM-CSF and mGM-CSF, respectively), isolated from Escherichia coli cells expressing the corresponding human and mouse genes, have been characterized. The observed properties of the proteins have been compared with those properties which can be deduced from the DNA sequence alone and the published properties of natural GM-CSFs. The purified E. coli-derived proteins were found to have the expected molecular masses, amino acid compositions and N- and C-terminal amino acid sequences. The finding of 70-90% unprocessed N-terminal methionine for both proteins is discussed. The four Cys residues were found to be involved in two intramolecular disulphide bonds, linking the first and third, and second and fourth Cys residues. This disulphide bond arrangement is probably the one existing in natural material, since, although not glycosylated, both E. coli-derived proteins showed biological activity (colony stimulating assay for hGM-CSF, and cell proliferation assay for mGM-CSF) comparable with that reported for the respective proteins purified from animal cells.

scholarly journals Sequence Analysis and Structure Prediction of Malaysia SARS-CoV-2 Strain’s Structural and Accessory Proteins

2021 ◽  
Vol 12 (3) ◽  
pp. 3259-3304
Keyword(s):  
Structure Prediction ◽  
Active Sites ◽  
Homo Sapiens ◽  
Functional Characterization ◽  
Protein Structures ◽  
Three Dimensional ◽  
Experimental Models ◽  
Amino Acid Sequences ◽  
Accessory Proteins ◽  
Evolutionary Analysis

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that transmitted from animal to human became a life-threatening pandemic in 2020. Scientists are currently testing several drugs to eradicate the COVID-19 outbreak. However, there is no 100 % effective drug or vaccine against SARS-CoV-2 has been discovered so far. In this study, we explored the structure prediction and functional analysis of 75 Malaysia SARS-CoV-2 strain’s structural and accessory proteins without the presence of experimental models. Physiochemical analysis, secondary structure analysis, structure prediction, functional characterization, active site identification, and evolutionary analysis based on the amino acid sequences retrieved from National Centre for Biotechnology Information (NCBI). Three-dimensional (3-D) protein structures were built using the Swiss model. The quality of protein models was verified by ERRAT, PROCHECK, and Verify 3D tools. Active prediction analysis revealed the high potential active sites of proteins where the anti-viral drug or vaccine may bind and inhibit the viral activities. Molecular phylogenetic analysis of ORF10, ORF8, and ORF6 proteins from five different species was analyzed. The results from this analysis proved that Homo sapiens SARS-CoV-2 had high genetic similarity with the bat coronavirus. These analyses may help in designing structure-based anti-viral drugs or to develop potential vaccines for SARS-CoV-2.

scholarly journals Proteins sequence analysis of Contagious Caprine Pleuropneumonia

2017 ◽  
Vol 33 (3) ◽  
pp. 309-319
Author(s):  
Ayuba Dauda ◽  
Abdulmojeed Yakubu ◽  
Ihe Dim ◽  
Deeve Gwaza
Keyword(s):  
Amino Acid ◽  
Structure Prediction ◽  
Secondary Structure Prediction ◽  
Three Dimensional ◽  
Chemical Properties ◽  
Alpha Helix ◽  
Amino Acid Sequences ◽  
Contagious Bovine Pleuropneumonia ◽  
Isoleucine Leucine ◽  
Grand Average

A total of twenty (20) contagious bovine pleuropneumonia (CCPP) proteins were retrieved from the GenBank (www.ncbi.nlm.nih.gov). The proteins sequences were used to investigate the molecular identity of various CCPP proteins. The physico-chemical properties of CCPP proteins were performed using protparam tool. Isoelectric point (pI), molecular weight (MW), extinction coefficient (EC); instability index (II), aliphatic index (AI) and grand average of hydropathicity (GRAVY) were computed. The study revealed that the pI of CCPP proteins were acidic and basic in nature. The EC and II of CCPP proteins indicate better stability which is an indication of resistant to mutation and thermally stable. The GRAVY of CCPP proteins revealed some are positive while some are negative. The positive value indicates solubility (hydrophilic) in water while negative is not soluble (hydrophobic) in water. The amino acid composition of CCPP proteins indicates that they are rich in isoleucine, leucine and lysine. The three dimensional structures (3D) of the CCPP proteins were determine using Phyre2 server. The amino acid sequences of CCPP proteins were subjected to secondary structure prediction using ExPASy?s SOPMA tool. The proteins are more of alpha helix structure. The genetic information eminating from this study may bring insight into mutagenesis and pharmacogenetic. <br><br><font color="red"><b> This article has been retracted. Link to the retraction <u><a href="http://dx.doi.org/10.2298/BAH1803369E">10.2298/BAH1803369E</a><u></b></font>

scholarly journals Completion of the amino acid sequences of the A and B chains of subcomponent C1q of the first component of human complement

1982 ◽  
Vol 203 (3) ◽  
pp. 559-569 ◽  
Author(s):  
K B M Reid ◽  
J Gagnon ◽  
J Frampton
Keyword(s):  
Amino Acid ◽  
Structure Prediction ◽  
Sequence Data ◽  
Helical Structure ◽  
Amino Acid Sequences ◽  
Amino Acid Residues ◽  
Human Complement ◽  
Major Site ◽  
A Chain ◽  
Asparagine Residue

The sequences of amino acid residues 109-224 of the A chain, and residues 109-22 of the B chain, of human subcomponent C1q are given. These results, along with previously published sequence data on the N-terminal, collagen-like, regions of the A and B chains [Reid (1979) Biochem. J. 179, 367-371] yield the complete amino acid sequences of the A and B chains of subcomponent C1q. The asparagine residue at position A-124 has been identified as the major site of asparagine-linked carbohydrate in subcomponent C1q. When the sequences of the C-terminal, 135-residue-long, ‘globular’ regions of A and B chains are compared they show 40% homology. The degree of homology over certain stretches of 15-20 residues, within the C-terminal regions, rises up to values of 73%, indicating the presence of strongly conserved structures. Structure prediction studies indicate that both the A and B chain C-terminal regions may adopt a predominantly beta-type structure with apparently little alpha-helical structure.

scholarly journals Protein sequence design by conformational landscape optimization

2021 ◽  
Vol 118 (11) ◽  
pp. e2017228118
Author(s):  
Christoffer Norn ◽  
Basile I. M. Wicky ◽  
David Juergens ◽  
Sirui Liu ◽  
David Kim ◽  
...  
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Structure Prediction ◽  
Alternative Energy ◽  
De Novo ◽  
Amino Acid Sequences ◽  
Energy Landscapes ◽  
Point Energy ◽  
Sequence Design ◽  
Conformational Landscape

The protein design problem is to identify an amino acid sequence that folds to a desired structure. Given Anfinsen’s thermodynamic hypothesis of folding, this can be recast as finding an amino acid sequence for which the desired structure is the lowest energy state. As this calculation involves not only all possible amino acid sequences but also, all possible structures, most current approaches focus instead on the more tractable problem of finding the lowest-energy amino acid sequence for the desired structure, often checking by protein structure prediction in a second step that the desired structure is indeed the lowest-energy conformation for the designed sequence, and typically discarding a large fraction of designed sequences for which this is not the case. Here, we show that by backpropagating gradients through the transform-restrained Rosetta (trRosetta) structure prediction network from the desired structure to the input amino acid sequence, we can directly optimize over all possible amino acid sequences and all possible structures in a single calculation. We find that trRosetta calculations, which consider the full conformational landscape, can be more effective than Rosetta single-point energy estimations in predicting folding and stability of de novo designed proteins. We compare sequence design by conformational landscape optimization with the standard energy-based sequence design methodology in Rosetta and show that the former can result in energy landscapes with fewer alternative energy minima. We show further that more funneled energy landscapes can be designed by combining the strengths of the two approaches: the low-resolution trRosetta model serves to disfavor alternative states, and the high-resolution Rosetta model serves to create a deep energy minimum at the design target structure.

scholarly journals Suboptimal intermediates underlie evolution of the Bicoid homeodomain

2020 ◽  
Author(s):  
Pinar Onal ◽  
Himari Imaya Gunasinghe ◽  
Kristaley Yui Umezawa ◽  
Michael Zheng ◽  
Jia Ling ◽  
...  
Keyword(s):  
Amino Acid ◽  
Regulatory Networks ◽  
Phenotypic Diversity ◽  
Regulatory Elements ◽  
Amino Acid Sequences ◽  
The Body ◽  
Embryo Patterning ◽  
Dna And Rna ◽  
Evolutionary Changes ◽  
Transcription Networks

AbstractChanges in regulatory networks generate materials for evolution to create phenotypic diversity. For transcription networks, multiple studies have shown that alterations in binding sites of cis-regulatory elements correlate well with the gain or loss of specific features of the body plan. Less is known about alterations in the amino acid sequences of the transcription factors (TFs) that bind these elements. Here we study the evolution of Bicoid (Bcd), a homeodomain (HD) protein that is critical for anterior embryo patterning in Drosophila. The ancestor of Bcd (AncBcd) emerged after a duplication of a Zerknullt (Zen)-like ancestral protein (AncZB) in a suborder of flies. AncBcd diverged from AncZB, gaining novel transcriptional and translational activities. We focus on the evolution of the HD of AncBcd, which binds DNA and RNA, and is comprised of four subdomains: an N-terminal arm (NT) and three helices; H1, H2, and Recognition Helix (RH). Using chimeras of subdomains and gene rescue assays in Drosophila, we show that robust patterning activity of the Bcd HD (high frequency rescue to adulthood) is achieved only when amino acid substitutions in three separate subdomains (NT, H1, and RH) are combined. Other combinations of subdomains also yield full rescue, but with lower penetrance, suggesting alternative suboptimal activities. Our results suggest a multi-step pathway for the evolution of the Bcd HD that involved intermediate HD sequences with suboptimal activities, which constrained and enabled further evolutionary changes. They also demonstrate critical epistatic forces that contribute to the robust function of a DNA-binding domain.

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