Location of the carbohydrate groups of ovomucoid

Tryptic glycopeptides were purified from the sialic acid-free variant of ovomucoid, O1, and its CNBr fragments. The amino acid sequences adjacent to the four major sites of carbohydrate (Carb.) attachment were: (1), Phe-Pro-Asn(Carb.)-Ala-Thr-Asp-Lys-Glu-Gly-Lys; (2), Ala-Try-Ser-Ile-Glu-Phe-Gly-Thr-Asn (Carb.)-Ile-Ser-Lys; (3), Glu, Thr-Val-Pro-Met-Asn(Carb.)-cys-Ser; (4), Ser-Ser-Tyr-Ala-Asn (Carb.)-Thr-Thr-Ser-Glu-Asp-Gly-Lys, Glycosylated Asn residues were located at position 10, between residues 49 and 60, and at positions 69 and 75, in the primary sequence. All of these carbohydrate groups contained GlcNAc, Man and Gal in the approximate molar proprotions 5:3:0.5. A further glycopeptide containing His was isolated in low yield, suggesting that some carbohydrate is attached at a fifth site. Two of the carbohydrate-attachment sites (Asn-10 and Asn-75) occur in sequences that show internal homologies. These are presumed to have evolved as a consequence of partial gene duplication. Three of the carbohydrate-attachment sites occur in similar positions to the carbohydrate groups in quail ovomucoid [Laskowski (1976) Protides Biol. Fluids Proc. Colloq. 23, in the press]. Prediction of peptide conformation from the sequence data by the method of Chou & Fasman [(1974) Biochemistry 13, 222-225] indicated that four glycosylated Asn residues in hen ovomucoid are very close to groups of amino acids that occur with high frequency in β-turns. The possible significance of peptide-chain conformation in the attachment of carbohydrate to glycoproteins is briefly discussed.

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Revealing evolutionary constraints on proteins through sequence analysis

10.1101/397521 ◽

2018 ◽

Author(s):

Shou-Wen Wang ◽

Anne-Florence Bitbol ◽

Ned S. Wingreen

Keyword(s):

Amino Acids ◽

Covariance Matrix ◽

Sequence Data ◽

Amino Acid Sequences ◽

Elastic Network Model ◽

Sequence Alignments ◽

Cellular Processes ◽

Large Numbers ◽

Protein Properties ◽

Selected Traits

AbstractStatistical analysis of alignments of large numbers of protein sequences has revealed “sectors” of collectively coevolving amino acids in several protein families. Here, we show that selection acting on any functional property of a protein, represented by an additive trait, can give rise to such a sector. As an illustration of a selected trait, we consider the elastic energy of an important conformational change within an elastic network model, and we show that selection acting on this energy leads to correlations among residues. For this concrete example and more generally, we demonstrate that the main signature of functional sectors lies in the small-eigenvalue modes of the covariance matrix of the selected sequences. However, secondary signatures of these functional sectors also exist in the extensively-studied large-eigenvalue modes. Our simple, general model leads us to propose a principled method to identify functional sectors, along with the magnitudes of mutational effects, from sequence data. We further demonstrate the robustness of these functional sectors to various forms of selection, and the robustness of our approach to the identification of multiple selected traits.Author summaryProteins play crucial parts in all cellular processes, and their functions are encoded in their amino-acid sequences. Recently, statistical analyses of protein sequence alignments have demonstrated the existence of “sectors” of collectively correlated amino acids. What is the origin of these sectors? Here, we propose a simple underlying origin of protein sectors: they can arise from selection acting on any collective protein property. We find that the main signature of these functional sectors lies in the low-eigenvalue modes of the covariance matrix of the selected sequences. A better understanding of protein sectors will make it possible to discern collective protein properties directly from sequences, as well as to design new functional sequences, with far-reaching applications in synthetic biology.

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Amino acid distributions around O-linked glycosylation sites

Biochemical Journal ◽

10.1042/bj2750529 ◽

1991 ◽

Vol 275 (2) ◽

pp. 529-534 ◽

Cited By ~ 200

Author(s):

I B Wilson ◽

Y Gavel ◽

G von Heijne

Keyword(s):

Amino Acids ◽

Amino Acid ◽

Sequence Data ◽

Prominent Feature ◽

Primary Sequence ◽

Hydroxy Amino ◽

Glycosylation Sites ◽

Sequence Requirements ◽

Primary Sequence Data ◽

Glycosylated Proteins

To study the sequence requirements for addition of O-linked N-acetylgalactosamine to proteins, amino acid distributions around 174 O-glycosylation sites were compared with distributions around non-glycosylated sites. In comparison with non-glycosylated serine and threonine residues, the most prominent feature in the vicinity of O-glycosylated sites is a significantly increased frequency of proline residues, especially at positions -1 and +3 relative to the glycosylated residues. Alanine, serine and threonine are also significantly increased. The high serine and threonine content of O-glycosylated regions is due to the presence of clusters of several closely spaced glycosylated hydroxy amino acids in many O-glycosylated proteins. Such clusters can be predicted from the primary sequence in some cases, but there is no apparent possibility of predicting isolated O-glycosylation sites from primary sequence data.

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Anticoagulant serine fibrinogenases from Vipera lebetinavenom: structure-function relationships

Thrombosis and Haemostasis ◽

10.1055/s-0037-1613468 ◽

2003 ◽

Vol 89 (05) ◽

pp. 826-831 ◽

Cited By ~ 15

Author(s):

Anu Aaspõllu ◽

Jüri Siigur ◽

Ene Siigur

Keyword(s):

Amino Acids ◽

Snake Venom ◽

Sequence Data ◽

Research Society ◽

Catalytic Triad ◽

Amino Acid Sequences ◽

Serine Proteinases ◽

Significant Similarity ◽

Cdna Sequences ◽

Vipera Lebetina

SummaryAmino acid sequences of two anticoagulant serine fibrinogenases – α- and β-fibrinogenase (VLAF and VLBF) from Vipera lebetina venom have been deduced from the cDNA sequences encoding the enzymes. The mature protein sequences of 234 amino acids (VLAF) and 233 amino acids (VLBF) exhibit significant similarity with other snake venom serine proteinases. Both enzymes contain the catalytic triad His57, Asp102, Ser195, and twelve conserved cysteines forming six disulfide bridges. Unlike typical trypsin-like serine proteinases, they lack the third aspartate, Asp189 which is replaced by Gly189. VLBF is a typical representative of arginine esterases – β-fibrinogenases. α-Fibrinogenase, VLAF, is unique among snake venom serine proteinases with homologous structure. Until now there is no evidence of the anticoagulant serine enzymes degrading fibrinogen α-chain only and lacking esterolytic activity.Parts of this paper were presented at the 17th International Fibrinogen Workshop of the International Fibrinogen Research Society (IFRS) held in Munich, Germany, September, 2002.The sequence data of Vipera lebetina mRNA for α- and β-fibrinogenase have been deposited in the GenBank database under accession numbers AF528193 (VLAF) and AF536235 (VLBF).

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The V-region sequence of the H chain from a third rabbit anti-pneumococcal antibody

Biochemical Journal ◽

10.1042/bj1570449 ◽

1976 ◽

Vol 157 (2) ◽

pp. 449-459 ◽

Cited By ~ 5

Author(s):

J C Jaton

Keyword(s):

Amino Acids ◽

Amino Acid ◽

Sequence Data ◽

Hypervariable Region ◽

Variable Region ◽

Amino Acid Sequences ◽

Rabbit Antibody ◽

Simple Correlation ◽

Type Iii ◽

V Region

The amino acid sequence of the V (variable) region of the heavy (H) chain of rabbit antibody BS-1, raised against type III pneumococcal vaccine, is reported. Together with the sequence data of the V region of the light (L) chain previously determined [Jaton (1974a) Biochem. J. 141, 1-13], the present work completes the analysis of the V domain of the homogeneous antibody BS-1. The V domains (VL + VH regions) of this antibody are compared with those of two other anti-(type III) pneumococcal antibodies BS-5 and K-25 [Jaton (1975) Biochem. J. 147, 235-247]. Except for the second hypervariable section of the L chains, these antibodies have very different sequences in the hypervariable segments of the V domains. Within the third hypervariable region of the H chain, each antibody has a different length: BS-1 is three amino acids shorter than K-25 and two amino acids shorter than BS-5. When the sequences in that section are aligned for maximal homology, only two residues, glycine-97 and leucine-101, are common to the three antibodies. On the basis of the amino acid sequences of these three anti-pneumococcal antibodies, the results do not support the concept of a simple correlation between primary structure in the hypervariable sections (known to determine the shape of the combining site) and antigen-binding specificity.

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Isolation and classification of a family of cyclin gene homologues in Lupinus luteus.

Acta Biochimica Polonica ◽

10.18388/abp.1997_4437 ◽

1997 ◽

Vol 44 (1) ◽

pp. 37-42 ◽

Cited By ~ 5

Author(s):

J Deckert ◽

J Jeleńska ◽

Z Zaborowska ◽

A B Legocki

Keyword(s):

Cell Cycle ◽

Amino Acids ◽

Phylogenetic Analysis ◽

Amino Acid Sequences ◽

Lupinus Luteus ◽

Cdna Clones ◽

Conserved Residues ◽

The Press ◽

Cyclin Gene

The lupine (Lupinus luteus cv. Ventus) cDNA clones encoding homologues of cyclin (CycB1;2, CycB1;3, CycB1;4) have been isolated from cDNA library prepared from roots inoculated with Bradyrhizobium lupini. Comparison of the deduced amino-acid sequences of CycB1;2, CycB1;3, CycB1;4 and previously described CycB1;1 (Deckert et al. 1996, Biochimie 78, 90-94) showed that they share 46-65% of identical amino acids. The presence of conserved residues (Renaudin et. al., in The Plant Cell Cycle, in the press; Renaudin et al., Plant Mol. Biol, in the press) along with phylogenetic analysis of known plant cyclins revealed that the four lupine sequences belong to subgroup 1 of B-like mitotic cyclins.

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Elevated Sporulation Efficiency in Fission Yeast Schizosaccharomyces japonicus Strains Isolated from Drosophila

Journal of Fungi ◽

10.3390/jof7050350 ◽

2021 ◽

Vol 7 (5) ◽

pp. 350

Author(s):

Taisuke Seike ◽

Natsue Sakata ◽

Fumio Matsuda ◽

Chikara Furusawa

Keyword(s):

Signal Transduction ◽

Fission Yeast ◽

High Frequency ◽

Type Strain ◽

Hyphal Growth ◽

Amino Acid Sequences ◽

Iodine Vapor ◽

Sporulation Efficiency ◽

Yeast Ecology ◽

Wild Strains

The fission yeast Schizosaccharomyces japonicus, comprising S. japonicus var. japonicus and S. japonicus var. versatilis varieties, has unique characteristics such as striking hyphal growth not seen in other Schizosaccharomyces species; however, information on its diversity and evolution, in particular mating and sporulation, remains limited. Here we compared the growth and mating phenotypes of 17 wild strains of S. japonicus, including eight S. japonicus var. japonicus strains newly isolated from an insect (Drosophila). Unlike existing wild strains isolated from fruits/plants, the strains isolated from Drosophila sporulated at high frequency even under nitrogen-abundant conditions. In addition, one of the strains from Drosophila was stained by iodine vapor, although the type strain of S. japonicus var. japonicus is not stained. Sequence analysis further showed that the nucleotide and amino acid sequences of pheromone-related genes have diversified among the eight strains from Drosophila, suggesting crossing between S. japonicus cells of different genetic backgrounds occurs frequently in this insect. Much of yeast ecology remains unclear, but our findings suggest that insects such as Drosophila might be a good niche for mating and sporulation, and will provide a basis for the understanding of sporulation mechanisms via signal transduction, as well as the ecology and evolution of yeast.

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AC2: An Efficient Protein Sequence Compression Tool Using Artificial Neural Networks and Cache-Hash Models

Entropy ◽

10.3390/e23050530 ◽

2021 ◽

Vol 23 (5) ◽

pp. 530

Author(s):

Milton Silva ◽

Diogo Pratas ◽

Armando J. Pinho

Keyword(s):

Protein Sequence ◽

Sequence Data ◽

Specific Protein ◽

General Purpose ◽

Amino Acid Sequences ◽

Input Size ◽

Protein Sequence Data ◽

Analysis Application ◽

Straightforward Solution ◽

Human Coronaviruses

Recently, the scientific community has witnessed a substantial increase in the generation of protein sequence data, triggering emergent challenges of increasing importance, namely efficient storage and improved data analysis. For both applications, data compression is a straightforward solution. However, in the literature, the number of specific protein sequence compressors is relatively low. Moreover, these specialized compressors marginally improve the compression ratio over the best general-purpose compressors. In this paper, we present AC2, a new lossless data compressor for protein (or amino acid) sequences. AC2 uses a neural network to mix experts with a stacked generalization approach and individual cache-hash memory models to the highest-context orders. Compared to the previous compressor (AC), we show gains of 2–9% and 6–7% in reference-free and reference-based modes, respectively. These gains come at the cost of three times slower computations. AC2 also improves memory usage against AC, with requirements about seven times lower, without being affected by the sequences’ input size. As an analysis application, we use AC2 to measure the similarity between each SARS-CoV-2 protein sequence with each viral protein sequence from the whole UniProt database. The results consistently show higher similarity to the pangolin coronavirus, followed by the bat and human coronaviruses, contributing with critical results to a current controversial subject. AC2 is available for free download under GPLv3 license.

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Roles of the C-Terminal Amino Acids of Non-Hexameric Helicases: Insights from Escherichia coli UvrD

International Journal of Molecular Sciences ◽

10.3390/ijms22031018 ◽

2021 ◽

Vol 22 (3) ◽

pp. 1018

Author(s):

Hiroaki Yokota

Keyword(s):

Escherichia Coli ◽

Amino Acids ◽

Amino Acid ◽

Single Molecule ◽

Underlying Mechanism ◽

Amino Acid Sequences ◽

E Coli ◽

X Ray Crystallography ◽

Terminal Amino

Helicases are nucleic acid-unwinding enzymes that are involved in the maintenance of genome integrity. Several parts of the amino acid sequences of helicases are very similar, and these quite well-conserved amino acid sequences are termed “helicase motifs”. Previous studies by X-ray crystallography and single-molecule measurements have suggested a common underlying mechanism for their function. These studies indicate the role of the helicase motifs in unwinding nucleic acids. In contrast, the sequence and length of the C-terminal amino acids of helicases are highly variable. In this paper, I review past and recent studies that proposed helicase mechanisms and studies that investigated the roles of the C-terminal amino acids on helicase and dimerization activities, primarily on the non-hexermeric Escherichia coli (E. coli) UvrD helicase. Then, I center on my recent study of single-molecule direct visualization of a UvrD mutant lacking the C-terminal 40 amino acids (UvrDΔ40C) used in studies proposing the monomer helicase model. The study demonstrated that multiple UvrDΔ40C molecules jointly participated in DNA unwinding, presumably by forming an oligomer. Thus, the single-molecule observation addressed how the C-terminal amino acids affect the number of helicases bound to DNA, oligomerization, and unwinding activity, which can be applied to other helicases.

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Interactions of mouse glycophorin A with the dRTA-related mutant G719D of the mouse Cl–/HCO3– exchanger Ae1This paper is one of a selection of papers published in a Special Issue entitled CSBMCB 53rd Annual Meeting — Membrane Proteins in Health and Disease, and has undergone the Journal’s usual peer review process.

Biochemistry and Cell Biology ◽

10.1139/o10-147 ◽

2011 ◽

Vol 89 (2) ◽

pp. 224-235 ◽

Cited By ~ 2

Author(s):

Andrew K. Stewart ◽

Fouad T. Chebib ◽

Syed W. Akbar ◽

Maria J. Salas ◽

Rajan A. Sonik ◽

...

Keyword(s):

Amino Acids ◽

Transmembrane Domain ◽

Peer Review Process ◽

Surface Expression ◽

Amino Acid Sequences ◽

Glycophorin A ◽

Specific Expression ◽

Health And Disease ◽

Renal Tubular

The AE1 mutation G701D, associated with recessive distal renal tubular acidosis (dRTA), produces only minimal erythroid phenotype, reflecting erythroid-specific expression of stimulatory AE1 subunit glycophorin A (GPA). GPA transgene expression could theoretically treat recessive dRTA in patients and in mice expressing cognate Ae1 mutation G719D. However, human (h) GPA and mouse (m) Gpa amino acid sequences are widely divergent, and mGpa function in vitro has not been investigated. We therefore studied in Xenopus oocytes the effects of coexpressed mGpa and hGPA on anion transport by erythroid (e) and kidney (k) isoforms of wild-type mAe1 (meAe1, mkAe1) and of mAe1 mutant G719D. Coexpression of hGPA or mGpa enhanced the function of meAe1 and mkAe1 and rescued the nonfunctional meAe1 and mkAe1 G719D mutants through increased surface expression. Progressive N-terminal truncation studies revealed a role for meAe1 amino acids 22–28 in GPA-responsiveness of meAe1 G719D. MouseN-cyto/humanTMD and humanN-cyto/mouseTMD kAE1 chimeras were active and GPA-responsive. In contrast, whereas chimera mkAe1N-cyto/hkAE1 G701DTMD was GPA-responsive, chimera hkAE1N-cyto/mkAe1 G719DTMD was GPA-insensitive. Moreover, whereas the isolated transmembrane domain (TMD) of hAE1 G701D was GPA-responsive, that of mAe1 G719D was GPA-insensitive. Thus, mGpa increases surface expression and activity of meAe1 and mkAe1. However, the G719D mutation renders certain mAe1 mutant constructs GPA-unresponsive and highlights a role for erythroid-specific meAe1 amino acids 22–28 in GPA-responsiveness.

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Occurrence and Origin of Supernumerary Chromosomes in Partamona (Hymenoptera: Apidae: Meliponini)

Cytogenetic and Genome Research ◽

10.1159/000452290 ◽

2016 ◽

Vol 150 (1) ◽

pp. 68-75 ◽

Cited By ~ 1

Author(s):

Diana P. Machado ◽

Elder A. Miranda ◽

Mariana C. Dessi ◽

Camila P. Sabadini ◽

Marco A. Del Lama

Keyword(s):

High Frequency ◽

Scar Marker ◽

Sequence Data ◽

Low Frequency ◽

B Chromosomes ◽

First Report ◽

Supernumerary Chromosomes

Samples from 861 colonies of 12 Partamona species from 125 Brazilian localities were analysed for a SCAR marker specific to the B chromosomes of P. helleri. We identified the SCAR marker in 6 of the 12 species analysed, including 2 (P. gregaria and P. chapadicola) from the pearsoni clade. This is the first report on the presence of this marker in Partamona species that are not included in the cupira clade, which indicates that the B chromosomes probably are more widespread in this genus than previously thought. The analysis revealed a high frequency of the SCAR marker in the samples of P. helleri (0.47), P. cupira (0.46), and P. rustica (0.29), and a low frequency in P. aff. helleri (0.06). The frequency of the marker in P. helleri was correlated with the latitude of the sampling locality, decreasing from north to south. Sequence data on the SCAR marker from 50 individuals of the 6 species in which the presence of this marker was shown revealed a new scenario for the origin of the B chromosomes in Partamona.

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