Ribosome-binding protein p34 is a member of the leucine-rich-repeat-protein superfamily

Protein p34 is a non-glycosylated membrane protein characteristic of rough microsomes and is believed to play a role in the ribosome-membrane association. In the present study we isolated cDNA encoding p34 from a rat liver cDNA library and determined its complete amino acid sequence. p34 mRNA is 3.2 kb long and encodes a polypeptide of 307 amino acids with a molecular mass of about 34.9 kDa. Primary sequence analysis, coupled with biochemical studies on the topology, suggested that p34 is a type II signal-anchor protein; it is composed of a large cytoplasmic domain, a membrane-spanning segment and a 38-amino-acid-long luminally disposed C-terminus. The cytoplasmic domain of p34 has several noteworthy structural features, including a region of 4.5 tandem repeats of 23-24 amino acids. The repeated motif shows structural similarity to the leucine-rich repeat which is found in a variety of proteins widely distributed among eukaryotic cells and which potentially functions in mediating protein-protein interactions. The cytoplasmic domain also contains a characteristic hydrophilic region with abundant charged amino acids. These structural regions may be important for the observed ribosome-binding activity of the p34 protein.

Download Full-text

MATHEMATICAL MODELS FOR THE SYNTHESIS OF PLANT-BASED COMPOSITIONS WITH IMPROVED AMINO ACID COMPOSITION

10.32008/geolinks2021/b1/v3/12 ◽

2021 ◽

Author(s):

Irina Gaivoronskaya ◽

Valenitna Kolpakova

Keyword(s):

Amino Acids ◽

Amino Acid ◽

Mathematical Models ◽

Functional Properties ◽

Amino Nitrogen ◽

Essential Amino Acids ◽

Major Allergen ◽

Structural Features ◽

Covalent Bonds ◽

Pea Protein

The aim of the work was to optimize the process of obtaining multicomponent protein compositions with high biological value and higher functional properties than the original vegetable protein products. Was realized studies to obtain biocomposites on the base of pea protein-oat protein and pea protein-rice protein. Developed composites were enriched with all limited amino acids. For each of the essential amino acids, the amino acid score was 100% and higher. Protein products used in these compositions are not in major allergen list, which allows to use these compositions in allergen-free products and specialized nutrition. To determine biosynthesis parameters for compositions from pea protein and various protein concentrates with the use of transglutaminase enzyme, was studied effect of concentration and exposition time on the amount of amino nitrogen released during the reaction. Decreasing of amino nitrogen in the medium indicated the occurrence of a protein synthesis reaction with the formation of new covalent bonds. Were determined optimal parameters of reaction: the hydromodule, the exposure time, the concentration of EP of the preparation, were obtained mathematical models. Studies on the functional properties of composites, the physicochemical properties of the proteins that make up their composition, and structural features will make it possible to determine the uses in the manufacture of food products based on their ability to bind fat, water, form foam, gels, and etc.

Download Full-text

Isolation and characterization of some novel genes of the apolipoprotein A-I family in Japanese eel, Anguilla japonica

Open Life Sciences ◽

10.2478/s11535-011-0042-8 ◽

2011 ◽

Vol 6 (4) ◽

pp. 545-557 ◽

Cited By ~ 2

Author(s):

Malay Choudhury ◽

Takahiro Oku ◽

Shoji Yamada ◽

Masaharu Komatsu ◽

Keita Kudoh ◽

...

Keyword(s):

Amino Acids ◽

Molecular Weight ◽

Amino Acid ◽

Consensus Sequence ◽

Structural Features ◽

Lipid Binding ◽

Japanese Eel ◽

Amino Acid Sequences ◽

Novel Genes ◽

Isolation And Characterization

AbstractApolipoproteins such as apolipoprotein (apo) A-I, apoA-IV, and apoE are lipid binding proteins synthesized mainly in the liver and the intestine and play an important role in the transfer of exogenous or endogenous lipids through the circulatory system. To investigate the mechanism of lipid transport in fish, we have isolated some novel genes of the apoA-I family, apoIA-I (apoA-I isoform) 1–11, from Japanese eel by PCR amplification. Some of the isolated genes of apoIA-I corresponded to 28kDa-1 cDNAs which had already been deposited into the database and encoded an apolipoprotein with molecular weight of 28 kDa in the LDL, whereas others seemed to be novel genes. The structural organization of all apoIA-Is consisted of four exons separated by three introns. ApoIA-I10 had a total length of 3232 bp, whereas other genes except for apoIA-I9 ranged from 1280 to 1441 bp. The sequences of apoIA-Is at the exon-intron junctions were mostly consistent with the consensus sequence (GT/AG) at exon-intron boundaries, whereas the sequences of 3′ splice acceptor in intron 1 of apoIA-I1-7 were (AC) but not (AG). The deduced amino acid sequences of all apoIA-Is contained a putative signal peptide and a propeptide of 17 and 5 amino acid residues, respectively. The mature proteins of apoIA-I1-3, 7, and 8 consisted of 237 amino acids, whereas those of apoIA-I4-6 consisted of 239 amino acids. The mature apoIA-I10 sequence showed 65% identity to amino acid sequence of apoIA-I11 which was associated with an apolipoprotein with molecular weight of 23 kDa in the VLDL. All these mature apoIA-I sequences satisfied the common structural features depicted for the exchangeable apolipoproteins such as apoA-I, apoA-IV, and apoE but apoIA-I11 lacked internal repeats 7, 8, and 9 when compared with other members of apoA-I family. Phylogenetic analysis showed that these novel apoIA-Is isolated from Japanese eel were much closer to apoA-I than apoA-IV and apoE, suggesting new members of the apoA-I family.

Download Full-text

Role of the Varicella-Zoster Virus gB Cytoplasmic Domain in gB Transport and Viral Egress

Journal of Virology ◽

10.1128/jvi.76.2.591-599.2002 ◽

2002 ◽

Vol 76 (2) ◽

pp. 591-599 ◽

Cited By ~ 31

Author(s):

Thomas C. Heineman ◽

Susan L. Hall

Keyword(s):

Amino Acids ◽

Plasma Membrane ◽

Amino Acid ◽

Varicella Zoster Virus ◽

Cultured Cells ◽

Signal Sequence ◽

Cytoplasmic Domain ◽

Varicella Zoster ◽

Golgi Transport ◽

Viral Egress

ABSTRACT To study the function of the varicella-zoster virus (VZV) gB cytoplasmic domain during viral infection, we produced a VZV recombinant virus that expresses a truncated form of gB lacking the C-terminal 36 amino acids of its cytoplasmic domain (VZV gB-36). VZV gB-36 replicates in noncomplementing cells and grows at a rate similar to that of native VZV. However, cells infected with VZVgB-36 form extensive syncytia compared to the relatively small syncytia formed during native VZV infection. In addition, electron microscopy shows that very little virus is present on the surfaces of cells infected with VZV gB-36, while cells infected with native VZV exhibit abundant virions on the cell surface. The C-terminal 36 amino acids of the gB cytoplasmic domain have been shown in transfection-based experiments to contain both an endoplasmic reticulum-to-Golgi transport signal (the C-terminal 17 amino acids) and a consensus YXXφ (where Y is tyrosine, X is any amino acid, and φ is any bulky hydrophobic amino acid) signal sequence (YSRV) that mediates the internalization of gB from the plasma membrane. As predicted based on these data, gB-36 expressed during the infection of cultured cells is transported inefficiently to the Golgi. Despite lacking the YSRV signal sequence, gB-36 is internalized from the plasma membrane; however, in contrast to native gB, it fails to localize to the Golgi. Therefore, the C-terminal 36 amino acids of the VZV gB cytoplasmic domain are required for normal viral egress and for both the pre- and post-Golgi transport of gB.

Download Full-text

Engineering an acetyllysine reader with photocrosslinking amino acid for interactome profiling

Chemical Communications ◽

10.1039/d1cc04611j ◽

2021 ◽

Author(s):

Babu Sudhamalla ◽

Anirban Roy ◽

Soumen Barman ◽

Jyotirmayee Padhan

Keyword(s):

Amino Acids ◽

Amino Acid ◽

Protein Interactions ◽

Unnatural Amino Acids ◽

Protein Protein Interactions ◽

Site Specific ◽

Powerful Approach

The site-specific installation of light-activable crosslinker unnatural amino acids offers a powerful approach to trap transient protein-protein interactions both in vitro and in vivo. Herein, we engineer a bromodomain to...

Download Full-text

Structural basis for divergent and convergent evolution of catalytic machineries in plant aromatic amino acid decarboxylase proteins

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1920097117 ◽

2020 ◽

Vol 117 (20) ◽

pp. 10806-10817 ◽

Cited By ~ 6

Author(s):

Michael P. Torrens-Spence ◽

Ying-Chih Chiang ◽

Tyler Smith ◽

Maria A. Vicent ◽

Yi Wang ◽

...

Keyword(s):

Amino Acids ◽

Amino Acid ◽

Convergent Evolution ◽

Structural Features ◽

Divergent Evolution ◽

Structural Basis ◽

Acid Decarboxylase ◽

Substrate Selectivity ◽

Amino Acid Decarboxylase ◽

Catalytic Mechanisms

Radiation of the plant pyridoxal 5′-phosphate (PLP)-dependent aromatic l-amino acid decarboxylase (AAAD) family has yielded an array of paralogous enzymes exhibiting divergent substrate preferences and catalytic mechanisms. Plant AAADs catalyze either the decarboxylation or decarboxylation-dependent oxidative deamination of aromatic l-amino acids to produce aromatic monoamines or aromatic acetaldehydes, respectively. These compounds serve as key precursors for the biosynthesis of several important classes of plant natural products, including indole alkaloids, benzylisoquinoline alkaloids, hydroxycinnamic acid amides, phenylacetaldehyde-derived floral volatiles, and tyrosol derivatives. Here, we present the crystal structures of four functionally distinct plant AAAD paralogs. Through structural and functional analyses, we identify variable structural features of the substrate-binding pocket that underlie the divergent evolution of substrate selectivity toward indole, phenyl, or hydroxyphenyl amino acids in plant AAADs. Moreover, we describe two mechanistic classes of independently arising mutations in AAAD paralogs leading to the convergent evolution of the derived aldehyde synthase activity. Applying knowledge learned from this study, we successfully engineered a shortened benzylisoquinoline alkaloid pathway to produce (S)-norcoclaurine in yeast. This work highlights the pliability of the AAAD fold that allows change of substrate selectivity and access to alternative catalytic mechanisms with only a few mutations.

Download Full-text

Positive and Negative Regulation of Poly(A) Nuclease

Molecular and Cellular Biology ◽

10.1128/mcb.24.12.5521-5533.2004 ◽

2004 ◽

Vol 24 (12) ◽

pp. 5521-5533 ◽

Cited By ~ 57

Author(s):

David A. Mangus ◽

Matthew C. Evans ◽

Nathan S. Agrin ◽

Mandy Smith ◽

Preetam Gongidi ◽

...

Keyword(s):

Amino Acids ◽

Amino Acid ◽

Protein Interactions ◽

Binding Pocket ◽

Negative Regulation ◽

Single Amino Acid ◽

Carboxy Terminus ◽

Protein Protein Interactions ◽

C Terminus

ABSTRACT PAN, a yeast poly(A) nuclease, plays an important nuclear role in the posttranscriptional maturation of mRNA poly(A) tails. The activity of this enzyme is dependent on its Pan2p and Pan3p subunits, as well as the presence of poly(A)-binding protein (Pab1p). We have identified and characterized the associated network of factors controlling the maturation of mRNA poly(A) tails in yeast and defined its relevant protein-protein interactions. Pan3p, a positive regulator of PAN activity, interacts with Pab1p, thus providing substrate specificity for this nuclease. Pab1p also regulates poly(A) tail trimming by interacting with Pbp1p, a factor that appears to negatively regulate PAN. Pan3p and Pbp1p both interact with themselves and with the C terminus of Pab1p. However, the domains required for Pan3p and Pbp1p binding on Pab1p are distinct. Single amino acid changes that disrupt Pan3p interaction with Pab1p have been identified and define a binding pocket in helices 2 and 3 of Pab1p's carboxy terminus. The importance of these amino acids for Pab1p-Pan3p interaction, and poly(A) tail regulation, is underscored by experiments demonstrating that strains harboring substitutions in these residues accumulate mRNAs with long poly(A) tails in vivo.

Download Full-text

The cDNA-deduced amino acid sequence for trichohyalin, a differentiation marker in the hair follicle, contains a 23 amino acid repeat.

The Journal of Cell Biology ◽

10.1083/jcb.110.2.427 ◽

1990 ◽

Vol 110 (2) ◽

pp. 427-436 ◽

Cited By ~ 33

Author(s):

M J Fietz ◽

R B Presland ◽

G E Rogers

Keyword(s):

Amino Acids ◽

Amino Acid ◽

Amino Acid Sequence ◽

Intermediate Filament ◽

Tandem Repeats ◽

Single Copy ◽

Hair Follicles ◽

Helical Structures ◽

Differentiation Marker ◽

Carboxy Terminal

Trichohyalin is a highly expressed protein within the inner root sheath of hair follicles and is similar, or identical, to a protein present in the hair medulla. In situ hybridization studies have shown that trichohyalin is a very early differentiation marker in both tissues and that in each case the trichohyalin mRNA is expressed from the same single copy gene. A partial cDNA clone for sheep trichohyalin has been isolated and represents approximately 40% of the full-length trichohyalin mRNA. The carboxy-terminal 458 amino acids of trichohyalin are encoded, and the first 429 amino acids consist of full- or partial-length tandem repeats of a 23 amino acid sequence. These repeats are characterized by a high proportion of charged amino acids. Secondary structure analyses predict that the majority of the encoded protein could form alpha-helical structures that might form filamentous aggregates of intermediate filament dimensions, even though the heptad motif obligatory for the intermediate filament structure itself is absent. The alternative structural role of trichohyalin could be as an intermediate filament-associated protein, as proposed from other evidence.

Download Full-text

Total 4EBP1 Is Elevated in Liver of Rats in Response to Low Sulfur Amino Acid Intake

Journal of Amino Acids ◽

10.1155/2013/864757 ◽

2013 ◽

Vol 2013 ◽

pp. 1-11 ◽

Cited By ~ 12

Author(s):

Angelos K. Sikalidis ◽

Kevin M. Mazor ◽

Minji Kang ◽

Hongyun Liu ◽

Martha H. Stipanuk

Keyword(s):

Amino Acids ◽

Amino Acid ◽

Dietary Treatment ◽

Binding Activity ◽

Initiation Factor ◽

Sulfur Amino Acid ◽

Sulfur Amino Acids ◽

Protein Levels ◽

Cellular Stresses

Translation initiation is known to be regulated by the binding of eukaryotic initiation factor 4E (eIF4E) by binding proteins (4EBPs), and there is evidence that amino acid deprivation and other cellular stresses upregulate 4EBP1 expression. To pursue the question of whether diets limited in an essential amino acid lead to induction of 4EBP1 expression in vivo, diets that varied in methionine and cystine content were fed to rats for 7 days, and 4EBP1 mRNA and protein levels and 4EBP1 phosphorylation state were determined. Total 4EBP1 mRNA and protein abundance increased in liver of rats with severely deficient intakes of sulfur amino acids (0.23% or 0.11% methionine without cystine) but not in animals with a less restricted intake of sulfur amino acids (0.11% methionine plus 0.35% cystine) but a similarly restricted intake of total diet (53 to 62% of control). The amount of 4EBP1 binding activity (α + β forms) was elevated in liver of rats fed sulfur amino acid-deficient diets, whereas the hyperphosphorylation of 4EBP1 was not affected by dietary treatment. Results suggest that changes in total 4EBP1 expression should be considered when examining mechanisms that attenuate protein synthesis during amino acid deficiency states.

Download Full-text

Amino acid sequence of HSP-1, a major protein of stallion seminal plasma: effect of glycosylation on its heparin- and gelatin-binding capabilities

Biochemical Journal ◽

10.1042/bj3100615 ◽

1995 ◽

Vol 310 (2) ◽

pp. 615-622 ◽

Cited By ~ 70

Author(s):

J J Calvete ◽

K Mann ◽

W Schäfer ◽

L Sanz ◽

M Reinert ◽

...

Keyword(s):

Amino Acids ◽

Amino Acid ◽

Amino Acid Sequence ◽

Seminal Plasma ◽

Binding Activity ◽

Size Exclusion ◽

Major Protein ◽

Heparin Binding ◽

Aggregation State ◽

Consensus Pattern

We report the complete amino acid sequence of HSP-1, a major protein isolated from stallion seminal plasma or acid extracts of ejaculated spermatozoa. The protein consists of 121 amino acids organized in two types of homologous repeats arranged in the pattern AA‘BB’. Each of the 13-15-residue A-type repeats contains two O-linked oligosaccharide chains. The B-type repeats span 44-47 amino acids each, are not glycosylated, and have the consensus pattern of the gelatin-binding fibronectin type-II module. This domain also occurs in the major bovine seminal plasma heparin-binding proteins PDC-109 (BSP-A1/A2) and BSP-A3. However, unlike the bovine proteins which bind quantitatively to a heparin-Sepharose column, stallion HSP-1 was recovered in both the flow-through and the heparin-bound fractions. Structural analysis showed that the two HSP-1 forms contain identical polypeptide chains which are differently glycosylated. Moreover, size-exclusion chromatography showed that heparin-bound HSP-1 associates with HSP-2, another major seminal plasma protein, into a 90 kDa product, whereas the non-heparin-bound glycoform of HSP-1 is eluted as a monomeric (14 kDa) protein. This suggests that glycosylation may have an indirect effect on the heparin-binding ability of HSP-1 through modulation of its aggregation state. On the other hand, both glycoforms of HSP-1 displayed gelatin-binding activity, indicating that the molecular determinants for binding heparin and gelatin are different.

Download Full-text

NUCLEOTIDE SEQUENCE OF THE STAPHYLOCOAGULASE GENE FROM STAPHYLOCOCCUS AUREUS STRAIN BB

10.1055/s-0038-1644607 ◽

1987 ◽

Author(s):

S Kaida ◽

T Miyata ◽

S Kawabata ◽

T Morita ◽

Y Yoshizawa ◽

...

Keyword(s):

Amino Acids ◽

Staphylococcus Aureus ◽

Amino Acid ◽

Tandem Repeats ◽

Molar Ratio ◽

Clotting Factor ◽

Aureus Strain ◽

Activation Process ◽

Coding Region ◽

Flanking Region

Staphylocoagulase (SC) is a secretary protein produced by several strains of Staphylococcus aureus (S. aureus). This protein forms a molecular complex ("staphylothrombin") with human prothrombin in a molar ratio of 1:1. The complex displays the ability to clot fibrinogen and to hydrolyze the synthetic tripeptide substrates for α-thrombin. The formation of staphylothrombin does not require proteolytic cleavage of the prothrombin molecule, and this mechanism differs markedly from the activation process by either blood-clotting factor Xa or snake venom procoagulant.In the present studies, a pAT153 library containing partial Mbo I-digested DNA prepared from aureus strain BB has been screened with a fibrin gel formation method. The identity of these clones with SC was confirmed by DNA sequence analysis and by comparison of the derived amino acid sequence with that determined for the purified SC protein. One of the positive colonies was isolated and 3.1 Kb of the insert DNA was determined by the dideoxy chain termination method. The results indicated that the insert DNA consists of 148 bp 5' flanking region, protein coding region of 715 amino acids and 746 bp 3' flanking region, and that SC from strain BB is synthesized as a precursor with a signal peptide of 26 amino acids. Thus, the mature form was composed of 689 amino acids with a molecular weight of 77,337- The NH2-terminal sequence (324 amino acids) of SC isolated from S. aureus strain 213 (S. Kawabata et al. (1986): J. Biol. Chem. 261, 527-531) was compared with that of SC derived from strain BB. The sequence homology between them was found to show 57 %. It was also found that SC derived from strain BB was composed of 8 tandem repeats (27 amino acid residues in length) in the COOH-terminal region, although their functions are not known.

Download Full-text