scholarly journals Charge influences substrate recognition and self-assembly of hydrophobic FG sequences

2016 ◽  
Author(s):  
Wesley G. Chen ◽  
Jacob Witten ◽  
Scott C. Grindy ◽  
Niels Holten-Andersen ◽  
Katharina Ribbeck
Keyword(s):  
Amino Acid ◽  
Self Assembly ◽  
Amino Acid Sequences ◽  
Nuclear Pore ◽  
Selective Binding ◽  
Charged Amino Acids ◽  
Essential Components ◽  
Transport Receptors

AbstractThe nuclear pore complex controls the passage of molecules via hydrophobic phenylalanine-glycine (FG) domains on nucleoporins. Such FG-domains consist of repeating units of FxFG, FG, or GLFG sequences, which can be interspersed with highly charged amino acid sequences. Despite the high density of charge exhibited in certain FG-domains, if and how charge influences FG-domain self-assembly and selective binding of nuclear transport receptors is largely unexplored. Studying how individual charged amino acids contribute to nuclear pore selectivity is challenging with modern in vivo and in vitro techniques due to the complexity of nucleoporin sequences. Here, we present a rationally designed approach to deconstruct essential components of nucleoporins down to 14 amino acid sequences. With these nucleoporin-based peptides, we systematically dissect how charge type and placement of charge influences self-assembly and selective binding of FG-containing gels. Specifically, we find that charge type determines which hydrophobic substrates FG sequences recognize while spatial localization of charge tunes hydrophobic self-assembly and receptor selectivity of FG sequences.

scholarly journals Molecular characterization of three newly recognized rat parvoviruses

2002 ◽  
Vol 83 (8) ◽  
pp. 2075-2083 ◽  
Author(s):  
Cho-Hua Wan ◽  
Maria Söderlund-Venermo ◽  
David J. Pintel ◽  
Lela K. Riley
Keyword(s):  
Amino Acid ◽  
Nucleotide Sequence ◽  
Molecular Characterization ◽  
Amino Acid Sequences ◽  
Minute Virus ◽  
Genomic Nucleotide Sequence ◽  
Kilham Rat Virus

Rodent parvoviruses have been documented to interfere with both in vivo and in vitro research. In this study, three rat parvoviruses distinct from previously characterized rodent parvoviruses were identified from naturally infected rats obtained from four discrete sources. These three newly recognized parvoviruses were designated rat minute virus (RMV)-1a, -1b and -1c. In this study, the genomic nucleotide sequence and the predicted amino acid sequences of proteins for each of the three RMV-1 variants and Kilham rat virus (KRV) were determined and compared with previously characterized rodent parvoviruses. The three RMV-1 variants were shown to be closely related to each other, to be distinct from but closely related to KRV and H-1 virus, and to be significantly different from the previously identified rat parvovirus isolate, RPV-1a.

scholarly journals Residues critical for retroviral integrative recombination in a region that is highly conserved among retroviral/retrotransposon integrases and bacterial insertion sequence transposases.

1992 ◽  
Vol 12 (5) ◽  
pp. 2331-2338 ◽  
Author(s):  
J Kulkosky ◽  
K S Jones ◽  
R A Katz ◽  
J P Mack ◽  
A M Skalka
Keyword(s):  
Human Immunodeficiency Virus ◽  
Amino Acid ◽  
Rous Sarcoma Virus ◽  
Amino Acid Sequences ◽  
Rous Sarcoma ◽  
Essential Components ◽  
Immunodeficiency Virus ◽  
Sarcoma Virus ◽  
E Region

Our comparison of deduced amino acid sequences for retroviral/retrotransposon integrase (IN) proteins of several organisms, including Drosophila melanogaster and Schizosaccharomyces pombe, reveals strong conservation of a constellation of amino acids characterized by two invariant aspartate (D) residues and a glutamate (E) residue, which we refer to as the D,D(35)E region. The same constellation is found in the transposases of a number of bacterial insertion sequences. The conservation of this region suggests that the component residues are involved in DNA recognition, cutting, and joining, since these properties are shared among these proteins of divergent origin. We introduced amino acid substitutions in invariant residues and selected conserved and nonconserved residues throughout the D,D(35)E region of Rous sarcoma virus IN and in human immunodeficiency virus IN and assessed their effect upon the activities of the purified, mutant proteins in vitro. Changes of the invariant and conserved residues typically produce similar impairment of both viral long terminal repeat (LTR) oligonucleotide cleavage referred to as the processing reaction and the subsequent joining of the processed LTR-based oligonucleotides to DNA targets. The severity of the defects depended upon the site and the nature of the amino acid substitution(s). All substitutions of the invariant acidic D and E residues in both Rous sarcoma virus and human immunodeficiency virus IN dramatically reduced LTR oligonucleotide processing and joining to a few percent or less of wild type, suggesting that they are essential components of the active site for both reactions.(ABSTRACT TRUNCATED AT 250 WORDS)

Molecular self-assembly of a tyroservatide-derived octapeptide and hydroxycamptothecin for enhanced therapeutic efficacy

Nanoscale ◽  
2021 ◽  
Vol 13 (9) ◽  
pp. 5094-5102
Author(s):  
Jing Liu ◽  
Can Wu ◽  
Guoru Dai ◽  
Feng Feng ◽  
Yuquan Chi ◽  
...  
Keyword(s):  
Amino Acid ◽  
Self Assembly ◽  
Therapeutic Efficacy ◽  
Self Assembling

A pure l-amino acid-based molecular hydrogel was designed through conjugation of an anticancer tripeptide tyroservatide (YSV) with a self-assembling moiety, which enhanced therapeutic efficacy of both YSV and hydroxycamptothecin in vitro and in vivo.

Residues critical for retroviral integrative recombination in a region that is highly conserved among retroviral/retrotransposon integrases and bacterial insertion sequence transposases

1992 ◽  
Vol 12 (5) ◽  
pp. 2331-2338
Author(s):  
J Kulkosky ◽  
K S Jones ◽  
R A Katz ◽  
J P Mack ◽  
A M Skalka
Keyword(s):  
Human Immunodeficiency Virus ◽  
Amino Acid ◽  
Rous Sarcoma Virus ◽  
Amino Acid Sequences ◽  
Rous Sarcoma ◽  
Essential Components ◽  
Immunodeficiency Virus ◽  
Sarcoma Virus ◽  
E Region

Our comparison of deduced amino acid sequences for retroviral/retrotransposon integrase (IN) proteins of several organisms, including Drosophila melanogaster and Schizosaccharomyces pombe, reveals strong conservation of a constellation of amino acids characterized by two invariant aspartate (D) residues and a glutamate (E) residue, which we refer to as the D,D(35)E region. The same constellation is found in the transposases of a number of bacterial insertion sequences. The conservation of this region suggests that the component residues are involved in DNA recognition, cutting, and joining, since these properties are shared among these proteins of divergent origin. We introduced amino acid substitutions in invariant residues and selected conserved and nonconserved residues throughout the D,D(35)E region of Rous sarcoma virus IN and in human immunodeficiency virus IN and assessed their effect upon the activities of the purified, mutant proteins in vitro. Changes of the invariant and conserved residues typically produce similar impairment of both viral long terminal repeat (LTR) oligonucleotide cleavage referred to as the processing reaction and the subsequent joining of the processed LTR-based oligonucleotides to DNA targets. The severity of the defects depended upon the site and the nature of the amino acid substitution(s). All substitutions of the invariant acidic D and E residues in both Rous sarcoma virus and human immunodeficiency virus IN dramatically reduced LTR oligonucleotide processing and joining to a few percent or less of wild type, suggesting that they are essential components of the active site for both reactions.(ABSTRACT TRUNCATED AT 250 WORDS)

scholarly journals Expression of CD14 by Hepatocytes: Upregulation by Cytokines during Endotoxemia

1998 ◽  
Vol 66 (11) ◽  
pp. 5089-5098 ◽  
Author(s):  
Shubing Liu ◽  
Lajwanti S. Khemlani ◽  
Richard A. Shapiro ◽  
Mark L. Johnson ◽  
Kaihong Liu ◽  
...  
Keyword(s):  
Amino Acid ◽  
Rat Hepatocytes ◽  
Amino Acid Sequences ◽  
Mrna Levels ◽  
Soluble Cd14 ◽  
Protein Levels ◽  
Cd14 Mrna ◽  
Lps Treatment

ABSTRACT Studies were undertaken to examine hepatocyte CD14 expression during endotoxemia. Our results show that lipopolysaccharide (LPS) treatment in vivo caused a marked upregulation in CD14 mRNA and protein levels in rat hepatocytes. Detectable increases in mRNA were seen as early as 1.5 h after LPS treatment; these increases peaked at 20-fold by 3 h and returned to baseline levels by 24 h. In situ hybridization localized the CD14 mRNA expression to hepatocytes both in vitro and in vivo. Increases in hepatic CD14 protein levels were detectable by 3 h and peaked at 12 h. Hepatocytes from LPS-treated animals expressed greater amounts of cell-associated CD14 protein, and more of the soluble CD14 was released by hepatocytes from LPS-treated rats in vitro. The increases in hepatocyte CD14 expression during endotoxemia occurred in parallel to increases of CD14 levels in plasma. To provide molecular identification of the hepatocyte CD14, we cloned the rat liver CD14 cDNA. The longest clone consists of a 1,591-bp insert containing a 1,116-bp open reading frame. The deduced amino acid sequence is 372 amino acids long, has 81.8 and 62.8% homology to the amino acid sequences of mouse and human CD14, respectively, and is identical to the rat macrophage CD14. The expressed CD14 protein from this clone was functional, as indicated by NF-κB activation in response to LPS and fluorescein isothiocyanate-LPS binding in CHO cells stably transfected with rat CD14. A nuclear run-on assay showed that CD14 transcription rates were significantly increased in hepatocytes from LPS-treated animals, indicating that the upregulation in CD14 mRNA levels observed in rat hepatocytes after LPS treatment is dependent, in part, on increased transcription. In vitro and in vivo experiments indicated that interleukin-1β and/or tumor necrosis factor α participate in the upregulation of CD14 mRNA levels in hepatocytes. Our data indicate that hepatocytes express CD14 and that hepatocyte CD14 mRNA and protein levels increase rapidly during endotoxemia. Our observations also support the idea that soluble CD14 is an acute-phase protein and that hepatocytes could be a source for soluble CD14 production.

Amino Acid Degrading Enzymes and their Application in Cancer Therapy

2019 ◽  
Vol 26 (3) ◽  
pp. 446-464 ◽  
Author(s):  
Vadim S. Pokrovsky ◽  
Olga E. Chepikova ◽  
Denis Zh. Davydov ◽  
Andrey A. Zamyatnin Jr ◽  
Alexander N. Lukashev ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Cancer Therapy ◽  
Cancer Treatment ◽  
Arginine Deiminase ◽  
In Vivo Studies ◽  
Degrading Enzymes ◽  
Essential Components

Background:Amino acids are essential components in various biochemical pathways. The deprivation of certain amino acids is an antimetabolite strategy for the treatment of amino acid-dependent cancers which exploits the compromised metabolism of malignant cells. Several studies have focused on the development and preclinical and clinical evaluation of amino acid degrading enzymes, namely L-asparaginase, L-methionine γ-lyase, L-arginine deiminase, L-lysine α-oxidase. Further research into cancer cell metabolism may therefore define possible targets for controlling tumor growth.Objective:The purpose of this review was to summarize recent progress in the relationship between amino acids metabolism and cancer therapy, with a particular focus on Lasparagine, L-methionine, L-arginine and L-lysine degrading enzymes and their formulations, which have been successfully used in the treatment of several types of cancer.Methods:We carried out a structured search among literature regarding to amino acid degrading enzymes. The main aspects of search were in vitro and in vivo studies, clinical trials concerning application of these enzymes in oncology.Results:Most published research are on the subject of L-asparaginase properties and it’s use for cancer treatment. L-arginine deiminase has shown promising results in a phase II trial in advanced melanoma and hepatocellular carcinoma. Other enzymes, in particular Lmethionine γ-lyase and L-lysine α-oxidase, were effective in vitro and in vivo.Conclusion:The findings of this review revealed that therapy based on amino acid depletion may have the potential application for cancer treatment but further clinical investigations are required to provide the efficacy and safety of these agents.

scholarly journals The blp Bacteriocins of Streptococcus pneumoniae Mediate Intraspecies Competition both In Vitro and In Vivo

2006 ◽  
Vol 75 (1) ◽  
pp. 443-451 ◽  
Author(s):  
Suzanne Dawid ◽  
Aoife M. Roche ◽  
Jeffrey N. Weiser
Keyword(s):  
Streptococcus Pneumoniae ◽  
Amino Acid ◽  
Response Regulator ◽  
Strain Analysis ◽  
Amino Acid Sequences ◽  
Bacteriocin Activity ◽  
Nasopharyngeal Colonization ◽  
Intraspecies Competition

ABSTRACT The introduction of the conjugate seven-valent pneumococcal vaccine has led to the replacement of vaccine serotypes with nonvaccine serotypes of Streptococcus pneumoniae. This observation implies that intraspecies competition between pneumococci occurs during nasopharyngeal colonization, allowing one strain or set of strains to predominate over others. We investigated the contribution of the blp locus, encoding putative bacteriocins and cognate immunity peptides, to intraspecies competition. We sequenced the relevant regions of the blp locus of a type 6A strain able to inhibit the growth of the type 4 strain, TIGR4, in vitro. Using deletional analysis, we confirmed that inhibitory activity is regulated by the function of the response regulator, BlpR, and requires the two putative bacteriocin genes blpM and blpN. Comparison of the TIGR4 BlpM and -N amino acid sequences demonstrated that only five amino acid differences were sufficient to target the heterologous strain. Analysis of a number of clinical isolates suggested that the BlpMN bacteriocins divide into two families. A mutant in the blpMN operon created in the clinically relevant type 19A background was deficient in both bacteriocin activity and immunity. This strain was unable to compete with both its parent strain and a serotype 4 isolate during cocolonization in the mouse nasopharynx, suggesting that the locus is functional in vivo and confirming its role in promoting intraspecies competition.

scholarly journals Pseudomonas aeruginosa MutL protein functions in Escherichia coli

2005 ◽  
Vol 388 (3) ◽  
pp. 879-887 ◽  
Author(s):  
Daniela K. JACQUELÍN ◽  
Adrián FILIBERTI ◽  
Carlos E. ARGARAÑA ◽  
José L. BARRA
Keyword(s):  
Escherichia Coli ◽  
Pseudomonas Aeruginosa ◽  
Amino Acid ◽  
Amino Acid Sequences ◽  
Single Amino Acid ◽  
Repair System ◽  
E Coli ◽  
New Findings

Escherichia coli MutS, MutL and MutH proteins act sequentially in the MMRS (mismatch repair system). MutH directs the repair system to the newly synthesized strand due to its transient lack of Dam (DNA-adenine methylase) methylation. Although Pseudomonas aeruginosa does not have the corresponding E. coli MutH and Dam homologues, and consequently the MMRS seems to work differently, we show that the mutL gene from P. aeruginosa is capable of complementing a MutL-deficient strain of E. coli. MutL from P. aeruginosa has conserved 21 out of the 22 amino acids known to affect functioning of E. coli MutL. We showed, using protein affinity chromatography, that the C-terminal regions of P. aeruginosa and E. coli MutL are capable of specifically interacting with E. coli MutH and retaining the E. coli MutH. Although, the amino acid sequences of the C-terminal regions of these two proteins are only 18% identical, they are 88% identical in the predicted secondary structure. Finally, by analysing (E. coli–P. aeruginosa) chimaeric MutL proteins, we show that the N-terminal regions of E. coli and P. aeruginosa MutL proteins function similarly, in vivo and in vitro. These new findings support the hypothesis that a large surface, rather than a single amino acid, constitutes the MutL surface for interaction with MutH, and that the N- and C-terminal regions of MutL are involved in such interactions.

scholarly journals Health Benefits of Antioxidative Peptides Derived from Legume Proteins with a High Amino Acid Score

Antioxidants ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 316
Author(s):  
Athanasia Matemu ◽  
Soichiro Nakamura ◽  
Shigeru Katayama
Keyword(s):  
Amino Acid ◽  
Protein Hydrolysates ◽  
Amino Acid Sequences ◽  
In Vivo Studies ◽  
Antioxidant Peptides ◽  
High Amino Acid ◽  
Potential Applications ◽  
Amino Acid Score

Legumes such as soybean, chickpea, lentil, cowpea, and mung bean, are valuable sources of protein with a high amino acid score and can provide bioactive peptides. This manuscript presents a review on legume-derived peptides, focusing on in vitro and in vivo studies on the potential antioxidative activities of protein hydrolysates and their characterization, amino acid sequences, or purified/novel peptides. The health implications of legume-derived antioxidative peptides in reducing the risks of cancer and cardiovascular diseases are linked with their potent action against oxidation and inflammation. The molecular weight profiles and amino acid sequences of purified and characterized legume-derived antioxidant peptides are not well established. Therefore, further exploration of legume protein hydrolysates is necessary for assessing the potential applications of antioxidant-derived peptides in the functional food industry.

In vitro and in vivo polysaccharides assembly: ultrastructural and cytochemical study of growing plant cell wall components.

1978 ◽  
Vol 36 (2) ◽  
pp. 434-435
Author(s):  
D. Reis ◽  
B. Vian ◽  
J. C. Roland
Keyword(s):  
Cell Wall ◽  
Self Assembly ◽  
Plant Cell Wall ◽  
Higher Plants ◽  
Three Dimensional ◽  
Cytochemical Study ◽  
Wall Components

Wall morphogenesis in higher plants is a problem still open to controversy. Until now the possibility of a transmembrane control and the involvement of microtubules were mostly envisaged. Self-assembly processes have been observed in the case of walls of Chlamydomonas and bacteria. Spontaneous gelling interactions between xanthan and galactomannan from Ceratonia have been analyzed very recently. The present work provides indications that some processes of spontaneous aggregation could occur in higher plants during the formation and expansion of cell wall.Observations were performed on hypocotyl of mung bean (Phaseolus aureus) for which growth characteristics and wall composition have been previously defined.In situ, the walls of actively growing cells (primary walls) show an ordered three-dimensional organization (fig. 1). The wall is typically polylamellate with multifibrillar layers alternately transverse and longitudinal. Between these layers intermediate strata exist in which the orientation of microfibrils progressively rotates. Thus a progressive change in the morphogenetic activity occurs.

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