scholarly journals The role of the IT-state in D76N β2-microglobulin amyloid assembly: A crucial intermediate or an innocuous bystander?

2020 ◽  
Vol 295 (35) ◽  
pp. 12474-12484 ◽  
Author(s):  
Hugh I. Smith ◽  
Nicolas Guthertz ◽  
Emma E. Cawood ◽  
Roberto Maya-Martinez ◽  
Alexander L. Breeze ◽  
...  
Keyword(s):  
Amino Acids ◽  
Single Amino Acid ◽  
Folding Intermediate ◽  
Exposed Site ◽  
Aggregation Propensity ◽  
Amyloid Disease ◽  
Aggregation Rate ◽  
Amyloid Assembly

The D76N variant of human β2-microglobulin (β2m) is the causative agent of a hereditary amyloid disease. Interestingly, D76N-associated amyloidosis has a distinctive pathology compared with aggregation of WT-β2m, which occurs in dialysis-related amyloidosis. A folding intermediate of WT-β2m, known as the IT-state, which contains a nonnative trans Pro-32, has been shown to be a key precursor of WT-β2m aggregation in vitro. However, how a single amino acid substitution enhances the rate of aggregation of D76N-β2m and gives rise to a different amyloid disease remained unclear. Using real-time refolding experiments monitored by CD and NMR, we show that the folding mechanisms of WT- and D76N-β2m are conserved in that both proteins fold slowly via an IT-state that has similar structural properties. Surprisingly, however, direct measurement of the equilibrium population of IT using NMR showed no evidence for an increased population of the IT-state for D76N-β2m, ruling out previous models suggesting that this could explain its enhanced aggregation propensity. Producing a kinetically trapped analog of IT by deleting the N-terminal six amino acids increases the aggregation rate of WT-β2m but slows aggregation of D76N-β2m, supporting the view that although the folding mechanisms of the two proteins are conserved, their aggregation mechanisms differ. The results exclude the IT-state as the origin of the rapid aggregation of D76N-β2m, suggesting that other nonnative states must cause its high aggregation rate. The results highlight how a single substitution at a solvent-exposed site can affect the mechanism of aggregation and the resulting disease.

scholarly journals Phylogenetic analysis and predicted functional effect of protein mutations of E6 and E7 HPV16 strains isolated in Indonesia

2015 ◽  
Vol 24 (4) ◽  
pp. 197-205
Author(s):  
Dwi Wulandari ◽  
Lisnawati Rachmadi ◽  
Tjahjani M. Sudiro
Keyword(s):  
Amino Acids ◽  
Phylogenetic Analysis ◽  
Amino Acid ◽  
Asian American ◽  
Protein Function ◽  
Single Amino Acid ◽  
Hpv16 E6 ◽  
E6 And E7 ◽  
Neutral Mutations

Background: E6 and E7 are oncoproteins of HPV16. Natural amino acid variation in HPV16 E6 can alter its carcinogenic potential. The aim of this study was to analyze phylogenetically E6 and E7 genes and proteins of HPV16 from Indonesia and predict the effects of single amino acid substitution on protein function. This analysis could be used to reduce time, effort, and research cost as initial screening in selection of protein or isolates to be tested in vitro or in vivo.Methods: In this study, E6 and E7 gene sequences were obtained from 12 samples of  Indonesian isolates, which  were compared with HPV16R (prototype) and 6 standard isolates in the category of European (E), Asian (As), Asian-American (AA), African-1 (Af-1), African-2 (Af-2), and North American (NA) branch from Genbank. Bioedit v.7.0.0 was used to analyze the composition and substitution of single amino acids. Phylogenetic analysis of E6 and E7 genes and proteins was performed using Clustal X (1.81) and NJPLOT softwares. Effects of single amino acid substitutions on protein function of E6 and E7 were analysed by SNAP.Results: Java variants and isolate ui66* belonged to European branch, while the others belonged to Asian and African branches. Twelve changes of amino acids were found in E6 and one in E7 proteins. SNAP analysis showed two non neutral mutations, i.e. R10I and C63G in E6 proteins. R10I mutations were found in Af-2 genotype (AF472509) and Indonesian isolates (Af2*), while C63G mutation was found only in Af2*.Conclusion: E6 proteins of HPV16 variants were more variable than E7. SNAP analysis showed that only E6 protein of African-2 branch had functional differences compared to HPV16R.

scholarly journals Enhancement of aromatase activity by D-aspartic acid in the ovary of the lizard Podarcis s. sicula

Reproduction ◽  
2001 ◽  
pp. 803-808 ◽  
Author(s):  
L Assisi ◽  
V Botte ◽  
A D'Aniello ◽  
MM Di Fiore
Keyword(s):  
Amino Acids ◽  
Aspartic Acid ◽  
Reproductive Cycle ◽  
Catalytic Properties ◽  
Ovarian Tissue ◽  
Experimental Treatment ◽  
Tissue Homogenate ◽  
Aromatase Activity

The present study investigated the role of D-aspartic acid (D-Asp) in ovarian steroidogenesis and its effect on aromatase activity in the lizard, Podarcis s. sicula. It was determined that D-Asp concentrations vary significantly during phases of the reproductive cycle: they vary inversely with testosterone concentrations and directly with oestradiol concentrations in the ovary and plasma. Experimental treatment showed that administration of D-Asp induces a decrease in testosterone and an increase in oestradiol, and that treatment with other amino acids (L-Asp, D-Glu and D-Ala) instead of D-Asp has no effects. Experiments in vitro confirmed these results. Furthermore, these experiments showed an increase in aromatase activity, as the addition of D-Asp either to fresh ovarian tissue homogenate or to acetonic powder of ovarian follicles induced a significant increase in the conversion of testosterone to oestradiol. Aromatase activity is four times greater in the presence of D-Asp than in its absence. However, almost equivalent values of the two K(m) values (both approximately 25 nmol l(-1)) indicate that aromatase has the same catalytic properties in both cases.

scholarly journals Identification of a talin binding site in the cytoskeletal protein vinculin.

1989 ◽  
Vol 109 (6) ◽  
pp. 2917-2927 ◽  
Author(s):  
P Jones ◽  
P Jackson ◽  
G J Price ◽  
B Patel ◽  
V Ohanion ◽  
...  
Keyword(s):  
Amino Acids ◽  
In Vitro Transcription ◽  
Binding Activity ◽  
Cytoskeletal Protein ◽  
Translation System ◽  
Cos Cells ◽  
Cell Matrix ◽  
Do So

Binding of the cytoskeletal protein vinculin to talin is one of a number of interactions involved in linking F-actin to cell-matrix junctions. To identify the talin binding domain in vinculin, we expressed the NH2-terminal region of the molecule encoded by two closely similar, but distinct vinculin cDNAs, using an in vitro transcription translation system. The 5' Eco RI-Bam HI fragment of a partial 2.89-kb vinculin cDNA encodes a 45-kD polypeptide containing the first 398 amino acids of the molecule. The equivalent restriction enzyme fragment of a second vinculin cDNA (cVin5) lacks nucleotides 746-867, and encodes a 41-kD polypeptide missing amino acids 167-207. The radiolabeled 45-kD vinculin polypeptide bound to microtiter wells coated with talin, but not BSA, and binding was inhibited by unlabeled vinculin. In contrast, the 41-kD vinculin polypeptide was devoid of talin binding activity. The role of residues 167-207 in talin binding was further analyzed by making a series of deletions spanning this region, each deletion of seven amino acids contiguous with the next. Loss of residues 167-173, 174-180, 181-187, 188-194, or 195-201 resulted in a marked reduction in talin binding activity, although loss of residues 202-208 had much less effect. When the 45-kD vinculin polypeptide was expressed in Cos cells, it localized to cell matrix junctions, whereas the 41-kD polypeptide, lacking residues 167-207, was unable to do so. Interestingly, some deletion mutants with reduced ability to bind talin in vitro, were still able to localize to cell matrix junctions.

Amino Acid Transporter X Is Required for Hematopoietic Stem Cell Maintenance through Regulating Specific Amino Acids Level

Blood ◽  
2015 ◽  
Vol 126 (23) ◽  
pp. 1166-1166 ◽  
Author(s):  
Zhenrui Li ◽  
Keiyo Takubo ◽  
Pengxu Qian ◽  
Toshio Suda ◽  
Linheng Li
Keyword(s):  
Amino Acids ◽  
Stem Cell ◽  
Amino Acid ◽  
Acid Metabolism ◽  
Hematopoietic Stem ◽  
Cell Pool ◽  
Stem Cell Pool

Abstract Hematopoietic stem cells (HSCs) maintenance is required to preserve stem cell pool and compensate the dynamic loss of blood cells. Previous studies of HSCs maintenance mainly focus on the quiescent versus active state of HSCs and accumulated evidence indicates that metabolism plays a critical role in coordinating divergent stem cell states. While recent reports largely emphasized the role of catabolic glycolysis on long-term (LT) HSC maintenance, we found that free amino acids are enriched in primitive stem cell by ~1.5 fold. Given that amino acid metabolism in HSCs is largely unknown, we first cultured bone marrow (BM) cells with individual amino acid deprived medium to study the function of individual amino acids on HSCs in vitro. Surprisingly, we found that specific amino acids, including valine, methionine and threonine (VMT), are essential for maintaining primitive HSCs, as removing them (VMT) individually from media dramatically reduced primitive HSC number by over 95%. Thus, we hypothesize that specific amino acids are critical for preserving the stem cell pool and maintaining their function. To test it, we transplanted equal number of cells cultured with complete or individual VMT deprived media into lethally irradiated recipient mice and found VMT deprivation in vitro impaired stem cell repopulation ability. We also identified the amino acid transporter X (AATX) that is specifically expressed in HSCs and maintain VMT levels within the cell. Furthermore, inhibition of AATX reduced LT-HSC (LSK CD34- Flk2-) number in vivo. BM transplantation indicated that AATX inhibition impaired stem cell long-term reconstitution ability by over 2 fold. Our studies uncovered a role of amino acid metabolism in HSC maintenance and discovered the underlying molecular mechanism related to the amino acid transport. This finding may impact clinical treatment of blood disorders including leukemia. Disclosures No relevant conflicts of interest to declare.

scholarly journals The Role of Amino Acids for the In Vitro Culture of Some Species of Forage Legumes I. Trifolium pratense L

2013 ◽  
Vol 70 (1) ◽  
pp. 87-92
Author(s):  
Gabriela Maria VICAȘ ◽  
Mircea SAVATTI
Keyword(s):  
Amino Acids ◽  
In Vitro Culture ◽  
Culture Medium ◽  
Trifolium Pratense ◽  
Basal Medium ◽  
Red Clover ◽  
Forage Legumes ◽  
Trifolium Pratense L

Establishing the effect of the amino acids as additional additives to the culture medium is and will be in the future one of our concerns of interest for the in vitro culture of some plants. The present study examines the effect of the glicocol added to the LS basal medium over the embryos of the Trifolium pratense L specie cultivated in vitro. There were followed: the percentage of plant regeneration of the red clover, its multiplication capacity and the formation of the root system, and also the evolution of the callus obtained on mediums with 2,4D, BA and amino acid.

Role of Tissue Factor in Adhesion of Mononuclear Phagocytes to and Trafficking Through Endothelium In Vitro

Blood ◽  
1998 ◽  
Vol 92 (11) ◽  
pp. 4167-4177 ◽  
Author(s):  
Gwendalyn J. Randolph ◽  
Thomas Luther ◽  
Sybille Albrecht ◽  
Viktor Magdolen ◽  
William A. Muller
Keyword(s):  
Amino Acids ◽  
Endothelial Cells ◽  
Tissue Factor ◽  
Mononuclear Phagocytes ◽  
Adhesive Protein ◽  
Endothelial Surface ◽  
Apical Direction ◽  
Vitro Model

Abstract An in vitro model consisting of endothelium grown on collagen was used to investigate how mononuclear phagocytes traverse endothelium in the basal-to-apical direction (reverse transmigration), a process that mimics their migration across vascular and/or lymphatic endothelium during atherosclerosis and resolution of inflammation, respectively. Monoclonal antibody (MoAb) VIC7 against tissue factor (TF) inhibited reverse transmigration by 77%. Recombinant tissue factor fragments containing at least six amino acids C-terminal to residue 202 also strongly inhibited reverse transmigration. TF was absent on resting monocytes but was induced on these cells after initial apical-to-basal transendothelial migration. Two additional observations suggest that TF is involved in adhesion between mononuclear phagocytes and endothelium: (1) when monocytes were incubated with lipopolysaccharide (LPS) to stimulate expression of TF before they were added to endothelium, VIC7 or soluble TF modestly inhibited their adhesion to the apical endothelial surface, each by about 35%; and (2) endothelial cells specifically bound to surfaces coated with TF fragments containing amino acids 202-219. This binding was blocked by anti-TF MoAb, suggesting that endothelial cells bear a receptor for TF. These data suggest that mononuclear phagocytes use TF, perhaps as an adhesive protein, to exit sites of inflammation.

scholarly journals Evaluating the role of conserved amino acids in bacterial O-oligosaccharyltransferases by in vivo, in vitro and limited proteolysis assays

Glycobiology ◽  
2013 ◽  
Vol 24 (1) ◽  
pp. 39-50 ◽  
Author(s):  
M. A. Musumeci ◽  
A. Faridmoayer ◽  
Y. Watanabe ◽  
M. F. Feldman
Keyword(s):  
Amino Acids ◽  
Limited Proteolysis ◽  
Conserved Amino Acids

scholarly journals Reconstruction of the immunogenic peptide RNase(43-56) by identification and transfer of the critical residues into an unrelated peptide backbone.

1989 ◽  
Vol 170 (1) ◽  
pp. 203-215 ◽  
Author(s):  
R G Lorenz ◽  
A N Tyler ◽  
P M Allen
Keyword(s):  
Amino Acid ◽  
T Cell ◽  
Single Amino Acid ◽  
Amino Acid Residues ◽  
Peptide Backbone ◽  
Chimeric Peptide ◽  
Critical Residues

The involvement of each of the amino acid residues of the I-Ak-restricted T cell determinant RNase(43-56) was examined in detail using a series of peptides containing single amino acid substitutions. Four positions were identified as being essential for the formation of the determinant, Phe-46, Val-47, His-48, and Leu-51. When these four residues were substituted into the backbone of the unrelated peptide HA(130-144), a nonstimulatory peptide was obtained. The inclusion of an additional residue, Val-54, resulted in a chimeric peptide, RN/HA2, which was nearly as active as the native molecule. The peptide RN/HA2 was able to prime in vivo for RNase reactivity, confirming that these five residues contained all of the specificity of the RNase(43-56) determinant. The role of three of these critical residues was examined using both a functional competition assay and an in vivo priming assay. It was ascertained that the Phe-46 was directly involved in contacting the TCR, while the His-48 and Leu-51 were either involved in binding to the I-Ak molecule or in determining the conformation of the peptide. Thus, by critically evaluating the contribution of each of the amino acid residues in a T cell determinant, we were able to generate a chimeric peptide only containing 5 of 15 residues from the RNase(43-56) sequence that was functionally identical to the native RNase(43-56) molecule both in vitro and in vivo.

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