scholarly journals Peripheral cyclic β-amino acids balance the stability and edge-protection of β-sandwiches

2018 ◽  
Vol 16 (30) ◽  
pp. 5492-5499 ◽  
Author(s):  
Gábor Olajos ◽  
Anasztázia Hetényi ◽  
Edit Wéber ◽  
Titanilla Szögi ◽  
Lívia Fülöp ◽  
...  

cis-2-Aminocyclohexanecarboxylic acid replacements at the edges of β-sandwiches reduce β-sheet propensities just enough to prevent aggregation but still maintain a compact structure.

2000 ◽  
Vol 83 (06) ◽  
pp. 896-901 ◽  
Author(s):  
Guang-Chao Sui ◽  
Björn Wiman

SummaryWe have investigated the B β-sheet in PAI-1 regarding its role for the stability of the molecule. The residues from His219 to Tyr241 (except for Gly230 and Pro240), covering the s2B and s3B strands, and in addition His185 and His190 were substituted by amino acids with opposite properties. The 23 generated single-site changed mutants and also wild type PAI-1 (wtPAI-1) were expressed in E. coli. Subsequently they were purified by heparin-Sepharose and anhydrotrypsin agarose affinity chromatographies. The stability of the purified PAI-1 variants was analyzed at 37° C and at different pHs (5.5, 6.5 or 7.5). At pH 7.5 and 37° C, single substitutions of the residues in the central portions of both strands 2 and 3 in the B β-sheet (Ile223 to Leu226 on s2B and Met235 to Ile237 on s3B), caused a significant decrease in stability, yielding half-lives of about 10–25% as compared to wtPAI-1. On the other hand, mutations at both sides of the central portion of the B β-sheet (Tyr221, Asp222, Tyr228 and Thr232) frequently resulted in an increased PAI-1 stability (up to 7-fold). While wtPAI-1 exhibited prolonged half-lives at pH 6.5 and 5.5, the PAI-1 variant Y228S was more stable at neutral pH (half-life of 9.6 h at pH 7.5) as compared to its half-life at pH 5.5 (1.1 h). One of the 4 modified histidine residues (His229) resulted in a variant with a clearly affected stability as a function of pH, suggesting that it may, at least in part, be of importance for the pH dependence of the PAI-1 stability. Thus, our data demonstrate that the B β-sheet is of great importance for the stability of the molecule. Modifications in this part causes decreased or increased stability in a certain pattern, suggesting effects on the insertion rate of the reactive center loop into the A β-sheet of the molecule.


PLoS ONE ◽  
2021 ◽  
Vol 16 (12) ◽  
pp. e0261123
Author(s):  
Thu-Thuy Nguyen ◽  
Trang Hoang ◽  
Kiet N. Tran ◽  
Hyeonji Kim ◽  
Sei-Heon Jang ◽  
...  

Thioredoxin (Trx), a small redox protein, exhibits thermal stability at high temperatures regardless of its origin, including psychrophiles. Trxs have a common structure consisting of the central β-sheet flanked by an aliphatic cluster on one side and an aromatic cluster on the other side. Although the roles of aromatic amino acids in the folding and stability of proteins have been studied extensively, the contributions of aromatic residues to the stability and function of Trx, particularly Trxs from cold-adapted organisms, have not been fully elucidated. This study examined the roles of aromatic amino acids in the aromatic cluster of a Trx from the psychrophilic Arctic bacterium Sphingomonas sp. PAMC 26621 (SpTrx). The aromatic cluster of SpTrx was comprised of W11, F26, F69, and F80, in which F26 at the β2 terminus was buried inside. The substitution of tyrosine for F26 changed the SpTrx conformation substantially compared to that of F69 and F80. Further biochemical and spectroscopic investigations on F26 showed that the F26Y, F26W, and F26A mutants resulted in structural instability of SpTrx in both urea- and temperature-induced unfolding and lower insulin reduction activities. The Trx reductase (SpTR) showed lower catalytic efficiencies against F26 mutants compared to the wild-type SpTrx. These results suggest that buried F26 is essential for maintaining the active-site conformation of SpTrx as an oxidoreductase and its structural stability for interactions with SpTR at colder temperatures.


2004 ◽  
Vol 13 (4) ◽  
pp. 1134-1147 ◽  
Author(s):  
Clara M. Santiveri ◽  
Jorge Santoro ◽  
Manuel Rico ◽  
M. Angeles Jiménez

1988 ◽  
Vol 253 (1) ◽  
pp. 139-151 ◽  
Author(s):  
C Domenicucci ◽  
H A Goldberg ◽  
T Hofmann ◽  
D Isenman ◽  
S Wasi ◽  
...  

Osteonectin, extracted from foetal porcine calvariae with 0.5 M-EDTA, was purified to homogeneity by using gel filtration and polyanion anion-exchange fast protein liquid chromatography under dissociative conditions without the need of reducing agents. The purified protein migrated with an Mr of 40,300 on SDS/polyacrylamide gels and was similar to bovine osteonectin in both amino acid composition and in its ability to bind to hydroxyapatite in the presence of 4 M-guanidinium hydrochloride (GdmCl). However, unlike the bovine protein, porcine osteonectin did not bind selectively to hydroxyapatite when EDTA tissue extracts were used. In addition, purified porcine osteonectin did not show any apparent affinity for either native or denatured type I collagen, but did bind to serum albumin. Primary sequence analysis revealed an N-terminal alanine residue, with approximately one-half of the subsequent 35 residues identified as small hydrophobic amino acids and one-quarter as acidic amino acids. The only significant difference between the N-terminal sequences of the bovine and porcine proteins was the deletion of the tripeptide Val-Ala-Glu in porcine osteonectin. In contrast with bovine osteonectin, far-u.v.c.d. of porcine osteonectin revealed considerable secondary structure, of which 27% was alpha-helix and 39% was beta-sheet. Cleavage of the molecule with CNBr under non-reducing conditions generated five fragments, of which two major fragments (Mr 27,900 and 12,400) stained blue with Stains All, a reagent that stains sialic-acid-rich proteins/phosphate-containing proteins and/or Ca2+-binding proteins blue while staining other proteins pink. The 12,400-Mr fragment bound 45Ca2+ selectively, indicating a Ca2+-binding site in this part of the molecule. The 27,900-Mr fragment did not bind Ca2+, and since biosynthetic studies with 32PO4(3-) did not show phosphorylation of porcine osteonectin, this fragment is likely to be highly acidic. The incomplete cleavage of the molecule with CNBr and the ability of the molecule to regain its secondary structure after exposure to 7 M-urea are features consistent with the molecule having a compact structure that is stabilized by numerous disulphide bridges. The chemical and binding properties of porcine osteonectin are closely similar to the recently described ‘culture shock’, SPARC and BM-40 proteins, indicating that these are homologous proteins.


Author(s):  
LEILA D. FALCÃO ◽  
DENISE M. BARROS ◽  
CONY GAUCHE ◽  
MARILDE T. BORDIGNON LUIZ

Este trabalho apresenta revisão de literatura sobre a reação de copigmentação intra e intermolecular e sua relevância na estabilização de antocianinas. Flavonóides não-antociânicos, alcalóides, aminoácidos e nucleosídios, entre outros, podem atuar como copigmentos de antocianinas. O aumento na estabilidade das antocianinas ocorre devido à proteção fornecida pelo copigmento frente à reação de hidratação do cátion flavilium. Estudos ainda são necessários para avaliar a estabilidade de antocianinas adicionadas de copigmentos em sistemas modelos de alimentos, visando aumentar o espectro de aplicação dessas como corantes em alimentos e bebidas. ANTHOCYANINS INTRA AND INTERMOLECULAR COPIGMENTATION: A REVIEW Abstract This research presents literature review about the reaction of intra and intermolecular copigmentation and its revealance in anthocyanins stabilization. Non-anthocyanic flavonoids, alkaloids, amino acids, nucleosides, and others, can act as anthocyanins copigments. The increase in the stability of anthocyanins occurs due to protection supplied by the copigment towards the hydratation reaction of colored flavylium cation. Studies to evaluate anthocyanins stabilization added of copigments in food models system are still necessary, aiming to enhance the application spectra as colorants in foods and beverages.


1995 ◽  
Vol 181 (5) ◽  
pp. 1817-1825 ◽  
Author(s):  
J M Vyas ◽  
J R Rodgers ◽  
R R Rich

The major histocompatibility (MHC) class I-b molecule H-2M3a binds and presents N-formylated peptides to cytotoxic T lymphocytes. This requirement potentially places severe constraints on the number of peptides that M3a can present to the immune system. Consistent with this idea, the M3a-Ld MHC class I chimera is expressed at very low levels on the cell surface, but can be induced significantly by the addition of specific peptides at 27 degrees C. Using this assay, we show that M3a binds many very short N-formyl peptides, including N-formyl chemotactic peptides and canonical octapeptides. This observation is in sharp contrast to the paradigmatic size range of peptides of 8-10 amino acids binding to most class I-a molecules and the class I-b molecule Qa-2. Stabilization by fMLF-benzyl amide could be detected at peptide concentrations as low as 100 nM. While N-formyl peptides as short as two amino acids in length stabilized expression of M3a-Ld, increasing the length of these peptides added to the stability of peptide-MHC complexes as determined by 27-37 degrees C temperature shift experiments. We propose that relaxation of the length rule may represent a compensatory adaptation to maximize the number of peptides that can be presented by H-2M3a.


2005 ◽  
Vol 387 (2) ◽  
pp. 401-409 ◽  
Author(s):  
Jolanta KOPEC ◽  
Alexander BERGMANN ◽  
Gerhard FRITZ ◽  
Elisabeth GROHMANN ◽  
Walter KELLER

TraA is the DNA relaxase encoded by the broad-host-range Grampositive plasmid pIP501. It is the second relaxase to be characterized from plasmids originating from Gram-positive organisms. Full-length TraA (654 amino acids) and the N-terminal domain (246 amino acids), termed TraAN246, were expressed as 6×His-tagged fusions and purified. Small-angle X-ray scattering and chemical cross-linking proved that TraAN246 and TraA form dimers in solution. Both proteins revealed oriTpIP501 (origin of transfer of pIP501) cleavage activity on supercoiled plasmid DNA in vitro. oriT binding was demonstrated by electrophoretic mobility shift assays. Radiolabelled oligonucleotides covering different parts of oriTpIP501 were subjected to binding with TraA and TraAN246. The KD of the protein–DNA complex encompassing the inverted repeat, the nick site and an additional 7 bases was found to be 55 nM for TraA and 26 nM for TraAN246. The unfolding of both protein constructs was monitored by measuring the change in the CD signal at 220 nm upon temperature change. The unfolding transition of both proteins occurred at approx. 42 °C. CD spectra measured at 20 °C showed 30% α-helix and 13% β-sheet for TraA, and 27% α-helix and 18% β-sheet content for the truncated protein. Upon DNA binding, an enhanced secondary structure content and increased thermal stability were observed for the TraAN246 protein, suggesting an induced-fit mechanism for the formation of the specific relaxase–oriT complex.


Gaia Scientia ◽  
2016 ◽  
Vol 10 (4) ◽  
pp. 372-389
Author(s):  
João Paulo de Sousa Prado ◽  
José Marcelino Oliveira Cavalheiro ◽  
Thiago Brandão Cavalheiro ◽  
Fernanda Vanessa Gomes da Silva

The Brazilian shrimp farming uses mainly commercial feed for shrimp nutrition. This choice occurs because of the advantages related to convenience and good adaptation of Litopenaeus vannanmei to feed intake. Thus, the quality of feed is a determining factor for maximum performance of the shrimp farms, making the right selection of suppliers and control of the storage conditions as ways to prevent contamination and spoilage of feed. The objective of this study was to evaluate the stability of amino acids in meals and commercial feed with different protein levels, subjected to high-temperature storage. The samples were exposed to temperature of 50 oC and evaluated every 5 days for 30 days.The analyses of the degradation of amino acids were performed using an elution gradient in HPLC system.In evaluated meals it was observed that valine and arginine were the amino acids that suffered greater loss during the experiment and histidine and alanine suffered less degradation.Significant difference was observed in the content of all amino acids analyzed after exposure of the feed to the temperature of 50 oC; with reduce in values of its amino acid content. The results obtained in this study indicate that meals and feed exposed to elevated temperatures significantly reduced the content of its amino acids.


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