scholarly journals Complex kinetics and residual structure in the thermal unfolding of yeast triosephosphate isomerase

2015 ◽  
Vol 16 (1) ◽  
Author(s):  
Ariana Labastida-Polito ◽  
Georgina Garza-Ramos ◽  
Menandro Camarillo-Cadena ◽  
Rafael A. Zubillaga ◽  
Andrés Hernández-Arana
2007 ◽  
Vol 26 (7) ◽  
pp. 491-498 ◽  
Author(s):  
Edgar Mixcoha-Hernández ◽  
Liliana M. Moreno-Vargas ◽  
Arturo Rojo-Domínguez ◽  
Claudia G. Benítez-Cardoza

Biochemistry ◽  
2008 ◽  
Vol 47 (44) ◽  
pp. 11665-11673 ◽  
Author(s):  
Luis A. Tellez ◽  
Luis M. Blancas-Mejia ◽  
Ernesto Carrillo-Nava ◽  
Guillermo Mendoza-Hernández ◽  
David A. Cisneros ◽  
...  

2019 ◽  
Vol 476 (21) ◽  
pp. 3333-3353 ◽  
Author(s):  
Malti Yadav ◽  
Kamalendu Pal ◽  
Udayaditya Sen

Cyclic dinucleotides (CDNs) have emerged as the central molecules that aid bacteria to adapt and thrive in changing environmental conditions. Therefore, tight regulation of intracellular CDN concentration by counteracting the action of dinucleotide cyclases and phosphodiesterases (PDEs) is critical. Here, we demonstrate that a putative stand-alone EAL domain PDE from Vibrio cholerae (VcEAL) is capable to degrade both the second messenger c-di-GMP and hybrid 3′3′-cyclic GMP–AMP (cGAMP). To unveil their degradation mechanism, we have determined high-resolution crystal structures of VcEAL with Ca2+, c-di-GMP-Ca2+, 5′-pGpG-Ca2+ and cGAMP-Ca2+, the latter provides the first structural basis of cGAMP hydrolysis. Structural studies reveal a typical triosephosphate isomerase barrel-fold with substrate c-di-GMP/cGAMP bound in an extended conformation. Highly conserved residues specifically bind the guanine base of c-di-GMP/cGAMP in the G2 site while the semi-conserved nature of residues at the G1 site could act as a specificity determinant. Two metal ions, co-ordinated with six stubbornly conserved residues and two non-bridging scissile phosphate oxygens of c-di-GMP/cGAMP, activate a water molecule for an in-line attack on the phosphodiester bond, supporting two-metal ion-based catalytic mechanism. PDE activity and biofilm assays of several prudently designed mutants collectively demonstrate that VcEAL active site is charge and size optimized. Intriguingly, in VcEAL-5′-pGpG-Ca2+ structure, β5–α5 loop adopts a novel conformation that along with conserved E131 creates a new metal-binding site. This novel conformation along with several subtle changes in the active site designate VcEAL-5′-pGpG-Ca2+ structure quite different from other 5′-pGpG bound structures reported earlier.


2019 ◽  
Vol 20 (4) ◽  
pp. 304-315 ◽  
Author(s):  
Mónica Rodríguez-Bolaños ◽  
Ruy Perez-Montfort

Triosephosphate isomerase is the fifth enzyme in glycolysis and its canonical function is the reversible isomerization of glyceraldehyde-3-phosphate and dihydroxyacetone phosphate. Within the last decade multiple other functions, that may not necessarily always involve catalysis, have been described. These include variations in the degree of its expression in many types of cancer and participation in the regulation of the cell cycle. Triosephosphate isomerase may function as an auto-antigen and in the evasion of the immune response, as a factor of virulence of some organisms, and also as an important allergen, mainly in a variety of seafoods. It is an important factor to consider in the cryopreservation of semen and seems to play a major role in some aspects of the development of Alzheimer's disease. It also seems to be responsible for neurodegenerative alterations in a few cases of human triosephosphate isomerase deficiency. Thus, triosephosphate isomerase is an excellent example of a moonlighting protein.


Author(s):  
A. B. Edwards

During a petrological examination of samples of bauxite from Boolarra, in south Gippsland, Victoria, it was noted that some specimens of the bauxite, which is largely derived from Tertiary olivine-basalt, contained numerous grains of yellow-brown to amber-yellow leucoxene. The leucoxene is clearly pseudo-morphous after ilmenite, residual particles of ilmenite being enclosed in many of the leucoxene grains. Most of the leucoxene grains are opaque, but occasional grains are translucent to transparent, though isotropic. Some of them show parallel markings suggestive of cleavage, but probably a residual structure from the replaced ilmenite. In view of the highly aluminous nature of the enclosing rock, there seemed some possibility that this mineral might be the little-known aluminium titanate, xanthitane. It was thought, therefore, that if a pure sample of the mineral could be prepared, a chemical analysis would establish its identity.


2021 ◽  
Vol 125 (3) ◽  
pp. 780-788
Author(s):  
Jennifer Fischer ◽  
Aurel Radulescu ◽  
Peter Falus ◽  
Dieter Richter ◽  
Ralf Biehl

2021 ◽  
Vol 11 (12) ◽  
pp. 5656
Author(s):  
Yufan Zeng ◽  
Jiashan Tang

Graph neural networks (GNNs) have been very successful at solving fraud detection tasks. The GNN-based detection algorithms learn node embeddings by aggregating neighboring information. Recently, CAmouflage-REsistant GNN (CARE-GNN) is proposed, and this algorithm achieves state-of-the-art results on fraud detection tasks by dealing with relation camouflages and feature camouflages. However, stacking multiple layers in a traditional way defined by hop leads to a rapid performance drop. As the single-layer CARE-GNN cannot extract more information to fix the potential mistakes, the performance heavily relies on the only one layer. In order to avoid the case of single-layer learning, in this paper, we consider a multi-layer architecture which can form a complementary relationship with residual structure. We propose an improved algorithm named Residual Layered CARE-GNN (RLC-GNN). The new algorithm learns layer by layer progressively and corrects mistakes continuously. We choose three metrics—recall, AUC, and F1-score—to evaluate proposed algorithm. Numerical experiments are conducted. We obtain up to 5.66%, 7.72%, and 9.09% improvements in recall, AUC, and F1-score, respectively, on Yelp dataset. Moreover, we also obtain up to 3.66%, 4.27%, and 3.25% improvements in the same three metrics on the Amazon dataset.


Proteomes ◽  
2021 ◽  
Vol 9 (1) ◽  
pp. 10
Author(s):  
Bernadette B. Bagon ◽  
Valerie Diane V. Valeriano ◽  
Ju Kyoung Oh ◽  
Edward Alain B. Pajarillo ◽  
Ji Yoon Lee ◽  
...  

Probiotics must not only exert a health-promoting effect but also be capable of adapting to the harsh environment of the gastrointestinal (GI) tract. Probiotics in the GI tract must survive the cell wall-disrupting effect of bile acids. We investigated the exoproteome of Lactobacillus johnsonii PF01 and C1-10 under bile stress. A comparative analysis revealed the similarities between the two L. johnsonii exoproteomes, as well as their different responses to bile. The large number of metabolic proteins in L. johnsonii revealed its metabolic adaptation to meet protein synthesis requirements under bile stress. In addition, cell wall modifications occurred in response to bile. Furthermore, some extracellular proteins of L. johnsonii may have moonlighting function in the presence of bile. Enolase, L-lactate dehydrogenase, glyceraldehyde-3-phosphate dehydrogenase, triosephosphate isomerase, 50s ribosomal protein L7/L12, and cellobiose-specific phosphotransferase system (PTS) sugar transporter were significantly upregulated under bile stress, suggesting a leading role in the collective bile stress response of L. johnsonii from its exoproteome perspective.


2021 ◽  
Vol 11 (12) ◽  
pp. 5570
Author(s):  
Binbin Wang ◽  
Jingze Liu ◽  
Zhifu Cao ◽  
Dahai Zhang ◽  
Dong Jiang

Based on the fixed interface component mode synthesis, a multiple and multi-level substructure method for the modeling of complex structures is proposed in this paper. Firstly, the residual structure is selected according to the structural characteristics of the assembled complex structure. Secondly, according to the assembly relationship, the parts assembled with the residual structure are divided into a group of substructures, which are named the first-level substructure, the parts assembled with the first-level substructure are divided into a second-level substructure, and consequently the multi-level substructure model is established. Next, the substructures are dynamically condensed and assembled on the boundary of the residual structure. Finally, the substructure system matrix, which is replicated from the matrix of repeated physical geometry, is obtained by preserving the main modes and the constrained modes and the system matrix of the last level of the substructure is assembled to the upper level of the substructure, one level up, until it is assembled in the residual structure. In this paper, an assembly structure with three panels and a gear box is adopted to verify the method by simulation and a rotor is used to experimentally verify the method. The results show that the proposed multiple and multi-level substructure modeling method is not unique to the selection of residual structures, and different classification methods do not affect the calculation accuracy. The selection of 50% external nodes can further improve the analysis efficiency while ensuring the calculation accuracy.


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