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Journal articles on the topic 'Triosephosphate Isomerase Barrel'

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Published: 6 September 2023

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1

Carcamo-Noriega, Edson N., and Gloria Saab-Rincon. "Identification of fibrillogenic regions in human triosephosphate isomerase." PeerJ 4 (February 4, 2016): e1676. http://dx.doi.org/10.7717/peerj.1676.

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Background.Amyloid secondary structure relies on the intermolecular assembly of polypeptide chains through main-chain interaction. According to this, all proteins have the potential to form amyloid structure, nevertheless, in nature only few proteins aggregate into toxic or functional amyloids. Structural characteristics differ greatly among amyloid proteins reported, so it has been difficult to link the fibrillogenic propensity with structural topology. However, there are ubiquitous topologies not represented in the amyloidome that could be considered as amyloid-resistant attributable to stru
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2

Ravindra, Gudihal, and Padmanabhan Balaram. "Plasmodium falciparum triosephosphate isomerase: New insights into an old enzyme." Pure and Applied Chemistry 77, no. 1 (2005): 281–89. http://dx.doi.org/10.1351/pac200577010281.

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Triosephosphate isomerase (TIM), a central enzyme in the glycolytic pathway, has been the subject of extensive structural and mechanistic investigations over the past 30 years. The TIM barrel is the prototype of the (β/α)8 barrel fold, which is one of the most extensively used structural motifs in enzymes. Mechanistic studies on TIM from a variety of sources have emphasized the importance of loop 6 dynamics for enzyme activity. Several conserved residues in TIM have been investigated by extensive site-directed mutagenesis of the enzyme from yeast, chicken, and trypanosoma. The cloning and sequ
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3

Yang, Trent C., Steve Legault, Emery A. Kayiranga, Jyothi Kumaran, Kazuhiko Ishikawa та Wing L. Sung. "The N-Terminal β-Sheet of the Hyperthermophilic Endoglucanase from Pyrococcus horikoshii Is Critical for Thermostability". Applied and Environmental Microbiology 78, № 9 (2012): 3059–67. http://dx.doi.org/10.1128/aem.07576-11.

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ABSTRACTThe β-1,4-endoglucanase (EC 3.2.1.4) from the hyperthermophilic archaeonPyrococcus horikoshii(EGPh) has strong hydrolyzing activity toward crystalline cellulose. When EGPh is used in combination with β-glucosidase (EC 3.2.1.21), cellulose is completely hydrolyzed to glucose at high temperature, suggesting great potential for EGPh in bioethanol industrial applications. The crystal structure of EGPh shows a triosephosphate isomerase (TIM) (β/α)8-barrel fold with an N-terminal antiparallel β-sheet at the opposite side of the active site and a very short C-terminal sequence outside of the
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4

Garrido, Francisco, María Gasset, Juliana Sanz-Aparicio, Carlos Alfonso, and María A. Pajares. "Rat liver betaine–homocysteine S-methyltransferase equilibrium unfolding: insights into intermediate structure through tryptophan substitutions." Biochemical Journal 391, no. 3 (2005): 589–99. http://dx.doi.org/10.1042/bj20050505.

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Equilibrium folding of rat liver BHMT (betaine–homocysteine methyltransferase), a TIM (triosephosphate isomerase)-barrel tetrameric protein, has been studied using urea as denaturant. A combination of activity measurements, tryptophan fluorescence, CD and sedimentation-velocity studies suggested a multiphasic process including two intermediates, a tetramer (I4) and a monomer (J). Analysis of denaturation curves for single- and six-tryptophan mutants indicated that the main changes leading to the tetrameric intermediate are related to alterations in the helix α4 of the barrel, as well as in the
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5

Halloran, Kevin T., Yanming Wang, Karunesh Arora, et al. "Frustration and folding of a TIM barrel protein." Proceedings of the National Academy of Sciences 116, no. 33 (2019): 16378–83. http://dx.doi.org/10.1073/pnas.1900880116.

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Triosephosphate isomerase (TIM) barrel proteins have not only a conserved architecture that supports a myriad of enzymatic functions, but also a conserved folding mechanism that involves on- and off-pathway intermediates. Although experiments have proven to be invaluable in defining the folding free-energy surface, they provide only a limited understanding of the structures of the partially folded states that appear during folding. Coarse-grained simulations employing native centric models are capable of sampling the entire energy landscape of TIM barrels and offer the possibility of a molecul
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6

Kumar, Jay Prakash, Harshvardhan Rao, Vinod Nayak, and S. Ramaswamy. "Crystal structures and kinetics ofN-acetylneuraminate lyase fromFusobacterium nucleatum." Acta Crystallographica Section F Structural Biology Communications 74, no. 11 (2018): 725–32. http://dx.doi.org/10.1107/s2053230x18012992.

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N-Acetyl-D-neuraminic acid lyase (NanA) catalyzes the breakdown of sialic acid (Neu5Ac) toN-acetyl-D-mannosamine (ManNAc) and pyruvate. NanA plays a key role in Neu5Ac catabolism in many pathogenic and bacterial commensals where sialic acid is available as a carbon and nitrogen source. Several pathogens or commensals decorate their surfaces with sialic acids as a strategy to escape host innate immunity. Catabolism of sialic acid is key to a range of host–pathogen interactions. In this study, atomic resolution structures of NanA fromFusobacterium nucleatum(FnNanA) in ligand-free and ligand-boun
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7

Shi, Rong, Marco Pineda, Eunice Ajamian, Qizhi Cui, Allan Matte, and Miroslaw Cygler. "Structure of l-Xylulose-5-Phosphate 3-Epimerase (UlaE) from the Anaerobic l-Ascorbate Utilization Pathway of Escherichia coli: Identification of a Novel Phosphate Binding Motif within a TIM Barrel Fold." Journal of Bacteriology 190, no. 24 (2008): 8137–44. http://dx.doi.org/10.1128/jb.01049-08.

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ABSTRACT Three catabolic enzymes, UlaD, UlaE, and UlaF, are involved in a pathway leading to fermentation of l-ascorbate under anaerobic conditions. UlaD catalyzes a β-keto acid decarboxylation reaction to produce l-xylulose-5-phosphate, which undergoes successive epimerization reactions with UlaE (l-xylulose-5-phosphate 3-epimerase) and UlaF (l-ribulose-5-phosphate 4-epimerase), yielding d-xylulose-5-phosphate, an intermediate in the pentose phosphate pathway. We describe here crystallographic studies of UlaE from Escherichia coli O157:H7 that complete the structural characterization of this
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8

Mahanta, Pranjal, Amit Bhardwaj, Krishan Kumar, Vanga S. Reddy та Suryanarayanarao Ramakumar. "Structural insights into N-terminal to C-terminal interactions and implications for thermostability of a (β/α)8-triosephosphate isomerase barrel enzyme". FEBS Journal 282, № 18 (2015): 3543–55. http://dx.doi.org/10.1111/febs.13355.

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9

Yadav, Malti, Kamalendu Pal, and Udayaditya Sen. "Structures of c-di-GMP/cGAMP degrading phosphodiesterase VcEAL: identification of a novel conformational switch and its implication." Biochemical Journal 476, no. 21 (2019): 3333–53. http://dx.doi.org/10.1042/bcj20190399.

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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 Ca
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10

Dinis, Pedro, Daniel L. M. Suess, Stephen J. Fox, et al. "X-ray crystallographic and EPR spectroscopic analysis of HydG, a maturase in [FeFe]-hydrogenase H-cluster assembly." Proceedings of the National Academy of Sciences 112, no. 5 (2015): 1362–67. http://dx.doi.org/10.1073/pnas.1417252112.

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Hydrogenases use complex metal cofactors to catalyze the reversible formation of hydrogen. In [FeFe]-hydrogenases, the H-cluster cofactor includes a diiron subcluster containing azadithiolate, three CO, and two CN− ligands. During the assembly of the H cluster, the radical S-adenosyl methionine (SAM) enzyme HydG lyses the substrate tyrosine to yield the diatomic ligands. These diatomic products form an enzyme-bound Fe(CO)x(CN)y synthon that serves as a precursor for eventual H-cluster assembly. To further elucidate the mechanism of this complex reaction, we report the crystal structure and EPR
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11

Shukla, Anshuman, та Purnananda Guptasarma. "Folding of β/α-unit scrambled forms of S. cerevisiae triosephosphate isomerase: Evidence for autonomy of substructure formation and plasticity of hydrophobic and hydrogen bonding interactions in core of (β/α)8-barrel". Proteins: Structure, Function, and Bioinformatics 55, № 3 (2004): 548–57. http://dx.doi.org/10.1002/prot.20066.

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12

Saab-Rincón, Gloria, Leticia Olvera, Maricela Olvera та ін. "Evolutionary Walk between (β/α)8 Barrels: Catalytic Migration from Triosephosphate Isomerase to Thiamin Phosphate Synthase". Journal of Molecular Biology 416, № 2 (2012): 255–70. http://dx.doi.org/10.1016/j.jmb.2011.12.042.

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13

NÁJERA, Hugo, Miguel COSTAS, and D. Alejandro FERNÁNDEZ-VELASCO. "Thermodynamic characterization of yeast triosephosphate isomerase refolding: insights into the interplay between function and stability as reasons for the oligomeric nature of the enzyme." Biochemical Journal 370, no. 3 (2003): 785–92. http://dx.doi.org/10.1042/bj20021439.

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The reasons underlying the oligomeric nature of some proteins such as triosephosphate isomerase (TIM) are unclear. It has been proposed that this enzyme is an oligomer, mainly because of its stability rather than for functional reasons. To address this issue, the reversible denaturation and renaturation of the homodimeric TIM from baker's yeast (Saccharomyces cerevisiae) induced by guanidinium chloride and urea have been characterized by spectroscopic, functional and hydrodynamic techniques. The unfolding and refolding of this enzyme are not coincident after ‘conventional’ equilibrium times. U
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14

Matsui, Motomu, and Wataru Iwasaki. "Graph Splitting: A Graph-Based Approach for Superfamily-Scale Phylogenetic Tree Reconstruction." Systematic Biology, August 17, 2019. http://dx.doi.org/10.1093/sysbio/syz049.

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Abstract A protein superfamily contains distantly related proteins that have acquired diverse biological functions through a long evolutionary history. Phylogenetic analysis of the early evolution of protein superfamilies is a key challenge because existing phylogenetic methods show poor performance when protein sequences are too diverged to construct an informative multiple sequence alignment (MSA). Here, we propose the Graph Splitting (GS) method, which rapidly reconstructs a protein superfamily-scale phylogenetic tree using a graph-based approach. Evolutionary simulation showed that the GS
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15

Borisenko, Ilya, Maria Daugavet, Alexander Ereskovsky, Andrey Lavrov, and Olga Podgornaya. "Novel protein from larval sponge cells, ilborin, is related to energy turnover and calcium binding and is conserved among marine invertebrates." Open Biology 12, no. 2 (2022). http://dx.doi.org/10.1098/rsob.210336.

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Sponges (phylum Porifera) are early-branching animals, whose outwardly simple body plan is underlain by a complex genetic repertoire. The transition from a mobile larva to an attached filter-feeding organism occurs by metamorphosis, a process accompanied by a radical change of the body plan and cell transdifferentiation. The continuity between larval cells and adult tissues is still obscure. In a previous study, we have produced polyclonal antibodies against the major protein of the flagellated cells covering the larva of the sponge Halisarca dujardini , used them to trace the fate of these ce
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