Triosephosphate isomerase
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<i>Giardia duodenalis</i>genetic assemblages and hosts Open
Techniques for sub-classifying morphologically identical Giardia duodenalis trophozoites have included comparisons of the electrophoretic mobility of enzymes and of chromosomes, and sequencing of genes encoding β-giardin, triose phosphate …
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Protein Flexibility and Stiffness Enable Efficient Enzymatic Catalysis Open
The enormous rate accelerations observed for many enzyme catalysts are due to strong stabilizing interactions between the protein and reaction transition state. The defining property of these catalysts is their specificity for binding the …
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Loop Motion in Triosephosphate Isomerase Is Not a Simple Open and Shut Case Open
Conformational changes are crucial for the catalytic action of many enzymes. A prototypical and well-studied example is loop opening and closure in triosephosphate isomerase (TIM), which is thought to determine the rate of catalytic turnov…
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A Mutation in CsYL2.1 Encoding a Plastid Isoform of Triose Phosphate Isomerase Leads to Yellow Leaf 2.1 (yl2.1) in Cucumber (Cucumis Sativus L.) Open
The leaf is an important photosynthetic organ and plays an essential role in the growth and development of plants. Leaf color mutants are ideal materials for studying chlorophyll metabolism, chloroplast development, and photosynthesis. In …
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A Cytosolic Bypass and G6P Shunt in Plants Lacking Peroxisomal Hydroxypyruvate Reductase Open
The oxygenation of ribulose 1,5-bisphosphate by Rubisco is the first step in photorespiration and reduces the efficiency of photosynthesis in C3 plants. Our recent data indicate that mutants in photorespiration have increased rates of phot…
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Overexpression of Sedoheptulose-1,7-Bisphosphatase Enhances Photosynthesis in Chlamydomonas reinhardtii and Has No Effect on the Abundance of Other Calvin-Benson Cycle Enzymes Open
The productivity of plants and microalgae needs to be increased to feed the growing world population and to promote the development of a low-carbon economy. This goal can be achieved by improving photosynthesis via genetic engineering. In …
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The Glycolytic Enzyme Triosephosphate Isomerase of Trichomonas vaginalis Is a Surface-Associated Protein Induced by Glucose That Functions as a Laminin- and Fibronectin-Binding Protein Open
Triosephosphate isomerase of Trichomonas vaginalis ( Tv TIM) is a 27-kDa cytoplasmic protein encoded by two genes, tvtim1 and tvtim2 , that participates in glucose metabolism. Tv TIM is also localized to the parasite surface. Thus, the goa…
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Enzyme Architecture: Modeling the Operation of a Hydrophobic Clamp in Catalysis by Triosephosphate Isomerase Open
Triosephosphate isomerase (TIM) is a proficient catalyst of the reversible isomerization of dihydroxyacetone phosphate (DHAP) to d-glyceraldehyde phosphate (GAP), via general base catalysis by E165. Historically, this enzyme has been an ex…
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ClustENM: ENM-Based Sampling of Essential Conformational Space at Full Atomic Resolution Open
Accurate sampling of conformational space and, in particular, the transitions between functional substates has been a challenge in molecular dynamic (MD) simulations of large biomolecular systems. We developed an Elastic Network Model (ENM…
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The Activating Oxydianion Binding Domain for Enzyme-Catalyzed Proton Transfer, Hydride Transfer, and Decarboxylation: Specificity and Enzyme Architecture Open
The kinetic parameters for activation of yeast triosephosphate isomerase (ScTIM), yeast orotidine monophosphate decarboxylase (ScOMPDC), and human liver glycerol 3-phosphate dehydrogenase (hlGPDH) for catalysis of reactions of their respec…
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Comparative Transcriptome Analysis of Litopenaeus vannamei Reveals That Triosephosphate Isomerase-Like Genes Play an Important Role During Decapod Iridescent Virus 1 Infection Open
Decapod iridescent virus 1 (DIV1) results in severe economic losses in shrimp aquaculture. However, little is known about the physiological effect of DIV1 infection on the host. In this study, we found that the lethal dose 50 of DIV1-infec…
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Enabling Role of Ligand-Driven Conformational Changes in Enzyme Evolution Open
Many enzymes that show a large specificity in binding the enzymatic transition state with a higher affinity than the substrate utilize substrate binding energy to drive protein conformational changes to form caged substrate complexes. Thes…
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Molecular Docking of Selective Binding Affinity of Sulfonamide Derivatives as Potential Antimalarial Agents Targeting the Glycolytic Enzymes: GAPDH, Aldolase and TPI Open
The parasite Plasmodium falciparum is responsible for the major world scourge malaria, a disease that affects 3.3 billion people worldwide. The development of new drugs is critical because of the diminished effectiveness of current antimal…
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Aging, Alzheimer’s Disease and Dysfunctional Glycolysis; Similar Effects of Too Much and Too Little Open
Aging and much related dysfunction can be delayed by decreased glycolysis, however dysfunctional glycolysis appears to play a causative role in Alzheimer's disease (AD). It is proposed here that this apparent contradiction can be reconcile…
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Role of Loop-Clamping Side Chains in Catalysis by Triosephosphate Isomerase Open
The side chains of Y208 and S211 from loop 7 of triosephosphate isomerase (TIM) form hydrogen bonds to backbone amides and carbonyls from loop 6 to stabilize the caged enzyme-substrate complex. The effect of seven mutations [Y208T, Y208S, …
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Cytosolic Triosephosphate Isomerase from Arabidopsis thaliana Is Reversibly Modified by Glutathione on Cysteines 127 and 218 Open
In plant cells, an increase in cellular oxidants can have multiple effects, including the promotion of mixed disulfide bonds between glutathione and some proteins (S-glutathionylation). The present study focuses on the cytosolic isoform of…
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Newly discovered roles of triosephosphate isomerase including functions within the nucleus Open
Triosephosphate isomerase (TPI) is best known as a glycolytic enzyme that interconverts the 3-carbon sugars dihydroxyacetone phosphate (DHAP) and glyceraldehyde-3-phosphate (G3P). TPI is an essential enzyme that is required for the catabol…
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Enzyme activation through the utilization of intrinsic dianion binding energy Open
We consider 'the proposition that the intrinsic binding energy that results from the noncovalent interaction of a specific substrate with the active site of the enzyme is considerably larger than is generally believed. An important part of…
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Disulfiram as a novel inactivator of Giardia lamblia triosephosphate isomerase with antigiardial potential Open
Giardiasis, the infestation of the intestinal tract by Giardia lamblia, is one of the most prevalent parasitosis worldwide. Even though effective therapies exist for it, the problems associated with its use indicate that new therapeutic op…
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Role of Ligand-Driven Conformational Changes in Enzyme Catalysis: Modeling the Reactivity of the Catalytic Cage of Triosephosphate Isomerase Open
We have previously performed empirical valence bond calculations of the kinetic activation barriers, Δ G‡calc, for the deprotonation of complexes between TIM and the whole substrate glyceraldehyde-3-phosphate (GAP, Kulkarni et al. J. Am. C…
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Molecular Basis of Sulfosugar Selectivity in Sulfoglycolysis Open
The sulfosugar sulfoquinovose (SQ) is produced by essentially all photosynthetic organisms on Earth and is metabolized by bacteria through the process of sulfoglycolysis. The sulfoglycolytic Embden-Meyerhof-Parnas pathway metabolizes SQ to…
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A Cytosolic Triosephosphate Isomerase Is a Key Component in XA3/XA26-Mediated Resistance Open
Bacterial blight caused by Xanthomonas oryzae pv oryzae (Xoo) causes severe damage to rice (Oryza sativa) production worldwide. The major disease resistance gene, Xa3/Xa26, confers broad-spectrum and durable resistance to Xoo at both seedl…
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Sampling of Protein Conformational Space Using Hybrid Simulations: A Critical Assessment of Recent Methods Open
Recent years have seen several hybrid simulation methods for exploring the conformational space of proteins and their complexes or assemblies. These methods often combine fast analytical approaches with computationally expensive full atomi…
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Suppression of chloroplast triose phosphate isomerase evokes inorganic phosphate-limited photosynthesis in rice Open
The availability of inorganic phosphate (Pi) for ATP synthesis is thought to limit photosynthesis at elevated [CO2] when Pi regeneration via sucrose or starch synthesis is limited. We report here another mechanism for the occurrence of Pi-…
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Structural Effects of Protein Aging: Terminal Marking by Deamidation in Human Triosephosphate Isomerase Open
Deamidation, the loss of the ammonium group of asparagine and glutamine to form aspartic and glutamic acid, is one of the most commonly occurring post-translational modifications in proteins. Since deamidation rates are encoded in the prot…
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Enzyme Architecture: Amino Acid Side-Chains That Function To Optimize the Basicity of the Active Site Glutamate of Triosephosphate Isomerase Open
We report pH rate profiles for kcat and Km for the isomerization reaction of glyceraldehyde 3-phosphate catalyzed by wildtype triosephosphate isomerase (TIM) from three organisms and by ten mutants of TIM; and, for Ki for inhibition of thi…
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Structural and Genetic Studies Demonstrate Neurologic Dysfunction in Triosephosphate Isomerase Deficiency Is Associated with Impaired Synaptic Vesicle Dynamics Open
Triosephosphate isomerase (TPI) deficiency is a poorly understood disease characterized by hemolytic anemia, cardiomyopathy, neurologic dysfunction, and early death. TPI deficiency is one of a group of diseases known as glycolytic enzymopa…
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Structure–Function Studies of Hydrophobic Residues That Clamp a Basic Glutamate Side Chain during Catalysis by Triosephosphate Isomerase Open
Kinetic parameters are reported for the reactions of whole substrates (kcat/Km, M(-1) s(-1)) (R)-glyceraldehyde 3-phosphate (GAP) and dihydroxyacetone phosphate (DHAP) and for the substrate pieces [(kcat/Km)E·HPi/Kd, M(-2) s(-1)] glycolald…
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Complex Loop Dynamics Underpin Activity, Specificity, and Evolvability in the (βα) <sub>8</sub> Barrel Enzymes of Histidine and Tryptophan Biosynthesis Open
Enzymes are conformationally dynamic, and their dynamical properties play an important role in regulating their specificity and evolvability. In this context, substantial attention has been paid to the role of ligand-gated conformational c…
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Regulation of SESAME-mediated H3T11 phosphorylation by glycolytic enzymes and metabolites Open
Cancer cells prefer aerobic glycolysis, but little is known about the underlying mechanism. Recent studies showed that the rate-limiting glycolytic enzymes, pyruvate kinase M2 (PKM2) directly phosphorylates H3 at threonine 11 (H3T11) to re…