scholarly journals Detection and Time Course of Formation of Major Thiamin Diphosphate-Bound Covalent Intermediates Derived from a Chromophoric Substrate Analogue on Benzoylformate Decarboxylase†

Biochemistry ◽  
2009 ◽  
Vol 48 (5) ◽  
pp. 981-994 ◽  
Author(s):  
Sumit Chakraborty ◽  
Natalia S. Nemeria ◽  
Anand Balakrishnan ◽  
Gabriel S. Brandt ◽  
Malea M. Kneen ◽  
...  
Keyword(s):  
Time Course ◽  
Thiamin Diphosphate ◽  
Benzoylformate Decarboxylase ◽  
Substrate Analogue

The Crystal Structure of Benzoylformate Decarboxylase at 1.6 Å Resolution:  Diversity of Catalytic Residues in Thiamin Diphosphate-Dependent Enzymes†,‡

Biochemistry ◽  
1998 ◽  
Vol 37 (28) ◽  
pp. 9918-9930 ◽  
Author(s):  
Miriam S. Hasson ◽  
Angelika Muscate ◽  
Michael J. McLeish ◽  
Lena S. Polovnikova ◽  
John A. Gerlt ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Thiamin Diphosphate ◽  
Catalytic Residues ◽  
Benzoylformate Decarboxylase

scholarly journals Computational characterization of enzyme-bound thiamin diphosphate reveals a surprisingly stable tricyclic state: implications for catalysis

2019 ◽  
Vol 15 ◽  
pp. 145-159 ◽  
Author(s):  
Ferran Planas ◽  
Michael J McLeish ◽  
Fahmi Himo
Keyword(s):  
Density Functional ◽  
Density Functional Theory Calculations ◽  
Thiamin Diphosphate ◽  
Diverse Range ◽  
Factors Affecting ◽  
Benzoylformate Decarboxylase ◽  
Carbon Carbon Bond ◽  
Activated State ◽  
Catalyzed Reactions ◽  
The Individual

Thiamin diphosphate (ThDP)-dependent enzymes constitute a large class of enzymes that catalyze a diverse range of reactions. Many are involved in stereospecific carbon–carbon bond formation and, consequently, have found increasing interest and utility as chiral catalysts in various biocatalytic applications. All ThDP-catalyzed reactions require the reaction of the ThDP ylide (the activated state of the cofactor) with the substrate. Given that the cofactor can adopt up to seven states on an enzyme, identifying the factors affecting the stability of the pre-reactant states is important for the overall understanding of the kinetics and mechanism of the individual reactions. In this paper we use density functional theory calculations to systematically study the different cofactor states in terms of energies and geometries. Benzoylformate decarboxylase (BFDC), which is a well characterized chiral catalyst, serves as the prototypical ThDP-dependent enzyme. A model of the active site was constructed on the basis of available crystal structures, and the cofactor states were characterized in the presence of three different ligands (crystallographic water, benzoylformate as substrate, and (R)-mandelate as inhibitor). Overall, the calculations reveal that the relative stabilities of the cofactor states are greatly affected by the presence and identity of the bound ligands. A surprising finding is that benzoylformate binding, while favoring ylide formation, provided even greater stabilization to a catalytically inactive tricyclic state. Conversely, the inhibitor binding greatly destabilized the ylide formation. Together, these observations have significant implications for the reaction kinetics of the ThDP-dependent enzymes, and, potentially, for the use of unnatural substrates in such reactions.

Mechanism-Based Inactivation of Benzoylformate Decarboxylase, A Thiamin Diphosphate-Dependent Enzyme

2007 ◽  
Vol 129 (14) ◽  
pp. 4120-4121 ◽  
Author(s):  
Asim K. Bera ◽  
Lena S. Polovnikova ◽  
Juliatek Roestamadji ◽  
Theodore S. Widlanski ◽  
George L. Kenyon ◽  
...  
Keyword(s):  
Thiamin Diphosphate ◽  
Benzoylformate Decarboxylase

Structural and Kinetic Analysis of Catalysis by a Thiamin Diphosphate-Dependent Enzyme, Benzoylformate Decarboxylase†

Biochemistry ◽  
2003 ◽  
Vol 42 (7) ◽  
pp. 1820-1830 ◽  
Author(s):  
Elena S. Polovnikova ◽  
Michael J. McLeish ◽  
Eduard A. Sergienko ◽  
John T. Burgner ◽  
Natalie L. Anderson ◽  
...  
Keyword(s):  
Kinetic Analysis ◽  
Thiamin Diphosphate ◽  
Benzoylformate Decarboxylase

Spectroscopic Detection of Transient Thiamin Diphosphate-Bound Intermediates on Benzoylformate Decarboxylase†

Biochemistry ◽  
2000 ◽  
Vol 39 (45) ◽  
pp. 13862-13869 ◽  
Author(s):  
Eduard A. Sergienko ◽  
Jue Wang ◽  
Lena Polovnikova ◽  
Miriam S. Hasson ◽  
Michael J. McLeish ◽  
...  
Keyword(s):  
Thiamin Diphosphate ◽  
Benzoylformate Decarboxylase

Ultrastructural Changes of the Symbiotic Chlorella-Like Alga Isolated from Hydra Viridis

1982 ◽  
Vol 40 ◽  
pp. 320-321
Author(s):  
K.W. Lee ◽  
R.H. Meints ◽  
D. Kuczmarski ◽  
J.L. Van Etten
Keyword(s):  
Time Course ◽  
Reciprocal Cross ◽  
Ultrastructural Level ◽  
Ultrastructural Changes ◽  
Symbiotic Relationship ◽  
Cell Recognition ◽  
Green Hydra ◽  
Different Strains ◽  
Hydra Viridis

The physiological, biochemical, and ultrastructural aspects of the symbiotic relationship between the Chlorella-like algae and the hydra have been intensively investigated. Reciprocal cross-transfer of the Chlorellalike algae between different strains of green hydra provide a system for the study of cell recognition. However, our attempts to culture the algae free of the host hydra of the Florida strain, Hydra viridis, have been consistently unsuccessful. We were, therefore, prompted to examine the isolated algae at the ultrastructural level on a time course.

Destruction of Actin Filaments by Osmium Tetroxide

1977 ◽  
Vol 35 ◽  
pp. 466-467
Author(s):  
P. Maupin-Szamier ◽  
T. D. Pollard
Keyword(s):  
Actin Filaments ◽  
Time Course ◽  
Osmium Tetroxide ◽  
Rabbit Muscle ◽  
Muscle Actin ◽  
Sodium Phosphate Buffer ◽  
Transmission Electron ◽  
The Difference ◽  
Rates Of Decay ◽  
Short Time

We have studied the destruction of rabbit muscle actin filaments by osmium tetroxide (OSO4) to develop methods which will preserve the structure of actin filaments during preparation for transmission electron microscopy.Negatively stained F-actin, which appears as smooth, gently curved filaments in control samples (Fig. 1a), acquire an angular, distorted profile and break into progressively shorter pieces after exposure to OSO4 (Fig. 1b,c). We followed the time course of the reaction with viscometry since it is a simple, quantitative method to assess filament integrity. The difference in rates of decay in viscosity of polymerized actin solutions after the addition of four concentrations of OSO4 is illustrated in Fig. 2. Viscometry indicated that the rate of actin filament destruction is also dependent upon temperature, buffer type, buffer concentration, and pH, and requires the continued presence of OSO4. The conditions most favorable to filament preservation are fixation in a low concentration of OSO4 for a short time at 0°C in 100mM sodium phosphate buffer, pH 6.0.

The time course of calcium deposition in shells of the barnacle (Balanus amphititre amphititre) during cyprid-juvenile metamorphosis

1994 ◽  
Vol 52 ◽  
pp. 178-179
Author(s):  
Nancy R. Wallace ◽  
Craig C. Freudenrich ◽  
Karl Wilbur ◽  
Peter Ingram ◽  
Ann LeFurgey
Keyword(s):  
Electron Microscopy ◽  
Scanning Electron Microscopy ◽  
Time Course ◽  
Vertical Plane ◽  
Mantle Cavity ◽  
Qualitative Assessment ◽  
Calcium Deposition ◽  
Free Swimming ◽  
Freeze Dried ◽  
Scanning Electron

The morphology of balanomorph barnacles during metamorphosis from the cyprid larval stage to the juvenile has been examined by light microscopy and scanning electron microscopy (SEM). The free-swimming cyprid attaches to a substrate, rotates 90° in the vertical plane, molts, and assumes the adult shape. The resulting metamorph is clad in soft cuticle and has an adult-like appearance with a mantle cavity, thorax with cirri, and incipient shell plates. At some time during the development from cyprid to juvenile, the barnacle begins to mineralize its shell, but it is not known whether calcification occurs before, during, or after ecdysis. To examine this issue, electron probe x-ray microanalysis (EPXMA) was used to detect calcium in cyprids and juveniles at various times during metamorphosis.Laboratory-raised, free-swimming cyprid larvae were allowed to settle on plastic coverslips in culture dishes of seawater. The cyprids were observed with a dissecting microscope, cryopreserved in liquid nitrogen-cooled liquid propane at various times (0-24 h) during metamorphosis, freeze dried, rotary carbon-coated, and examined with scanning electron microscopy (SEM). EPXMA dot maps were obtained in parallel for qualitative assessment of calcium and other elements in the carapace, wall, and opercular plates.

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