scholarly journals X-ray Structure of the R69D Phosphatidylinositol-Specific Phospholipase C Enzyme:  Insight into the Role of Calcium and Surrounding Amino Acids in Active Site Geometry and Catalysis

Biochemistry ◽  
2005 ◽  
Vol 44 (30) ◽  
pp. 9980-9989 ◽  
Author(s):  
David Apiyo ◽  
Li Zhao ◽  
Ming-Daw Tsai ◽  
Thomas L. Selby
Keyword(s):  
Amino Acids ◽  
Phospholipase C ◽  
Active Site ◽  
X Ray ◽  
Insight Into

Crystal structure and lattice energetics of 10-methylacridinium halides

2000 ◽  
Vol 53 (8) ◽  
pp. 627 ◽  
Author(s):  
Piotr Storoniak ◽  
Karol Krzyminski ◽  
Pawel Dokurno ◽  
Antoni Konitz ◽  
Jerzy Blazejowski
Keyword(s):  
Crystal Lattice ◽  
Lattice Energy ◽  
Enthalpies Of Formation ◽  
Triclinic Space Group ◽  
X Ray ◽  
Molecular Arrangement ◽  
Van Der Waals Contacts ◽  
Chloride Monohydrate ◽  
Insight Into

The crystal structures of 10-methylacridinium chloride monohydrate, bromide monohydrate and iodide were determined by X-ray analysis. The compounds crystallize in the triclinic space group, P¯1, with 2 molecules in the unit cell. The molecular arrangement in the crystals revealed that hydrogen bonds (in hydrates) and van der Waals contacts play a significant part in intermolecular interactions. To discover their nature, contributions to the crystal lattice energy arising from electrostatic (the most important since the compounds form ionic crystals), dispersive and repulsive interactions were calculated. Enthalpies of formation of the salts, their stability and susceptibility to decomposition could be predicted from a combination of crystal lattice energies with values of other thermochemical characteristics obtained theoretically or taken from the literature. The role of water in the stabilization of the crystal lattice of the hydrates is also explained. The information gathered has given an insight into the features and behaviour of compounds which can be regarded as models of a large group of aromatic quaternary nitrogen salts.

Diamond growth on thin Ti wafers via chemical vapor deposition

1995 ◽  
Vol 10 (11) ◽  
pp. 2685-2688 ◽  
Author(s):  
Qijin Chen ◽  
Zhangda Lin
Keyword(s):  
Chemical Vapor Deposition ◽  
Vapor Deposition ◽  
Titanium Substrate ◽  
Chemical Vapor ◽  
Low Pressure ◽  
Diamond Growth ◽  
X Ray ◽  
Hot Filament ◽  
Insight Into

Diamond film was synthesized on thin Ti wafers (as thin as 40 μm) via hot filament chemical vapor deposition (HFCVD). The hydrogen embrittlement of the titanium substrate and the formation of a thick TiC interlayer were suppressed. A very low pressure (133 Pa) was employed to achieve high-density rapid nucleation and thus to suppress the formation of TiC. Oxygen was added to source gases to lower the growth temperature and therefore to slow down the hydrogenation of the thin Ti substrate. The role of the very low pressure during nucleation is discussed, providing insight into the nucleation mechanism of diamond on a titanium substrate. The as-grown diamond films were characterized by scanning electron microscopy (SEM), Raman spectroscopy, and x-ray analysis.

Peroxovanadates and Its Bio-Mimicking Relation with Vanadium Haloperoxidases

2016 ◽  
pp. 197-219
Author(s):  
Pranjal Saikia ◽  
Saitanya Kumar Bharadwaj ◽  
Abu Taleb Miah
Keyword(s):  
Amino Acids ◽  
Active Site ◽  
High Efficiency ◽  
Recombinant Enzymes ◽  
Vanadium Compounds ◽  
Reaction Conditions ◽  
The Cost ◽  
Major Emphasis ◽  
Protein Active Site

Vanadium Haloperoxidases (VHPOs) have been used in a variety of biotransformations showing remarkable stereoselectivity and regiospecificity. The high efficiency of the enzyme is influenced by the protein active site and the role of certain amino acids in activation of vanadium(V)-bound peroxide for halide oxidation. The use of natural or recombinant enzymes, or biomimetic vanadium compounds brings up issues regarding the cost of production and reaction conditions. In this chapter, the primary intent is to provide a simple and clear picture of functional mimicking nature of peroxovanadium compounds with haloperoxidases enzymes to the readers. Major emphasis would be given to examine the reactivity of the vanadium haloperoxidases with mechanism.

Conservation of structure in ATP-depleted proximal tubules: role of calcium, polyphosphoinositides, and glycine

1993 ◽  
Vol 265 (5) ◽  
pp. F605-F623 ◽  
Author(s):  
R. Garza-Quintero ◽  
J. M. Weinberg ◽  
J. Ortega-Lopez ◽  
J. A. Davis ◽  
M. A. Venkatachalam
Keyword(s):  
Amino Acids ◽  
Phospholipase C ◽  
Cell Structure ◽  
Proximal Tubules ◽  
Atp Depletion ◽  
The Other ◽  
Antimycin A ◽  
Phospholipid Hydrolysis ◽  
Hydrolysis Of

Increases of intracellular free Ca2+ (Caf) may mediate phospholipid hydrolysis and disintegration in energy-compromised cells; on the other hand, glycine and related amino acids preserve structure. We have examined the effects of increased Caf on phospholipids and structure in ATP-depleted cells, as well as how these actions may be modified by glycine. Incubation of isolated proximal tubules with antimycin A led to ATP depletion, delayed increases of Caf to micromolar levels, polyphosphoinositide (PPI) hydrolysis by phospholipase C, and generalized disintegration of cell structure. Glycine inhibited PPI hydrolysis and preserved cell structure in entirety but did not apparently modify the Caf increases. When overwhelming increases of Caf were induced by the additional presence of a Ca2+ ionophore, glycine did not inhibit either the hydrolysis of PPI or disruption of mitochondria and microvilli. However, the cells remained integrated and unbroken. Incubation in low-Ca2+ medium prevented Caf increases, inhibited PPI hydrolysis, and preserved the structure of mitochondria and microvilli. Nevertheless, there was lethal damage by disintegration of all other membranes. This damage was prevented specifically and completely by glycine. Thus compartments of cells were shown to be differentially susceptible to injury from increased Caf or lack of glycine. Although damage by either factor occurs by distinct mechanisms, glycine also appears to have effects that suppress the deleterious effects of Ca2+ so long as Caf increases are not overwhelming. Our results also suggest that the PPI have a major structural role, which may be compromised by Caf increase during ATP depletion.

scholarly journals The three-dimensional structure of a class-Pi glutathione S-transferase complexed with glutathione: the active-site hydration provides insights into the reaction mechanism

1998 ◽  
Vol 333 (3) ◽  
pp. 811-816 ◽  
Author(s):  
Antonio PÁRRAGA ◽  
Isabel GARCÍA-SÁEZ ◽  
Sinead B. WALSH ◽  
Timothy J. MANTLE ◽  
Miquel COLL
Keyword(s):  
Conformational Changes ◽  
Active Site ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Water Molecules ◽  
X Ray Diffraction ◽  
Glutathione S Transferase ◽  
X Ray ◽  
The Right

The structure of mouse liver glutathione S-transferase P1-1 complexed with its substrate glutathione (GSH) has been determined by X-ray diffraction analysis. No conformational changes in the glutathione moiety or in the protein, other than small adjustments of some side chains, are observed when compared with glutathione adduct complexes. Our structure confirms that the role of Tyr-7 is to stabilize the thiolate by hydrogen bonding and to position it in the right orientation. A comparison of the enzyme–GSH structure reported here with previously described structures reveals rearrangements in a well-defined network of water molecules in the active site. One of these water molecules (W0), identified in the unliganded enzyme (carboxymethylated at Cys-47), is displaced by the binding of GSH, and a further water molecule (W4) is displaced following the binding of the electrophilic substrate and the formation of the glutathione conjugate. The possibility that one of these water molecules participates in the proton abstraction from the glutathione thiol is discussed.

scholarly journals GlcNAcstatins are nanomolar inhibitors of human O-GlcNAcase inducing cellular hyper-O-GlcNAcylation

2009 ◽  
Vol 420 (2) ◽  
pp. 221-227 ◽  
Author(s):  
Helge C. Dorfmueller ◽  
Vladimir S. Borodkin ◽  
Marianne Schimpl ◽  
Daan M. F. van Aalten
Keyword(s):  
Active Site ◽  
Cell Biology ◽  
Rational Design ◽  
Catalytic Mechanism ◽  
Conserved Residues ◽  
Cellular Processes ◽  
Acetyl Group ◽  
Nanomolar Range ◽  
Insight Into

O-GlcNAcylation is an essential, dynamic and inducible post-translational glycosylation of cytosolic proteins in metazoa and can show interplay with protein phosphorylation. Inhibition of OGA (O-GlcNAcase), the enzyme that removes O-GlcNAc from O-GlcNAcylated proteins, is a useful strategy to probe the role of this modification in a range of cellular processes. In the present study, we report the rational design and evaluation of GlcNAcstatins, a family of potent, competitive and selective inhibitors of human OGA. Kinetic experiments with recombinant human OGA reveal that the GlcNAcstatins are the most potent human OGA inhibitors reported to date, inhibiting the enzyme in the sub-nanomolar to nanomolar range. Modification of the GlcNAcstatin N-acetyl group leads to up to 160-fold selectivity against the human lysosomal hexosaminidases which employ a similar substrate-assisted catalytic mechanism. Mutagenesis studies in a bacterial OGA, guided by the structure of a GlcNAcstatin complex, provides insight into the role of conserved residues in the human OGA active site. GlcNAcstatins are cell-permeant and, at low nanomolar concentrations, effectively modulate intracellular O-GlcNAc levels through inhibition of OGA, in a range of human cell lines. Thus these compounds are potent selective tools to study the cell biology of O-GlcNAc.

scholarly journals Role of Computational Methods in Going beyond X-ray Crystallography to Explore Protein Structure and Dynamics

2018 ◽  
Vol 19 (11) ◽  
pp. 3401 ◽  
Author(s):  
Ashutosh Srivastava ◽  
Tetsuro Nagai ◽  
Arpita Srivastava ◽  
Osamu Miyashita ◽  
Florence Tama
Keyword(s):  
Protein Dynamics ◽  
Computational Methods ◽  
Protein Structures ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
X Ray ◽  
X Ray Crystallography ◽  
Insight Into

Protein structural biology came a long way since the determination of the first three-dimensional structure of myoglobin about six decades ago. Across this period, X-ray crystallography was the most important experimental method for gaining atomic-resolution insight into protein structures. However, as the role of dynamics gained importance in the function of proteins, the limitations of X-ray crystallography in not being able to capture dynamics came to the forefront. Computational methods proved to be immensely successful in understanding protein dynamics in solution, and they continue to improve in terms of both the scale and the types of systems that can be studied. In this review, we briefly discuss the limitations of X-ray crystallography in studying protein dynamics, and then provide an overview of different computational methods that are instrumental in understanding the dynamics of proteins and biomacromolecular complexes.

scholarly journals The mechanism of action of dd-peptidases: the role of Threonine-299 and -301 in the Streptomyces R61 dd-peptidase

1994 ◽  
Vol 301 (2) ◽  
pp. 477-483 ◽  
Author(s):  
J M Wilkin ◽  
A Dubus ◽  
B Joris ◽  
J M Frère
Keyword(s):  
Amino Acids ◽  
Active Site ◽  
Site Directed Mutagenesis ◽  
Directed Mutagenesis ◽  
Peptide Substrate ◽  
Binding Properties ◽  
Beta Lactamases ◽  
Penicillin Binding Proteins ◽  
Active Site Cavity

The side chains of residues Thr299 and Thr301 in the Streptomyces R61 DD-peptidase have been modified by site-directed mutagenesis. These amino acids are part of a beta-strand which forms a wall of the active-site cavity. Thr299 corresponds to the second residue of the Lys-Thr(Ser)-Gly triad, highly conserved in active-site beta-lactamases and penicillin-binding proteins (PBPs). Modification of Thr301 resulted only in minor alterations of the catalytic and penicillin-binding properties of the enzyme. No selective decrease of the rate of acylation was observed for any particular class of compounds. By contrast, the loss of the hydroxy group of the residue in position 299 yielded a seriously impaired enzyme. The rates of inactivation by penicillins were decreased 30-50-fold, whereas the reactions with cephalosporins were even more affected. The efficiency of hydrolysis against the peptide substrate was also seriously decreased. More surprisingly, the mutant was completely unable to catalyse transpeptidation reactions. The conservation of an hydroxylated residue in this position in PBPs is thus easily explained by these results.

scholarly journals New insights into the mechanism of substrates trafficking in Glyoxylate/Hydroxypyruvate reductases

2016 ◽  
Vol 6 (1) ◽  
Author(s):  
Louise Lassalle ◽  
Sylvain Engilberge ◽  
Dominique Madern ◽  
Pierre Vauclare ◽  
Bruno Franzetti ◽  
...  
Keyword(s):  
Renal Failure ◽  
Active Site ◽  
Ternary Complex ◽  
Substrate Recognition ◽  
Binding Mode ◽  
X Ray ◽  
Hyperoxaluria Type

Abstract Glyoxylate accumulation within cells is highly toxic. In humans, it is associated with hyperoxaluria type 2 (PH2) leading to renal failure. The glyoxylate content within cells is regulated by the NADPH/NADH dependent glyoxylate/hydroxypyruvate reductases (GRHPR). These are highly conserved enzymes with a dual activity as they are able to reduce glyoxylate to glycolate and to convert hydroxypyruvate into D-glycerate. Despite the determination of high-resolution X-ray structures, the substrate recognition mode of this class of enzymes remains unclear. We determined the structure at 2.0 Å resolution of a thermostable GRHPR from Archaea as a ternary complex in the presence of D-glycerate and NADPH. This shows a binding mode conserved between human and archeal enzymes. We also determined the first structure of GRHPR in presence of glyoxylate at 1.40 Å resolution. This revealed the pivotal role of Leu53 and Trp138 in substrate trafficking. These residues act as gatekeepers at the entrance of a tunnel connecting the active site to protein surface. Taken together, these results allowed us to propose a general model for GRHPR mode of action.

Geometric and Electronic Structure Studies of the Binuclear Nonheme Ferrous Active Site of Toluene-4-monooxygenase: Parallels with Methane Monooxygenase and Insight into the Role of the Effector Proteins in O2Activation

2008 ◽  
Vol 130 (22) ◽  
pp. 7098-7109 ◽  
Author(s):  
Jennifer K. Schwartz ◽  
Pin-pin Wei ◽  
Kevin H. Mitchell ◽  
Brian G. Fox ◽  
Edward I. Solomon
Keyword(s):  
Electronic Structure ◽  
Active Site ◽  
Methane Monooxygenase ◽  
Effector Proteins ◽  
Insight Into
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