Conformational basis for substrate recognition and regulation of catalytic activity in Staphylococcus aureus nucleoside di-phosphate kinase

Nucleoside diphosphate kinases (NDK) are characterized by high catalytic turnover rates and diverse substrate specificity. These features make this enzyme an effective activator of a pro-drug an application that has been actively pursued for a variety of therapeutic strategies. The catalytic mechanism of this enzyme is governed by a conserved histidine that coordinates a magnesium ion at the active site. Despite substantial structural and biochemical information on NDK, the mechanistic feature of the phospho-transfer that leads to auto-phosphorylation remains unclear. While the role of the histidine residue is well documented, the other active site residues, in particular the conserved serine remains poorly characterized. Studies on some homologues suggest no role for the serine residue at the active site, while others suggest a crucial role for this serine in the regulation and quaternary association of this enzyme in some species. Here we report the biochemical features of the Staphylococcus aureus NDK and the mutant enzymes. We also describe the crystal structures of the apo-NDK, as a transition state mimic with vanadate and in complex with different nucleotide substrates. These structures formed the basis for molecular dynamics simulations to understand the broad substrate specificity of this enzyme and the role of active site residues in the phospho-transfer mechanism and oligomerization. Put together, these data suggest that concerted changes in the conformation of specific residues facilitate the stabilization of nucleotide complexes thereby enabling the steps involved in the ping-pong reaction mechanism without large changes to the overall structure of this enzyme. (C) 2011 Elsevier B.V. All rights reserved.

High Rate Capability Lithium Iron Phosphate Wired by Carbon Nanotubes and Galvanostatic Transformed to Graphitic Carbon

Lithium iron phosphate (LiFePO4) electronically wired by multi-walled carbon nanotubes (MWCNTs) and in-situ transformed graphitic carbon for lithium-ion batteries are discussed here. Presence of MWCNTs up to a maximum of 0.5% in porous LiFePO4 (abbreviated as LFP-CNT) resulted in remarkable reversible cyclability and rate capability compared to LFP coated with highly disordered carbon (abbreviated as LFP-C). In the current range (30-1500) mAg(-1), specific capacity of LFP-CNT (approximate to 150-50 mAhg(-1)) is observed to be always higher compared to LFP-C (approximate to 120-0 mAhg(-1)). At higher currents of 250-1500 mAg(-1) LFP-C performed poorly compared to LFP-CNT. LFP-C showed considerable decay in capacity with increase in cycle number at intermediate high currents (approximate to 250 mAg(-1)) whereas at very high currents (approximate to 750 mAg(-1)) it is nearly zero. The LFP-CNT showed no such detrimental behavior in battery performance. The exemplary performance of the LFP-CNT is attributed to combination of both enhanced LFP structural stability, as revealed by Raman spectra and formation of an efficient percolative network of carbon nanotubes which during the course of galvanostatic cycling gets gradually transformed to graphitic carbon. (C) 2012 The Electrochemical Society. [DOI: 10.1149/2.015204jes] All rights reserved.

Electrochemical, phosphate hydrolysis, DNA binding and DNA cleavage properties of new polyaza macrobicyclic dinickel(II) complexes

A new class of macrobicyclic dinickel(II) complexes Ni2L1,2 B](ClO4)(4) (1-6), where L-1,L-2 are polyaza macrobicyclic binucleating ligands, and B is a N,N-donor heterocyclic base (viz. 2,2'-bipyridine (bipy) and 1,10-phenanthroline (phen)) are synthesized and characterized. The redox, catalytic, DNA binding and DNA cleavage properties were studied. They exhibit two irreversible waves in the cathodic region around E-pc = -0.95 V and E-pa = -0.85 V vs. Ag/Ag+ in CH3CN-0.1 M TBAP, respectively. The first order rate constants for the hydrolysis of 4-nitrophenylphosphate to 4-nitrophenolate by the dinickel(II) complexes 1-6 are in the range from 3.36 x 10(-5) to 10.83 x 10(-5) Ms-1. The complexes 3 and 6 show good binding propensity to calf thymus DNA giving binding constant values (K-b) in the range from 3.08 x 10(5) to 5.37 x 10(5) M-1. The binding site sizes and viscosity data suggest the DNA intercalative and/or groove binding nature of the complexes. The complexes display significant hydrolytic cleavage of supercoiled pBR322DNA at pH 7.2 and 37 degrees C. The hydrolytic cleavage of DNA by the complexes is supported by the evidence from free radical quenching and T4 ligase ligation. The pseudo Michaelis-Menten kinetic parameters k(cat) = 5.44 x 10(-2) h(-1) and K-M = 6.23 x 10(-3) M for complex 3 were obtained. Complex 3 also shows an enormous enhancement of the cleavage rate, of 1.5 x 10(6), in comparison to the uncatalysed hydrolysis rate (k = 3.6 x 10(-8) h(-1)) of ds-DNA.

Modulation of glyceraldehyde-3-phosphate dehydrogenase activity by surface functionalized quantum dots

Enzymatic regulation is a fast and reliable diagnosis tool via identification and design of inhibitors for modulation of enzyme function. Previous reports on quantum dots (QDs)-enzyme interactions reveal a protein-surface recognition ability leading to promising applications in protein stabilization, protein delivery, bio-sensing and detection. However, the direct use of QDs to control enzyme inhibition has never been revealed to date. Here we show that a series of biocompatible surface-functionalized metal-chalcogenide QDs can be used as potent inhibitors for malignant cells through the modulation of enzyme activity, while normal cells remain unaffected. The in vitro activity of glyceraldehyde-3-phosphate dehydrogenase (GAPDH), an enzyme involved critically in the glycolysis of cancer cells, is inactivated selectively in a controlled way by the QDs at a significantly low concentration (nM). Cumulative kinetic studies delineate that the QDs undergo both reversible and irreversible inhibition mechanisms owing to the site-specific interactions, enabling control over the inhibition kinetics. These complementary loss-of-function probes may offer a novel route for rapid clinical diagnosis of malignant cells and biomedical applications.

An oxygen evolution Co-Ac catalyst - the synergistic effect of phosphate ions

Formation of an amorphous cobalt based oxygen evolution catalyst called Co-Pi has been recently reported from a neutral phosphate buffer solution containing Co2+. But the concentration of Co2+ is as low as 0.5 mM due to poor solubility of a cobalt salt in phosphate medium. In the present study, a cobalt acetate based oxygen evolution catalyst (Co-Ac) is prepared from a neutral acetate buffer solution, where the solubility of Co2+ is very high (>100 times in comparison with phosphate buffer solution). The Co-Ac possesses better catalytic activity than the Co-Pi with an additional advantage of easy bulk scale preparation. The comparative studies on the oxygen evolution reaction (OER) activity of Co-Ac and Co-Pi in phosphate and acetate buffer electrolytes reveal that the Co-Ac exhibits enhanced synergistic catalytic activity in phosphate solution, probably due to partial substitution of acetate in the catalyst layer by phosphate, resulting in the formation of a Co-Ac-Pi catalyst.

FOLD TYPE II PYRIDOXAL 5 `-PHOSPHATE DEPENDENT ENZYMES: STRUCTURE, SUBSTRATE RECOGNITION AND CATALYSIS

Enzymes utilizing pyridoxal 5'-phosphate dependent mechanism for catalysis are observed in all cellular forms of living organisms. PLP-dependent enzymes catalyze a wide variety of reactions involving amino acid substrates and their analogs. Structurally, these ubiquitous enzymes have been classified into four major fold types. We have carried out investigations on the structure and function of fold type I enzymes serine hydroxymethyl transferase and acetylornithine amino transferase, fold type n enzymes catabolic threonine deaminase, D-serine deaminase, D-cysteine desulfhydrase and diaminopropionate ammonia lyase. This review summarizes the major findings of investigations on fold type II enzymes in the context of similar studies on other PLP-dependent enzymes. Fold type II enzymes participate in pathways of both degradation and synthesis of amino acids. Polypeptide folds of these enzymes, features of their active sites, nature of interactions between the cofactor and the polypeptide, oligomeric structure, catalytic activities with various ligands, origin of specificity and plausible regulation of activity are briefly described. Analysis of the available crystal structures of fold type II enzymes revealed five different classes. The dimeric interfaces found in these enzymes vary across the classes and probably have functional significance.

Effect of solvent; enhancing the wettability and engineering the porous structure of a calcium phosphate/agarose composite for drug delivery

Tissue engineering deals with the regeneration of tissues for bone repair, wound healing, drug delivery, etc., and a highly porous 3D artificial scaffold is required to accommodate the cells and direct their growth. We prepared 3D porous calcium phosphate ((hydroxyapatite/beta-tricalcium phosphate)/agarose, (HAp/beta-TCP)/agarose) composite scaffolds by sol-gel technique with water (WBS) and ethanol (EBS) as solvents. The crystalline phases of HAp and beta-TCP in the scaffolds were confirmed by X-ray diffraction (XRD) analysis. The EBS had reduced crystallinity and crystallite size compared to WBS. WBS and EBS revealed interconnected pores of 1 mu m and 100 nm, respectively. The swelling ratio was higher for EBS in water and phosphate buffered saline (PBS). An in vitro drug loading/release experiment was carried out on the scaffolds using gentamicin sulphate (GS) and amoxicillin (AMX). We observed initial burst release followed by sustained release from WBS and EBS. In addition, GS showed more extended release than AMX from both the scaffolds. GS and AMX loaded scaffolds showed greater efficacy against Pseudomonas than Bacillus species. WBS exhibited enhanced mechanical properties, wettability, drug loading and haemocompatibility compared to EBS. In vitro cell studies showed that over the scaffolds, MC3T3 cells attached and proliferated and there was a significant increase in live MC3T3 cells. Both scaffolds supported MC3T3 proliferation and mineralization in the absence of osteogenic differentiation supplements in media which proves the scaffolds are osteoconducive. Microporous scaffolds (WBS) could assist the bone in-growth, whereas the presence of nanopores (EBS) could enhance the degradation process. Hence, WBS and EBS could be used as scaffolds for tissue engineering and drug delivery. This is a cost effective technique to produce scaffolds of degradable 3D ceramic-polymer composites.

Phase stability of silver particles embedded calcium phosphate bioceramics

In this paper, we report the compositional variation-dependent phase stability of hydroxyapatite (Ca-10(PO4)(6)(OH)(2)) on doping with silver. The transformation of hydroxyapatite to (beta/alpha) tricalcium phosphate phases during sintering has been explored using Raman spectroscopy and X-ray diffraction techniques. The optical absorption spectroscopy analysis reveals the presence of Ag+ ions at low doping levels. As the doping increases, abundance of Ag particles is enhanced.

Structures of substrate- and nucleotide-bound propionate kinase from Salmonella typhimurium: substrate specificity and phosphate-transfer mechanism

Kinases are ubiquitous enzymes that are pivotal to many biochemical processes. There are contrasting views on the phosphoryl-transfer mechanism in propionate kinase, an enzyme that reversibly transfers a phosphoryl group from propionyl phosphate to ADP in the final step of non-oxidative catabolism of L-threonine to propionate. Here, X-ray crystal structures of propionate- and nucleotide-bound Salmonella typhimurium propionate kinase are reported at 1.8-2.0 angstrom resolution. Although the mode of nucleotide binding is comparable to those of other members of the ASKHA superfamily, propionate is bound at a distinct site deeper in the hydrophobic pocket defining the active site. The propionate carboxyl is at a distance of approximate to 5 angstrom from the -phosphate of the nucleotide, supporting a direct in-line transfer mechanism. The phosphoryl-transfer reaction is likely to occur via an associative S(N)2-like transition state that involves a pentagonal bipyramidal structure with the axial positions occupied by the nucleophile of the substrate and the O atom between the - and the -phosphates, respectively. The proximity of the strictly conserved His175 and Arg236 to the carboxyl group of the propionate and the -phosphate of ATP suggests their involvement in catalysis. Moreover, ligand binding does not induce global domain movement as reported in some other members of the ASKHA superfamily. Instead, residues Arg86, Asp143 and Pro116-Leu117-His118 that define the active-site pocket move towards the substrate and expel water molecules from the active site. The role of Ala88, previously proposed to be the residue determining substrate specificity, was examined by determining the crystal structures of the propionate-bound Ala88 mutants A88V and A88G. Kinetic analysis and structural data are consistent with a significant role of Ala88 in substrate-specificity determination. The active-site pocket-defining residues Arg86, Asp143 and the Pro116-Leu117-His118 segment are also likely to contribute to substrate specificity.

Synthesis, and crystal and electronic structure of sodium metal phosphate for use as a hybrid capacitor in non-aqueous electrolyte

Energy storage devices based on sodium have been considered as an alternative to traditional lithium based systems because of the natural abundance, cost effectiveness and low environmental impact of sodium. Their synthesis, and crystal and electronic properties have been discussed, because of the importance of electronic conductivity in supercapacitors for high rate applications. The density of states of a mixed sodium transition metal phosphate (maricite, NaMn1/3Co1/3Ni1/3PO4) has been determined with the ab initio generalized gradient approximation (GGA)+Hubbard term (U) method. The computed results for the mixed maricite are compared with the band gap of the parent NaFePO4 and the electrochemical experimental results are in good agreement. A mixed sodium transition metal phosphate served as an active electrode material for a hybrid supercapacitor. The hybrid device (maricite versus carbon) in a nonaqueous electrolyte shows redox peaks in the cyclic voltammograms and asymmetric profiles in the charge-discharge curves while exhibiting a specific capacitance of 40 F g(-1) and these processes are found to be quasi-reversible. After long term cycling, the device exhibits excellent capacity retention (95%) and coulombic efficiency (92%). The presence of carbon and the nanocomposite morphology, identified through X-ray photoelectron spectroscopy (XPS) and transmission electron microscopy (TEM) studies, ensures the high rate capability while offering possibilities to develop new cathode materials for sodium hybrid devices.

Strength reliability and in vitro degradation of three-dimensional powder printed strontium-substituted magnesium phosphate scaffolds

Strontium ions (Sr2+) are known to prevent osteoporosis and also encourage bone formation. Such twin requirements have motivated researchers to develop Sr-substituted biomaterials for orthopaedic applications. The present study demonstrates a new concept of developing Sr-substituted Mg-3(PO4)(2) - based biodegradable scaffolds. In particular, this work reports the fabrication, mechanical properties with an emphasis on strength reliability as well as in vitro degradation of highly biodegradable strontium-incorporated magnesium phosphate cements. These implantable scaffolds were fabricated using three-dimensional powder printing, followed by high temperature sintering and/or chemical conversion, a technique adaptable to develop patient-specific implants. A moderate combination of strength properties of 36.7 MPa (compression), 242 MPa (bending) and 10.7 MPa (tension) were measured. A reasonably modest Weibull modulus of up to 8.8 was recorded after uniaxial compression or diametral tensile tests on 3D printed scaffolds. A comparison among scaffolds with varying compositions or among sintered or chemically hardened scaffolds reveals that the strength reliability is not compromised in Sr-substituted scaffolds compared to baseline Mg-3(PO4)(2). The micro-computed tomography analysis reveals the presence of highly interconnected porous architecture in three-dimension with lognormal pore size distribution having median in the range of 17.74-26.29 mu m for the investigated scaffolds. The results of extensive in vitro ion release study revealed passive degradation with a reduced Mg2+ release and slow but sustained release of Sr2+ from strontium-substituted magnesium phosphate scaffolds. Taken together, the present study unequivocally illustrates that the newly designed Sr-substituted magnesium phosphate scaffolds with good strength reliability could be used for biomedical applications requiring consistent Sr2+-release, while the scaffold degrades in physiological medium. Statement of significance The study investigates the additive manufacturing of scaffolds based on different strontium-substituted magnesium phosphate bone cements by means of three-dimensional powder printing technique (3DPP). Magnesium phosphates were chosen due to their higher biodegradability compared to calcium phosphates, which is due to both a higher solubility as well as the absence of phase changes (to low soluble hydroxyapatite) in vivo. Since strontium ions are known to promote bone formation by stimulating osteoblast growth, we aimed to establish such a highly degradable magnesium phosphate ceramic with an enhanced bioactivity for new bone ingrowth. After post-processing, mechanical strengths of up to 36.7 MPa (compression), 24.2 MPa (bending) and 10.7 MPa (tension) could be achieved. Simultaneously, the failure reliability of those bioceramic implant materials, measured by Weibull modulus calculations, were in the range of 4.3-8.8. Passive dissolution studies in vitro proved an ion release of Mg2+ and PO43- as well as Sr2+, which is fundamental for in vivo degradation and a bone growth promoting effect. In our opinion, this work broadens the range of bioceramic bone replacement materials suitable for additive manufacturing processing. The high biodegradability of MPC ceramics together with the anticipated promoting effect on osseointegration opens up the way for a patient-specific treatment with the prospect of a fast and complete healing of bone fractures. (C) 2015 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

Electrochemical deposition of manganese oxide-phosphate-reduced graphene oxide composite and electrocatalysis of the oxygen evolution reaction

A composite of manganese oxide and reduced graphene oxide (rGO) is prepared in a single step electrochemical reduction process in a phosphate buffer solution for studying as an electrocatalyst for the oxygen evolution reaction (OER). The novel composite catalyst, namely, MnOx-Pi-rGO, is electrodeposited from a suspension of graphene oxide (GO) in a neutral phosphate buffer solution containing KMnO4. The manganese oxide incorporates phosphate ions and deposits on the rGO sheet, which in turn is formed on the substrate electrode by electrochemical reduction of GO in the suspension. The OER is studied with the MnOx-Pi-rGO catalyst in a neutral phosphate electrolyte by linear sweep voltammetry. The results indicate a positive influence of rGO in the catalyst. By varying the ratio of KMnO4 and GO in the deposition medium and performing linear sweep voltammetry for the OER, the optimum composition of the deposition medium is obtained as 20 mM KMnO4 + 6.5% GO in 0.1 M phosphate buffer solution of pH 7. Under identical conditions, the MnOx-Pi-rGO catalyst exhibits 6.2 mA cm(-2) OER current against 2.9 mA cm(-2) by MnOx-Pi catalyst at 2.05 V in neutral phosphate solution. The Tafel slopes measured for OER at MnOx-Pi and MnOx-Pi-rGO are similar in magnitude at about 0.180 V decade(-1). The high Tafel slopes are attributed to partial dissolution of the catalyst during oxygen evolution. The O-2 evolved at the catalyst is measured by the water displacement method and the positive role of rGO on catalytic activity of MnOx-Pi is demonstrated.