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Molecule Binds (molecule + bind)
Selected AbstractsLabel-Free Impedance Biosensors: Opportunities and ChallengesELECTROANALYSIS, Issue 12 2007Jonathan Abstract Impedance biosensors are a class of electrical biosensors that show promise for point-of-care and other applications due to low cost, ease of miniaturization, and label-free operation. Unlabeled DNA and protein targets can be detected by monitoring changes in surface impedance when a target molecule binds to an immobilized probe. The affinity capture step leads to challenges shared by all label-free affinity biosensors; these challenges are discussed along with others unique to impedance readout. Various possible mechanisms for impedance change upon target binding are discussed. We critically summarize accomplishments of past label-free impedance biosensors and identify areas for future research. [source] The effect of the sixth sulfur ligand in the catalytic mechanism of periplasmic nitrate reductaseJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 15 2009N. M. F. S. A. Cerqueira Abstract The catalytic mechanism of nitrate reduction by periplasmic nitrate reductases has been investigated using theoretical and computational means. We have found that the nitrate molecule binds to the active site with the Mo ion in the +6 oxidation state. Electron transfer to the active site occurs only in the proton-electron transfer stage, where the MoV species plays an important role in catalysis. The presence of the sulfur atom in the molybdenum coordination sphere creates a pseudo-dithiolene ligand that protects it from any direct attack from the solvent. Upon the nitrate binding there is a conformational rearrangement of this ring that allows the direct contact of the nitrate with MoVI ion. This rearrangement is stabilized by the conserved methionines Met141 and Met308. The reduction of nitrate into nitrite occurs in the second step of the mechanism where the two dimethyl-dithiolene ligands have a key role in spreading the excess of negative charge near the Mo atom to make it available for the chemical reaction. The reaction involves the oxidation of the sulfur atoms and not of the molybdenum as previously suggested. The mechanism involves a molybdenum and sulfur-based redox chemistry instead of the currently accepted redox chemistry based only on the Mo ion. The second part of the mechanism involves two protonation steps that are promoted by the presence of MoV species. MoVI intermediates might also be present in this stage depending on the availability of protons and electrons. Once the water molecule is generated only the MoVI species allow water molecule dissociation, and, the concomitant enzymatic turnover. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009 [source] X-ray structure and characterization of carbamate kinase from the human parasite Giardia lambliaACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 4 2010Andrey Galkin Carbamate kinase catalyzes the reversible conversion of carbamoyl phosphate and ADP to ATP and ammonium carbamate, which is hydrolyzed to ammonia and carbonate. The three-dimensional structure of carbamate kinase from the human parasite Giardia lamblia (glCK) has been determined at 3,Å resolution. The crystals belonged to the monoclinic space group P21, with unit-cell parameters a = 69.77, b = 85.41, c = 102.1,Å, , = 106.8°. The structure was refined to a final R factor of 0.227. The essentiality of glCK together with its absence in humans makes the enzyme an attractive candidate for anti- Giardia drug development. Steady-state kinetic rate constants have been determined. The kcat for ATP formation is 319 ± 9,s,1. The Km values for carbamoyl phosphate and ADP are 85 ± 6 and 70 ± 5,µM, respectively. The structure suggests that three invariant lysine residues (Lys131, Lys216 and Lys278) may be involved in the binding of substrates and phosphoryl transfer. The structure of glCK reveals that a glycerol molecule binds in the likely carbamoyl phosphate-binding site. [source] Inhibitor design for ribonuclease A: the binding of two 5,-phosphate uridine analoguesACTA CRYSTALLOGRAPHICA SECTION F (ELECTRONIC), Issue 7 2009Vicky G. Tsirkone In the quest for the rational design of selective and potent inhibitors for members of the pancreatic ribonuclease A (RNase A) family of biomedical interest, the binding of uridine 5,-phosphate (U5P) and uridine 5,-diphosphate (UDP) to RNase A have been investigated using kinetic studies and X-ray crystallography. Both nucleotides are competitive inhibitors of the enzyme, with Ki values of 4.0 and 0.65,mM, respectively. They bind to the active site of the enzyme by anchoring two molecules connected to each other by hydrogen bonds and van der Waals interactions. While the first of the inhibitor molecules binds with its nucleobase in the pyrimidinyl-binding subsite, the second is bound at the purine-preferring subsite. The unexpected binding of a pyrimidine at the purine-binding subsite has added new important elements to the rational design approach for the discovery of new potent inhibitors of the RNase A superfamily. [source] |