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Bound Water Molecules (bound + water_molecule)
Selected AbstractsStructure-based prediction of modifications in glutarylamidase to allow single-step enzymatic production of 7-aminocephalosporanic acid from cephalosporin CPROTEIN SCIENCE, Issue 1 2002Karin Fritz-Wolf Abstract Glutarylamidase is an important enzyme employed in the commercial production of 7-aminocephalosporanic acid, a starting compound in the synthesis of cephalosporin antibiotics. 7-aminocephalosporanic acid is obtained from cephalosporin C, a natural antibiotic, either chemically or by a two-step enzymatic process utilizing the enzymes D-amino acid oxidase and glutarylamidase. We have investigated possibilities for redesigning glutarylamidase for the production of 7-aminocephalosporanic acid from cephalosporin C in a single enzymatic step. These studies are based on the structures of glutarylamidase, which we have solved with bound phosphate and ethylene glycol to 2.5 Å resolution and with bound glycerol to 2.4 Å. The phosphate binds near the catalytic serine in a way that mimics the hemiacetal that develops during catalysis, while the glycerol occupies the side-chain binding pocket. Our structures show that the enzyme is not only structurally similar to penicillin G acylase but also employs essentially the same mechanism in which the ,-amino group of the catalytic serine acts as a base. A subtle difference is the presence of two catalytic dyads, His B23/Glu B455 and His B23/Ser B1, that are not seen in penicillin G acylase. In contrast to classical serine proteases, the central histidine of these dyads interacts indirectly with the O, through a hydrogen bond relay network involving the ,-amino group of the serine and a bound water molecule. A plausible model of the enzyme,substrate complex is proposed that leads to the prediction of mutants of glutarylamidase that should enable the enzyme to deacylate cephalosporin C into 7-aminocephalosporanic acid. [source] The metabolic component of cellular refractivity and its importance for optical cytometryJOURNAL OF BIOPHOTONICS, Issue 8-9 2009V. TychinskyArticle first published online: 30 JUL 200 Abstract Initially, it has been shown that the phase thickness and refractivity (the latter interpreted as the difference of the refractivity indices of an object and surrounding medium) depend on the functional state of mitochondria. The refractivity of various objects decreased in response to energy depletion. This dependence was then demonstrated for other biological objects such as cyanobacteria, chloroplasts and human cells. This general response brought about the hypothesis of a certain "universal" factor that links the variable (or metabolic) component of refractivity with the object's functional state. However, the origin of this phenomenon remains unknown. Our hypothesis is founded on the dependence of polarization of bound water molecules and the activity of metabolic processes. Here, we show the results of measurements of metabolic component of refractivity different bio-objects (mitochondria, chloroplasts, spores, cancer cells) obtained using the Coherent Phase Microscope "Airyscan". Estimations indicated high (up to n , 1.41,1.45) values for the equivalent refractive index of structured water in cells. (© 2009 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] Identification of bound waters in the solution structure of ribonuclease T1 using the double pulsed field gradient spin-echo NMR technique for selective water excitationMAGNETIC RESONANCE IN CHEMISTRY, Issue 9 2002Mitsuru Tashiro Abstract Novel pulse sequences incorporating the double pulsed field gradient spin-echo technique are presented that have particular use in identifying macromolecular bound water. The use of these sequences is illustrated using ribonuclease T1. Five amide protons cross-relaxing with bound water protons were observed. Examination of the crystal structure revealed that all of these amide protons donate hydrogen bonds or are in close proximity to water molecules with very low temperature factors, indicating that these amide protons are highly correlated with the bound water molecules. This method rapidly provides reliable information for characterizing macromolecular bound water molecules. Copyright © 2002 John Wiley & Sons, Ltd. [source] Water and Carboxyl Group Environments in the Dehydration Blueshift of Bacteriorhodopsin,PHOTOCHEMISTRY & PHOTOBIOLOGY, Issue 5 2000Robert Renthal ABSTRACT The proton channels of the bacteriorhodopsin (BR) proton pump contain bound water molecules. The channels connect the purple membrane surfaces with the protonated retinal Schiff base at the membrane center. Films of purple membrane equilibrated at low relative humidity display a shift of the 570 nm retinal absorbance maximum to 528 nm, with most of the change occurring below 15% relative humidity. Purple membrane films were dehydrated to defined humidities between about 50 and 4.5% and examined by Fourier transform infrared difference spectroscopy. In spectra of dehydrated-minus-hydrated purple membrane, troughs are observed at 3645 and 3550 cm,1, and peaks are observed at 3665 and 3500 cm,1. We attribute these changes to water dissociation from the proton uptake channel and the resulting changes in hydrogen bonding of water that remains bound. Also, in the carboxylic acid spectral region, a trough was observed at 1742 cm,1 and a peak at 1737 cm,1. The magnitude of the trough to peak difference between 1737 and 1742 cm,1 correlates linearly with the extent of the 528 nm pigment. This suggests that a carboxylic acid group or groups is undergoing a change in environment as a result of dehydration, and that this change is linked to the appearance of the 528 nm pigment. Dehydration difference spectra with BR mutants D96N and D115N show that the 1737,1742 cm,1 change is due to Asp 96 and Asp 115. A possible mechanism is suggested that links dissociation of water in the proton uptake channel to the environmental change at the Schiff base site. [source] Structure of tetragonal crystals of human erythrocyte catalaseACTA CRYSTALLOGRAPHICA SECTION D, Issue 1 2001Martin K. Safo The structure of catalase from human erythrocytes (HEC) was determined in tetragonal crystals of space group I41 by molecular-replacement methods, using the orthorhombic crystal structure as a search model. It was then refined in a unit cell of dimensions a = b = 203.6 and c = 144.6,Å, yielding R and Rfree of 0.196 and 0.244, respectively, for all data at 2.4,Å resolution. A major difference of the HEC structure in the tetragonal crystal compared with the orthorhombic structure was the omission of a 20-residue N-terminal segment corresponding to the first exon of the human catalase gene. The overall structures were otherwise identical in both crystal forms. The NADPH-binding sites were empty in all four subunits and bound water molecules were observed at the active sites. The structure of the C-terminal segment, which corresponds to the last exon, remained undetermined. The tetragonal crystals showed a pseudo-4122 symmetry in molecular packing. Two similar types of lattice contact interfaces between the HEC tetramers were observed; they were related by the pseudo-dyad axes. [source] | ||||||||||