ライフサイエンスコーパス: bound water

1 of the water (i.e., converting free water to bound water).

2 ith heavy association of tightly and loosely bound water.

3 is; the pK(a1) was assigned to the manganese-bound water.

4 a1) = 8.7 +/- 0.1 corresponds to the cadmium-bound water.

5 distal His-64 forms a hydrogen bond with the bound water.

6 udies revealed a pK(a) of 10.4 for the metal-bound water.

7 for deprotonation and activation of the zinc-bound water.

8 s indirect contacts with the bases through a bound water.

9 econd TST binding causes displacement of the bound water.

10 ectra show evidence for minor carbonates and bound water.

11 the proton to solvent through an additional bound water.

12 O bond by transferring a proton from a metal-bound water.

13 ase regardless of the presence or absence of bound water.

14 molecule, with retention of a third, axially bound water.

15 e to the deprotonation of the catalytic zinc-bound water.

16 and would predict a lower pKa for the metal-bound water.

17 y reflects groove-specific reorganization of bound water.

18 ond with a subtilisin hydrogen-bond donor or bound water.

19 to date for low-valent reductants containing bound water.

20 te dissociation and deprotonation of surface bound water.

21 en-bonded network between His64 and the zinc-bound water.

22 o the order of the pK's for these four metal-bound waters.

23 xyl oxygens are positioned near a network of bound waters.

24 to obtain sites corresponding to kinetically bound waters.

25 (AdoHcy) hydrolase and/or addition of enzyme-bound water across the conjugated enyne system.

26 combination with cooperative interactions of bound water along the backbone chain.

27 The active form of LuxS contains a metal-bound water and a thiolate ion at Cys-83, consistent wit

28 shuttle to transfer protons between the zinc-bound water and bulk water.

29 ogen bond was identified between a magnesium-bound water and Cys1p, bridging the two metallic binding

30 of an effective solvent bridge between zinc-bound water and H64 and thereby hinders solvent-mediated

31 fore, the active solvent bridge between zinc-bound water and H64 is disrupted by substitutions at pos

32 Intramolecular proton transfer between zinc-bound water and H64 is significantly inhibited by the in

33 presence of a zinc-bound hydroxide or a zinc-bound water and in the protonation state of the essentia

34 ug covers the minor groove of DNA, displaces bound water and interacts with neighbouring DNA molecule

35 orption near Ceres and previous detection of bound water and OH near and on Ceres have raised interes

36 to previous work investigating the states of bound water and provide a new approach for probing water

37 s64 in transferring protons between the zinc-bound water and solution was confirmed by the 100-fold l

38 the proton transfer pathway between the zinc-bound water and solution.

39 e active site uniformly by mobile and weakly bound water and some structural water similar to that in

40 on shuttle accepting a proton from the metal-bound water and subsequently acts as a general acid duri

41 rface enabled discrimination between surface-bound water and that in the double layer.

42 lues for the apparent pKa at 6.2 to the zinc-bound water and the pKa of 7.5 to His 64.

43 in relaxation represents the behavior of the bound water and the spin-lattice relaxation that of tota

44 d to contribute to the low pK(a) of the zinc-bound water and to promote proton transfer in catalysis.

45 increase in prototropic exchange rate of the bound water and/or phenolic protons.

46 ndicated that the inactivity might be due to bound waters and high flexibility of residues within the

47 erve the pivotal interactions between the Mg-bound waters and the N-oxide of pyridine.

48 had per-voxel signal-to-noise ratios of 18 (bound water) and 14 (pore water) and inter-study standar

49 of several key residues (e.g., His334, Cu(B)-bound water, and PRD(a3)) on the computed microscopic pK

50 uences the headgroup conformation, amount of bound water, and the lipid-packing density, without pert

51 ro-time covariance patterns between protein, bound waters, and ligand vary between the different simu

52 tered at the pK(a)'s for the respective zinc-bound waters, and limiting second-order rate constants a

53 conformation, as well as favorably oriented bound waters, and the proximity of the backbone carbonyl

54 dent in which movements of protein atoms and bound water are coordinated with relaxation of the initi

55 nformational changes of the compound and the bound water are essential for strong binding to DNA by R

56 elastin fibers and conclude (i) that tightly bound waters are absent in both dry and hydrated elastin

57 Bound waters are identified by high site occupancies usi

58 Within the selectivity filter, four bound waters are localized along three hydrophilic nodes

59 and, one by the substrate and the other by a bound water, are found, consistent with the proposed pro

60 265 as a general acid-base pair and the zinc-bound water as a nucleophile.

61 nalyzed plant stem water as a proxy for soil-bound water as well as total soil water by cryogenic dis

62 cilitating the formation of the ionized zinc-bound water at close to neutral pH and in providing addi

63 in vivo electron transfer, had a more weakly bound water at one position (W1).

64 drase requires proton transfer from the zinc-bound water at the active site to solution for each cycl

65 results from the nucleophilic attack of zinc-bound water at the active site.

66 ffective active site of HCA II from the zinc-bound water at the base of the conical cavity in the enz

67 usion that a proton transfer occurs in which bound water at the catalytic site acts as a primary prot

68 d for the correct assembly of metal ions and bound water at the catalytic site, functions important i

69 dies have revealed structure and dynamics of bound waters at atomic resolution.

70 dines, one unibidentate acidic ligand, and a bound water), but their histidine tautomeric geometries

71 rotein-water coupled motions, referred to as bound water (BW).

72 ring nitrogens, inhibits displacement of the bound water by added protein and also suppresses intermo

73 Stereo-specific interrogation of bound water by chemical synthesis provides a general met

74 cally less costly than that of more strongly bound water by up to several kBT and thus can lower the

75 s described by the single ionization of zinc-bound water, CA VII exhibits a pH profile for Kcat/K(m)

76 Tightly bound water can be removed from soybean and pea seeds by

77 lements in the pumping mechanism may include bound water, carboxylates, and the heme propionates, arg

78 a member of the aquaporin family of membrane-bound water channels.

79 s as indicated by a decreased pKa for the Zn-bound water compared to CA II (6.2 vs 6.9), as well as l

80 Purpose To quantify free and bound water components of cortical bone with a model-bas

81 Results The mean free water concentration, bound water concentration, free water T1, and bound wate

82 to stabilise the structure, and kinetically bound water detected in the minor groove of such DNA spe

83 pper of the binuclear center, displacing the bound water, followed by sequential deprotonation throug

84 A higher pK(a) for the metal-bound water for cadmium and manganese BCII leads to more

85 ars to activate a proton of the type 2 Cu(+)-bound water for participation in the transition state.

86 The release of bound water from the hydration layers of macromolecules

87 The catalytic zinc-bound water, His-51 (which interacts with the 2'- and 3'

88 n-bound hydroxyl/His64+ (charged) and the Zn-bound water/His64 (uncharged) HCA II states.

89 structure observed is most likely in the Zn-bound water/His64 state.

90 orption resistance is caused by the strongly bound water hydration layer and characterized by the sim

91 the excess proton between the catalytic zinc-bound water/hydroxide and the proton shuttling residue,

92 ses with fluoride ion, suggest that a Zn(II)-bound water/hydroxide exists at the dimetal active site

93 acid side chain as in tyrosine or to already-bound water in a second solvation shell around the ammon

94 lacetate indicate that the pK(a) of the zinc-bound water in CA XII is 7.1.

95 Deprotonation of zinc-bound water in carbonic anhydrase II is the rate-limitin

96 factor of phi approximately 0.5 for the zinc-bound water in conjunction with a transition-state proto

97 ls pK(a) values of 6.5 and 5.6 for the metal-bound water in E133A and E133D Co-PDF, respectively, sug

98 This result suggests a role for bound water in electron transfer to P700+.

99 active site and leave primarily the tightly bound water in that region.

100 om these findings, and from the locations of bound water in the extracellular region in the crystal s

101 es the strength of the O-H bond in the metal-bound water in the Mn(II) complex to be 82 (+/-2) kcal m

102 reliably estimating the amount of capillary-bound water in the rock, which is important for efficien

103 inders as well as to the location of protein-bound water in the surroundings of the ligand.

104 The pK(a) of this bound water in the zinc(II) complex of L(1) and L(2) is

105 In two different soil types, soil-bound water in two sets of 19-l pots, each with a 2-yr-o

106 ding and measure the millisecond dynamics of bound waters in protein crevices.

107 e with theoretical simulations employing two bound waters in the region of the Asp-85 and Asp-212 res

108 release, we demonstrate the participation of bound waters in the sequence discrimination of substrate

109 Escherichia coli aquaglyceroporin GlpF with bound water, in native (2.7 angstroms) and in W48F/F200T

110 increase with increasing pK(a) of the metal-bound water, in the order Zn < Co < Mn < Cd.

111 of hydrogen bonding as well as the amount of bound water increases.

112 ps that either address or substitute protein-bound water, information of utmost importance for drug d

113 -based readout to identify sites of bulk and bound water interactions with surface and internal resid

114 ed MS to measure the millisecond dynamics of bound water interactions with various internal residue s

115 the structural chemistry influencing whether bound water is displaced or participates in ligand bindi

116 conservation or displacement of active-site bound water is independent of the ligand, and shows that

117 nconsistent with the suggestion that a metal-bound water is involved in hydrolysis.

118 nd water, and for the H64G mutant, where the bound water is no longer stabilized by hydrogen bonding

119 files, showing that deprotonation of a metal-bound water is partially rate-limiting.

120 to flip into the enzyme active site, where a bound water is poised for nucleophilic attack.

121 arriers of 0.36 eV and find that molecularly bound water is preferred over the surface-bound hydroxyl

122 After the second PT event and when the zinc-bound water is regenerated, the His64 is again favored t

123 If the zinc-bound water is the nucleophile in the reaction, the role

124 hat water from bulk solvent, but not tightly bound water, is involved in the hydrolytic release of ch

125 Seventy-five to 95% of the bound water isotopically exchanged with the mobile water

126 e free/quasifree water molecules and surface-bound water layer (minimum binding energy of 1-2 kcal/mo

127 Results show that a tightly bound water layer adjacent to the OEG-SAMs is mainly res

128 posed to play a role in activating the metal-bound water ligand for subsequent nucleophilic attack on

129 lost, suggesting the existence of two weakly bound water ligands near the cation-binding site in bact

130 gamma-class enzyme contains additional metal-bound water ligands, so the overall coordination geometr

131 Ionization of the zinc-bound water may be responsible for this pKa since the th

132 mitive biochemical reactions within membrane-bound water micro-droplets is considered an essential st

133 ese results suggest that increases in enzyme-bound water mobility mediated by the presence of salt ac

134 uperfamily abstracts a proton from the metal-bound water molecule (or hydroxide) to promote the hydro

135 ioned inhibitor heteroatom and one between a bound water molecule and a second inhibitor heteroatom.

136 components: a motif intended to stabilize a bound water molecule and hydrophobic substrate binding i

137 le proton transfer pathways between the zinc-bound water molecule and solution.

138 n transfer likely proceeds, bridges the zinc-bound water molecule and the C131-MI imidazole group.

139 gateway residues Tyr34, His30 and a tightly bound water molecule are implicated in closing-off the a

140 resent the first identification of an enzyme-bound water molecule at a subunit interface (active site

141 y the abstraction of a proton from the metal-bound water molecule by the side chain imidazole of His-

142 a consequence of the lower pK(a) of a Co(2+)-bound water molecule compared with a Mn(2+)-bound water

143 results in a frequency shift of 56 ppm in a bound water molecule exchange peak between pH 5 and 8.

144 so that it might in turn activate a tightly bound water molecule for nucleophilic attack.

145 A pKa of 6.6 was estimated for the zinc-bound water molecule in mCA IV.

146 e 2Fe subcluster at the site of a terminally bound water molecule in the as crystallized native state

147 eneral base to accept a proton from the zinc-bound water molecule in the initial rate-determining nuc

148 One extra bound water molecule is coupled with the loss of approxi

149 ee-energy increase due to the removal of the bound water molecule is not more than compensated by the

150 The residence time of the Cd(2+)-bound water molecule is tens of nanoseconds at 20 degree

151 ted thiolate group of GSH (GS(-)), and a GSH-bound water molecule may donate a hydrogen bond to the 3

152 To better understand the role of the bound water molecule observed in the X-ray crystal struc

153 on of metal-bound hydroxide ion from a metal-bound water molecule requires proton transfer to bulk so

154 the position and orientation of a metal ion-bound water molecule that is located in the active site

155 le, facilitating the deprotonation of a zinc-bound water molecule to regenerate the nucleophilic zinc

156 imal velocity by proton transfer from a zinc-bound water molecule to the proton shuttle His64.

157 ructures of those ligands were determined, a bound water molecule was observed interacting with the a

158 een these proton shuttle groups and the zinc-bound water molecule were estimated as the predominant r

159 Gln-450 interacts through a bound water molecule with the phosphoryl moiety and may

160 leaving oxoanion is protonated by an Mg(2+)-bound water molecule within the same elementary reaction

161 nked movements of the zinc ion, a zinc-bound bound water molecule, and the substrate during progressi

162 g as a general base catalyst toward the zinc-bound water molecule, on the basis of mechanistic propos

163 eric demand, required displacement of a well-bound water molecule, or changes of trigonal-planar to t

164 ng interactions with a tyrosine hydroxyl and bound water molecule, rather than the highly specific hy

165 -bound water molecule compared with a Mn(2+)-bound water molecule, strengthens electrostatic interact

166 m, a species most likely containing a weakly bound water molecule, which accumulates during storage o

167 through a proton shuttle via a pyrophosphate-bound water molecule.

168 n the abstraction of a proton from the metal-bound water molecule.

169 by mutagenesis), a histidine residue, and a bound water molecule.

170 ere assigned to the deprotonation of a metal-bound water molecule.

171 on atom is hexacoordinated with a covalently bound water molecule.

172 a pseudobridging coordination with a calcium-bound water molecule.

173 r of a hydrogen atom from this newly formed, bound, water molecule to the ferryl oxygen with a concom

174 Two tightly bound water molecules appear to stabilize this network b

175 metal sites are fully occupied, and tightly bound water molecules at metal site 1 ("Water 1") and me

176 Mn2+-bound water molecules at the binuclear metal centre coor

177 partner is quite variable and also involves bound water molecules at the TCR/pMHC interface.

178 nges involving hydrogen-bonding residues and bound water molecules begin to propagate from the retina

179 of these effects may increase the number of bound water molecules by 50%.

180 Rather, the complete exchange of protein-bound water molecules by translational displacement seem

181 hbors classifier/genetic algorithm, predicts bound water molecules conserved between free and ligand-

182 sequence discrimination wherein specifically bound water molecules couple flanking backbone contacts

183 Metal-bound water molecules facilitate the PCET necessary for

184 Flexible side chains and bound water molecules form the majority of the base cont

185 c model comprising residues 19 to 245 and 28 bound water molecules has been refined at 2.6 angstrom r

186 dies enabled us to determine how transiently bound water molecules impact the rate and mechanism of S

187 potential hydrogen bonds, utilizing several bound water molecules in addition to protein atoms, that

188 he results indicate extensive involvement of bound water molecules in both the structure and the func

189 , and supports a possible role of restricted/bound water molecules in C-type inactivation gating.

190 There are 4-5 strongly bound water molecules in hydrogen bonds to the conformer

191 ted in the identification of several tightly bound water molecules in key structural positions.

192 hotooxidation of P(700) perturbs internal or bound water molecules in PSI and that the P(700)(+)-minu

193 and acetonitrile) replace mobile and weakly bound water molecules in the active site and leave prima

194 e parts of the protein globule together with bound water molecules in the early stages of radiation d

195 arly visible Na(+), and specific patterns of bound water molecules in the four non-equivalent grooves

196 elf-assembly of the nanostructure as well as bound water molecules in the nanotube's channel.

197 importance of proper recognition of protein bound water molecules in the protein-ligand binding and

198 till underappreciated roles for specifically bound water molecules in the structural dynamics and fun

199 tudies aimed at examining whether internally bound water molecules interact with the chromophore and

200 No measurable net change in the number of bound water molecules is observed when neomycin binds th

201 Hydrogen bonding to metal-bound water molecules is the dominant stabilizing intera

202 ributed to the Bronsted acidity of the metal-bound water molecules located inside the nanocavity, whi

203 hat rearrangement of flexible side-chains or bound water molecules may contribute to degenerate Py-tr

204 A chain of bound water molecules may provide such a connection, whi

205 This number of bound water molecules neglects the possibility of local

206 that remains is attributed to motion of the bound water molecules on the protein or to internal prot

207 (+) monocations, Mg(2+) better polarizes the bound water molecules resulting in stronger Mg(2+)-water

208 trehalose skeleton with a minimal number of bound water molecules scattered in the bulk.

209 rther identified the contribution of surface-bound water molecules to bands in the far-IR and, throug

210 The dynamic behavior of surface-bound water molecules under each study environment is id

211 A total of seven tightly bound water molecules were found in the FGF-2 structure,

212 These waters, distinct from bound water molecules within the SRII receptor, appear t

213 idin binding site (specifically expulsion of bound water molecules).

214 The interface also includes 11 bound water molecules, 3 of which are completely buried

215 t the FabE8-cytc interface is enhanced by 48 bound water molecules, and by local movements of up to 4

216 esence of significant quantities of strongly bound water molecules, and the relatively high concentra

217 water with a maximum of four dissociatively bound water molecules, and they exhibit structural fluxi

218 sights from the crystal structure on tightly bound water molecules, conformational strain, and packin

219 01 non-H protein atoms and approximately 200 bound water molecules, has been determined ab initio (us

220 romophore to the bulk solvent via Ser147 and bound water molecules, resulting in green emission from

221 e flavin-binding site, including the tightly bound water molecules, the mode of NADP(+) binding, and

222 chanism is proposed involving the two enzyme-bound water molecules, W2 and W4, in acid/base catalysis

223 Binding is coupled to the dissociation of bound water molecules, which is greater for CaATP-actin

224 ly hydrophilic surface that includes tightly bound water molecules.

225 ot necessarily correspond to the presence of bound water molecules.

226 Arg-381 but, unusually, does not involve any bound water molecules.

227 hanging groups of amino acid side chains and bound water molecules.

228 he multivalent hydrogen-bonding potential of bound water molecules.

229 vary inversely with the pKa values of their bound water molecules.

230 nisation of hydrogen-bond networks involving bound water molecules.

231 protein side chains, the inhibitor, and two bound water molecules.

232 ctions between backbone and substituent, and bound water molecules.

233 ive, extended conformation in the state with bound water molecules.

234 site region (comprising Cys32 and Cys35) via bound water molecules.

235 o protein-based metal ligands, and two metal-bound water molecules.

236 gen bonds to protein polar atoms and to site-bound water molecules.

237 esults in stabilization of a large number of bound water molecules.

238 trigonal bipyramidal geometry and two metal-bound water molecules.

239 cylinder is polar in character and includes bound water molecules.

240 and ROESY experiments identifies only a few "bound" water molecules with long residence times.

241 It is suggested that the presence of "bound" water molecules within the pore may reduce the ef

242 Mutational analysis suggested that the bound water motif does not contribute to the rate accele

243 (to isolate the effect of the catalytic zinc-bound water) mutations were used to test the roles of th

244 catalytic lysine are slightly different; the bound water network appears to be more extensive; and th

245 tB, reveals structural similarities with the bound water network in the OEC.

246 , consistent with Asp-282 activating a metal-bound water nucleophile.

247 is, consistent with deprotonation of a metal-bound water nucleophile.

248 rement that the ligand must displace loosely bound water on binding.

249 ion was used to examine the motion of enzyme-bound water on subtilisin Carlsberg co-lyophilized with

250 sp-His intersubunit dyad to activate a metal-bound water or hydroxide for proton transfer during cata

251 re limited by proton transfer involving zinc-bound water or hydroxide in the active site.

252 it only O/N ligands to the zinc atom, a zinc-bound water or hydroxide may serve as a general base for

253 euterium-to-hydrogen (D/H) ratio in strongly bound water or hydroxyl groups in ancient martian clays

254 entified with polar moieties in the protein, bound waters, or Arg-82 is an important mechanistic ques

255 tprocessing algorithms, to quantify free and bound water parameters (concentration [rho] and longitud

256 zing the sites and measuring the dynamics of bound waters, particularly on timescales relevant to cat

257 onsistent with earlier indications that site-bound water plays a prominent role in substrate activati

258 to proton-catalyzed exchange of the Ln(3+) -bound water protons even though their pKa 's are much hi

259 Thus, the free water-to-bound water ratio decreases with increasing pressure, de

260 ormation content of the model by identifying bound water sites based on peak electron densities, and

261 at other locations were excluded by tightly-bound waters so that only the hot-spot cluster remained

262 e transfer from the metal oxide to a surface-bound water species.

263 samples, we allowed for the possibility that bound water spectra differ from the bulk water spectra.

264 ound water concentration, free water T1, and bound water T1 in the recruited population were 5.9%, 19

265 act that coarse and PE bran hold more weakly bound water than ground bran, which is most probably wat

266 can hold about 25 per cent more structurally bound water than those in metamorphosed terrestrial basa

267 onal network of hydrogen-bonded residues and bound water that accounts for the changed pKa values (wh

268 Moreover, an intense band due to weakly bound water that is peculiar for L was already present i

269 d) 4 formed by cryoreduction of 3 involves a bound water that may convey a proton from L-Arg, while t

270 osmotic stress technique is measuring weakly bound waters that are not measured via the heat capacity

271 The first is "non-freezing bound" water that gradually becomes mobile with increasi

272 ange from approximately 0.6 milliseconds for bound water to 41 seconds and 13 hours for the two disti

273 gyrase are illustrative of the importance of bound water to binding thermodynamics.

274 (HCA II) requires proton transfer from zinc-bound water to solution assisted by His 64.

275 e of which is to transfer a proton from zinc-bound water to solution in the hydration direction to re

276 the oxidative addition of a proton from the bound water to the metal center and finally an alpha-H a

277 We mapped ferrous-iron-bearing minerals, bound water, trapped CO2, probable phyllosilicates, orga

278 orrelate with the dipole moments of the zinc-bound water upon deprotonation.

279 at residues Arg-404, Glu-290, Asp-356, and a bound water (WAT185) participate in a unique H-bonding n

280 xtent of dissociation, or pK(a), of the zinc-bound water, we apply quantum chemistry calculations to

281 es between these shuttle groups and the zinc-bound water were estimated as the rate-determining step

282 ation techniques three types of structurally-bound water were observed in these materials.

283 l forces causes bran to retain only strongly bound water which is most likely bound in cell wall nano

284 Mutation of the triad results in loss of the bound water, which destabilizes LacY, and the cavities o

285 ions and HG gelation increase the amount of bound water, which facilitates spin diffusion, while cal

286 five distinct water pools: three are peptide-bound water, while two are highly dynamic water that can

287 y hopping between bound and free states, (2) bound water with internal motion, and (3) free diffusion

288 sence of halothane, the exchange rate of the bound waters with bulk water was increased.

289 iously attributed to ionization of the metal-bound water yielding the hydroxyl group attacking CO(2).