ライフサイエンスコーパス: protein backbone

1 A backbone, comparable to phi and psi in the protein backbone.

2 elding a probe that is rigid relative to the protein backbone.

3 ails of the interaction between urea and the protein backbone.

4 ncluding unanticipated hydrogen bonds to the protein backbone.

5 lly stabilizes the fold without altering the protein backbone.

6 nd fifth bonds linking the spin-label to the protein backbone.

7 glycine peptide, which is a good model for a protein backbone.

8 the second cysteine was introduced into the protein backbone.

9 ment linkers that position dyes far from the protein backbone.

10 the spin label and the local dynamics of the protein backbone.

11 to form within a compact conformation of the protein backbone.

12 level that has so far been reserved for the protein backbone.

13 moved from the 12C=16O band of the unlabeled protein backbone.

14 es or by engaging in hydrogen bonds with the protein backbone.

15 orientation and distance with respect to the protein backbone.

16 n unprecedented covalent modification of the protein backbone.

17 eferentially excluded/accumulated around the protein backbone.

18 d by covalent linkage of the cysteine to the protein backbone.

19 ereas beta(var) allows accumulation of alpha protein backbone.

20 om dissociation of the N-Calpha bonds of the protein backbone.

21 ing through a cis-trans isomerization of the protein backbone.

22 kbone dynamics are propagated throughout the protein backbone.

23 together with additional small shifts of the protein backbone.

24 e, on the structure and dynamics of the TPMT protein backbone.

25 he flexibility of amino acid residues of the protein backbone.

26 ns to determine the relative mobility of the protein backbone.

27 mino acid sequences compatible with a target protein backbone.

28 erimental method to assess the motion of the protein backbone.

29 dical species that then propagates along the protein backbone.

30 ese residues induce strain in the DNA and/or protein backbone.

31 ave been used to assign the signals from the protein backbone.

32 e oxazolidinedione ring oxygen and the CA II protein backbone.

33 tes in a water-mediated hydrogen bond to the protein backbone.

34 between the Trp ring and its linkage to the protein backbone.

35 s directly attached to the asparagine of the protein backbone.

36 ecause of constraints imposed by P225 on the protein backbone.

37 by incorporating 13C at two positions in the protein backbone.

38 Cross-linking was to His62, mainly to the protein backbone.

39 stiffness to springs that connect along the protein backbone.

40 chitectures to predict phi and psi angles of protein backbone.

41 adily be used in simulations with a flexible protein backbone.

42 lates fluorophilic sites in proximity to the protein backbone.

43 of ligands, amino acid side chains, and the protein backbone.

44 due that links the polysaccharide chain to a protein backbone.

45 t mainly using the carbonyl oxygens from the protein backbone.

46 es its conformation, now pointing toward the protein backbone.

47 e (NGT) at every possible position along the protein backbone.

48 to which probe dynamics reflect those of the protein backbone.

49 by genetically tuning the charge density of protein backbones.

50 TD and SCWRL4) on both native and non-native protein backbones.

51 nergy sequences for nine naturally occurring protein backbones.

52 s a simple mimic of cation interactions with protein backbones.

53 lactose (Gal) to hydroxyproline (Hyp) in AGP protein backbones.

54 y apparent adverse affects on the glycans or protein backbones.

55 hed a spin label as close as possible to the protein backbone, achieving high resolution in double el

56 Early in the folding process, the protein backbone adopts a nativelike topology while cert

57 trace unambiguously approximately 85% of the protein backbone, allowing us to identify the structural

58 linked through the same 376-Da sugar to the protein backbone, also in O-linkage.

59 (15)N labeling to structural changes of the protein backbone, although no such bands were previously

60 NMR results show that the protein backbone amide chemical shift deviations correla

61 ts that correlate with the distances between protein backbone amides and spin-labeled probes.

62 engths of all six key hydrogen bonds between protein backbone amides and the sulfur atoms of the four

63 een recognized that hydrogen bonds formed by protein backbone amides with cysteinyl S(gamma) atoms pl

64 (1)H, (13)C, and (15)N spin probes along the protein backbone and amino-acid side chains, reveals a p

65 We observe changes in the protein backbone and aromatic residues as well as disulf

66 uniform distributions of cleavages along the protein backbone and consequently higher sequence covera

67 lecular contacts were determined between the protein backbone and glycosite glycan based on available

68 HIV-1 Env N-glycans shield the protein backbone and have been shown to play key roles i

69 , and hydrogen bond interactions between the protein backbone and heme functional groups are readily

70 ion implies that the interaction between the protein backbone and osmolyte polar groups is more favor

71 ns two potential ET pathways: P1 through the protein backbone and P2 through the H-bond between the C

72 HIV-1 Env N-glycans shield the protein backbone and play key roles in determining Env s

73 in alkanediols mediate interactions with the protein backbone and polar amino acid side chains, while

74 CD provides more homogeneous cleavage of the protein backbone and preserves labile PTMs.

75 itional electrostatic interactions with both protein backbone and side chain atoms.

76 dispersion interaction between urea and the protein backbone and side chains is stronger than for wa

77 ypothesis that rapid Monte-Carlo sampling of protein backbone and side-chain conformational space wit

78 Unfavorable entropic contributions from the protein backbone and side-chain residues in the vicinity

79 nance experiments of the kind used to assign protein backbone and side-chain resonances.

80 Furthermore, effects of the protein backbone and side-chains, as well as of the aque

81 ad to underestimation of the dynamics of the protein backbone and the entropy contained therein.

82 A side-chain interacts with the protein backbone and the probability-weighted average of

83 revealed a significant rearrangement of the protein backbone and the side chains of the Glu167 and A

84 t from proximity of Ala(beta) methyls to the protein backbone and their high degree of ordering.

85 a combination of hydrogen bonds between the protein backbone and uracil, with the pocket shaped to p

86 Protein backbones and pyridine-carboxylic acids dominate

87 Protein backbones and side chains display varying degree

88 ee Cys residues, two N-amide groups from the protein backbone, and one OH(-).

89 ng of tryptophan side-chains relative to the protein backbone, and orientational fluctuations of enti

90 inent and sensitive vibrational bands of the protein backbone, and they relate to protein secondary s

91 However, we observe that in the protein backbone angle prediction research, there is an

92 AP) to train simpler DNN models that enhance protein backbone angle prediction.

93 gen bonds between the N-acetyl group and the protein backbone are an important integral part of the o

94 Their protein backbones are rich in the disordering amino acid

95 lation results identified the motions of the protein backbone as the gorge opens.

96 eters can yield complementary information on protein backbone as well as side chain dynamics.

97 water-mediated interaction of TMAO with the protein backbone, as suggested by recent experimental st

98 e of (4,2)D triple-resonance experiments for protein backbone assignment and a Hybrid Backprojection/

99 duce the acquisition time required to obtain protein backbone assignment data.

100 ese observations is scission of the collagen protein backbone at N-alkylamide bonds.

101 fluence exerted by the carbonyl group of the protein backbone at residue 57.

102 oteolytic DNA can be activated to cleave the protein backbone at sites near the DNA.

103 ragmentation was observed to occur along the protein backbone at the C-terminal of aspartic acid resi

104 DAs) from bacterial pathogens, modifying the protein backbone at the Calpha atom of a Pro residue to

105 ately portray the motional properties of the protein backbone at the probe attachment site.

106 in the pattern of anticorrelated motions for protein backbone atoms when the transition state occupie

107 es are found to repeatedly interact with the protein backbone atoms, weakening individual interstrand

108 tron capture dissociation (ECD) for cleaving protein backbone bonds while preserving noncovalent inte

109 to the concurrent cleavages of disulfide and protein backbone bonds.

110 Primary amines as indicator for protein backbone breakage increased in early stages of o

111 fects were not exhibited uniformly along the protein backbone but occurred in a site-specific manner,

112 of the monosaccharides located close to the protein backbone, but failed to detect those further fro

113 ding caused no significant alteration of the protein backbone, but movements of several amino acid si

114 ucture or the sub-nanosecond dynamics of the protein backbone, but resulted in a >100-fold increase i

115 n state, involves little or no change in the protein backbones, but there are conformational rearrang

116 est that long-range dynamical changes in the protein backbone can have a significant effect on the fu

117 Interactions of cations with protein backbone carbonyl oxygens, in particular, play a

118 Knotting has been previously identified in protein backbone chains, for which these mechanical cons

119 The spectra are dominated by amide I/II protein backbone changes.

120 nts, for example, cause site-specific capsid protein backbone cleavage that inhibits viral genome inj

121 rotein aggregates by disulfide exchange, and protein backbone cleavage.

122 The protein backbone cleavages mainly occurred at the amide

123 helps to impede proton permeation due to the protein backbone collective macrodipoles that create an

124 base region of the substrate are made by the protein backbone, complicating the identification of res

125 to provide high-resolution insight into the protein backbone conformation and dynamics in fibrils fo

126 A previously unobserved protein backbone conformation is found within the oxygen

127 Far-UV CD spectra of G473D indicate that the protein backbone conformation is remarkably changed, and

128 sed to measure the temperature-dependence of protein backbone conformational fluctuations in the ther

129 have devised two novel automated methods in protein backbone conformational state prediction: one me

130 a web server designed to sample alternative protein backbone conformations in loop regions.

131 l lattices and essentially indistinguishable protein backbone conformations that are unlikely to be d

132 h alterations in both protein side-chain and protein backbone conformations, and allows for changes i

133 ysteine side chain of the T1 Cu site and the protein backbone couple to the Cu-S vibration.

134 We describe a protein backbone design method for generating a wide ran

135 CE2-RBD interface using a two-stage flexible protein backbone design process that improved affinity f

136 an overall, average sense, DeltaC(p) for the protein backbone, determined from the NMR dynamics measu

137 In natural photosynthesis, the protein backbone directs and positions primary and secon

138 ter molecule makes an H-bond with either the protein backbone donor or acceptor atom.

139 Analysis of protein backbone dynamics based on NMR relaxation reveal

140 To determine whether membrane protein backbone dynamics could be mapped with SDSL, a n

141 spectrometry demonstrates that it increases protein backbone dynamics in domain-domain interfaces at

142 Such inhibition of protein backbone dynamics may be a general mechanism of

143 Local protein backbone dynamics of the camphor hydroxylase cyt

144 e-directed spin labeling of T4 lysozyme, and protein backbone dynamics, as also shown by model peptid

145 riance with the common crank-shaft model for protein backbone dynamics, which predicts the opposite b

146 and allow a more accurate interpretation of protein backbone dynamics.

147 compensated by the counter influence of the protein backbone ( E sq/hq upshift of 260 mV).

148 l shift (ACS) of a particular nucleus in the protein backbone empirically correlates well to its seco

149 The increased flexibility in the protein backbone enhanced the accessibility of the flavi

150 he structural repertoire of alphaS by tuning protein backbone entropy, however entropy of the water r

151 owed by deformation of covalent bonds in the protein backbone, eventually leading to molecular fractu

152 nit is covalently connected to its PD by the protein backbone (far connection) and non-covalently to

153 mers with intradomain PREs only, keeping the protein backbone fixed in the open form.

154 fluence a biocatalyst's function by altering protein backbone flexibility and active site accessibili

155 rtual screening, especially with modeling of protein backbone flexibility, may be broadly useful for

156 Alternatively, dynamic protein backbone fluctuation may occur, enabling Cys532

157 e role played by the coupling between subtle protein backbone fluctuations and the solvation by water

158 mental motion of the ligand was modulated by protein backbone fluctuations.

159 ion experiments, we show that, in the mutant protein, backbone fluctuations are restricted to the pic

160 c temperatures minimally perturb the overall protein backbone fold.

161 used to probe the flow of energy through the protein backbone following excitation of a heater dye, a

162 g bases or side chains coming off the DNA or protein backbone-for example, the bases participating in

163 uggest that the subdiffusional motion of the protein backbone found here may promote rapid folding of

164 oreceptors where signals propagate along the protein backbone from an N-terminal sensor to HAMP.

165 ation and eccentricity, the deviation of the protein backbone from the x-ray crystal structure, the o

166 key observation: the transfer free energy of protein backbone from water to a water/osmolyte solution

167 aspartate inserts a methylene group into the protein backbone, generating a "kink", and may drastical

168 modelling, probably due to the complexity of protein backbone geometry and sequence-structure relatio

169 d dihedral angle restraints to determine the protein backbone geometry with a precision paralleling t

170 A protein backbone has two degrees of conformational freed

171 olar interactions involving fluorine and the protein backbone have been frequently observed in protei

172 erent conformation in which the atoms of the protein backbone have moved by as much as 6.5 A from the

173 The TTS protein backbones have a deduced molecular mass of about

174 Protein backbones have characteristic secondary structur

175 there is a shift in the 1-CPI complex of the protein backbone in helices F and I, repositioning the s

176 with OmpA(+) E. coli, indicating the role of protein backbone in mediating the OmpA binding to HBMEC.

177 to study the role of the amide bonds of the protein backbone in protein structure, function, and fol

178 By explicitly including the protein backbone in the model, we are able to associate

179 hich is likely to involve the motions of the protein backbone in the random-coiled state.

180 The protein backbone in the vicinity of M95 is then free to

181 orientation of the N-H bonds relative to the protein backbone in these rodlike systems.

182 the linkage of oligosaccharides to the BclA protein backbone, in its absence, GlcNAc can serve as a

183 Movements of the protein backbone, in response to inhibitor binding, enla

184 he D. vulgaris flavodoxin, the corresponding protein backbone influence on E sq/hq is significantly s

185 ironments because of the competition between protein backbone intramolecular and protein-water interm

186 ation shell, large structural changes in the protein backbone, involving both solvent accessible and

187 that the direct-binding model of urea to the protein backbone is compatible with available experiment

188 by proteolysis, suggesting that the albumin protein backbone is essential.

189 t the flexibility of certain portions of the protein backbone is increased in the partially structure

190 Results indicate that the protein backbone is most rigid at the dimer interface, m

191 cate that one H-bonding interaction from the protein backbone is needed to reproduce the experimental

192 High flexibility of the protein backbone is observed for the residues in the loo

193 of a strong hydrogen bond from A1(-) to the protein backbone is possible only in the case of A1A(-).

194 eferences of sequentially local regions of a protein backbone is presented.

195 he histidine tether between the heme and the protein backbone is replaced by bound imidazole.

196 These data show that the majority of the protein backbone is rigid on the nanosecond to picosecon

197 The results show that, on average, the protein backbone is slightly more dynamic in the oxidize

198 y restricts conformational entropy along the protein backbone is used to identify putative allosteric

199 gy for photochemical cleavage of peptide and protein backbones is described, which is based on a sele

200 many-fold more rapidly than turnover of the protein backbone itself, consistent with a regulatory ro

201 s a probabilistic model to infer an accurate protein backbone layout.

202 anges to be metastable and reversible at the protein backbone level.

203 recognition that utilizes both alpha-helical protein backbone matching to the (2 -1 0) surface topogr

204 he resulting pyrenyl cation radical with the protein backbone may be responsible for the protein clea

205 lded protein of moderate or larger size, the protein backbone may weave through itself in complex way

206 ration", which is highly atypical in being a protein backbone-modifying activity, rather than a side-

207 listic way to observe microsecond time-scale protein backbone motion both in solution and in the soli

208 cation network within a protein subunit tune protein backbone motions at a distal site to enable allo

209 s, slow protein side-chain motions, and fast protein backbone motions being activated consecutively.

210 A new model for the prediction of protein backbone motions is presented.

211 ated coarse-grained models that describe the protein backbone motions of the CRP/FNR family transcrip

212 rect information on the collective nature of protein backbone motions.

213 druggability estimation to account for light protein backbone movement and protein side-chain flexibi

214 iously, an approach to loop remodeling where protein backbone movement is directed by side-chain rota

215 Through perturbing the protein backbone network by introducing additional nodes

216 The amplitude of protein backbone NH group motions on a time-scale faster

217 via the formation of hydrogen bonds between protein backbone nitrogens and DNA phosphate groups.

218 ant conformational change in the surrounding protein backbone occurs.

219 For example, cleavage of the protein backbone of alpha-hemoglobin is observed selecti

220 GALACTAN-PROTEIN1 [GhPLA1]) that encoded the protein backbone of an AGP in the active fraction.

221 N-glycosylated cell surface molecule with a protein backbone of approximately 21 kDa.

222 is dependent on sialic acids as well as the protein backbone of glycophorin A.

223 ROA indicated that the protein backbone of MUC5B is dominated by unordered conf

224 l enzyme that initiates glycosylation of the protein backbone of PGs, xylosyltransferase-1.

225 e site of covalent attachment of heme to the protein backbone of rabbit CYP4B1; (ii) this I-helix glu

226 receptors by Opa variants is mediated by the protein backbone of the CD66 N-domains.

227 f a novel covalent ester linkage between the protein backbone of the CYP4 family of mammalian P450s a

228 That is, evolution has crafted the protein backbone of the enzyme to direct vibrations in s

229 and two hydrogen-bonding interactions to the protein backbone of the receptor.

230 we used amide-to-ester substitutions in the protein backbone of the selectivity filter to alter ion

231 gnificant difference in the influence of the protein backbone of the so-called 60s loop region betwee

232 The protein backbone of two loops near the active site was r

233 NMR measurements of a large set of protein backbone one-bond dipolar couplings have been ca

234 a resolution that made it possible to trace protein backbones or even to build atomic models.

235 Direct anchoring of quinone to the protein backbone permits secure and adaptable control of

236 eins with amide linkages), when termini of a protein backbone pierce through an auxiliary surface of

237 d by DFT calculations, which reveal that the protein backbone plays a significant role in controlling

238 Templates based on protein backbone positions are more discriminating than

239 served amide modes suggest alteration of the protein backbone (possibly in the vicinity of A(1)) upon

240 barkeri as a model enzyme, we show that the protein backbone provides a strained chelating scaffold

241 terms of conformational distributions of the protein backbone rather than of individual high-resoluti

242 we find a surprisingly high stiffness of the protein backbone, reflected by a persistence length of 1

243 ritical ligand-binding induced movement of a protein backbone region which increases the pocket size

244 A new approach for simultaneous protein backbone resonance assignment and structure dete

245 Using NMR techniques optimized for large proteins, backbone resonance assignments were also deter

246 Chemical-shift changes of protein-backbone resonances and side-chain-amide resonan

247 strained--compared to secondary contacts--by proteins' backbone rigidity.

248 in this regime and to identify signatures of protein backbone secondary (and tertiary) structure.

249 ra show sporadic fragmentation over the full protein backbone sequence of the subunits with a bias to

250 GlcNAc, Glc, Glc and GlcNAc residues to the protein backbone sequentially.

251 GlcNAc, Glc, Glc, and GlcNAc residues to the protein backbone sequentially.

252 major hydrogen bonding interactions with the protein backbone similar to darunavir (1) or inhibitor 2

253 ce changes that remodel the structure of the protein backbone so that the functional groups are prope

254 nal design afforded four hCAII variants with protein backbone-stabilizing and hydrophobic cofactor-em

255 The manipulation of protein backbone structure to control interaction and fu

256 distance constraints that relate directly to protein-backbone structure and flexibility.

257 to ambiguity in relating ESR measurements to protein-backbone structure.

258 free energy sequences were generated for 108 protein backbone structures by using a Monte Carlo optim

259 l (HMM) to connect predicted atoms and build protein backbone structures.

260 catalytic site giving vibrational changes of protein backbone, substrate, amino acid residues, and co

261 000 cm(-1) region that arise from changes of protein backbone, substrate, amino acid side chain, and

262 show that, even in the presence of the polar protein backbone, sufficiently hydrophobic protein surfa

263 predominantly by inhibiting rotations of the protein backbone that are coupled to the global closing

264 tion compounds mediate interactions with the protein backbone that are critical for antagonizing viru

265 olate bridge, reveals the following: (i) The protein backbones (the "SOD rack") remain essentially un

266 cterized and compared the fluctuation of the protein backbone, the volumes in the intracellular pocke

267 accharide side chains are linked to the BclA protein backbone through an N-acetylgalactosamine (GalNA

268 ct evidence of charge transport control in a protein backbone through external mutagenesis and a uniq

269 The remodeling of short fragment(s) of the protein backbone to accommodate new function(s), fine-tu

270 p10-Nhp2 ternary complex and positioning the protein backbone to interact with the H/ACA RNA.

271 t ssDNA-free Pot1pN adopts a similar overall protein backbone topology as ssDNA-bound Pot1pN does.

272 Protein backbone torsion angle prediction provides usefu

273 Predictions of protein backbone torsion angles ( and psi) and secondary

274 Accurate prediction of protein backbone torsion angles will substantially impro

275 omic radii in combination with adjusting the protein backbone torsional energetics.

276 main undergoes conformational changes of the protein backbone upon CO photolysis and that the changes

277 iew of the dynamic changes that occur in the protein backbone upon ligand binding.

278 ernately optimizing the sequence for a fixed protein backbone using rotamer based sequence search, an

279 glycoproteins contain glycans linked to the protein backbone via amino acid residues such as Asn for

280 ircular dichroism), and (3) fragmentation of protein backbones (via sodium dodecyl sulfate-polyacryla

281 -type CID case, extensive cleavage along the protein backbone was noted, which yielded richer sequenc

282 , extensive nonspecific fragmentation of the protein backbone was observed, with 50% sequence coverag

283 A mesostate representation of the protein backbone was then used to extract likely candida

284 Here, we probe these protein backbone-water molecule and side chain-side chai

285 ate spin label behavior when attached to the protein backbone we developed a novel approach that enha

286 ntrast based on the Amide I resonance of the protein backbone, we identify the protein distribution w

287 group in the normal position relative to the protein backbone were active.

288 p in the normal position with respect to the protein backbone were active; the relative activities co

289 The amide-to-ester substitutions in the protein backbone were introduced using protein semisynth

290 ic surfaces, as well as those regions of the protein backbone where fluctuations in different timesca

291 re strongly favored in interactions with the protein backbone, whereas there is little preference for

292 ta-carbon, affording the shortest linkage to protein backbone which is essential for advanced studies

293 re prominent spectroscopic signatures of the protein backbone, which are routinely used in ultraviole

294 ydrophobicity and restricted mobility of the protein backbone, which can explain the nucleation and f

295 structural analysis, because one probes the protein backbone, while the other probes side chains.

296 residue forms a stabilizing contact with the protein backbone, while the second makes a base-specific

297 arisen, viz. that they lack the character of protein backbones whose interactions would limit the fol

298 ractions of amide and carbonyl groups in the protein backbone with the edge of the RNA base.

299 nd II regions involves rearrangements of the protein backbone within these regions, rather than rigid

300 llocate the deuterium distribution along the protein backbone, yielding a backbone-amide protection m