ライフサイエンスコーパス: rotamer

1 reduction in the population of the reactive rotamer.

2 state that is unable to populate a reactive rotamer.

3 eas Trp-41 can be of either the t-105 or t90 rotamer.

4 nitrogen site, whereas Trp-41 adopts the t90 rotamer.

5 component to the major NMR-determined chi(1) rotamer.

6 e represents the major chi(2) = -100 degrees rotamer.

7 fetime component to the chi(1) = 180 degrees rotamer.

8 t the thermodynamic prevalence for the trans-rotamer.

9 sformation of the first kind toward a single rotamer.

10 of three distinct solvent-exposed side-chain rotamers.

11 ermining bond lengths, angles, dihedrals and rotamers.

12 d is poorly packed, with multiple side-chain rotamers.

13 degrees) and GG (omega = 300 +/- 60 degrees) rotamers.

14 hm that approximates side chains as discrete rotamers.

15 f the side chains are modeled in the correct rotamers.

16 ther than a drop in the number of accessible rotamers.

17 through sampling of libraries of side chain rotamers.

18 ctions were the thermodynamically favored sp rotamers.

19 rrelations between psi/theta; and C5-C6 bond rotamers.

20 of nine IR bands of the 1cTc, 1cTt, and 1tTt rotamers.

21 nfiguration and revealed the presence of two rotamers.

22 hain conformations toward physically allowed rotamers.

23 s biosynthesized as a mixture of two proline rotamers.

24 oton- and electron-transfer rates in various rotamers.

25 3)) bond that led to two unequally populated rotamers.

26 ) energy calculations to identify side-chain rotamers.

27 rete, low-energy states, which we call rigid rotamers.

28 grees with an average span of the side-chain rotamers.

29 temporal evolution of the lowest-energy O-H rotamers (1cTc, 1cTt, 1tTt) of oxalic acid for up to 19

30 phosgene-powered unidirectional rotation to rotamer 6 (see Figure 5 in the full article), 7 was desi

31 The tryptophan side chain has three chi(1) rotamers: a major chi(1) = -60 degrees rotamer with a po

32 uces from 2.05 to 0.75 Hz when using the new rotamer analysis instead of the 1.1-A X-ray structure as

33 Rotamer analysis of amino acid side-chain conformations

34 SGPB), the equivalent Phe adopts a different rotamer and is undistorted.

35 he His-37 residue most likely adopts the t60 rotamer and should be monoprotonated at the delta-nitrog

36 ation of the TG (omega = 180 +/- 60 degrees) rotamer and the barriers at omega= 120 and 240 degrees b

37 pt that the relationship between the peptide rotamer and the handedness of the helix is reversed.

38 tion of the Cys 38 side chain between chi(1) rotamers and a previously uncharacterized process on a f

39 This tension between favorable bond rotamers and favorable molecular interactions may be rep

40 Adaptations of active site side-chain rotamers and polypeptide conformations were evident betw

41 The dyad has no rotamers and possesses a fixed distance between ZnPc and

42 ntly high to allow for separation of the two rotamers and to observe their isomerization kinetics.

43 tion adopted by some amino-acid side chains (rotamers) and resolving ordered water molecules, in agre

44 e electrostatic interaction, minimization of rotamers, and possible differences in hydration phenomen

45 s, populations greater than 10% for a second rotamer are observed, and four residues require sampling

46 The relative energies of these rotamers are 0.0 (1cTc), 2.6 (1cTt), and 4.0 (1tTt) kcal

47 quilibrium angles and distribution of chi(1) rotamers are largely determined by the backbone phi/psi

48 nal motion of R1 and the number of preferred rotamers are limited, translating interspin distance mea

49 A model in which favorable bond rotamers are opposed by favorable stacking and pairing i

50 xposure with relatively extended sidechains, rotamers are selected that exhibit maximal packing with

51 d the central C=C bonds in solution, and the rotamers are stabilized by intramolecular hydrogen bondi

52 barriers of interconversion between the two rotamers are strongly influenced by ICT, whereas the rat

53 rom initial Calpha traces and the side-chain rotamers are then refined together with the backbone ato

54 egrees ; chi(2) congruent with +60 degrees ) rotamers as the likely conduction-catalyzing conformatio

55 an atomic-resolution structure with accurate rotamer assignments for many side chains.

56 , indicating that for side chains undergoing rotamer averaging that is fast on the chemical shift tim

57 e and denatured states are used to calculate rotamer-backbone, rotamer-intrinsic, and rotamer-rotamer

58 sequence for a fixed protein backbone using rotamer based sequence search, and optimizing the backbo

59 The rotamer-based approach is tested here for the S1' pocket

60 ere, we take advantage of recent advances in rotamer-based protein design and the large number of str

61 h backbone flexibility, guaranteeing that no rotamers belonging to the flexible-backbone GMEC are pru

62 s and/or the restriction to high probability rotamer bins.

63 ctron transfer also occurs in the 80 degrees rotamer, but the major quenching process is intramolecul

64 ctrostatic model used in the optimization of rotamers by iterative techniques (ORBIT) force-field, wh

65 mization was performed using optimization of rotamers by iterative techniques (ORBIT), a protein desi

66 e so low (<9 kcal/mol) that the syn and anti rotamers cannot be observed as separate signals by 500 M

67 p-279(5.43) is crucial for the Trp-356(6.48) rotamer change toward receptor activation through the ri

68 ry dictates the degree to which the cysteine rotamers change upon metal complexation.

69 e of Conformational Memories showed that the rotamer changes among Cys/Ser/Thr(6.47), Trp(6.48), and

70 facilitate sequence changes equally well as rotamer changes.

71 r populations (including those of side-chain rotamers), changes in NMR parameters [chemical shifts, J

72 mma1 by 1.71 ppm, while the next populated m rotamer (chi(1) = -60 degrees) shows the opposite trend

73 2.89 ppm is found for the most populated mt rotamer (chi(1) = -60 degrees, chi(2) = 180 degrees), wh

74 r alpha-helical Val residues, the dominant t rotamer (chi(1) = 180 degrees) has more downfield Cgamma

75 0.73 ppm is found for the next populated tp rotamer (chi(1) = 180 degrees, chi(2) = 60 degrees).

76 l energy function, DEE identifies and prunes rotamer choices that are provably not part of the Global

77 This secondary amide displays 16-19% E-rotamer (cis) around the carbonyl-nitrogen bond in apola

78 tes are such that two of them "fall" in each rotamer class.

79 was generated using an exhaustive search of rotamer combinations on a template crystal structure.

80 ese rules consistently reduces the number of rotamer combinations that need to be searched to trivial

81 gn involves the searching of vast numbers of rotamer combinations.

82 rough specific interactions in its different rotamer configurations.

83 in and by adoption of alternative side chain rotamer conformations of ligand-proximal amino acids.

84 ues (Phe9, Tyr15, and Phe19) adopt different rotamer conformations or become disordered in the enzyme

85 dges more commonly, utilize a wider range of rotamer conformations, and are more dynamic than Glu-Lys

86 in CDR H3, Trp100a and Asp100b, which change rotamer conformations.

87 This analysis suggests that preferred rotamers contribute directly to specificity in protein c

88 Such rotamer-dependencies are not limited to specific type or

89 In this potential, named "rotamer-dependent atomic statistical potential" (ROTAS),

90 by active site residues that adopt alternate rotamers depending on the ligand bound.

91 influenced by ICT, whereas the ratio of such rotamers depends primarily on the character of the hydro

92 The ratio of the two rotamers depends strongly on the character of the substi

93 Residue and rotamer design choices are driven by a globally converge

94 Mixtures of two rotamers differing in the orientation of the nitroso gro

95 ofactor and substrate, respectively, exhibit rotamer disorder in the ternary folate:NADP+ complex.

96 Thr, which in an alpha-helix has a different rotamer distribution from Cys and Ser, produced a consti

97 A rotamer distribution model based on the crystal structur

98 is shown to significantly impact side-chain rotamer distribution.

99 s the resolution of the X-ray data improves (rotamer distributions from 3.4 and 2.3 A X-ray structure

100 sented for determining Val side-chain chi(1) rotamer distributions in proteins based exclusively on m

101 Rotamer distributions were influenced by whether the res

102 es that could not be explained by spin-label rotamer diversity.

103 Remarkably, these rotamers do not detectably interconvert at temperatures

104 rsor-dependent product ratios based on amide rotamer effects are ruled out.

105 heuristics such as patterning of residues or rotamers, EGAD has a minimalist philosophy; it uses very

106 tural variations on the cis-trans amide bond rotamer equilibria in a selection of monomer model syste

107 The quantitatively defined side chain rotamer equilibria obtained from our study set new bench

108 We show that this process is related to chi1 rotamer exchange of Y101 and that mutation of this aroma

109 ll iMinDEE, that makes the use of continuous rotamers feasible in larger systems.

110 elical propensity and a gauche(-) side-chain rotamer for one of the valine residues.

111 mechanics calculations suggested two chi(2) rotamers for cis-W3 in solution, -100 degrees and 80 deg

112 ed as 1/n where n is the number of potential rotamers for each residue type.

113 uilibrium angles and distributions of chi(1) rotamers for mobile surface side chains of the small, 63

114 mbrane environment considerably perturbs the rotamer frequencies compared to soluble proteins.

115 apidly equilibrating small molecules such as rotamers from nonequilibrating diastereomers.

116 e equilibrium anti and gauche percentages of rotamers from the averaged NMR-time scale couplings.

117 ic criterion for excluding rare, high-energy rotamers from the library.

118 tilized to effectively eliminate trans-amide rotamers from the peptoid backbone, yielding the most co

119 -chain flexibility (which we call continuous rotamers) greatly improves protein flexibility modeling.

120 In one peptide the chi(1) = 180 degrees rotamer has a 0.5-ns lifetime.

121 ime represents the minor chi(2) = 80 degrees rotamer having the ammonium group closer to C4 of the in

122 with the presence of the chi(2) = 80 degrees rotamer in solution.

123 We measured the frequency of side-chain rotamers in 14 alpha-helical and 16 beta-barrel membrane

124 The existence of rotamers in a solution of analyte complicates (1)H NMR a

125 ation, resulting in the absence of the trans rotamers in CDCl(3).

126 from the use of fixed backbones and discrete rotamers in protein design calculations, and describes t

127 The relative populations of two rotamers in the hydrazone of 2H-perfluoro-2-methyl-3-pen

128 Several of the side-chain rotamers in the predicted structure of Core-10 differ fr

129 Rotamers in the unit cell of a single crystal of I(t)BuP

130 ups, with the beta-anomer enriched in the gt rotamer, in agreement with recent multi-J redundant coup

131 differences of the calculated ECD of its two rotamers indicate that the rotational restrictions signi

132 At the same time, transitions between rotamers induced by interactions across the interface or

133 te mimics for the enzyme-catalyzed cis-trans rotamer interconversion of amides involved in peptide an

134 design of compounds with increased rates of rotamer interconversion.

135 n barriers in these azetidines indicate that rotamer interconversions do not occur at the temperature

136 ates are used to calculate rotamer-backbone, rotamer-intrinsic, and rotamer-rotamer conformational en

137 The key role of such rotamer is confirmed by newly synthesized derivatives wh

138 major quenching process in the -100 degrees rotamer is electron transfer from the excited indole to

139 One of these rotamers is rarely observed within crystal structures of

140 at is coupled to dynamic two-state sidechain rotamer jumps, as evidenced by alternate conformations i

141 In alphaLP, the only allowed rotamer leads to the deformation of Phe228 due to steric

142 Splitting the search space at the rotamer level instead of at the amino acid level further

143 Splitting the search space at the rotamer level instead of at the amino acid level further

144 SIDEpro programs and Web server, rotamer libraries and data are available through the SCR

145 structural data to allow parametrization of rotamer libraries and energies.

146 use of molecular mechanics for constructing rotamer libraries for non-natural foldamer backbones.

147 ures active-site geometries than traditional rotamer libraries in the systems tested.

148 We have incorporated our peptoid rotamer libraries into ROSETTA, a molecular design packa

149 luding side chain conformations derived from rotamer libraries, are combined with random sampling of

150 A spin label rotamer library based on a molecular dynamics simulation

151 We evaluated two rotamer library development methods that employ quantum

152 states to provide a backbone-dependent (BBD) rotamer library for a set of 54 different peptoid side c

153 pled from a Protein Data Bank-based backbone rotamer library generated by either ignoring or includin

154 The MD simulations and an analysis of a rotamer library suggest that dynamic decoupling of the t

155 rmational parameters, especially the type of rotamer library used, significantly affect the ability o

156 ze the intracellular peptide conformation, a rotamer library was set up to take the conformational fl

157 fixed, side-chain conformations come from a rotamer library, and a pairwise energy function is optim

158 By using a fixed backbone template, a rotamer library, and a potential energy function, DEE id

159 determines alternative conformations using a rotamer library.

160 their 5'-end tetrads, and multiple stacking rotamers may be present due to a high symmetry at the st

161 rotamers was never better than a continuous-rotamer model and almost always resulted in higher energ

162 eover, the sequences found by the continuous-rotamer model are more similar to the native sequences.

163 designs the sequence found by the continuous-rotamer model is different and has a lower energy than t

164 xylic acid, cis-W3, was designed to test the rotamer model of tryptophan photophysics.

165 s in 69 protein-core redesigns using a rigid-rotamer model versus a continuous-rotamer model.

166 lower energy than the one found by the rigid-rotamer model.

167 ng a rigid-rotamer model versus a continuous-rotamer model.

168 not a practical alternative to a continuous-rotamer model: at computationally feasible resolutions,

169 ed water molecules calculated using solvated rotamer models met with mixed success; however, we were

170 observe that the toggling of the W265(6.48) rotamer modulates the bend angle of TM6 around the conse

171 conformations, while guaranteeing that only rotamers not belonging to the GMEC are pruned.

172 199, which prevents Phe228 from adopting the rotamer observed in many other chymotrypsin family membe

173 accuracy of the measured DEER distance, the rotamers observed in the crystal structure of the domain

174 rature experiments is formed by the minority rotamer of (R)-NEA and pro-S MTFP.

175 sp orbital of the carbene carbon in the s-Z rotamer of 13 and the antibonding sigma orbital between

176 interaction that is not observed in the s-E rotamer of 13.

177 that of AFB(1)-N7-Gua, and (ii) one proposed rotamer of AFB(1)-FAPY is a block to replication, even w

178 The reactive rotamer of the nucleophile determines which neighboring

179 rizontal lineN core but also in favoring one rotamer of the resulting Ni(III)-imide, by locking the p

180 ith the relative energy of the corresponding rotamer of the uncomplexed reactant aldehyde, indicating

181 In five peptides the chi(1) = -60 degrees rotamer of tryptophan has lifetimes of 2.7-5.5 ns, depen

182 mation, analogous to the chi(1) = 60 degrees rotamer of tryptophan.

183 Two rotamers of 3a were identified and characterized.

184 d B3LYP hybrid DFT calculations performed on rotamers of 4 and 5 and related complexes, as well as Cp

185 scenarios is required: CH-I for the NN-trans-rotamers of 7-9 to undergo C-X cleavage or NN-isomerizat

186 mer with a population of 0.67, and two minor rotamers of equal population.

187 The relative energies of the rotamers of the carbanions derived from N-methylformamid

188 The barrier of interconversion between two rotamers of the compounds with two possible IMHBs is det

189 ntally measured distance data, and the known rotamers of the nitroxide side chain.

190 of site-directed spin labeling by resolving rotamers of the nitroxide spin-label side chain in a var

191 lculation of the energy profile of different rotamers of the substrate revealed that presence of a su

192 ple support to the notion that the different rotamers of these glutamates partition into two classes

193 ra, the electronic absorption spectra of the rotamers of triplet 3-thienylcarbene (13) are indistingu

194 ees, analogous to the chi(2) = +/-90 degrees rotamers of tryptophan.

195 Through minor adjustment of the rotamers of two amino acid side chains for this latter s

196 d on exhaustive conformational searching and rotamer optimization were in excellent agreement with ex

197 n simulated annealing molecular dynamics and rotamer optimization, and is applicable to the docking o

198 Each rotamer-oxyanion hole combination limits the location of

199 n the various target structures by using the rotamer packing routine and composite energy function of

200 nal space of the salt-bridging Glu(-)/Arg(+) rotamer pairs compared to Asp(-)/Arg(+) and Glu(-)/Lys(+

201 This t90 rotamer points the Nepsilon1-Cepsilon2-Czeta2 side of th

202 Either a shift in the rotamer population, or a loss of the tryptophan side cha

203 lished between O(axis)(2) and the side chain rotamer populations (rho).

204 rved in 1-4 were analyzed to yield preferred rotamer populations about omega and theta;.

205 secondary acetamides in which significant E-rotamer populations are rare due to steric contacts betw

206 Similar rotamer populations can be derived from side-chain dipol

207 Rotamer populations evaluated from the omega(C-C-C-O), t

208 e new Karplus curves permit determination of rotamer populations for the chi(1) torsion angles.

209 xes have been measured, together with chi(1) rotamer populations for threonine, isoleucine, and valin

210 Conversion of these rotamer populations into generalized order parameters, S

211 tions with the helical backbone perturbs the rotamer populations of Ser and His.

212 The solution structure and side-chain chi(1) rotamer populations of the peptides were determined by o

213 The -, psi-angles and chi(1) rotamer populations of tryptophan vary with position in

214 of the lifetime components match the chi(2) rotamer populations predicted by molecular mechanics.

215 odulate the EPR spectrum by modulating label rotamer populations.

216 rs, where the residues adopted favoured chi1 rotamer positions that allowed side-chain interactions t

217 Rather than changing to new rotamers predicted by the design process, side-chains te

218 backbone movement is directed by side-chain rotamers predicted to form interactions previously obser

219 e found statistically significant changes in rotamer preferences depending on the residue environment

220 to affect charge selectivity by changing the rotamer preferences of the ionized side chains in the fi

221 te an N to C-terminal composition bias, that rotamer preferences of TM side-chains are position-depen

222 ertion depth in the membrane, its side-chain rotamer preferences, and stabilizes the C-terminal helic

223 ers was altered considerably to favor the gt rotamer, presumably because of attraction between the 2-

224 residue 28; these are in good agreement with rotamers previously reported for helical structures.

225 Based on these parameters, de novo rotamer probabilities for secondary structures of peptid

226 lecular mechanics (MM) for the prediction of rotamer probability distributions in the crystal structu

227 A specific tryptophan side chain rotamer promotes the functional dynamic allostery by ind

228 inDEE, a state-of-the-art DEE criterion, for rotamer pruning to further improve SCPR with the conside

229 iction in the experimental dependence of the rotamer ratio on the Hammett constants for the arylamino

230 first time integrates residue reduction and rotamer reduction techniques previously developed for th

231 ddress this problem, we developed FDPB_MF, a rotamer repacking method that exhaustively samples side

232 g(+) and t rotameric angles, even though no rotamer restraint is used when deriving the sampled angl

233 The rotamer-restricted model we propose is supported further

234 ppended arsenic chelate: the fluorescence is rotamer-restricted.

235 elucidate the probabilities of all possible rotamer-rotamer combinations in a minimum Helmholtz free

236 ate rotamer-backbone, rotamer-intrinsic, and rotamer-rotamer conformational energies.

237 rved for the previously identified g+ and g- rotamer sampling by Tyr-106.

238 ight-chain variable domains using side-chain rotamer sampling in the interface and molecular-mechanic

239 t of protonation equilibria, high-resolution rotamer sampling, a final local energy minimization step

240 s in both three-dimensional space and in the rotamer search space to produce small, fast jobs that ar

241 space is split into overlapping regions and rotamer search spaces, accelerates the design process wh

242 cy in protein design requires a fine-grained rotamer search, multiple backbone conformations, and a d

243 Guided by the motif rotamer searches, we made improvements to the underlying

244 on states, heme redox states, and side chain rotamers simultaneously.

245 en conformation, which involves an alternate rotamer state of one of the gate residues, presents only

246 the active-site geometry and determines the rotamer state of the oxyanion hole-forming Asn295, and t

247 ters (O(axis)(2)), populations of side chain rotamer states (rho), conformational entropies (S(conf))

248 oximation that the decrease in the number of rotamer states available to the side chains forms the ma

249 A hierarchical grading of rotamer states based on the conformational free energy b

250 n shuffling model, in which exchange between rotamer states of a large aromatic ring in the middle of

251 uplings are proposed to arise from two C1-C2 rotamer states of the product radical that are present i

252 ion was due to decreased fluctuations within rotamer states of the side chains.

253 e free energy barriers separating side chain rotamer states range from 0.3 to 12 kcal/mol in all prot

254 d hydrogen binding may result in alternative rotamer structures of the diiron site in a single (Hred)

255 e broken in the activated state via a chi(1) rotamer switch (F3.36(201) trans, W6.48(357) g+) --> (F3

256 f the NPXXY motif, is likely to act as a new rotamer switch implicated in the activation of the recep

257 rimental support for the association of this rotamer switch with receptor activation.

258 n agonist binding, consistent with proposed "rotamer switch" models.

259 ent into structural changes at the conserved rotamer switches, thus leading to receptor activation.

260 observed to react 100 times faster than its rotamer that can employ only two hydrogen bonds.

261 liminate from consideration polar amino acid rotamers that do not form a minimum number of hydrogen b

262 The calculations identify those As-aryl rotamers that support fluorescence and those that do not

263 (DEE)-based criterion for pruning candidate rotamers that, in contrast to previous DEE algorithms, i

264 nted for possible presence of two rhodopsin "rotamers" that fit within the binding cavity.

265 nes is great enough to allow their sp and ap rotamers to be detected coexisting in solution, although

266 or NN-isomerization and CH-II for the NN-cis-rotamers to undergo C-X cleavage, C-N cleavage, or NN-is

267 dues in the sixth transmembrane segment by a rotamer toggle switch mechanism.

268 he DRY motif) and E247(6.30) on TM6, and the rotamer toggle switch on W265(6.48) on TM6.

269 he DRY motif) and E268(6.30) on TM6, and the rotamer toggle switch on W286(6.48) on TM6.

270 : Leu-41 and Ile-115, the former acting as a rotamer toggle switch to accommodate PTH/PTHrP sequence

271 thought to involve two molecular switches, a rotamer toggle switch within the transmembrane domain an

272 dopamine break the ionic lock and engage the rotamer toggle switch, whereas salbutamol, a noncatechol

273 d the weak agonist catechol only engages the rotamer toggle switch.

274 (6.52) are highly correlated, representing a rotamer "toggle switch" that may modulate the TM6 Pro-ki

275 The rotamer toggling is facilitated by the formation of a wa

276 Form(+) through water molecules, and 3) the rotamer transition is mediated by water traffic into the

277 s 15 are interpreted to result from a chi(1) rotamer transition of Cys 14 that converts the Cys 14-Cy

278 structures revealed a previously undescribed rotamer transition of the hydroxymethyl side chain of th

279 We find that peptoids can be described by a "rotamer" treatment, similar to that established for prot

280 in the number of conformations available per rotamer upon folding (OmegaU/OmegaN).

281 an expected drop in the number of accessible rotamers upon binding.

282 calculated for the six preferred side chain rotamers using Marcus theory.

283 nally feasible resolutions, using more rigid rotamers was never better than a continuous-rotamer mode

284 de of chi1 angle fluctuations within a given rotamer well is ca. 20 degrees .

285 The predicted Val rotamers were further verified by dipolar correlation ex

286 f decay of s-cis conformers to their s-trans rotamers were obtained in the solid-state by warming up

287 37 residue can be of either the t-160 or t60 rotamer, whereas Trp-41 can be of either the t-105 or t9

288 that the two arginines adopt new side-chain rotamers, whereas a 25-residue subdomain, forming a heli

289 ounding a conserved Phe side-chain dictate a rotamer which results in a ~6 degrees distortion along t

290 e chain could be characterized into discrete rotamers, which may reflect the observation of alternati

291 roduced the higher energy nonenantiomeric ap rotamers, which rapidly rotated into the sp products tha

292 are dependent on the ratio of two different rotamers, whose interconversion is poorly understood.

293 hi(1) rotamers: a major chi(1) = -60 degrees rotamer with a population of 0.67, and two minor rotamer

294 NMR with fluorescence data reveals that the rotamer with N...H-O bonding is predominant in the solut

295 clic N4 site, resulting in the anti-cytosine rotamer with respect to site N3 in its metal-stabilized

296 ough a HBO derivative typically exhibits two rotamers with O...H-O (e.g., 1a) and N...H-O bonding (e.

297 This is accomplished by including only those rotamers with probability greater than a given threshold

298 As a result, two rotamers with reversed orientation of the 5-nitroso grou

299 specific, staggered conformations, known as rotamers within protein structures.

300 emingly easy solution of sampling more rigid rotamers within the continuous region is not a practical