ライフサイエンスコーパス: rotamer

1 ed on the rotational isomers (hence the word rotamer).

2 reduction in the population of the reactive rotamer.

3 state that is unable to populate a reactive rotamer.

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

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

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

7 t the thermodynamic prevalence for the trans-rotamer.

8 sformation of the first kind toward a single rotamer.

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

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

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

12 ermining bond lengths, angles, dihedrals and rotamers.

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

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

15 hm that approximates side chains as discrete rotamers.

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

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

18 through sampling of libraries of side chain rotamers.

19 ctions were the thermodynamically favored sp rotamers.

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

21 nfiguration and revealed the presence of two rotamers.

22 hain conformations toward physically allowed rotamers.

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

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

25 ) energy calculations to identify side-chain rotamers.

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

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

28 would like to encourage researchers to apply rotamer analyses beyond their traditional use.

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

30 Rotamer analysis of amino acid side-chain conformations

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

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

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

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

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

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

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

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

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

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

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

42 ithout manual intervention or any additional rotamer- and backbone-specific restraints.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

57 the field of computational protein design as rotamer-based sequence optimization protocols have enabl

58 mation-dependent manner, with some glutamate rotamers being much more effective at conferring selecti

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

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

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

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

63 facilitate sequence changes equally well as rotamer changes.

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

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

66 2.89 ppm is found for the most populated mt rotamer (chi(1) = -60 degrees, chi(2) = 180 degrees), wh

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

68 0.73 ppm is found for the next populated tp rotamer (chi(1) = 180 degrees, chi(2) = 60 degrees).

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

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

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

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

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

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

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

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

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

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

79 rm several muoniated radicals with different rotamer conformations; b) bulky Dur-substituted phosphas

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

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

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

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

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

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

86 Given by chi torsional angles, rotamers describe the side-chain conformations of amino

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

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

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

90 A rotamer distribution model based on the crystal structur

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

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

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

94 Rotamer distributions were influenced by whether the res

95 rom, respectively, dihedral angle values and rotamer distributions.

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

97 we used simple computational tools to study rotamer dynamics (RD) in MD simulations.

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

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

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

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

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

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

104 somer is rationalized by invoking a reactive rotamer featuring two ammonium-boronate hydrogen bonds,

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

123 These proved to be two stable rotamers, in which the carbonyl group of the tert-butyl

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

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

126 In addition, we apply pools of side chain rotamers interacting with the target ligand to augment R

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

128 design of compounds with increased rates of rotamer interconversion.

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

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

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

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

133 Reducing the side-chain rotamer isomerization barriers in the all-atom force fie

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

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

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

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

138 Rotamer libraries are routinely used in structure modeli

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

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

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

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

143 Constructed rotamer libraries, based on either protein crystal struc

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

145 We evaluated two rotamer library development methods that employ quantum

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

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

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

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

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

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

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

153 determines alternative conformations using a rotamer library.

154 also done in R according to the penultimate rotamer library.

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

156 beta; L, left) of the XDF motif and the Phe rotamer (minus, plus, trans).

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

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

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

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

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

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

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

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

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

166 rances of the substituents on various linker rotamers, MOFs with various topologies can be obtained.

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

168 199, which prevents Phe228 from adopting the rotamer observed in many other chymotrypsin family membe

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

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

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

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

173 We have found that the rotamer of His is not influenced by the environmental pH

174 The reactive rotamer of the nucleophile determines which neighboring

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

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

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

178 Two rotamers of 3a were identified and characterized.

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

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

181 otamers were akin to the s- trans and s- cis rotamers of alpha,beta-unsaturated carbonyl compounds.

182 EPR spectroscopic evidence for two rotamers of the analogous methyl ester containing NHC-ox

183 Indeed, whereas some rotamers of the buried arginines at position 0' conferre

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

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

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

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

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

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

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

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

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

193 Each rotamer-oxyanion hole combination limits the location of

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

209 odulate the EPR spectrum by modulating label rotamer populations.

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

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

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

213 a short model peptide to determine the amide rotamer preference N-terminal to the cyclic residue.

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

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

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

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

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

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

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

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

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

223 -delta-azaproline exhibit strong trans amide rotamer propensities irrespective of ring conformation,

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

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

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

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

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

229 The rotamer-restricted model we propose is supported further

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

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

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

233 plications such as protein folding, study of rotamer-rotamer relationship in protein-protein interact

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

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

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

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

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

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

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

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

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

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

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

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

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

247 By examining the accuracy of side-chain rotamer states in subensembles of structures that have v

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

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

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

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

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

253 correlation between secondary structures and rotamers, study of flexibility of side chains in binding

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

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

256 ivity of HisKA HKs based on the pH-dependent rotamer switch of the phosphorylatable His.

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

274 amics studies, are the tools for classifying rotamers (torsional angles) in a way that reflect their

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

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

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

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

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

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

281 ore the DFGmotif, and the DFG-Phe side-chain rotamer, utilizing a density-based clustering algorithm.

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

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

284 These rotamers were akin to the s- trans and s- cis rotamers o

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

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

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

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

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

298 We identified a single alternative rotamer within the recognition helix itself as an import

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