ライフサイエンスコーパス: sidechain

1 ctivities owing to repositioning of the K145 sidechain.

2 which in some cases involves a phenylalanine sidechain.

3 N-termini, formed as a thioester on the C143 sidechain.

4 y modify each naturally occurring amino acid sidechain.

5 by relocating to replace the missing Arg85' sidechain.

6 (<25), indicating only partial burial of the sidechains.

7 ionalized with sequence-defined biomolecular sidechains.

8 h the formation of hydrogen bonds with polar sidechains.

9 sion between the negatively charged arginine sidechains.

10 selective cleavage of modifications at other sidechains.

11 f native gammaCH(2) to gammaCF(2) in protein sidechains.

12 g phosphorylated, methylated, and acetylated sidechains.

13 hydrogen bonds, and loosely stacked aromatic sidechains.

14 er-subunit sites near betaM286 and alphaL232 sidechains.

15 nificant modifications of rhamnogalacturonan sidechains.

16 nvironments precisely created by the ordered sidechains.

17 e-helical staircase coordinate the substrate sidechains.

18 odification of peptides featuring nonnatural sidechains.

19 charide with a rhamnose backbone and glucose sidechains.

20 anonical amino acids (ncAAs) bearing diverse sidechains.

21 ite with unambiguous density for interacting sidechains.

22 enzyme-triggered cleavage of coronal peptide sidechains.

23 substituted by aromatic, non-polar, or polar sidechains.

24 ches proteins for networks of proton-binding sidechains.

25 ate in interactions that are unique to polar sidechains?

26 The ion is coordinated by three acidic sidechains, a water molecule, a serine and a main-chain

27 otein folding is directed by the sequence of sidechains along the polypeptide backbone, but despite t

28 leation of hinge helices creates TS, burying sidechain amide nitrogens.

29 on but that lysine's electronically isolated sidechain amine likely provides an evolutionary advantag

30 e addition of two DOPAL molecules to the Lys sidechain amine through their aldehyde moieties and the

31 critical catalytic roles in provision of the sidechain amino groups of tryptophan, phenylalanine, and

32 ion allows the installation of difluorinated sidechain analogs of proteinogenic amino acids, in both

33 with the size of the substituted amino acid sidechain and affects a variety of modified nucleotide s

34 e suggestive that steric effects of the D254 sidechain and the N260-linked oligosaccharide may contri

35 is second sodium site involves two threonine sidechains and a backbone carbonyl from helix 3, a pheny

36 estimates of the distance between beta3M286C sidechains and anesthetics (etomidate and propofol) boun

37 istant sites around the IDP chains, with Arg sidechains and backbone carbonyls the favored partners o

38 ubstrates with catalytic or cofactor-binding sidechains and catalyse reactions such as oxidation and

39 ilibria-H-bond self-assembed stacking of the sidechains and dynamic covalent polymerization of the ba

40 Polyglycine, a poly secondary-amide, has no sidechains and is a useful model system for generic poly

41 odeling whole proteins and their parts (e.g. sidechains and loops) as well as interactions between pr

42 ligible contribution to solvation by protein sidechains and observed that the hydration dynamics at t

43 ungin rigidifies beta-1,6-glucans and mannan sidechains and reduces water permeability during beta-1,

44 s tend to form "water bridges" between their sidechains and TiO2 surface, thus displaying an indirect

45 diverse sidechain-to-backbone, sidechain-to-sidechain, and sidechain-to-water interactions.

46 peptide, indicating that it is the arginine sidechains, and not their contribution to the helical st

47 The W74 sidechains are flexible, sampling conformations that ran

48 In peptide natural products, amino acid sidechains are frequently used as sites of modification

49 ture of the M63F mutant, the Phe37 and Phe63 sidechains are in contact, plausibly forming an edge-fac

50 Glycol sidechains are often used to enhance the performance of

51 transition state analog shows that catalytic sidechains are properly aligned for catalysis.

52 The sidechains are recognised because each one forces the co

53 the range of 0.35-0.44, suggesting that the sidechains are relatively collapsed in comparison to the

54 ts form a four-layered beta-sheet core whose sidechains are stabilized by numerous polar and hydropho

55 to protonation of solvent-exposed histidine sidechains as the pH is reduced from a near neutral pH o

56 increasing the solvent exposure of the Lys22 sidechain, as indicated by molecular dynamics simulation

57 eriments focused on threonine and isoleucine sidechains, as well as magic angle spinning solid-state

58 crystal contacts reduce the dynamics of the sidechain at position 12 by stabilizing the Switch I reg

59 gramming spatial and temporal projections of sidechains at the segmental level can be effective in re

60 rs many possibilities for backbone-backbone, sidechain-backbone, and sidechain-sidechain interactions

61 exocyclic fluoromethylene pushes the Met184 sidechain backward, and the resultant enlarged hydrophob

62 tic sums of individual ANS(-)-polyamino acid sidechain binding enthalpies (polyhistidine, polyarginin

63 rains to sample the full range of amino acid sidechain biochemical properties, including acidic, basi

64 Thus, reducing sidechain bulkiness and expanding surface loops results

65 lpha subunits contain networks of pH-sensing sidechains buried between their Ras and helical domains.

66 L-Arg residues attached to the B-carboxylate sidechains by isopeptide bonds.

67 carbon-centered C* radicals that install the sidechain can be synthesized in two to six steps from co

68 develop a rapid method to evaluate whether a sidechain can form a hydrogen-bond.

69 Here we show that different sidechains can be ordered over a metal-organic framework

70 Second, correlations between amino acid sidechains can convey allosteric signals even in the abs

71 nticipated that (13)C shift data for protein sidechains can provide a useful basis for the analysis o

72 ests the involvement of carboxylate ion, and sidechain carbon-oxygen of aspartate/glutamate and serin

73 conformation in which the first two residue sidechains complement hydrophobic residues around the ac

74 formed from three rhamnose units and a short sidechain composed of two glucose units.

75 he other opposing the attendant reduction in sidechain conformational entropy on helix and turn forma

76 design have been much more limited than for sidechain conformational search.

77 ndMPNN generates not only sequences but also sidechain conformations to allow detailed evaluation of

78 he26 indicate that both residues exhibit two sidechain conformations, which coexist within each chann

79 an extremely large number of combinations of sidechain conformers and backbone fragments to locally e

80 phoglycolipid 5 to form the (C25) moenocinyl-sidechain-containing lipid 7.

81 For the trisaccharide sidechain-containing oligosaccharide as found in pea XG,

82 VP39's R107 sidechain contributes to specificity at the downstream r

83 cted, in the range that is unaffected by its sidechain contributions.

84 A series of polyethylene glycol (PEG)-based sidechain copolymers were synthesized to form sidechain

85 ided the core of beraprost to which both its sidechains could be appended through a 1,4-conjugate add

86 on of model peptides containing nucleophilic sidechains (Cys, His, and Lys) and selected proteins (bo

87 duced via nucleophilic attacks by the lysine sidechains degradation.

88 tural integrity of ectodomain where aromatic sidechain deletion increases thermal instability, interf

89 4d with a carboxyl sidechain demonstrated the highest incorporation.

90 Some sidechain densities are clearly resolved and show the su

91 t distribution of the observed mainchain and sidechain dihedral angles (< ,psi,chi1,chi2,...>) of any

92 se angular bins, and cluster combinations of sidechain dihedral angles (<chi1,chi2,...>) as a functio

93 developed two scores of correlation between sidechain dihedral angles.

94 ithms, which model continuous flexibility in sidechain dihedrals, to model continuous, appropriately

95 urenine attracts more waters and other polar sidechains due to its additional amino and carbonyl grou

96 labelling experiments, and uses backbone and sidechain dynamics as well as secondary structure propen

97 et there is no experimental evidence for how sidechain dynamics control allosteric transitions betwee

98 ctural changes in A2AR, and that patterns of sidechain dynamics substantially differ between agonist

99 ng proteins through modulation of fast ps-ns sidechain dynamics.

100 Inward displacement of TM2 might alter the sidechain environment of control cable residues at the m

101 Their imidazole sidechains experience simple, uncoupled Henderson-Hassel

102 t are comprised exclusively of four cysteine sidechains fall into three clusters, representing bindin

103 ing experiments were initially analyzed with sidechain FEP simulations, performed on alternate bindin

104 mong binding site residues permits increased sidechain flexibility.

105 1,4-conjugate addition process (lower omega-sidechain), followed by de novo construction of berapros

106 Completion of the sidechains, followed by global deprotection, resulted in

107 stages of ATP hydrolysis show that the K854 sidechain forms polar bonds that constrain the conformat

108 act as a signaling switch by movement of its sidechain from a hydrophilic pocket in the TMH bundle to

109 sing numbers of oligoethyleneglycol (OEG; g) sidechains from 1 g to 3 g, affording OMIECs 1gY, 2gY, a

110 Significantly, HS sidechains from a neuroepithelial perlecan variant that

111 Our results demonstrate that different HS sidechains from the same core protein differentially aff

112 frameworks that recognize and order multiple sidechain functionality by conformational control offers

113 1,2- and 1,3-linked rhamnose units, and the sidechain has a terminal glucose linked to a 1,6-glucose

114 eptide conformations via linkage of aromatic sidechains has been developed.

115 ntacts: a turn-hydrogen bond, a mainchain-to-sidechain hydrogen bond, and an end-to-end hydrophobic c

116 NHBn in order to probe the interplay between sidechain hydrogen bonding and backbone conformational p

117 condary structure, solvent accessibility and sidechain hydrogen bonds, XSuLT annotates each amino aci

118 Thus, sidechain hydrogen-bonding potential is satisfied in a m

119 P/WARP--in terms of main chain completeness, sidechain identification and crystallographic R factor.

120 Using this example, we show that sidechain immobilization occurs downstream of the major

121 433) and that substitution with the Val(433) sidechain imparts a broader, more DnaK-like, substrate r

122 Reducing the volume of the sidechain in both rings leads to a partially conductive,

123 The oscillation of the R262 sidechain in CaiT indicates how a positive charge trigge

124 ics bind within 1 angstrom of the alpha1L232 sidechain in functional receptors, consistent with cryog

125 yze the removal of methyl groups from lysine sidechain in histones to modulate gene transcription.

126 elix suggest an important role for its bulky sidechain in the allosteric mechanism; we show that the

127 The approach comprises identifying hotspot sidechains in a functional protein-protein interaction a

128 ansfer of arginine to aspartate or glutamate sidechains in a protein.

129 Long sidechains in S2 are "bent" and co-locate with the homoa

130 The only charged sidechains in the core are those of D23 and K28, which f

131 oitin sulfate proteoglycan glycosaminoglycan sidechains in the periphery of the lesion.

132 ub84B/D are glutamylated at several glutamyl sidechains in various combinations.

133 Measured interhelical distances between W23 sidechains indicate that the pore constriction at W23 in

134 that constitutes the dimer interface; their sidechains interact with the Pro767 of the other monomer

135 contrast, compound 7 disrupts the catalytic sidechain interaction network of Sco GlgE1-V279S via ste

136 unique sequences that directly decrease the sidechain interactions around the B sheet and indirectly

137 dity on the structure than sequence-specific sidechain interactions between sheets, and that electros

138 ckbone, but despite this the developement of sidechain interactions during folding is not well unders

139 and a weaker dependence of such exposure on sidechain interactions than other trinucleotides.

140 gy by site-selectively installing an N(e) Ac sidechain into recombinantly expressed ubiquitin (Ub).

141 ite-selective installation of N(e) -modified sidechains into peptides and proteins of interest.

142 for the behavior of a protein when a mutant sidechain is abruptly changed to the wild-type residue a

143 en conformational state; the heme a farnesyl sidechain is H-bonded to S382, and loop-I-II adopts a di

144 The apolar outer barrel surface with large sidechains is immersed in the lipid bilayer, while the i

145 se interactions, which are typically through sidechains, is an important need in protein design.

146 While sidechain length and/or branching had no effect on their

147 ls that alpha1L232W, which increases maximal sidechain length by 2.1 angstrom, displaces etomidate cl

148 xi also scales with sidechain length to a power in the range of 0.35-0.44, s

149 conformationally tunable where backbone and sidechain lengths were precisely altered, grafting densi

150 s clearly demonstrated that, when a cationic sidechain (Lys or Arg) is near an aromatic sidechain (Ph

151 haracterized by the installation of distinct sidechain macrocycles by enzymes known as burpitide cycl

152 tics of surface salt-bridge interactions and sidechain-mainchain interactions.

153 ons from sheet length, aligned leucines, and sidechain membrane insertion.

154 enters on two prominent, sequential, peptide sidechains, methionine-tryptophan.

155 nsisting of a protein sequence, backbone and sidechain NMR resonance assignments, and 3D-NOESY ((13)C

156 The sidechain of Arg is more likely than that of Lys to be i

157 and have indicated that reorientation of the sidechain of Arg38, such that access to the haem is much

158 In one model, the sidechain of Asn122 is proposed to make interactions wit

159 with residues in the TMH bundle and that the sidechain of Asp-83 does not interact with Arg-143.

160 nteractions between Y30 of p.MT-ND1 with the sidechain of E4 and backbone carbonyl group of M1 of NDU

161 ge upon protonation that moves the imidazole sidechain of H64 away from the CO into the high-dielectr

162 ha5-helix breaks a hydrogen bond between the sidechain of His373 in the C-terminal alpha5-helix and t

163 ted by the disaccharide-modified hydrophobic sidechain of oritavancin interactions with the pentaglyc

164 These include the native state in which the sidechain of Phe114 is exposed to solvent (E state) and

165 zation for modification of a specific lysine sidechain of the cGTPase (K572) within human Miro1 is de

166 structural constraints onto the backbone and sidechain of the peptide and preorganize it to the bound

167 reason is interactions between the aliphatic sidechain of V12 and the Switch II region of K-Ras4B(G12

168 e that normally accommodates the hydrophobic sidechains of a canonical D-site, retaining a significan

169 at of the same framework decorated only with sidechains of a single kind.

170 Through the sidechains of aromatic amino acids, novel binding sites

171 In fact, naphthyridinols with sidechains of eight or more carbons had affinities for T

172 key step in the biosynthesis of fucosylated sidechains of galactoxyloglucan.

173 ed by a plethora of hydrogen bonds involving sidechains of Gln, Asn, Ser, and Tyr residues, both alon

174 rate constant faster than energy minima for sidechains of H402 and R404 from SCR7(H402).

175 ine chitin/chitosan layer, stabilized by the sidechains of hydrophobic amino acid residues, and situa

176 of an unusual carbon-carbon bond between the sidechains of lysine (Lys) and tryptophan (Trp) in the b

177 ly by analyzing to what extent the different sidechains of pea cell wall XG and nasturtium seed stora

178 Molecular dynamics simulations show that Arg sidechains of protamine each form hydrogen bonds with mu

179 between the beta-sheet 2, alpha-helix 2, and sidechains of residues Lys38 and Lys72.

180 favorable interactions of the osmolytes with sidechains of residues that lie at the interfaces of the

181 Positively charged sidechains of the ECL2 (R177 of NK1R and K180 of NK2R) a

182 oggle switch tryptophan indole group and the sidechains of the microswitch motif Pro-Ile-Phe (PIF).

183 e strong dispersion interactions between the sidechains of these solvent-exposed basic residues and t

184 nine-scanning mutagenesis indicated that the sidechains of three phenylalanines (at positions 473, 47

185 presented which suggested that the different sidechains of XG may play a role in controlling cellulos

186 We observe energy minima for sidechains of Y402 and R404 from SCR7(Y402) that are pre

187 compared to simply placing the best-matching sidechains on ACMI's trace.

188 he energetic impact of individual amino acid sidechains on nucleotide translocation through the pore

189 cules attach electrostatically to the lysine sidechains on the fibrils' surfaces, generating a double

190 The resulting sidechain ordering affords hexane isomer separation perf

191 ements have been made in sequence alignment, sidechain orientation and loop building.

192 ntaining oligosaccharide as found in pea XG, sidechain orientation appeared to regulate the gradual a

193 form of XG, forms in which the trisaccharide sidechain orientation enables increased backbone planari

194 nd polymorphs with differences in amino acid sidechain orientations, lengths of structurally ordered

195 kbone residue torsional distribution and the sidechain orientations.

196 on to modify the methylation state of lysine sidechains, other proteins recognize specific histone me

197 and found to direct their imidazole-bearing sidechains outward (exo).

198 Design strategies that positionally order sidechains over a defined porous framework to diversify

199 In alpha1L232Wbeta3M286Cgamma2L receptors, sidechain overlap with bound etomidate was inferred for

200 atoms of the residues at positions 2, 9 and sidechain oxygen atoms of the residue at position 12 (N(

201 show that inclusion of this term in Rosetta sidechain packing calculations substantially reduces the

202 ating the interplay among backbone ordering, sidechain packing, and desolvation arises from these cal

203 n rotamers such that following combinatorial sidechain packing, buried unsaturated polar atoms are pe

204 gy-based criterion for selecting significant sidechain pairs.

205 In addition, the C=O group of each Gln sidechain participates in a seven-membered ring hydrogen

206 c sidechain (Lys or Arg) is near an aromatic sidechain (Phe, Tyr, or Trp), the geometry is biased tow

207 (1-aza[6]helicene) and intrinsically chiral-sidechain polymers using a combination of spectroscopic

208 idechain copolymers were synthesized to form sidechain polypseudorotaxanes with a-cyclodextrins (a-CD

209 sign to fabricate a sea cucumber mimic using sidechain polypseudorotaxanes with tunable nano-to-macro

210 replacement of the distal amine on the C-17 sidechain present in 4 with a tertiary alcohol in combin

211 n the presence of DTNB allowed the degree of sidechain protection in any rapidly formed intermediate

212 behaviour we describe as stimulus-responsive sidechain reconfiguration.

213 perimental structures than the more extended sidechain regime.

214 quality, diversity, and novelty metrics, and sidechains reproduce the chemical features and behavior

215 tom models, resulting in fewer chains, lower sidechain RMS error and reduced R factor, compared to si

216 ations, that is coupled to dynamic two-state sidechain rotamer jumps, as evidenced by alternate confo

217 Sidechain rotamer libraries of the common amino acids of

218 ubtle changes in the distribution of sampled sidechain rotameric states.

219 tify a set of residues whose "collaborative" sidechain rotamerization immediately preceded or accompa

220 assigning a pairwise-decomposable energy to sidechain rotamers such that following combinatorial sid

221 ng solvent exposure with relatively extended sidechains, rotamers are selected that exhibit maximal p

222 R structures suggests only a minor change in sidechain rotation of toggle switch residues upon activa

223 Macrocycles c5a and c5b with hydrophobic sidechains serve as carriers that mediate efficient sulf

224 distinct mutations identified as disrupting sidechain-sidechain hydrogen bonding from 181 in our pre

225 rings the two beta-sheets in contact through sidechain-sidechain interactions.

226 r backbone-backbone, sidechain-backbone, and sidechain-sidechain interactions.

227 acid remodeling but also reduced GPI anchor sidechain size on mature GPI-anchored procyclin glycopro

228 This reduction in GPI anchor sidechain size was reversed upon the re-addition of Tb92

229 Mutation of one of these sites, R195, whose sidechain stabilizes both backbone and base of a bound n

230 tructure, Protpardelle, which represents all sidechain states at once as a "superposition" state; sup

231 virtually unlimited alteration of amino acid sidechain structures.

232 a-tocopherol (alpha-TOH, right) with varying sidechain substitution was synthesized to determine how

233 hese findings suggest potential roles for XG sidechain substitution, enabling XG to function in a var

234 results are presented as mappings of matched sidechain superpositions.

235 the C(alpha)-C(beta) bond, and its imidazole sidechain swings out of the heme pocket into the solvent

236 ine how protein structure enforces histidine sidechain tautomerization.

237 ith LC-MS/MS analysis to distinguish the two sidechain tautomers of histidine residues in peptides an

238 2) will also allow for selective decaging of sidechains that are candidates for covalent modification

239 and overall tertiary structure, but with the sidechains that make up the hydrophobic protein core dyn

240 trichomes produce defensive acylsugars, with sidechains that vary in length across the family.

241 of poly(ADP-ribose) (PAR) chains to protein sidechains then signals for assembly of DNA repair compo

242 s used to probe the exposure of the cysteine sidechain thiols in the kinetic folding intermediates of

243 nd carbonyl groups on the damaged tryptophan sidechain, thus breaching the integrity of nearby dry ce

244 (ptE) that constrained both the backbone and sidechain to the bound conformation was synthesized and

245 yrrolopyrrole-based polymers with engineered sidechains to investigate the impact of several molecula

246 uter mannan fibrils rely on alpha-1,2-linked sidechains to maintain contact with the inner wall.

247 e fibril growth direction, including diverse sidechain-to-backbone, sidechain-to-sidechain, and sidec

248 on, including diverse sidechain-to-backbone, sidechain-to-sidechain, and sidechain-to-water interacti

249 ain-to-backbone, sidechain-to-sidechain, and sidechain-to-water interactions.

250 Knowledge of the effect of sidechain type on assembly dynamics and fibrillar struct

251 vealed the unexpected presence of a tyrosine sidechain (Tyr54) near the coordination sphere of one of

252 calculations were made with no repacking of sidechains upon complexation, and only minimal packing u

253 f beraprost's dihydrobenzofuran (upper alpha-sidechain) using our newly developed methodology.

254 f dunked conformations of the protonated Glu sidechain, which exhibit a higher pK(a) shift.

255 cating that pea XG possesses a trisaccharide sidechain, which is not found in nasturtium XG.

256 alternating orientations of the buried R262 sidechain, which mimic sodium binding and unbinding in t

257 'zero-size-zero-background' label in protein sidechains, which may be used to probe biological phenom

258 Overlap of modified cysteine sidechains with bound anesthetic was inferred when anest

259 Decoration of its alpha-xylosyl sidechains with further sugars is critical for plant gro

260 ng of the local nuclear motion at the chiral sidechains with the delocalized electronic motion of mol

261 nding, but also that it uses a common set of sidechains with which it captures key groups of UCN-01 a

262 d to attack C1 in GPP to form the moenocinyl sidechain, with the more distal regions of 5 aligning wi

263 Mutation of amino acids whose sidechains would directly coordinate bound ligands affec