ライフサイエンスコーパス: secondary structure

1 ), only two enantiomeric isomers are formed (secondary structure).

2 m outside binding motifs through altered RNA secondary structure.

3 in can be associated with disruptions to the secondary structure.

4 e covariations are a signal of conserved RNA secondary structure.

5 into fibrils that have a parallel-beta-sheet secondary structure.

6 cid/base frustration enforced by the protein secondary structure.

7 d the adoption of a predominantly beta-sheet secondary structure.

8 ide coupling, which is directly dependent on secondary structure.

9 mere structure and also modified the protein secondary structure.

10 s while containing short regions of residual secondary structure.

11 as high proline content, and lacks predicted secondary structure.

12 -40) was less prone to adopt the alpha-helix secondary structure.

13 e expected complexity of the predicted local secondary structure.

14 -3-3, leading to destabilization of TOMM34's secondary structure.

15 on, while another helps unwinding the target secondary structure.

16 stry, respectively, without affecting the Ub secondary structure.

17 d DNA damage by way of G-quadruplex (G4) DNA secondary structure.

18 nstraints are relieved in the absence of RNA secondary structure.

19 w similarity in the primary sequence and the secondary structure.

20 pyrrolidine units mimics natural PPII helix secondary structure.

21 SUVs were similar and indicated beta-barrel secondary structure.

22 Rosetta could be adjusted based on the local secondary structure.

23 NA-binding protein motif enrichment, and RNA secondary structure.

24 l states (ESs) that remodel local aspects of secondary structure.

25 a greater ability to form highly stable DNA secondary structures.

26 DNA and RNA can adopt various secondary structures.

27 s emerging class of RNAs has been limited to secondary structures.

28 gions is likely due to its tendency to break secondary structures.

29 ding potential is strongly influenced by RNA secondary structures.

30 analyze the spectra of proteins with stable secondary structures.

31 A replication, which tends to stall at these secondary structures.

32 different flanking bases within diverse DNA secondary structures.

33 k model over a thermodynamic ensemble of RNA secondary structures.

34 rbohydrases differently affected polypeptide secondary structures.

35 vely regulates translation by resolving mRNA secondary structures.

36 o test the functional relevance of viral RNA secondary structures.

37 their sequences upon their G-quadruplex and secondary structures.

38 rgence in their nucleotide sequences and RNA secondary structures.

39 The features used were secondary structure, accessible surface area and the loc

40 thod to directly compare levels of predicted secondary structure across SARS-CoV-2 domains.

41 coarse-grained tree graphs to represent RNA secondary structure, allowing the application of graph t

42 We observed two distinct secondary structures, alpha-helix and beta-sheet, which

43 In silico secondary structure analyses from NGS indicated extensiv

44 ic PSMalpha3-NH(2) displays an alpha-helical secondary structure and a packing pattern that is remini

45 scopy (TERS) could be used to reveal protein secondary structure and amino acid composition of the vi

46 Protein secondary structure and backbone torsion angle predictio

47 oteins from the Protein Data Bank, comparing secondary structure and disorder predictions with simula

48 effect on structure (amino acid composition, secondary structure and electrophoresis pattern) and tec

49 lymer-OP conjugate (PDOP) adopts alpha-helix secondary structure and induces robust immunogenic cell

50 solid-state NMR measurements of beta-strand secondary structure and inter-strand organization within

51 corresponding to structures with a prefolded secondary structure and ligand-induced-folding versions

52 Furthermore, conserved secondary structure and mutagenesis analyses revealed a

53 e significant destabilizing perturbations of secondary structure and remove correlated motions likely

54 his is accompanied with strengthening of the secondary structure and surface exposure of hydrophobic

55 e RNAs by jointly predicting their consensus secondary structure and the optimal sequence alignment.

56 ameter affects proteins in the cheese, their secondary structure and the resulting cream cheese.

57 drug-like molecules can modulate the amyloid secondary structure and therefore have raised significan

58 more, STARR-seq readout is confounded by RNA secondary structure and thermodynamic stability.

59 ay mapping was used to additionally validate secondary structure and to discover regions that easy bi

60 ragile sequences that when expanded form DNA secondary structures and cause human disease.

61 ws that it has a propensity to form multiple secondary structures and contacts, indicating that it co

62 Protein loops connect regular secondary structures and contain 4-residue beta turns wh

63 fficient conversion of RNAs that form stable secondary structures and double-stranded RNA targets rem

64 kground, the review gives an introduction to secondary structures and experimental methods as well as

65 e duplications, anticodon mutations, loss of secondary structures and high gene translocation rates.

66 icity to identify potentially functional RNA secondary structures and identified 23 regions within th

67 al connections between DNA modification, DNA secondary structures and large chromatin domains in earl

68 me contains a number of unique, specific RNA secondary structures and provides a strategy for testing

69 e ITS itself, such as the propensity to form secondary structures and telomeric protein binding, pose

70 promoter-proximal pausing, nucleosomes, RNA secondary structures and the underlying DNA sequence.

71 ], using a correlation score (which assesses secondary structure), and an RMSD score (which measures

72 ngle nucleotide polymorphisms can affect RNA secondary structure, and here we show that single nucleo

73 the inner workings of a cell at the protein, secondary structure, and perhaps even side-chain levels.

74 f panels connected by elastic backbones into secondary structures; and hierarchical assembly of 2-dim

75 Protein hydration and secondary structure appeared to be key factors affecting

76 New data indicate that RNA length and secondary structure are features sensed by MDA5.

77 eferences as well as the competition between secondary structures are discussed.

78 s with the ability to form highly stable DNA secondary structures are enriched for endogenous DSBs in

79 ements of the interactions of S1 with simple secondary structures are known, mechanistic details of t

80 aterally along the substrate and must bypass secondary structures as well as protein barriers.

81 We disrupted secondary structures associated with vPAR-CL sites using

82 ich are measures of uncertainty in predicted secondary structure at each position in the sequence; th

83 arried out, monitoring the change in protein secondary structure at increasing temperature by Fourier

84 side chain are determined by the type of the secondary structure at the attachment site.

85 bservation by inferring the strengthening of secondary structure at the expense of tertiary structure

86 state-of-the-art performance for predicting secondary structures, backbone torsion angles, beta-turn

87 Compared to recent secondary structure based methods, the proposed solution

88 ed Rosetta modeling of mutations, and use of secondary structure-based energetic calculations to mode

89 atory regions in the genome has emerged as a secondary structure-based epigenetic mechanism for regul

90 s finding appears to go against the dogma of secondary structure being a key determinant of function

91 ous studies found little conservation in RNA secondary structure between alphaviruses, and this struc

92 e deglycosylation does not change hemocyanin secondary structure but alters their refolding mechanism

93 have enabled transcriptome-wide maps of RNA secondary structure, called 'RNA structuromes'.

94 A short, single-stranded segment within the secondary structure can be used as a toehold for initiat

95 istics, the complete enumeration of possible secondary structures can be accomplished quickly despite

96 ansition to the inactivated state involves a secondary structure change of the pore-lining helix, whi

97 We used circular dichroism to show secondary structure changes and isothermal titration cal

98 uce the location of both local and non-local secondary structure changes due to the Val66Met mutation

99 nant Arabidopsis MDLs (AtMDLs) share similar secondary structure characteristics with human MIF, yet

100 differs from the ground state by a change in secondary structure, consistent with previous prediction

101 alysis indicated that Asp t 36 shows similar secondary structure content and temperature sensitivity

102 Obtaining protein secondary structure content from high-resolution structu

103 re definitions result in large variations in secondary structure content that are not equivalent in v

104 is currently widely used to evaluate protein secondary structure content, is a good choice when deali

105 ently used and can have a profound impact on secondary structure content.

106 g restrictions and suggests that the protein secondary structure defines not only tertiary geometry,

107 The paper demonstrates that different secondary structure definitions result in large variatio

108 visiae form distinct Hoogsteen pairing-based secondary structures, depending on their length.

109 The close agreement of NMR secondary structure determination of isolated RNA elemen

110 , their large-scale production and NMR-based secondary structure determination.

111 With no significant changes in secondary structure, determined through FTIR, the observ

112 posure of thiol groups as well as a shift in secondary structure distribution, while sheeting only ha

113 the alpha-helix and gain beta-sheets in the secondary structure during adsorption on hematite.

114 e successfully identified changes in protein secondary structure during pH- and heparin-induced fibri

115 ted with a disputed oligomeric form exhibits secondary structure, dynamics, and solvent accessibility

116 r certain interfaces the mimicry of a single secondary structure element is insufficient to obtain hi

117 This model predicts secondary structure elements (SSEs), backbone structure,

118 rformed on larger RNA regions shows that the secondary structure elements fold independently.

119 Regions that connect secondary structure elements in a protein are known as l

120 Transient formation of secondary structure elements in the acid unfolded and pr

121 c and aromatic interactions between distinct secondary structure elements in the ancestral forms that

122 FUS LC adopts conformations with traditional secondary structure elements in the condensed phase; rat

123 e been described as useful mimics of protein secondary structure elements, enabling for example the d

124 ed a suppression of the response of specific secondary structure elements, indicating that the intrac

125 ehavior of food proteins by determination of secondary structure elements.

126 the actual properties and functions of these secondary-structure elements in their native contexts ar

127 Modified nucleotides that stabilize mRNA secondary structure enabled high expression across a wid

128 with a single cysteine residue in different secondary structures, enabling Cys labeling with Alexa F

129 efine our computational model of the peptide secondary structure ensemble produced by all-atom molecu

130 We were also able to probe the secondary structure evolution of individual oligomers.

131 that saponin changes the beta-galactosidase secondary structure, favoring its protein-substrate inte

132 mation in terms of mutations affecting PTMs, secondary structure features and per-residue solvent acc

133 econvolution of experimental CD spectra into secondary structure features of the IDP ensemble.

134 formation without the necessity of computing secondary structure features which is computationally ex

135 es and provides a strategy for testing these secondary structures for functional importance in CHIKV

136 ulations indicate different contact maps and secondary structures for the different variants along th

137 es may be important for resolving the unique secondary structures formed by GGGGCC-DNA during transcr

138 presses R-loop formation in genes harbouring secondary structure-forming sequences, exemplified by G

139 lar dynamics simulations, are used to deduce secondary structure from backbone and side-chain chemica

140 The scoutRNA differs in secondary structure from previously described tracrRNAs

141 -fibroin phosphoserines (pSs) and a shift in secondary structure from random coils to beta-structures

142 otein backbone torsion angles ( and psi) and secondary structure from sequence are crucial subproblem

143 NPs could change their corresponding miRNA's secondary structure from stable to unstable.

144 DNAproDB now supports any DNA secondary structure from typical B-form DNA to single-st

145 l dynamics of the carotenoid and the protein secondary structure, from femtoseconds to 0.5 ms.

146 emonstrated links between these nucleic acid secondary structures, gene expression, and DNA replicati

147 Algorithms that predict secondary structure given only the primary sequence, and

148 How the replisome senses and deals with DNA secondary structures has been a mystery.

149 Since RNA secondary structures have only been defined for a small

150 g and aggregation, along with changes in the secondary structure, have been correlated with its toxic

151 y on small protein fragments, often isolated secondary structures; however, there has lately been a g

152 t, the exchange rates depend strongly on the secondary structure (hydrogen bonding status) of the oli

153 no decrease in capsule binding, but did lose secondary structure in a capsule-dependent fashion compa

154 In contrast, beta-sheets, the main secondary structure in cooked pasta, negatively correlat

155 We investigated the role of in vivo RNA secondary structure in miRNA cleavage by developing the

156 pha-helix is the most commonly found natural secondary structure in proteins and is intrinsic to many

157 We found that mRNAs that have complex secondary structure in the 5' untranslated region (UTR)

158 BID fibers display both types of secondary structure in the fiber, whereas BAX was conver

159 highlights an underappreciated role of mRNA secondary structure in the regulation of mRNA stability.

160 RNA secondary structure in the viral genome plays an importa

161 eceding peptide bond and induce well-defined secondary structures in a biomimetic environment.

162 NA sequencing and machine learning to detect secondary structures in cellular RNAs.

163 we show that replication hurdles, including secondary structures in template, slowed helicase, or un

164 hat Nm preferentially stabilizes alternative secondary structures in which the Nm-modified nucleotide

165 folds with significant differences in their secondary structure, in which each fold is stabilized by

166 00 W, 75-125 degrees C, and 5-15 min) on the secondary structures, in-vitro protein digestibility, mi

167 ad utility of this approach across different secondary structures, including both beta-sheet and heli

168 and enhanced thermal resistance to change in secondary structure, indicating that these two molecules

169 FTIR studies revealed alterations in protein secondary structure induced by plasma, particularly cont

170 essfully proven to predict RNA function from secondary structure information.

171 Archetypal biologically relevant secondary structures investigated by molecular beam spec

172 We establish that control by RNA secondary structure is chiefly mediated by highly folded

173 It is widely known that secondary structure is determinant to know RNA function

174 isons of NMR to crystal structures show that secondary structure is equally accurate, but crystal str

175 e two types of Abeta42 fibrils show that the secondary structure is similar in both fibril polymorphs

176 hese feature selection analyses suggest that secondary structure is the most important peptide sequen

177 of beta-peptides sequences to adopt regular secondary structures is an important challenge in peptid

178 However, obtaining stable secondary structures is challenging, and designing these

179 How the replisome detects and responds to secondary structures is poorly understood.

180 The synthesis of biomimetic helical secondary structures is sought after for the constructio

181 en recognized as an all-important element of secondary structure, it generally requires stabilization

182 hough the N-terminal region of RNF4 bears no secondary structure, it maintains a compact global archi

183 bi-functional role is modulated through RNA secondary structures known as G-Quadruplexes.

184 Cytosine-rich DNA can fold into secondary structures known as i-motifs.

185 The complexity of the secondary structures makes RNA targets inaccessible for

186 reveals a direct role for TOP2 in generating secondary structure-mediated DNA fragility, advancing ou

187 ications, global restrictions and the use of secondary structure mimetics.

188 Results from secondary structure modeling and analysis of RNase E cle

189 However, traditional RNA secondary structure models cannot treat loop-sequence an

190 Caenorhabditis and possesses three essential secondary structure motifs but no essential open reading

191 ciency between the probe and target RNA with secondary structure motifs.

192 may impair the peptoid's adoption of stable secondary structures, notably the all-cis polyproline I-

193 The secondary structure of AFs was preserved as observed by

194 ratio (DAR) of 1 (ALDC1) retained the native secondary structure of albumin compared to conjugate wit

195 CD analysis revealed that the secondary structure of all variants was retained compare

196 ex"-a normalized function of the primary and secondary structure of an individual molecule that measu

197 scriptional efficiency, gene expression, the secondary structure of both mRNA and proteins, and has b

198 G-quadruplex (G4) is a noncanonical secondary structure of DNA or RNA which can enhance or r

199 A role for the secondary structure of IAV mRNAs has been hypothesized a

200 been predicted to affect the expression and secondary structure of long noncoding RNAs (lncRNAs), bu

201 We propose that secondary structure of miRNA precursors induced by their

202 ed significant conformational changes in the secondary structure of polyaniline chitosan silver nanoc

203 ours were mitigated through the unfolding of secondary structure of PPI by forming solid dispersions

204 results also indicate that the dictionary of secondary structure of proteins (DSSP) algorithm, which

205 have been used to differentiate between the secondary structure of proteins in bulk solution and tho

206 The changes in secondary structure of proteins with heating were charac

207 geting of not only the sequence but also the secondary structure of RNA.

208 ngly associated with the modification of the secondary structure of shrimp proteins, including the in

209 ty enables the accurate determination of the secondary structure of single protein molecules with ove

210 The CD spectra suggested that the secondary structure of the betaLG remains unaffected by

211 bsequent scanning require the removal of the secondary structure of the by RNA helicases such as eIF4

212 erride locally the preferred global 12-helix secondary structure of the corresponding tACBC homooligo

213 ontacts form before or concurrently with the secondary structure of the disordered protein)-an observ

214 onjugates within 2 h, avoiding damage to the secondary structure of the protein and providing easily

215 the putative client-binding loop altered the secondary structure of the UCS domain (by decreasing the

216 Furthermore, we defined the RNA secondary structure of three CHIKV 3'UTR variants that d

217 tent of hydrogen-deuterium exchange in local secondary structures of A1 within multimeric VWF.

218 Secondary structures of beta-proline tripeptides in solu

219 tal reflectance (ATR) analysis modes and the secondary structures of cheese proteins determined.

220 a chemical probing method to define the RNA secondary structures of CHIKV genomic RNA.

221 r knowledge, novel way to solve the ensemble secondary structures of IDPs in solution, which is impor

222 s, the atomic-level contributions of various secondary structures of luciferase to its fold's mechani

223 We also analyzed the RNA flexibility and secondary structures of multiple 3'UTR variants of CHIKV

224 nfrared spectroscopy analysis elucidated the secondary structures of protein in the composite flour w

225 ated in different nitration degrees, and the secondary structures of proteins were determined by circ

226 ecular crowding conditions to better predict secondary structures of RNAs in vivo.

227 ysed by several spectroscopic techniques the secondary structures of two artificial miRNAs selected b

228 d interrogate the impact of STR sequence and secondary structure on their genomic representation and

229 t impact the amino acid composition, protein secondary structure or gluten protein composition.

230 -binding groove did not alter the UCS domain secondary structure or structural stability but reduced

231 To link secondary structure prediction algorithms developed for

232 Finally, DeepMSA was used for secondary structure prediction and resulted in statistic

233 Chemical shift-based secondary structure prediction confirms that in solution

234 state-of-the-art tools when computing their secondary structure prediction do not explicitly leverag

235 Protein secondary structure prediction is a fundamental precurso

236 RNA secondary structure prediction is widely used to underst

237 In this model, secondary structure prediction programs are used to calc

238 The most popular RNA secondary structure prediction programs utilize free ene

239 We present a new hybrid approach to secondary structure prediction that gains the advantages

240 both backbone torsion angles prediction and secondary structure prediction.

241 currently available for both 3- and 8-state secondary structure prediction.

242 ively, and the accuracies for 3- and 8-state secondary structure predictions are 87.72 and 77.15%, re

243 The potential for improving secondary structure predictions from FTIR spectra has be

244 ons, and 89.06 and 78.87% for 3- and 8-state secondary structure predictions, respectively.

245 ntage of the high accuracy of sequence-based secondary structure predictions, we showed the value of

246 While disorder databases continue to expand, secondary structure predictors and molecular simulations

247 man spectroscopy to estimate the ensemble of secondary structures present in proteins.

248 The NMR data are corroborated with secondary structure probing by DMS footprinting experime

249 Furthermore, divergence in secondary structure profiles often occurred for LCDs enr

250 We also observed an enrichment of DNA secondary structure-prone sites overlapping transcriptio

251 ucture tendencies with numerous pre-existing secondary structure propensity scales resulted in relati

252 RNA G-quadruplexes (G4s) are secondary structures proposed to function as regulators

253 mi scaffolds as general promoters of unusual secondary structures, proteinaceous side chains have bee

254 red an increase in DSBs at highly stable DNA secondary structure regions, in response to etoposide, a

255 ike domain that are predicted to disrupt the secondary structure resulted in up to a 10,000-fold drop

256 ism showed that the altered protein acquired secondary structure resulting in an increase in alpha-he

257 compute the entire free energy landscape of secondary structures resulting from a primary RNA sequen

258 eCLIP experiments align with long-range RNA secondary structure, revealing discrete XIST domains tha

259 ic acid sequences have the potential to form secondary structures such as G-quadruplexes and i-motifs

260 that can fold into thermodynamically stable secondary structures such as hairpins and quadruplexes.

261 tly increased tendency to fold into branched secondary structures, supporting the predicted mechanism

262 Secondary structures tend to be recognizable because the

263 een enrichment of individual amino acids and secondary structure tendencies across the entire PDB pro

264 indicating that these scales may not capture secondary structure tendencies as sequence complexity de

265 Secondary structure tendencies varied as a function of t

266 Comparison of LCD secondary structure tendencies with numerous pre-existin

267 sed of related amino acids can have distinct secondary structure tendencies.

268 5' UTR and is predicted to form an extensive secondary structure that overlaps the ribosome binding s

269 include naturally occurring DNA lesions and secondary structures that are difficult to replicate.

270 The CHIKV genome contains functional RNA secondary structures that are essential for proper virus

271 lso counteracts replication conflicts at DNA secondary structures that arise within telomeres and acr

272 n-binding sites and/or have stable predicted secondary structures that could afford protection from p

273 of ribosomes on mRNA is often interrupted by secondary structures that present mechanical barriers an

274 used our approach to elucidate the specific secondary structures that provide the largest contributi

275 lar dynamics simulations to examine specific secondary structures that resist mechanical unfolding wh

276 Expanded TA repeats form non-B DNA secondary structures that stall replication forks, activ

277 ur frequently at the terminal regions of the secondary structures, the propensity for proline at thes

278 ansfer rate, textural, functional groups and secondary structure, thermal, crystallinity, and antioxi

279 used SHAPE-MaP to inform the modeling of RNA secondary structure throughout the genome of a CHIKV iso

280 r: samples tree graph topologies from an RNA secondary structure to predict corresponding tertiary to

281 ontributions of factors like codon usage and secondary structure to regulating protein expression are

282 winding helicase, which unfolds these stable secondary structures to regulate LANA translation.IMPORT

283 ontrolling the formation of higher-order DNA secondary structures to regulate transcription beyond it

284 Fold-switch pathways remodel the secondary structure topology of proteins in response to

285 It provides predictions of protein secondary structures, torsion angles, beta-turns and gam

286 thium buds, through spatial conformation and secondary structure transformation from alpha-helix to b

287 ical conformation to a short-lived different secondary structure transiently before reaching the acti

288 2+) binding by NS2 triggered a helix-to-coil secondary structure transition.

289 in-base hydrogen bonds favor strand and coil secondary structure types in highly specific DNA-binding

290 roles of individual DNA strands and protein secondary structure types in specific protein-DNA recogn

291 ealed that there is no significant change in secondary structures up to 2 M concentration of GuHCl.

292 that BII forms a rigid and helically ordered secondary structure upon binding to DPC micelles, wherea

293 Amyloid beta-sheet secondary structure was detected in cataract lenses alon

294 hitherto undescribed, higher-order, G4-based secondary structure we term a 'G4 Kiss or G4K'.

295 is of predicting a stable G-quadruplex and a secondary structure, we truncated 19 nucleotides (nt) fr

296 Protein solubility, accessible thiols and secondary structures were measured in dough, sheeted and

297 spectral features of proteins with different secondary structures were successfully identified at con

298 , and understanding the evolution of various secondary structures with respect to each other during u

299 cture probing analysis reveals a decrease in secondary structure within stem-loop regions of these tr

300 d proximal MMP-3 interface and by changes in secondary structure within the TIMP-1 C-terminal domain