ライフサイエンスコーパス: knot

1 tion joins together one end of each overhand knot.

2 ugh not as compact as, e.g., the synchrotron knot.

3 n the medial plantar nerve (MPN) and Henry's knot.

4 ling centers: the initiation knot and enamel knot.

5 s in the dynamics of the loops that form the knot.

6 es probed, the human genome is often free of knots.

7 e composition of fungal communities in olive knots.

8 time, reveal the existence of rare composite knots.

9 r strand enables it to be tied into multiple knots.

10 ance of nanopores in future investigation of knots.

11 ting the shape of biopolymers, including DNA knots.

12 -conjugation and electronic structure of the knots.

13 topologies such as Mobius, ribbon strips and knots.

14 amine the genome in vivo for the presence of knots.

15 f PE, with particular reference to syncytial knots.

16 nslocation of 10-kbp-long DNA rings that are knotted.

17 n unknot (0(1)) macrocycle, a trefoil (3(1)) knot(6-15), and a three-twist (5(2)) knot-were each sele

18 eed with stereoinduction: in the case of one knot, a lanthanide(III)-coordinated crossing pattern for

19 l to understanding the interplay between the knot, activation of the methyltransferase, and the impli

20 ail suggests that ClpXP tightens the trefoil knot against GFP, which prevents GFP unfolding.

21 ] for the folding of the [Formula: see text]-knotted alpha-haloacid dehalogenase (DehI) protein, we i

22 btain different RT-PCR patterns for an ssRNA knot and circle of the same sequence.

23 Both root-knot and cyst nematodes are endoparasites that have co-e

24 Sedentary endoparasitic nematodes, root-knot and cyst nematodes in particular, as well as gall-i

25 hytoplasma, rust fungi, Ustilago smuts, root knot and cyst nematodes, and gall midges.

26 t with two signaling centers: the initiation knot and enamel knot.

27 view of the conformational mechanics of the knot and its relationship to the activation of the ligan

28 if of Celtic interlace, the smallest Chinese knot and one of the eight auspicious symbols of Buddhism

29 ssembly dynamics of an imine-based pentafoil knot and related pentameric circular helicates, each der

30 d to define the relationship between Henry's knot and the plantar nerves.

31 n on 491 different substrate topologies, 166 knots and 325 links, and distinguish between pathways co

32 ith large-scale simulations of various nodal knots and an experiment which maps out the topological d

33 gs, in turn catalyzing the simplification of knots and links by TopoII enzymes even in crowded and co

34 Knots and links have been conjectured to play a fundamen

35 Although both knots and open circular helicates self-assemble under th

36 llects information about proteins which form knots and other entangled structures.

37 ew of synthetic strategies towards molecular knots and outline the principles of knot, braid, and tan

38 synthesis of imine-based pentafoil molecular knots and pentameric circular helicates despite, in prac

39 predict the relative mechanical stability of knots and tangles, in agreement with simulations and exp

40 ure and topology of individual helical field knots and the various hierarchical crystalline organizat

41 ith large statistics, we explore the complex knots and, for the first time, reveal the existence of r

42 ty of the native state with reference to the knotted and unknotted denatured state we find that knott

43 In achiral liquid crystals, dopant knotted and unknotted strands induce supramolecular heli

44 Though knotting and entanglement have been observed in DNA and

45 dynamic switching achievable through in situ knotting and unknotting events.

46 Here we demonstrate that the knotting and unknotting of a molecular strand can be use

47 to six Hopf and two Solomon links, a trefoil knot, and a [3]catenate.

48 d a (Fe(II))(5)-coordinated pentafoil (5(1)) knot are found to selectively transport anions across ph

49 The composite knots are assembled by combining two entanglement syntho

50 Equilibrium knots are common in biological polymers-their prevalence

51 The properties of knots are exploited in a range of applications, from sho

52 Although knots are found in DNA and proteins(2), and form randoml

53 Knots are intricate structures that cannot be unambiguou

54 Knots are natural topologies of chains.

55 despite their being open curves in which the knots are not mathematically well defined; knotting can

56 Knots are remarkable topological features in nature.

57 These knots are robust and topologically distinct from the hos

58 n which the topological properties of framed knots are used in conjunction with prime factorization t

59 By using a constructed ssRNA knot as a highly sensitive topological probe, we find th

60 rint data from crystal structures of protein knots as evidence that particular protein knots may fold

61 inear regression with 2 linear splines and a knot at January 2015 was used to compare the slope of th

62 l loops and basal constriction around enamel knot at the center of the cap.

63 Linear spline models with a single knot at time of switch accounted for nonlinear trends.

64 lows undistorted propagation of polarization knots at a rate of 28 GHz along a 10 km length of normal

65 he C=C linkages topologically connect pyrene knots at regular intervals into a 2D lattice with pi con

66 systematic investigation of the influence of knotting at the molecular level.

67 esidues, ClpXP tightens and translocates the knot before it reaches GFP, enabling the complete unfold

68 e demonstrate the use of a constructed ssDNA knot both to probe the topological conversion catalysed

69 olecular knots and outline the principles of knot, braid, and tangle theory appropriate to chemistry

70 rase IV, supercoiled DNA relaxation, and DNA knotting but not intermolecular reactions such as decate

71 These results support that a protein knot can be formed during a single cooperative step of f

72 ties of the strand: whereas the tighter 5(2) knot can bind two different metal ions simultaneously, t

73 restrictions imposed on molecular strands by knotting can impart significant physical and chemical pr

74 e knots are not mathematically well defined; knotting can only be identified by closing the termini o

75 tensioning and sliding of the translocating knotted chains.

76 Despite possessing the trefoil knot characteristic of SPOUT enzymes, Trm10 does not sha

77 Our nodal knot circuits can be characterized with impedance measur

78 The MXene-knotted CNT composite electrodes achieve high capacitanc

79 The large, knot-like structures in the knotted CNTs prevent the usual restacking of the Ti(3)C(

80 MXene Ti(3)C(2) by using specially designed knotted CNTs.

81 ot crossing number <m>, a natural measure of knot complexity and, correspondingly, we find E C to be

82 atural product which possess a unique lariat knot conformation.

83 se in writhe (topological strain) in the new knotted conformation.

84 Knots contain both at once a stable core as well as movi

85 e note a potential source of bias insofar as knotted contours may be more difficult to reliably resol

86 Interestingly, if the linker between the knot core of MJ0366 and GFP is longer than 36 residues,

87 functionals have been related to the average knot crossing number <m>, a natural measure of knot comp

88 different length and stiffness, and minimum knot crossing number values m for a wide class of knot t

89 tic routes to all but the simplest molecular knots currently prevents systematic investigation of the

90 resulted in the discovery of a new class of knotted cyclic peptides from the marine sponge Axinella

91 arboxylase, proteasomal subunit, or cysteine knot (defensin) protein; and the first report of a proka

92 t than the (Fe(II))(5)-coordinated pentafoil knot, derived from a cyclic pentamer of the same buildin

93 a regime of open curves in which the virtual knotting description is likely to be important.

94 roteins and the most deeply embedded protein knot discovered so far.

95 rom a functional point of view, most protein knots discovered so far are either enzymes or DNA-bindin

96 th the first of a unique structural class of knotted disulfide-rich peptides and defines a previously

97 ted membrane proteins and argue that a novel knotted DNA-binding protein constitutes a new fold.

98 we find E C to be directly related to <m> of knotted DNA.

99 a comprises two homologous inhibitor cystine knot domains separated by a short, structurally well-def

100 re, particularly of the glomerular capillary knot, dysregulation of nephrin and collagen IV, and ultr

101 enerated radicals are confined on the pyrene knots, enabling the formation of a paramagnetic carbon s

102 The resolved metal-free 819 knot enantiomers have pronounced features in their circu

103 free terminus, or one in which the tightened knot enters the translocation pore of ClpXP.

104 are often misdiagnosed as nematode-mediated knots, even by experts, because the gall symptoms in bot

105 enables two-step assembly of a molecular 819 knot featuring eight nonalternating crossings in a 192-a

106 ments with theory and simulations to analyze knotted fibers that change their color under mechanical

107 represents their complexity in the form of a knotting fingerprint, and presents many biological and g

108 nt strategies for the synthesis of molecular knots focus on twisting, folding and/or threading molecu

109 s confirm Taylor's twisted hairpin theory of knot folding for the [Formula: see text]-knotted protein

110 n, we introduce a topological description of knot folding that could describe pathways for the format

111 We study the percentage of molecules with knots for DNA molecules of up to 166 kilobase pairs in l

112 Yet, little is known about spontaneous knot formation in a polypeptide chain-an event that can

113 lue, indicating that the free energy cost of knot formation is of entropic origin.

114 oaches have been used to investigate protein knot formation.

115 lding pathway based on the idea that a loose knot forms at a terminus and slides to its native positi

116 physical filaments are naturally tangled and knotted, from macroscopic string down to long-chain mole

117 n the numerical simulation, we find that the knot function can be embedded into the acoustic field by

118 ower for the analogous closed-loop pentafoil knot (>60 days).

119 Knotting has been previously identified in protein backb

120 y been associated with the inhibitor cystine knot (ICK) fold.

121 RTX-Preg1a, exhibiting an inhibitory cystine knot (ICK) motif, and N-BUTX-Ptr1a, a short scorpion-CSa

122 d to adopt a well-defined inhibitory cystine knot (ICK) scaffold structure.

123 Finally, we have also discovered a knot in an artificially designed protein structure.

124 This record involved the participant tying a knot in ribbons worn under the clothing each time they h

125 that the free energy cost to form a trefoil knot in the denatured state of a polypeptide chain of 12

126 ,4), methods for tying(5) different sorts of knots in a synthetic nanoscale strand are lacking.

127 walls in the form of localized polarization knots in conventional optical fibres.

128 The presence of knots in crystallographic structures of proteins have st

129 Starting with Gauss and Kelvin, knots in fields were postulated to behave like particles

130 oduce energetically stable, micrometer-sized knots in helical fields of chiral liquid crystals.

131 The statistics of virtual knots in protein chains are compared with those of open

132 Knots in proteins are hypothesized to make them resistan

133 Knots in proteins are increasingly being recognized as a

134 Twenty years after their discovery, knots in proteins are now quite well understood.

135 r understanding the possible implications of knots in proteins for cellular degradation.

136 Recently, tying isolated vortex knots in the complex optical field has been realized.

137 Knots in the human genome would greatly impact diverse c

138 long to the SpoU-TrmD family contain trefoil knots in their backbone fold.

139 ysis to determine if a genomic trajectory is knotted in the setting of experimental noise.

140 The existence of knotting in a filament naturally affects its configurati

141 We introduce a new method for resolving knotting in open curves using virtual knots, which are a

142 ny knot; of opposite handedness for a square knot) in three synthetic steps: first, a CuAAC reaction

143 Momentum space knots, in particular, have been elusive due to their req

144 These observations suggest that a knot-induced stall during degradation of multidomain pro

145 exploited to associate to each vortex loop a knot invariant called the Alexander polynomial whose deg

146 owever, how to construct the acoustic vortex knot is still an unknown problem.

147 We further investigate the case in which a knot is tied along the chromatin fibre, and find that th

148 topology, which means that only one type of knot is usually possible.

149 effect induced by the tying of the molecular knots is similar to that famously used to rotate a glass

150 easily degrade a protein with a shallow 3(1) knot, it cannot degrade 5(2)-knotted proteins if degrada

151 knotted proteins and the [Formula: see text]-knotted ketol-acid reductoisomerases and present alterna

152 The large, knot-like structures in the knotted CNTs prevent the usu

153 Class I KNOTTED-LIKE HOMEOBOX (KNOX) proteins regulate developme

154 e propose that SHOOT MERISTEMLESS, a class I KNOTTED-LIKE HOMEOBOX gene, is likely to play a role in

155 inuation of PrEP, with age included as a one-knot linear spline.

156 etathesis (RCM) then affords the closed-loop knot, locking the topology.

157 The knot loops form the S-adenosyl-methionine (SAM)-binding

158 in knots as evidence that particular protein knots may fold according to specific pathways from our t

159 Knots may ultimately prove just as versatile and useful

160 the evolutionary origin of a novel class of knotted membrane proteins and argue that a novel knotted

161 The cystine-knot miniproteins present in tomato fruit (TCMPs) have b

162 k reveals several novel structures including knotted mitochondrial proteins and the most deeply embed

163 slocate an entanglement from one region of a knotted molecular structure to another, resulting in an

164 insight into the topology of interlocked and knotted molecules, even when they exist in complex mixtu

165 model, including a previously unappreciated 'knotted' morphology to pathological vascular tufts, abno

166 eir head-to-tail cyclic backbone and cystine knot motif, which render them to be exceptionally stable

167 mino acid-long cyclic backbone and a cystine knot motif.

168 diverse stresses such as water deficit, root-knot nematode (RKN) infection, and UV exposure, with an

169 anic compounds used by the subterranean root-knot nematode (RKN) Meloidogyne incognita for host locat

170 Here, we report that the root-knot nematode (RKN) Meloidogyne incognita induces the sy

171 de (BCN), Heterodera schachtii, and the root-knot nematode (RKN), Meloidogyne incognita.

172 otypes using root tissue harvested from root-knot nematode infected plants at 0, 3, 7 days after inoc

173 Root-knot nematode is a very destructive pathogen, to which m

174 t nematode Heterodera schachtii and the root-knot nematode Meloidogyne incognita.

175 ibility to H. schachtii, but not to the root-knot nematode Meloidogyne incognita.

176 In this study, a total of 244 root-knot nematode populations from various hosts from 39 cou

177 Resistance to root-knot nematode was introgressed into cultivated peanut Ar

178 Root-knot nematodes (Meloidogyne spp.) are the most common ma

179 Root-knot nematodes (RKN) such as Meloidogyne spp. are among

180 sm by which plants defend against plant root-knot nematodes (RKNs) is largely unknown.

181 Root knot nematodes (RKNs) penetrate into the root vascular c

182 ided and evolutionary trends within the root-knot nematodes are discussed.

183 Cyst and root-knot nematodes are obligate parasites of economic import

184 feeding sites induced by both cyst and root-knot nematodes are surrounded by endodermis during early

185 stainable management strategies against root-knot nematodes in Arkansas.

186 Both cyst and root-knot nematodes induce specialized long-term feeding stru

187 ression analysis provides evidence that root-knot nematodes modulate biological pathways involved in

188 The root-knot nematodes of the genus Meloidogyne are highly adapt

189 sly reported related cyst nematodes and root-knot nematodes revealed a subset of esophageal gland rel

190 N in a way similar to that reported for root-knot nematodes, but opposite to that suggested for the s

191 lant responses to infection by cyst and root-knot nematodes, with a focus on the functions of microRN

192 ry endoparasites that includes cyst and root-knot nematodes.

193 6 kilobase pairs in length and find that the knotting occurrence rises with the length of the DNA mol

194 point-chiral centres folds into an overhand knot of single handedness upon coordination to lanthanid

195 Molecular knots of high symmetry have previously been synthesized

196 ks of defined stereochemistry (here overhand knots of Lambda- or Delta-handed entanglement) is remini

197 ugh the use of lanthanide-complexed overhand knots of specific handedness as three-crossing "entangle

198 is quantum turbulence always contains vortex knots of very large degree which keep forming, vanishing

199 experiments aimed at probing the spontaneous knotting of biopolymers.

200 eas topological assays based on Cre-mediated knotting of plasmid DNAs are consistent with a right-han

201 synthons (of the same chirality for a granny knot; of opposite handedness for a square knot) in three

202 ility to tie nanoscale chains into different knots offers opportunities to explore the modification o

203 In this study, the impact of olive knot (OK) disease caused by the bacteria Pseudomonas sav

204 impair its folding-and about the effect of a knot on the stability and folding kinetics of a protein.

205 n the viewing angle of the observed emitting knots or jet regions have also been suggested as an expl

206 allow the protein to refold from either the knotted or the unknotted denatured state to characterize

207 or both modes the pore obstruction caused by knot passage has a brief duration and typically occurs a

208 engineering and validation of a new cystine knot peptide (knottin) that selectively recognizes human

209 een velvet tarantula is an inhibitor cystine-knot peptide and selective antagonist of the human Nav1.

210 Recently, we demonstrated that the cystine-knot peptide EETI-II is internalized into cells and that

211 Cystine-knot peptides are attractive templates in drug discovery

212 to enhance the cytosolic delivery of cystine-knot peptides.

213 Our results indicate that these cystine knot PET tracers may have potential utility in multiple

214 lding mechanisms for the [Formula: see text]-knotted phytochromes and the [Formula: see text]- and [F

215 Knots play a fundamental role in the dynamics of biologi

216 Although the potential of such cyclized/knot polymer architectures is far from being fulfilled,

217 DRP has led to the formation of new cyclized/knotted polymer structures.

218 y molecular dynamics simulations to generate knotted polymeric configurations having different length

219 se ratios should be useful in characterizing knotted polymers experimentally.

220 and the intrinsic viscosity of semi-flexible knotted polymers in comparison to the linear polymeric c

221 We then compute E C for all these knotted polymers using the program ZENO and find that th

222 the wider literature, demonstrating that the knotting probability of the vortex tangle grows with the

223 the DNA molecule, consistent with a constant knotting probability per unit length.

224 Results of experiments on knotted protein fusions with a highly stable domain show

225 we characterized the effects of the trefoil-knotted protein MJ0366 from Methanocaldococcus jannaschi

226 that ClpXP can easily degrade a deeply 3(1)-knotted protein.

227 uropeptide hormone consisting of two cystine-knot proteins (burs alpha and burs beta), responsible fo

228 of knot folding for the [Formula: see text]-knotted proteins and the [Formula: see text]-knotted ket

229 es of the degradation of both 3(1)- and 5(2)-knotted proteins by ClpXP using numerous constructs wher

230 Therefore, we conclude that naturally knotted proteins cannot attain their knot randomly in th

231 How knotted proteins fold has remained controversial since t

232 a shallow 3(1) knot, it cannot degrade 5(2)-knotted proteins if degradation is initiated at the C-te

233 Mechanical stretching of knotted proteins is also of importance for understanding

234 roversial since the identification of deeply knotted proteins nearly two decades ago.

235 ly published work on the degradation of 5(2)-knotted proteins, our results show that the ClpXP machin

236 [Formula: see text]- and [Formula: see text]-knotted proteins.

237 nitude close to the energy cost of forming a knot randomly in the denatured state.

238 turally knotted proteins cannot attain their knot randomly in the unfolded state but must pay the cos

239 show the occurrence of both tight and loose knots, reconciling previous contradictory results from d

240 The primary outcome was change in number of knots (recorded leakage episodes) from recruitment to 24

241 g on the biophysical characterization of the knot region by NMR spectroscopy, we identify the SAM-bin

242 ealed that Myo6 and the transcription factor Knot regulate transient surges of microtubule polymeriza

243 ay between topology and mechanics in elastic knots remains poorly understood.

244 mination of whether genomic trajectories are knotted remains challenging because small errors in the

245 ew scheme, recovering and extending previous knotting results, and identifying topological interest i

246 along the chromatin fibre, and find that the knotted segment enhances local epigenetic order, giving

247 nsistent with mechanisms in which either the knot simply slips along the polypeptide chain and falls

248 opy revealed that roseltide rT7 is a cystine-knotted, six-cysteine hevein-like cysteine-rich peptide.

249 by the knot translocation velocity than the knot size.

250 d into topologically complex shapes, such as knots, slipknots or complex lassos.

251 Paradigmatic knotted solitons, Hopfions, that are characterized by to

252 f topologies which we quantify in terms of a knot spectrum and its scaling law.

253 d mass spectrometry and the chirality of the knot stereoisomers compared by circular dichroism.

254 sion scores, error scores, leak volumes, and knot tensile strengths.

255 ncreasingly useful for chemists to adopt the knot terminology employed by other disciplines.

256 Links are generalization of knots, that consist of several components.

257 d and unknotted denatured state we find that knotting the polypeptide chain of MJ0366 increase the fo

258 the identification of the so-called cysteine knots, the possibility to analyze all or a non-redundant

259 ynthesis of both molecular granny and square knots through the use of lanthanide-complexed overhand k

260 the unfolded state but must pay the cost of knotting through contacts along their folding landscape.

261 ium structure of DNA knots, without spurious knot tightening and sliding.

262 nding/unwinding in helical propensity as the knot tightens to secure the SAM cofactor.

263 onstruction of the Seifert surface and hence knot topological invariants like the Alexander polynomia

264 the way for the synthesis of other molecular knot topologies and to woven polymer materials.

265 t few years that more complex small-molecule knot topologies have been realized through chemical synt

266 umber and complexity of accessible molecular knot topologies increases, it will become increasingly u

267 The knot topology affects the chemical properties of the str

268 This 7(4) knot topology corresponds to that of an endless knot, wh

269 owever, how a protein substrate containing a knotted topology affects this process remains unknown.

270 derstand allosteric effects modulated by the knotted topology.

271 m several venoms and characterized a cystine knot toxin called JZTx-27 from the venom of tarantula Ch

272 laborated knottin domains, as well as double-knot toxins, that likely evolved from a single ancestral

273 nsform an unknotted trajectory into a highly knotted trajectory and vice versa.

274 nce of two quantitatively different modes of knot translocation through the nanopores, involving very

275 obstruction event is more controlled by the knot translocation velocity than the knot size.

276 rather two qualitatively different modes of knot translocation.

277 Tying the molecular knot transmits information regarding asymmetry across le

278 rrors and duration on 5 basic robotic tasks (knot tying, continuous suturing, cutting, dissection, an

279 Participants completed a knot-tying task within a collective reward ("cooperation

280 losed, double-stranded DNA is defined by the knot type $K$ and the linking-number difference $\Delta

281 the formation of all currently known protein knot types and predicts knot types that might be identif

282 crossing number values m for a wide class of knot types relevant to the real DNA.

283 rently known protein knot types and predicts knot types that might be identified in the future.

284 range of applications, from shoelaces to the knots used for climbing, fishing and sailing(1).

285 perimentally the creation of acoustic vortex knots using metamaterials, with decoupled modulation of

286 e acoustic fields with Hopf link and trefoil knot vortex lines have been observed experimentally.

287 The results suggest that knotted vortex structures are generic in complex three-d

288 between the medial plantar nerve and Henry's knot was 5.96 mm (range, 3.34 to 7.84, SD = 1.12).

289 The first synthetic molecular trefoil knot was prepared in the late 1980s.

290 e domain protein harboring a shallow trefoil knot, we allow the protein to refold from either the kno

291 The composite knots were characterized by (1)H and (13)C NMR spectrosc

292 (3(1)) knot(6-15), and a three-twist (5(2)) knot-were each selectively prepared from the same molecu

293 ought to address is as follows: How does the knot, which constricts the backbone as well as forms the

294 t topology corresponds to that of an endless knot, which is a basic motif of Celtic interlace, the sm

295 olving knotting in open curves using virtual knots, which are a wider class of topological objects th

296 inks-entangled structures, more complex than knots, which consist of several components.

297 interlocked [2]catenane (Solomon link) and a knot with seven crossings in a 258-atom-long closed loop

298 essarily break reciprocity, by pairing nodal knots with their mirror image partners in a fully recipr

299 th free and bound homologs indicate that the knot within the polypeptide backbone plays a significant

300 al realization of structures known as framed knots within optical polarization fields.

301 rs that map the equilibrium structure of DNA knots, without spurious knot tightening and sliding.