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3 y a structural rearrangement that places the scissile amide into an oxyanion hole and forces the nucl
5 onal asymmetry of abasic interference on the scissile and nonscissile strands highlights the importan
6 analog indole at individual positions of the scissile and nonscissile strands on the rate of single-t
7 basic lesions at individual positions of the scissile and nonscissile strands on the rate of single-t
8 specificity depends on the stability of the scissile base-sugar bond by determining the maximal acti
9 ptide was developed based on the fibronectin scissile bond (269)RAA downward arrowVal(272), and this
10 a double latch structure that sequesters the scissile bond (between Arg(234) and Lys(235)) and minimi
11 d the eight residues flanking the prelamin A scissile bond (TRSY LLGN) to all other 19 amino acids, c
12 d to an unfolded state, in which the cryptic scissile bond (Y1605-M1606) is exposed and can then be p
13 tes for the ubiquitins on either side of the scissile bond allow hOtu1 to discriminate among differen
14 pproximately 9-10 residues C-terminal of the scissile bond and acts as an inducer of conformational f
16 propeptide cleavage, thereby identifying the scissile bond and characterizing the basic amino acids r
17 ding of the VWF A2 domain, which exposes the scissile bond and exosite for interaction with complemen
18 ysis requires mechanical force to expose the scissile bond and is regulated by a calcium-binding site
19 nt of cleavage-optimal residues flanking the scissile bond and modulate the mechanism for procofactor
21 of enzyme-mediated scission at the opposite scissile bond and was sufficient to stimulate the format
24 ophilic attack on the carbonyl carbon of the scissile bond are present; it is also the first peptidog
25 ible that quinolone interactions at a single scissile bond are sufficient to distort both strands of
27 te composition to the C-terminal side of the scissile bond as well as interactions of larger substrat
30 membrane alpha-helices, which results in the scissile bond being positioned adjacent to a glutamate-a
31 is remarkable that the peptide spanning the scissile bond binds to but bypasses cleavage by the enzy
32 nserved A9 and A10 bases reside close to the scissile bond but make distinct contributions to catalys
33 ement of two residues that contribute to the scissile bond by Ala did not eliminate cleavage, but rat
34 pin ribozyme-vanadate complex, indicated the scissile bond can adopt a variety of conformations resul
35 or CG bp at the pb position adjacent to the scissile bond can suppress cleavage without inhibiting b
36 ility were most likely caused by alternative scissile bond choices by tissue-specific gamma-secretase
37 B and TeNT: residues adjacent to the site of scissile bond cleavage (cleavage region) and residues lo
38 ', P3, and P5 sites of SNAP25 contributed to scissile bond cleavage by LC/A, whereas the P1' and P2 s
42 the active site of the enzyme and across the scissile bond contribute to defining the rate of process
43 indicate that the presence of a nick at one scissile bond dramatically increases the rate of cleavag
44 riants were prepared with mutations swapping scissile bond flanking sequences in the heavy chain indi
47 ine) folded properly, but exhibited nonideal scissile bond geometries (tau ranging from 118 degrees t
50 or conformational change to expose the first scissile bond in prothrombin, which is the likely event
51 nding site and resultant displacement of the scissile bond in the active site results in the observed
52 force is transduced from the polymer to the scissile bond in the mechanophore (i.e., mechanochemical
54 presence of the quinolone CP-115,953 at one scissile bond increased the extent of enzyme-mediated sc
55 rtially coordinated and that cleavage at one scissile bond increases the degree of cleavage at the ot
56 ge at Gly(2196)-Leu(2197) We noted that this scissile bond is in the linker between fibronectin modul
59 form of CPD was determined and revealed the scissile bond Leu(3428)-Ala(3429) captured in the cataly
60 horothioate substitution is installed at the scissile bond normally cleaved by the HHRz, Pt(II) cross
65 rmational changes in C4 are induced, and its scissile bond region becomes ordered and inserted into t
66 n GLP-1 and GIP, a single thioamide near the scissile bond renders these peptides up to 750-fold more
69 tended peptide sequences before or after the scissile bond showed endopeptidase to be superior to dip
70 of the metalloprotease domain of ADAMTS13 in scissile bond specificity, we identified 3 variable regi
72 yl, so as to enable the nitrogen atom of the scissile bond to accept the proton that is necessary for
75 orts the binding loop in the vicinity of the scissile bond was found to be important both for enzyme
76 that replaced the 3'-bridging oxygen of the scissile bond with a sulfur atom (i.e. 3'-bridging phosp
79 VWF) unfolding which exposes the Y1605-M1606 scissile bond within the VWF A2 domain for cleavage by A
81 (at the +2 or +3 position 3' relative to the scissile bond), 3,N(4)-ethenodeoxycytidine, 3,N(4)-ethen
83 f short amino acid sequences surrounding the scissile bond, -Pro(12)-Asn(13)-, indicated that P2 Gly
85 NA and DNA IBS1 targets, presentation of the scissile bond, and stabilization of the structure by met
86 s a hydroxyethylamine moiety in place of the scissile bond, binds in two equivalent antiparallel orie
88 intact fibronectin at the Ala(271)/Val(272) scissile bond, generating an approximately 30-kd fragmen
89 ds the leucine 10 residues C-terminal to the scissile bond, is critical for collagenolysis and repres
90 neurotoxin (TeNT) cleave VAMP-2 at the same scissile bond, their mechanism(s) of VAMP-2 recognition
91 bunit favors acidic residues proximal to the scissile bond, while the alpha subunit prefers small or
110 in conjunction with the phosphate 3' to the scissile bond; the same Lys is also hydrogen bonded with
111 ve site suggested that Asp195 may facilitate scissile-bond activation and that His247 is oriented to
113 Moreover, we identified multiple additional scissile bonds in an N-terminal linker region of LTBP4 t
114 uential presentation and cleavage of the two scissile bonds in prothrombin activation is accomplished
115 t CA and UA dinucleotides, preferentially at scissile bonds located more than five nucleotides away f
116 , the human enzyme appears to ligate the two scissile bonds of a cleavage site in a nonconcerted fash
119 urface for optimum proteolytic attack on the scissile bonds of membrane-bound protein substrates such
121 core sequence of amino acids surrounding the scissile bonds responsible for governing the relative pr
122 for etoposide, which must be present at both scissile bonds to stabilize a double-stranded DNA break.
124 , interacts with the sequences distal to the scissile bonds whereas the CTD beta1-beta2 loop binds to
126 of polymers bearing three putatively "weak" scissile bonds: the carbon-nitrogen bond of an azobisdia
129 ne mass unit is added to the carbon end of a scissile C-H bond and when one mass unit is added to the
130 hydroxylation that correlated well with the scissile C-H bond energy, indicating a homolytic hydroge
131 an inhibitor carbonyl carbon that mimics the scissile carbonyl of substrates is pyramidalized and jus
132 hat substrate binding forces the substrate's scissile carboxylate group into the neighborhood of seve
133 DCase) furnishes a counterion that helps the scissile carboxylate group of the substrate leave water
135 ne metal ion shifts away from binding at the scissile DNA phosphate to a position near the 3'-adjacen
136 the small subunit and the nicked ends of the scissile DNA strand, mimicking the previously unseen tra
141 particular interest is the activation of non-scissile mechanophores in which latent reactivity can be
146 eases cleave the serpin reactive center loop scissile P1-P1' bond, resulting in serpin-protease suici
147 The (1)J(NC') coupling constant for the (-1) scissile peptide bond at the N-extein-intein junction wa
148 ity to both the active site Cys(184) and the scissile peptide bond between threonine and glycine.
149 loy a splicing pathway in which the upstream scissile peptide bond is consecutively rearranged into t
153 ature, a highly strained conformation at the scissile peptide bond, had been identified and was hypot
159 revious work showed that substitution of the scissile phosphate (P) by methylphosphonate (MeP) permit
160 ious work we showed that substitution of the scissile phosphate (P) by the charge neutral methylphosp
161 VRR nuc) domain, enabling FAN1 to incise the scissile phosphate a few bases distant from the junction
163 ) in the active site that interacts with the scissile phosphate and anchors the general base guanine
164 Five of the metals bind within 12 A of the scissile phosphate and coordinate the majority of the ox
165 y be required for correct positioning of the scissile phosphate and coordination of catalytic residue
166 interaction with the 3'-bridging atom of the scissile phosphate and facilitates DNA scission by the b
167 ltured in isolation, and it shows an ordered scissile phosphate and nucleotide 5' to the cleavage sit
168 ed at 3.1-A resolution exhibits a disordered scissile phosphate and nucleotide 5' to the cleavage sit
170 del suggests that the pro-R(P) oxygen of the scissile phosphate and the 2'-hydroxyl nucleophile are i
171 Trp330 also assists in the activation of the scissile phosphate and the departure of the 5'-hydroxyl
172 O2' nucleophile, and the conformation at the scissile phosphate and the position of the general base
174 e optimal spacing between the 5' end and the scissile phosphate appears to be eight nucleotides for R
176 r, a single phosphorothioate in place of the scissile phosphate blocks cleavage; the phosphorothioate
178 a fully assembled active site including the scissile phosphate bound by a divalent metal ion cofacto
179 ied at the end of the active site, while the scissile phosphate bridges two active site Mg(2+) ions.
180 nt is mediated by nucleophilic attack on the scissile phosphate by a conserved tyrosine residue, form
182 by replacement of the 5'-oxygen atom at the scissile phosphate by sulfur (5'-PS), which is a much be
183 eway, and double-base unpairing flanking the scissile phosphate control precise flap incision by the
184 ft in position together with movement of the scissile phosphate deeper into the active site cleft.
187 nt manganese rescue was not observed for the scissile phosphate diester linkage implying that electro
188 double nucleotide unpairing that places the scissile phosphate diester on active site divalent metal
189 unpairing the 5'-end of duplex to permit the scissile phosphate diester to contact catalytic divalent
190 interactions that successively position the scissile phosphate for bottom-strand cleavage at the DNA
191 hree-base interaction may be to position the scissile phosphate for cleavage, rather than to directly
194 cond hydrated Mg(2+) ion that approaches the scissile phosphate from its binding site in the pre-clea
196 nt metal ion and the 3'-bridging atom of the scissile phosphate greatly enhances enzyme-mediated DNA
197 eaturing a common, novel conformation of the scissile phosphate group as compared to all previous Eco
200 S1 nucleotide) or 3' (S1' nucleotide) of the scissile phosphate had large effects on substrate utiliz
201 t 1.95 A, reveals an Mg(2+) ion bound to the scissile phosphate in a position corresponding to Mg(B)
203 om in place of the 3'-bridging oxygen of the scissile phosphate in the presence of Mg2+, Mn2+, or Ca2
206 tereospecific phosphorothioate effect at the scissile phosphate is consistent with a significant stab
207 rate helix docking event that constrains the scissile phosphate linkage and positions G8 and A38 for
208 tonated C75 to the nonbridging oxygen of the scissile phosphate occurs to stabilize the phosphorane i
211 I domain, which can be extended to place the scissile phosphate of the target strand adjacent to the
212 Ruler to form a protein-DNA complex with the scissile phosphate positioned at the active site for opt
213 catalysis, the nucleophile is aligned with a scissile phosphate positioned proximal to the A-9 phosph
216 cond metal ion and a nonbridging atom of the scissile phosphate that stimulates DNA cleavage mediated
217 ics; neutralizing the negative charge on the scissile phosphate through methylphosphonate (MeP) subst
218 ween the two catalytic sites, in order for a scissile phosphate to attract a metal ion to the A-site
219 by compensatory charge neutralization of the scissile phosphate via methylphosphonate (MeP) modificat
220 roup (the non-bridging 3'-oxygen atom of the scissile phosphate) during the hydrolysis reaction.
221 PPT positions -2, -4 and +1 (relative to the scissile phosphate) substantially reduces (+)-strand pri
222 tive site and the non-bridging oxygen of the scissile phosphate, a feature found previously also for
223 taining the complete intron, both exons, the scissile phosphate, and all of the functional groups imp
224 s state, the nucleophile is in line with the scissile phosphate, and the N1 position of G33 and N3 po
225 coordinated by a conserved aspartate and the scissile phosphate, as observed in the restriction endon
226 a U-1 forms the most robust kink around the scissile phosphate, exposing it to the catalytic C75 in
227 2') to G40 is concomitant with attack of the scissile phosphate, followed by the remainder of the cle
228 ting SRL, containing a 3'-sulfur atom at the scissile phosphate, reacts at a fully diffusion-limited
229 R(p) oxygen of the phosphate group 3' of the scissile phosphate, suggesting possible roles for these
231 the modeled G53 2'-OH group that attacks the scissile phosphate, thus suggesting a direct role in gen
232 The citrate fills the binding site for the scissile phosphate, wherein it is coordinated by Arg237,
233 cleophile requiring a closer approach to the scissile phosphate, which in turn increases the barrier.
234 interaction with the 3'-bridging atom of the scissile phosphate, while the other (M(2)(2+)) is believ
235 ng oligodeoxynucleotides substituted, at the scissile phosphate, with isomeric phosphorothioates and
257 ated to the non-bridging oxygen atoms of the scissile phosphate; for the latter, additional evidence
259 more ambiguous third site bridges the A9 and scissile phosphates in a manner consistent with that of
261 aining a phosphoramidate substitution at the scissile phosphates were resistant to cleavage by the en
263 We find that resolution is optimal when the scissile phosphodiester (Tp/N) is located two nucleotide
264 The residues in ONC that are proximal to the scissile phosphodiester bond (His10, Lys31, and His97) a
267 mal structure, integrase gains access to the scissile phosphodiester bonds by lifting DNA off the his
268 ed at the catalytic center, bringing the two scissile phosphodiester bonds into close proximity.
271 1Cas9, the active site is seen poised at the scissile phosphodiester linkage of the target strand, pr
272 6-deoxyadenosine (dA) positions flanking the scissile phosphodiester slow the rate of DNA religation
274 icked-site substrate at the positions of the scissile phosphodiesters result in abolition or inhibiti
275 water molecule to the phosphorus atom of the scissile phosphoester bond, with the attacking water bei
276 s via an in-line-attack by CYT 17 O2' on the scissile phosphorous (ADE 1.1 P), and is therefore consi
277 with an abortive 3'-terminal dC close to the scissile position in the enzyme active site, providing i
278 design, the adenosine ribonucleotide at the scissile position of the 8-17 DNAzyme was replaced by 2'
280 troducing tetrahydrofuran lesions around the scissile PPT/unique 3'-sequence junction indicate that t
281 limited by modest force-free stability or a scissile response that caps mechanoacid generation at on
283 the AT(1)R-associated short form suggested a scissile site located within the Arg(363)-Arg(393) regio
284 delivery to the active site of the selected scissile sites further implicates the existence of a pre
285 ed to determine the timing of three selected scissile sites in lambdaN approaching the proteolytic si
286 ts the "almost complete" delivery of all the scissile sites in lambdaN to the proteolytic site in an
288 eptide bond cleavage and the delivery of the scissile sites near the amino- versus carboxyl-terminal
290 ns become energetically more damaging as the scissile strand is shortened from 32 to 24 and 18 nucleo
291 rand in the context of duplexes in which the scissile strand length was progressively shortened.
292 -Oxo substitutions at the -1 position in the scissile strand slowed single-turnover cleavage by a fac
293 s effects of eliminating the +2T base on the scissile strand were rectified by introducing the nonpol
294 aced the -1N, +1T, +2T, and +4C bases of the scissile strand, but abasic lesions at +5C and +3C had l
295 basic sites within the CCCTT sequence of the scissile strand, but an abasic lesion at the 5'-OH nucle
298 eus cleaves LPXTG-containing proteins at the scissile T-G peptide bond and ligates protein-LPXT to th
300 leavage by analyzing the conformation of the scissile X-Pro peptide bond, and by comparing the rate c