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1 ons within the catalytic core which forms a "closed complex".
2 art codon, indicating destabilization of the closed complex.
3 lymerase which leads to the formation of the closed complex.
4 is required to describe the formation of the closed complex.
5 getic barrier for docking into the reactive, closed complex.
6 tic core via tertiary interactions to give a closed complex.
7 ymerase to a promoter DNA and formation of a closed complex.
8 the subsequent remodelling of the Esigma(54) closed complex.
9 ouble-stranded DNA is present in the initial closed complex.
10 se and promoter DNA may adequately model the closed complex.
11 s with features similar to those of a stable closed complex.
12 re used to mimic RNAP-promoter contacts in a closed complex.
13  R383 is not proximal to promoter DNA in the closed complex.
14  shown to have a destabilizing effect on the closed complex.
15 site inhibits or eliminates formation of the closed complex.
16 hree failed in transcription after forming a closed complex.
17 sigma54-holoenzyme to the promoter to form a closed complex.
18 aking place in the polymerase holoenzyme and closed complex.
19 h the formation of a catalytically competent closed complex.
20 AP to promoter DNA to form the RNAP-promoter closed complex.
21 ved in the heparin sensitivity of the sigmaN closed complex.
22  X-ray crystal structure), consistent with a closed complex.
23 T) and sequesters RNA polymerase (RNAP) in a closed complex.
24 e activity in the formation of a prokaryotic closed complex.
25 ed on a variety of crystallographic open and closed complexes.
26 ), the equilibrium constant for formation of closed complexes.
27 e sufficient to ensure stable docking in the closed complex, added functional groups give stronger bi
28 ilar in energy to those of the corresponding closed complexes after chemistry, in marked contrast to
29 fold in this work) increases affinity in the closed complex and accelerates promoter opening.
30 ts (UDP plus GalNAc) representing an initial closed complex and later open form primed for product re
31 gma factor (sigma(54)), which forms a stable closed complex and requires its activator that belongs t
32 cture-function relationships in the reactive closed complex and targeted engineering is hampered by h
33 rase was the lowest for constructs mimicking closed complex and the highest for the constructs mimick
34  mutant enzyme are in rapid equilibrium with closed complexes and, unlike the wild-type complexes, ar
35 ith the P-site tRNA-head interaction in the 'closed' complex and is likely ejected from the P-site up
36 ), the equilibrium constant for formation of closed complexes, and decreased K(B)k(f) by a factor of
37 AP to promoter DNA to form the RNAP-promoter closed complex; and (ii) protein-protein interactions be
38    Since T-9 is melted in open complexes the closed complex appears poised for melting.
39 Consequently, the urea moieties in the fully closed complex are able to catalyze a Diels-Alder reacti
40 ons between the activator and the Esigma(54) closed complex are in themselves insufficient for formin
41                  We propose a model in which closed complexes are established in the upstream region
42  scanning and to impede rearrangement to the closed complex at non-AUG codons.
43 54)-RNA polymerase holoenzyme forms a stable closed complex at the promoter site that rarely isomeris
44  R13P and K16D substitutions destabilize the closed complex at UUG codons in reconstituted PICs.
45 consistent with its ability to stabilize the closed complex at UUG.
46 nteractions are deterred in the rigid, fully closed complex because of geometric and steric restraint
47 res have revealed interactions unique to the closed complex between arginines R55/R57 of eIF2alpha wi
48 catalyzes the ATP-dependent isomerization of closed complexes between sigma 54-RNA polymerase holoenz
49 transcription by catalyzing isomerization of closed complexes between sigma54-holoenzyme and a promot
50  promoter by catalysing the isomerization of closed complexes between sigma54-RNA polymerase holoenzy
51 a54-holoenzyme catalyze the isomerization of closed complexes between this polymerase and a promotor
52 r DNA is bent slightly by <40 degrees in the closed complex but bent more sharply by 86 degrees in th
53  isomerization) because isomerization to the closed complex commits the substrate to react.
54  was changed to an alanine crystallized in a closed complex containing dethiaacetyl-CoA, which adopts
55 to a promoter to form an inactive, unstable, closed complex (described by an equilibrium constant, K(
56       Detailed quantification shows that the closed complex detected has the same binding constant as
57                                       In the closed complex, DNA sequences melted upon activation are
58           The initial collision complex or a closed complex, ED(c) is formed with a K(d) of 1.8 micro
59                               Apart from the closed complex formation and promoter clearance, we were
60 inhibits transcription at the early stage of closed complex formation by blocking interaction of RNA
61                        Band shift assays for closed complex formation implicated a series of arginine
62                     The first step after the closed complex formation leads to a rapid increase of 2-
63 formational change leads to a stable ternary closed complex formation only when the correct nucleotid
64                 The effect of temperature on closed complex formation was found to be small over the
65 Pol II from properly engaging the DNA during closed complex formation, resulting in complexes with an
66 ent or steps of transcription after promoter closed complex formation.
67 stream and downstream of the TATA box during closed complex formation.
68 ments of functionally important domains upon closed complex formation.
69 cts a step in transcription initiation after closed-complex formation in addition to its stimulatory
70 that the -13 and -15 positions contribute to closed-complex formation, whereas the -12 position has a
71  the function of sigma54 at some point after closed-complex formation.
72 teps of transcription initiation that follow closed-complex formation.
73 detailed DNase I footprinting studies of the closed complex formed on the phage lambda prmup-1 Delta2
74 ilarities to as well as differences from the closed complex formed under standard transcription condi
75 nanocircuit-based observations, the enzyme's closed complex forms a phosphodiester bond in a highly e
76 r efficient transcription initiation, once a closed complex has formed.
77             Comparison of the holoenzyme and closed complex hydroxyl radical footprints revealed that
78                  Although the formation of a closed complex in the presence of a non-hydrogen-bonding
79 DNA and to form an RNA polymerase holoenzyme closed complex in vitro.
80 s several intermediates, the first being the closed complex in which the DNA is fully base-paired.
81  solely by base-pairing interactions, or the closed complex, in which the duplex is docked into terti
82  for the AAA activator within the Esigma(54) closed complex includes a complex interface contributed
83 romoter of bacteriophage lambda to model the closed complex intermediate at physiologically relevant
84 of an initial RNA polymerase (RNAP)-promoter closed complex into a catalytically competent RNAP-promo
85 ich occurs during the isomerization from the closed complex into the open complex, contributes to the
86 quilibrium binding process, formation of the closed complex is entropy driven.
87  with zero ribonucleotides present, when the closed complex is favored, we find reduced tension sensi
88                            Finally, a stable closed complex is not formed in the presence of a ddNTP
89 complexes, we explain why the RNAP-sigma(54) closed complex is unable to access the DNA template and
90 m dissociation constant of RNA polymerase-P1 closed complexes is largely unaffected in the presence o
91         A "threshold" model for the open and closed complexes is presented that provides a framework
92 onstant describing formation of the initial (closed) complex is close to that expected for a diffusio
93   sigmaN (sigma54) RNA polymerase holoenzyme closed complexes isomerize to open complexes in a reacti
94  using x-ray structure data for the open and closed complexes of the Taq enzyme with DNA revealed tha
95 t binding of the activator to the Esigma(54) closed complex results in the re-organization of Esigma(
96             Our results indicate that in the closed complex, RNA polymerase recognizes base pairs as
97 he composite rate constant for conversion of closed complexes (RP(c)) to open complexes (RP(o)) but d
98 A DNA fork junction structure present within closed complexes serves as a nucleation point for the DN
99              The footprinting pattern of the closed complex shows major differences from that of the
100 lted in arrest of initiation at the earliest closed complex, suggesting that region 1.2 is required f
101 pon formation of the wild-type holoenzyme or closed complex, suggesting that, in the mutants, alterat
102 ted with stress responses and forms a stable closed complex that does not spontaneously isomerize to
103 se holoenzyme binds to promoters as a stable closed complex that is silent for transcription unless a
104                                          The closed complexes, then isomerize to open complexes.
105  activation sequences (UAS) and contacts the closed complex through DNA looping to activate transcrip
106 ium constant, K(B)) and isomerization of the closed complex to an active, stable, open complex (descr
107  isomerization step in the conversion of the closed complex to an open one indicates that there are a
108 (0.26(+/-0.02) s-1) in the conversion of the closed complex to an open one was an order of magnitude
109  at least two steps in the conversion of the closed complex to an open one.
110 o a three-step model for the transition from closed complex to elongation complex, two steps of which
111 tial recognition of the duplex promoter in a closed complex to the final RPo.
112  increasing the isomerization of the initial closed complex to the open complex.
113 isomerization of the RNA polymerase promoter closed complex to the RNA polymerase promoter open compl
114 cilitates isomerization of the RNAP-promoter closed complex to the RNAP-promoter open complex.
115 ilitating isomerization of the RNAP-promoter closed complex to the transcriptionally competent open c
116 olthetai binding to the Poltheta-pol:DNA/DNA closed complex traps the polymerase on DNA for more than
117                   This initial RNAP-promoter closed complex undergoes a series of conformational chan
118  variant sigma factor sigma(54) remains as a closed complex until ATP hydrolysis-dependent remodeling
119  in that it forms a transcriptionally silent closed complex upon promoter binding.
120 binding step leading to the formation of the closed complex were linear.
121 ding of T7 RNAP to the promoter results in a closed complex, which is then converted into an open com
122 c for AZT because HIV-1 RT, which can form a closed complex with a dideoxy-terminated primer and an i
123 oside triphosphate (dNTP), does not form the closed complex with an AZTMP-terminated primer and an in
124 c13 catalyzes the transit of syntaxin from a closed complex with Munc18 into the ternary SNARE comple
125 bunit sigma(N) (sigma(54)) can form a stable closed complex with promoter DNA but only undergo transi
126 ndent mechanism by associating with open and closed complexes with different affinities.
127 tures, including reversible formation of two closed complexes with greatly differing stabilities, mul

 
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