Split (1)

train · 816k rows

paragraph_index int64	sec string	p_has_citation int64	cites string	citeids list	pmid int64	cited_id string	sentences string	all_sent_cites list	sent_len int64	sentence_batch_index int64	sent_has_citation float64	qc_fail bool	cited_sentence string	cites_in_sentence list	cln_sentence string	is_cap bool	is_alpha bool	ends_wp bool	cit_qc bool	lgtm bool	__index_level_0__ int64
3	INTRODUCTION	1	16	[ "b4", "b16", "b12", "b16" ]	16,738,132	pmid-7715723\|pmid-10660627\|pmid-9245598\|pmid-10660627\|pmid-10499579	The interactions with Thr30 and Thr49 have been shown to be essential for activation of TRAP whereas the hydrogen bond with Ser53 is dispensable (16).	[ "4", "16", "12", "16" ]	150	8,100	1	false	The interactions with Thr30 and Thr49 have been shown to be essential for activation of TRAP whereas the hydrogen bond with Ser53 is dispensable.	[ "16" ]	The interactions with Thr30 and Thr49 have been shown to be essential for activation of TRAP whereas the hydrogen bond with Ser53 is dispensable.	true	true	true	true	true	1,313
3	INTRODUCTION	1	4	[ "b4", "b16", "b12", "b16" ]	16,738,132	pmid-7715723\|pmid-10660627\|pmid-9245598\|pmid-10660627\|pmid-10499579	The interaction of Thr52 with tryptophan has only a limited role in activation of TRAP.	[ "4", "16", "12", "16" ]	87	8,101	0	false	The interaction of Thr52 with tryptophan has only a limited role in activation of TRAP.	[]	The interaction of Thr52 with tryptophan has only a limited role in activation of TRAP.	true	true	true	true	true	1,313
3	INTRODUCTION	1	4	[ "b4", "b16", "b12", "b16" ]	16,738,132	pmid-7715723\|pmid-10660627\|pmid-9245598\|pmid-10660627\|pmid-10499579	In addition, each bound tryptophan hydrogen bonds with the main-chain portions of several TRAP residues, including Thr25, Gly27, Asp29 and Gln47.	[ "4", "16", "12", "16" ]	145	8,102	0	false	In addition, each bound tryptophan hydrogen bonds with the main-chain portions of several TRAP residues, including Thr25, Gly27, Asp29 and Gln47.	[]	In addition, each bound tryptophan hydrogen bonds with the main-chain portions of several TRAP residues, including Thr25, Gly27, Asp29 and Gln47.	true	true	true	true	true	1,313
3	INTRODUCTION	1	4	[ "b4", "b16", "b12", "b16" ]	16,738,132	pmid-7715723\|pmid-10660627\|pmid-9245598\|pmid-10660627\|pmid-10499579	Of these, only the interactions with Thr25 and Gln47 have been shown to play a role in activation (12,16).	[ "4", "16", "12", "16" ]	106	8,103	0	false	Of these, only the interactions with Thr25 and Gln47 have been shown to play a role in activation.	[ "12,16" ]	Of these, only the interactions with Thr25 and Gln47 have been shown to play a role in activation.	true	true	true	true	true	1,313
4	INTRODUCTION	1	16	[ "b16", "b16", "b17" ]	16,738,132	pmid-10660627\|pmid-10660627\|pmid-14687568\|pmid-12381302	The importance of Thr30 in tryptophan binding and activation of TRAP is demonstrated by the dramatic effects of two substitutions (Ala and Val) at this position.	[ "16", "16", "17" ]	161	8,104	0	false	The importance of Thr30 in tryptophan binding and activation of TRAP is demonstrated by the dramatic effects of two substitutions (Ala and Val) at this position.	[]	The importance of Thr30 in tryptophan binding and activation of TRAP is demonstrated by the dramatic effects of two substitutions (Ala and Val) at this position.	true	true	true	true	true	1,314
4	INTRODUCTION	1	16	[ "b16", "b16", "b17" ]	16,738,132	pmid-10660627\|pmid-10660627\|pmid-14687568\|pmid-12381302	Substituting Ala for Thr30 (T30A) disrupts both the tryptophan- and RNA-binding activities of the protein (16).	[ "16", "16", "17" ]	111	8,105	1	false	Substituting Ala for Thr30 (T30A) disrupts both the tryptophan- and RNA-binding activities of the protein.	[ "16" ]	Substituting Ala for Thr30 (T30A) disrupts both the tryptophan- and RNA-binding activities of the protein.	true	true	true	true	true	1,314
4	INTRODUCTION	1	16	[ "b16", "b16", "b17" ]	16,738,132	pmid-10660627\|pmid-10660627\|pmid-14687568\|pmid-12381302	In contrast, T30V TRAP, with valine at position 30, does not bind tryptophan, but binds RNA constitutively, although with ∼100-fold lower affinity than tryptophan-activated WT TRAP (16).	[ "16", "16", "17" ]	186	8,106	1	false	In contrast, T30V TRAP, with valine at position 30, does not bind tryptophan, but binds RNA constitutively, although with ∼100-fold lower affinity than tryptophan-activated WT TRAP.	[ "16" ]	In contrast, T30V TRAP, with valine at position 30, does not bind tryptophan, but binds RNA constitutively, although with ∼100-fold lower affinity than tryptophan-activated WT TRAP.	true	true	true	true	true	1,314
4	INTRODUCTION	1	17	[ "b16", "b16", "b17" ]	16,738,132	pmid-10660627\|pmid-10660627\|pmid-14687568\|pmid-12381302	Characterization of the interaction of T30V TRAP with RNA showed that the mutant protein recognizes similar features of the RNA as does WT TRAP (17).	[ "16", "16", "17" ]	149	8,107	1	false	Characterization of the interaction of T30V TRAP with RNA showed that the mutant protein recognizes similar features of the RNA as does WT TRAP.	[ "17" ]	Characterization of the interaction of T30V TRAP with RNA showed that the mutant protein recognizes similar features of the RNA as does WT TRAP.	true	true	true	true	true	1,314
4	INTRODUCTION	1	16	[ "b16", "b16", "b17" ]	16,738,132	pmid-10660627\|pmid-10660627\|pmid-14687568\|pmid-12381302	This observation suggests that the T30V substitution may activate TRAP in a manner similar to how tryptophan binding activates WT TRAP.	[ "16", "16", "17" ]	135	8,108	0	false	This observation suggests that the T30V substitution may activate TRAP in a manner similar to how tryptophan binding activates WT TRAP.	[]	This observation suggests that the T30V substitution may activate TRAP in a manner similar to how tryptophan binding activates WT TRAP.	true	true	true	true	true	1,314
5	INTRODUCTION	1	11	[ "b11" ]	16,738,132	pmid-10499579\|pmid-14687568\|pmid-15050822\|pmid-10499579\|pmid-9245598	To provide a better understanding of the role of Thr30 in activation of TRAP, we introduced several additional substitutions at position 30 and examined the RNA binding and tryptophan binding properties of the resulting mutant proteins.	[ "11" ]	236	8,109	0	false	To provide a better understanding of the role of Thr30 in activation of TRAP, we introduced several additional substitutions at position 30 and examined the RNA binding and tryptophan binding properties of the resulting mutant proteins.	[]	To provide a better understanding of the role of Thr30 in activation of TRAP, we introduced several additional substitutions at position 30 and examined the RNA binding and tryptophan binding properties of the resulting mutant proteins.	true	true	true	true	true	1,315
5	INTRODUCTION	1	11	[ "b11" ]	16,738,132	pmid-10499579\|pmid-14687568\|pmid-15050822\|pmid-10499579\|pmid-9245598	We also determined that in general, the same amino acid residues in WT TRAP and T30V TRAP are important for RNA binding.	[ "11" ]	120	8,110	0	false	We also determined that in general, the same amino acid residues in WT TRAP and T30V TRAP are important for RNA binding.	[]	We also determined that in general, the same amino acid residues in WT TRAP and T30V TRAP are important for RNA binding.	true	true	true	true	true	1,315
5	INTRODUCTION	1	11	[ "b11" ]	16,738,132	pmid-10499579\|pmid-14687568\|pmid-15050822\|pmid-10499579\|pmid-9245598	However, the side chain of Lys37, which plays an important role in the WT complex, does not contribute to the stability of the T30V TRAP–RNA complex.	[ "11" ]	149	8,111	0	false	However, the side chain of Lys37, which plays an important role in the WT complex, does not contribute to the stability of the T30V TRAP–RNA complex.	[]	However, the side chain of Lys37, which plays an important role in the WT complex, does not contribute to the stability of the T30V TRAP–RNA complex.	true	true	true	true	true	1,315
5	INTRODUCTION	1	11	[ "b11" ]	16,738,132	pmid-10499579\|pmid-14687568\|pmid-15050822\|pmid-10499579\|pmid-9245598	Additionally, we found that altering residues in T30V TRAP that contact the RNA affects the tryptophan binding properties of the resulting double mutant proteins.	[ "11" ]	162	8,112	0	false	Additionally, we found that altering residues in T30V TRAP that contact the RNA affects the tryptophan binding properties of the resulting double mutant proteins.	[]	Additionally, we found that altering residues in T30V TRAP that contact the RNA affects the tryptophan binding properties of the resulting double mutant proteins.	true	true	true	true	true	1,315
5	INTRODUCTION	1	11	[ "b11" ]	16,738,132	pmid-10499579\|pmid-14687568\|pmid-15050822\|pmid-10499579\|pmid-9245598	This finding indicates that information can be transferred from the RNA binding region to the tryptophan binding site even though these sites are distinct and ≥7.5 Å apart (11).	[ "11" ]	177	8,113	1	false	This finding indicates that information can be transferred from the RNA binding region to the tryptophan binding site even though these sites are distinct and ≥7.5 Å apart.	[ "11" ]	This finding indicates that information can be transferred from the RNA binding region to the tryptophan binding site even though these sites are distinct and ≥7.5 Å apart.	true	true	true	true	true	1,315
0	DISCUSSION	1	17	[ "b17" ]	16,738,132	pmid-9383185\|pmid-8022289\|pmid-10369778\|pmid-7715723\|pmid-8419914\|pmid-7544009\|pmid-14687568	Tryptophan-activation of TRAP to bind its target RNAs is central to regulation of expression of the trp genes in B.subtilis.	[ "17" ]	124	8,114	0	false	Tryptophan-activation of TRAP to bind its target RNAs is central to regulation of expression of the trp genes in B.subtilis.	[]	Tryptophan-activation of TRAP to bind its target RNAs is central to regulation of expression of the trp genes in B.subtilis.	true	true	true	true	true	1,316
0	DISCUSSION	1	17	[ "b17" ]	16,738,132	pmid-9383185\|pmid-8022289\|pmid-10369778\|pmid-7715723\|pmid-8419914\|pmid-7544009\|pmid-14687568	However, the precise mechanism of tryptophan-activation is not known, in part due to lack of a high resolution structure of apo-TRAP (i.e.	[ "17" ]	138	8,115	0	false	However, the precise mechanism of tryptophan-activation is not known, in part due to lack of a high resolution structure of apo-TRAP (i.e.	[]	However, the precise mechanism of tryptophan-activation is not known, in part due to lack of a high resolution structure of apo-TRAP (i.e.	true	true	true	true	true	1,316
0	DISCUSSION	1	17	[ "b17" ]	16,738,132	pmid-9383185\|pmid-8022289\|pmid-10369778\|pmid-7715723\|pmid-8419914\|pmid-7544009\|pmid-14687568	TRAP in the absence of bound tryptophan).	[ "17" ]	41	8,116	0	false	TRAP in the absence of bound tryptophan).	[]	TRAP in the absence of bound tryptophan).	true	true	true	true	true	1,316
0	DISCUSSION	1	17	[ "b17" ]	16,738,132	pmid-9383185\|pmid-8022289\|pmid-10369778\|pmid-7715723\|pmid-8419914\|pmid-7544009\|pmid-14687568	In this study, we provide insight into tryptophan-activation of TRAP by studying a mutant protein (T30V) that binds RNA in the absence of bound tryptophan.	[ "17" ]	155	8,117	0	false	In this study, we provide insight into tryptophan-activation of TRAP by studying a mutant protein (T30V) that binds RNA in the absence of bound tryptophan.	[]	In this study, we provide insight into tryptophan-activation of TRAP by studying a mutant protein (T30V) that binds RNA in the absence of bound tryptophan.	true	true	true	true	true	1,316
0	DISCUSSION	1	17	[ "b17" ]	16,738,132	pmid-9383185\|pmid-8022289\|pmid-10369778\|pmid-7715723\|pmid-8419914\|pmid-7544009\|pmid-14687568	T30V TRAP recognizes similar RNA features as does WT TRAP (17).	[ "17" ]	63	8,118	1	false	T30V TRAP recognizes similar RNA features as does WT TRAP.	[ "17" ]	T30V TRAP recognizes similar RNA features as does WT TRAP.	true	true	true	true	true	1,316
0	DISCUSSION	1	17	[ "b17" ]	16,738,132	pmid-9383185\|pmid-8022289\|pmid-10369778\|pmid-7715723\|pmid-8419914\|pmid-7544009\|pmid-14687568	Our results show that three of the four principal RNA binding residues, Glu36, Lys56 and Arg58, are important for interacting with RNA in both WT and T30V TRAP (Table 3).	[ "17" ]	170	8,119	0	false	Our results show that three of the four principal RNA binding residues, Glu36, Lys56 and Arg58, are important for interacting with RNA in both WT and T30V TRAP (Table 3).	[]	Our results show that three of the four principal RNA binding residues, Glu36, Lys56 and Arg58, are important for interacting with RNA in both WT and T30V TRAP (Table 3).	true	true	true	true	true	1,316
0	DISCUSSION	1	17	[ "b17" ]	16,738,132	pmid-9383185\|pmid-8022289\|pmid-10369778\|pmid-7715723\|pmid-8419914\|pmid-7544009\|pmid-14687568	Lys37 is important for RNA binding to WT TRAP but not for binding to T30V TRAP.	[ "17" ]	79	8,120	0	false	Lys37 is important for RNA binding to WT TRAP but not for binding to T30V TRAP.	[]	Lys37 is important for RNA binding to WT TRAP but not for binding to T30V TRAP.	true	true	true	true	true	1,316
1	DISCUSSION	1	4	[ "b4", "b17" ]	16,738,132	pmid-15050822\|pmid-9245598\|pmid-10369778\|pmid-7715723\|pmid-14687568	The side chain of Thr30 hydrogen bonds with the amino group of the bound tryptophan (4).	[ "4", "17" ]	88	8,121	1	false	The side chain of Thr30 hydrogen bonds with the amino group of the bound tryptophan.	[ "4" ]	The side chain of Thr30 hydrogen bonds with the amino group of the bound tryptophan.	true	true	true	true	true	1,317
1	DISCUSSION	1	4	[ "b4", "b17" ]	16,738,132	pmid-15050822\|pmid-9245598\|pmid-10369778\|pmid-7715723\|pmid-14687568	Our results with mutant proteins bearing substitutions at position 30 indicate that as long as the hydrogen bonding potential of this side chain is maintained, TRAP can bind tryptophan and become activated to bind RNA.	[ "4", "17" ]	218	8,122	0	false	Our results with mutant proteins bearing substitutions at position 30 indicate that as long as the hydrogen bonding potential of this side chain is maintained, TRAP can bind tryptophan and become activated to bind RNA.	[]	Our results with mutant proteins bearing substitutions at position 30 indicate that as long as the hydrogen bonding potential of this side chain is maintained, TRAP can bind tryptophan and become activated to bind RNA.	true	true	true	true	true	1,317
1	DISCUSSION	1	4	[ "b4", "b17" ]	16,738,132	pmid-15050822\|pmid-9245598\|pmid-10369778\|pmid-7715723\|pmid-14687568	Some mutant proteins bind RNA with lower affinity than WT TRAP even though they are fully saturated with tryptophan (Table 2: T30D, T30E, T30N and T30Q).	[ "4", "17" ]	153	8,123	0	false	Some mutant proteins bind RNA with lower affinity than WT TRAP even though they are fully saturated with tryptophan (Table 2: T30D, T30E, T30N and T30Q).	[]	Some mutant proteins bind RNA with lower affinity than WT TRAP even though they are fully saturated with tryptophan (Table 2: T30D, T30E, T30N and T30Q).	true	true	true	true	true	1,317
1	DISCUSSION	1	4	[ "b4", "b17" ]	16,738,132	pmid-15050822\|pmid-9245598\|pmid-10369778\|pmid-7715723\|pmid-14687568	The tryptophan analog indole-3-propionic acid lacks the amino group of tryptophan and thus is unable to hydrogen bond with Thr30.	[ "4", "17" ]	129	8,124	0	false	The tryptophan analog indole-3-propionic acid lacks the amino group of tryptophan and thus is unable to hydrogen bond with Thr30.	[]	The tryptophan analog indole-3-propionic acid lacks the amino group of tryptophan and thus is unable to hydrogen bond with Thr30.	true	true	true	true	true	1,317
1	DISCUSSION	1	17	[ "b4", "b17" ]	16,738,132	pmid-15050822\|pmid-9245598\|pmid-10369778\|pmid-7715723\|pmid-14687568	This analog does not bind to either WT or T30V further demonstrating the importance of this interaction (17).	[ "4", "17" ]	109	8,125	1	false	This analog does not bind to either WT or T30V further demonstrating the importance of this interaction.	[ "17" ]	This analog does not bind to either WT or T30V further demonstrating the importance of this interaction.	true	true	true	true	true	1,317
1	DISCUSSION	1	4	[ "b4", "b17" ]	16,738,132	pmid-15050822\|pmid-9245598\|pmid-10369778\|pmid-7715723\|pmid-14687568	Together these observations provide further support for the importance of residue 30 in both tryptophan binding and activation of RNA binding as well as show that these processes can be distinct from each other.	[ "4", "17" ]	211	8,126	0	false	Together these observations provide further support for the importance of residue 30 in both tryptophan binding and activation of RNA binding as well as show that these processes can be distinct from each other.	[]	Together these observations provide further support for the importance of residue 30 in both tryptophan binding and activation of RNA binding as well as show that these processes can be distinct from each other.	true	true	true	true	true	1,317
2	DISCUSSION	1	16	[ "b16", "b29", "b30" ]	16,738,132	pmid-15099736\|pmid-11805104\|pmid-11805104\|pmid-12381302\|pmid-10660627\|NA\|NA	To date, mutants with substitutions at Thr30 are the only examples of altered TRAP proteins that bind RNA constitutively in the absence of bound tryptophan.	[ "16", "29", "30" ]	156	8,127	0	false	To date, mutants with substitutions at Thr30 are the only examples of altered TRAP proteins that bind RNA constitutively in the absence of bound tryptophan.	[]	To date, mutants with substitutions at Thr30 are the only examples of altered TRAP proteins that bind RNA constitutively in the absence of bound tryptophan.	true	true	true	true	true	1,318
2	DISCUSSION	1	16	[ "b16", "b29", "b30" ]	16,738,132	pmid-15099736\|pmid-11805104\|pmid-11805104\|pmid-12381302\|pmid-10660627\|NA\|NA	These include T30V and T30I, which suggests that constitutive binding is the result of the presence of a intermediate sized hydrophobic side chain at position 30 that cannot hydrogen bond with tryptophan (16).	[ "16", "29", "30" ]	209	8,128	1	false	These include T30V and T30I, which suggests that constitutive binding is the result of the presence of a intermediate sized hydrophobic side chain at position 30 that cannot hydrogen bond with tryptophan.	[ "16" ]	These include T30V and T30I, which suggests that constitutive binding is the result of the presence of a intermediate sized hydrophobic side chain at position 30 that cannot hydrogen bond with tryptophan.	true	true	true	true	true	1,318
2	DISCUSSION	1	16	[ "b16", "b29", "b30" ]	16,738,132	pmid-15099736\|pmid-11805104\|pmid-11805104\|pmid-12381302\|pmid-10660627\|NA\|NA	However, T30L TRAP, with Leu at position 30, does not bind RNA constitutively but instead shows tryptophan-dependent RNA binding.	[ "16", "29", "30" ]	129	8,129	0	false	However, T30L TRAP, with Leu at position 30, does not bind RNA constitutively but instead shows tryptophan-dependent RNA binding.	[]	However, T30L TRAP, with Leu at position 30, does not bind RNA constitutively but instead shows tryptophan-dependent RNA binding.	true	true	true	true	true	1,318
2	DISCUSSION	1	16	[ "b16", "b29", "b30" ]	16,738,132	pmid-15099736\|pmid-11805104\|pmid-11805104\|pmid-12381302\|pmid-10660627\|NA\|NA	Hence, a hydrophobic residue at position 30 alone is not sufficient to activate TRAP to bind RNA (and the ability of the side chain at residue 30 to hydrogen bond is not essential for tryptophan binding or activation).	[ "16", "29", "30" ]	218	8,130	0	false	Hence, a hydrophobic residue at position 30 alone is not sufficient to activate TRAP to bind RNA.	[ "and the ability of the side chain at residue 30 to hydrogen bond is not essential for tryptophan binding or activation" ]	Hence, a hydrophobic residue at position 30 alone is not sufficient to activate TRAP to bind RNA.	true	true	true	true	true	1,318
2	DISCUSSION	1	16	[ "b16", "b29", "b30" ]	16,738,132	pmid-15099736\|pmid-11805104\|pmid-11805104\|pmid-12381302\|pmid-10660627\|NA\|NA	While Val, Ile and Leu all have small aliphatic side chains, only the Val and Ile side chains are β-branched, suggesting this property may be important to induce tryptophan-independent RNA binding.	[ "16", "29", "30" ]	197	8,131	0	false	While Val, Ile and Leu all have small aliphatic side chains, only the Val and Ile side chains are β-branched, suggesting this property may be important to induce tryptophan-independent RNA binding.	[]	While Val, Ile and Leu all have small aliphatic side chains, only the Val and Ile side chains are β-branched, suggesting this property may be important to induce tryptophan-independent RNA binding.	true	true	true	true	true	1,318
2	DISCUSSION	1	16	[ "b16", "b29", "b30" ]	16,738,132	pmid-15099736\|pmid-11805104\|pmid-11805104\|pmid-12381302\|pmid-10660627\|NA\|NA	β-Branching of the side chain restricts the conformations that the peptide backbone can adopt due to steric considerations (29,30).	[ "16", "29", "30" ]	131	8,132	0	false	β-Branching of the side chain restricts the conformations that the peptide backbone can adopt due to steric considerations.	[ "29,30" ]	β-Branching of the side chain restricts the conformations that the peptide backbone can adopt due to steric considerations.	false	true	true	true	false	1,318
2	DISCUSSION	1	16	[ "b16", "b29", "b30" ]	16,738,132	pmid-15099736\|pmid-11805104\|pmid-11805104\|pmid-12381302\|pmid-10660627\|NA\|NA	Hence, the presence of the β-branched Val or Ile residues at position 30 may bring about changes in the protein backbone that activate these mutant proteins to bind RNA.	[ "16", "29", "30" ]	169	8,133	0	false	Hence, the presence of the β-branched Val or Ile residues at position 30 may bring about changes in the protein backbone that activate these mutant proteins to bind RNA.	[]	Hence, the presence of the β-branched Val or Ile residues at position 30 may bring about changes in the protein backbone that activate these mutant proteins to bind RNA.	true	true	true	true	true	1,318
3	DISCUSSION	1	11	[ "b11" ]	16,738,132	pmid-7715723\|pmid-10660627\|pmid-9245598\|pmid-10660627\|pmid-10499579	Perhaps one reason that Thr30 plays a key role in activation of TRAP is that it is the only residue in the protein that interacts with both the bound tryptophan and bound RNA.	[ "11" ]	175	8,134	0	false	Perhaps one reason that Thr30 plays a key role in activation of TRAP is that it is the only residue in the protein that interacts with both the bound tryptophan and bound RNA.	[]	Perhaps one reason that Thr30 plays a key role in activation of TRAP is that it is the only residue in the protein that interacts with both the bound tryptophan and bound RNA.	true	true	true	true	true	1,319
3	DISCUSSION	1	11	[ "b11" ]	16,738,132	pmid-7715723\|pmid-10660627\|pmid-9245598\|pmid-10660627\|pmid-10499579	The side chain hydroxyl of Thr30 hydrogen bonds with the amino group of the bound tryptophan.	[ "11" ]	93	8,135	0	false	The side chain hydroxyl of Thr30 hydrogen bonds with the amino group of the bound tryptophan.	[]	The side chain hydroxyl of Thr30 hydrogen bonds with the amino group of the bound tryptophan.	true	true	true	true	true	1,319
3	DISCUSSION	1	11	[ "b11" ]	16,738,132	pmid-7715723\|pmid-10660627\|pmid-9245598\|pmid-10660627\|pmid-10499579	In the complex with (GAGAU)11, the main chain carbonyl oxygen of Thr30 hydrogen bonds with the NH2 of the third G of each repeat (Figure 2), and makes a hydrogen bond to the 2′ sugar hydroxyl of the preceding A via a bridging water molecule (11).	[ "11" ]	246	8,136	1	false	In the complex with (GAGAU)11, the main chain carbonyl oxygen of Thr30 hydrogen bonds with the NH2 of the third G of each repeat (Figure 2), and makes a hydrogen bond to the 2′ sugar hydroxyl of the preceding A via a bridging water molecule.	[ "11" ]	In the complex with (GAGAU)11, the main chain carbonyl oxygen of Thr30 hydrogen bonds with the NH2 of the third G of each repeat (Figure 2), and makes a hydrogen bond to the 2′ sugar hydroxyl of the preceding A via a bridging water molecule.	true	true	true	true	true	1,319
3	DISCUSSION	1	11	[ "b11" ]	16,738,132	pmid-7715723\|pmid-10660627\|pmid-9245598\|pmid-10660627\|pmid-10499579	Therefore, changes at residue 30 have the potential to directly affect both the tryptophan and RNA binding properties of TRAP.	[ "11" ]	126	8,137	0	false	Therefore, changes at residue 30 have the potential to directly affect both the tryptophan and RNA binding properties of TRAP.	[]	Therefore, changes at residue 30 have the potential to directly affect both the tryptophan and RNA binding properties of TRAP.	true	true	true	true	true	1,319
4	DISCUSSION	1	15	[ "b15" ]	16,738,132	pmid-10660627\|pmid-10660627\|pmid-14687568\|pmid-12381302	NMR studies have demonstrated that tryptophan binding reduces the flexibility of TRAP (15).	[ "15" ]	91	8,138	1	false	NMR studies have demonstrated that tryptophan binding reduces the flexibility of TRAP.	[ "15" ]	NMR studies have demonstrated that tryptophan binding reduces the flexibility of TRAP.	true	true	true	true	true	1,320
4	DISCUSSION	1	15	[ "b15" ]	16,738,132	pmid-10660627\|pmid-10660627\|pmid-14687568\|pmid-12381302	These authors also showed that tryptophan binding to WT TRAP results in changes in the vicinity of residue 31 that reduce accessibility of this residue to trypsin.	[ "15" ]	163	8,139	0	false	These authors also showed that tryptophan binding to WT TRAP results in changes in the vicinity of residue 31 that reduce accessibility of this residue to trypsin.	[]	These authors also showed that tryptophan binding to WT TRAP results in changes in the vicinity of residue 31 that reduce accessibility of this residue to trypsin.	true	true	true	true	true	1,320
4	DISCUSSION	1	15	[ "b15" ]	16,738,132	pmid-10660627\|pmid-10660627\|pmid-14687568\|pmid-12381302	However, it was not clear whether these changes affecting residue 31 are directly tied to activation of TRAP to bind RNA.	[ "15" ]	121	8,140	0	false	However, it was not clear whether these changes affecting residue 31 are directly tied to activation of TRAP to bind RNA.	[]	However, it was not clear whether these changes affecting residue 31 are directly tied to activation of TRAP to bind RNA.	true	true	true	true	true	1,320
4	DISCUSSION	1	15	[ "b15" ]	16,738,132	pmid-10660627\|pmid-10660627\|pmid-14687568\|pmid-12381302	Given that we have shown that Thr30 plays a key role in activation of TRAP, it was reasonable to propose that these changes in the protein in the vicinity of residue 31 might be associated with activation.	[ "15" ]	205	8,141	0	false	Given that we have shown that Thr30 plays a key role in activation of TRAP, it was reasonable to propose that these changes in the protein in the vicinity of residue 31 might be associated with activation.	[]	Given that we have shown that Thr30 plays a key role in activation of TRAP, it was reasonable to propose that these changes in the protein in the vicinity of residue 31 might be associated with activation.	true	true	true	true	true	1,320
4	DISCUSSION	1	15	[ "b15" ]	16,738,132	pmid-10660627\|pmid-10660627\|pmid-14687568\|pmid-12381302	However our results with several mutant proteins do not support this hypothesis.	[ "15" ]	80	8,142	0	false	However our results with several mutant proteins do not support this hypothesis.	[]	However our results with several mutant proteins do not support this hypothesis.	true	true	true	true	true	1,320
4	DISCUSSION	1	15	[ "b15" ]	16,738,132	pmid-10660627\|pmid-10660627\|pmid-14687568\|pmid-12381302	Both T30V and T30VD39A TRAP, which bind RNA constitutively, are susceptible to cleavage by trypsin.	[ "15" ]	99	8,143	0	false	Both T30V and T30VD39A TRAP, which bind RNA constitutively, are susceptible to cleavage by trypsin.	[]	Both T30V and T30VD39A TRAP, which bind RNA constitutively, are susceptible to cleavage by trypsin.	true	true	true	true	true	1,320
4	DISCUSSION	1	15	[ "b15" ]	16,738,132	pmid-10660627\|pmid-10660627\|pmid-14687568\|pmid-12381302	Hence the changes that protect residue 31 are not essential for RNA binding, at least not with these mutant proteins.	[ "15" ]	117	8,144	0	false	Hence the changes that protect residue 31 are not essential for RNA binding, at least not with these mutant proteins.	[]	Hence the changes that protect residue 31 are not essential for RNA binding, at least not with these mutant proteins.	true	true	true	true	true	1,320
4	DISCUSSION	1	15	[ "b15" ]	16,738,132	pmid-10660627\|pmid-10660627\|pmid-14687568\|pmid-12381302	Moreover, comparing the properties of WT, T30V, T30VD39A TRAP shows that there is no correlation between the affinities of these proteins for RNA and their sensitivity to trypsin cleavage.	[ "15" ]	188	8,145	0	false	Moreover, comparing the properties of WT, T30V, T30VD39A TRAP shows that there is no correlation between the affinities of these proteins for RNA and their sensitivity to trypsin cleavage.	[]	Moreover, comparing the properties of WT, T30V, T30VD39A TRAP shows that there is no correlation between the affinities of these proteins for RNA and their sensitivity to trypsin cleavage.	true	true	true	true	true	1,320
4	DISCUSSION	1	15	[ "b15" ]	16,738,132	pmid-10660627\|pmid-10660627\|pmid-14687568\|pmid-12381302	In addition, T30VD39A TRAP binds tryptophan (with no effect on the affinity for RNA) yet this protein is cleaved by trypsin equally well in the absence or presence of tryptophan.	[ "15" ]	178	8,146	0	false	In addition, T30VD39A TRAP binds tryptophan (with no effect on the affinity for RNA) yet this protein is cleaved by trypsin equally well in the absence or presence of tryptophan.	[]	In addition, T30VD39A TRAP binds tryptophan (with no effect on the affinity for RNA) yet this protein is cleaved by trypsin equally well in the absence or presence of tryptophan.	true	true	true	true	true	1,320
4	DISCUSSION	1	15	[ "b15" ]	16,738,132	pmid-10660627\|pmid-10660627\|pmid-14687568\|pmid-12381302	Together these observations show that the changes in the vicinity of residue 31 which protect TRAP from trypsin cleavage are not required for TRAP to bind RNA.	[ "15" ]	159	8,147	0	false	Together these observations show that the changes in the vicinity of residue 31 which protect TRAP from trypsin cleavage are not required for TRAP to bind RNA.	[]	Together these observations show that the changes in the vicinity of residue 31 which protect TRAP from trypsin cleavage are not required for TRAP to bind RNA.	true	true	true	true	true	1,320
4	DISCUSSION	1	15	[ "b15" ]	16,738,132	pmid-10660627\|pmid-10660627\|pmid-14687568\|pmid-12381302	It is also possible that the changes at residue 31 reflect an alteration in the protein required for tryptophan-activation of WT TRAP, and the mutant proteins are activated to bind RNA by a different means.	[ "15" ]	206	8,148	0	false	It is also possible that the changes at residue 31 reflect an alteration in the protein required for tryptophan-activation of WT TRAP, and the mutant proteins are activated to bind RNA by a different means.	[]	It is also possible that the changes at residue 31 reflect an alteration in the protein required for tryptophan-activation of WT TRAP, and the mutant proteins are activated to bind RNA by a different means.	true	true	true	true	true	1,320
4	DISCUSSION	1	15	[ "b15" ]	16,738,132	pmid-10660627\|pmid-10660627\|pmid-14687568\|pmid-12381302	However our data showing that T30V TRAP recognizes similar features of the RNA and uses most of the same residues in the protein to bind to it, suggests that the mutant proteins are activated by at least a similar mechanism as tryptophan binding to WT TRAP.	[ "15" ]	257	8,149	0	false	However our data showing that T30V TRAP recognizes similar features of the RNA and uses most of the same residues in the protein to bind to it, suggests that the mutant proteins are activated by at least a similar mechanism as tryptophan binding to WT TRAP.	[]	However our data showing that T30V TRAP recognizes similar features of the RNA and uses most of the same residues in the protein to bind to it, suggests that the mutant proteins are activated by at least a similar mechanism as tryptophan binding to WT TRAP.	true	true	true	true	true	1,320
5	DISCUSSION	1	17	[ "b17", "b10", "b11", "b12" ]	16,738,132	pmid-10499579\|pmid-14687568\|pmid-15050822\|pmid-10499579\|pmid-9245598	Our results suggest that although WT and T30V TRAP recognize similar features of RNA (17), these two proteins interact differently with the first base of each (G/U)AG repeat.	[ "17", "10", "11", "12" ]	174	8,150	1	false	Our results suggest that although WT and T30V TRAP recognize similar features of RNA, these two proteins interact differently with the first base of each (G/U)AG repeat.	[ "17" ]	Our results suggest that although WT and T30V TRAP recognize similar features of RNA, these two proteins interact differently with the first base of each (G/U)AG repeat.	true	true	true	true	true	1,321
5	DISCUSSION	1	17	[ "b17", "b10", "b11", "b12" ]	16,738,132	pmid-10499579\|pmid-14687568\|pmid-15050822\|pmid-10499579\|pmid-9245598	Several crystal structures of TRAP complexed with RNA show that both Lys37 and Asp39 interact with the first G or U of the repeats (10,11) (Figure 2).	[ "17", "10", "11", "12" ]	150	8,151	0	false	Several crystal structures of TRAP complexed with RNA show that both Lys37 and Asp39 interact with the first G or U of the repeats (Figure 2).	[ "10,11" ]	Several crystal structures of TRAP complexed with RNA show that both Lys37 and Asp39 interact with the first G or U of the repeats (Figure 2).	true	true	true	true	true	1,321
5	DISCUSSION	1	17	[ "b17", "b10", "b11", "b12" ]	16,738,132	pmid-10499579\|pmid-14687568\|pmid-15050822\|pmid-10499579\|pmid-9245598	We found that substitutions at Lys37 and Asp39 have different effects on WT and T30V TRAP.	[ "17", "10", "11", "12" ]	90	8,152	0	false	We found that substitutions at Lys37 and Asp39 have different effects on WT and T30V TRAP.	[]	We found that substitutions at Lys37 and Asp39 have different effects on WT and T30V TRAP.	true	true	true	true	true	1,321
5	DISCUSSION	1	17	[ "b17", "b10", "b11", "b12" ]	16,738,132	pmid-10499579\|pmid-14687568\|pmid-15050822\|pmid-10499579\|pmid-9245598	Consistent with the structural data, substitution of Lys37 with Ala in WT TRAP is deleterious to binding RNA (Table 3).	[ "17", "10", "11", "12" ]	119	8,153	0	false	Consistent with the structural data, substitution of Lys37 with Ala in WT TRAP is deleterious to binding RNA (Table 3).	[]	Consistent with the structural data, substitution of Lys37 with Ala in WT TRAP is deleterious to binding RNA (Table 3).	true	true	true	true	true	1,321
5	DISCUSSION	1	17	[ "b17", "b10", "b11", "b12" ]	16,738,132	pmid-10499579\|pmid-14687568\|pmid-15050822\|pmid-10499579\|pmid-9245598	In contrast, this change has no significant effect on the RNA binding affinity of the T30V protein.	[ "17", "10", "11", "12" ]	99	8,154	0	false	In contrast, this change has no significant effect on the RNA binding affinity of the T30V protein.	[]	In contrast, this change has no significant effect on the RNA binding affinity of the T30V protein.	true	true	true	true	true	1,321
5	DISCUSSION	1	17	[ "b17", "b10", "b11", "b12" ]	16,738,132	pmid-10499579\|pmid-14687568\|pmid-15050822\|pmid-10499579\|pmid-9245598	Conversely, changing Asp39 to Ala has no effect on WT TRAP binding to RNA yet this change increases affinity for RNA with T30V TRAP.	[ "17", "10", "11", "12" ]	132	8,155	0	false	Conversely, changing Asp39 to Ala has no effect on WT TRAP binding to RNA yet this change increases affinity for RNA with T30V TRAP.	[]	Conversely, changing Asp39 to Ala has no effect on WT TRAP binding to RNA yet this change increases affinity for RNA with T30V TRAP.	true	true	true	true	true	1,321
5	DISCUSSION	1	17	[ "b17", "b10", "b11", "b12" ]	16,738,132	pmid-10499579\|pmid-14687568\|pmid-15050822\|pmid-10499579\|pmid-9245598	The results with Asp39 are particularly interesting because several crystal structures indicate that this residue forms a hydrogen bond with the first G or U in the RNA repeats, yet we can find no evidence that this interaction contributes to the stability of the complex of WT TRAP with RNA [Table 3; (12)].	[ "17", "10", "11", "12" ]	308	8,156	0	false	The results with Asp39 are particularly interesting because several crystal structures indicate that this residue forms a hydrogen bond with the first G or U in the RNA repeats, yet we can find no evidence that this interaction contributes to the stability of the complex of WT TRAP with RNA.	[ "Table 3; (12)" ]	The results with Asp39 are particularly interesting because several crystal structures indicate that this residue forms a hydrogen bond with the first G or U in the RNA repeats, yet we can find no evidence that this interaction contributes to the stability of the complex of WT TRAP with RNA.	true	true	true	true	true	1,321
5	DISCUSSION	1	17	[ "b17", "b10", "b11", "b12" ]	16,738,132	pmid-10499579\|pmid-14687568\|pmid-15050822\|pmid-10499579\|pmid-9245598	In T30V TRAP it seems that the side chain of residue 39 interferes with RNA binding when it is larger than the methyl group of Ala.	[ "17", "10", "11", "12" ]	131	8,157	0	false	In T30V TRAP it seems that the side chain of residue 39 interferes with RNA binding when it is larger than the methyl group of Ala.	[]	In T30V TRAP it seems that the side chain of residue 39 interferes with RNA binding when it is larger than the methyl group of Ala.	true	true	true	true	true	1,321
5	DISCUSSION	1	17	[ "b17", "b10", "b11", "b12" ]	16,738,132	pmid-10499579\|pmid-14687568\|pmid-15050822\|pmid-10499579\|pmid-9245598	These differences between T30V and WT TRAP were observed regardless of whether there was a G or a U in the first position of the RNA repeats.	[ "17", "10", "11", "12" ]	141	8,158	0	false	These differences between T30V and WT TRAP were observed regardless of whether there was a G or a U in the first position of the RNA repeats.	[]	These differences between T30V and WT TRAP were observed regardless of whether there was a G or a U in the first position of the RNA repeats.	true	true	true	true	true	1,321
5	DISCUSSION	1	17	[ "b17", "b10", "b11", "b12" ]	16,738,132	pmid-10499579\|pmid-14687568\|pmid-15050822\|pmid-10499579\|pmid-9245598	Together these observations suggest that the orientations of Lys37 and Asp39 are different between complexes of T30V and tryptophan-activated WT TRAP with RNA.	[ "17", "10", "11", "12" ]	159	8,159	0	false	Together these observations suggest that the orientations of Lys37 and Asp39 are different between complexes of T30V and tryptophan-activated WT TRAP with RNA.	[]	Together these observations suggest that the orientations of Lys37 and Asp39 are different between complexes of T30V and tryptophan-activated WT TRAP with RNA.	true	true	true	true	true	1,321
5	DISCUSSION	1	17	[ "b17", "b10", "b11", "b12" ]	16,738,132	pmid-10499579\|pmid-14687568\|pmid-15050822\|pmid-10499579\|pmid-9245598	These differences may, at least in part explain the lower affinity of T30V TRAP than WT TRAP for RNA.	[ "17", "10", "11", "12" ]	101	8,160	0	false	These differences may, at least in part explain the lower affinity of T30V TRAP than WT TRAP for RNA.	[]	These differences may, at least in part explain the lower affinity of T30V TRAP than WT TRAP for RNA.	true	true	true	true	true	1,321
6	DISCUSSION	1	4	[ "b4", "b4", "b15" ]	16,738,132	pmid-7715723\|pmid-7715723\|pmid-12381302	Altering residues in the RNA binding region of T30V TRAP to Ala had the unexpected effect of restoring tryptophan binding activity to this protein, which otherwise does not bind tryptophan (Table 3).	[ "4", "4", "15" ]	199	8,161	0	false	Altering residues in the RNA binding region of T30V TRAP to Ala had the unexpected effect of restoring tryptophan binding activity to this protein, which otherwise does not bind tryptophan (Table 3).	[]	Altering residues in the RNA binding region of T30V TRAP to Ala had the unexpected effect of restoring tryptophan binding activity to this protein, which otherwise does not bind tryptophan (Table 3).	true	true	true	true	true	1,322
6	DISCUSSION	1	4	[ "b4", "b4", "b15" ]	16,738,132	pmid-7715723\|pmid-7715723\|pmid-12381302	Further investigation of this finding by making changes at Lys56 showed that residues with smaller side chains at position 56 allow the mutant proteins to bind tryptophan, whereas those with larger side chains do not (Table 4).	[ "4", "4", "15" ]	227	8,162	0	false	Further investigation of this finding by making changes at Lys56 showed that residues with smaller side chains at position 56 allow the mutant proteins to bind tryptophan, whereas those with larger side chains do not.	[ "Table 4" ]	Further investigation of this finding by making changes at Lys56 showed that residues with smaller side chains at position 56 allow the mutant proteins to bind tryptophan, whereas those with larger side chains do not.	true	true	true	true	true	1,322
6	DISCUSSION	1	4	[ "b4", "b4", "b15" ]	16,738,132	pmid-7715723\|pmid-7715723\|pmid-12381302	There are two possible explanations for these observations.	[ "4", "4", "15" ]	59	8,163	0	false	There are two possible explanations for these observations.	[]	There are two possible explanations for these observations.	true	true	true	true	true	1,322
6	DISCUSSION	1	4	[ "b4", "b4", "b15" ]	16,738,132	pmid-7715723\|pmid-7715723\|pmid-12381302	First, the side chain of residue 56 could directly interfere with tryptophan accessing its binding site.	[ "4", "4", "15" ]	104	8,164	0	false	First, the side chain of residue 56 could directly interfere with tryptophan accessing its binding site.	[]	First, the side chain of residue 56 could directly interfere with tryptophan accessing its binding site.	true	true	true	true	true	1,322
6	DISCUSSION	1	4	[ "b4", "b4", "b15" ]	16,738,132	pmid-7715723\|pmid-7715723\|pmid-12381302	Alternatively, changes at residue 56 could affect the conformation of the protein and thereby influence its tryptophan binding properties indirectly.	[ "4", "4", "15" ]	149	8,165	0	false	Alternatively, changes at residue 56 could affect the conformation of the protein and thereby influence its tryptophan binding properties indirectly.	[]	Alternatively, changes at residue 56 could affect the conformation of the protein and thereby influence its tryptophan binding properties indirectly.	true	true	true	true	true	1,322
6	DISCUSSION	1	4	[ "b4", "b4", "b15" ]	16,738,132	pmid-7715723\|pmid-7715723\|pmid-12381302	The structure of TRAP complexed with RNA shows that Lys56 is over 10 Å from the bound tryptophan (4).	[ "4", "4", "15" ]	101	8,166	1	false	The structure of TRAP complexed with RNA shows that Lys56 is over 10 Å from the bound tryptophan.	[ "4" ]	The structure of TRAP complexed with RNA shows that Lys56 is over 10 Å from the bound tryptophan.	true	true	true	true	true	1,322
6	DISCUSSION	1	4	[ "b4", "b4", "b15" ]	16,738,132	pmid-7715723\|pmid-7715723\|pmid-12381302	This would seem to argue against the simple steric hindrance model.	[ "4", "4", "15" ]	67	8,167	0	false	This would seem to argue against the simple steric hindrance model.	[]	This would seem to argue against the simple steric hindrance model.	true	true	true	true	true	1,322
6	DISCUSSION	1	4	[ "b4", "b4", "b15" ]	16,738,132	pmid-7715723\|pmid-7715723\|pmid-12381302	However, the location of Lys56 in apo-TRAP is not known.	[ "4", "4", "15" ]	56	8,168	0	false	However, the location of Lys56 in apo-TRAP is not known.	[]	However, the location of Lys56 in apo-TRAP is not known.	true	true	true	true	true	1,322
6	DISCUSSION	1	4	[ "b4", "b4", "b15" ]	16,738,132	pmid-7715723\|pmid-7715723\|pmid-12381302	Several observations suggest there must be a significant difference in the arrangement of the tryptophan binding site in apo-TRAP as compared to the complex with tryptophan, which could also be the case in T30V TRAP.	[ "4", "4", "15" ]	216	8,169	0	false	Several observations suggest there must be a significant difference in the arrangement of the tryptophan binding site in apo-TRAP as compared to the complex with tryptophan, which could also be the case in T30V TRAP.	[]	Several observations suggest there must be a significant difference in the arrangement of the tryptophan binding site in apo-TRAP as compared to the complex with tryptophan, which could also be the case in T30V TRAP.	true	true	true	true	true	1,322
6	DISCUSSION	1	4	[ "b4", "b4", "b15" ]	16,738,132	pmid-7715723\|pmid-7715723\|pmid-12381302	For example, in the WT TRAP–tryptophan complex the bound tryptophan is almost completely buried in the binding pocket (4).	[ "4", "4", "15" ]	122	8,170	1	false	For example, in the WT TRAP–tryptophan complex the bound tryptophan is almost completely buried in the binding pocket.	[ "4" ]	For example, in the WT TRAP–tryptophan complex the bound tryptophan is almost completely buried in the binding pocket.	true	true	true	true	true	1,322
6	DISCUSSION	1	4	[ "b4", "b4", "b15" ]	16,738,132	pmid-7715723\|pmid-7715723\|pmid-12381302	Hence for tryptophan to enter the binding site, it must be in a more open conformation in apo-TRAP.	[ "4", "4", "15" ]	99	8,171	0	false	Hence for tryptophan to enter the binding site, it must be in a more open conformation in apo-TRAP.	[]	Hence for tryptophan to enter the binding site, it must be in a more open conformation in apo-TRAP.	true	true	true	true	true	1,322
6	DISCUSSION	1	15	[ "b4", "b4", "b15" ]	16,738,132	pmid-7715723\|pmid-7715723\|pmid-12381302	Consistent with this proposal, NMR studies show that the tryptophan binding region of the protein is disordered in the absence of tryptophan and then becomes ordered when tryptophan binds (15).	[ "4", "4", "15" ]	193	8,172	1	false	Consistent with this proposal, NMR studies show that the tryptophan binding region of the protein is disordered in the absence of tryptophan and then becomes ordered when tryptophan binds.	[ "15" ]	Consistent with this proposal, NMR studies show that the tryptophan binding region of the protein is disordered in the absence of tryptophan and then becomes ordered when tryptophan binds.	true	true	true	true	true	1,322
6	DISCUSSION	1	4	[ "b4", "b4", "b15" ]	16,738,132	pmid-7715723\|pmid-7715723\|pmid-12381302	Thus with T30V TRAP it is possible that a large side chain at position 56 might directly create steric hindrance to tryptophan binding in its binding pocket.	[ "4", "4", "15" ]	157	8,173	0	false	Thus with T30V TRAP it is possible that a large side chain at position 56 might directly create steric hindrance to tryptophan binding in its binding pocket.	[]	Thus with T30V TRAP it is possible that a large side chain at position 56 might directly create steric hindrance to tryptophan binding in its binding pocket.	true	true	true	true	true	1,322
7	DISCUSSION	1	31	[ "b31", "b33", "b33", "b34", "b34", "b35", "b35" ]	16,738,132	pmid-16285852\|pmid-10706627\|pmid-10706627\|pmid-11557884\|pmid-11557884\|pmid-11786553\|pmid-11786553	In addition to TRAP-mediated regulation of the trp genes in response to changes in intracellular free tryptophan, B.subtilis also regulates expression of these genes in response to accumulation of uncharged tRNATrp (31–33).	[ "31", "33", "33", "34", "34", "35", "35" ]	223	8,174	0	false	In addition to TRAP-mediated regulation of the trp genes in response to changes in intracellular free tryptophan, B.subtilis also regulates expression of these genes in response to accumulation of uncharged tRNATrp.	[ "31–33" ]	In addition to TRAP-mediated regulation of the trp genes in response to changes in intracellular free tryptophan, B.subtilis also regulates expression of these genes in response to accumulation of uncharged tRNATrp.	true	true	true	true	true	1,323
7	DISCUSSION	1	31	[ "b31", "b33", "b33", "b34", "b34", "b35", "b35" ]	16,738,132	pmid-16285852\|pmid-10706627\|pmid-10706627\|pmid-11557884\|pmid-11557884\|pmid-11786553\|pmid-11786553	Accumulation of uncharged tRNATrp leads to expression of the anti-TRAP (AT) protein, which antagonizes TRAP activity, thus increasing expression of the trp genes (33,34).	[ "31", "33", "33", "34", "34", "35", "35" ]	170	8,175	0	false	Accumulation of uncharged tRNATrp leads to expression of the anti-TRAP (AT) protein, which antagonizes TRAP activity, thus increasing expression of the trp genes.	[ "33,34" ]	Accumulation of uncharged tRNATrp leads to expression of the anti-TRAP (AT) protein, which antagonizes TRAP activity, thus increasing expression of the trp genes.	true	true	true	true	true	1,323
7	DISCUSSION	1	31	[ "b31", "b33", "b33", "b34", "b34", "b35", "b35" ]	16,738,132	pmid-16285852\|pmid-10706627\|pmid-10706627\|pmid-11557884\|pmid-11557884\|pmid-11786553\|pmid-11786553	AT does not bind to apo-TRAP but specifically binds to tryptophan-activated TRAP and prevents it from binding to RNA (34,35).	[ "31", "33", "33", "34", "34", "35", "35" ]	125	8,176	0	false	AT does not bind to apo-TRAP but specifically binds to tryptophan-activated TRAP and prevents it from binding to RNA.	[ "34,35" ]	AT does not bind to apo-TRAP but specifically binds to tryptophan-activated TRAP and prevents it from binding to RNA.	true	true	true	true	true	1,323
7	DISCUSSION	1	35	[ "b31", "b33", "b33", "b34", "b34", "b35", "b35" ]	16,738,132	pmid-16285852\|pmid-10706627\|pmid-10706627\|pmid-11557884\|pmid-11557884\|pmid-11786553\|pmid-11786553	Studies of AT binding to mutant TRAP proteins suggest that AT recognizes similar features of TRAP that are essential for binding RNA, including Lys37, Lys56 and Arg58 (35).	[ "31", "33", "33", "34", "34", "35", "35" ]	172	8,177	1	false	Studies of AT binding to mutant TRAP proteins suggest that AT recognizes similar features of TRAP that are essential for binding RNA, including Lys37, Lys56 and Arg58.	[ "35" ]	Studies of AT binding to mutant TRAP proteins suggest that AT recognizes similar features of TRAP that are essential for binding RNA, including Lys37, Lys56 and Arg58.	true	true	true	true	true	1,323
7	DISCUSSION	1	31	[ "b31", "b33", "b33", "b34", "b34", "b35", "b35" ]	16,738,132	pmid-16285852\|pmid-10706627\|pmid-10706627\|pmid-11557884\|pmid-11557884\|pmid-11786553\|pmid-11786553	Preliminary studies indicate that AT does not bind to T30V TRAP in vitro (Y. Chen, D. Paul and P. Gollnick unpublished data).	[ "31", "33", "33", "34", "34", "35", "35" ]	125	8,178	0	false	Preliminary studies indicate that AT does not bind to T30V TRAP in vitro (Y. Chen, D. Paul and P. Gollnick unpublished data).	[]	Preliminary studies indicate that AT does not bind to T30V TRAP in vitro (Y. Chen, D. Paul and P. Gollnick unpublished data).	true	true	true	true	true	1,323
7	DISCUSSION	1	31	[ "b31", "b33", "b33", "b34", "b34", "b35", "b35" ]	16,738,132	pmid-16285852\|pmid-10706627\|pmid-10706627\|pmid-11557884\|pmid-11557884\|pmid-11786553\|pmid-11786553	These observations suggest that while T30V TRAP functions similarly as tryptophan-activated WT TRAP, the RNA binding surfaces of the two proteins are not identical.	[ "31", "33", "33", "34", "34", "35", "35" ]	164	8,179	0	false	These observations suggest that while T30V TRAP functions similarly as tryptophan-activated WT TRAP, the RNA binding surfaces of the two proteins are not identical.	[]	These observations suggest that while T30V TRAP functions similarly as tryptophan-activated WT TRAP, the RNA binding surfaces of the two proteins are not identical.	true	true	true	true	true	1,323
7	DISCUSSION	1	31	[ "b31", "b33", "b33", "b34", "b34", "b35", "b35" ]	16,738,132	pmid-16285852\|pmid-10706627\|pmid-10706627\|pmid-11557884\|pmid-11557884\|pmid-11786553\|pmid-11786553	Our studies suggest that Lys37 may be positioned differently between the two proteins, which may explain why T30V TRAP is not recognized by AT.	[ "31", "33", "33", "34", "34", "35", "35" ]	143	8,180	0	false	Our studies suggest that Lys37 may be positioned differently between the two proteins, which may explain why T30V TRAP is not recognized by AT.	[]	Our studies suggest that Lys37 may be positioned differently between the two proteins, which may explain why T30V TRAP is not recognized by AT.	true	true	true	true	true	1,323
8	DISCUSSION	1	36	[ "b36", "b37", "b39", "b40", "b37", "b41", "b15" ]	16,738,132	pmid-1574585\|pmid-8433368\|pmid-3881764\|pmid-2182120\|pmid-8433368\|pmid-2991205\|pmid-12381302	One of the most extensively studied proteins that shows ligand induced activation of nucleic acid binding is the Trp repressor of E.coli (36).	[ "36", "37", "39", "40", "37", "41", "15" ]	142	8,181	1	false	One of the most extensively studied proteins that shows ligand induced activation of nucleic acid binding is the Trp repressor of E.coli.	[ "36" ]	One of the most extensively studied proteins that shows ligand induced activation of nucleic acid binding is the Trp repressor of E.coli.	true	true	true	true	true	1,324
8	DISCUSSION	1	36	[ "b36", "b37", "b39", "b40", "b37", "b41", "b15" ]	16,738,132	pmid-1574585\|pmid-8433368\|pmid-3881764\|pmid-2182120\|pmid-8433368\|pmid-2991205\|pmid-12381302	Upon binding two molecules of l-tryptophan, the Trp repressor dimer binds to its operator DNA and blocks RNA polymerase from binding to the promoter.	[ "36", "37", "39", "40", "37", "41", "15" ]	149	8,182	0	false	Upon binding two molecules of l-tryptophan, the Trp repressor dimer binds to its operator DNA and blocks RNA polymerase from binding to the promoter.	[]	Upon binding two molecules of l-tryptophan, the Trp repressor dimer binds to its operator DNA and blocks RNA polymerase from binding to the promoter.	true	true	true	true	true	1,324
8	DISCUSSION	1	36	[ "b36", "b37", "b39", "b40", "b37", "b41", "b15" ]	16,738,132	pmid-1574585\|pmid-8433368\|pmid-3881764\|pmid-2182120\|pmid-8433368\|pmid-2991205\|pmid-12381302	Each monomer is composed of six α helices, two of which form a helix–turn–helix (HTH) motif that contains the amino acid residues that interact directly with the DNA (37–39).	[ "36", "37", "39", "40", "37", "41", "15" ]	174	8,183	0	false	Each monomer is composed of six α helices, two of which form a helix–turn–helix (HTH) motif that contains the amino acid residues that interact directly with the DNA.	[ "37–39" ]	Each monomer is composed of six α helices, two of which form a helix–turn–helix (HTH) motif that contains the amino acid residues that interact directly with the DNA.	true	true	true	true	true	1,324
8	DISCUSSION	1	40	[ "b36", "b37", "b39", "b40", "b37", "b41", "b15" ]	16,738,132	pmid-1574585\|pmid-8433368\|pmid-3881764\|pmid-2182120\|pmid-8433368\|pmid-2991205\|pmid-12381302	Tryptophan binding induces the HTH substructures from each subunit to move apart so that they can fit into the two successive major grooves of the DNA, which is essential for operator specific recognition (40).	[ "36", "37", "39", "40", "37", "41", "15" ]	210	8,184	1	false	Tryptophan binding induces the HTH substructures from each subunit to move apart so that they can fit into the two successive major grooves of the DNA, which is essential for operator specific recognition.	[ "40" ]	Tryptophan binding induces the HTH substructures from each subunit to move apart so that they can fit into the two successive major grooves of the DNA, which is essential for operator specific recognition.	true	true	true	true	true	1,324
8	DISCUSSION	1	36	[ "b36", "b37", "b39", "b40", "b37", "b41", "b15" ]	16,738,132	pmid-1574585\|pmid-8433368\|pmid-3881764\|pmid-2182120\|pmid-8433368\|pmid-2991205\|pmid-12381302	In addition, tryptophan binding also stabilizes the HTH substructures, which are more flexible in the absence of tryptophan (37,41).	[ "36", "37", "39", "40", "37", "41", "15" ]	132	8,185	0	false	In addition, tryptophan binding also stabilizes the HTH substructures, which are more flexible in the absence of tryptophan.	[ "37,41" ]	In addition, tryptophan binding also stabilizes the HTH substructures, which are more flexible in the absence of tryptophan.	true	true	true	true	true	1,324
8	DISCUSSION	1	15	[ "b36", "b37", "b39", "b40", "b37", "b41", "b15" ]	16,738,132	pmid-1574585\|pmid-8433368\|pmid-3881764\|pmid-2182120\|pmid-8433368\|pmid-2991205\|pmid-12381302	Therefore, in part, tryptophan binding activates the Trp repressor to bind operator DNA by a similar mechanism involving changes in protein flexibility that has been proposed for TRAP activation (15).	[ "36", "37", "39", "40", "37", "41", "15" ]	200	8,186	1	false	Therefore, in part, tryptophan binding activates the Trp repressor to bind operator DNA by a similar mechanism involving changes in protein flexibility that has been proposed for TRAP activation.	[ "15" ]	Therefore, in part, tryptophan binding activates the Trp repressor to bind operator DNA by a similar mechanism involving changes in protein flexibility that has been proposed for TRAP activation.	true	true	true	true	true	1,324
9	DISCUSSION	1	12	[ "b12" ]	16,738,132	pmid-9245598	Our results suggest that changes in the RNA binding and tryptophan binding regions of TRAP influence one another.	[ "12" ]	113	8,187	0	false	Our results suggest that changes in the RNA binding and tryptophan binding regions of TRAP influence one another.	[]	Our results suggest that changes in the RNA binding and tryptophan binding regions of TRAP influence one another.	true	true	true	true	true	1,325
9	DISCUSSION	1	12	[ "b12" ]	16,738,132	pmid-9245598	These changes may reflect the pathway that normally conveys changes when tryptophan binds to activate RNA binding.	[ "12" ]	114	8,188	0	false	These changes may reflect the pathway that normally conveys changes when tryptophan binds to activate RNA binding.	[]	These changes may reflect the pathway that normally conveys changes when tryptophan binds to activate RNA binding.	true	true	true	true	true	1,325
9	DISCUSSION	1	12	[ "b12" ]	16,738,132	pmid-9245598	One possible means for this transfer of information between the two binding regions would be via the residues that most directly connect the two binding sites.	[ "12" ]	159	8,189	0	false	One possible means for this transfer of information between the two binding regions would be via the residues that most directly connect the two binding sites.	[]	One possible means for this transfer of information between the two binding regions would be via the residues that most directly connect the two binding sites.	true	true	true	true	true	1,325
9	DISCUSSION	1	12	[ "b12" ]	16,738,132	pmid-9245598	According to this model, tryptophan binding would introduce changes in residues in its binding site—particularly Thr30—and these changes would be transmitted to the RNA binding site via residues most directly adjacent along the polypeptide backbone to one or more residues that contact the RNA.	[ "12" ]	294	8,190	0	false	According to this model, tryptophan binding would introduce changes in residues in its binding site—particularly Thr30—and these changes would be transmitted to the RNA binding site via residues most directly adjacent along the polypeptide backbone to one or more residues that contact the RNA.	[]	According to this model, tryptophan binding would introduce changes in residues in its binding site—particularly Thr30—and these changes would be transmitted to the RNA binding site via residues most directly adjacent along the polypeptide backbone to one or more residues that contact the RNA.	true	true	true	true	true	1,325
9	DISCUSSION	1	12	[ "b12" ]	16,738,132	pmid-9245598	Two key residues that contact the RNA, Glu36 and Lys37, are directly linked to Thr30 by a portion of the loop made up of residues 25–33 and by the β-strand composed of residues 34 to 38 (Indicated in dark blue on Figure 2).	[ "12" ]	223	8,191	0	false	Two key residues that contact the RNA, Glu36 and Lys37, are directly linked to Thr30 by a portion of the loop made up of residues 25–33 and by the β-strand composed of residues 34 to 38 (Indicated in dark blue on Figure 2).	[]	Two key residues that contact the RNA, Glu36 and Lys37, are directly linked to Thr30 by a portion of the loop made up of residues 25–33 and by the β-strand composed of residues 34 to 38.	true	true	true	true	true	1,325
9	DISCUSSION	1	12	[ "b12" ]	16,738,132	pmid-9245598	The hypothesis that this means of communication is important in the activation mechanism is supported by results from previous mutagenesis studies (12).	[ "12" ]	152	8,192	1	false	The hypothesis that this means of communication is important in the activation mechanism is supported by results from previous mutagenesis studies.	[ "12" ]	The hypothesis that this means of communication is important in the activation mechanism is supported by results from previous mutagenesis studies.	true	true	true	true	true	1,325
9	DISCUSSION	1	12	[ "b12" ]	16,738,132	pmid-9245598	These studies showed that Ala substitutions in several of these connecting residues, including Lys31 and His33, interfere with TRAP-mediated regulation of the trp operon in vivo even though neither residue directly interacts with either tryptophan or RNA.	[ "12" ]	255	8,193	0	false	These studies showed that Ala substitutions in several of these connecting residues, including Lys31 and His33, interfere with TRAP-mediated regulation of the trp operon in vivo even though neither residue directly interacts with either tryptophan or RNA.	[]	These studies showed that Ala substitutions in several of these connecting residues, including Lys31 and His33, interfere with TRAP-mediated regulation of the trp operon in vivo even though neither residue directly interacts with either tryptophan or RNA.	true	true	true	true	true	1,325
9	DISCUSSION	1	12	[ "b12" ]	16,738,132	pmid-9245598	Determining the tryptophan and RNA binding properties of these mutant proteins may provide additional insight into the role of these residues in the activation mechanism of TRAP.	[ "12" ]	178	8,194	0	false	Determining the tryptophan and RNA binding properties of these mutant proteins may provide additional insight into the role of these residues in the activation mechanism of TRAP.	[]	Determining the tryptophan and RNA binding properties of these mutant proteins may provide additional insight into the role of these residues in the activation mechanism of TRAP.	true	true	true	true	true	1,325
0	INTRODUCTION	1	1	[ "B1", "B2", "B3", "B4" ]	17,670,797	pmid-10807004\|pmid-1962210\|pmid-12691534\|pmid-15025524\|pmid-17226957	Steric-blocking antisense oligonucleotides (AOs) are considered potential therapeutics for genetic diseases such as Duchenne muscular dystrophy (DMD) and β-thalassemia.	[ "1", "2", "3", "4" ]	168	8,195	0	false	Steric-blocking antisense oligonucleotides (AOs) are considered potential therapeutics for genetic diseases such as Duchenne muscular dystrophy (DMD) and β-thalassemia.	[]	Steric-blocking antisense oligonucleotides (AOs) are considered potential therapeutics for genetic diseases such as Duchenne muscular dystrophy (DMD) and β-thalassemia.	true	true	true	true	true	1,326
0	INTRODUCTION	1	1	[ "B1", "B2", "B3", "B4" ]	17,670,797	pmid-10807004\|pmid-1962210\|pmid-12691534\|pmid-15025524\|pmid-17226957	For their potential to be realized, however, the AOs must be effectively delivered to cell nuclei.	[ "1", "2", "3", "4" ]	98	8,196	0	false	For their potential to be realized, however, the AOs must be effectively delivered to cell nuclei.	[]	For their potential to be realized, however, the AOs must be effectively delivered to cell nuclei.	true	true	true	true	true	1,326
0	INTRODUCTION	1	1	[ "B1", "B2", "B3", "B4" ]	17,670,797	pmid-10807004\|pmid-1962210\|pmid-12691534\|pmid-15025524\|pmid-17226957	Cationic lipoplex- or PEI-based transfection methods used to deliver charged AOs are not suitable for the delivery of uncharged AOs such as phosphorodiamidate morpholino oligomers (PMO, Figure 1) (1) and peptide nucleic acids (PNAs) (2).	[ "1", "2", "3", "4" ]	237	8,197	1	false	Cationic lipoplex- or PEI-based transfection methods used to deliver charged AOs are not suitable for the delivery of uncharged AOs such as phosphorodiamidate morpholino oligomers and peptide nucleic acids (PNAs).	[ "PMO, Figure 1", "1", "2" ]	Cationic lipoplex- or PEI-based transfection methods used to deliver charged AOs are not suitable for the delivery of uncharged AOs such as phosphorodiamidate morpholino oligomers and peptide nucleic acids (PNAs).	true	true	true	true	true	1,326
0	INTRODUCTION	1	1	[ "B1", "B2", "B3", "B4" ]	17,670,797	pmid-10807004\|pmid-1962210\|pmid-12691534\|pmid-15025524\|pmid-17226957	Conjugation of PMO to short CPPs is a good method to enhance the cytoplasmic and nuclear delivery of PMO because the conjugates are simple to use and because the short peptides and their AO conjugates can be easily manufactured and characterized in a quality-controlled manner.	[ "1", "2", "3", "4" ]	277	8,198	0	false	Conjugation of PMO to short CPPs is a good method to enhance the cytoplasmic and nuclear delivery of PMO because the conjugates are simple to use and because the short peptides and their AO conjugates can be easily manufactured and characterized in a quality-controlled manner.	[]	Conjugation of PMO to short CPPs is a good method to enhance the cytoplasmic and nuclear delivery of PMO because the conjugates are simple to use and because the short peptides and their AO conjugates can be easily manufactured and characterized in a quality-controlled manner.	true	true	true	true	true	1,326
0	INTRODUCTION	1	1	[ "B1", "B2", "B3", "B4" ]	17,670,797	pmid-10807004\|pmid-1962210\|pmid-12691534\|pmid-15025524\|pmid-17226957	Examples of well-studied CPP−PMO conjugates include those with Tat and oligoarginine peptides (3,4)	[ "1", "2", "3", "4" ]	99	8,199	0	false	Examples of well-studied CPP−PMO conjugates include those with Tat and oligoarginine peptides	[ "3,4" ]	Examples of well-studied CPP−PMO conjugates include those with Tat and oligoarginine peptides	true	true	false	true	false	1,326

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