Hi Susume,
Here is a reply from one of the scientists in Jim's lab.
- It is hard to pin-point the RNA interacting residues from the sequence alignments - sequence homology is too low, so you may end up being severely misled. On top of it, Mtb Hfq has extra strands on N-terminus (predicted to form beta-clasp), but it is not clear how it would fit into classic Hfq doughnut arrangement.
- From studying solved Hfqs with RNA bound few potentially useful observations could be made:
- RNA interacting spots located at the edges of secondary structure elements and/or in between them
- Most common interactions with RNA include: Q and N - H-bonding with the base; F (or Y) - stacking with the base ring; Y - stacking or bonding with the sugar; H - H-bonding with the sugar O and/or with the phosphate group. Mtb Hfq has one of each for those within the useful positions (I would pair this with the secondary structure predictions):
10 20 30 40 50 60 70
| | | | | | |
VEVKIGITDSPRELVFSSAQTPSEVEELVSNALRDDSGLLTLTDERGRRFLIHTARIAYVEIGVADARRV
GFGVGVDAAAGSAGKVATSG
- Yes, there are H-bonds with RNA (see above in (2). Structures were solved with polyU (pdb entry 4Y91)
Hi Susume,
Here is a reply from one of the scientists in Jim's lab.
- It is hard to pin-point the RNA interacting residues from the sequence alignments - sequence homology is too low, so you may end up being severely misled. On top of it, Mtb Hfq has extra strands on N-terminus (predicted to form beta-clasp), but it is not clear how it would fit into classic Hfq doughnut arrangement.
- From studying solved Hfqs with RNA bound few potentially useful observations could be made:
- RNA interacting spots located at the edges of secondary structure elements and/or in between them
- Most common interactions with RNA include: Q and N - H-bonding with the base; F (or Y) - stacking with the base ring; Y - stacking or bonding with the sugar; H - H-bonding with the sugar O and/or with the phosphate group. Mtb Hfq has one of each for those within the useful positions (I would pair this with the secondary structure predictions):
10 20 30 40 50 60 70
| | | | | | |
VEVKIGITDSPRELVFSSAQTPSEVEELVSNALRDDSGLLTLTDERGRRFLIHTARIAYVEIGVADARRV
GFGVGVDAAAGSAGKVATSG
- Yes, there are H-bonds with RNA (see above in (2). Structures were solved with polyU (pdb entry 4Y91)
Hi Susume,
Here is a reply from one of the scientists in Jim's lab.
- It is hard to pin-point the RNA interacting residues from the sequence alignments - sequence homology is too low, so you may end up being severely misled. On top of it, Mtb Hfq has extra strands on N-terminus (predicted to form beta-clasp), but it is not clear how it would fit into classic Hfq doughnut arrangement.
- From studying solved Hfqs with RNA bound few potentially useful observations could be made:
- RNA interacting spots located at the edges of secondary structure elements and/or in between them
- Most common interactions with RNA include: Q and N - H-bonding with the base; F (or Y) - stacking with the base ring; Y - stacking or bonding with the sugar; H - H-bonding with the sugar O and/or with the phosphate group. Mtb Hfq has one of each for those within the useful positions (I would pair this with the secondary structure predictions):
10 20 30 40 50 60 70
| | | | | | |
VEVKIGITDSPRELVFSSAQTPSEVEELVSNALRDDSGLLTLTDERGRRFLIHTARIAYVEIGVADARRV
GFGVGVDAAAGSAGKVATSG
- Yes, there are H-bonds with RNA (see above in (2). Structures were solved with polyU (pdb entry 4Y91)
I wonder if you'll give it with ED. Wait and see.
Hi Susume,
Here is a reply from one of the scientists in Jim's lab.
- It is hard to pin-point the RNA interacting residues from the sequence alignments - sequence homology is too low, so you may end up being severely misled. On top of it, Mtb Hfq has extra strands on N-terminus (predicted to form beta-clasp), but it is not clear how it would fit into classic Hfq doughnut arrangement.
- From studying solved Hfqs with RNA bound few potentially useful observations could be made:
- RNA interacting spots located at the edges of secondary structure elements and/or in between them
- Most common interactions with RNA include: Q and N - H-bonding with the base; F (or Y) - stacking with the base ring; Y - stacking or bonding with the sugar; H - H-bonding with the sugar O and/or with the phosphate group. Mtb Hfq has one of each for those within the useful positions (I would pair this with the secondary structure predictions):
10 20 30 40 50 60 70
| | | | | | |
VEVKIGITDSPRELVFSSAQTPSEVEELVSNALRDDSGLLTLTDERGRRFLIHTARIAYVEIGVADARRV
GFGVGVDAAAGSAGKVATSG
- Yes, there are H-bonds with RNA (see above in (2). Structures were solved with polyU (pdb entry 4Y91)
Hi Susume,
Here is a reply from one of the scientists in Jim's lab.
- It is hard to pin-point the RNA interacting residues from the sequence alignments - sequence homology is too low, so you may end up being severely misled. On top of it, Mtb Hfq has extra strands on N-terminus (predicted to form beta-clasp), but it is not clear how it would fit into classic Hfq doughnut arrangement.
- From studying solved Hfqs with RNA bound few potentially useful observations could be made:
- RNA interacting spots located at the edges of secondary structure elements and/or in between them
- Most common interactions with RNA include: Q and N - H-bonding with the base; F (or Y) - stacking with the base ring; Y - stacking or bonding with the sugar; H - H-bonding with the sugar O and/or with the phosphate group. Mtb Hfq has one of each for those within the useful positions (I would pair this with the secondary structure predictions):
10 20 30 40 50 60 70
| | | | | | |
VEVKIGITDSPRELVFSSAQTPSEVEELVSNALRDDSGLLTLTDERGRRFLIHTARIAYVEIGVADARRV
GFGVGVDAAAGSAGKVATSG
- Yes, there are H-bonds with RNA (see above in (2). Structures were solved with polyU (pdb entry 4Y91)
Hi Susume,
Here is a reply from one of the scientists in Jim's lab.
- It is hard to pin-point the RNA interacting residues from the sequence alignments - sequence homology is too low, so you may end up being severely misled. On top of it, Mtb Hfq has extra strands on N-terminus (predicted to form beta-clasp), but it is not clear how it would fit into classic Hfq doughnut arrangement.
- From studying solved Hfqs with RNA bound few potentially useful observations could be made:
- RNA interacting spots located at the edges of secondary structure elements and/or in between them
- Most common interactions with RNA include: Q and N - H-bonding with the base; F (or Y) - stacking with the base ring; Y - stacking or bonding with the sugar; H - H-bonding with the sugar O and/or with the phosphate group. Mtb Hfq has one of each for those within the useful positions (I would pair this with the secondary structure predictions):
10 20 30 40 50 60 70
| | | | | | |
VEVKIGITDSPRELVFSSAQTPSEVEELVSNALRDDSGLLTLTDERGRRFLIHTARIAYVEIGVADARRV
GFGVGVDAAAGSAGKVATSG
- Yes, there are H-bonds with RNA (see above in (2). Structures were solved with polyU (pdb entry 4Y91)
