Ronald Beavis ❌
@ronbeavis.bsky.social
Doing science for money since 1981.
Putting it online since 1995.
Does not engage in cancer research.
QA >> QC
I enjoy doing things I am not very good at doing.
Putting it online since 1995.
Does not engage in cancer research.
QA >> QC
I enjoy doing things I am not very good at doing.
While ankyrin tandem repeat domains can stretch across big chunks of sequence, they don't have to be large. Ankyrin repeat domain 11 (ANKRD11:p) has a 100 residue domain (3 repeats) flanked by pS acceptors. The rest of the protein is made up of IDRs & a conserved constellation of pS acceptors.
November 12, 2025 at 12:32 PM
While ankyrin tandem repeat domains can stretch across big chunks of sequence, they don't have to be large. Ankyrin repeat domain 11 (ANKRD11:p) has a 100 residue domain (3 repeats) flanked by pS acceptors. The rest of the protein is made up of IDRs & a conserved constellation of pS acceptors.
Ankyrin repeat domain 17 (ANKRD17:p) actually has 2 of them, with the regular striping artifact frequently found in calculated structures for this type of domain. The pS acceptor action near the N-terminus and the broader cward pIDR are not identical but clearly evolutionarily conserved. #proteomics
November 11, 2025 at 2:13 PM
Ankyrin repeat domain 17 (ANKRD17:p) actually has 2 of them, with the regular striping artifact frequently found in calculated structures for this type of domain. The pS acceptor action near the N-terminus and the broader cward pIDR are not identical but clearly evolutionarily conserved. #proteomics
Tetratricopeptide repeat, ankyrin repeat & coiled-coil containing 2 (TANC2:p) appears very similar to TANC1:p in this representation, even though they share only a few tryptic peptides (~2% of residues). The same domains (incl. no coiled-coils) & dazzle patterned pIDRs. #proteomics
November 10, 2025 at 12:18 PM
Tetratricopeptide repeat, ankyrin repeat & coiled-coil containing 2 (TANC2:p) appears very similar to TANC1:p in this representation, even though they share only a few tryptic peptides (~2% of residues). The same domains (incl. no coiled-coils) & dazzle patterned pIDRs. #proteomics
Tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 1 (TANC1:p) is one of those sequences in which its coiled-coil seems to have gone missing with time. The sequence is bedazzled with pS acceptors that nicely confirm the location of its IDRs. #proteomics
November 9, 2025 at 2:25 PM
Tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 1 (TANC1:p) is one of those sequences in which its coiled-coil seems to have gone missing with time. The sequence is bedazzled with pS acceptors that nicely confirm the location of its IDRs. #proteomics
The eye wall of Very Strong Typhoon Fung-wong is making landfall on Luzon this morning.
November 9, 2025 at 12:05 PM
The eye wall of Very Strong Typhoon Fung-wong is making landfall on Luzon this morning.
JUN:p proto-oncogene, activator protein-1 transcription factor subunit is in a family of proteins that form homo/hetero-dimers via their cward basic L-zipper domains with different DNA specificities. They also share pS/T-IDRs: one flanking the L-zipper & a more complex nward set of acceptors.
November 8, 2025 at 2:17 PM
JUN:p proto-oncogene, activator protein-1 transcription factor subunit is in a family of proteins that form homo/hetero-dimers via their cward basic L-zipper domains with different DNA specificities. They also share pS/T-IDRs: one flanking the L-zipper & a more complex nward set of acceptors.
Snow is very possible on the 10th & 11th. Unfortunately Toronto is very much like Vancouver in that its people like to pretend that it doesn't snow there (even though it does), so try to stay off the roads when it is snowing and about 24 hours afterwards.
November 7, 2025 at 3:31 PM
Snow is very possible on the 10th & 11th. Unfortunately Toronto is very much like Vancouver in that its people like to pretend that it doesn't snow there (even though it does), so try to stay off the roads when it is snowing and about 24 hours afterwards.
Activating transcription factor 2 (ATF2:p) has 2 prominent pS/T acceptors on the cward flank of its C2H2 zinc finger & 2 on the nward flank of its basic L-zipper. To function, it must form a dimer with a complementary basic L-zipper containing sequence. #proteomics
November 7, 2025 at 1:56 PM
Activating transcription factor 2 (ATF2:p) has 2 prominent pS/T acceptors on the cward flank of its C2H2 zinc finger & 2 on the nward flank of its basic L-zipper. To function, it must form a dimer with a complementary basic L-zipper containing sequence. #proteomics
Once again, I would like to thank reviewer number 5 for their perspicacity wrt to this additional figure.
November 6, 2025 at 10:59 PM
Once again, I would like to thank reviewer number 5 for their perspicacity wrt to this additional figure.
Human RNF149:p is a leukocyte type I membrane protein. It has 7 experimentally observed ubiquitin acceptors on its cytoplasmic domain. These acceptors are all within its RING/FYVE/PHD-type Zn-finger domain. How many E3 ligases would you expect to be responsible for these modifications? #proteomics
November 6, 2025 at 7:39 PM
Human RNF149:p is a leukocyte type I membrane protein. It has 7 experimentally observed ubiquitin acceptors on its cytoplasmic domain. These acceptors are all within its RING/FYVE/PHD-type Zn-finger domain. How many E3 ligases would you expect to be responsible for these modifications? #proteomics
Activating transcription factor 1 (ATF1:p) has 2 distinct pIDRs. There is an nward, low complexity S/T pIDR & another on the nward flank of its basic zipper DNA binding domain. The lace-curtain region in the middle may be largely β strands (based on modest evidence). #proteomics
November 6, 2025 at 1:52 PM
Activating transcription factor 1 (ATF1:p) has 2 distinct pIDRs. There is an nward, low complexity S/T pIDR & another on the nward flank of its basic zipper DNA binding domain. The lace-curtain region in the middle may be largely β strands (based on modest evidence). #proteomics
ZEB1:p (zinc finger E-box binding homeobox 1) is a transcription factor that has a couple of peripheral zinc fingers & a central homeobox domain. The pS/T acceptor occupancy pattern is pretty much what I would expect, esp. the rather artful pattern cward of the homeobox. #proteomics
November 5, 2025 at 1:50 PM
ZEB1:p (zinc finger E-box binding homeobox 1) is a transcription factor that has a couple of peripheral zinc fingers & a central homeobox domain. The pS/T acceptor occupancy pattern is pretty much what I would expect, esp. the rather artful pattern cward of the homeobox. #proteomics
Figure added in response to reviewer number 4's suggestions.
November 4, 2025 at 2:21 PM
Figure added in response to reviewer number 4's suggestions.
Human TCF3:p (transcription factor 3) is a neat example of how an alternate version of an exon can change things. No one seems to have taught these things canon law!
November 4, 2025 at 1:21 PM
Human TCF3:p (transcription factor 3) is a neat example of how an alternate version of an exon can change things. No one seems to have taught these things canon law!
Transcription factors really don't like Pauling-type structures, except for the bits that stick to DNA. Transcription factor 12 (TCF12:p) has a cward bright patch resulting from the basic helix-loop-helix gadget that fits into adjacent major grooves. #proteomics
November 3, 2025 at 1:24 PM
Transcription factors really don't like Pauling-type structures, except for the bits that stick to DNA. Transcription factor 12 (TCF12:p) has a cward bright patch resulting from the basic helix-loop-helix gadget that fits into adjacent major grooves. #proteomics
Yesterday's major news: the introduction of Coco.
November 2, 2025 at 2:09 PM
Yesterday's major news: the introduction of Coco.
Transcription factor 20 (TCF20:p) is pretty typical of transcription factors in that the structured sequence (2 small zinc fingers) is necessary for its function, but there is clearly a much larger game being played in their pIDRs & we don't know the rules. #proteomics
November 2, 2025 at 12:21 PM
Transcription factor 20 (TCF20:p) is pretty typical of transcription factors in that the structured sequence (2 small zinc fingers) is necessary for its function, but there is clearly a much larger game being played in their pIDRs & we don't know the rules. #proteomics
As their mouse tissue protein distributions show, all 4 of the SAL-family have a fondness for embryonic tissue but show some diversification starting at the next tier down.
November 1, 2025 at 12:23 PM
As their mouse tissue protein distributions show, all 4 of the SAL-family have a fondness for embryonic tissue but show some diversification starting at the next tier down.
The last of the SAL-family of transcription factors (SALL4:p) is just as stingy with αβ structure as its other family members, with only 5 small C2H2 zinc fingers. It phosphorylation patterns rhyme reasonably well between mouse & man, but some regions show possible evolutionary changes. #proteomics
November 1, 2025 at 12:11 PM
The last of the SAL-family of transcription factors (SALL4:p) is just as stingy with αβ structure as its other family members, with only 5 small C2H2 zinc fingers. It phosphorylation patterns rhyme reasonably well between mouse & man, but some regions show possible evolutionary changes. #proteomics
The 3rd instalment, embryo/brain/stem cell enriched SALL3:p (spalt like transcription factor 3), also has multiple small C2H2 type zinc fingers providing specific DNA sequence binding. Its phosphorylation pattern shows some species-specificity, although there is a general rhyming pattern.
October 31, 2025 at 1:14 PM
The 3rd instalment, embryo/brain/stem cell enriched SALL3:p (spalt like transcription factor 3), also has multiple small C2H2 type zinc fingers providing specific DNA sequence binding. Its phosphorylation pattern shows some species-specificity, although there is a general rhyming pattern.
The spalt-like proteins have several small C2H2 zinc finger structures. The embryo+brain+stem cell protein SALL2:p (spalt like transcription factor 2) fits this general scheme, but has a very different phosphorylation pattern than yesterday's exemplar, SALL1:p. #proteomics
October 30, 2025 at 11:31 AM
The spalt-like proteins have several small C2H2 zinc finger structures. The embryo+brain+stem cell protein SALL2:p (spalt like transcription factor 2) fits this general scheme, but has a very different phosphorylation pattern than yesterday's exemplar, SALL1:p. #proteomics
Spalt-like transcription factors don't have much in the way of Pauling-style structure. Even though SALL1:p (spalt like transcription factor 1) has 5 small C2H2 zinc finger domains, 87% of the sequence is made up of pIDRs with conserved/rhyming pS/T acceptor patterns. #proteomics
October 29, 2025 at 12:03 PM
Spalt-like transcription factors don't have much in the way of Pauling-style structure. Even though SALL1:p (spalt like transcription factor 1) has 5 small C2H2 zinc finger domains, 87% of the sequence is made up of pIDRs with conserved/rhyming pS/T acceptor patterns. #proteomics