TJ McCorvie
@allostericstate.bsky.social
Revealing the hidden world of shape shifting enzymes using Cryo-EM. Senior research associate at Newcastle University, UK. Currently working as part of Recon4IMD https://www.recon4imd.org Views are my own.
Coupled with recently reported thermophilic structures of the MTR homologue MeTH from the Ando and Koutmos labs we have attempted to contextualise these conformations within cobalamin loading, reactivation, and catalytic cycles.
November 11, 2025 at 1:22 PM
Coupled with recently reported thermophilic structures of the MTR homologue MeTH from the Ando and Koutmos labs we have attempted to contextualise these conformations within cobalamin loading, reactivation, and catalytic cycles.
Using recombinant material, we could confirm that MTR does form a complex with MTRR and that complex formation can still occur (albeit weakly) without the FMN domain present.
November 11, 2025 at 1:19 PM
Using recombinant material, we could confirm that MTR does form a complex with MTRR and that complex formation can still occur (albeit weakly) without the FMN domain present.
We next turned to AlphaFold to understand how MTR interacts with its binding partners. AlphaFold of MTR with its rescue partner MTRR threw a surprise our way: AF3 suggested two regions of interaction with one newly suggested that deviated from the previously known interaction with MTRR’s FMN domain.
November 11, 2025 at 1:13 PM
We next turned to AlphaFold to understand how MTR interacts with its binding partners. AlphaFold of MTR with its rescue partner MTRR threw a surprise our way: AF3 suggested two regions of interaction with one newly suggested that deviated from the previously known interaction with MTRR’s FMN domain.
Douglas also collected cryo-EM data of MTR with hydroxycobalamin which does not support activity and methylcobalamin which is the active form of the cofactor. Though MTR again behaves as two separate bodies, we were able to observe conformational changes due to cobalamin binding.
November 11, 2025 at 1:10 PM
Douglas also collected cryo-EM data of MTR with hydroxycobalamin which does not support activity and methylcobalamin which is the active form of the cofactor. Though MTR again behaves as two separate bodies, we were able to observe conformational changes due to cobalamin binding.
These structures demonstrate that MTR without cofactor acts as two separate modules with the C-half organised as what is called the reactivation state. A state productive for the binding of Cbl and its reactivation aided by MTRR.
November 11, 2025 at 1:05 PM
These structures demonstrate that MTR without cofactor acts as two separate modules with the C-half organised as what is called the reactivation state. A state productive for the binding of Cbl and its reactivation aided by MTRR.
Due to its flexibility MTR is a tricky protein to study by classical structural techniques however cryo-EM is well suited for this type of sample. Douglas could successfully purify full-length MTR which allowed him to determine two separate classes of MTR without cbl.
November 11, 2025 at 1:03 PM
Due to its flexibility MTR is a tricky protein to study by classical structural techniques however cryo-EM is well suited for this type of sample. Douglas could successfully purify full-length MTR which allowed him to determine two separate classes of MTR without cbl.
MTR also operates with other assisting proteins such as MMADHC which loads cobalamin into MTR and methionine synthase reductase (MTRR) also rescues MTR from oxidative inactivation of the cbl cofactor by supporting reductive methylation.
November 11, 2025 at 12:58 PM
MTR also operates with other assisting proteins such as MMADHC which loads cobalamin into MTR and methionine synthase reductase (MTRR) also rescues MTR from oxidative inactivation of the cbl cofactor by supporting reductive methylation.
MTR is the link between the folate and methionine cycles. It produces methionine while recycling folate using methylcobalamin/vitamin B12 (cbl) as a cofactor. As substrates bind to different active sites MTR requires a high degree of flexibility to function.
November 11, 2025 at 12:54 PM
MTR is the link between the folate and methionine cycles. It produces methionine while recycling folate using methylcobalamin/vitamin B12 (cbl) as a cofactor. As substrates bind to different active sites MTR requires a high degree of flexibility to function.
As far as I understand leads me to ask why merge the same micelle density twice into a map? This is an unusual map of a cytosolic protein embedded in the membrane of a liposome. There is no explanation for how this map was derived in the associated paper. www.ebi.ac.uk/emdb/EMD-47001
November 10, 2025 at 11:24 AM
As far as I understand leads me to ask why merge the same micelle density twice into a map? This is an unusual map of a cytosolic protein embedded in the membrane of a liposome. There is no explanation for how this map was derived in the associated paper. www.ebi.ac.uk/emdb/EMD-47001
Spiral deposition of samples for cryo-EM looks interesting! PS Glad to see the Dreamcast (logo) is back in some form...
November 3, 2025 at 2:26 PM
Spiral deposition of samples for cryo-EM looks interesting! PS Glad to see the Dreamcast (logo) is back in some form...
Yes it probably doesn't help but I'm stuck with orientation bias with my target. I get nice 2D classes but sadly they are all the same view:
October 27, 2025 at 1:57 PM
Yes it probably doesn't help but I'm stuck with orientation bias with my target. I get nice 2D classes but sadly they are all the same view:
Equipped with a Falcon C detector, optimised for 100 keV, the Tundra TEM is located at Newcastle University Structural Biology Facility @nusbf.bsky.social This will enable users to not only screen their samples but also collect high resolution datasets in-house. #CryoEM
October 21, 2025 at 9:50 AM
Equipped with a Falcon C detector, optimised for 100 keV, the Tundra TEM is located at Newcastle University Structural Biology Facility @nusbf.bsky.social This will enable users to not only screen their samples but also collect high resolution datasets in-house. #CryoEM
The Northern Eye is a joint project with @newcastleuni.bsky.social , @durham.ac.uk , & @northumbriauni.bsky.social to enable researchers in the North East to easily access cryo-EM for their structural biology projects.
October 21, 2025 at 9:38 AM
The Northern Eye is a joint project with @newcastleuni.bsky.social , @durham.ac.uk , & @northumbriauni.bsky.social to enable researchers in the North East to easily access cryo-EM for their structural biology projects.
The authors show these cryoSPARC FSC plots for their maps with Fig. S4B being for the "Fern"-like map of plasminogen (EMD-42462). It is unlikely to be the FSC plot for that map as it's a plot for a map with a larger pixel size. The supplied half-maps into cryoSPARC actually give the FSC plot below:
October 17, 2025 at 4:07 PM
The authors show these cryoSPARC FSC plots for their maps with Fig. S4B being for the "Fern"-like map of plasminogen (EMD-42462). It is unlikely to be the FSC plot for that map as it's a plot for a map with a larger pixel size. The supplied half-maps into cryoSPARC actually give the FSC plot below:
Sneaky proteasome
October 16, 2025 at 5:18 PM
Sneaky proteasome
It has been back a lot from the looks of it....
October 15, 2025 at 8:43 PM
It has been back a lot from the looks of it....
It's a possibility. Here are the model to map FSC curves for the original map and then the manipulated map (which I had to rescale to the original pixel size):
October 15, 2025 at 7:58 PM
It's a possibility. Here are the model to map FSC curves for the original map and then the manipulated map (which I had to rescale to the original pixel size):
EMD-46967 is oddly deposited as a composite map and is ten times bigger than EMD-42429. I also thought that EMD-46967 was a masked local refinement of EMD-42429 but the projection slices show the use of a spherical eraser tool:
October 15, 2025 at 12:21 PM
EMD-46967 is oddly deposited as a composite map and is ten times bigger than EMD-42429. I also thought that EMD-46967 was a masked local refinement of EMD-42429 but the projection slices show the use of a spherical eraser tool:
Zoom-ins to show the remaining parts of these erased curves in the upper left of the plot and the gridlines:
October 14, 2025 at 10:02 PM
Zoom-ins to show the remaining parts of these erased curves in the upper left of the plot and the gridlines:
I'm I going crazy? Do we usually edit out the spherical (orange), tight (red) and corrected mask (purple) FSC curves and relabel the loose mask (green) FSC as corrected???? #cryoEM
www.sciencedirect.com/science/arti...
www.sciencedirect.com/science/arti...
October 14, 2025 at 7:00 PM
I'm I going crazy? Do we usually edit out the spherical (orange), tight (red) and corrected mask (purple) FSC curves and relabel the loose mask (green) FSC as corrected???? #cryoEM
www.sciencedirect.com/science/arti...
www.sciencedirect.com/science/arti...
The other maps reported in the paper (with associated PDBs not reported in the paper) are not great either:
October 14, 2025 at 12:20 PM
The other maps reported in the paper (with associated PDBs not reported in the paper) are not great either:
Seeing these projections and the corrected FSC curve (purple) cutting abruptly below a FSC of zero should be a warning sign to someone with cryo-EM experience
October 12, 2025 at 11:10 AM
Seeing these projections and the corrected FSC curve (purple) cutting abruptly below a FSC of zero should be a warning sign to someone with cryo-EM experience