Marcelo D. Polêto
@mdpoleto.bsky.social
Computational Biochemist @uspoficial.bsky.social - Molecular simulations | Drude Polarizable FF | Enzyme engineering | Sustainability ♻️. Trying to grow my own agroforestry system 🌳🫒. he/him 🇧🇷
https://mdpoleto.github.io/
https://mdpoleto.github.io/
Excited to finally share that our work is featured as the front cover of ACS Macromolecules' new issue!
Image was powered by the one and only MolecularNodes (thx @bradyajohnston.bsky.social) while I was playing around with surface transparency 😁
#chemsky #compchem
Image was powered by the one and only MolecularNodes (thx @bradyajohnston.bsky.social) while I was playing around with surface transparency 😁
#chemsky #compchem
January 14, 2025 at 11:28 AM
Excited to finally share that our work is featured as the front cover of ACS Macromolecules' new issue!
Image was powered by the one and only MolecularNodes (thx @bradyajohnston.bsky.social) while I was playing around with surface transparency 😁
#chemsky #compchem
Image was powered by the one and only MolecularNodes (thx @bradyajohnston.bsky.social) while I was playing around with surface transparency 😁
#chemsky #compchem
"Ceeeelebrate good times, c'mon!" 🥳
December 15, 2024 at 3:56 PM
"Ceeeelebrate good times, c'mon!" 🥳
December 13, 2024 at 12:23 PM
Obrigado pela resposta. Mas agora eu to confuso: o relatorio do BEN diz na pag 13:
www.epe.gov.br/pt/publicaco...
www.epe.gov.br/pt/publicaco...
December 13, 2024 at 12:12 PM
Obrigado pela resposta. Mas agora eu to confuso: o relatorio do BEN diz na pag 13:
www.epe.gov.br/pt/publicaco...
www.epe.gov.br/pt/publicaco...
It’s finally out! 🥳
We extended the Drude polarizable force field to model PET polymer and demonstrated interesting applications in modeling protein-PET interactions.
Feel free to check it out! DMs are open for feedback 😁
We extended the Drude polarizable force field to model PET polymer and demonstrated interesting applications in modeling protein-PET interactions.
Feel free to check it out! DMs are open for feedback 😁
September 4, 2024 at 2:35 PM
It’s finally out! 🥳
We extended the Drude polarizable force field to model PET polymer and demonstrated interesting applications in modeling protein-PET interactions.
Feel free to check it out! DMs are open for feedback 😁
We extended the Drude polarizable force field to model PET polymer and demonstrated interesting applications in modeling protein-PET interactions.
Feel free to check it out! DMs are open for feedback 😁
The winds of change are blowing! 🎐
The past 4 years at Virginia Tech in @justinlemkulvt.bsky.social's lab have been an incredible joyride. I've had the privilege of working with an amazing mentor and friends who have truly shaped this incredible experience♥️
Exciting things to come!😁
The past 4 years at Virginia Tech in @justinlemkulvt.bsky.social's lab have been an incredible joyride. I've had the privilege of working with an amazing mentor and friends who have truly shaped this incredible experience♥️
Exciting things to come!😁
August 22, 2024 at 1:52 PM
The winds of change are blowing! 🎐
The past 4 years at Virginia Tech in @justinlemkulvt.bsky.social's lab have been an incredible joyride. I've had the privilege of working with an amazing mentor and friends who have truly shaped this incredible experience♥️
Exciting things to come!😁
The past 4 years at Virginia Tech in @justinlemkulvt.bsky.social's lab have been an incredible joyride. I've had the privilege of working with an amazing mentor and friends who have truly shaped this incredible experience♥️
Exciting things to come!😁
This effort was only possible due to @jmaemontgomery who came up with a very cool code prototype for it and really helped with discussions.
November 16, 2024 at 10:17 AM
This effort was only possible due to @jmaemontgomery who came up with a very cool code prototype for it and really helped with discussions.
These electric fields also explain why K+ frequently dissociates in telomeric GQ: not only the field sensed by K+ at S3 is weaker than TERRA in magnitude (full lines), it also contains a negative Z-axis contribution (dotted lines), repelling the ion towards the bulk region.
November 16, 2024 at 10:48 AM
These electric fields also explain why K+ frequently dissociates in telomeric GQ: not only the field sensed by K+ at S3 is weaker than TERRA in magnitude (full lines), it also contains a negative Z-axis contribution (dotted lines), repelling the ion towards the bulk region.
And, of course, explicit electronic polarization makes a huge difference whether K+ is bound (A) or not (B), impacting the electric field magnitude to up to 50%
November 16, 2024 at 10:40 AM
And, of course, explicit electronic polarization makes a huge difference whether K+ is bound (A) or not (B), impacting the electric field magnitude to up to 50%
The GQs electric field are not only driving K+ binding, but they peak at S1/S3 even before ion binding. Again, differences are noticeable between telomeric and TERRA GQ.
Upon K+ binding at S3, the electric field at the site increases, somewhat trapping the bound ion there.
Upon K+ binding at S3, the electric field at the site increases, somewhat trapping the bound ion there.
November 16, 2024 at 10:33 AM
The GQs electric field are not only driving K+ binding, but they peak at S1/S3 even before ion binding. Again, differences are noticeable between telomeric and TERRA GQ.
Upon K+ binding at S3, the electric field at the site increases, somewhat trapping the bound ion there.
Upon K+ binding at S3, the electric field at the site increases, somewhat trapping the bound ion there.
To check how such differences impact ion binding thermodynamics, we employed volume-based metadynamics (thks @plumed_org ) to calculate ion binding free energy profiles, showing a higher propensity for K+ ions to bind to TERRA in relation to telomeric GQ (by nearly 1 kcal/mol)
November 16, 2024 at 9:59 AM
To check how such differences impact ion binding thermodynamics, we employed volume-based metadynamics (thks @plumed_org ) to calculate ion binding free energy profiles, showing a higher propensity for K+ ions to bind to TERRA in relation to telomeric GQ (by nearly 1 kcal/mol)
Upon K+ binding to S3, we noted a clear modulation of the GQ tetrad core dynamics , albeit with differing effects on telomeric and TERRA GQs
(Deoxy)ribose puckering analyses show distinct patterns as well: mostly C2' for telomeric GQ and mixed C2'/C3' conformations for TERRA GQ.
(Deoxy)ribose puckering analyses show distinct patterns as well: mostly C2' for telomeric GQ and mixed C2'/C3' conformations for TERRA GQ.
November 16, 2024 at 9:43 AM
Upon K+ binding to S3, we noted a clear modulation of the GQ tetrad core dynamics , albeit with differing effects on telomeric and TERRA GQs
(Deoxy)ribose puckering analyses show distinct patterns as well: mostly C2' for telomeric GQ and mixed C2'/C3' conformations for TERRA GQ.
(Deoxy)ribose puckering analyses show distinct patterns as well: mostly C2' for telomeric GQ and mixed C2'/C3' conformations for TERRA GQ.
Like many GQ simulations, it's common to observe ion binding events at the tetrad-water interface, where they align with the guanine O6 core axis (S1 and S3 shown below).
November 16, 2024 at 9:34 AM
Like many GQ simulations, it's common to observe ion binding events at the tetrad-water interface, where they align with the guanine O6 core axis (S1 and S3 shown below).
Hey #BPS2023 folks, on Feb 22 I will be giving a talk about PET-degrading enzymes ♻️, how they modulate the electronic properties of PET plastic and reaction electric fields ⚡
It has been a 2-year long journey that I am happy to share with everyone. See you all! 😉
It has been a 2-year long journey that I am happy to share with everyone. See you all! 😉
November 16, 2024 at 9:11 AM
Hey #BPS2023 folks, on Feb 22 I will be giving a talk about PET-degrading enzymes ♻️, how they modulate the electronic properties of PET plastic and reaction electric fields ⚡
It has been a 2-year long journey that I am happy to share with everyone. See you all! 😉
It has been a 2-year long journey that I am happy to share with everyone. See you all! 😉
To demonstrate that, we quantified the electric field throughout the NaK2K ion channel. We aligned the channel core with the box Z-axis and iteratively ran TUPÃ for each position. The effects of multiple parts of the environment set is discussed in the paper.
November 16, 2024 at 11:35 AM
To demonstrate that, we quantified the electric field throughout the NaK2K ion channel. We aligned the channel core with the box Z-axis and iteratively ran TUPÃ for each position. The effects of multiple parts of the environment set is discussed in the paper.
Speaking of them, we reproduced some of their results in our paper. We studied the electric field exerted by Ketosteroid isomerase (KSI) on its ligand (19-nortestosterone). We were able to identify the same important residues, while also visualizing the field orientation.
November 16, 2024 at 11:12 AM
Speaking of them, we reproduced some of their results in our paper. We studied the electric field exerted by Ketosteroid isomerase (KSI) on its ligand (19-nortestosterone). We were able to identify the same important residues, while also visualizing the field orientation.
TUPÃ has 4 calculation modes.
In ATOM MODE, the position of an atom (or COG of multiple atoms) is tracked throughout a trajectory; In our paper, we describe the electric field sensed by a benzene ligand exerted by its receptor (lysozyme) using the Drude polarizable force field.
In ATOM MODE, the position of an atom (or COG of multiple atoms) is tracked throughout a trajectory; In our paper, we describe the electric field sensed by a benzene ligand exerted by its receptor (lysozyme) using the Drude polarizable force field.
November 16, 2024 at 10:48 AM
TUPÃ has 4 calculation modes.
In ATOM MODE, the position of an atom (or COG of multiple atoms) is tracked throughout a trajectory; In our paper, we describe the electric field sensed by a benzene ligand exerted by its receptor (lysozyme) using the Drude polarizable force field.
In ATOM MODE, the position of an atom (or COG of multiple atoms) is tracked throughout a trajectory; In our paper, we describe the electric field sensed by a benzene ligand exerted by its receptor (lysozyme) using the Drude polarizable force field.
Volleyball (or as a call, "blowing off some steam") season is open 🙌🖐️🏐!!!!
November 16, 2024 at 11:04 AM
Volleyball (or as a call, "blowing off some steam") season is open 🙌🖐️🏐!!!!
Wife: "Hey, how was your day?"
Me: "I tried to refine some parameters..."
😮💨
Me: "I tried to refine some parameters..."
😮💨
November 16, 2024 at 11:20 AM
Wife: "Hey, how was your day?"
Me: "I tried to refine some parameters..."
😮💨
Me: "I tried to refine some parameters..."
😮💨
We made sure analyses were present. By using PyTraj and Matplotlib, we covered the basic MD structural analyses (such as RMSD, RMSF, Rg, etc) and users can see those graphs plotted in the notebook and saved as raw output files
November 16, 2024 at 1:16 PM
We made sure analyses were present. By using PyTraj and Matplotlib, we covered the basic MD structural analyses (such as RMSD, RMSF, Rg, etc) and users can see those graphs plotted in the notebook and saved as raw output files
We present 3 workflows: A) taking a input structure directly from PDB; B) using your own input coordinate/topology files and C) predicting the 3D structure of a protein and directly plugging it into a MD pipeline. (shout out to @sokrypton
et. al for their amazing ColabFold!)
et. al for their amazing ColabFold!)
November 16, 2024 at 12:26 PM
We present 3 workflows: A) taking a input structure directly from PDB; B) using your own input coordinate/topology files and C) predicting the 3D structure of a protein and directly plugging it into a MD pipeline. (shout out to @sokrypton
et. al for their amazing ColabFold!)
et. al for their amazing ColabFold!)
Hi @LatinXChem, this is our work ‘Making it Rain: cloud-based molecular simulations for everyone’, a great collaboration between @pablitoarantes @ConradoPedebos @ligabue_braun and myself.
Time for a thread! 🧵👇
#LatinXChem #LXChemComp #Comp166
Time for a thread! 🧵👇
#LatinXChem #LXChemComp #Comp166
November 16, 2024 at 12:08 PM
Hi @LatinXChem, this is our work ‘Making it Rain: cloud-based molecular simulations for everyone’, a great collaboration between @pablitoarantes @ConradoPedebos @ligabue_braun and myself.
Time for a thread! 🧵👇
#LatinXChem #LXChemComp #Comp166
Time for a thread! 🧵👇
#LatinXChem #LXChemComp #Comp166
Very excited to be an early-career reviewer with @eLife ! 🥳
I've always been a fan of innovative peer-reviewing strategies and I am happy to be part of a team that is pursuing that.
Looking forward for great science and tons of learning!
I've always been a fan of innovative peer-reviewing strategies and I am happy to be part of a team that is pursuing that.
Looking forward for great science and tons of learning!
November 16, 2024 at 12:26 PM
Very excited to be an early-career reviewer with @eLife ! 🥳
I've always been a fan of innovative peer-reviewing strategies and I am happy to be part of a team that is pursuing that.
Looking forward for great science and tons of learning!
I've always been a fan of innovative peer-reviewing strategies and I am happy to be part of a team that is pursuing that.
Looking forward for great science and tons of learning!
Thanks for reading this! Any suggestions are very welcome!
November 16, 2024 at 3:39 PM
Thanks for reading this! Any suggestions are very welcome!