Michael Bakker

Michael Bakker

Postdoctoral Researcher

Sitemap

A list of all the posts and pages found on the site. For you robots out there is an XML version available for digesting as well.

Pages

Posts

portfolio

Targeting Orphan Nuclear Receptors for Novel Therapies

Utilizing virtual screening, molecular dynamics, and free energy calculations to discover and optimize ligands for orphan nuclear receptors (e.g., NR2F family) with the goal of developing first-in-class targeted therapies.

Unraveling Protein Phosphorylation Dynamics

Investigating how phosphorylation and phosphomimetic modifications influence protein structure and dynamics, focusing on biomolecular size, secondary structure changes, and effects on protein-protein interactions.

publications

3D printed NMR spectra: From 1D and 2D acquisition to 3D visualization

Published in Concepts in Magnetic Resonance Part A, 2019

This paper discusses a method for creating 3D printed models of NMR data using Mathematica and a 3D printer, which can serve as a helpful teaching tool for students to understand complex information in NMR spectra.

Recommended citation: Bakker, M., Boyd, B., & Meints, G. A. (2019). 3D printed NMR spectra: From 1D and 2D acquisition to 3D visualization. Concepts in Magnetic Resonance Part A, 47A(1), e21470. https://doi.org/10.1002/cmr.a.21470

Improving IDP theoretical chemical shift accuracy and efficiency through a combined MD/ADMA/DFT and machine learning approach

Published in Physical Chemistry Chemical Physics, 2022

This paper is about the generation of NMR chemical shifts ab-inito from IDP trajectories using a multiscale approach.

Recommended citation: Bakker, M. J., Mládek, A., Semrád, H., Zapletal, V., & Pavlíková Přecechtělová, J. (2022). Improving IDP theoretical chemical shift accuracy and efficiency through a combined MD/ADMA/DFT and machine learning approach. Physical Chemistry Chemical Physics, 24(44), 27678–27692. https://doi.org/10.1039/D2CP01638A

Atomistic Details of Methyl Linoleate Pyrolysis: Direct Molecular Dynamics Simulation of Converting Biodiesel to Petroleum Products

Published in Energies, 2024

The long-term unsustainability of petroleum-based products is addressed by investigating the direct molecular dynamics simulation of the pyrolysis of methyl linoleate (a biodiesel substitute) to understand the atomistic details of its decomposition and identify alternative, renewable pathways to produce valuable petrochemical precursors like ethene and propene.

Recommended citation: Bakker, M. J., & Siebert, M. R. (2024). Atomistic Details of Methyl Linoleate Pyrolysis: Direct Molecular Dynamics Simulation of Converting Biodiesel to Petroleum Products. Energies, 17(10), 2433. https://doi.org/10.3390/en17102433

Streamlining NMR Chemical Shift Predictions for Intrinsically Disordered Proteins: Design of Ensembles with Dimensionality Reduction and Clustering

Published in Journal of Chemical Information and Modeling, 2024

This study streamlines the sampling procedure for predicting NMR chemical shifts (CS) in intrinsically disordered proteins (IDPs) by merging dimensionality reduction (DR) (specifically using solvent-accessible surface area (SASA)) and clustering algorithms (CA) to generate clustered ensembles (CEs) that outperform traditional sequential ensembles.

Recommended citation: Bakker, M. J., Gaffour, A., Juhás, M., Zapletal, V., Stošek, J., Bratholm, L. A., & Pavlíková Přecechtělová, J. (2024). Streamlining NMR Chemical Shift Predictions for Intrinsically Disordered Proteins: Design of Ensembles with Dimensionality Reduction and Clustering. Journal of Chemical Information and Modeling, 64(16), 6542–6556. https://doi.org/10.1021/acs.jcim.4c00809

Deeper Insight of the Conformational Ensemble of Intrinsically Disordered Proteins

Published in Journal of Chemical Information and Modeling, 2024

This study introduces an approach to better understand the conformational ensemble (CoE) of intrinsically disordered proteins (IDPs) by decomposing the ensemble of the model peptide histatin 5 into groups separated by their radius of gyration (Rg​) using a combination of small-angle X-ray scattering (SAXS) and all-atomistic molecular dynamics simulations.

Recommended citation: Svensson, O., Bakker, M. J., & Skepö, M. (2024). Deeper Insight of the Conformational Ensemble of Intrinsically Disordered Proteins. Journal of Chemical Information and Modeling, 64(15), 6105–6114. https://doi.org/10.1021/acs.jcim.4c00941

Exploring the Functional Landscape of the p53 Regulatory Domain: The Stabilizing Role of Post-Translational Modifications.

Published in Journal of Chemical Theory and Computation, 2024

This study uses fully atomistic explicit water molecular dynamics simulations to explore the functional landscape of the intrinsically disordered p53 regulatory domain, revealing a detailed understanding of how varying the number of phosphorylated amino acids impacts its conformational dynamics, flexibility, structural effects, protein interactivity, and energy landscapes.

Recommended citation: Bakker, M. J., Svensson, O., Sørensen, H. V., & Skepö, M. (2024). Exploring the Functional Landscape of the p53 Regulatory Domain: The Stabilizing Role of Post-Translational Modifications. Journal of Chemical Theory and Computation, 20(14), 5842–5853. https://doi.org/10.1021/acs.jctc.4c00570

Exploring the Role of Globular Domain Locations on an Intrinsically Disordered Region of p53: A Molecular Dynamics Investigation

Published in Journal of Chemical Theory and Computation, 2024

This paper is about an investigation made into the disordered regions of p53 using molecular dynamics and machine learning techniques.

Recommended citation: Bakker, M. J., Sørensen, H. V., & Skepö, M. (2024). Exploring the Role of Globular Domain Locations on an Intrinsically Disordered Region of p53: A Molecular Dynamics Investigation. Journal of Chemical Theory and Computation, 20(3), 1423–1433. https://doi.org/10.1021/acs.jctc.3c00971

The discovery of a new nonbile acid modulator of Takeda G protein-coupled receptor 5: An integrated computational approach

Published in Archiv der Pharmazie, 2025

An integrated computational approach led to the discovery of Hit-3 (CSC089939231), a new nonsteroidal Takeda G protein-coupled receptor 5 (TGR5) modulator, with molecular dynamics simulations suggesting its activation is supported by a hydrogen bond interaction with Tyr240.

Recommended citation: Salam, R., Bakker, M., Krutáková, M., Štefela, A., Pávek, P., Duintjer Tebbens, J., & Zitko, J. (2025). The discovery of a new nonbile acid modulator of Takeda G protein-coupled receptor 5: An integrated computational approach. Archiv der Pharmazie, 358(1), e2400423. https://doi.org/10.1002/ardp.202400423

Reduced Binding of Tau(210-240) to BIN1: Phosphate Charges Prefer n-Src/Distal Loops over RT-Src Loops

Published in Biophysical Journal, 2025

All-atomistic molecular dynamics simulations of the Tau(210-240)/BIN1 SH3 complex reveal that additional phosphate charges reduce salt-bridge formation by up to 32% and cause a strong preference in Tau for contact with the distal and n-Src loops instead of the RT-Src loop.

Recommended citation: Gaffour, A., Bakker, M., Bera, K., & Pavlíková Přecechtělová, J. (2025). Reduced Binding of Tau(210-240) to BIN1: Phosphate Charges Prefer n-Src/Distal Loops over RT-Src Loops. Biophysical Journal, 124(21), 3800–3810. https://doi.org/10.1016/j.bpj.2025.09.037

Conformational flexibility and transient structure of the proline-rich domain in p53

Published in Biophysical Journal, 2026

Molecular dynamics simulations and biophysical measurements characterize the disordered ensemble of the p53 proline-rich domain, including transient polyproline II structure, domain constraints, and mutation-dependent changes.

Recommended citation: Berggren, A., Bakker, M., Fisher, H., & Skepö, M. (2026). Conformational flexibility and transient structure of the proline-rich domain in p53. Biophysical Journal, 125(8), 1914–1925. https://doi.org/10.1016/j.bpj.2026.03.024

Comparative analysis of drop mass variance for manual and automatic delivery of large-scale eye drop poultry vaccine

Published in Poultry Science, 2026

Statistical modeling compares manual and automated ocular vaccine dispensing, examining how delivery conditions affect drop mass consistency.

Recommended citation: Bakker, M., Vraníková, B., Duintjer Tebbens, E. J., & Šklubalová, Z. (2026). Comparative analysis of drop mass variance for manual and automatic delivery of large-scale eye drop poultry vaccine. Poultry Science, 105(11), 107159. https://doi.org/10.1016/j.psj.2026.107159

talks

Intrinsically Disordered Regions in p53 Tumor Suppressor Protein

Published:

The p53 protein is also known as the ”Guardian of the Genome” as it can trigger cell cycle arrest, DNA repair, and apoptosis. Mutations in p53 is quite common in the development of cancer. The protein is also quite complex with multiple domains, and also contains four signficantly disorderd regions as seen below.

teaching

Organic Chemistry Tutor

University Sponsored Tutoring, Missouri State University, Department of Chemistry, 2016

Worked with students through collaboration from the faculty (Professor Siebert) to provide supplemental support for the Organic Chemistry course.

Organic Chemistry Lab Instructor

Lab Instructor, Missouri State University, Department of Chemistry, 2018

Instructed students on hands-on wet chemistry related to their lessons in Organic Chemistry I and II.

ACT Lecturer

Practical Classes, Charles University, Faculty of Pharmacy, 2025

Taught practical classes focused on utilizing simple publicly available office tools to overcome minor obstacles in computational work and data presentations.

Calculus and Statistics Teaching Assistant

Teaching Assistant, Charles University, Faculty of Pharmacy, Department of Inorganic and Organic Chemistry, 2025

Provided supplementary instruction and support for students enrolled in the introductory Calculus and Statistics courses.