Herre Jelger Risselada
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View article: Automated parametrization of small molecules within the Martini 3 coarse-grained model guided by experimental log P values
Automated parametrization of small molecules within the Martini 3 coarse-grained model guided by experimental log P values Open
View article: Physics-based evolution of transmembrane helices reveals mechanisms of cholesterol attraction
Physics-based evolution of transmembrane helices reveals mechanisms of cholesterol attraction Open
View article: Membrane curvature regulates Ups1 dependent phosphatidic acid transfer across lipid bilayers
Membrane curvature regulates Ups1 dependent phosphatidic acid transfer across lipid bilayers Open
Mitochondria are essential organelles in eukaryotic cells, enclosed by two membranes with distinct compositions and functions. In addition to the endoplasmic reticulum, mitochondria are major sites of cellular lipids production. Cardiolipi…
View article: Membrane curvature regulates Ups1 dependent phosphatidic acid transfer across lipid bilayers
Membrane curvature regulates Ups1 dependent phosphatidic acid transfer across lipid bilayers Open
Mitochondria are essential organelles in eukaryotic cells, enclosed by two membranes with distinct compositions and functions. In addition to the endoplasmic reticulum, mitochondria are major sites of cellular lipids production. Cardiolipi…
View article: Author response: Membrane curvature regulates Ups1 dependent phosphatidic acid transfer across lipid bilayers
Author response: Membrane curvature regulates Ups1 dependent phosphatidic acid transfer across lipid bilayers Open
View article: Membrane curvature regulates Ups1 dependent phosphatidic acid transfer across lipid bilayers
Membrane curvature regulates Ups1 dependent phosphatidic acid transfer across lipid bilayers Open
Mitochondria are essential organelles in eukaryotic cells, enclosed by two membranes with distinct compositions and functions. In addition to the endoplasmic reticulum, mitochondria are major sites of cellular lipids production. Cardiolipi…
View article: SMARTINI3 parametrization of multi-scale membrane models via unsupervised learning methods
SMARTINI3 parametrization of multi-scale membrane models via unsupervised learning methods Open
In this study, we utilize genetic algorithms to develop a realistic implicit solvent ultra-coarse-grained (ultra-CG) membrane model comprising only three interaction sites. The key philosophy of the ultra-CG membrane model SMARTINI3 is its…
View article: SMARTINI3: Systematic Parametrization of Realistic Multi-Scale Membrane Models via Unsupervised Learning and Multi-Objective Evolutionary Algorithms
SMARTINI3: Systematic Parametrization of Realistic Multi-Scale Membrane Models via Unsupervised Learning and Multi-Objective Evolutionary Algorithms Open
In this study, we utilize genetic algorithms to develop a realistic implicit solvent ultra-coarse-grained (PC) membrane model comprising only three interaction sites. The key philosophy of the ultra-CG membrane model SMARTINI3 is its compa…
View article: SMARTINI3: Systematic Parametrization of Realistic Multi-Scale Membrane Models via Unsupervised Learning and Multi-Objective Evolutionary Algorithms
SMARTINI3: Systematic Parametrization of Realistic Multi-Scale Membrane Models via Unsupervised Learning and Multi-Objective Evolutionary Algorithms Open
In this study, we utilize genetic algorithms to develop a realistic implicit solvent ultra-coarse-grained (PC) membrane model comprising only three interaction sites. The key philosophy of the ultra-CG membrane model SMARTINI3 is its compa…
View article: Physics-Based Evolution of Cholesterol-Attracting Transmembrane Helices: Deciphering Cholesterol Attraction in Native Membrane Proteins
Physics-Based Evolution of Cholesterol-Attracting Transmembrane Helices: Deciphering Cholesterol Attraction in Native Membrane Proteins Open
The existence of linear cholesterol-recognition motifs in alpha-helical transmembrane domains has long been debated. Our study introduces an innovative approach, evolutionary molecular dynamics (Evo-MD), which utilizes a genetic algorithm …
View article: When Data Are Lacking: Physics-Based Inverse Design of Biopolymers Interacting with Complex, Fluid Phases
When Data Are Lacking: Physics-Based Inverse Design of Biopolymers Interacting with Complex, Fluid Phases Open
Biomolecular research traditionally revolves around comprehending the mechanisms through which peptides or proteins facilitate specific functions, often driven by their relevance to clinical ailments. This conventional approach assumes tha…
View article: Atypical cofilin signaling drives dendritic cell migration through the extracellular matrix via nuclear deformation
Atypical cofilin signaling drives dendritic cell migration through the extracellular matrix via nuclear deformation Open
View article: PMIpred: a physics-informed web server for quantitative protein–membrane interaction prediction
PMIpred: a physics-informed web server for quantitative protein–membrane interaction prediction Open
Motivation Many membrane peripheral proteins have evolved to transiently interact with the surface of (curved) lipid bilayers. Currently, methods to quantitatively predict sensing and binding free energies for protein sequences or structur…
View article: Data from molecular dynamics (MD) simulations of gold surfaces related to publication "Impact of nanoparticles on amyloid peptide and protein aggregation: a review with a focus on gold nanoparticles"
Data from molecular dynamics (MD) simulations of gold surfaces related to publication "Impact of nanoparticles on amyloid peptide and protein aggregation: a review with a focus on gold nanoparticles" Open
The data provided refer to our published article: T. John, A. Gladytz, C. Kubeil, L. L. Martin, H. J. Risselada, B. Abel*, Impact of nanoparticles on amyloid peptide and protein aggregation: a review with a focus on gold nanoparticles, …
View article: Data from molecular dynamics (MD) simulations of gold surfaces related to publication "Impact of nanoparticles on amyloid peptide and protein aggregation: a review with a focus on gold nanoparticles"
Data from molecular dynamics (MD) simulations of gold surfaces related to publication "Impact of nanoparticles on amyloid peptide and protein aggregation: a review with a focus on gold nanoparticles" Open
The data provided refer to our published article: T. John, A. Gladytz, C. Kubeil, L. L. Martin, H. J. Risselada, B. Abel*, Impact of nanoparticles on amyloid peptide and protein aggregation: a review with a focus on gold nanoparticles, Nan…
View article: Phase‐Separated Lipid‐Based Nanoparticles: Selective Behavior at the Nano‐Bio Interface
Phase‐Separated Lipid‐Based Nanoparticles: Selective Behavior at the Nano‐Bio Interface Open
The membrane‐protein interface on lipid‐based nanoparticles influences their in vivo behavior. Better understanding may evolve current drug delivery methods toward effective targeted nanomedicine. Previously, the cell‐selective accumulatio…
View article: CGCompiler: Automated Coarse-Grained Molecule Parametrization via Noise-Resistant Mixed-Variable Optimization
CGCompiler: Automated Coarse-Grained Molecule Parametrization via Noise-Resistant Mixed-Variable Optimization Open
Coarse-grained force fields (CG FFs) such as the Martini model entail a predefined, fixed set of Lennard-Jones parameters (building blocks) to model virtually all possible nonbonded interactions between chemically relevant molecules. Owing…
View article: Pure Graphene Acts as an “Entropic Surfactant” at the Octanol–Water Interface
Pure Graphene Acts as an “Entropic Surfactant” at the Octanol–Water Interface Open
[Image: see text] Graphene oxide (GO) has proved itself as a nanomaterial capable of acting as a surfactant by lowering the interfacial tension of the oil–water interface due to its polar oxygen groups. However, the surfactant behavior of …
View article: Cofilin-Driven Nuclear Deformation Drives Dendritic Cell Migration through the Extracellular Matrix
Cofilin-Driven Nuclear Deformation Drives Dendritic Cell Migration through the Extracellular Matrix Open
To mount an adaptive immune response, dendritic cells must process antigens, migrate to lymph nodes and form synapses with T cells. Critical to 3D migration and mechano-sensing is the nucleus, which is the size-limiting barrier for navigat…
View article: CGCompiler: Automated coarse-grained molecule parameterization via noise-resistant mixed-variable optimization
CGCompiler: Automated coarse-grained molecule parameterization via noise-resistant mixed-variable optimization Open
Coarse-grained force-fields (CG FF) such as the Martini model entail a predefined, fixed set of Lennard-Jones parameters (building blocks) to model virtually all possible non-bonded interactions between chemically relevant molecules. Owing…
View article: PMIpred: A physics-informed web server for quantitative Protein-Membrane Interaction prediction
PMIpred: A physics-informed web server for quantitative Protein-Membrane Interaction prediction Open
Motivation Many membrane peripheral proteins have evolved to transiently interact with the surface of (curved) lipid bilayers. Currently, methods to quantitatively predict sensing and binding free energies for protein sequences or structur…
View article: Physics-based generative model of curvature sensing peptides; distinguishing sensors from binders
Physics-based generative model of curvature sensing peptides; distinguishing sensors from binders Open
Proteins can specifically bind to curved membranes through curvature-induced hydrophobic lipid packing defects. The chemical diversity among such curvature “sensors” challenges our understanding of how they differ from general membrane “bi…
View article: Data for publication "Lipid oxidation controls peptide self-assembly near membranes through a surface attraction mechanism"
Data for publication "Lipid oxidation controls peptide self-assembly near membranes through a surface attraction mechanism" Open
The data provided refer to our published article: T. John,* S. Piantavigna, T. J. A. Dealey, B. Abel, H. J. Risselada, L. L. Martin*, Lipid oxidation controls peptide self-assembly nearmembranes through a surface attraction mechanism, Chem…
View article: Data for publication "Lipid oxidation controls peptide self-assembly near membranes through a surface attraction mechanism"
Data for publication "Lipid oxidation controls peptide self-assembly near membranes through a surface attraction mechanism" Open
<p>The data provided refer to our published article:</p>\n<p>T. John,* S. Piantavigna, T. J. A. Dealey, B. Abel, H. J. Risselada, L. L. Martin*, Lipid oxidation controls peptide self-assembly near<br>membranes throu…
View article: Azobenzene-Based Amino Acids for the Photocontrol of Coiled-Coil Peptides
Azobenzene-Based Amino Acids for the Photocontrol of Coiled-Coil Peptides Open
Coiled-coil peptides are high-affinity, selective, self-assembling binding motifs, making them attractive components for the preparation of functional biomaterials. Photocontrol of coiled-coil self-assembly allows for the precise localizat…
View article: Lipid oxidation controls peptide self-assembly near membranes through a surface attraction mechanism
Lipid oxidation controls peptide self-assembly near membranes through a surface attraction mechanism Open
Oxidized model membranes have differential effects on peptide fibril formation, driven by surface attraction, peptide charge and secondary structure stabilization.
View article: Cofilin-Driven Nuclear Deformation Drives Dendritic Cell Migration Through the Extracellular Matrix
Cofilin-Driven Nuclear Deformation Drives Dendritic Cell Migration Through the Extracellular Matrix Open
View article: Activated Dendritic Cells Round their Nuclei through Adhesion Loss and Atypical Cofilin Signaling
Activated Dendritic Cells Round their Nuclei through Adhesion Loss and Atypical Cofilin Signaling Open
To mount a secondary immune response, dendritic cells must process antigens, migrate to lymph nodes and form synapses with T cells. Critical to 3D migration and mechano-sensing is the nucleus, which is the size-limiting barrier for navigat…
View article: Curvature model for nanoparticle size effects on peptide fibril stability and molecular dynamics simulation data
Curvature model for nanoparticle size effects on peptide fibril stability and molecular dynamics simulation data Open
View article: Physics-based generative model of curvature sensing peptides; distinguishing sensors from binders
Physics-based generative model of curvature sensing peptides; distinguishing sensors from binders Open
Proteins can specifically bind to curved membranes through curvature-induced hydrophobic lipid packing defects. The chemical diversity among such curvature ‘sensors’ challenges our understanding of how they differ from general membrane ‘bi…