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Herre Jelger Risselada

Herre Jelger Risselada
1) Technische Universität Dortmund - Germany 2) Leiden University -The Netherlands 3) Georg-August University Goettingen - Germany · Physics - Computational Interface Physics

Prof. Dr.

About

82
Publications
16,354
Reads
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8,600
Citations
Citations since 2016
37 Research Items
5261 Citations
20162017201820192020202120220200400600800
20162017201820192020202120220200400600800
20162017201820192020202120220200400600800
20162017201820192020202120220200400600800
Additional affiliations
June 2018 - present
Leiden University
Position
  • Fellow
May 2014 - June 2016
Leibniz Institute of Surface Engineering (IOM)
Position
  • Junior research group leader
April 2009 - April 2014
Max Planck Institute for Biophysical Chemistry
Position
  • PostDoc Position

Publications

Publications (82)
Article
Highly curved toroidal micelles with diameters as small as 100 nm have been successfully constructed by self-assembly of amphiphilic block copolymers. These structures may have potential applications in gene or drug delivery. Experimental observations suggest that toroidal micelles likely originate from spherical or disc-like micelles which are tri...
Preprint
The occurrence of linear cholesterol-recognition motifs in alpha-helical transmembrane domains has long been debated. Here, we demonstrate the ability of a genetic algorithm guided by coarse-grained molecular dynamics simulations—a method coined evolutionary molecular dynamics (evo-MD)—to directly resolve the sequence which maximally attracts/sorts...
Article
Membrane curvature plays an essential role in the organization and trafficking of membrane associated proteins. Comparison or prediction of the experimentally resolved protein concentrations adopted at different membrane curvatures requires direct quantification of the relative partitioning free energy. Here, we present a highly efficient and simpl...
Article
Full-text available
In biological systems, proteins can be attracted to curved or stretched regions of lipid bilayers by sensing hydrophobic defects in the lipid packing on the membrane surface. Here, we present an efficient end-state free energy calculation method to quantify such sensing in molecular dynamics simulations. We illustrate that lipid packing defect sens...
Article
Full-text available
Heterogeneities (e.g., membrane proteins and lipid domains) and deformations (e.g., highly curved membrane regions) in biological lipid membranes cause lipid packing defects that may trigger functional sorting of lipids and membrane-associated proteins. To study these phenomena in a controlled and efficient way within molecular simulations, we deve...
Preprint
Full-text available
The self-assembly of peptides into supramolecular fibril structures has been linked to neurodegenerative diseases such as Alzheimer's disease but has also been observed in functional roles. Peptides are physiologically exposed to crowded environments of biomacromolecules, and particularly membrane lipids, within a cellular milieu. Previous research...
Article
Full-text available
The twin-arginine translocation (Tat) system serves to translocate folded proteins across energy-transducing membranes in bacteria, archaea, plastids and some mitochondria. In Escherichia coli, TatA, TatB, and TatC constitute functional translocons. TatA and TatB both possess an N-terminal transmembrane helix (TMH) followed by an amphipathic helix...
Article
The aggregation of peptides into amyloid fibrils has been linked to ageing-related diseases, such as Alzheimer’s and type 2 diabetes. Interfaces, particularly those with large nanostructured surfaces, can affect the kinetics of peptide aggregation, which ranges from complete inhibition to strong acceleration. While a number of physiochemical parame...
Preprint
The mitochondrial inner membrane is an integral part of the cellular lipid biosynthesis network. Intramitochondrial lipid transfer shuttles specific lipid species between the two mitochondrial membranes. This pathway is facilitated by designated protein complexes in the intermembrane space. A hetero-dimeric complex of Ups1 and Mdm35 has been identi...
Preprint
In biological systems, proteins can be attracted to curved or stretched regions of lipid bilayers by sensing hydrophobic defects in the lipid packing on the membrane surface. Here, we present an efficient end-state free energy calculation method to quantify such sensing in molecular dynamics simulations. We illustrate that lipid packing defect sens...
Preprint
Full-text available
The aggregation of peptides into amyloid fibrils is linked to ageing-related diseases, such as Alzheimer's disease and type 2 diabetes. Interfaces, particularly those with large nanostructured surface areas, can affect the kinetics of peptide aggregation, ranging from a complete inhibition to strong acceleration. While a number of physiochemical pa...
Preprint
The Tat system translocates folded proteins across energy-transducing prokaryotic membranes. In the bacterial model system Escherichia coli , the three components TatA, TatB, and TatC assemble to functional translocons. TatA and TatB both possess an N-terminal transmembrane helix (TMH) that is followed by an amphipathic helix (APH). The TMHs of Tat...
Article
Souza et al. present the latest release of the popular and widely used force field for near-atomistic coarse-grained biomolecular simulations.
Article
Full-text available
Fusion proteins can play a versatile and involved role during all stages of the fusion reaction. Their roles go far beyond forcing the opposing membranes into close proximity to drive stalk formation and fusion. Molecular simulations have played a central role in providing a molecular understanding of how fusion proteins actively overcome the free...
Presentation
Nanostructured material surfaces are abundant in nature, such as in the form of self-assembled liposomes and synthetic inorganic nanoparticles. These surfaces are coated with a biofilm ‘corona’ once they are exposed to a solution of peptides or proteins. The resulting peptide or protein ‘corona’ then defines the activity of the surface toward biolo...
Article
Thermodynamic integration is one of the most established methods to quantify excess free energies between different meta-stable states. Excess intermolecular inter-actions in surfactant assemblies are on the scale of the energy of thermal fluctuations.Therefore, these materials can be deformed and topologically altered via relatively small mechanic...
Article
Full-text available
Solid substrates often induce non-uniform strain and doping in graphene monolayer, therefore altering the intrinsic properties of graphene, reducing its charge carrier mobilities and, consequently, the overall electrical performance. Here, we exploit confocal Raman spectroscopy to study graphene directly free-floating on the surface of water, and s...
Article
Full-text available
Physiological membrane vesicles are built to separate reaction spaces in a stable manner, even when they accidentally collide or are kept in apposition by spatial constraints in the cell. This requires a natural resistance to fusion and mixing of their content, which originates from substantial energetic barriers to membrane fusion [1]. To facilita...
Article
Biological transmission of vesicular content occurs by opening of a fusion pore. Recent experimental observations have illustrated that fusion pores between vesicles that are docked by an extended flat contact zone are located at the edge (vertex) of this zone. We modeled this experimentally observed scenario by coarse-grained molecular simulations...
Article
The islet amyloid polypeptide (IAPP) is a regulatory peptide that can aggregate into fibrillar structures associated with type 2 diabetes. In this study, the IAPP21-27 segment was modified with a biotin linker at the N-terminus (Btn-GNNFGAIL) to immobilize peptide fibrils on streptavidin coated surfaces. Key residues for fibril formation of the N-t...
Article
Full-text available
Fat storage is an essential mechanism whereby cells store energy that can be later used to perform basal functions when food intake is reduced or insufficient. In cells, fat is deposited in organelles called lipid droplets (LDs). LDs are not mere inert storage pools, but they are active sites of lipid metabolism and remodeling. Furthermore, they ar...
Article
Significance The isolated transmembrane domains (TMDs) of fusion proteins such as SNARE molecules drastically lower the free energy of both the stalk barrier and metastable stalk, which is not trivially explained by molecular shape arguments. The here-demonstrated methodology may have far-reaching applications in the fields of medicine and pharmaco...
Article
Society is increasingly exposed to nanoparticles as they are ubiquitous in nature and introduced as man-made air pollutants and as functional ingredients in cosmetic products as well as in nanomedicine. Nanoparticles differ in size, shape and material properties. In addition to their intended function, the side effects on biochemical processes in o...
Article
Full-text available
The importance of curvature as a structural feature of biological membranes has been recognized for many years and has fascinated scientists from a wide range of different backgrounds. On the one hand, changes in membrane morphology are involved in a plethora of phenomena involving the plasma membrane of eukaryotic cells, including endo- and exocyt...
Article
Constitutive membrane fusion within eukaryotic cells is thought to be controlled at its initial steps, membrane tethering and SNARE complex assembly, and to rapidly proceed from there to full fusion. Although theory predicts that fusion pore expansion faces a major energy barrier and might hence be a rate-limiting and regulated step, corresponding...
Article
Full-text available
Membrane fusion in eukaryotic cells mediates the biogenesis of organelles, vesicular traffic between them, and exo- and endocytosis of important signalling molecules, such as hormones and neurotransmitters. Distinct tasks in intracellular membrane fusion have been assigned to conserved protein systems. Tethering proteins mediate the initial recogni...
Article
Coarse-grained molecular dynamics simulations are applied to explore the experimentally observed ability of the liquid-ordered (lo)/liquid-disordered (ld) phase boundary to facilitate viral membrane fusion. Surprisingly, a formed fusion stalk can be both attracted (i.e., stalkophilic) and repelled (i.e., stalkophobic) by the lo/ld phase boundary. T...
Article
Full-text available
SNAREs fuse membranes in several steps. Trans-SNARE complexes juxtapose membranes, induce hemifused stalk structures, and open the fusion pore. A recent penetration model of fusion proposed that SNAREs force the hydrophilic C-termini of their transmembrane domains through the hydrophobic core of the membrane(s). In contrast, the indentation model s...
Article
A complete physical description of membrane remodeling processes, such as fusion or fission, requires knowledge of the underlying free energy landscapes, particularly in barrier regions involving collective shape changes, topological transitions, and high curvature, where Canham-Helfrich (CH) continuum descriptions may fail. To calculate these free...
Article
Die Frage, wie Amyloidfibrillenbildung von Oberflächen beeinflusst wird, ist entscheidend für das Verständnis des Prozesses in vivo. Wir haben eine Kombination von kinetischen Experimenten und Moleküldynamiksimulationen angewendet, um aufzuklären, wie (Modell-)Oberflächen die Fibrillenbildung der amyloidbildenden Sequenzen des Prionenproteins SUP35...
Article
Full-text available
The question of how amyloid fibril formation is influenced by surfaces is crucial for a detailed understanding of the process in vivo. We applied a combination of kinetic experiments and molecular dynamics simulations to elucidate how (model) surfaces influence fibril formation of the amyloid-forming sequences of prion protein SUP35 and human islet...
Article
Full-text available
Investigating the adsorption of peptides on inorganic surfaces, on the molecular level, is fundamental for medicinal and analytical applications. Peptides can be potent as linkers between surfaces and living cells in biochips or in implantation medicine. Here, we studied the adsorption process of the positively charged pentapeptide RTHRK, a recentl...
Article
Phage shock protein A (PspA) belongs to the highy conserved PspA/IM30 family and is a key component of the stress inducible Psp system in Escherichia coli. One of its central roles is the regulatory interaction with the transcriptional activator of this system, the σ(54) enhancer binding protein PspF, a member of the AAA+ protein family. The PspA/F...
Article
Full-text available
The Tat system can transport folded, signal peptide-containing proteins (Tat substrates) across energized membranes of prokaryotes and plant plastids. A twin-arginine motif in the signal peptide of Tat substrates is recognized by TatC-containing complexes, and TatA permits the membrane passage. Often, as in the model Tat systems of Escherichia coli...
Article
In this issue of Structure, Reddy and colleagues combined various experimental data to build a realistic near-atomic model of the complete lipidic influenza A virion. Here, we illustrate the advances made by this pioneering simulation study and discuss ongoing challenges. Copyright © 2015 Elsevier Ltd. All rights reserved.
Article
Full-text available
The clustering of proteins and lipids in distinct microdomains is emerging as an important principle for the spatial patterning of biological membranes. Such domain formation can be the result of hydrophobic and ionic interactions with membrane lipids as well as of specific protein–protein interactions. Here using plasma membrane-resident SNARE pro...
Article
Full-text available
The clustering of proteins and lipids in distinct microdomains is emerging as an important principle for the spatial patterning of biological membranes. Such domain formation can be the result of hydrophobic and ionic interactions with membrane lipids as well as of specific protein–protein interactions. Here using plasma membrane-resident SNARE pro...
Article
The productive fusion pore in membrane fusion is generally thought to be toroidally shaped. Theoretical studies and recent experiments suggest that its formation, in some scenarios, may be preceded by an initial pore formed near the rim of the extended hemifusion diaphragm (HD), a rim-pore. This rim-pore is characterized by a nontoroidal shape that...
Article
Full-text available
Significance We focus on computing lipidic fusion pathway energetics and interpret them in a biological context. We illustrate that the progression of fast synaptic fusion may not rely on the point-like forces that are being transmitted to the membrane via the transmembrane domains of SNARE molecules. Our work bridges the many present gaps between...
Article
Full-text available
Here we report studies on biologically important intermembrane repulsion forces using molecular dynamics (MD) simulations and experimental (osmotic stress) investigations of repulsion forces between 1-palmitoyl-2-oleyl-sn-glycero-3-phosphocholine bilayers. We show that the repulsion between tension-free membranes can be determined from MD simulatio...
Article
Full-text available
Synaptic-vesicle exocytosis is mediated by the vesicular Ca(2+) sensor synaptotagmin-1. Synaptotagmin-1 interacts with the SNARE protein syntaxin-1A and acidic phospholipids such as phosphatidylinositol 4,5-bisphosphate (PIP2). However, it is unclear how these interactions contribute to triggering membrane fusion. Using PC12 cells from Rattus norve...
Article
SNARE molecules and influenza hemagglutinin are thought to facilitate a similar fusion mechanism. Yet, fusion occurs under different physiological conditions and time-scales, and thus the underlying free-energy landscapes and reaction pathways might be rather different. Here, we have applied CG-MD simulations to elucidate how these different fusion...
Article
Full-text available
In experiments on model membranes, formation of large domains of different lipid composition is readily observed. However, no such phase separation is observed in the membranes of intact cells. Instead, small transient inhomogeneities called lipid rafts are expected in these systems. One of the numerous attempts to explain small domains refers to t...
Article
Full-text available
Our molecular simulations reveal that wild-type influenza fusion peptides are able to stabilize a highly fusogenic pre-fusion structure, i.e. a peptide bundle formed by four or more trans-membrane arranged fusion peptides. We rationalize that the lipid rim around such bundle has a non-vanishing rim energy (line-tension), which is essential to (i) s...
Data
Calculation of the line-tension of the elongated stalk and HD. (TIF)
Data
Splayed lipid intermediate observed before the stalk disappears. (TIF)
Data
Bundle-mediated stalk formation. (TIF)
Data
Additional bundle-mediated fusion simulations. (TIF)
Article
At mesoscopic length scales and small curvatures, Helfrich's well established continuum model [1] provides accurate membrane bending and stretching energies. For the small nanometer scales and extreme curvatures relevant for fundamental biological processes like synaptic fusion and tubulation, however, its validity is unclear. To test whether or no...
Article
Full-text available
Neuronal exocytosis is catalysed by the SNAP receptor protein syntaxin-1A, which is clustered in the plasma membrane at sites where synaptic vesicles undergo exocytosis. However, how syntaxin-1A is sequestered is unknown. Here we show that syntaxin clustering is mediated by electrostatic interactions with the strongly anionic lipid phosphatidylinos...
Article
Neurotransmitter release at the synapse requires fusion of synaptic vesicles with the presynaptic plasma membrane. SNAREs are the core constituents of the protein machinery responsible for this membrane fusion, but the actual fusion mechanism remains unclear. Here, we have simulated neuronal SNARE-mediated membrane fusion in molecular detail. In ou...
Article
Full-text available
Synaptotagmin-1 triggers Ca(2+)-sensitive, rapid neurotransmitter release by promoting interactions between SNARE proteins on synaptic vesicles and the plasma membrane. How synaptotagmin-1 promotes this interaction is unclear, and the massive increase in membrane fusion efficiency of Ca(2+)-bound synaptotagmin-1 has not been reproduced in vitro. Ho...
Article
Full-text available
Using a coarse-grained molecular model we study the spatial distribution of lipid domains on a 20-nm-sized vesicle. The lipid mixture laterally phase separates into a raftlike, liquid-ordered (l(o)) phase and a liquid-disordered phase. As we uniaxially compress the mixed vesicle keeping the enclosed volume constant, we impart tension onto the membr...
Article
Full-text available
Mechano-sensitive channels are ubiquitous membrane proteins that activate in response to increasing tension in the lipid membrane. They facilitate a sudden, nonselective release of solutes and water that safeguards the integrity of the cell in hypo- or hyper-osmotic shock conditions. We have simulated the rapid release of content from a pressurized...
Article
We present an algorithm to reconstruct atomistic structures from their corresponding coarse-grained (CG) representations and its implementation into the freely available molecular dynamics (MD) program package GROMACS. The central part of the algorithm is a simulated annealing MD simulation in which the CG and atomistic structures are coupled via r...
Article
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Article
Full-text available
At present very little is known about the kinetic barriers which a small vesicle will face during the transformation from the liquid-crystalline to the gel phase, and what the structure of frozen vesicles looks like at the molecular level. The formation of gel domains in the strongly curved bilayer of a small vesicle seems almost paradoxical and is...
Article
The asymmetric insertion of amphiphiles into biological membranes compromises the balance between the inner and outer monolayers. As a result, area expansion of the receiving leaflet and curvature strain may lead to membrane permeation, shape changes, or membrane fusion events. We have conducted both atomistic and coarse-grained molecular dynamics...