Publications

Electroporation Simulation

Published 7 July 2020 in Biophysical Journal (v. 119 pp. 190–205):

Pulsed electric fields can create pores in the voltage sensors of voltage-gated ion channels

Lea Rems, Marina A Kasimova, Ilaria Testa, Lucie Delemotte

Pulsed electric fields are increasingly used in medicine to transiently increase the cell membrane permeability via electroporation to deliver therapeutic molecules into the cell. One type of event that contributes to this increase in membrane permeability is the formation of pores in the membrane lipid bilayer. However, electrophysiological measurements suggest that membrane proteins are affected as well, particularly voltage-gated ion channels (VGICs). The molecular mechanisms by which the electric field could affects these molecules remain unidentified. In this study, we used molecular dynamics simulations to unravel the molecular events that take place in different VGICs when exposing them to electric fields mimicking electroporation conditions. We show that electric fields can induce pores in the voltage-sensor domains (VSDs) of different VGICs and that these pores form more easily in some channels than in others. We demonstrate that poration is more likely in VSDs that are more hydrated and are electrostatically more favorable for the entry of ions. We further show that pores in VSDs can expand into so-called complex pores, which become stabilized by lipid headgroups. Our results suggest that such complex pores are considerably more stable than conventional lipid pores, and their formation can lead to severe unfolding of VSDs from the channel. We anticipate that such VSDs become dysfunctional and unable to respond to changes in transmembrane voltage, which is in agreement with previous electrophysiological measurements showing a decrease in the voltage-dependent transmembrane ionic currents after pulse treatment. Finally, we discuss the possibility of activation of VGICs by submicrosecond-duration pulses. Overall, our study reveals a new, to our knowledge, mechanism of electroporation through membranes containing VGICs.

Read the full publication here.

Publications

Dramatic Domains of DeCLIC

Published 16 June 2020 in Proceedings of the National Academy of Sciences of the USA (v. 117 pp. 13437–13446):

Structural basis for allosteric transitions of a multidomain pentameric ligand-gated ion channel

Haidai Hu, Rebecca J Howard, Ugo Bastolla, Erik Lindahl, Marc Delarue

Pentameric ligand-gated ion channels (pLGICs) are allosteric receptors that mediate rapid electrochemical signal transduction in the animal nervous system through the opening of an ion pore upon binding of neurotransmitters. Orthologs have been found and characterized in prokaryotes and they display highly similar structure–function relationships to eukaryotic pLGICs; however, they often encode greater architectural diversity involving additional amino-terminal domains (NTDs). Here we report structural, functional, and normal-mode analysis of two conformational states of a multidomain pLGIC, called DeCLIC, from a Desulfofustis deltaproteobacterium, including a periplasmic NTD fused to the conventional ligand-binding domain (LBD). X-ray structure determination revealed an NTD consisting of two jelly-roll domains interacting across each subunit interface. Binding of Ca2+ at the LBD subunit interface was associated with a closed transmembrane pore, with resolved monovalent cations intracellular to the hydrophobic gate. Accordingly, DeCLIC-injected oocytes conducted currents only upon depletion of extracellular Ca2+; these were insensitive to quaternary ammonium block. Furthermore, DeCLIC crystallized in the absence of Ca2+ with a wide-open pore and remodeled periplasmic domains, including increased contacts between the NTD and classic LBD agonist-binding sites. Functional, structural, and dynamical properties of DeCLIC paralleled those of sTeLIC, a pLGIC from another symbiotic prokaryote. Based on these DeCLIC structures, we would reclassify the previous structure of bacterial ELIC (the first high-resolution structure of a pLGIC) as a “locally closed” conformation. Taken together, structures of DeCLIC in multiple conformations illustrate dramatic conformational state transitions and diverse regulatory mechanisms available to ion channels in pLGICs, particularly involving Ca2+ modulation and periplasmic NTDs.

Read the full publication here.

Publications

Library Building for CryoEM

Published 1 April 2020 in Acta Crystallographica Section D (v. 76 pp. 350–356):

Development of basic building blocks for cryo-EM: the emcore and emvis software libraries

José Miguel de la Rosa-Trevín, Pedro Alberto Hernández Viga, Joaquín Otónc, Erik Lindahl

Image-processing software has always been an integral part of structure determination by cryogenic electron microscopy (cryo-EM). Recent advances in hardware and software are recognized as one of the key factors in the so-called cryo-EM resolution revolution. Increasing computational power has opened many possibilities to consider more demanding algorithms, which in turn allow more complex biological problems to be tackled. Moreover, data processing has become more accessible to many experimental groups, with computations that used to last for many days at supercomputing facilities now being performed in hours on personal workstations. All of these advances, together with the rapid expansion of the community, continue to pose challenges and new demands on the software-development side. In this article, the development of emcore and emvis, two basic software libraries for image manipulation and data visualization in cryo-EM, is presented. The main goal is to provide basic functionality organized in modular components that other developers can reuse to implement new algorithms or build graphical applications. An additional aim is to showcase the importance of following established practices in software engineering, with the hope that this could be a first step towards a more standardized way of developing and distributing software in the field.

Read the full publication here.

Publications

Microswitch Control of GPCRs

Published 7 February 2020 in Biochemistry (v. 59 pp. 880–891):

Energy landscapes reveal agonist control of G protein-coupled receptor activation via microswitches

Oliver Fleetwood, Pierre Matricon, Jens Carlsson, Lucie Delemotte

Agonist binding to G protein-coupled receptors (GPCRs) leads to conformational changes in the transmembrane region that activate cytosolic signaling pathways. Although high-resolution structures of different receptor states are available, atomistic details of allosteric signaling across the membrane remain elusive. We calculated free energy landscapes of β2 adrenergic receptor activation using atomistic molecular dynamics simulations in an optimized string of swarms framework, which shed new light on how microswitches govern the equilibrium between conformational states. Contraction of the extracellular binding site in the presence of the agonist BI-167107 is obligatorily coupled to conformational changes in a connector motif located in the core of the transmembrane region. The connector is probabilistically coupled to the conformation of the intracellular region. An active connector promotes desolvation of a buried cavity, a twist of the conserved NPxxY motif, and an interaction between two conserved tyrosines in transmembrane helices 5 and 7 (Y–Y motif), which lead to a larger population of active-like states at the G protein binding site. This coupling is augmented by protonation of the strongly conserved Asp792.50. The agonist binding site hence communicates with the intracellular region via a cascade of locally connected microswitches. Characterization of these can be used to understand how ligands stabilize distinct receptor states and contribute to development drugs with specific signaling properties. The developed simulation protocol can likely be transferred to other class A GPCRs.

Read the full publication here.

Publications

Machine Learning Demystifies Biomolecular Simulations

Published 4 February 2020 in Biophysical Journal (v. 118 pp. 765-780):

Molecular insights from conformational ensembles via machine learning

Oliver Fleetwood, Marina A Kasimova, Annie M Westerlund, Lucie Delemotte

Biomolecular simulations are intrinsically high dimensional and generate noisy data sets of ever-increasing size. Extracting important features from the data is crucial for understanding the biophysical properties of molecular processes, but remains a big challenge. Machine learning (ML) provides powerful dimensionality reduction tools. However, such methods are often criticized as resembling black boxes with limited human-interpretable insight. We use methods from supervised and unsupervised ML to efficiently create interpretable maps of important features from molecular simulations. We benchmark the performance of several methods, including neural networks, random forests, and principal component analysis, using a toy model with properties reminiscent of macromolecular behavior. We then analyze three diverse biological processes: conformational changes within the soluble protein calmodulin, ligand binding to a G protein-coupled receptor, and activation of an ion channel voltage-sensor domain, unraveling features critical for signal transduction, ligand binding, and voltage sensing. This work demonstrates the usefulness of ML in understanding biomolecular states and demystifying complex simulations.

Read the full publication here.

Publications

Seeing and Simulating Malarial Sugar Transport

Published 29 January 2020 in Nature (v. 578 pp. 321–325):

The molecular basis for sugar import in malaria parasites

Abdul Aziz Qureshi, Albert Suades, Rei Matsuoka, Joseph Brock, Sarah E McComas, Emmanuel Nji, Laura Orellana, Magnus Claesson, Lucie Delemotte, David Drew

Elucidating the mechanism of sugar import requires a molecular understanding of how transporters couple sugar binding and gating events. Whereas mammalian glucose transporters (GLUTs) are specialists1, the hexose transporter from the malaria parasite Plasmodium falciparum PfHT12,3 has acquired the ability to transport both glucose and fructose sugars as efficiently as the dedicated glucose (GLUT3) and fructose (GLUT5) transporters. Here, to establish the molecular basis of sugar promiscuity in malaria parasites, we determined the crystal structure of PfHT1 in complex with D-glucose at a resolution of 3.6 Å. We found that the sugar-binding site in PfHT1 is very similar to those of the distantly related GLUT3 and GLUT5 structures4,5. Nevertheless, engineered PfHT1 mutations made to match GLUT sugar-binding sites did not shift sugar preferences. The extracellular substrate-gating helix TM7b in PfHT1 was positioned in a fully occluded conformation, providing a unique glimpse into how sugar binding and gating are coupled. We determined that polar contacts between TM7b and TM1 (located about 15 Å from D-glucose) are just as critical for transport as the residues that directly coordinate D-glucose, which demonstrates a strong allosteric coupling between sugar binding and gating. We conclude that PfHT1 has achieved substrate promiscuity not by modifying its sugar-binding site, but instead by evolving substrate-gating dynamics.

Read the full publication here.

Publications

Gating by Breaking

Released 27 November 2019 in eLife (v. 8 art. e53400):

Helix breaking transition in the S4 of HCN channel is critical for hyperpolarization-dependent gating

Marina A Kasimova, Debanjan Tewari, John B Cowgill, Willy Carrasquel Ursuleaz, Jenna L Lin, Lucie Delemotte, Baron Chanda

In contrast to most voltage-gated ion channels, hyperpolarization- and cAMP gated (HCN) ion channels open on hyperpolarization. Structure-function studies show that the voltage-sensor of HCN channels are unique but the mechanisms that determine gating polarity remain poorly understood. All-atom molecular dynamics simulations (~20 μs) of HCN1 channel under hyperpolarization reveals an initial downward movement of the S4 voltage-sensor but following the transfer of last gating charge, the S4 breaks into two sub-helices with the lower sub-helix becoming parallel to the membrane. Functional studies on bipolar channels show that the gating polarity strongly correlates with helical turn propensity of the substituents at the breakpoint. Remarkably, in a proto-HCN background, the replacement of breakpoint serine with a bulky hydrophobic amino acid is sufficient to completely flip the gating polarity from inward to outward-rectifying. Our studies reveal an unexpected mechanism of inward rectification involving a linker sub-helix emerging from HCN S4 during hyperpolarization.

Read the full publication here.

Publications

Clustering Calmodulin

From the October 2019 issue of Journal of Chemical Theory & Computation (v. 15 pp. 6752–6759):

InfleCS: clustering free energy landscapes with Gaussian mixtures

Annie M. Westerlund, Lucie Delemotte

Free energy landscapes provide insights into conformational ensembles of biomolecules. In order to analyze these landscapes and elucidate mechanisms underlying conformational changes, there is a need to extract metastable states with limited noise. This has remained a formidable task, despite a plethora of existing clustering methods. We present InfleCS, a novel method for extracting well-defined core states from free energy landscapes. The method is based on a Gaussian mixture free energy estimator and exploits the shape of the estimated density landscape. The core states that naturally arise from the clustering allow for detailed characterization of the conformational ensemble. The clustering quality is evaluated on three toy models with different properties, where the method is shown to consistently outperform other conventional and state-of-the-art clustering methods. Finally, the method is applied to a temperature enhanced molecular dynamics simulation of Ca2+ -bound Calmodulin. Through the free energy landscape, we discover a pathway between a canonical and a compact state, revealing conformational changes driven by electrostatic interactions.

Read the full publication here.

Publications

Models for MD Sharing

Published 17 September 2019 in the Journal of Chemical Information and Modeling (v. 59 pp. 4093–4099):

Sharing data from molecular simulations

Mark Abraham, Rossen Apostolov, Jonathan Barnoud, Paul Bauer, Christian Blau, Alexandre MJJ Bonvin, Matthieu Chavent, John Chodera, Karmen Čondić-Jurkić, Lucie Delemotte, Helmut Grubmüller, Rebecca J Howard, E Joseph Jordan, Erik Lindahl, OH Samuli Ollila, Jana Selent, Daniel GA Smith, Phillip J Stansfeld, Johanna KS Tiemann, Mikael Trellet, Christopher Woods, Artem Zhmurov

Given the need for modern researchers to produce open, reproducible scientific output, the lack of standards and best practices for sharing data and workflows used to produce and analyze molecular dynamics (MD) simulations has become an important issue in the field. There are now multiple well-established packages to perform molecular dynamics simulations, often highly tuned for exploiting specific classes of hardware, each with strong communities surrounding them, but with very limited interoperability/transferability options. Thus, the choice of the software package often dictates the workflow for both simulation production and analysis. The level of detail in documenting the workflows and analysis code varies greatly in published work, hindering reproducibility of the reported results and the ability for other researchers to build on these studies. An increasing number of researchers are motivated to make their data available, but many challenges remain in order to effectively share and reuse simulation data. To discuss these and other issues related to best practices in the field in general, we organized a workshop in November 2018. Here, we present a brief overview of this workshop and topics discussed. We hope this effort will spark further conversation in the MD community to pave the way toward more open, interoperable, and reproducible outputs coming from research studies using MD simulations.

Read the full publication here.

Publications

Nicotinic Structure & Dynamics

For the November 2019 issue of Neuron (v. 104 pp. 501–511.e6):

Agonist selectivity and ion permeation in the α3β4 ganglionic nicotinic receptor

Anant Gharpure, Jinfeng Teng, Yuxuan Zhuang, Colleen M. Noviello, Richard M. Walsh Jr., Rico Cabuco, Rebecca J. Howard, Nurulain T. Zaveri, Erik Lindahl, Ryan E. Hibbs

Nicotinic acetylcholine receptors are pentameric ion channels that mediate fast chemical neurotransmission. The α3β4 nicotinic receptor subtype forms the principal relay between the central and peripheral nervous systems in the autonomic ganglia. This receptor is also expressed focally in brain areas that affect reward circuits and addiction. Here, we present structures of the α3β4 nicotinic receptor in lipidic and detergent environments, using functional reconstitution to define lipids appropriate for structural analysis. The structures of the receptor in complex with nicotine, as well as the α3β4-selective ligand AT-1001, complemented by molecular dynamics, suggest principles of agonist selectivity. The structures further reveal much of the architecture of the intracellular domain, where mutagenesis experiments and simulations define residues governing ion conductance.

Read the full publication here.

Publications

Otop Proton Paths

From the June 2019 issue of Nature Structural & Molecular Biology (v. 26 pp. 528–530):

Outlining the proton-conduction pathway in otopetrin channels

Lucie Delemotte

New structural work sheds light on the architecture of otopetrin channels, offering insights into the mechanisms for proton permeation in this family.

Read the full News & Views article here, referencing the publication Structures of the otopetrin proton channels Otop1 and Otop3 by Saotome & colleagues.

Publications

Elastic Networks on the Net

For the September 2019 issue of Bioinformatics (v. 35 pp. 3505–3507):

eBDIMS server: protein transition pathways with ensemble analysis in 2D-motion spaces

Laura Orellana, Johan Gustavsson, Cathrine Bergh, Ozge Yoluk, Erik Lindahl

Understanding how proteins transition between different conformers, and how conformers relate to each other in terms of structure and function, is not trivial. Here, we present an online tool for transition pathway generation between two protein conformations using Elastic Network Driven Brownian Dynamics Importance Sampling, a coarse-grained simulation algorithm, which spontaneously predicts transition intermediates trapped experimentally. In addition to path-generation, the server provides an interactive 2D-motion landscape graphical representation of the transitions or any additional conformers to explore their structural relationships.

Read the full publication here.

Publications

Reproducibility rules

Released 17 January 2019 in PLOS Computational Biology (v. 15 art. e1006649):

Ten simple rules on how to create open access and reproducible molecular simulations of biological systems

Arne Elofsson, Berk Hess, Erik Lindahl, Alexey Onufriev, David van der Spoel, Anders Wallqvist

All PLOS journals have an open data policy that, amongst other things, states that all data and related metadata underlying the findings reported in a submitted manuscript should be deposited in an appropriate public repository, or for smaller datasets, as supporting information. This should obviously apply to computational methods as well, but unfortunately this is not always applied in practice, although it is of greatest importance for the scientific quality of simulations and other modeling projects.

Molecular dynamics and other type of simulations have become a fundamental part of life sciences. The simulations are dependent on a number of parameters such as force fields, initial configurations, simulation protocols, and software. Researchers have different opinions about the types of software they prefer, and in general, we believe authors should be free to choose the tools that best fit their needs. However, as scientists, we also have a common obligation to critically test each other’s statements to find mistakes (including errors in the algorithms and bugs in the code), which can be exemplified by a heated debate over simulations of supercooled water that ended up being due to a subtle algorithmic issue, and we believe PLOS has a particularly strong responsibility to lead this development even if it might cause some short-term grief.

In particular, all published results should, in principle, be possible to reproduce independently by scientists in other labs using different tools. To ensure this, we propose a set of standards that any publication in PLOS Computational Biology, and hopefully, publications in other journals as well, should follow. We do believe that the sooner such policies are widely adapted, the more open and collaborative science will flourish.

These 10 simple rules should not be limited to molecular dynamics but also include Monte Carlo simulations, quantum mechanics calculations, molecular docking, and any other computational methods involving computations on biological molecules.

Read the full publication here.

Publications

e-Science in Scandinavia

From the December 2018 release of Informatik Spektrum (v. 41 pp. 398–404):

e-Science in Scandinavia: The Case of the Swedish e-Science Research Center

Olivia Eriksson, Erwin Laure, Erik Lindahl, Dan Henningson & Anders Ynnerman

The Swedish e-Science Research Centre (SeRC) is based on a collaboration between four Swedish universities: The KTH Royal Institute of Technology (KTH), Stockholm University (SU), Karolinska Institutet (KI) and Linköping University (LiU). SeRC’s mission statement is to develop state-of-the-art eScience tools and provide e-infrastructure support to existing and emerging e-Science research communities to help bring about scientific breakthroughs in Sweden. SeRC was founded in 2010 as the result of the Strategic Research Area (SRA) initiative launched by the Swedish Government Bill on Research Policy in 2008, where a total of 24 different strategic research areas were defined – one of which was e-Science. Initially SeRC was granted funding for 5 years. During those first 5 years, SeRC built up an organization for e-Science research, which has been highly successful. This was reflected in the excellent grades that SeRC received when the SRAs in Sweden were evaluated in 2015, and the fact that after this, SeRC received funding for at least 5 more years. This new phase of SeRC partly focuses on activities relating to emerging technologies (such as exascale systems and data-driven science) while also consolidating SeRC’s ongoing efforts in working towards a long-lasting e-Science environment in Sweden.

Read the full publication here.

Publications

RELION Refined

Accepted manuscript, posted ahead of online November 9, 2018 in eLife (v. 7 art. e42166):

New tools for automated high-resolution cryo-EM structure determination in RELION-3

Jasenko Zivanov, Takanori Nakane, Björn O Forsberg, Dari Kimanius, Wim JH Hagen, Erik Lindahl & Sjors HW Scheres

Here, we describe the third major release of RELION. CPU-based vector acceleration has been added in addition to GPU support, which provides flexibility in use of resources and avoids memory limitations. Reference-free autopicking with Laplacian-of-Gaussian filtering and execution of jobs from python allows non-interactive processing during acquisition, including 2D-classification, de novo model generation and 3D-classification. Per-particle refinement of CTF parameters and correction of estimated beam tilt provides higher-resolution reconstructions when particles are at different heights in the ice, and/or coma-free alignment has not been optimal. Ewald sphere curvature correction improves resolution for large particles. We illustrate these developments with publicly available data sets: together with a Bayesian approach to beam-induced motion correction it leads to resolution improvements of 0.2–0.7 Å compared to previous RELION versions.

Read the full publication here.

Publications

Dynamic Basis for Drug Binding

From the October 16, 2018 issue of Proceedings of the National Academy of Sciences of the USA (v. 115 pp. 10672–10677):

Allosteric potentiation of a ligand-gated ion channel is mediated by access to a deep membrane-facing cavity

Stephanie A Heusser, Marie Lycksell, Xueqing Wang, Sarah E McComas, Rebecca J Howard & Erik Lindahl

Molecular mechanisms of general anesthetic modulation in pentameric ligand-gated ion channels remain controversial. Here we present molecular simulations and functional data that reveal correlations between dynamic differences in a membrane-accessible cavity and dramatic anesthetic effects, separate inhibitory and potentiating effects within the same electrophysiology recordings, and support a model for communication between the lipid bilayer and ion channel pore. In particular, enhanced electrostatic interactions in the membrane-accessible site were associated with a unique mode of anesthetic potentiation, persisting tens of minutes after washout. These results offer a bridge between lipid- and receptor-based theories of anesthesia, with the potential to inform both mechanistic understanding and drug development.

Read the full publication here.

Publications

Sweet Simulations

From the September 25, 2018 issue of Scientific Reports (v. 8 art. 14324):

Uptake dynamics in the Lactose permease (LacY) membrane protein transporter

Dari Kimanius, Erik Lindahl & Magnus Andersson

The sugar transporter Lactose permease (LacY) of Escherichia coli has become a prototype to understand the underlying molecular details of membrane transport. Crystal structures have trapped the protein in sugar-bound states facing the periplasm, but with narrow openings unable to accommodate sugar. Therefore, the molecular details of sugar uptake remain elusive. In this work, we have used extended simulations and metadynamics sampling to explore a putative sugar-uptake pathway and associated free energy landscape. We found an entrance at helix-pair 2 and 11, which involved lipid head groups and residues Gln 241 and Gln 359. Furthermore, the protein displayed high flexibility on the periplasmic side of Phe 27, which is located at the narrowest section of the pathway. Interactions to Phe 27 enabled passage into the binding site, which was associated with a 24 ± 4 kJ/mol binding free energy in excellent agreement with an independent binding free energy calculation and experimental data. Two free energy minima corresponding to the two possible binding poses of the lactose analog β-D-galactopyranosyl-1-thio-β-D-galactopyranoside (TDG) were aligned with the crystal structure-binding pocket. This work outlines the chemical environment of a putative periplasmic sugar pathway and paves way for understanding substrate affinity and specificity in LacY.

Corresponding author and former group member Magnus Andersson can now be reached at Umeå University. Read the full publication here.

Publications

Commentary: Opening Leads to Closing

Commentary for the October 1, 2018 issue of the Journal of General Physiology (v. 150 art. 1356):

Opening leads to closing: Allosteric crosstalk between the activation and inactivation gates in KcsA

Lucie Delemotte

Voltage-gated potassium (Kv) channels control a number of different physiological processes, including the firing rate in axons. Such K+ channels display a reduction of conductance after exposure to a prolonged activating stimulus. This process, referred to as inactivation, causes repolarization of the cell membrane after the depolarizing phase of an action potential. The transient openings that result from it also allow neurons to readily fire a new action potential. Two types of inactivation mechanisms have been described in Kv channels (Hoshi et al., 1990). Fast inactivation, also called N-type inactivation, results from a mechanism that has been ascribed to pore blocking by a N-terminal peptide. Slow inactivation, or C-type inactivation, is revealed upon suppression of fast inactivation and is thought to be due to a conformational change occurring within the pore of the channel. While the structural basis of C-type inactivation appears to have been established, how it is dynamically coupled to channel activation remains to be understood in detail. In the Journal of General Physiology, a new study (see Li et al. 2018) proposes an intriguing mechanism for the allosteric control of C-type inactivation by the activation gate in the bacterial K+ channel KcsA.

Read the full commentary here.

Publications

Who Dances With an Electric Beat?

For the October 1, 2018 issue of the Journal of General Physiology (v. 150 art. 1444):

Determining the molecular basis of voltage sensitivity in membrane proteins

Marina A. Kasimova, Erik Lindahl & Lucie Delemotte

Voltage-sensitive membrane proteins are united by their ability to transform changes in membrane potential into mechanical work. They are responsible for a spectrum of physiological processes in living organisms, including electrical signaling and cell-cycle progression. Although the mechanism of voltage-sensing has been well characterized for some membrane proteins, including voltage-gated ion channels, even the location of the voltage-sensing elements remains unknown for others. Moreover, the detection of these elements by using experimental techniques is challenging because of the diversity of membrane proteins. Here, we provide a computational approach to predict voltage-sensing elements in any membrane protein, independent of its structure or function. It relies on an estimation of the propensity of a protein to respond to changes in membrane potential. We first show that this property correlates well with voltage sensitivity by applying our approach to a set of voltage-sensitive and voltage-insensitive membrane proteins. We further show that it correctly identifies authentic voltage-sensitive residues in the voltage-sensor domain of voltage-gated ion channels. Finally, we investigate six membrane proteins for which the voltage-sensing elements have not yet been characterized and identify residues and ions that might be involved in the response to voltage. The suggested approach is fast and simple and enables a characterization of voltage sensitivity that goes beyond mere identification of charges. We anticipate that its application before mutagenesis experiments will significantly reduce the number of potential voltage-sensitive elements to be tested.

Read the commentary in the same issue by Caitlin Sedwick, or see the paper here!

Publications

Human Skin Barrier Structure

Featured on the August 2018 cover of Journal of Structural Biology (v. 203 pp. 149–161):

Human skin barrier structure and function analyzed by cryo-EM and molecular dynamics simulation

Magnus Lundborg, Ali Narangifard, Christian L Wennberg, Erik Lindahl, Bertil Daneholt & Lars Norlén

In the present study we have analyzed the molecular structure and function of the human skin’s permeability barrier using molecular dynamics simulation validated against cryo-electron microscopy data from near native skin.

The skin’s barrier capacity is located to an intercellular lipid structure embedding the cells of the superficial most layer of skin – the stratum corneum. According to the splayed bilayer model (Iwai et al., 2012) the lipid structure is organized as stacked bilayers of ceramides in a splayed chain conformation with cholesterol associated with the ceramide sphingoid moiety and free fatty acids associated with the ceramide fatty acid moiety. However, knowledge about the lipid structure’s detailed molecular organization, and the roles of its different lipid constituents, remains circumstantial.

Starting from a molecular dynamics model based on the splayed bilayer model, we have, by stepwise structural and compositional modifications, arrived at a thermodynamically stable molecular dynamics model expressing simulated electron microscopy patterns matching original cryo-electron microscopy patterns from skin extremely closely. Strikingly, the closer the individual molecular dynamics models’ lipid composition was to that reported in human stratum corneum, the better was the match between the models’ simulated electron microscopy patterns and the original cryo-electron microscopy patterns. Moreover, the closest-matching model’s calculated water permeability and thermotropic behaviour were found compatible with that of human skin.

The new model may facilitate more advanced physics-based skin permeability predictions of drugs and toxicants. The proposed procedure for molecular dynamics based analysis of cellular cryo-electron microscopy data might be applied to other biomolecular systems.

Read the full publication here.

Publications

Boosting Efficiency With Riemann Metrics

From the August 30, 2018 issue of Physical Review E (v. 98 art. 023312):

Riemann metric approach to optimal sampling of multidimensional free-energy landscapes

Viveca Lindahl, Jack Lidmar & Berk Hess

Exploring the free-energy landscape along reaction coordinates or system parameters λ is central to many studies of high-dimensional model systems in physics, e.g., large molecules or spin glasses. In simulations this usually requires sampling conformational transitions or phase transitions, but efficient sampling is often difficult to attain due to the roughness of the energy landscape. For Boltzmann distributions, crossing rates decrease exponentially with free-energy barrier heights. Thus, exponential acceleration can be achieved in simulations by applying an artificial bias along λ tuned such that a flat target distribution is obtained. A flat distribution is, however, an ambiguous concept unless a proper metric is used and is generally suboptimal. Here we propose a multidimensional Riemann metric, which takes the local diffusion into account, and redefine uniform sampling such that it is invariant under nonlinear coordinate transformations. We use the metric in combination with the accelerated weight histogram method, a free-energy calculation and sampling method, to adaptively optimize sampling toward the target distribution prescribed by the metric. We demonstrate that for complex problems, such as molecular dynamics simulations of DNA base-pair opening, sampling uniformly according to the metric, which can be calculated without significant computational overhead, improves sampling efficiency by 50%–70%.

Read the full publication here.

Publications

Predicting Permeability through Skin

From the August 10, 2018 release of Journal of Controlled Release (v. 283 pp. 269–279):

Predicting drug permeability through skin using molecular dynamics simulation

Magnus Lundborg, Christian L Wennberg, Ali Narangifard, Erik Lindahl & Lars Norlén

Understanding and predicting permeability of compounds through skin is of interest for transdermal delivery of drugs and for toxicity predictions of chemicals. We show, using a new atomistic molecular dynamics model of the skin’s barrier structure, itself validated against near-native cryo-electron microscopy data from human skin, that skin permeability to the reference compounds benzene, DMSO (dimethyl sulfoxide), ethanol, codeine, naproxen, nicotine, testosterone and water can be predicted. The permeability results were validated against skin permeability data in the literature. We have investigated the relation between skin barrier molecular organization and permeability using atomistic molecular dynamics simulation. Furthermore, it is shown that the calculated mechanism of action differs between the five skin penetration enhancers Azone, DMSO, oleic acid, stearic acid and water. The permeability enhancing effect of a given penetration enhancer depends on the permeating compound and on the concentration of penetration enhancer inside the skin’s barrier structure. The presented method may open the door for computer based screening of the permeation of drugs and toxic compounds through skin.

Read the full publication here.

Publications

Contact Line Friction in Dynamic Wetting

From the July 2018 release of Physical Review Fluids (v. 3 art. 074201):

Molecular origin of contact line friction in dynamic wetting

Petter Johansson & Berk Hess

A hydrophilic liquid, such as water, forms hydrogen bonds with a hydrophilic substrate. The strength and locality of the hydrogen bonding interactions prohibit slip of the liquid over the substrate. The question then arises how the contact line can advance during wetting. Using large-scale molecular dynamics simulations we show that the contact line advances by single molecules moving ahead of the contact line through two distinct processes: either moving over or displacing other liquid molecules. In both processes friction occurs at the molecular scale. We measure the energy dissipation at the contact line and show that it is of the same magnitude as the dissipation in the bulk of a droplet. The friction increases significantly as the contact angle decreases, which suggests suggests thermal activation plays a role. We provide a simple model that is consistent with the observations.

Read the full publication here.

Publications

Frozen in Motion

From the June 1, 2018 release of eLife (v. 7 art. e36861):

Characterisation of molecular motions in cryo-EM single-particle data by multi-body refinement in RELION

Takanori Nakane, Dari Kimanius, Erik Lindahl & Sjors HW Scheres

Macromolecular complexes that exhibit continuous forms of structural flexibility pose a challenge for many existing tools in cryo-EM single-particle analysis. We describe a new tool, called multi-body refinement, which models flexible complexes as a user-defined number of rigid bodies that move independently from each other. Using separate focused refinements with iteratively improved partial signal subtraction, the new tool generates improved reconstructions for each of the defined bodies in a fully automated manner. Moreover, using principal component analysis on the relative orientations of the bodies over all particle images in the data set, we generate movies that describe the most important motions in the data. Our results on two test cases, a cytoplasmic ribosome from Plasmodium falciparum, and the spliceosomal B-complex from yeast, illustrate how multi-body refinement can be useful to gain unique insights into the structure and dynamics of large and flexible macromolecular complexes.

Read the full publication here.

Publications

K-Channel Models Go Viral

From the June 2018 release of The Journal of Membrane Biology (v. 251 pp. 419–430):

Exploring the viral channel Kcv(PBCV-1) function via computation

Alma EV Andersson, Marina A Kasimova & Lucie Delemotte

Viral potassium channels (Kcv) are homologous to the pore module of complex K⁺-selective ion channels of cellular organisms. Due to their relative simplicity, they have attracted interest towards understanding the principles of K⁺ conduction and channel gating. In this work, we construct a homology model of the Kcv(PBCV-1) open state, which we validate by studying the binding of known blockers and by monitoring ion conduction through the channel. Molecular dynamics simulations of this model reveal that the re-orientation of selectivity filter carbonyl groups coincides with the transport of potassium ions, suggesting a possible mechanism for fast gating. In addition, we show that the voltage sensitivity of this mechanism can originate from the relocation of potassium ions inside the selectivity filter. We also explore the interaction of Kcv(PBCV-1) with the surrounding bilayer and observe the binding of lipids in the area between two adjacent subunits. The model is available to the scientific community to further explore the structure/function relationship of Kcv channels.

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