Publications

Drugging COVID-19 with Dynamics

Published 16 March 2021 in ACS Pharmacology & Translational Sciences (doi 10.1021/acsptsci.0c00215):

A blueprint for high affinity SARS-CoV-2 Mpro inhibitors from activity-based compound library screening guided by analysis of protein dynamics

Jonas Gossen, Simone Albani, Anton Hanke, Benjamin P Joseph, Cathrine Bergh, Maria Kuzikov, Elisa Costanzi, Candida Manelfi, Paola Storici, Philip Gribbon, Andrea R Beccari, Carmine Talarico, Francesca Spyrakis, Erik Lindahl, Andrea Zaliani, Paolo Carloni, Rebecca C Wade, Francesco Musiani, Daria B Kokh, and Giulia Rossetti

The SARS-CoV-2 coronavirus outbreak continues to spread at a rapid rate worldwide. The main protease (Mpro) is an attractive target for anti-COVID-19 agents. Unexpected difficulties have been encountered in the design of specific inhibitors. Here, by analyzing an ensemble of ∼30 000 SARS-CoV-2 Mpro conformations from crystallographic studies and molecular simulations, we show that small structural variations in the binding site dramatically impact ligand binding properties. Hence, traditional druggability indices fail to adequately discriminate between highly and poorly druggable conformations of the binding site. By performing ∼200 virtual screenings of compound libraries on selected protein structures, we redefine the protein’s druggability as the consensus chemical space arising from the multiple conformations of the binding site formed upon ligand binding. This procedure revealed a unique SARS-CoV-2 Mpro blueprint that led to a definition of a specific structure-based pharmacophore. The latter explains the poor transferability of potent SARS-CoV Mpro inhibitors to SARS-CoV-2 Mpro, despite the identical sequences of the active sites. Importantly, application of the pharmacophore predicted novel high affinity inhibitors of SARS-CoV-2 Mpro, that were validated by in vitro assays performed here and by a newly solved X-ray crystal structure. These results provide a strong basis for effective rational drug design campaigns against SARS-CoV-2 Mpro and a new computational approach to screen protein targets with malleable binding sites.

Read the full publication here.

Publications

A Range of Sites for Resin Acids

Published 8 March 2021 in the Journal of General Physiology (doi 10.1085/jgp.202012676):

Resin-acid derivatives bind to multiple sites on the voltage-sensor domain of the Shaker potassium channel

Malin Silverå Ejneby, Arina Gromova, Nina E Ottosson, Stina Borg, Argel Estrada-Mondragón, Samira Yazdi, Panagiotis Apostolakis, Fredrik Elinder, Lucie Delemotte

Voltage-gated potassium (Kv) channels can be opened by negatively charged resin acids and their derivatives. These resin acids have been proposed to attract the positively charged voltage-sensor helix (S4) toward the extracellular side of the membrane by binding to a pocket located between the lipid-facing extracellular ends of the transmembrane segments S3 and S4. By contrast to this proposed mechanism, neutralization of the top gating charge of the Shaker KV channel increased resin-acid–induced opening, suggesting other mechanisms and sites of action. Here, we explore the binding of two resin-acid derivatives, Wu50 and Wu161, to the activated/open state of the Shaker KV channel by a combination of in silico docking, molecular dynamics simulations, and electrophysiology of mutated channels. We identified three potential resin-acid–binding sites around S4: (1) the S3/S4 site previously suggested, in which positively charged residues introduced at the top of S4 are critical to keep the compound bound, (2) a site in the cleft between S4 and the pore domain (S4/pore site), in which a tryptophan at the top of S6 and the top gating charge of S4 keeps the compound bound, and (3) a site located on the extracellular side of the voltage-sensor domain, in a cleft formed by S1–S4 (the top-VSD site). The multiple binding sites around S4 and the anticipated helical-screw motion of the helix during activation make the effect of resin-acid derivatives on channel function intricate. The propensity of a specific resin acid to activate and open a voltage-gated channel likely depends on its exact binding dynamics and the types of interactions it can form with the protein in a state-specific manner.

Read the full publication here.

Publications

Hotspots of Efficacy in GPCRs

Published 28 January 2021 in eLife (doi 10.7554/eLife.60715):

Identification of ligand-specific G-protein coupled receptor states and prediction of downstream efficacy via data-driven modeling

Oliver Fleetwood, Jens Carlsson, Lucie Delemotte

Ligand binding stabilizes different G protein-coupled receptor states via a complex allosteric process that is not completely understood. Here, we have derived free energy landscapes describing activation of the β2 adrenergic receptor bound to ligands with different efficacy profiles using enhanced sampling molecular dynamics (MD) simulations. These reveal shifts towards active-like states at the G protein binding site for receptors bound to partial and full agonists and that the ligands modulate the conformational ensemble of the receptor by tuning protein microswitches. We indeed find an excellent correlation between the conformation of the microswitches close to the ligand binding site and in the transmembrane region and experimentally reported cAMP signaling responses. Dimensionality reduction further reveals the similarity between the unique conformational states induced by different ligands and examining the output of classifiers highlights two distant hotspots governing agonism on transmembrane helices 5 and 7.

Read the full publication here.

Publications

Homegrown Tests for COVID-19

Published 19 January 2021 in Scientific Reports (doi 10.1038/s41598-020-80352-8):

Direct detection of SARS-CoV-2 using non-commercial RT-LAMP reagents on heat-inactivated samples

Alisa Alekseenko, Donal Barrett, Yerma Pareja-Sanchez, Rebecca J Howard, Emilia Strandback, Henry Ampah-Korsah, Urška Rovšnik, Silvia Zuniga-Veliz, Alexander Klenov, Jayshna Malloo, Shenglong Ye, Xiyang Liu, Björn Reinius, Simon J. Elsässer, Tomas Nyman, Gustaf Sandh, Xiushan Yin & Vicent Pelechano

RT-LAMP detection of SARS-CoV-2 has been shown to be a valuable approach to scale up COVID-19 diagnostics and thus contribute to limiting the spread of the disease. Here we present the optimization of highly cost-effective in-house produced enzymes, and we benchmark their performance against commercial alternatives. We explore the compatibility between multiple DNA polymerases with high strand-displacement activity and thermostable reverse transcriptases required for RT-LAMP. We optimize reaction conditions and demonstrate their applicability using both synthetic RNA and clinical patient samples. Finally, we validate the optimized RT-LAMP assay for the detection of SARS-CoV-2 in unextracted heat-inactivated nasopharyngeal samples from 184 patients. We anticipate that optimized and affordable reagents for RT-LAMP will facilitate the expansion of SARS-CoV-2 testing globally, especially in sites and settings where the need for large scale testing cannot be met by commercial alternatives.

Read the full publication here.

Publications

Switching on a CaM

Published 11 December 2020 in Science Advances (doi 10.1126/sciadv.abd6798):

Calmodulin acts as a state-dependent switch to control a cardiac potassium channel opening

Po Wei Kang,* Annie M Westerlund,* Jingyi Shi, Kelli McFarland White, Alex K Dou, Amy H Cui, Jonathan R Silva, Lucie Delemotte, Jianmin Cui
*contributed equally to this work

Calmodulin (CaM) and phosphatidylinositol 4,5-bisphosphate (PIP2) are potent regulators of the voltage-gated potassium channel KCNQ1 (KV7.1), which conducts the cardiac IKs current. Although cryo–electron microscopy structures revealed intricate interactions between the KCNQ1 voltage-sensing domain (VSD), CaM, and PIP2, the functional consequences of these interactions remain unknown. Here, we show that CaM-VSD interactions act as a state-dependent switch to control KCNQ1 pore opening. Combined electrophysiology and molecular dynamics network analysis suggest that VSD transition into the fully activated state allows PIP2 to compete with CaM for binding to VSD. This leads to conformational changes that alter VSD-pore coupling to stabilize open states. We identify a motif in the KCNQ1 cytosolic domain, which works downstream of CaM-VSD interactions to facilitate the conformational change. Our findings suggest a gating mechanism that integrates PIP2and CaM in KCNQ1 voltage-dependent activation, yielding insights into how KCNQ1 gains the phenotypes critical for its physiological function.

Read the full publication here.

Publications

Skin Structures Simulated

Published 22 October 2020 in Journal of Investigative Dermatology (doi 10.1016/j.jid.2020.07.040):

Molecular reorganization during formation of the human skin barrier studied in situ

Ali Narangifard, Christian L Wennberg, Lianne den Hollander, Ichiro Iwai, HongMei Han, Magnus Lundborg, Sergej Masich, Erik Lindahl, Bertil Daneholt, Lars Norlén

In vertebrates, skin upholds homeostasis by preventing body water loss. The skin’s permeability barrier is located intercellularly in stratum corneum and consists of stacked lipid lamellae composed of ceramides, cholesterol and free fatty acids. We have combined cryo-EM with molecular dynamics modelling and EM-simulation in our analysis of the lamellae’s formation, a maturation process beginning in stratum granulosum and ending in stratum corneum. Previously, we have revealed the lipid lamellae’s initial- and end-stage molecular organizations. Here, we reveal two cryo-EM patterns representing intermediate stages in the lamellae’s maturation process: a single-band pattern with 2.0-2.5 nm periodicity and a two-band pattern with 5.5-6.0 nm periodicity, that may be derived from lamellar lipid structures with 4.0-5.0 nm and 5.5-6.0 nm periodicity, respectively. Based on the analysis of the data now available on the four maturation stages identified, we can present a tentative molecular model for the complete skin barrier formation process.

Read the full publication here.

Publications

Elucidating Lipid Allostery

Published 9 October 2020 in The Journal of Chemical Physics (doi 10.1063/5.0020974):

Network analysis reveals how lipids and other cofactors influence membrane protein allostery

Annie M Westerlund, Oliver Fleetwood, Sergio Pérez-Conesa, Lucie Delemotte

Many membrane proteins are modulated by external stimuli, such as small molecule binding or change in pH, transmembrane voltage, or temperature. This modulation typically occurs at sites that are structurally distant from the functional site. Revealing the communication, known as allostery, between these two sites is key to understanding the mechanistic details of these proteins. Residue interaction networks of isolated proteins are commonly used to this end. Membrane proteins, however, are embedded in a lipid bilayer, which may contribute to allosteric communication. The fast diffusion of lipids hinders direct use of standard residue interaction networks. Here, we present an extension that includes cofactors such as lipids and small molecules in the network. The novel framework is applied to three membrane proteins: a voltage-gated ion channel (KCNQ1), a G-protein coupled receptor (GPCR—β2 adrenergic receptor), and a pH-gated ion channel (KcsA). Through systematic analysis of the obtained networks and their components, we demonstrate the importance of lipids for membrane protein allostery. Finally, we reveal how small molecules may stabilize different protein states by allosterically coupling and decoupling the protein from the membrane.

Read the full publication here.

Publications

Speedier Simulations with Parallelization

Published 5 October 2020 in The Journal of Chemical Physics (doi 10.1063/5.0018516):

Heterogeneous parallelization and acceleration of molecular dynamics simulations in GROMACS

Szilárd Páll, Artem Zhmurov, Paul Bauer, Mark Abraham, Magnus Lundborg, Alan Gray, Berk Hess, Erik Lindahl

The introduction of accelerator devices such as graphics processing units (GPUs) has had profound impact on molecular dynamics simulations and has enabled order-of-magnitude performance advances using commodity hardware. To fully reap these benefits, it has been necessary to reformulate some of the most fundamental algorithms, including the Verlet list, pair searching, and cutoffs. Here, we present the heterogeneous parallelization and acceleration design of molecular dynamics implemented in the GROMACS codebase over the last decade. The setup involves a general cluster-based approach to pair lists and non-bonded pair interactions that utilizes both GPU and central processing unit (CPU) single instruction, multiple data acceleration efficiently, including the ability to load-balance tasks between CPUs and GPUs. The algorithm work efficiency is tuned for each type of hardware, and to use accelerators more efficiently, we introduce dual pair lists with rolling pruning updates. Combined with new direct GPU–GPU communication and GPU integration, this enables excellent performance from single GPU simulations through strong scaling across multiple GPUs and efficient multi-node parallelization.

Read the full publication here.

Publications

Fungal Metabolism at its Core

Published 16 September 2020 in Nature Communications (doi 10.1038/s41467-020-18401-z):

Arrangement and symmetry of the fungal E3BP-containing core of the pyruvate dehydrogenase complex

Björn O Forsberg, Shintaro Aibara, Rebecca J Howard, Narges Mortezaei, Erik Lindahl

The pyruvate dehydrogenase complex (PDC) is a multienzyme complex central to aerobic respiration, connecting glycolysis to mitochondrial oxidation of pyruvate. Similar to the E3-binding protein (E3BP) of mammalian PDC, PX selectively recruits E3 to the fungal PDC, but its divergent sequence suggests a distinct structural mechanism. Here, we report reconstructions of PDC from the filamentous fungus Neurospora crassa by cryo-electron microscopy, where we find protein X (PX) interior to the PDC core as opposed to substituting E2 core subunits as in mammals. Steric occlusion limits PX binding, resulting in predominantly tetrahedral symmetry, explaining previous observations in Saccharomyces cerevisiae. The PX-binding site is conserved in (and specific to) fungi, and complements possible C-terminal binding motifs in PX that are absent in mammalian E3BP. Consideration of multiple symmetries thus reveals a differential structural basis for E3BP-like function in fungal PDC.

Read the full publication here.

Publications

Unveiling Valium

Published 2 September 2020 in Nature (doi 10.1038/s41586-020-2654-5):

Shared structural mechanisms of general anaesthetics and benzodiazepines

Jeong Joo Kim, Anant Gharpure, Jinfeng Teng, Yuxuan Zhuang, Rebecca J Howard, Shaotong Zhu, Colleen M Noviello, Richard M Walsh Jr, Erik Lindahl, Ryan E Hibbs

Most general anaesthetics and classical benzodiazepine drugs act through positive modulation of γ-aminobutyric acid type A (GABAA) receptors to dampen neuronal activity in the brain. However, direct structural information on the mechanisms of general anaesthetics at their physiological receptor sites is lacking. Here we present cryo-electron microscopy structures of GABAA receptors bound to intravenous anaesthetics, benzodiazepines and inhibitory modulators. These structures were solved in a lipidic environment and are complemented by electrophysiology and molecular dynamics simulations. Structures of GABAA receptors in complex with the anaesthetics phenobarbital, etomidate and propofol reveal both distinct and common transmembrane binding sites, which are shared in part by the benzodiazepine drug diazepam. Structures in which GABAA receptors are bound by benzodiazepine-site ligands identify an additional membrane binding site for diazepam and suggest an allosteric mechanism for anaesthetic reversal by flumazenil. This study provides a foundation for understanding how pharmacologically diverse and clinically essential drugs act through overlapping and distinct mechanisms to potentiate inhibitory signalling in the brain.

Read the full publication here.

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

Friction in the Field

Published 29 June 2020 in Physical Review Fluids (v. 5 p. 064203):

Electrowetting diminishes contact line friction in molecular wetting

Petter JohanssonBerk Hess

We use large-scale molecular dynamics to study the dynamics at the three-phase contact line in electrowetting of water and electrolytes on no-slip substrates. Under the applied electrostatic potential the line friction at the contact line is diminished. The effect is consistent for droplets of different sizes as well as for both pure water and electrolyte solution droplets. We analyze the electric field at the contact line to show how it assists ions and dipolar molecules to advance the contact line. Without an electric field, the interaction between a substrate and a liquid has a very short range, mostly affecting the bottom, immobilized layer of liquid molecules which leads to high friction since mobile molecules are not pulled towards the surface. In electrowetting, the electric field attracts charged and polar molecules over a longer range, which diminishes the friction.

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.

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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.