Molecular Biophysics and COVID-19

Like so many of our colleagues worldwide, Molecular Biophysics Stockholm (MBS) has been engaged in various efforts to navigate and combat the novel coronavirus. Although the group’s past research rarely intersected with virology or clinical work, and none of us are are experts in the field, we hope to help where we can.

Membrane-Protein Modeling team members, prior to social distancing

Among others, members of the Membrane-Protein Modeling and GROMACS Development teams have joined the Folding@home consortium to apply the power of distributed computing to understanding SARS-CoV-2 membrane proteins. Listen to Professor Erik Lindahl speak about this work on Sveriges Radio (Swedish), read about it on (Danish)—or contribute your own compute time to active projects managed by Associate Professor Lucie Delemotte!

Summary by Erik Lindahl, 21-Apr 2020 on Exscalate4CoV and related projects

Members of the GROMACS team and BioExcel Centre also contribute to Exscalate4CoV, a consortium awarded €3 million by the European Commission for research on COVID-19 vaccines, treatment, and diagnostics. Key tasks at MBS include deployment of molecular-dynamics code and free-energy calculations for coronavirus protein simulations and drug-candidate scoring. For an overview of relevant targets, data repositories, and community collaborations, watch Lindahl’s presentation to the Centre Européen de Calcul Atomique et Moléculaire (English, 4:13–36:04).

Marie Lycksell and other SU chemists involved in hand-sanitizer production

On the clinical side, members of the Ligand-Gated Ion Channels (LGICs) team have worked with fellow chemists at Stockholm University to alleviate urgent needs for medical supplies, helping coordinate donations of masks, gloves, and other personal protective equipment from SciLifeLab to local hospitals. With reagents contributed by academic groups, the Museum of Natural History, and companies including GE Health, Petrolia, Runa and Absolut Vodka, we also assisted in the department’s production and distribution of over 20,000 liters of hand sanitizer to medical and care facilities. Read more in recent coverage by the university (English) and national (Swedish) media.

Reba Howard producing enzymes for rapid COVID-19 tests

MBS is also involved in an accelerated grant by the KAW Foundation to iLACO-Sweden, a multi-institution project led by Professor Vicent Pelechano (Karolinska Institute) to develop a rapid, low-cost color-based test for COVID-19 infection. The method was recently covered on Sveriges Television, including an interview with LGICs team-lead Reba Howard (Swedish, some English audio).

We are deeply grateful for the dedication and compassion of all MBS members, who continue to find creative paths to productivity even at a distance. Many have managed unprecedented disruptions to academic, research, and development work, including DIS students Jojo Scott and Phaedra Robinson, whose time abroad was truncated months early by US travel restrictions. We so look forward to collaborating again at higher density on the other side of this pandemic.


Agonist Control of G Protein-Coupled Receptor via Microswitches

Published 7 February 2020 in Biochemistry

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.


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.


Grattis till Professor Hess

Members of Molecular Biophysics Stockholm celebrated Berk Hess‘ promotion to full Professor in Applied Physics at KTH Royal Institute of Technology, 15 November 2019, conferred by President Sigbritt Karlsson at Konserthuset in Stockholm, Sweden. With funding recently awarded by Vetenskapsrådet to the INTERFACE project, Hess’ team stands poised grow in size and contribution; check back soon for new openings!

Promotion video, Professor Berk Hess, Fall 2019

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.


2019 Fall Retreat

Twenty-three members of Molecular Biophysics Stockholm gathered for our fall off-site retreat, 24–25 October 2019 at historic Vår Gård in Saltsjöbaden, Sweden, workshopping topics related to individual core competencies, academic and industry CVs, group networking, and team communication. Thanks to co-organizers Annie, Joe, Lucie, Reba, and Urška, and to Vår Gård for a beautiful autumn getaway!


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.


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.


Channels on the Coast

Four current and former members of Molecular Biophysics Stockholm, along with multiple collaborators, presented their research at the 2019 Jacques Monod Conference Canaux ioniques activés par les ligands: de la structure atomique à la transmission synaptique (Ligand-gated ion channels from atomic structure to synaptic transmission) 24–29 May 2019 in Roscoff, France. Among others, Reba Howard gave an invited talk on Biochemical and simulation studies of allosteric mechanisms in a model Cys-loop receptor.


Biophysics Abroad

Molecular Biophysics Stockholm again hosted two US undergraduates through the DIS-Study Abroad in Scandinavia Stockholm program in Spring 2019. Under the supervision of Reba Howard and Urška Rovšnik, Sarah Komon (Wheaton College) and Nicole Sanford (St Olaf College) worked ≥20 hours per week on independent projects in the Ligand-Gated Ion Channels team throughout the term, including data collection at both the Science for Life Laboratory and Umeå University. Each presented a research poster at the DIS End-of-Semester Symposium, 7 May 2019 at Stockholm’s Kungliga Musikhögskolan. For an interview with Komon and Sanford regarding their experiences, visit the DIS blog Discover Study Abroad.

Two new DIS students will initiate research projects with the team in Fall 2019. For more information, contact Reba or DIS-Stockholm.


2019 Spring Workshop

Thirty members of Molecular Biophysics Stockholm, representing thirteen countries and a range of research areas, gathered for a spring mini-retreat on 8 April 2019 at the Science for Life Laboratory in Solna, Sweden. Gabriella Fägerlind of Uppsala’s Implement Diversity AB led a workshop on inclusivity and psychological safety in the academic workplace, followed by small- and large-group exercises around goal-setting and group resource development, and an evening pizza party.


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.


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.


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.


Workshopping Sharing

Eight members of Molecular Biophysics Stockholm helped host an international workshop on Sharing Data from Molecular Simulations, 25–27 November on Lidingö in the Stockholm archipelago. Researchers from 13 institutions in 8 countries sought to explore and improve the dissemination of data and code related to molecular simulations and related methods in computational biology/chemistry. Major topics included:

  • Standardization of file formats
  • Tools for trajectory sharing
  • Streamlining molecular simulations data
  • Reproducibility of molecular simulations

Lucie Delemotte and Reba Howard co-organized the workshop with Matthieu Chavent (IPBS), Daniel Smith (MolSSI), and Mikael Trellet (Utrecht), with sponsorship from Rossen Apostolov at BioExcel. Among the participants were session chair Mark Abraham and invited speaker Erik Lindahl.

Although this exploratory workshop was limited in scale, organizers sought to maximize transparency by live-tweeting the proceedings (#SDMS18) and making videos of all talks and roundtable discussions, as well as original presentation slides, available for download via BioExcel.

A follow-up event, organized by MolSSI, is planned for 2019 in the USA.


Biophysics Abroad

Molecular Biophysics Stockholm was the first external research site to host US undergraduates through the recently launched DIS-Study Abroad in Scandinavia Stockholm program in Fall 2018. Under the supervision of Reba Howard, Isabel Anaya (Northwestern University) and Jaewon Kang (Vassar College) worked ≥20 hours per week on independent research projects in the Ligand-Gated Ion Channels team throughout the term. Both presented posters on their work at the DIS End-of-Semester Symposium, 11 December 2018 at Stockholm’s Kungliga Musikhögskolan.

Two new DIS students will initiate research projects with the team in Spring 2019. For more information, contact Reba or DIS-Stockholm.


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.


Multiscale Modeling in Tokyo

Five members of Molecular Biophysics Stockholm presented their research and discussed prospective collaborations at the 2nd Stockholm-Tokyo University Partnership Workshop, held this year in Japan, 28–30 October 2018. Among others, Erik Lindahl co-chaired a plenary session on Biological Mechanisms Regulating Healthy and Maladaptive Aging, and co-coordinated a satellite workshop on New Technologies: Multiscale Computation. Following the workshop, group members were generously hosted by their University of Tokyo colleagues in multiscale simulations and electron microscopy for a traditional meal in the Hongō district.


Grattis till Docent Delemotte

Members of Molecular Biophysics Stockholm celebrated Lucie Delemotte’s Swedish-language Docent Lecture in Applied Physics at KTH Royal Institute of Technology, Structural dynamics of voltage-gated ion channels and implications for health and disease, 24 October 2018 at AlbaNova Universitetscentrum in Stockholm, Sweden. With new funding recently awarded by Vetenskapsrådet, the Delemotte team stands poised grow in size and contribution. Check back soon for new openings!


GROMACS Workshop October 2018

The 2018 workshop, 17–19 October in Göttingen, set out to provide opportunities for GROMACS developers and power-users to use or implement their own enhanced simulation protocols, involving for example fast multipole methods, constant pH, or experimental constraints from microscopy/spectroscopy. Key questions included:

  • How can a highly optimized, parallel simulation code provide a general infrastructure that allows incorporation of new methods in a straightforward way?
  • Can it do so without sacrificing (parallel) performance?
  • Can the software be made less monolithic and blackbox-like, but more modular and extensible?
  • Can providing an own method become less of a challenge for the average scientist who is not at the same time a GROMACS coding expert?

Thanks to sponsors BioExcel and SPPEXA, and to the Theoretical and Computational Biophysics group at the Max Planck Institute for Biophysical Chemistry for venue and other support.


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.


Grattis till Licentiate Westerlund

Members of Molecular Biophysics Stockholm celebrated Annie Westerlund’s successful defense of her Licentiate thesis in Biophysics from KTH Royal Institute of Technology, Computational Study of Calmodulin’s Ca2+-dependent Conformational Ensembles, 3 October 2018 at the Science for Life Laboratory in Solna, Sweden. Professor Björn Wallner (Linköping University) served as opponent, and Professors Lucie Delemotte (KTH) and Erik Lindahl (KTH & Stockholm University) led a toast to their advisee of two years.


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.