Publications by authors named "Gregory A Voth"

377 Publications

Key Factors Governing Initial Stages of Lipid Droplet Formation.

J Phys Chem B 2022 Jan 6. Epub 2022 Jan 6.

Department of Chemistry, Chicago Center for Theoretical Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637 United States.

Lipid droplets (LDs) are neutral lipid storage organelles surrounded by a phospholipid (PL) monolayer. LD biogenesis from the endoplasmic reticulum is driven by phase separation of neutral lipids, overcoming surface tension and membrane deformation. However, the core biophysics of the initial steps of LD formation remains relatively poorly understood. Here, we use a tunable, phenomenological coarse-grained model to study triacylglycerol (TG) nucleation in a bilayer membrane. We show that PL rigidity has a strong influence on TG lensing and membrane remodeling: when membrane rigidity increases, TG clusters remain more planar with high anisotropy but a minor degree of phase nucleation. This finding is confirmed by advanced sampling simulations that calculate nucleation free energy as a function of the degree of nucleation and anisotropy. We also show that asymmetric tension, controlled by the number of PL molecules on each membrane leaflet, determines the budding direction. A TG lens buds in the direction of the monolayer containing excess PL molecules to allow for better PL coverage of TG, consistent with the reported experiments. Finally, two governing mechanisms of the LD growth, Ostwald ripening and merging, are observed. Taken together, this study characterizes the interplay between two thermodynamic quantities during the initial LD phases, the TG bulk free energy and membrane remodeling energy.
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http://dx.doi.org/10.1021/acs.jpcb.1c09683DOI Listing
January 2022

Multiscale Simulation of an Influenza A M2 Channel Mutant Reveals Key Features of Its Markedly Different Proton Transport Behavior.

J Am Chem Soc 2022 Jan 5. Epub 2022 Jan 5.

Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics and James Franck Institute, The University of Chicago, Chicago, Illinois 60637, United States.

The influenza A M2 channel, a prototype for viroporins, is an acid-activated viroporin that conducts protons across the viral membrane, a critical step in the viral life cycle. Four central His37 residues control channel activation by binding subsequent protons from the viral exterior, which opens the Trp41 gate and allows proton flux to the interior. Asp44 is essential for maintaining the Trp41 gate in a closed state at high pH, resulting in asymmetric conduction. The prevalent D44N mutant disrupts this gate and opens the C-terminal end of the channel, resulting in increased conduction and a loss of this asymmetric conduction. Here, we use extensive Multiscale Reactive Molecular Dynamics (MS-RMD) and quantum mechanics/molecular mechanics (QM/MM) molecular dynamics simulations with an explicit, reactive excess proton to calculate the free energy of proton transport in this M2 mutant and to study the dynamic molecular-level behavior of D44N M2. We find that this mutation significantly lowers the barrier of His37 deprotonation in the activated state and shifts the barrier for entry to the Val27 tetrad. These free energy changes are reflected in structural shifts. Additionally, we show that the increased hydration around the His37 tetrad diminishes the effect of the His37 charge on the channel's water structure, facilitating proton transport and enabling activation from the viral interior. Altogether, this work provides key insight into the fundamental characteristics of PT in WT M2 and how the D44N mutation alters this PT mechanism, and it expands understanding of the role of emergent mutations in viroporins.
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http://dx.doi.org/10.1021/jacs.1c09281DOI Listing
January 2022

Using Machine Learning to Greatly Accelerate Path Integral Molecular Dynamics.

J Chem Theory Comput 2022 Jan 4. Epub 2022 Jan 4.

Department of Chemistry, Chicago Center for Theoretical Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States.

molecular dynamics (AIMD) has become one of the most popular and robust approaches for modeling complicated chemical, liquid, and material systems. However, the formidable computational cost often limits its widespread application in simulations of the largest-scale systems. The situation becomes even more severe in cases where the hydrogen nuclei may be better described as quantized particles using a path integral representation. Here, we present a computational approach that combines machine learning with recent advances in path integral contraction schemes, and we achieve a 2 orders of magnitude acceleration over direct path integral AIMD simulation while at the same time maintaining its accuracy.
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http://dx.doi.org/10.1021/acs.jctc.1c01085DOI Listing
January 2022

A quantitative paradigm for water-assisted proton transport through proteins and other confined spaces.

Proc Natl Acad Sci U S A 2021 12;118(49)

Department of Chemistry, The University of Chicago, Chicago, IL 60637;

Water-assisted proton transport through confined spaces influences many phenomena in biomolecular and nanomaterial systems. In such cases, the water molecules that fluctuate in the confined pathways provide the environment and the medium for the hydrated excess proton migration via Grotthuss shuttling. However, a definitive collective variable (CV) that accurately couples the hydration and the connectivity of the proton wire with the proton translocation has remained elusive. To address this important challenge-and thus to define a quantitative paradigm for facile proton transport in confined spaces-a CV is derived in this work from graph theory, which is verified to accurately describe water wire formation and breakage coupled to the proton translocation in carbon nanotubes and the Cl/H antiporter protein, ClC-ec1. Significant alterations in the conformations and thermodynamics of water wires are uncovered after introducing an excess proton into them. Large barriers in the proton translocation free-energy profiles are found when water wires are defined to be disconnected according to the new CV, even though the pertinent confined space is still reasonably well hydrated and-by the simple measure of the mere existence of a water structure-the proton transport would have been predicted to be facile via that oversimplified measure. In this paradigm, however, the simple presence of water is not sufficient for inferring proton translocation, since an excess proton itself is able to drive hydration, and additionally, the water molecules themselves must be adequately connected to facilitate any successful proton transport.
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http://dx.doi.org/10.1073/pnas.2113141118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8670507PMC
December 2021

Preservation of HIV-1 Gag Helical Bundle Symmetry by Bevirimat Is Central to Maturation Inhibition.

J Am Chem Soc 2021 Nov 5;143(45):19137-19148. Epub 2021 Nov 5.

Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago, Chicago, Illinois 60637, United States.

The assembly and maturation of human immunodeficiency virus type 1 (HIV-1) require proteolytic cleavage of the Gag polyprotein. The rate-limiting step resides at the junction between the capsid protein CA and spacer peptide 1, which assembles as a six-helix bundle (6HB). Bevirimat (BVM), the first-in-class maturation inhibitor drug, targets the 6HB and impedes proteolytic cleavage, yet the molecular mechanisms of its activity, and relatedly, the escape mechanisms of mutant viruses, remain unclear. Here, we employed extensive molecular dynamics (MD) simulations and free energy calculations to quantitatively investigate molecular structure-activity relationships, comparing wild-type and mutant viruses in the presence and absence of BVM and inositol hexakisphosphate (IP6), an assembly cofactor. Our analysis shows that the efficacy of BVM is directly correlated with preservation of 6-fold symmetry in the 6HB, which exists as an ensemble of structural states. We identified two primary escape mechanisms, and both lead to loss of symmetry, thereby facilitating helix uncoiling to aid access of protease. Our findings also highlight specific interactions that can be targeted for improved inhibitor activity and support the use of MD simulations for future inhibitor design.
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http://dx.doi.org/10.1021/jacs.1c08922DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8610020PMC
November 2021

Resolving the Structural Debate for the Hydrated Excess Proton in Water.

J Am Chem Soc 2021 Nov 1;143(44):18672-18683. Epub 2021 Nov 1.

Department of Chemistry, Chicago Center for Theoretical Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, 5735 South Ellis Avenue, Chicago, Illinois 60637, United States.

It has long been proposed that the hydrated excess proton in water (aka the solvated "hydronium" cation) likely has two limiting forms, that of the Eigen cation (HO) and that of the Zundel cation (HO). There has been debate over which of these two is the more dominant species and/or whether intermediate (or "distorted") structures between these two limits are the more realistic representation. Spectroscopy experiments have recently provided further results regarding the excess proton. These experiments show that the hydrated proton has an anisotropy reorientation time scale on the order of 1-2 ps. This time scale has been suggested to possibly contradict the picture of the more rapid "special pair dance" phenomenon for the hydrated excess proton, which is a signature of a distorted Eigen cation. The special pair dance was predicted from prior computational studies in which the hydrated central core hydronium structure continually switches (O-H···O)* special pair hydrogen-bond partners with the closest three water molecules, yielding on average a distorted Eigen cation with three equivalent and dynamically exchanging distortions. Through state-of-art simulations it is shown here that anisotropy reorientation time scales of the same magnitude are obtained that also include structural reorientations associated with the special pair dance, leading to a reinterpretation of the experimental results. These results and additional analyses point to a distorted and dynamic Eigen cation as the most prevalent hydrated proton species in aqueous acid solutions of dilute to moderate concentration, as opposed to a stabilized or a distorted (but not "dancing") Zundel cation.
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http://dx.doi.org/10.1021/jacs.1c08552DOI Listing
November 2021

Molecular interactions of the M and E integral membrane proteins of SARS-CoV-2.

Faraday Discuss 2021 12 24;232(0):49-67. Epub 2021 Dec 24.

Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and The James Franck Institute, The University of Chicago, Chicago, Illinois, 60637, USA.

Specific lipid-protein interactions are key for cellular processes, and even more so for the replication of pathogens. The COVID-19 pandemic has drastically changed our lives and caused the death of nearly four million people worldwide, as of this writing. SARS-CoV-2 is the virus that causes the disease and has been at the center of scientific research over the past year. Most of the research on the virus is focused on key players during its initial attack and entry into the cellular host; namely the S protein, its glycan shield, and its interactions with the ACE2 receptors of human cells. As cases continue to rise around the globe, and new mutants are identified, there is an urgent need to understand the mechanisms of this virus during different stages of its life cycle. Here, we consider two integral membrane proteins of SARS-CoV-2 known to be important for viral assembly and infectivity. We have used microsecond-long all-atom molecular dynamics to examine the lipid-protein and protein-protein interactions of the membrane (M) and envelope (E) structural proteins of SARS-CoV-2 in a complex membrane model. We contrast the two proposed protein complexes for each of these proteins, and quantify their effect on their local lipid environment. This ongoing work also aims to provide molecular-level understanding of the mechanisms of action of this virus to possibly aid in the design of novel treatments.
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http://dx.doi.org/10.1039/d1fd00031dDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8712422PMC
December 2021

Accurate and Transferable Reactive Molecular Dynamics Models from Constrained Density Functional Theory.

J Phys Chem B 2021 09 14;125(37):10471-10480. Epub 2021 Sep 14.

Department of Chemistry, Chicago Center for Theoretical Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois 60637, United States.

Chemical reactions constitute the central feature of many liquid, material, and biomolecular processes. Conventional molecular dynamics (MD) is inadequate for simulating chemical reactions given the fixed bonding topology of most force fields, while modeling chemical reactions using molecular dynamics is limited to shorter time and length scales given its high computational cost. As such, the multiscale reactive molecular dynamics method provides one promising alternative for simulating complex chemical systems at atomistic detail on a reactive potential energy surface. However, the parametrization of such models is a key barrier to their applicability and success. In this work, we present reactive MD models derived from constrained density functional theory that are both accurate and transferable. We illustrate the features of these models for proton dissociation reactions of amino acids in both aqueous and protein environments. Specifically, we present models for ionizable glutamate and lysine that predict accurate absolute p values in water as well as their significantly shifted p in staphylococcal nuclease (SNase) without any modification of the models. As one outcome of the new methodology, the simulations show that the deprotonation of ionizable residues in SNase can be closely coupled with side chain rotations, which is a concept likely generalizable to many other proteins. Furthermore, the present approach is not limited to only p prediction but can enable the fully atomistic simulation of many other reactive systems along with a determination of the key aspects of the reaction mechanisms.
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http://dx.doi.org/10.1021/acs.jpcb.1c05992DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8480781PMC
September 2021

Integrin-based mechanosensing through conformational deformation.

Biophys J 2021 10 10;120(20):4349-4359. Epub 2021 Sep 10.

Yale Cardiovascular Research Center, Department of Cardiovascular Medicine, Yale University, New Haven, Connecticut; Department of Cell Biology, New Haven, Connecticut; Department of Biomedical Engineering, School of Engineering and Applied Science, Yale University, New Haven, Connecticut.

Conversion of integrins from low to high affinity states, termed activation, is important in biological processes, including immunity, hemostasis, angiogenesis, and embryonic development. Integrin activation is regulated by large-scale conformational transitions from closed, low affinity states to open, high affinity states. Although it has been suggested that substrate stiffness shifts the conformational equilibrium of integrin and governs its unbinding, here, we address the role of integrin conformational activation in cellular mechanosensing. Comparison of wild-type versus activating mutants of integrin αVβ3 show that activating mutants shift cell spreading, focal adhesion kinase activation, traction stress, and force on talin toward high stiffness values at lower stiffness. Although all activated integrin mutants showed equivalent binding affinity for soluble ligands, the β3 S243E mutant showed the strongest shift in mechanical responses. To understand this behavior, we used coarse-grained computational models derived from molecular level information. The models predicted that wild-type integrin αVβ3 displaces under force and that activating mutations shift the required force toward lower values, with S243E showing the strongest effect. Cellular stiffness sensing thus correlates with computed effects of force on integrin conformation. Together, these data identify a role for force-induced integrin conformational deformation in cellular mechanosensing.
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http://dx.doi.org/10.1016/j.bpj.2021.09.010DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8553792PMC
October 2021

Using Constrained Density Functional Theory to Track Proton Transfers and to Sample Their Associated Free Energy Surface.

J Chem Theory Comput 2021 Sep 1;17(9):5759-5765. Epub 2021 Sep 1.

Department of Chemistry, Chicago Center for Theoretical Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois 60637, United States.

Ab initio molecular dynamics (AIMD) and quantum mechanics/molecular mechanics (QM/MM) methods are powerful tools for studying proton solvation, transfer, and transport processes in various environments. However, due to the high computational cost of such methods, achieving sufficient sampling of rare events involving excess proton motion-especially when Grotthuss proton shuttling is involved-usually requires enhanced free energy sampling methods to obtain informative results. Moreover, an appropriate collective variable (CV) that describes the effective position of the net positive charge defect associated with an excess proton is essential both for tracking the trajectory of the defect and for the free energy sampling of the processes associated with the resulting proton transfer and transport. In this work, such a CV is derived from first principles using constrained density functional theory (CDFT). This CV is applicable to a broad array of proton transport and transfer processes as studied via AIMD and QM/MM simulations.
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http://dx.doi.org/10.1021/acs.jctc.1c00609DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8444337PMC
September 2021

The hopping mechanism of the hydrated excess proton and its contribution to proton diffusion in water.

J Chem Phys 2021 May;154(19):194506

Department of Chemistry, Chicago Center for Theoretical Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, USA.

In this work, a series of analyses are performed on ab initio molecular dynamics simulations of a hydrated excess proton in water to quantify the relative occurrence of concerted hopping events and "rattling" events and thus to further elucidate the hopping mechanism of proton transport in water. Contrary to results reported in certain earlier papers, the new analysis finds that concerted hopping events do occur in all simulations but that the majority of events are the product of proton rattling, where the excess proton will rattle between two or more waters. The results are consistent with the proposed "special-pair dance" model of the hydrated excess proton wherein the acceptor water molecule for the proton transfer will quickly change (resonate between three equivalent special pairs) until a decisive proton hop occurs. To remove the misleading effect of simple rattling, a filter was applied to the trajectory such that hopping events that were followed by back hops to the original water are not counted. A steep reduction in the number of multiple hopping events is found when the filter is applied, suggesting that many multiple hopping events that occur in the unfiltered trajectory are largely the product of rattling, contrary to prior suggestions. Comparing the continuous correlation function of the filtered and unfiltered trajectories, we find agreement with experimental values for the proton hopping time and Eigen-Zundel interconversion time, respectively.
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http://dx.doi.org/10.1063/5.0040758DOI Listing
May 2021

Formin Cdc12's specific actin assembly properties are tailored for cytokinesis in fission yeast.

Biophys J 2021 08 30;120(15):2984-2997. Epub 2021 Jun 30.

Department of Molecular Genetics and Cell Biology, Chicago, Illinois; Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, Illinois. Electronic address:

Formins generate unbranched actin filaments by a conserved, processive actin assembly mechanism. Most organisms express multiple formin isoforms that mediate distinct cellular processes and facilitate actin filament polymerization by significantly different rates, but how these actin assembly differences correlate to cellular activity is unclear. We used a computational model of fission yeast cytokinetic ring assembly to test the hypothesis that particular actin assembly properties help tailor formins for specific cellular roles. Simulations run in different actin filament nucleation and elongation conditions revealed that variations in formin's nucleation efficiency critically impact both the probability and timing of contractile ring formation. To probe the physiological importance of nucleation efficiency, we engineered fission yeast formin chimera strains in which the FH1-FH2 actin assembly domains of full-length cytokinesis formin Cdc12 were replaced with the FH1-FH2 domains from functionally and evolutionarily diverse formins with significantly different actin assembly properties. Although Cdc12 chimeras generally support life in fission yeast, quantitative live-cell imaging revealed a range of cytokinesis defects from mild to severe. In agreement with the computational model, chimeras whose nucleation efficiencies are least similar to Cdc12 exhibit more severe cytokinesis defects, specifically in the rate of contractile ring assembly. Together, our computational and experimental results suggest that fission yeast cytokinesis is ideally mediated by a formin with properly tailored actin assembly parameters.
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http://dx.doi.org/10.1016/j.bpj.2021.06.023DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8390969PMC
August 2021

Advanced Materials for Energy-Water Systems: The Central Role of Water/Solid Interfaces in Adsorption, Reactivity, and Transport.

Chem Rev 2021 08 2;121(15):9450-9501. Epub 2021 Jul 2.

Advanced Materials for Energy-Water Systems (AMEWS) Energy Frontier Research Center (EFRC), Argonne National Laboratory, 9700 South Cass Avenue, Lemont, Illinois 60439 United States.

The structure, chemistry, and charge of interfaces between materials and aqueous fluids play a central role in determining properties and performance of numerous water systems. Sensors, membranes, sorbents, and heterogeneous catalysts almost uniformly rely on specific interactions between their surfaces and components dissolved or suspended in the water-and often the water molecules themselves-to detect and mitigate contaminants. Deleterious processes in these systems such as fouling, scaling (inorganic deposits), and corrosion are also governed by interfacial phenomena. Despite the importance of these interfaces, much remains to be learned about their multiscale interactions. Developing a deeper understanding of the molecular- and mesoscale phenomena at water/solid interfaces will be essential to driving innovation to address grand challenges in supplying sufficient fit-for-purpose water in the future. In this Review, we examine the current state of knowledge surrounding adsorption, reactivity, and transport in several key classes of water/solid interfaces, drawing on a synergistic combination of theory, simulation, and experiments, and provide an outlook for prioritizing strategic research directions.
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http://dx.doi.org/10.1021/acs.chemrev.1c00069DOI Listing
August 2021

Structural Characterization of Protonated Water Clusters Confined in HZSM-5 Zeolites.

J Am Chem Soc 2021 Jul 1;143(27):10203-10213. Epub 2021 Jul 1.

Department of Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States.

A molecular description of the structure and behavior of water confined in aluminosilicate zeolite pores is a crucial component for understanding zeolite acid chemistry under hydrous conditions. In this study, we use a combination of ultrafast two-dimensional infrared (2D IR) spectroscopy and molecular dynamics (AIMD) to study HO confined in the pores of highly hydrated zeolite HZSM-5 (∼13 and ∼6 equivalents of HO per Al atom). The 2D IR spectrum reveals correlations between the vibrations of both terminal and H-bonded O-H groups and the continuum absorption of the excess proton. These data are used to characterize the hydrogen-bonding network within the cluster by quantifying single-, double-, and non-hydrogen-bond donor water molecules. These results are found to be in good agreement with the statistics calculated from an AIMD simulation of an H(HO) cluster in HZSM-5. Furthermore, IR spectral assignments to local O-H environments are validated with DFT calculations on clusters drawn from AIMD simulations. The simulations reveal that the excess charge is detached from the zeolite and resides near the more highly coordinated water molecules in the cluster. When they are taken together, these results unambiguously assign the complex IR spectrum of highly hydrated HZSM-5, providing quantitative information on the molecular environments and hydrogen-bonding topology of protonated water clusters under extreme confinement.
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http://dx.doi.org/10.1021/jacs.1c03205DOI Listing
July 2021

Physical Characterization of Triolein and Implications for Its Role in Lipid Droplet Biogenesis.

J Phys Chem B 2021 07 17;125(25):6874-6888. Epub 2021 Jun 17.

Department of Chemistry, Chicago Center for Theoretical Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States.

Lipid droplets (LDs) are neutral lipid-storing organelles surrounded by a phospholipid (PL) monolayer. At present, how LDs are formed in the endoplasmic reticulum (ER) bilayer is poorly understood. In this study, we present a revised all-atom (AA) triolein (TG) model, the main constituent of the LD core, and characterize its properties in a bilayer membrane to demonstrate the implications of its behavior in LD biogenesis. In bilayer simulations, TG resides at the surface, adopting PL-like conformations (denoted in this work as SURF-TG). Free energy sampling simulation results estimate the barrier for TG relocating from the bilayer surface to the bilayer center to be ∼2 kcal/mol in the absence of an oil lens. SURF-TG is able to modulate membrane properties by increasing PL ordering, decreasing bending modulus, and creating local negative curvature. The other neutral lipid, dioleoyl-glycerol (DAG), also reduces the membrane bending modulus and populates negative curvature regions. A phenomenological coarse-grained (CG) model is also developed to observe larger-scale SURF-TG-mediated membrane deformation. CG simulations confirm that TG nucleates between the bilayer leaflets at a critical concentration when SURF-TG is evenly distributed. However, when one monolayer contains more SURF-TG, the membrane bends toward the other leaflet, followed by TG nucleation if a concentration is higher than the critical threshold. The central conclusion of this study is that SURF-TG is a negative curvature inducer, as well as a membrane modulator. To this end, a model is proposed in which the accumulation of SURF-TG in the luminal leaflet bends the ER bilayer toward the cytosolic side, followed by TG nucleation.
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http://dx.doi.org/10.1021/acs.jpcb.1c03559DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8314861PMC
July 2021

Key computational findings reveal proton transfer as driving the functional cycle in the phosphate transporter PiPT.

Proc Natl Acad Sci U S A 2021 06;118(25)

Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics and James Frank Institute, University of Chicago, Chicago, IL 60637;

Phosphate is an indispensable metabolite in a wide variety of cells and is involved in nucleotide and lipid synthesis, signaling, and chemical energy storage. Proton-coupled phosphate transporters within the major facilitator family are crucial for phosphate uptake in plants and fungi. Similar proton-coupled phosphate transporters have been found in different protozoan parasites that cause human diseases, in breast cancer cells with elevated phosphate demand, in osteoclast-like cells during bone reabsorption, and in human intestinal Caco2BBE cells for phosphate homeostasis. However, the mechanism of proton-driven phosphate transport remains unclear. Here, we demonstrate in a eukaryotic, high-affinity phosphate transporter from (PiPT) that deprotonation of aspartate 324 (D324) triggers phosphate release. Quantum mechanics/molecular mechanics molecular dynamics simulations combined with free energy sampling have been employed here to identify the proton transport pathways from D324 upon the transition from the occluded structure to the inward open structure and phosphate release. The computational insights so gained are then corroborated by studies of D45N and D45E amino acid substitutions via mutagenesis experiments. Our findings confirm the function of the structurally predicted cytosolic proton exit tunnel and suggest insights into the role of the titratable phosphate substrate.
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http://dx.doi.org/10.1073/pnas.2101932118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8237618PMC
June 2021

Cooperative multivalent receptor binding promotes exposure of the SARS-CoV-2 fusion machinery core.

bioRxiv 2021 Jun 7. Epub 2021 Jun 7.

The molecular events that permit the spike glycoprotein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) to bind, fuse, and enter cells are important to understand for both fundamental and therapeutic reasons. Spike proteins consist of S1 and S2 domains, which recognize angiotensin-converting enzyme 2 (ACE2) receptors and contain the viral fusion machinery, respectively. Ostensibly, the binding of spike trimers to ACE2 receptors promotes the preparation of the fusion machinery by dissociation of the S1 domains. We report the development of bottom-up coarse-grained (CG) models validated with cryo-electron tomography (cryo-ET) data, and the use of CG molecular dynamics simulations to investigate the dynamical mechanisms involved in viral binding and exposure of the S2 trimeric core. We show that spike trimers cooperatively bind to multiple ACE2 dimers at virion-cell interfaces. The multivalent interaction cyclically and processively induces S1 dissociation, thereby exposing the S2 core containing the fusion machinery. Our simulations thus reveal an important concerted interaction between spike trimers and ACE2 dimers that primes the virus for membrane fusion and entry.
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http://dx.doi.org/10.1101/2021.05.24.445443DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8202425PMC
June 2021

Synthesis, Characterization, and Simulation of Four-Armed Megamolecules.

Biomacromolecules 2021 06 12;22(6):2363-2372. Epub 2021 May 12.

Departments of Chemistry and Biomedical Engineering, Northwestern University, Evanston, Illinois 60208, United States.

This paper describes the synthesis, characterization, and modeling of a series of molecules having four protein domains attached to a central core. The molecules were assembled with the "megamolecule" strategy, wherein enzymes react with their covalent inhibitors that are substituted on a linker. Three linkers were synthesized, where each had four oligo(ethylene glycol)-based arms terminated in a -nitrophenyl phosphonate group that is a covalent inhibitor for cutinase. This enzyme is a serine hydrolase and reacts efficiently with the phosphonate to give a new ester linkage at the Ser-120 residue in the active site of the enzyme. Negative-stain transmission electron microscopy (TEM) images confirmed the architecture of the four-armed megamolecules. These cutinase tetramers were also characterized by X-ray crystallography, which confirmed the active-site serine-phosphonate linkage by electron-density maps. Molecular dynamics simulations of the tetracutinase megamolecules using three different force field setups were performed and compared with the TEM observations. Using the Amberff99SB-disp + pH7 force field, the two-dimensional projection distances of the megamolecules were found to agree with the measured dimensions from TEM. The study described here, which combines high-resolution characterization with molecular dynamics simulations, will lead to a comprehensive understanding of the molecular structures and dynamics for this new class of molecules.
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http://dx.doi.org/10.1021/acs.biomac.1c00118DOI Listing
June 2021

Molecular interactions of the M and E integral membrane proteins of SARS-CoV-2.

bioRxiv 2021 Apr 29. Epub 2021 Apr 29.

Specific lipid-protein interactions are key for cellular processes, and even more so for the replication of pathogens. The COVID-19 pandemic has drastically changed our lives and cause the death of nearly three million people worldwide, as of this writing. SARS-CoV-2 is the virus that causes the disease and has been at the center of scientific research over the past year. Most of the research on the virus is focused on key players during its initial attack and entry into the cellular host; namely the S protein, its glycan shield, and its interactions with the ACE2 receptors of human cells. As cases continue to raise around the globe, and new mutants are identified, there is an urgent need to understand the mechanisms of this virus during different stages of its life cycle. Here, we consider two integral membrane proteins of SARS-CoV-2 known to be important for viral assembly and infectivity. We have used microsecond-long all-atom molecular dynamics to examine the lipid-protein and protein-protein interactions of the membrane (M) and envelope (E) structural proteins of SARS-CoV-2 in a complex membrane model. We contrast the two proposed protein complexes for each of these proteins, and quantify their effect on their local lipid environment. This ongoing work also aims to provide molecular-level understanding of the mechanisms of action of this virus to possibly aid in the design of novel treatments.
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http://dx.doi.org/10.1101/2021.04.29.442018DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8095202PMC
April 2021

Constructing many-body dissipative particle dynamics models of fluids from bottom-up coarse-graining.

J Chem Phys 2021 Feb;154(8):084122

Department of Chemistry, Chicago Center for Theoretical Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, USA.

Since their emergence in the 1990s, mesoscopic models of fluids have been widely used to study complex organization and transport phenomena beyond the molecular scale. Even though these models are designed based on results from physics at the meso- and macroscale, such as fluid mechanics and statistical field theory, the underlying microscopic foundation of these models is not as well defined. This paper aims to build such a systematic connection using bottom-up coarse-graining methods. From the recently developed dynamic coarse-graining scheme, we introduce a statistical inference framework of explicit many-body conservative interaction that quantitatively recapitulates the mesoscopic structure of the underlying fluid. To further consider the dissipative and fluctuation forces, we design a novel algorithm that parameterizes these forces. By utilizing this algorithm, we derive pairwise decomposable friction kernels under both non-Markovian and Markovian limits where both short- and long-time features of the coarse-grained dynamics are reproduced. Finally, through these new developments, the many-body dissipative particle dynamics type of equations of motion are successfully derived. The methodologies developed in this work thus open a new avenue for the construction of direct bottom-up mesoscopic models that naturally bridge the meso- and macroscopic physics.
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http://dx.doi.org/10.1063/5.0035184DOI Listing
February 2021

Compressive and Tensile Deformations Alter ATP Hydrolysis and Phosphate Release Rates in Actin Filaments.

J Chem Theory Comput 2021 Mar 17;17(3):1900-1913. Epub 2021 Feb 17.

Department of Chemistry, Chicago Center for Theoretical Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, The University of Chicago, Chicago, Illinois 60637, United States.

Actin filament networks in eukaryotic cells are constantly remodeled through nucleotide state controlled interactions with actin binding proteins, leading to macroscopic structures such as bundled filaments, branched filaments, and so on. The nucleotide (ATP) hydrolysis, phosphate release, and polymerization/depolymerization reactions that lead to the formation of these structures are correlated with the conformational fluctuations of the actin subunits at the molecular scale. The resulting structures generate and experience varying levels of force and impart cells with several functionalities such as their ability to move, divide, transport cargo, etc. Models that explicitly connect the structure to reactions are essential to elucidate a fundamental level of understanding of these processes. In this regard, a bottom-up Ultra-Coarse-Grained (UCG) model of actin filaments that can simulate ATP hydrolysis, inorganic phosphate release (Pi), and depolymerization reactions is presented in this work. In this model, actin subunits are represented using coarse-grained particles that evolve in time and undergo reactions depending on the conformations sampled. The reactions are represented through state transitions, with each state represented by a unique effective coarse-grained potential. Effects of compressive and tensile strains on the rates of reactions are then analyzed. Compressive strains tend to unflatten the actin subunits, reduce the rate of ATP hydrolysis, and increase the Pi release rate. On the other hand, tensile strain flattens subunits, increases the rate of ATP hydrolysis, and decrease the Pi release rate. Incorporating these predictions into a Markov State Model highlighted that strains alter the steady-state distribution of subunits with ADPPi and ADP nucleotide, thus identifying possible additional factors underlying the cooperative binding of regulatory proteins to actin filaments.
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http://dx.doi.org/10.1021/acs.jctc.0c01186DOI Listing
March 2021

A new one-site coarse-grained model for water: Bottom-up many-body projected water (BUMPer). I. General theory and model.

J Chem Phys 2021 Jan;154(4):044104

Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago, Chicago, Illinois 60637, USA.

Water is undoubtedly one of the most important molecules for a variety of chemical and physical systems, and constructing precise yet effective coarse-grained (CG) water models has been a high priority for computer simulations. To recapitulate important local correlations in the CG water model, explicit higher-order interactions are often included. However, the advantages of coarse-graining may then be offset by the larger computational cost in the model parameterization and simulation execution. To leverage both the computational efficiency of the CG simulation and the inclusion of higher-order interactions, we propose a new statistical mechanical theory that effectively projects many-body interactions onto pairwise basis sets. The many-body projection theory presented in this work shares similar physics from liquid state theory, providing an efficient approach to account for higher-order interactions within the reduced model. We apply this theory to project the widely used Stillinger-Weber three-body interaction onto a pairwise (two-body) interaction for water. Based on the projected interaction with the correct long-range behavior, we denote the new CG water model as the Bottom-Up Many-Body Projected Water (BUMPer) model, where the resultant CG interaction corresponds to a prior model, the iteratively force-matched model. Unlike other pairwise CG models, BUMPer provides high-fidelity recapitulation of pair correlation functions and three-body distributions, as well as N-body correlation functions. BUMPer extensively improves upon the existing bottom-up CG water models by extending the accuracy and applicability of such models while maintaining a reduced computational cost.
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http://dx.doi.org/10.1063/5.0026651DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7826168PMC
January 2021

A new one-site coarse-grained model for water: Bottom-up many-body projected water (BUMPer). II. Temperature transferability and structural properties at low temperature.

J Chem Phys 2021 Jan;154(4):044105

Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, and James Franck Institute, The University of Chicago, Chicago, Illinois 60637, USA.

A number of studies have constructed coarse-grained (CG) models of water to understand its anomalous properties. Most of these properties emerge at low temperatures, and an accurate CG model needs to be applicable to these low-temperature ranges. However, direct use of CG models parameterized from other temperatures, e.g., room temperature, encounters a problem known as transferability, as the CG potential essentially follows the form of the many-body CG free energy function. Therefore, temperature-dependent changes to CG interactions must be accounted for. The collective behavior of water at low temperature is generally a many-body process, which often motivates the use of expensive many-body terms in the CG interactions. To surmount the aforementioned problems, we apply the Bottom-Up Many-Body Projected Water (BUMPer) CG model constructed from Paper I to study the low-temperature behavior of water. We report for the first time that the embedded three-body interaction enables BUMPer, despite its pairwise form, to capture the growth of ice at the ice/water interface with corroborating many-body correlations during the crystal growth. Furthermore, we propose temperature transferable BUMPer models that are indirectly constructed from the free energy decomposition scheme. Changes in CG interactions and corresponding structures are faithfully recapitulated by this framework. We further extend BUMPer to examine its ability to predict the structure, density, and diffusion anomalies by employing an alternative analysis based on structural correlations and pairwise potential forms to predict such anomalies. The presented analysis highlights the existence of these anomalies in the low-temperature regime and overcomes potential transferability problems.
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http://dx.doi.org/10.1063/5.0026652DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7826166PMC
January 2021

Structural basis of fast- and slow-severing actin-cofilactin boundaries.

J Biol Chem 2021 Jan-Jun;296:100337. Epub 2021 Jan 27.

Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, USA. Electronic address:

Members of the ADF/cofilin family of regulatory proteins bind actin filaments cooperatively, locally change actin subunit conformation and orientation, and sever filaments at "boundaries" between bare and cofilin-occupied segments. A cluster of bound cofilin introduces two distinct classes of boundaries due to the intrinsic polarity of actin filaments, one at the "pointed" end side and the other at the "barbed" end-side of the cluster; severing occurs more readily at the pointed end side of the cluster ("fast-severing" boundary) than the barbed end side ("slow-severing" boundary). A recent electron-cryomicroscopy (cryo-EM) model of the slow-severing boundary revealed structural "defects" at the interface that potentially contribute to severing. However, the structure of the fast-severing boundary remains uncertain. Here, we use extensive molecular dynamics simulations to produce atomic resolution models of both severing boundaries. Our equilibrated simulation model of the slow-severing boundary is consistent with the cryo-EM structural model. Simulations indicate that actin subunits at both boundaries adopt structures intermediate between those of bare and cofilin-bound actin subunits. These "intermediate" states have compromised intersubunit contacts, but those at the slow-severing boundary are stabilized by cofilin bridging interactions, accounting for its lower fragmentation probability. Simulations where cofilin proteins are removed from cofilactin filaments favor a mechanism in which a cluster of two contiguously bound cofilins is needed to fully stabilize the cofilactin conformation, promote cooperative binding interactions, and accelerate filament severing. Together, these studies provide a molecular-scale foundation for developing coarse-grained and theoretical descriptions of cofilin-mediated actin filament severing.
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http://dx.doi.org/10.1016/j.jbc.2021.100337DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7961102PMC
August 2021

Coarse-Grained Force Fields from the Perspective of Statistical Mechanics: Better Understanding of the Origins of a MARTINI Hangover.

J Chem Theory Comput 2021 Feb 21;17(2):1170-1180. Epub 2021 Jan 21.

Department of Chemistry, Chicago Center for Theoretical Chemistry, James Franck Institute, and Institute for Biophysical Dynamics, University of Chicago, Chicago, Illinois 60637, United States.

The popular MARTINI coarse-grained model is used as a test case to analyze the adherence of top-down coarse-grained molecular dynamics models (i.e., models primarily parametrized to match experimental results) to the known features of statistical mechanics for the underlying all-atom representations. Specifically, the temperature dependence of various pair distribution functions, and hence their underlying potentials of mean force via the reversible work theorem, are compared between MARTINI 2.0, Dry MARTINI, and all-atom simulations mapped onto equivalent coarse-grained sites for certain lipid bilayers. It is found that the MARTINI models do not completely capture the lipid structure seen in atomistic simulations as projected onto the coarse-grained mappings and that issues of accuracy and temperature transferability arise due to an incorrect enthalpy-entropy decomposition of these potentials of mean force. The potential of mean force for the association of two amphipathic helices in a lipid bilayer is also calculated, and especially at shorter ranges, the MARTINI and all-atom projection results differ substantially. The former is much less repulsive and hence will lead to a higher probability of MARTINI helix association in the MARTINI bilayer than occurs in the actual all-atom case. Additionally, the bilayer height fluctuation spectra are calculated for the MARTINI model, and compared to the all-atom results, it is found that the magnitude of thermally averaged amplitudes at intermediate length scales are quite different, pointing to a number of possible consequences for realistic modeling of membrane processes. Taken as a whole, the results presented here show disagreement in the enthalpic and entropic driving forces driving lateral structure in lipid bilayers as well as quantitative differences in association of embedded amphipathic helices, which can help direct future efforts to parametrize CG models with better agreement to the all-atom systems they aspire to represent.
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http://dx.doi.org/10.1021/acs.jctc.0c00638DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7876797PMC
February 2021

Immature HIV-1 assembles from Gag dimers leaving partial hexamers at lattice edges as potential substrates for proteolytic maturation.

Proc Natl Acad Sci U S A 2021 01;118(3)

Structural Studies Division, Medical Research Council Laboratory of Molecular Biology, Cambridge Biomedical Campus, CB2 0QH Cambridge, United Kingdom;

The CA (capsid) domain of immature HIV-1 Gag and the adjacent spacer peptide 1 (SP1) play a key role in viral assembly by forming a lattice of CA hexamers, which adapts to viral envelope curvature by incorporating small lattice defects and a large gap at the site of budding. This lattice is stabilized by intrahexameric and interhexameric CA-CA interactions, which are important in regulating viral assembly and maturation. We applied subtomogram averaging and classification to determine the oligomerization state of CA at lattice edges and found that CA forms partial hexamers. These structures reveal the network of interactions formed by CA-SP1 at the lattice edge. We also performed atomistic molecular dynamics simulations of CA-CA interactions stabilizing the immature lattice and partial CA-SP1 helical bundles. Free energy calculations reveal increased propensity for helix-to-coil transitions in partial hexamers compared to complete six-helix bundles. Taken together, these results suggest that the CA dimer is the basic unit of lattice assembly, partial hexamers exist at lattice edges, these are in a helix-coil dynamic equilibrium, and partial helical bundles are more likely to unfold, representing potential sites for HIV-1 maturation initiation.
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http://dx.doi.org/10.1073/pnas.2020054118DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7826355PMC
January 2021

A multiscale coarse-grained model of the SARS-CoV-2 virion.

Biophys J 2021 03 28;120(6):1097-1104. Epub 2020 Nov 28.

Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics and James Franck Institute, The University of Chicago, Chicago, Illinois. Electronic address:

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the COVID-19 pandemic. Computer simulations of complete viral particles can provide theoretical insights into large-scale viral processes including assembly, budding, egress, entry, and fusion. Detailed atomistic simulations are constrained to shorter timescales and require billion-atom simulations for these processes. Here, we report the current status and ongoing development of a largely "bottom-up" coarse-grained (CG) model of the SARS-CoV-2 virion. Data from a combination of cryo-electron microscopy (cryo-EM), x-ray crystallography, and computational predictions were used to build molecular models of structural SARS-CoV-2 proteins, which were then assembled into a complete virion model. We describe how CG molecular interactions can be derived from all-atom simulations, how viral behavior difficult to capture in atomistic simulations can be incorporated into the CG models, and how the CG models can be iteratively improved as new data become publicly available. Our initial CG model and the detailed methods presented are intended to serve as a resource for researchers working on COVID-19 who are interested in performing multiscale simulations of the SARS-CoV-2 virion.
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http://dx.doi.org/10.1016/j.bpj.2020.10.048DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7695975PMC
March 2021

Lipid-Composition-Mediated Forces Can Stabilize Tubular Assemblies of I-BAR Proteins.

Biophys J 2021 01 26;120(1):46-54. Epub 2020 Nov 26.

Department of Chemistry, Chicago Center for Theoretical Chemistry, Institute for Biophysical Dynamics, The James Franck Institute, The University of Chicago, Chicago, Illinois. Electronic address:

Collective action by inverse-Bin/Amphiphysin/Rvs (I-BAR) domains drive micron-scale membrane remodeling. The macroscopic curvature sensing and generation behavior of I-BAR domains is well characterized, and computational models have suggested various mechanisms on simplified membrane systems, but there remain missing connections between the complex environment of the cell and the models proposed thus far. Here, we show a connection between the role of protein curvature and lipid clustering in the relaxation of large membrane deformations. When we include phosphatidylinositol 4,5-bisphosphate-like lipids that preferentially interact with the charged ends of an I-BAR domain, we find clustering of phosphatidylinositol 4,5-bisphosphate-like lipids that induce a directional membrane-mediated interaction between membrane-bound I-BAR domains. Lipid clusters mediate I-BAR domain interactions and cause I-BAR domain aggregates that would not arise through membrane fluctuation-based or curvature-based interactions. Inside of membrane protrusions, lipid cluster-mediated interaction draws long side-by-side aggregates together, resulting in more cylindrical protrusions as opposed to bulbous, irregularly shaped protrusions.
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http://dx.doi.org/10.1016/j.bpj.2020.11.019DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7820731PMC
January 2021

Structural basis for polarized elongation of actin filaments.

Proc Natl Acad Sci U S A 2020 12 16;117(48):30458-30464. Epub 2020 Nov 16.

Department of Chemistry, University of Chicago, Chicago, IL 60637;

Actin filaments elongate and shorten much faster at their barbed end than their pointed end, but the molecular basis of this difference has not been understood. We use all-atom molecular dynamics simulations to investigate the properties of subunits at both ends of the filament. The terminal subunits tend toward conformations that resemble actin monomers in solution, while contacts with neighboring subunits progressively flatten the conformation of internal subunits. At the barbed end the terminal subunit is loosely tethered by its DNase-1 loop to the third subunit, because its monomer-like conformation precludes stabilizing contacts with the penultimate subunit. The motions of the terminal subunit make the partially flattened penultimate subunit accessible for binding monomers. At the pointed end, unique contacts between the penultimate and terminal subunits are consistent with existing cryogenic electron microscopic (cryo-EM) maps, limit binding to incoming monomers, and flatten the terminal subunit, which likely promotes ATP hydrolysis and rapid phosphate release. These structures explain the distinct polymerization kinetics of the two ends.
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http://dx.doi.org/10.1073/pnas.2011128117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7720195PMC
December 2020
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