Analyzing the electrogenicity of cytochrome c oxidase

Measurements of voltage changes in response to charge separation within membrane proteins can offer fundamental information on spectroscopically “invisible” steps. For example, results from studies of voltage changes associated with electron and proton transfer in cytochrome c oxidase could, in principle, be used to discriminate between different theoretical models describing the molecular mechanism of proton pumping. Earlier analyses of data from these measurements have been based on macroscopic considerations that may not allow for exploring the actual molecular mechanisms. Here, we have used a coarse-grained model describing the relation between observed voltage changes and specific charge-transfer reactions, which includes an explicit description of the membrane, the electrolytes, and the electrodes. The results from these calculations offer mechanistic insights at the molecular level. Our main conclusion is that previously assumed mechanistic evidence that was based on electrogenic measurements is not unique. However, the ability of our calculations to obtain reliable voltage changes means that we have a tool that can be used to describe a wide range of electrogenic charge transfers in channels and transporters, by combining voltage measurements with other experiments and simulations to analyze new mechanistic proposals.

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Physical mechanisms of amyloid nucleation on fluid membranes

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.2007694117 ◽

2020 ◽

Vol 117 (52) ◽

pp. 33090-33098

Author(s):

Johannes Krausser ◽

Tuomas P. J. Knowles ◽

Anđela Šarić

Keyword(s):

Lipid Membranes ◽

Molecular Mechanisms ◽

Amyloid Fibrils ◽

Lipid Membrane ◽

Coarse Grained ◽

Coarse Grained Model ◽

Physical Mechanisms ◽

Fluid Membranes ◽

Protein Membrane ◽

Protein Rich

Biological membranes can dramatically accelerate the aggregation of normally soluble protein molecules into amyloid fibrils and alter the fibril morphologies, yet the molecular mechanisms through which this accelerated nucleation takes place are not yet understood. Here, we develop a coarse-grained model to systematically explore the effect that the structural properties of the lipid membrane and the nature of protein–membrane interactions have on the nucleation rates of amyloid fibrils. We identify two physically distinct nucleation pathways—protein-rich and lipid-rich—and quantify how the membrane fluidity and protein–membrane affinity control the relative importance of those molecular pathways. We find that the membrane’s susceptibility to reshaping and being incorporated into the fibrillar aggregates is a key determinant of its ability to promote protein aggregation. We then characterize the rates and the free-energy profile associated with this heterogeneous nucleation process, in which the surface itself participates in the aggregate structure. Finally, we compare quantitatively our data to experiments on membrane-catalyzed amyloid aggregation of α-synuclein, a protein implicated in Parkinson’s disease that predominately nucleates on membranes. More generally, our results provide a framework for understanding macromolecular aggregation on lipid membranes in a broad biological and biotechnological context.

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Quantitative insights into the cyanobacterial cell economy

eLife ◽

10.7554/elife.42508 ◽

2019 ◽

Vol 8 ◽

Cited By ~ 20

Author(s):

Tomáš Zavřel ◽

Marjan Faizi ◽

Cristina Loureiro ◽

Gereon Poschmann ◽

Kai Stühler ◽

...

Keyword(s):

Growth Rate ◽

Coarse Grained ◽

Translational Machinery ◽

Coarse Grained Model ◽

Green Biotechnology ◽

Photosynthetic Productivity ◽

Heterotrophic Microorganisms ◽

Wide Range ◽

Growth Laws ◽

Phototrophic Growth

Phototrophic microorganisms are promising resources for green biotechnology. Compared to heterotrophic microorganisms, however, the cellular economy of phototrophic growth is still insufficiently understood. We provide a quantitative analysis of light-limited, light-saturated, and light-inhibited growth of the cyanobacterium Synechocystis sp. PCC 6803 using a reproducible cultivation setup. We report key physiological parameters, including growth rate, cell size, and photosynthetic activity over a wide range of light intensities. Intracellular proteins were quantified to monitor proteome allocation as a function of growth rate. Among other physiological acclimations, we identify an upregulation of the translational machinery and downregulation of light harvesting components with increasing light intensity and growth rate. The resulting growth laws are discussed in the context of a coarse-grained model of phototrophic growth and available data obtained by a comprehensive literature search. Our insights into quantitative aspects of cyanobacterial acclimations to different growth rates have implications to understand and optimize photosynthetic productivity.

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Simulating the function of sodium/proton antiporters

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1516881112 ◽

2015 ◽

Vol 112 (40) ◽

pp. 12378-12383 ◽

Cited By ~ 14

Author(s):

Raphael Alhadeff ◽

Arieh Warshel

Keyword(s):

Conformational Changes ◽

Molecular Basis ◽

Molecular Level ◽

Structural Information ◽

Coarse Grained ◽

Charged State ◽

Transport Models ◽

Coarse Grained Model ◽

Effective Transport ◽

Molecular Origin

The molecular basis of the function of transporters is a problem of significant importance, and the emerging structural information has not yet been converted to a full understanding of the corresponding function. This work explores the molecular origin of the function of the bacterial Na+/H+ antiporter NhaA by evaluating the energetics of the Na+ and H+ movement and then using the resulting landscape in Monte Carlo simulations that examine two transport models and explore which model can reproduce the relevant experimental results. The simulations reproduce the observed transport features by a relatively simple model that relates the protein structure to its transporting function. Focusing on the two key aspartic acid residues of NhaA, D163 and D164, shows that the fully charged state acts as an Na+ trap and that the fully protonated one poses an energetic barrier that blocks the transport of Na+. By alternating between the former and latter states, mediated by the partially protonated protein, protons, and Na+ can be exchanged across the membrane at 2:1 stoichiometry. Our study provides a numerical validation of the need of large conformational changes for effective transport. Furthermore, we also yield a reasonable explanation for the observation that some mammalian transporters have 1:1 stoichiometry. The present coarse-grained model can provide a general way for exploring the function of transporters on a molecular level.

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Parameterization of a coarse-grained model with short-ranged interactions for modeling fuel cell membranes with controlled water uptake

Physical Chemistry Chemical Physics ◽

10.1039/c7cp02281f ◽

2017 ◽

Vol 19 (27) ◽

pp. 17698-17707 ◽

Cited By ~ 12

Author(s):

Jibao Lu ◽

Chance Miller ◽

Valeria Molinero

Keyword(s):

Fuel Cell ◽

Activity Coefficient ◽

Water Uptake ◽

Coarse Grained ◽

Fuel Cell Membranes ◽

Coarse Grained Model ◽

Experimental Activity ◽

Tetramethylammonium Chloride ◽

Atomistic Models ◽

Wide Range

The coarse-grained model FFpvap reproduces the experimental activity coefficient of water in tetramethylammonium chloride solutions over a wide range of concentrations, with a hundred-fold gain in computing efficiency with respect to atomistic models.

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Molecular mechanisms of the interhead coordination by interhead tension in cytoplasmic dyneins

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1806688115 ◽

2018 ◽

Vol 115 (40) ◽

pp. 10052-10057 ◽

Cited By ~ 6

Author(s):

Qian Wang ◽

Biman Jana ◽

Michael R. Diehl ◽

Margaret S. Cheung ◽

Anatoly B. Kolomeisky ◽

...

Keyword(s):

Binding Affinity ◽

Molecular Mechanisms ◽

Cytoplasmic Dynein ◽

Coarse Grained ◽

Cellular Transport ◽

Coarse Grained Model ◽

Detachment Rate ◽

The Moment ◽

Dynamics Simulations ◽

Molecular Picture

Cytoplasmic dyneins play a major role in retrograde cellular transport by moving vesicles and organelles along microtubule filaments. Dyneins are multidomain motor proteins with two heads that coordinate their motion via their interhead tension. Compared with the leading head, the trailing head has a higher detachment rate from microtubules, facilitating the movement. However, the molecular mechanism of such coordination is unknown. To elucidate this mechanism, we performed molecular dynamics simulations on a cytoplasmic dynein with a structure-based coarse-grained model that probes the effect of the interhead tension on the structure. The tension creates a torque that influences the head rotating about its stalk. The conformation of the stalk switches from the α registry to the β registry during the rotation, weakening the binding affinity to microtubules. The directions of the tension and the torque of the leading head are opposite to those of the trailing head, breaking the structural symmetry between the heads. The leading head transitions less often to the β registry than the trailing head. The former thus has a greater binding affinity to the microtubule than the latter. We measured the moment arm of the torque from a dynein structure in the simulations to develop a phenomenological model that captures the influence of the head rotating about its stalk on the differential detachment rates of the two heads. Our study provides a consistent molecular picture for interhead coordination via interhead tension.

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Coarse-grained molecular simulations of the binding of the SARS-CoV-2 spike protein RBD to the ACE2 receptor

10.1101/2020.05.07.083212 ◽

2020 ◽

Cited By ~ 3

Author(s):

David De Sancho ◽

José A. Gavira ◽

Raul Pérez-Jiménez

Keyword(s):

Bound States ◽

Dynamic Behaviour ◽

Molecular Level ◽

Molecular Simulations ◽

Bound State ◽

Spike Protein ◽

Coarse Grained ◽

Receptor Binding Domain ◽

Coarse Grained Model ◽

Dynamic Description

AbstractSince it was first observed, the COVID-19 pandemic has created a global emergency for national health systems due to millions of confirmed cases and hundreds of thousands of deaths. At a molecular level, the bottleneck for the infection is the binding of the receptor binding domain (RBD) of the viral spike protein to ACE2, an enzyme exposed on human cell membranes. Several experimental structures of the ACE2:RBD complex have been made available, however they offer only a static description of the arrangements of the molecules in either the free or bound states. In order to gain a dynamic description of the binding process that is key to infection, we use molecular simulations with a coarse grained model of the RBD and ACE2. We find that binding occurs in an all-or-none way, without intermediates, and that even in the bound state, the RBD exhibits a considerably dynamic behaviour. From short equilibrium simulations started in the unbound state we provide snapshots that result in a tentative mechanism of binding. Our findings may be important for the development of drug discovery strategies that target the RBD.

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Quantitative insights into the cyanobacterial cell economy

10.1101/446179 ◽

2018 ◽

Cited By ~ 1

Author(s):

Tomáš Zavřel ◽

Marjan Faizi ◽

Cristina Loureiro ◽

Gereon Poschmann ◽

Kai Stühler ◽

...

Keyword(s):

Growth Rate ◽

Coarse Grained ◽

Translational Machinery ◽

Coarse Grained Model ◽

Green Biotechnology ◽

Photosynthetic Productivity ◽

Heterotrophic Microorganisms ◽

Wide Range ◽

Growth Laws ◽

Phototrophic Growth

AbstractPhototrophic microorganisms are promising resources for green biotechnology. Compared to heterotrophic microorganisms, however, the cellular economy of phototrophic growth is still insufficiently understood. We provide a quantitative analysis of light-limited, light-saturated, and light-inhibited growth of the cyanobacteriumSynechocystissp. PCC 6803 using a reproducible cultivation setup. We report key physiological parameters, including growth rate, cell size, and photosynthetic activity over a wide range of light intensities. Intracellular proteins were quantified to monitor proteome allocation as a function of growth rate. Among other physiological adaptations, we identify an upregulation of the translational machinery and downregulation of light harvesting components with increasing light intensity and growth rate. The resulting growth laws are discussed in the context of a coarse-grained model of phototrophic growth and available data obtained by a comprehensive literature search. Our insights into quantitative aspects of cyanobacterial adaptations to different growth rates have implications to understand and optimize photosynthetic productivity.

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Viral genome structures are optimal for capsid assembly

eLife ◽

10.7554/elife.00632 ◽

2013 ◽

Vol 2 ◽

Cited By ~ 79

Author(s):

Jason D Perlmutter ◽

Cong Qiao ◽

Michael F Hagan

Keyword(s):

Negative Charge ◽

Tertiary Structure ◽

Theoretical Models ◽

Coarse Grained ◽

Capsid Assembly ◽

Optimal Length ◽

Viral Propagation ◽

Coarse Grained Model ◽

Virus Capsids ◽

Thermodynamic Basis

Understanding how virus capsids assemble around their nucleic acid (NA) genomes could promote efforts to block viral propagation or to reengineer capsids for gene therapy applications. We develop a coarse-grained model of capsid proteins and NAs with which we investigate assembly dynamics and thermodynamics. In contrast to recent theoretical models, we find that capsids spontaneously ‘overcharge’; that is, the negative charge of the NA exceeds the positive charge on capsid. When applied to specific viruses, the optimal NA lengths closely correspond to the natural genome lengths. Calculations based on linear polyelectrolytes rather than base-paired NAs underpredict the optimal length, demonstrating the importance of NA structure to capsid assembly. These results suggest that electrostatics, excluded volume, and NA tertiary structure are sufficient to predict assembly thermodynamics and that the ability of viruses to selectively encapsidate their genomic NAs can be explained, at least in part, on a thermodynamic basis.

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SNARE machinery is optimized for ultrafast fusion

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1820394116 ◽

2019 ◽

Vol 116 (7) ◽

pp. 2435-2442 ◽

Cited By ~ 11

Author(s):

Fabio Manca ◽

Frederic Pincet ◽

Lev Truskinovsky ◽

James E. Rothman ◽

Lionel Foret ◽

...

Keyword(s):

Synaptic Vesicles ◽

Snare Proteins ◽

Coarse Grained ◽

Optimum Number ◽

Biological Processes ◽

Cooperative Action ◽

Fusion Barrier ◽

Coarse Grained Model ◽

Wide Range

SNARE proteins zipper to form complexes (SNAREpins) that power vesicle fusion with target membranes in a variety of biological processes. A single SNAREpin takes about 1 s to fuse two bilayers, yet a handful can ensure release of neurotransmitters from synaptic vesicles much faster: in a 10th of a millisecond. We propose that, similar to the case of muscle myosins, the ultrafast fusion results from cooperative action of many SNAREpins. The coupling originates from mechanical interactions induced by confining scaffolds. Each SNAREpin is known to have enough energy to overcome the fusion barrier of 25–35 kBT; however, the fusion barrier only becomes relevant when the SNAREpins are nearly completely zippered, and from this state, each SNAREpin can deliver only a small fraction of this energy as mechanical work. Therefore, they have to act cooperatively, and we show that at least three of them are needed to ensure fusion in less than a millisecond. However, to reach the prefusion state collectively, starting from the experimentally observed half-zippered metastable state, the SNAREpins have to mechanically synchronize, which takes more time as the number of SNAREpins increases. Incorporating this somewhat counterintuitive idea in a simple coarse-grained model results in the prediction that there should be an optimum number of SNAREpins for submillisecond fusion: three to six over a wide range of parameters. Interestingly, in situ cryoelectron microscope tomography has very recently shown that exactly six SNAREpins participate in the fusion of each synaptic vesicle. This number is in the range predicted by our theory.

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Modeling structure, stability and flexibility of double-stranded RNAs in salt solutions

10.1101/332676 ◽

2018 ◽

Author(s):

L. Jin ◽

Y.Z. Shi ◽

C.J. Feng ◽

Y.L. Tan ◽

Z.J. Tan

Keyword(s):

Electrostatic Potential ◽

Cell Metabolism ◽

3D Structure ◽

Three Dimensional ◽

Coarse Grained ◽

Structure Stability ◽

Salt Solutions ◽

3D Structures ◽

Coarse Grained Model ◽

Wide Range

AbstractDouble-stranded (ds) RNAs play essential roles in many processes of cell metabolism. The knowledge of three-dimensional (3D) structure, stability and flexibility of dsRNAs in salt solutions is important for understanding their biological functions. In this work, we further developed our previously proposed coarse-grained model to predict 3D structure, stability and flexibility for dsRNAs in monovalent and divalent ion solutions through involving an implicit structure-based electrostatic potential. The model can make reliable predictions for 3D structures of extensive dsRNAs with/without bulge/internal loops from their sequences, and the involvement of the structure-based electrostatic potential and corresponding ion condition can improve the predictions on 3D structures of dsRNAs in ion solutions. Furthermore, the model can make good predictions on thermal stability for extensive dsRNAs over the wide range of monovalent/divalent ion concentrations, and our analyses show that thermally unfolding pathway of a dsRNA is generally dependent on its length as well as its sequence. In addition, the model was employed to examine the salt-dependent flexibility of a dsRNA helix and the calculated salt-dependent persistence lengths are in good accordance with experiments.

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