Nejvíce citovaný článek - PubMed ID 30623647
A ubiquitous property of bacteria is their ability to move toward more suitable environments, which can also facilitate host-associated activities like colonization and offer the cell several benefits such as bacteria moving towards a favorable gradient or away from a harmful gradient is known as chemotaxis. Bacteria achieve this by rotating flagella in clockwise and anticlockwise directions resulting in "run" and "tumble." This ability of bacteria to sense and respond to any type of change in the environmental factors like pH, osmolarity, redox potential, and temperature is a standard signal transduction system that depends on coupling proteins, which is the bacterial chemotaxis system. There are two architectures for the coupling proteins in the chemotaxis system: CheW and CheV. Typically, a signal transduction system for chemotaxis to form a core signaling complex couples CheA activity to chemoreceptor control: two CheW coupling protein molecules span a histidine kinase CheA dimer and two chemoreceptors (also known as methyl-accepting chemotaxis protein, MCP) trimers of dimers which further transfer the signal to the flagellar motor through CheY. The current review summarizes and highlights the molecular mechanism involved in bacterial chemotaxis, its physiological benefits such as locating suitable nutrients and niches for bacterial growth, and various assay techniques used for the detection of chemotactic motility.
- Klíčová slova
- Bacteria, Chemotaxis, Motility, Run, Tumble,
- MeSH
- Bacteria * metabolismus genetika MeSH
- bakteriální proteiny metabolismus genetika MeSH
- chemotaxe * fyziologie MeSH
- flagella fyziologie MeSH
- fyziologie bakterií * MeSH
- MCP systém metabolismus MeSH
- signální transdukce MeSH
- Publikační typ
- časopisecké články MeSH
- přehledy MeSH
- Názvy látek
- bakteriální proteiny MeSH
- MCP systém MeSH
Lipid-mediated delivery of active pharmaceutical ingredients (API) opened new possibilities in advanced therapies. By encapsulating an API into a lipid nanocarrier (LNC), one can safely deliver APIs not soluble in water, those with otherwise strong adverse effects, or very fragile ones such as nucleic acids. However, for the rational design of LNCs, a detailed understanding of the composition-structure-function relationships is missing. This review presents currently available computational methods for LNC investigation, screening, and design. The state-of-the-art physics-based approaches are described, with the focus on molecular dynamics simulations in all-atom and coarse-grained resolution. Their strengths and weaknesses are discussed, highlighting the aspects necessary for obtaining reliable results in the simulations. Furthermore, a machine learning, i.e., data-based learning, approach to the design of lipid-mediated API delivery is introduced. The data produced by the experimental and theoretical approaches provide valuable insights. Processing these data can help optimize the design of LNCs for better performance. In the final section of this Review, state-of-the-art of computer simulations of LNCs are reviewed, specifically addressing the compatibility of experimental and computational insights.
- Klíčová slova
- ionizable lipid, lipid nanocarrier, lipid nanoparticle, liposome, molecular simulation, vesicle,
- MeSH
- léčivé přípravky chemie aplikace a dávkování MeSH
- lékové transportní systémy * metody MeSH
- lidé MeSH
- lipidy * chemie MeSH
- nanočástice chemie MeSH
- nosiče léků * chemie MeSH
- počítačová simulace MeSH
- simulace molekulární dynamiky MeSH
- strojové učení MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- přehledy MeSH
- Názvy látek
- léčivé přípravky MeSH
- lipidy * MeSH
- nosiče léků * MeSH
All-atom molecular dynamics simulations are powerful tools for studying cell membranes and their interactions with proteins and other molecules. However, these processes occur on time scales determined by the diffusion rate of phospholipids, which are challenging to achieve in all-atom models. Here, we present a new all-atom model that accelerates lipid diffusion by splitting phospholipid molecules into head and tail groups. The bilayer structure is maintained by using external lateral potentials, which compensate for the lipid split. This split model enhances lateral lipid diffusion more than ten times, allowing faster and cheaper equilibration of large systems with different phospholipid types. The current model has been tested on membranes containing PSM, POPC, POPS, POPE, POPA, and cholesterol. We have also evaluated the interaction of the split model membranes with the Disheveled DEP domain and amphiphilic helix motif of the transcriptional repressor Opi1 as representative of peripheral proteins as well as the dimeric fragment of the epidermal growth factor receptor transmembrane domain and the Human A2A Adenosine of G protein-coupled receptors as representative of transmembrane proteins. The split model can predict the interaction sites of proteins and their preferred phospholipid type. Thus, the model could be used to identify lipid binding sites and equilibrate large membranes at an affordable computational cost.
- MeSH
- buněčná membrána * chemie metabolismus MeSH
- difuze MeSH
- fosfolipidy * chemie metabolismus MeSH
- lidé MeSH
- lipidové dvojvrstvy * chemie metabolismus MeSH
- simulace molekulární dynamiky * MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- fosfolipidy * MeSH
- lipidové dvojvrstvy * MeSH
Biological membranes play a crucial role in actively hosting, modulating and coordinating a wide range of molecular events essential for cellular function. Membranes are organized into diverse domains giving rise to dynamic molecular patchworks. However, the very definition of membrane domains has been the subject of continuous debate. For example, in the plant field, membrane domains are often referred to as nanodomains, nanoclusters, microdomains, lipid rafts, membrane rafts, signalling platforms, foci or liquid-ordered membranes without any clear rationale. In the context of plant-microbe interactions, microdomains have sometimes been used to refer to the large area at the plant-microbe interface. Some of these terms have partially overlapping meanings at best, but they are often used interchangeably in the literature. This situation generates much confusion and limits conceptual progress. There is thus an urgent need for us as a scientific community to resolve these semantic and conceptual controversies by defining an unambiguous nomenclature of membrane domains. In this Review, experts in the field get together to provide explicit definitions of plasma membrane domains in plant systems and experimental guidelines for their study. We propose that plasma membrane domains should not be considered on the basis of their size alone but rather according to the biological system being considered, such as the local membrane environment or the entire cell.
The transport of molecules across cell membranes is vital for proper cell function and effective drug delivery. While most cell membranes naturally possess an asymmetric lipid composition, research on membrane transport predominantly uses symmetric lipid membranes. The permeation through the asymmetric membrane is then calculated as a sum of the inverse permeabilities of leaflets from symmetric bilayers. In this study, we examined how two types of amphiphilic molecules translocate across both asymmetric and symmetric membranes. Using computer simulations with both coarse-grained and atomistic force fields, we calculated the free energy profiles for the passage of model amphiphilic peptides and a lipid across various membranes. Our results consistently demonstrate that while the free energy profiles for asymmetric membranes with a small differential stress concur with symmetric ones in the region of lipid headgroups, the profiles differ around the center of the membrane. In this region, the free energy for the asymmetric membrane transitions between the profiles for two symmetric membranes. In addition, we show that peptide permeability through an asymmetric membrane cannot always be predicted from the permeabilities of the symmetric membranes. This indicates that using symmetric membranes falls short in providing an accurate depiction of peptide translocation across asymmetric membranes.
The routinely employed periodic boundary conditions complicate molecular simulations of physiologically relevant asymmetric lipid membranes together with their distinct solvent environments. Therefore, separating the extracellular fluid from its cytosolic counterpart has often been performed using a costly double-bilayer setup. Here, we demonstrate that the lipid membrane and solvent asymmetry can be efficiently modeled with a single lipid bilayer by applying an inverted flat-bottom potential to ions and other solute molecules, thereby restraining them to only interact with the relevant leaflet. We carefully optimized the parameters of the suggested method so that the results obtained using the flat-bottom and double-bilayer approaches become mutually indistinguishable. Then, we apply the flat-bottom approach to lipid bilayers with various compositions and solvent environments, covering ions and cationic peptides to validate the approach in a realistic use case. We also discuss the possible limitations of the method as well as its computational efficiency and provide a step-by-step guide on how to set up such simulations in a straightforward manner.
- MeSH
- lipidové dvojvrstvy * chemie MeSH
- rozpouštědla MeSH
- simulace molekulární dynamiky * MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- lipidové dvojvrstvy * MeSH
- rozpouštědla MeSH
Cholesterol is a central building block in biomembranes, where it induces orientational order, slows diffusion, renders the membrane stiffer, and drives domain formation. Molecular dynamics (MD) simulations have played a crucial role in resolving these effects at the molecular level; yet, it has recently become evident that different MD force fields predict quantitatively different behavior. Although easily neglected, identifying such limitations is increasingly important as the field rapidly progresses toward simulations of complex membranes mimicking the in vivo conditions: pertinent multicomponent simulations must capture accurately the interactions between their fundamental building blocks, such as phospholipids and cholesterol. Here, we define quantitative quality measures for simulations of binary lipid mixtures in membranes against the C-H bond order parameters and lateral diffusion coefficients from NMR spectroscopy as well as the form factors from X-ray scattering. Based on these measures, we perform a systematic evaluation of the ability of commonly used force fields to describe the structure and dynamics of binary mixtures of palmitoyloleoylphosphatidylcholine (POPC) and cholesterol. None of the tested force fields clearly outperforms the others across the tested properties and conditions. Still, the Slipids parameters provide the best overall performance in our tests, especially when dynamic properties are included in the evaluation. The quality evaluation metrics introduced in this work will, particularly, foster future force field development and refinement for multicomponent membranes using automated approaches.
- MeSH
- cholesterol chemie MeSH
- fosfatidylcholiny * chemie MeSH
- lipidové dvojvrstvy * chemie MeSH
- simulace molekulární dynamiky MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- 1-palmitoyl-2-oleoylphosphatidylcholine MeSH Prohlížeč
- cholesterol MeSH
- fosfatidylcholiny * MeSH
- lipidové dvojvrstvy * MeSH
Membrane contact sites (MCSs) are interorganellar connections that allow for the direct exchange of molecules, such as lipids or Ca2+ between organelles, but can also serve to tether organelles at specific locations within cells. Here, we identified and characterized three proteins of Arabidopsis thaliana that form a lipid droplet (LD)-plasma membrane (PM) tethering complex in plant cells, namely LD-localized SEED LD PROTEIN (SLDP) 1 and SLDP2 and PM-localized LD-PLASMA MEMBRANE ADAPTOR (LIPA). Using proteomics and different protein-protein interaction assays, we show that both SLDPs associate with LIPA. Disruption of either SLDP1 and SLDP2 expression, or that of LIPA, leads to an aberrant clustering of LDs in Arabidopsis seedlings. Ectopic co-expression of one of the SLDPs with LIPA is sufficient to reconstitute LD-PM tethering in Nicotiana tabacum pollen tubes, a cell type characterized by dynamically moving LDs in the cytosolic streaming. Furthermore, confocal laser scanning microscopy revealed both SLDP2.1 and LIPA to be enriched at LD-PM contact sites in seedlings. These and other results suggest that SLDP and LIPA interact to form a tethering complex that anchors a subset of LDs to the PM during post-germinative seedling growth in Arabidopsis.
- MeSH
- Arabidopsis * genetika metabolismus MeSH
- buněčná membrána metabolismus MeSH
- lipidová tělíska metabolismus MeSH
- proteiny huseníčku * genetika metabolismus MeSH
- semena rostlinná genetika metabolismus MeSH
- semenáček genetika metabolismus MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- proteiny huseníčku * MeSH
Molecular dynamics (MD) simulations have become an indispensable tool to investigate phase separation in model membrane systems. In particular, simulations based on coarse-grained (CG) models have found widespread use due to their increased computational efficiency, allowing for simulations of multicomponent lipid bilayers undergoing phase separation into liquid-ordered and liquid-disordered domains. Here, we show that a significant temperature difference between molecule types can artificially arise in CG MD membrane simulations with the standard Martini simulation parameters in GROMACS. In particular, the linear constraint solver (LINCS) algorithm does not converge with its default settings, resulting in serious temperature differences between molecules in a time step-dependent manner. We demonstrate that the underlying reason for this behavior is the presence of highly constrained moieties, such as cholesterol. Their presence can critically impact numerous structural and dynamic membrane properties obtained from such simulations. Furthermore, any preference of these molecules toward a certain membrane phase can lead to spatial temperature gradients, which can amplify the degree of phase separation or even induce it in compositions that would otherwise mix well. We systematically investigated the effect of the integration time step and LINCS settings on membrane properties. Our data show that for cholesterol-containing membranes, a time step of 20 fs should be combined with at least lincs_iter = 2 and lincs_order = 12, while using a time step of 30 fs requires at least lincs_iter = 3 and lincs_order = 12 to bring the temperature differences to a level where they do not perturb central membrane properties. Moreover, we show that in cases where stricter LINCS settings are computationally too demanding, coupling the lipids in multiple groups to the temperature bath offers a practical workaround to the problem, although the validity of this approach should be further verified. Finally, we show that similar temperature gradients can also emerge in atomistic simulations using the CHARMM force field in combination with settings that allow for a 5 fs integration step.
- MeSH
- cholesterol MeSH
- lipidové dvojvrstvy * MeSH
- simulace molekulární dynamiky * MeSH
- teplota MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- cholesterol MeSH
- lipidové dvojvrstvy * MeSH
