Nejvíce citovaný článek - PubMed ID 29131844
Excessive aggregation of membrane proteins in the Martini model
Cellular homeostasis depends on the rapid, ATP-independent translocation of newly synthesized lipids across the endoplasmic reticulum (ER) membrane. Lipid translocation is facilitated by membrane proteins known as scramblases, a few of which have recently been identified in the ER. Our previous structure of the translocon-associated protein (TRAP) bound to the Sec61 translocation channel revealed local membrane thinning, suggesting that the Sec61/TRAP complex might be involved in lipid scrambling. Using complementary fluorescence spectroscopy assays, we detected nonselective scrambling by reconstituted translocon complexes. This activity was unaffected by Sec61 inhibitors that block its lateral gate, suggesting a second lipid scrambling pathway within the complex. Molecular dynamics simulations indicate that the trimeric TRAP subunit forms this alternative route, facilitating lipid translocation via a "credit card" mechanism, using a crevice lined with polar residues to shield lipid head groups from the hydrophobic membrane interior. Kinetic and thermodynamic analyses confirmed that local membrane thinning enhances scrambling efficiency and that both Sec61 and TRAP scramble phosphatidylcholine faster than phosphatidylethanolamine and phosphatidylserine, reflecting the intrinsic lipid flip-flop tendencies of these lipid species. As the Sec61 scrambling site lies in the lateral gate region, it is likely inaccessible during protein translocation, in line with our experiments on Sec61-inhibited samples. Hence, our findings suggest that the metazoan-specific trimeric TRAP bundle is a viable candidate for lipid scrambling activity that is insensitive to the functional state of the translocon.
- MeSH
- endoplazmatické retikulum metabolismus MeSH
- lidé MeSH
- membránové proteiny * metabolismus chemie MeSH
- simulace molekulární dynamiky MeSH
- translokační kanály SEC metabolismus MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- membránové proteiny * MeSH
- translokační kanály SEC MeSH
Peptides that form transmembrane barrel-stave pores are potential alternative therapeutics for bacterial infections and cancer. However, their optimization for clinical translation is hampered by a lack of sequence-function understanding. Recently, we have de novo designed the first synthetic barrel-stave pore-forming antimicrobial peptide with an identified function of all residues. Here, we systematically mutate the peptide to improve pore-forming ability in anticipation of enhanced activity. Using computer simulations, supported by liposome leakage and atomic force microscopy experiments, we find that pore-forming ability, while critical, is not the limiting factor for improving activity in the submicromolar range. Affinity for bacterial and cancer cell membranes needs to be optimized simultaneously. Optimized peptides more effectively killed antibiotic-resistant ESKAPEE bacteria at submicromolar concentrations, showing low cytotoxicity to human cells and skin model. Peptides showed systemic anti-infective activity in a preclinical mouse model of Acinetobacter baumannii infection. We also demonstrate peptide optimization for pH-dependent antimicrobial and anticancer activity.
- MeSH
- Acinetobacter baumannii účinky léků MeSH
- antibakteriální látky farmakologie chemie chemická syntéza MeSH
- antimikrobiální peptidy chemie farmakologie chemická syntéza MeSH
- kationické antimikrobiální peptidy farmakologie chemie chemická syntéza MeSH
- lidé MeSH
- mikrobiální testy citlivosti MeSH
- myši MeSH
- nádorové buněčné linie MeSH
- protinádorové látky * farmakologie chemie chemická syntéza MeSH
- racionální návrh léčiv * MeSH
- zvířata MeSH
- Check Tag
- lidé MeSH
- myši MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- antibakteriální látky MeSH
- antimikrobiální peptidy MeSH
- kationické antimikrobiální peptidy MeSH
- protinádorové látky * MeSH
In the last quarter-century, the field of molecular dynamics (MD) has undergone a remarkable transformation, propelled by substantial enhancements in software, hardware, and underlying methodologies. In this Perspective, we contemplate the future trajectory of MD simulations and their possible look at the year 2050. We spotlight the pivotal role of artificial intelligence (AI) in shaping the future of MD and the broader field of computational physical chemistry. We outline critical strategies and initiatives that are essential for the seamless integration of such technologies. Our discussion delves into topics like multiscale modeling, adept management of ever-increasing data deluge, the establishment of centralized simulation databases, and the autonomous refinement, cross-validation, and self-expansion of these repositories. The successful implementation of these advancements requires scientific transparency, a cautiously optimistic approach to interpreting AI-driven simulations and their analysis, and a mindset that prioritizes knowledge-motivated research alongside AI-enhanced big data exploration. While history reminds us that the trajectory of technological progress can be unpredictable, this Perspective offers guidance on preparedness and proactive measures, aiming to steer future advancements in the most beneficial and successful direction.
- Publikační typ
- časopisecké články MeSH
- přehledy MeSH
Cell membranes act as semi-permeable barriers, often restricting the entry of large or hydrophilic molecules. Nonetheless, certain amphiphilic molecules, such as antimicrobial and cell-penetrating peptides, can cross these barriers. In this study, we demonstrate that specific properties of transmembrane proteins/peptides can enhance membrane permeation of amphiphilic peptides. Using coarse-grained molecular dynamics with free-energy calculations, we identify key translocation-enhancing attributes of transmembrane proteins/peptides: a continuous hydrophilic patch, charged residues preferably in the membrane center, and aromatic hydrophobic residues. By employing both coarse-grained and atomistic simulations, complemented by experimental validation, we show that these properties not only enhance peptide translocation but also speed up lipid flip-flop. The enhanced flip-flop reinforces the idea that proteins such as scramblases and insertases not only share structural features but also operate through identical biophysical mechanisms enhancing the insertion and translocation of amphiphilic molecules. Our insights offer guidelines for the designing of translocation-enhancing proteins/peptides that could be used in medical and biotechnological applications.
- MeSH
- buněčná membrána metabolismus chemie MeSH
- hydrofobní a hydrofilní interakce * MeSH
- lipidové dvojvrstvy chemie metabolismus MeSH
- membránové proteiny * chemie metabolismus MeSH
- simulace molekulární dynamiky * MeSH
- transport proteinů MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- lipidové dvojvrstvy MeSH
- membránové proteiny * MeSH
Mitochondria are double-membrane-bounded organelles that depend critically on phospholipids supplied by the endoplasmic reticulum. These lipids must cross the outer membrane to support mitochondrial function, but how they do this is unclear. We identify the Voltage Dependent Anion Channel (VDAC), an abundant outer membrane protein, as a scramblase-type lipid transporter that catalyzes lipid entry. On reconstitution into membrane vesicles, dimers of human VDAC1 and VDAC2 catalyze rapid transbilayer translocation of phospholipids by a mechanism that is unrelated to their channel activity. Coarse-grained molecular dynamics simulations of VDAC1 reveal that lipid scrambling occurs at a specific dimer interface where polar residues induce large water defects and bilayer thinning. The rate of phospholipid import into yeast mitochondria is an order of magnitude lower in the absence of VDAC homologs, indicating that VDACs provide the main pathway for lipid entry. Thus, VDAC isoforms, members of a superfamily of beta barrel proteins, moonlight as a class of phospholipid scramblases - distinct from alpha-helical scramblase proteins - that act to import lipids into mitochondria.
- MeSH
- fosfolipidy * metabolismus MeSH
- lidé MeSH
- mitochondrie metabolismus MeSH
- napětím ovládané aniontové kanály metabolismus MeSH
- napětím ovládaný aniontový kanál 1 * metabolismus MeSH
- Saccharomyces cerevisiae metabolismus MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Research Support, N.I.H., Extramural MeSH
- Názvy látek
- fosfolipidy * MeSH
- napětím ovládané aniontové kanály MeSH
- napětím ovládaný aniontový kanál 1 * MeSH
Shear viscosity of lipid membranes dictates how fast lipids, proteins, and other membrane constituents travel along the membrane and rotate around their principal axis, thus governing the rates of diffusion-limited reactions taking place at membranes. In this framework, the heterogeneity of biomembranes indicates that cells could regulate these rates via varying local viscosities. Unfortunately, experiments to probe membrane viscosity under various conditions are tedious and error prone. Molecular dynamics simulations provide an attractive alternative, especially given that recent theoretical developments enable the elimination of finite-size effects in simulations. Here, we use a variety of different equilibrium methods to extract the shear viscosities of lipid membranes from both coarse-grained and all-atom molecular dynamics simulations. We systematically probe the variables relevant for cellular membranes, namely, membrane protein crowding, cholesterol concentration, and the length and saturation level of lipid acyl chains, as well as temperature. Our results highlight that in their physiologically relevant ranges, protein concentration, cholesterol concentration, and temperature have significantly larger effects on membrane viscosity than lipid acyl chain length and unsaturation level. In particular, the crowding with proteins has a significant effect on the shear viscosity of lipid membranes and thus on the diffusion occurring in the membranes. Our work also provides the largest collection of membrane viscosity values from simulation to date, which can be used by the community to predict the diffusion coefficients or their trends via the Saffman-Delbrück description. Additionally, it is worth emphasizing that diffusion coefficients extracted from simulations exploiting periodic boundary conditions must be corrected for the finite-size effects prior to comparison with experiment, for which the present collection of viscosity values can readily be used. Finally, our thorough comparison to experiments suggests that there is room for improvement in the description of bilayer dynamics provided by the present force fields.
- MeSH
- buněčná membrána metabolismus MeSH
- difuze MeSH
- lipidové dvojvrstvy metabolismus MeSH
- lipidy * MeSH
- simulace molekulární dynamiky * MeSH
- teplota MeSH
- viskozita MeSH
- Publikační typ
- časopisecké články MeSH
- Názvy látek
- lipidové dvojvrstvy MeSH
- lipidy * MeSH
Cell membranes are phospholipid bilayers with a large number of embedded transmembrane proteins. Some of these proteins, such as scramblases, have properties that facilitate lipid flip-flop from one membrane leaflet to another. Scramblases and similar transmembrane proteins could also affect the translocation of other amphiphilic molecules, including cell-penetrating or antimicrobial peptides. We studied the effect of transmembrane proteins on the translocation of amphiphilic peptides through the membrane. Using two very different models, we consistently demonstrate that transmembrane proteins with a hydrophilic patch enhance the translocation of amphiphilic peptides by stabilizing the peptide in the membrane. Moreover, there is an optimum amphiphilicity because the peptide could become overstabilized in the transmembrane state, in which the peptide-protein dissociation is hampered, limiting the peptide translocation. The presence of scramblases and other proteins with similar properties could be exploited for more efficient transport into cells. The described principles could also be utilized in the design of a drug-delivery system by the addition of a translocation-enhancing peptide that would integrate into the membrane.
The coarse-grained Martini force field is widely used in biomolecular simulations. Here we present the refined model, Martini 3 ( http://cgmartini.nl ), with an improved interaction balance, new bead types and expanded ability to include specific interactions representing, for example, hydrogen bonding and electronic polarizability. The updated model allows more accurate predictions of molecular packing and interactions in general, which is exemplified with a vast and diverse set of applications, ranging from oil/water partitioning and miscibility data to complex molecular systems, involving protein-protein and protein-lipid interactions and material science applications as ionic liquids and aedamers.
The Bcl-2 protein family comprises both pro- and antiapoptotic members that control the permeabilization of the mitochondrial outer membrane, a crucial step in the modulation of apoptosis. Recent research has demonstrated that the carboxyl-terminal transmembrane domain (TMD) of some Bcl-2 protein family members can modulate apoptosis; however, the transmembrane interactome of the antiapoptotic protein Mcl-1 remains largely unexplored. Here, we demonstrate that the Mcl-1 TMD forms homooligomers in the mitochondrial membrane, competes with full-length Mcl-1 protein with regards to its antiapoptotic function, and induces cell death in a Bok-dependent manner. While the Bok TMD oligomers locate preferentially to the endoplasmic reticulum (ER), heterooligomerization between the TMDs of Mcl-1 and Bok predominantly takes place at the mitochondrial membrane. Strikingly, the coexpression of Mcl-1 and Bok TMDs produces an increase in ER mitochondrial-associated membranes, suggesting an active role of Mcl-1 in the induced mitochondrial targeting of Bok. Finally, the introduction of Mcl-1 TMD somatic mutations detected in cancer patients alters the TMD interaction pattern to provide the Mcl-1 protein with enhanced antiapoptotic activity, thereby highlighting the clinical relevance of Mcl-1 TMD interactions.
- Klíčová slova
- Bcl-2, Bok, Mcl-1, apoptosis, transmembrane,
- MeSH
- apoptóza fyziologie MeSH
- buněčná smrt fyziologie MeSH
- endoplazmatické retikulum metabolismus MeSH
- HeLa buňky MeSH
- lidé MeSH
- mitochondriální membrány metabolismus MeSH
- mitochondrie metabolismus MeSH
- protein MCL-1 metabolismus MeSH
- proteinové domény MeSH
- protoonkogenní proteiny c-bcl-2 metabolismus MeSH
- zvířata MeSH
- Check Tag
- lidé MeSH
- zvířata MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- BOK protein, human MeSH Prohlížeč
- MCL1 protein, human MeSH Prohlížeč
- protein MCL-1 MeSH
- protoonkogenní proteiny c-bcl-2 MeSH
We addressed the onset of synergistic activity of the two well-studied antimicrobial peptides magainin 2 (MG2a) and PGLa using lipid-only mimics of Gram-negative cytoplasmic membranes. Specifically, we coupled a joint analysis of small-angle x-ray and neutron scattering experiments on fully hydrated lipid vesicles in the presence of MG2a and L18W-PGLa to all-atom and coarse-grained molecular dynamics simulations. In agreement with previous studies, both peptides, as well as their equimolar mixture, were found to remain upon adsorption in a surface-aligned topology and to induce significant membrane perturbation, as evidenced by membrane thinning and hydrocarbon order parameter changes in the vicinity of the inserted peptide. These effects were particularly pronounced for the so-called synergistic mixture of 1:1 (mol/mol) L18W-PGLa/MG2a and cannot be accounted for by a linear combination of the membrane perturbations of two peptides individually. Our data are consistent with the formation of parallel heterodimers at concentrations below a synergistic increase of dye leakage from vesicles. Our simulations further show that the heterodimers interact via salt bridges and hydrophobic forces, which apparently makes them more stable than putatively formed antiparallel L18W-PGLa and MG2a homodimers. Moreover, dimerization of L18W-PGLa and MG2a leads to a relocation of the peptides within the lipid headgroup region as compared to the individual peptides. The early onset of dimerization of L18W-PGLa and MG2a at low peptide concentrations consequently appears to be key to their synergistic dye-releasing activity from lipid vesicles at high concentrations.
- MeSH
- buněčná membrána metabolismus MeSH
- dimerizace MeSH
- fosfatidylethanolaminy MeSH
- fosfatidylglyceroly MeSH
- kationické antimikrobiální peptidy metabolismus MeSH
- lipidové dvojvrstvy chemie MeSH
- lipidy chemie MeSH
- magaininy metabolismus MeSH
- simulace molekulární dynamiky MeSH
- teplota MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Názvy látek
- 1-palmitoyl-2-oleoylphosphatidylethanolamine MeSH Prohlížeč
- 1,2-dioleoyl-sn-glycero-3-phosphoglycerol MeSH Prohlížeč
- fosfatidylethanolaminy MeSH
- fosfatidylglyceroly MeSH
- kationické antimikrobiální peptidy MeSH
- lipidové dvojvrstvy MeSH
- lipidy MeSH
- magaininy MeSH
- peptide-Gly-Leu-amide MeSH Prohlížeč
