Energetics of the Transmembrane Peptide Sorting by Hydrophobic Mismatch.

Hydrophobic mismatch between a lipid membrane and embedded transmembrane peptides or proteins plays a role in their lateral localization and function. Earlier studies have resolved numerous mechanisms through which the peptides and membrane proteins adapt to mismatch, yet the energetics of lateral sorting due to hydrophobic mismatch have remained elusive due to the lack of suitable computational or experimental protocols. Here, we pioneer a molecular dynamics simulation approach to study the sorting of peptides along a membrane thickness gradient. Peptides of different lengths tilt and diffuse along the membrane to eliminate mismatch with a rate directly proportional to the magnitude of mismatch. We extract the 2-dimensional free energy profiles as a function of local thickness and peptide orientation, revealing the relative contributions of sorting and tilting, and suggesting their thermally accessible regimes. Our approach can readily be applied to study other membrane systems of biological interest where hydrophobic mismatch, or membrane thickness in general, plays a role.

OrganL: Dynamic triangulation of biomembranes using curved elements.

We describe a method for simulating biomembranes of arbitrary shape. In contrast to other dynamically triangulated surface (DTS) algorithms, our method provides a rich, quasi-tangent-continuous, yet local description of the surface. We use curved Nagata triangles, which we generalize to cubic order to achieve the requisite flexibility. The resulting interpolation can be constructed locally without iterations, at the cost of having only approximate tangent continuity away from the vertices. This allows us to provide a parallelized and fine-tuned Monte Carlo implementation. As a first example of the potential benefits of the enhanced description, our method supports inhomogeneous lipid distributions as well as lipid mixing. It also supports restraints and constraints of various types and is constructed to be as easily extensible as possible. We validate the approach by testing its numerical accuracy, followed by reproducing the known Helfrich solutions for shapes with rotational symmetry. Finally, we present some example applications, including curvature-driven demixing and stylized effects of proteins. Input files for these examples, as well as the implementation itself, are freely available for researchers under the name OrganL (https://zenodo.org/doi/10.5281/zenodo.11204709).

Diffusion Analyses along Mean and Gaussian-Curved Membranes with CurD.

Curved cellular membranes are both abundant and functionally relevant. While novel tomography approaches reveal the structural details of curved membranes, their dynamics pose an experimental challenge. Curvature especially affects the diffusion of lipids and macromolecules, yet neither experiments nor continuum models distinguish geometric effects from those caused by curvature-induced changes in membrane properties. Molecular simulations could excel here, yet despite community interest toward curved membranes, tools for their analysis are still lacking. Here, we satisfy this demand by introducing CurD, our novel and openly available implementation of the Vertex-oriented Triangle Propagation algorithm to the study of lipid diffusion along membranes with mean and/or Gaussian curvature. This approach, aided by our highly optimized implementation, computes geodetic distances significantly faster than conventional implementations of path-finding algorithms. Our tool, applied to coarse-grained simulations, allows for the first time the analysis of curvature effects on diffusion at size scales relevant to physiological processes such as endocytosis. Our analyses with different membrane geometries reveal that Gaussian curvature plays a surprisingly small role on lipid motion, whereas mean curvature; i.e., the packing of lipid headgroups largely dictates their mobility.

Hydration of biologically relevant tetramethylammonium cation by neutron scattering and molecular dynamics.

Neutron scattering and molecular dynamics studies were performed on a concentrated aqueous tetramethylammonium (TMA) chloride solution to gain insight into the hydration shell structure of TMA, which is relevant for understanding its behavior in biological contexts of, e.g., properties of phospholipid membrane headgroups or interactions between DNA and histones. Specifically, neutron diffraction with isotopic substitution experiments were performed on TMA and water hydrogens to extract the specific correlation between hydrogens in TMA (HTMA) and hydrogens in water (HW). Classical molecular dynamics simulations were performed to help interpret the experimental neutron scattering data. Comparison of the hydration structure and simulated neutron signals obtained with various force field flavors (e.g. overall charge, charge distribution, polarity of the CH bonds and geometry) allowed us to gain insight into how sensitive the TMA hydration structure is to such changes and how much the neutron signal can capture them. We show that certain aspects of the hydration, such as the correlation of the hydrogen on TMA to hydrogen on water, showed little dependence on the force field. In contrast, other correlations, such as the ion-ion interactions, showed more marked changes. Strikingly, the neutron scattering signal cannot discriminate between different hydration patterns. Finally, ab initio molecular dynamics was used to examine the three-dimensional hydration structure and thus to benchmark force field simulations. Overall, while neutron scattering has been previously successfully used to improve force fields, in the particular case of TMA we show that it has only limited value to fully determine the hydration structure, with other techniques such as ab initio MD being of a significant help.

Neighbor List Artifacts in Molecular Dynamics Simulations.

Molecular dynamics (MD) simulations are widely used in biophysical research. To aid nonexpert users, most simulation packages provide default values for key input parameters. In MD simulations using the GROMACS package with default parameters, we found large membranes to deform under the action of a semi-isotropically coupled barostat. As the primary cause, we identified overly short outer cutoffs and infrequent neighbor list updates that resulted in missed nonbonded interactions. Small but systematic imbalances in the apparent pressure tensor then induce unphysical asymmetric box deformations that crumple the membrane. We also observed rapid oscillations in averages of the instantaneous pressure tensor components and traced these to the use of a dual pair list with dynamic pruning. We confirmed that similar effects are present in MD simulations of neat water in atomistic and coarse-grained representations. Whereas the slight pressure imbalances likely have minimal impact in most current atomistic MD simulations, we expect their impact to grow in studies of ever-larger systems with coarse-grained representation, in particular, in combination with anisotropic pressure coupling. We present measures to diagnose problems with missed interactions and guidelines for practitioners to avoid them, including estimates for appropriate values for the outer cutoff rl and the number of time steps nstlist between neighbor list updates.

Martini 3 Coarse-Grained Force Field for Cholesterol.

Cholesterol plays a crucial role in biomembranes by regulating various properties, such as fluidity, rigidity, permeability, and organization of lipid bilayers. The latest version of the Martini model, Martini 3, offers significant improvements in interaction balance, molecular packing, and inclusion of new bead types and sizes. However, the release of the new model resulted in the need to reparameterize many core molecules, including cholesterol. Here, we describe the development and validation of a Martini 3 cholesterol model, addressing issues related to its bonded setup, shape, volume, and hydrophobicity. The proposed model mitigates some limitations of its Martini 2 predecessor while maintaining or improving the overall behavior.

Efficient generation of random rotation matrices in four dimensions.

Four-dimensional (4D) rotations have applications in the fields of robotics, computer vision, and rigid-body mechanics. In the latter, they can be used to transform between equimomental systems of point masses. Here we provide an efficient algorithm to generate random 4D rotation matrices covering an arbitrary, predefined range of rotation angles. These matrices can be combined with Monte Carlo methods for the efficient sampling of the SO(4) group of 4D rotations. The matrices are unbiased and constructed such that repeated rotations result in uniform sampling over SO(4). The algorithm can be used to optimize the mass partitioning in coarse-grained simulation models of molecules involving coupled constraints for stable time integration.

Understanding the Molecular Mechanism of Anesthesia: Effect of General Anesthetics and Structurally Similar Non-Anesthetics on the Properties of Lipid Membranes.

General anesthesia can be caused by various, chemically very different molecules, while several other molecules, many of which are structurally rather similar to them, do not exhibit anesthetic effects at all. To understand the origin of this difference and shed some light on the molecular mechanism of general anesthesia, we report here molecular dynamics simulations of the neat dipalmitoylphosphatidylcholine (DPPC) membrane as well as DPPC membranes containing the anesthetics diethyl ether and chloroform and the structurally similar non-anesthetics n-pentane and carbon tetrachloride, respectively. To also account for the pressure reversal of anesthesia, these simulations are performed both at 1 bar and at 600 bar. Our results indicate that all solutes considered prefer to stay both in the middle of the membrane and close to the boundary of the hydrocarbon domain, at the vicinity of the crowded region of the polar headgroups. However, this latter preference is considerably stronger for the (weakly polar) anesthetics than for the (apolar) non-anesthetics. Anesthetics staying in this outer preferred position increase the lateral separation between the lipid molecules, giving rise to a decrease of the lateral density. The lower lateral density leads to an increased mobility of the DPPC molecules, a decreased order of their tails, an increase of the free volume around this outer preferred position, and a decrease of the lateral pressure at the hydrocarbon side of the apolar/polar interface, a change that might well be in a causal relation with the occurrence of the anesthetic effect. All these changes are clearly reverted by the increase of pressure. Furthermore, non-anesthetics occur in this outer preferred position in a considerably smaller concentration and hence either induce such changes in a much weaker form or do not induce them at all.

[Normative data on clinical neuropsychological tests in Hungary II.] / Klinikai neuropszichológiai tesztek magyarországi normatív adatai II.

INTRODUCTION: One basis of clinical neuropsychology is the application of objective, standardized measurements. Several internationally widespread measurements of memory and learning do not have normative data of the Hungarian population, hence it is crucial to provide a basis for future reference. OBJECTIVE: The purpose of this study was to provide normative data about neuropsychological instruments measuring executive functions, memory and verbal learning skills in relation to demographic factors. METHOD: Rey Auditory Verbal Learning Test (RAVLT), Montreal Cognitive Assessment (MoCA) and Prospective and Retrospective Memory Questionnaire (PRMQ) were administered to an adult, Hungarian representative sample (age, sex, education). RESULTS: Higher educated participants performed better on PRMQ, MoCA and RAVLT. Participants with primary education were identified as a risk group for poor verbal learning skills, executive functions and they committed more memory errors. Age had no significant effect on the results of PRMQ, while on MoCA and RAVLT a significant decline in performance was observed with the passage of lifetime. Females performed better in immediate and delayed recall on RAVLT. CONCLUSION: Application of the presented neuropsychological tests is recommended in clinical practice and scientific research as well. The presented normative data could be a valuable reference point for future studies and practical application, furthermore a basis for early identification of neurocognitive deficits. Orv Hetil. 2023; 164(16) 618-629.

[Normative data on clinical neuropsychological tests in Hungary I.] / Klinikai neuropszichológiai tesztek magyarországi normatív adatai I.

INTRODUCTION: Executive functions are crucial cognitive processes which enable us to manage our daily life, to be able to sustain goal-oriented behavior, to adapt to environmental changes and to regulate and coordinate the behavior during task situations. There are several means of evaluating executive functioning, but normative data for the Hungarian population were unavailable for detailed assessment. OBJECTIVE: The purpose of this study was to explore the effects of gender, age, and education on the performance of three neurocognitive tests measuring executive functions, and to provide normative data in the Hungarian population. METHOD: Victoria Stroop Test, Five-Point Test and Trail Making Test were administered to 316 individuals (175 female, 141 male). The sample was representative for Hungarian adults regarding age, gender and education. RESULTS: Performance scores decreased with increasing age, while scores increased by higher educational level. Performance was not influenced by gender. Significant correlations were observed between the measures. CONCLUSION: The provision of normative data should enhance the potential of the applied measures for clinical and research applications. These data provide a normative comparison for the assessment of executive functions and cognitive decline. Orv Hetil. 2023; 164(15): 577-585.

Protein Crowding and Cholesterol Increase Cell Membrane Viscosity in a Temperature Dependent Manner.

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.

Optimal Bond Constraint Topology for Molecular Dynamics Simulations of Cholesterol.

We recently observed artificial temperature gradients in molecular dynamics (MD) simulations of phase-separating ternary lipid mixtures using the Martini 2 force field. We traced this artifact to insufficiently converged bond length constraints with typical time steps and default settings for the linear constraint solver (LINCS). Here, we systematically optimize the constraint scaffold of cholesterol. With massive virtual sites in an equimomental arrangement, we accelerate bond constraint convergence while preserving the original cholesterol force field and dynamics. The optimized model does not induce nonphysical temperature gradients even at relaxed LINCS settings and is at least as fast as the original model at the strict LINCS settings required for proper thermal sampling. We provide a python script to diagnose possible problems with constraint convergence for other molecules and force fields. Equimomental constraint topology optimization can also be used to boost constraint convergence in atomistic MD simulations of molecular systems.

Nanoscale membrane curvature sorts lipid phases and alters lipid diffusion.

The precise spatiotemporal control of nanoscale membrane shape and composition is the result of a complex interplay of individual and collective molecular behaviors. Here, we employed single-molecule localization microscopy and computational simulations to observe single-lipid diffusion and sorting in model membranes with varying compositions, phases, temperatures, and curvatures. Supported lipid bilayers were created over 50-nm-radius nanoparticles to mimic the size of naturally occurring membrane buds, such as endocytic pits and the formation of viral envelopes. The curved membranes recruited liquid-disordered lipid phases while altering the diffusion and sorting of tracer lipids. Disorder-preferring fluorescent lipids sorted to and experienced faster diffusion on the nanoscale curvature only when embedded in a membrane capable of sustaining lipid phase separation at low temperatures. The curvature-induced sorting and faster diffusion even occurred when the sample temperature was above the miscibility temperature of the planar membrane, implying that the nanoscale curvature could induce phase separation in otherwise homogeneous membranes. Further confirmation and understanding of these results are provided by continuum and coarse-grained molecular dynamics simulations with explicit and spontaneous curvature-phase coupling, respectively. The curvature-induced membrane compositional heterogeneity and altered dynamics were achieved only with a coupling of the curvature with a lipid phase separation. These cross-validating results demonstrate the complex interplay of lipid phases, molecular diffusion, and nanoscale membrane curvature that are critical for membrane functionality.

Surface Properties of N,N-Dimethylformamide-Water Mixtures, As Seen from Computer Simulations.

The liquid-vapor interface of N,N-dimethylformamide (DMF)-water mixtures, spanning the entire composition range, is investigated in detail at 298 K by molecular dynamics simulation and intrinsic surface analysis. DMF molecules are found to adsorb strongly at the liquid surface, but this adsorption extends only to the first molecular layer. Water and DMF molecules mix with each other on the molecular scale even in the surface layer; thus, no marked self-association of any of the components is seen at the liquid surface. The major surface component prefers such orientation in which the molecular dipole vector lays parallel with the macroscopic plane of the surface. On the other hand, the preferred orientation of the minor component is determined, at both ends of the composition range, by the possibility of H-bond formation with the major component. The lack of H-donating ability of DMF leads to a rapid breakup of the percolating H-bond network at the surface; due to the strong adsorption of DMF, this breakup occurs below the bulk phase DMF mole fraction of 0.03. The disruption of the surface H-bond network also accelerates the exchange of both species between the liquid surface and bulk liquid phase, although, for water, this effect becomes apparent only above a bulk phase DMF mole fraction of 0.4. H-bonds formed by a DMF and a water molecule live, on average, 25-60% longer than those formed by two water molecules at the liquid surface. A similar, but smaller (i.e., about 10-20%) difference is seen in the bulk liquid phase. The enhanced surface mobility of the molecules results in 2-6 times larger diffusion coefficient and 2-5 times shorter H-bond lifetime values at the liquid surface than in the bulk liquid phase. The diffusion of both molecules is slowed down in the presence of the other species; in the case of DMF, this effect is caused by the formation of water-DMF H-bonds, whereas for water, steric hindrances imposed by the bulky DMF neighbors are responsible for this slowing down.

[Factors determining the quality of life in patients with Raynaud's syndrome]. / Az életminoséget meghatározó tényezok Raynaud-szindrómában.

INTRODUCTION: Raynaud's disease is a vasospastic phenomenon affecting acral areas, which manifests itself in characteristic color changes. Symptoms are affected by mundane things like stress or temperature. There are also differences in the presence and progression of the disease in terms of gender, age, health-damaging behaviors (e.g., smoking) and occupation. OBJECTIVE: The aim of our study was to examine how the risk factors assumed in the literature affect the quality of life of patients with Raynaud's disease. METHOD: 110 people diagnosed with Raynaud's disease completed a questionnaire on disease-specific quality of life and risk factors. RESULTS: There was a significant difference between the groups with good and less good quality of life in terms of age (p<0.001), education (p<0.01), type of diagnosis (p<0.001), duration of illness (p<0.001), headache frequency (p<0.01), the influence of cold (p<0.05) and emotions (p<0.01). The groups currently working (p<0.01), drinking coffee more often (p<0.05), attributing less influence to emotions (p<0.001) and cold (p<0.01) had a better quality of life. According to the regression analysis, the type of diagnosis, the duration of the disease, the influencing role of emotions and cold are the most important predictors of Raynaud-specific quality of life. CONCLUSION: Our results draw attention to the role of factors that potentially affect the long-term development of the quality of life, thereby identifying the possible focuses of prevention. Orv Hetil. 2022; 163(47): 1880-1885.

Depression and Anxiety Symptoms Are Associated with Mean Platelet Volume in Autoimmune Disorders.

Platelets are increasingly considered a bridge between mental and immunological disorders. However, data relating to platelet parameters in patients with autoimmune disorders are limited. The aim of the present study was to investigate, for the first time, the association of platelet parameters with the symptoms of affective disorders in patients with autoimmune conditions. In this cross-sectional study, we measured the complete blood count (CBC), the Generalized Anxiety Disorder Scale for anxiety (GAD-7), and the Beck Depression Inventory for depression (BDI) in 121 patients with autoimmune disorders. Mean platelet volume (MPV) was positively correlated with both anxiety and depression. Platelet distribution width (PDW) was negatively correlated with anxiety and depression. Before adjustment for covariates, logistic regression analysis revealed a significant association of MPV with depression and anxiety. After adjustment for covariates, only depression was associated with MPV. The area under the ROC curve of MPV for GAD-7 determined anxiety and BDI determined depression was 0.63. Our study showed that among the CBC hematological parameters, the MPV might be a useful biomarker of depression and anxiety in patients with autoimmune disorders. Further investigations of platelet parameters in controlled prospective studies are warranted to confirm our preliminary results.

Small ionic radii limit time step in Martini 3 molecular dynamics simulations.

Among other improvements, the Martini 3 coarse-grained force field provides a more accurate description of the solvation of protein pockets and channels through the consistent use of various bead types and sizes. Here, we show that the representation of Na+ and Cl- ions as "tiny" (TQ5) beads limits the accessible time step to 25 fs. By contrast, with Martini 2, time steps of 30-40 fs were possible for lipid bilayer systems without proteins. This limitation is relevant for systems that require long equilibration times. We derive a quantitative kinetic model of time-integration instabilities in molecular dynamics (MD) as a function of the time step, ion concentration and mass, system size, and simulation time. We demonstrate that ion-water interactions are the main source of instability at physiological conditions, followed closely by ion-ion interactions. We show that increasing the ionic masses makes it possible to use time steps up to 40 fs with minimal impact on static equilibrium properties and dynamical quantities, such as lipid and solvent diffusion coefficients. Increasing the size of the bead representing the ions (and thus changing their hydration) also permits longer time steps. For a soluble protein, we find that increasing the mass of tiny beads also on the protein permits simulations with 30-fs time steps. The use of larger time steps in Martini 3 results in a more efficient exploration of configuration space. The kinetic model of MD simulation crashes can be used to determine the maximum allowed time step upfront for an efficient use of resources and whenever sampling efficiency is critical.

The Two Faces of the Liquid Ordered Phase.

Coexisting liquid ordered (Lo) and liquid disordered (Ld) lipid phases in synthetic and plasma membrane-derived vesicles are commonly used to model the heterogeneity of biological membranes, including their putative ordered rafts. However, raft-associated proteins exclusively partition to the Ld and not the Lo phase in these model systems. We believe that the difference stems from the different microscopic structures of the lipid rafts at physiological temperature and the Lo phase studied at room temperature. To probe this structural diversity across temperatures, we performed atomistic molecular dynamics simulations, differential scanning calorimetry, and fluorescence spectroscopy on Lo phase membranes. Our results suggest that raft-associated proteins are excluded from the Lo phase at room temperature due to the presence of a stiff, hexagonally packed lipid structure. This structure melts upon heating, which could lead to the preferential solvation of proteins by order-preferring lipids. This structural transition is manifested as a subtle crossover in membrane properties; yet, both temperature regimes still fulfill the definition of the Lo phase. We postulate that in the compositionally complex plasma membrane and in vesicles derived therefrom, both molecular structures can be present depending on the local lipid composition. These structural differences must be taken into account when using synthetic or plasma membrane-derived vesicles as a model for cellular membrane heterogeneity below the physiological temperature.

Nonconverged Constraints Cause Artificial Temperature Gradients in Lipid Bilayer Simulations.

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.