SuAVE: A Tool for Analyzing Curvature-Dependent Properties in Chemical Interfaces

Abstract

Curvature is an intrinsic feature of biological membranes underlying vital cellular processes such as endocytosis, membrane fusion–fission, trafficking, and remodeling. The continuous expansion of the spatiotemporal scales accessible to computational simulations nowadays makes possible quasi-atomistic molecular dynamics simulations of these processes. In despite of that, computation of the shapes and curvatures associated with the dynamics of biological membranes remains challenging. For this reason, the effect of curvature is often neglected in the analysis of quantities essential for the accurate description of membrane properties (e.g., area and volume per lipid, density profiles, membrane thickness). We propose an algorithm for surface assessment via grid evaluation (SuAVE) that relies on the application of a radial base function to interpolate points scattered across an interface of any shape. This enables the representation of the chemical interface as fully differentiable so that related geometrical properties can be calculated through the straightforward employment of well-established differential geometry techniques. Hence, the effect of different types or degrees of curvature can be accurately taken into account in the calculations of structural properties of any interfaces regardless of chemical composition, asymmetry, and level of atom coarseness. The main functionalities implemented in SuAVE are featured for a number of tetraacylated and hexaacylated Lipid-A membranes of distinct curvatures and a surfactant micelle. We show that the properties calculated for moderately to highly curved membranes differ significantly between curvature-dependent and -independent algorithms. The SuAVE software is freely available from .

Impact of increased membrane realism on conformational sampling of proteins

“…Pure membrane simulations were analyzed for bulk physical properties using two software: Membrainy and SuAVE. 81,82 The following physical properties were calculated using these software: area-per-lipid (APL), entropy, gel fluidity, membrane thickness, membrane curvature order parameter, membrane curvature angle, lipid S CD order parameters, headgroup axial tilt angle, and headgroup lateral tilt angle. Electron density calculations were performed using the CPPTRAJ module found in AMBER.…”

“…Membrane curvature calculations lastly show that regardless of size, all Maximum Complexity membranes demonstrate the same curvature distribution, peaking at a curvature angle of 18º (indicative of a planar surface). 82 Meanwhile, the Top10 membrane construct differs, where the lower leaflet is slightly more planar and the upper leaflet more curved (Figure 4). Headgroup-specific properties measured include acyl chain order parameters, headgroup orientation, and electron density.…”

Estudo teórico da interação entre líquido iônico e bicamadas fosfolipídicas

“…A medida de APL portanto, pode ser corrigida a partir da superfície ajustada a cada monocamada -figura 25; procedimento aplicado através do software SuAVE (Surface Assessment Via grid Evaluation) [71]. A criação destas superfícies é feita a partir do ajuste numérico em uma rede, construída com base em átomos de referência da região de interface.…”

“…A precisão do ajuste é verificada pelo desvio quadrático médio entre a posição dos átomos de referência e a superfície ajustada, sendo menor quanto mais próximos, e portanto melhor ajustado. Os detalhes de implementação do software SuAVE são expostos na referência [71].…”

“…As figuras originais e reproduzidas deste trabalho foram geradas e editadas pelos softwares abertos VMD [77] e Inkscape [78]. Os gráficos e análises numéricas independentes do software de dinâmica molecular GROMACS foram realizados com auxílio da linguagem Python [79] e o software SuAVE [71].…”