Abstract Antibiotic resistant pathogens are a modern threat to the human health. As worldwide spreading problem, there is an urgency for new strategies minimize antibiotic resistance, particularly super‐resistant strains. Here, efficient design of carbohydrate‐coated silica nanoparticles reported which specifically target Gram‐negative bacteria cells. The system functionalized with gluconamide moieties and demonstrates increased binding ability bacterial membrane, enabling controlled drug...

Lipid-A is the causative agent of Gram-negative sepsis and responsible for an increasingly high mortality rate among hospitalized patients. Compounds that bind can limit this inflammatory process. The cationic antimicrobial peptide polymyxin B (Pmx-B) one simplest molecules capable selectively binding to may serve as a model further development agents. bacteria resistance Pmx-B relies on upregulation number regulatory systems, which promote chemical modifications lipopolysaccharide (LPS)...

Curvature is an intrinsic feature of biological membranes underlying vital cellular processes such as endocytosis, membrane fusion–fission, trafficking, and remodeling. The continuous expansion the spatiotemporal scales accessible to computational simulations nowadays makes possible quasi-atomistic molecular dynamics these processes. In despite that, computation shapes curvatures associated with remains challenging. For this reason, effect curvature often neglected in analysis quantities...

The complex solution behavior of polymer brushes is key to control their properties, including for biomedical applications and catalysis. swelling poly(dimethyl aminoethyl methacrylate) (PDMAEMA) poly(2-(methacryloyloxy)ethyl trimethylammonium chloride) (PMETAC) in response changes pH, solvent, salt types has been investigated using atomistic molecular dynamics simulations. PDMAEMA PMETAC have selected as canonical models weak strong polyelectrolytes whose conformational particularly...

Abstract Lipid droplets (LDs) are cellular organelles regulating energy and lipid metabolism. Generated in the endoplasmic reticulum (ER) by phase separation of neutral lipids (e.g., triglycerides), nascent LDs resemble lens-shaped blisters, grow into spherical droplets, eventually emerge from ER membrane, generally towards cytosol – a process known as budding. Images both mature available, but mechanism biogenesis has never been observed experimentally. Here we identify initial steps LD...

The surface assessment via grid evaluation (SuAVE) software was developed to account for the effect of curvature in calculations structural properties chemical interfaces regardless composition, asymmetry, and level atom coarseness. It employs differential geometry techniques, enabling representation surfaces as fully differentiable. In this article, we present novel developments SuAVE treat closed complex cavity shapes. These expand repertoire curvature-dependent analyses already available...

Recent developments of GROMACS v.2016 ceased to support methodological approaches used in the development and validation GROMOS force field.We investigated performance a previously developed extension field for lipopolysaccharides reproduce structural dynamics bacterial outer membrane (OM) using single cutoff nonbonded interactions atom-based charge truncation.We further compared this setup use with reaction (RF) or particle mesh Ewald (PME) approximations presence simple point (SPC)...

Molecular dynamics (MD) simulations represent an essential tool in the toolbox of modern chemistry, enabling prediction experimental observables for a variety chemical systems and processes majorly impacting study biological membranes. However, diversity complex lipids beyond phospholipids brings new challenges to well-established protocols used MD soft matter requires continuous assessment ensure simulation reproducibility minimize unphysical behavior. Lipopolysaccharides (LPS) are highly...

Lipid-A was previously shown to spontaneously aggregate into a vesicle via the hybrid particle field approach. We assess validity of proposed vesiculation mechanism by simulating resulting lipid-A at atom level. The spatial confinement imposed geometry on conformation and packing induces significant heterogeneity physical properties in inner outer leaflets. It also tighter molecular lower acyl chain order compared lamellar arrangement. Around 5% water molecules passively permeates membrane...

Rotational Profiler provides an analytical algorithm to compute sets of classical torsional dihedral parameters by fitting empirical energy profile a reference one that can be obtained experimentally or quantum-mechanical methods. The resulting profiles are compatible with the functional forms in most widely used biomolecular force fields (e.g., GROMOS, AMBER, OPLS, and CHARMM). linear least-squares regression method is generate best satisfy fitting. free use, analytical, field/package...

In article number 1904216, Mateus Borba Cardoso and co-workers demonstrate that nanoparticles fuctionalized with gluconamide moieties present selective targeting ability to Gram-negative bacteria membranes no significant toxicity mammalian or red blood cells. addition, functionality also provides tunable antibiotic delivery abilities, high stability in complex biological media, lack of non-specific protein adhesion.

Lipid-A can exhibit antagonist/agonist immunomodulatory properties depending on its chemical compostion. Computational simulations provide insights into the role of Al³⁺ and Na⁺ cations physical lipid-A aggregates, guidance in development vaccine adjuvants capable boosting immune system with decreased reactogenicity.

A análise de dados é um passo indispensável na engenharia modelos preditivos para sistema estudado. O sucesso do modelo depende diretamente quão precisas e, preferência, eficientes são as análises medição propriedades interesse. programa SuAVE (Surface Assessment Via grid Evaluation) baseado em Fortran desenvolvido analisar geométricas das superfícies tendo conta a morfologia estrutural dos sistemas. Para isso, esse conjunto rotinas numéricas processo montagem superfície estabelecido com...

O mosquito Aedes aegypti é o vetor primário responsável pela transmissão dos vírus zika, chikungunya, dengue e febre amarela.1 controle do uma tarefa árdua devido à sua grande adaptabilidade ambientes urbanos, alto comportamento antropofílico, além de outros fatores biológicos. Além disso, desenvolvimento vacinas contra todas as arboviroses seus múltiplos sorotipos tem um custo elevado requer longo período testes em pacientes.2 Portanto, a alternativa mais eficaz para inseto permanece sendo...

Escovas ou polímeros moleculares são formados por densos arranjos de cadeias poliméricas fixadas em uma superfície através das extremidades. O denso empacotamento resulta repulsão eletrostática e impedimento estérico entre vizinhas, fazendo com que as mesmas adotem conformação distendida quando solvente compatível. (BARBEY et al., 2009; KRISHNAMOORTHY 2014). A ligação covalente grupos funcionais na substrato perda entropia dos constituintes escovas comparativamente ao mesmo polímero livre...

A análise de dados é um passo indispensável na engenharia modelos preditivos para sistema estudado. O sucesso do modelo depende diretamente quão precisas e, preferência, eficientes são as análises medição propriedades interesse. programa SuAVE (Surface Assessment Via grid Evaluation) baseado em Fortran desenvolvido analisar geométricas das superfícies tendo conta a morfologia estrutural dos sistemas. Para isso, esse conjunto rotinas numéricas processo montagem superfície estabelecido com...

As escovas poliméricas constituem uma classe de polímeros covalentemente ligados à superfície por das extremidades da cadeia polimérica, seja em estado solvatado onde o polímero forma camada e solvente, ou fundido as cadeias ocupam inteiramente a adesão.1 Em regimes alta densidade poliméricas, repulsão estérica leva ao estiramento cadeia, conformação do tipo escova é adotada. sistemas baixa densidade, podem adotar inúmeros arranjos, e.g. cogumelo, panqueca, etc. Além disso, comportamento...

O primeiro conjunto de parâmetros atômicos para lipopolissacarídeos (LPS) foram desenvolvidos e validados [1,2] através simulações atomísticas membranas externas bacterianas;[3,4] porinas imersa nestas matrizes.[5,6]. Avanços na área caracterização experimental estruturas carboidratos tornaram necessário o refinamento re-parametrização um novo LPS compatíveis com os novos resultados experimentais. Com este intuito, específicos compatível campo força AMBER foi desenvolvido reproduzir...

Simulações computacionais, seja ao nível da representação atomístico ou coarse-grain têm contribuído singularmente para a caracterização estrutura e dinâmica de membranas lipídicas. (KHALILI-ARAGHI et al., 2009). O método computacional molecular (MD) oferece uma aproximação particularmente conveniente o estudo estrutural por abranger simultaneamente escalas temporal espacial, com precisão dificilmente acessível técnicas experimentais resolução atômica. Presentemente, sucesso (assim as...