The interaction of small molecules, such as drugs or metabolites, with proteins and biomembranes is of fundamental importance for their bioavailability. The systematic characterization of the binding affinity for structurally related ligands may provide rules that allow its prediction for any other relevant molecule. In this work we have studied a homologous series of fluorescent fatty amines with the fluorescent moiety 7-nitrobenz-2-oxa-1,3-diazol-4-yl covalently bound to the amine group (NBD-C(n); n = 4, 6, 8, 10, 12, 14, and 16) in aqueous solution and associated with BSA or lipid bilayers. We have found a linear dependence with the length of the alkyl chain, up to NBD-C(10), for the Gibb's free energy of partition between the aqueous solution and 1-palmitoyl-2-oleoyl phosphatidylcholine bilayers equal to ΔΔG = -2.5 ± 0.3 kJ/mol per methylene group. Additionally, the amphiphiles interacted efficiently with bovine serum albumin, and it was inhibited by fatty acids indicating that binding occurs to the fatty acids highest affinity binding site. The association of the amphiphiles with BSA and POPC bilayers was performed at different temperatures (15-35 °C) allowing for the calculation of the enthalpic and entropic contributions. A value of ΔH = -15 ± 4 kJ/mol was obtained for all amphiphiles and binding agents. The entropy contribution was always positive and increased with the length of the alkyl chain. The location of the ligand in the biological membrane is also of high relevance, namely because this will determine its effect on biomembrane properties at high ligand concentrations. With this goal, we have measured some photophysical properties of the amphiphiles inserted in POPC bilayers, and we found no significant variation along the series, indicating that the NBD group is located in a region with similar properties regardless of the length of the nonpolar group. An exception was noted for the case of NBD-C(14) whose parameters were somewhat different from the trend observed.
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http://dx.doi.org/10.1021/jp105163k | DOI Listing |
J Chem Inf Model
January 2025
Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-62500 Brno, Czech Republic.
Understanding the molecular mechanisms of pore formation is crucial for elucidating fundamental biological processes and developing therapeutic strategies, such as the design of drug delivery systems and antimicrobial agents. Although experimental methods can provide valuable information, they often lack the temporal and spatial resolution necessary to fully capture the dynamic stages of pore formation. In this study, we present two novel collective variables (CVs) designed to characterize membrane pore behavior, particularly its energetics, through molecular dynamics (MD) simulations.
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January 2025
Data Science, Amity Institute of Integrative Sciences and Health, Amity University Haryana, Gurugram, India.
The ATP-binding cassette transporter superfamily plays a pivotal role in cellular detoxification and drug efflux. ATP-binding cassette subfamily G member 2 (ABCG2) referred to as the Breast cancer resistance protein has emerged as a key member involved in multidrug resistance displayed by cancer cells. Understanding the molecular basis of substrate and inhibitor recognition, and binding within the transmembrane domain of ABCG2 is crucial for the development of effective therapeutic strategies.
View Article and Find Full Text PDFJ Chem Inf Model
January 2025
CEITEC─Central European Institute of Technology, Masaryk University, Kamenice 753/5, 625 00 Brno, Czech Republic.
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.
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December 2024
REQUIMTE, LAQV, Instituto de Ciências Biomédicas de Abel Salazar, Universidade do Porto, Rua Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal.
In this study, we synthesized a series of 3-hydroxy-4-pyridinone (3,4-HPO) chelators with varying lipophilicity by modifying the length of their alkyl chains. To investigate their interaction with lipid membranes, we employed differential scanning calorimetry (DSC) and electron paramagnetic resonance (EPR) spectroscopy using dimyristoylphosphatidylcholine (DMPC) and palmitoyloleoylphosphatidylcholine (POPC) liposomes as membrane model systems. DSC experiments on DMPC liposomes revealed that hexyl-substituted chelators significantly altered the thermotropic phase behavior of the lipid bilayer, indicating their potential as membrane property modulators.
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December 2024
Coimbra Chemistry Center, Institute of Molecular Sciences (CQC-IMS), University of Coimbra, 3004-535 Coimbra, Portugal.
The membrane dipole potential that arises from the interfacial water and constitutive dipolar groups of lipid molecules modulates the interaction of amphiphiles and proteins with membranes. Consequently, its determination for lipid mixtures resembling the existing diversity in biological membranes is very relevant. In this work, the dipole potentials of monolayers, formed at the air-water interface, from pure or mixed lipids (1-palmitoyl-2-oleoyl--glycero-3-phosphocholine (POPC), 1-palmitoyl-2-oleoyl--glycero-3-phosphoethanolamine (POPE), 1-palmitoyl-2-oleoyl--glycero-3-phosphatidyserine (POPS), sphingomyelin (SpM) and cholesterol) were measured and correlated with the mean area per lipid.
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