Diphenylhexatriene membrane probes DPH and TMA-DPH: A comparative molecular dynamics simulation study

Fluorescence spectroscopy andmicroscopy have been utilized as tools in membrane biophysics for decades now. Because phospholipids are non-fluorescent, the use of extrinsic membrane probes in this context is commonplace. Among the latter, 1,6-diphenylhexatriene (DPH) and its trimethylammonium derivative (TMA-DPH) have been extensively used. It is widely believed that, owing to its additional charged group, TMA-DPH is anchored at the lipid/water interface and reports on a bilayer region that is distinct from that of the hydrophobic DPH. In this study, we employ atomistic MD simulations to characterize the behavior of DPH and TMA-DPH in 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) and POPC/cholesterol (4:1) bilayers. We show that although the dynamics of TMA-DPH in thesemembranes is noticeably more hindered than that of DPH, the location of the average fluorophore of TMA-DPH is only ~3–4 Å more shallow than that of DPH. The hindrance observed in the translational and rotational motions of TMA-DPH compared to DPH is mainly not due to significant differences in depth, but to the favorable electrostatic interactions of the former with electronegative lipid atoms instead. By revealing detailed insights on the behavior of these two probes, our results are useful both in the interpretation of past work and in the planning of future experiments using themasmembrane reporters.

Diphenylhexatriene membrane probes DPH and TMA-DPH: A comparative molecular dynamics simulation study

Fluorescence spectroscopy andmicroscopy have been utilized as tools in membrane biophysics for decades now. Because phospholipids are non-fluorescent, the use of extrinsic membrane probes in this context is commonplace. Among the latter, 1,6-diphenylhexatriene (DPH) and its trimethylammonium derivative (TMA-DPH) have been extensively used. It is widely believed that, owing to its additional charged group, TMA-DPH is anchored at the lipid/water interface and reports on a bilayer region that is distinct from that of the hydrophobic DPH. In this study, we employ atomistic MD simulations to characterize the behavior of DPH and TMA-DPH in 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) and POPC/cholesterol (4:1) bilayers. We show that although the dynamics of TMA-DPH in thesemembranes is noticeably more hindered than that of DPH, the location of the average fluorophore of TMA-DPH is only ~3–4 Å more shallow than that of DPH. The hindrance observed in the translational and rotational motions of TMA-DPH compared to DPH is mainly not due to significant differences in depth, but to the favorable electrostatic interactions of the former with electronegative lipid atoms instead. By revealing detailed insights on the behavior of these two probes, our results are useful both in the interpretation of past work and in the planning of future experiments using themasmembrane reporters.

O comprimento descritivo mínimo na amostragem por transectos lineares

Apresenta·se um breve resumo histórico da evolução da amostragem por transectos lineares e desenvolve·se a sua teoria. Descrevemos a teoria de amostragem por transectos lineares, proposta por Buckland (1992), sendo apresentados os pontos mais relevantes, no que diz respeito à modelação da função de detecção. Apresentamos uma descrição do princípio CDM (Rissanen, 1978) e a sua aplicação à estimação de uma função densidade por um histograma (Kontkanen e Myllymãki, 2006), procedendo à aplicação de um exemplo prático, recorrendo a uma mistura de densidades. Procedemos à sua aplicação ao cálculo do estimador da probabilidade de detecção, no caso dos transectos lineares e desta forma estimar a densidade populacional de animais. Analisamos dois casos práticos, clássicos na amostragem por distâncias, comparando os resultados obtidos. De forma a avaliar a metodologia, simulámos vários conjuntos de observações, tendo como base o exemplo das estacas, recorrendo às funções de detecção semi-normal, taxa de risco, exponencial e uniforme com um cosseno. Os resultados foram obtidos com o programa DISTANCE (Thomas et al., in press) e um algoritmo escrito em linguagem C, cedido pelo Professor Doutor Petri Kontkanen (Departamento de Ciências da Computação, Universidade de Helsínquia). Foram desenvolvidos programas de forma a calcular intervalos de confiança recorrendo à técnica bootstrap (Efron, 1978). São discutidos os resultados finais e apresentadas sugestões de desenvolvimentos futuros. ABSTRACT; We present a brief historical note on the evolution of line transect sampling and its theoretical developments. We describe line transect sampling theory as proposed by Buckland (1992), and present the most relevant issues about modeling the detection function. We present a description of the CDM principle (Rissanen, 1978) and its application to histogram density estimation (Kontkanen and Myllymãki, 2006), with a practical example, using a mixture of densities. We proceed with the application and estimate probability of detection and animal population density in the context of line transect sampling. Two classical examples from the literature are analyzed and compared. ln order to evaluate the proposed methodology, we carry out a simulation study based on a wooden stakes example, and using as detection functions half normal, hazard rate, exponential and uniform with a cosine term. The results were obtained using program DISTANCE (Thomas et al., in press), and an algorithm written in C language, kindly offered by Professor Petri Kontkanen (Department of Computer Science, University of Helsinki). We develop some programs in order to estimate confidence intervals using the bootstrap technique (Efron, 1978). Finally, the results are presented and discussed with suggestions for future developments.