Molecular dynamics simulations of mixed DOPC–β-sitosterol bilayers and their interactions with DMSO

ell membrane phospholipid bilayers can be damaged by the large amounts of dimethyl sulphoxide (DMSO) commonly used in cryopreservation. The interaction of DMSO with model bilayers consisting of 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) and ß-sitosterol has been studied using molecular dynamics simulations. Initially the effect of sterol concentration and temperature upon bilayers solvated in pure water was determined, and membranes containing ß-sitosterol were compared with membranes containing cholesterol. These simulations showed that the presence of sterols has a condensing effect on the phospholipids, causing a reduction in the area per lipid as the sterol concentration increases, up to a phospholipid–sterol ratio of 2[thin space (1/6-em)]:[thin space (1/6-em)]1. The incorporation of sterols into the bilayer also increased the thickness and order of the phospholipid acyl tails. DOPC–ß-sitosterol bilayers at different relative concentrations were simulated in solutions of 2.5 and 25.0 mol% DMSO. The interaction of DMSO with the bilayers caused the bilayers to expand laterally, while thinning normal to the plane of the bilayer expansion. The same qualitative behaviour has been shown to occur in pure phosphocholine bilayers. However, the presence of sterols made the membranes more resistant to the effects of DMSO, to the extent that the membranes where able to maintain their integrity in 25.0 mol% DMSO, a concentration that would otherwise cause the destruction of a pure DOPC bilayer. Increasing the concentration of ß-sitosterol within the bilayers reduced the rate of DMSO diffusion across the bilayer and, if the concentration was large enough, caused the diffusion mechanism to change. DMSO was observed to disorder the membranes enough to cause an increase in the number of sterol “flip–flops”. The findings of this work provide a more realistic description of how DMSO interacts with cell membranes and the role of the composition of the membrane

What determines sub-diffusive behavior in crowded protein solutions?

This work used the ARCHER UK National Supercomputing Service (http://www.archer.ac.uk), access to which was provided by the UK High-End Computing Consortium for Biomolecular Simulation, HECBioSim (https://www.hecbiosim.ac.uk/), supported by EPSRC (grant no. EP/R029407/1). Analysis and visualization of the simulation data were conducted at the Pawsey Supercomputing Centre, therefore this work was supported by resources provided by the Pawsey Supercomputing Centre with funding from the Australian Government and the Government of Western Australia, as well as resources and services from the National Computational Infrastructure (NCI), which is supported by the Australian Government. V.K. gratefully acknowledges the receipt of a scholarship under the Aberdeen-Curtin Alliance collaborative PhD program.Peer reviewedPostprin

Definition Of The Minimal Contents For The Molecular Simulation Of The Yeast Cytoplasm

Funding VK gratefully acknowledges the receipt of a scholarship under the Aberdeen-Curtin Alliance collaborative Ph.D. program. Acknowledgments We thank Prof. Grant Brown (University of Toronto) for making the yeast proteomics datasets available to us.Peer reviewedPublisher PD

Identification and characterisation of putative drug binding sites in human ATP-binding cassette B5 (ABCB5) transporter

© 2020 The Author(s) The human ATP-binding cassette B5 (ABCB5) transporter, a member of the ABC transporter superfamily, is linked to chemoresistance in tumour cells by drug effluxion. However, little is known about its structure and drug-binding sites. In this study, we generated an atomistic model of the full-length human ABCB5 transporter with the highest quality using the X-ray crystal structure of mouse ABCB1 (Pgp1), a close homologue of ABCB5 and a well-studied member of the ABC family. Molecular dynamics simulations were used to validate the atomistic model of ABCB5 and characterise its structural properties in model cell membranes. Molecular docking simulations of known ABCB5 substrates such as taxanes, anthracyclines, camptothecin and etoposide were then used to identify at least three putative binding sites for chemotherapeutic drugs transported by ABCB5. The location of these three binding sites is predicted to overlap with the corresponding binding sites in Pgp1. These findings will serve as the basis for future in vitro studies to validate the nature of the identified substrate-binding sites in the full-length ABCB5 transporter

Biometry and plasmatic stress-related parameters in brill (Scophthalmus rhombus)cultured at different stocking densities.

The effects of the stocking density on the physiological stress and biometric features of the brill were studied. Fish (491&plusmn;20 g) were cultured at three different stocking densities: 1; 5 and 15 Kg m-2 (LSD, MSD and HSD) during 5 weeks. Survival and several biometric, feeding and plasmatic parameters were assessed. Although final weight and specific growth rate decreased in higher densities, there were not significant differences between MSD and HSD. Differences for survival rate, feed efficiency, conversion index and feed intake were not detected among treatments. The minimum HSI was found in the HSD treatment, and condition factor varied inversely regards to stocking density. Plasma cortisol and osmolality were directly related to stocking density though the former was not significantly different among treatments. Plasma lactate and glucose significantly increased while stocking density rose. Nevertheless, free fatty acids did not vary among treatments, and triglycerides only decreased in LSD. This work was supported by Interreg Project 0251_ECOAQUA_5_E, financed by the EDRF (European Regional Development Fund).www.juntadeandalucia.es/agriculturaypesca/ifapa/ecoaqua. &nbsp;Se estudiaron los efectos de la densidad de cultivo sobre el estr&eacute;s fisiol&oacute;gico y par&aacute;metros biom&eacute;tricos en el parracho. Los peces (491&plusmn;20 g) fueron cultivados a tres densidades diferentes: 1; 5 y 15 Kg m-2 (LSD, MSD y HSD) durante 5 semanas. El peso final y crecimiento decrecieron con la densidad, pero no hubo diferencias significativas entre MSD y HSD. No se detectaron diferencias significativas entre tratamientos para supervivencia, eficiencia alimentaria, &iacute;ndice de conversi&oacute;n y tasa de ingesti&oacute;n. El HIS m&iacute;nimo fue para la HSD y el factor de condici&oacute;n vari&oacute; inversamente a la densidad. La osmolalidad y el cortisol, glucosa y lactato plasm&aacute;ticos estuvieron directamente relacionados con la densidad. Sin embargo, los &aacute;cidos grasos libres no variaron entre tratamientos. Este trabajo fue apoyado por el proyecto Interreg 0251_ECOAQUA_5_E , financiado por el FEDER (Fondo Europeo de Desarrollo Regional).www.juntadeandalucia.es/agriculturaypesca/ifapa/ecoaqua.</p

FUS-DDIT3 Prevents the Development of Adipocytic Precursors in Liposarcoma by Repressing PPARγ and C/EBPα and Activating eIF4E

FUS-DDIT3 is a chimeric protein generated by the most common chromosomal translocation t(12;16)(q13;p11) linked to liposarcomas, which are characterized by the accumulation of early adipocytic precursors. Current studies indicate that FUS-DDIT3- liposarcoma develops from uncommitted progenitors. However, the precise mechanism whereby FUS-DDIT3 contributes to the differentiation arrest remains to be elucidated. METHODOLOGY/PRINCIPAL FINDINGS: Here we have characterized the adipocyte regulatory protein network in liposarcomas of FUS-DITT3 transgenic mice and showed that PPARgamma2 and C/EBPalpha expression was altered. Consistent with in vivo data, FUS-DDIT3 MEFs and human liposarcoma cell lines showed a similar downregulation of both PPARgamma2 and C/EBPalpha expression. Complementation studies with PPARgamma but not C/EBPalpha rescued the differentiation block in committed adipocytic precursors expressing FUS-DDIT3. Our results further show that FUS-DDIT3 interferes with the control of initiation of translation by upregulation of the eukaryotic translation initiation factors eIF2 and eIF4E both in FUS-DDIT3 mice and human liposarcomas cell lines, explaining the shift towards the truncated p30 isoform of C/EBPalpha in liposarcomas. Suppression of the FUS-DDIT3 transgene did rescue this adipocyte differentiation block. Moreover, eIF4E was also strongly upregulated in normal adipose tissue of FUS-DDIT3 transgenic mice, suggesting that overexpression of eIF4E may be a primary event in the initiation of liposarcomas. Reporter assays showed FUS-DDIT3 is involved in the upregulation of eIF4E in liposarcomas and that both domains of the fusion protein are required for affecting eIF4E expression. CONCLUSIONS/SIGNIFICANCE: Taken together, this study provides evidence of the molecular mechanisms involve in the disruption of normal adipocyte differentiation program in liposarcoma harbouring the chimeric gene FUS-DDIT3.Research in ISG group is supported partially by FEDER and by MEC (SAF2006-03726), Junta de Castilla y León (CSI03A05), FIS (PI050087, PI050116), Fundación de Investigación MMA, Federación de Cajas de Ahorro Castilla y León (I Convocatoria de Ayudas para Proyectos de Investigación Biosanitaria con Células Madre), CDTEAM project (CENIT-Ingenio 2010) and MEC Consolider-Ingenio 2010 (Ref. CSD2007-0017).Research in ISG group is supported partially by FEDER and by MEC (SAF2006-03726 and PETRI N° 95-0913.OP), Junta de Castilla y León (CSI03A05), FIS (PI050087, PI050116), Fundación de Investigación MMA, Federación de Cajas de Ahorro Castilla y León (I Convocatoria de Ayudas para Proyectos de Investigación Biosanitaria con Células Madre), CDTEAM project (CENIT-Ingenio 2010) and MEC Consolider-Ingenio 2010 (Ref. CSD2007-0017). MSM is supported by the Ramon y Cajal Scientific Spanish Program, Fondo Investigacion Sanitaria (FIS PI04-1271), Junta de Castilla y León (SA085A06) and Fundación Manuel Solorzano, University of Salamanca.Peer reviewe

Effect of hypobaric hypoxia on hematological parameters related to oxygen transport, blood volume and oxygen consumption in adolescent endurance-training athletes

Background/Objective:To analyze the effect of altitude on hematological and cardiorespiratory variables in adolescent athletes participating in aerobic disciplines. Methods:21 females and 89 males participated in the study. All were adolescent elite athletes engaged in endurance sports (skating, running and cycling) belonging to two groups: permanent residents in either low altitude (LA, 966 m) or moderate altitude (MA, 2640 m). Hematocrit (Hct), hemoglobin concentration ([Hb]), total hemoglobin mass (Hbt), blood, plasma and erythrocyte volumes (BV, PV and EV), VO2peak and other cardiorespiratory parameters were evaluated. Results:Sex differences were evident both in LA and HA skating practitioners, the males having higher significant values than the females in oxygen transport-related hematological parameters and VO2peak. The effect of altitude residence was also observed in Hct, [Hb], Hbt and EV with increased (14%–18%) values in the hematological parameters and higher EV (5%–24%). These results matched the significantly higher values of VO2peak measured in MA residents. However, BV and PV did not show differences between LA and MA residents in any case. Sports discipline influenced neither the hematological variables nor most of the cardiorespiratory parameters. Conclusions:LA and MA adolescent skaters showed sex differences in hematological variables. Endurance-trained male adolescent residents at MA had an increased erythropoietic response and a higher VO2peak compared to their counterparts residing and training at LA. These responses are similar in the three aerobic sports studied, indicating that the variables described are highly sensitive to hypoxia irrespective of the sports discipline