Structure of spheroidal HDL particles revealed by combined atomistic and coarse-grained simulations

Spheroidal high-density lipoprotein (HDL) particles circulating in the blood are formed through an enzymatic process activated by apoA-I, leading to the esterification of cholesterol, which creates a hydrophobic core of cholesteryl ester molecules in the middle of the discoidal phospholipid bilayer. In this study, we investigated the conformation of apoA-I in model spheroidal HDL (ms-HDL) particles using both atomistic and coarse-grained molecular dynamics simulations, which are found to provide consistent results for all HDL properties we studied. The observed small contribution of cholesteryl oleate molecules to the solvent-accessible surface area of the entire ms-HDL particle indicates that palmitoyloleoylphosphatidylcholines and apoA-I molecules cover the hydrophobic core comprised of cholesteryl esters particularly well. The ms-HDL particles are found to form a prolate ellipsoidal shape, with sizes consistent with experimental results. Large rigid domains and low mobility of the protein are seen in all the simulations. Additionally, the average number of contacts of cholesteryl ester molecules with apoA-I residues indicates that cholesteryl esters interact with protein residues mainly through their cholesterol moiety. We propose that the interaction of annular cholesteryl oleate molecules contributes to apoA-I rigidity stabilizing and regulating the structure and function of the ms-HDL particle.     

Fast-growing trees for cogongrass (Imperata cylindrica) suppression and enhanced colonization of understory plant species on a phosphate-mine clay settling area

Native plants rarely occur in cogongrass (Imperata cylindrica) dominated phosphate-mine clay settling areas (CSA) in central Florida. This is primarily due to the allelopathic nature and strong competitiveness of cogongrass and frequent fires in these grasslands. This study examined the performance of fast-growing 2.5-year-old cottonwood (Populus deltoides) and 2–3.5-year-old eucalypts (Eucalyptus grandis and Eucalyptus amplifolia) in suppressing cogongrass in an old CSA near Lakeland, Florida. Understory vegetation was studied in two-row cottonwood and one-row, two-row, and four-row E. grandis cultures in the commercial planting and a clone-configuration-fertilizer study (SRWC-90). Cogongrass was still dominant in two-row cottonwood and the first four treatments of study SRWC-90. A total of 57 herbs and 26 shrubs, mostly native, were present in the understory. More herbs and shrubs occurred in the commercial planting than in the cogongrass-dominated study SRWC-90. Stand age and proximity to natural areas positively affected species recruitment. Cogongrass importance value index (IVI) decreased with increasing stand density, cottonwood basal area in the commercial planting and with both E. grandis and E. amplifolia basal area in study SRWC-90. Fast-growing trees with good survival on intensively prepared CSAs produce early and permanent canopy closure and appear to suppress cogongrass.     

Apparent survival,territory turnover and site fidelity rates in Northern Goshawk Accipiter gentilis populations close to the northern range limit

Capsule: Mark–recapture data suggest low apparent survival and sex- and population-specific site fidelity and territory turnover in adult Northern Goshawks Accipiter gentilis breeding in northern Europe.

Aims: To understand how species cope with global environmental change requires knowledge of variation in population demographic rates, especially from populations close to the species’ northern range limit and from keystone species such as raptors. We analyse apparent survival and breeding dispersal propensity of adult Northern Goshawks breeding in northern Europe.

Methods: We used long-term mark–recapture data from two populations in Finland, northern Europe, and Cormack–Jolly–Seber models and binomial generalized linear models to investigate sex- and population-specific variation in apparent survival, territory turnover and site fidelity.

Results: We report low apparent survival (53–72%) of breeding adult Goshawks. Breeding dispersal propensity was higher in females than males, especially in northern Finland, contrasting with previous studies that suggest high site fidelity in both sexes.

Conclusion: Low apparent survival in females may be mainly due to permanent emigration outside the study areas, whereas in males the survival rate may truly be low. Both demographic aspects may be driven by the combination of sex-specific roles related to breeding and difficult environmental conditions prevailing in northern latitudes during the non-breeding season.     

Bayesian inference of ancestral recombination graphs

We present a novel algorithm, implemented in the software ARGinfer, for probabilistic inference of the Ancestral Recombination Graph under the Coalescent with Recombination. Our Markov Chain Monte Carlo algorithm takes advantage of the Succinct Tree Sequence data structure that has allowed great advances in simulation and point estimation, but not yet probabilistic inference. Unlike previous methods, which employ the Sequentially Markov Coalescent approximation, ARGinfer uses the Coalescent with Recombination, allowing more accurate inference of key evolutionary parameters. We show using simulations that ARGinfer can accurately estimate many properties of the evolutionary history of the sample, including the topology and branch lengths of the genealogical tree at each sequence site, and the times and locations of mutation and recombination events. ARGinfer approximates posterior probability distributions for these and other quantities, providing interpretable assessments of uncertainty that we show to be well calibrated. ARGinfer is currently limited to tens of DNA sequences of several hundreds of kilobases, but has scope for further computational improvements to increase its applicability.     

A mathematically defined motif for the radial distribution of charged residues on apolipoprotein amphipathic alpha helixes.

Multiple amphipathic alpha-helical candidate domains have been identified in exchangeable apolipoproteins by sequence analysis and indirect experimental evidence. The distribution of charged residues can differ within and between these apolipoproteins. Segrest et al. (Segrest, J. P., H. DeLoof, J. G. Dohlman, C. G. Brouillette, and G. M. Anantharamaiah. 1990. Proteins. 8:103-117.) argued that these differences are correlated with lipid affinity. A mathematically defined motif for the particular charge distribution associated with high lipid affinity (class A) is proposed. Primary sequence data from protein segments proposed previously to have an amphipathic alpha-helical structure are scanned. Counting formulas are presented for determining the conditional probability that the match between an observed charge distribution and the proposed motif would occur by chance. Because the preselected helical segments are short (the modal length is 22) and the motif definition imposes multiple constraints on the acceptable distributions, the computer-based algorithm is quite feasible computationally. 19 of the 20 segments previously assigned to class A match the motif sufficiently well (the remaining one is borderline), while very few others "erroneously" pass the screening test. These results confirm the original assignments of the candidate domains and, thus, support the hypothesis that there is a distinguishable subset of helixes having high lipid affinity. This counting approach is applicable to a growing subset of protein sequence analysis problems in which the segment lengths are short and the motif is complex.     

Properties of lipid complexes with amphipathic helix-forming peptides. Role of distribution of peptide charges

The peptides [Glu1,8,Leu11,17] 18A and [Glu4,9,Leu11,17] reverse-18A are 18-residue peptides designed to form amphipathic helices with opposite charge distribution; [Glu1,8,Leu11,17] 18A having positively charged residues at the hydrophobic/hydrophilic interface. Both [Glu1,8,Leu11,17] 18A and [Glu4,9,Leu11,17] reverse-18A strongly disrupt the bilayer structure as indicated by the relatively narrow lipid 1H and 31P NMR peaks. In addition, the 1H chemical shift of the quaternary ammonium methyl groups indicates that [Glu1,8,Leu11,17] 18A forms smaller lipoprotein particles with dimyristoylphosphatidylcholine (DMPC) than does [Glu4,9,Leu11,17] reverse-18A. However, motional properties of the lipid head group indicate that no specific salt bridges are formed between the phospholipid head group and the side chains of polar amino acids of either of the two peptides. In addition, the acyl chain conformation for the DMPC complexes with [Glu1,8,Leu11,17] 18A and with [Glu4,9,Leu11,17] reverse-18A are indistinguishable by the criterion of IR spectroscopy. The 2H linewidth of the solvent 2H2O remains narrower in frozen solutions of the DMPC-[Glu1,8,Leu11,17] 18A complexes suggesting the presence of more unfrozen bound water in this case. The two peptides exhibit many similarities in their interaction with lipids. However, [Glu1,8,Leu11,17] 18A can more readily lyse vesicles and activate lecithin:cholesterol acyltransferase. These differences do not appear to result from differences in specific charge interactions between the lipid and peptide but may be manifested through differences in hydration properties.     

Interactions of serum proteins with small unilamellar liposomes composed of dioleoylphosphatidylethanolamine and oleic acid: high-density lipoprotein, apolipoprotein A1, and amphipathic peptides stabilize liposomes

Small unilamellar liposomes composed to dioleoylphosphatidylethanolamine (DOPE) and oleic acid (OA) are stabilized by incubation with normal human serum or plasma [Liu, D., & Huang, L. (1989) Biochemistry 28, 7700-7707]. The present report describes a systematic study of interactions of purified serum proteins and lipoproteins with these liposomes. Albumin destabilized liposomes by extracting OA from the liposomes, whereas immunoglobulins and lipoproteins (HDL, LDL, and VLDL) had no effect. However, HDL and, to some extent, VLDL showed a rapid stabilization activity against the lytic effect of albumin. HDL added together with or shortly after the addition of albumin completely abolished the liposome leakage and aggregation effects induced by albumin. SDS-PAGE analysis of the HDL-stabilized liposomes revealed that apolipoprotein A1 was associated with liposomes. Purified apolipoprotein A1, but not a lipid mixture resembling the lipid composition of HDL, showed comparable liposome stabilization activity as HDL. Furthermore, synthetic peptides resembling the amphipathic helices found in apolipoprotein A1 also showed strong liposome stabilization activity. Peptides which were able to form amphipathic helixes of a wedge shape were more effective stabilizers than those which could not. These data indicate that HDL plays a major role in human serum or plasma for the liposome stabilization activity. HDL exerts its activity probably by the interactions of the amphipathic helices of apolipoprotein A1 with the hydrophobic voids found on the outer surface of the highly curved, small liposomes.     

The amphipathic helix in the exchangeable apolipoproteins: a review of secondary structure and function.

Site-directed mutagenesis and other molecular biology-based techniques are now available for probing the amphipathic alpha helix structural motif in the exchangeable apolipoproteins. Here we survey the published literature on lipid-binding and functional domains in apolipoproteins A-I, A-II, A-IV, C-I, C-II, C-III, and E and compare these results with recently developed computer methods for analysis of the location and properties of amphipathic helixes. This comparison suggests that there are at least three distinct classes of amphipathic helixes (classes A, Y, and G*) in the exchangeable apolipoproteins whose distribution varies within and between the seven apolipoproteins. This comparison further suggests that lipid affinity resides largely in class A amphipathic helixes (Segrest, J. P., et al. 1990. Proteins. 8: 103) and that variations in structure and/or numbers of class A domains in individual apolipoproteins allow a range of lipid affinities from high to low. The positions of the four alpha helixes recently shown to form a 4-helix bundle globular structure in apoE (Wilson, C., et al. 1991. Science. 252: 1817) correspond closely to the four amino-terminal class G* amphipathic helixes of apoE identified by our computer analysis. It is of particular interest, therefore, that all of the exchangeable apolipoproteins except apoA-II and C-I, contain amphipathic helixes of class G*. Additional implications of amphipathic helix heterogeneity for the structure and function of the exchangeable apolipoproteins will be discussed.     

The mechanism of lipid-binding by plasma lipoproteins

In this article, we review the current state of knowledge about the structure of human plasma high density lipoproteins. Recent advances in this field, including amino acid sequencing and lipid-binding studies, suggest that the plasma lipoproteins have specific sites with special structural features that account for their ability to bind and transport lipid. A hypothesis which describes the structure of these lipid-binding sites and their interaction with lipid is presented.