Molecular etiology of a dominant form of type III hyperlipoproteinemia caused by R142C substitution in apoE4

We have used adenovirus-mediated gene transfer in apolipoprotein (apo)E^−/− mice to elucidate the molecular etiology of a dominant form of type III hyperlipoproteinemia (HLP) caused by the R142C substitution in apoE4. It was found that low doses of adenovirus expressing apoE4 cleared cholesterol, whereas comparable doses of apoE4[R142C] greatly increased plasma cholesterol, triglyceride, and apoE levels, caused accumulation of apoE in VLDL/IDL/LDL region, and promoted the formation of discoidal HDL. Co-expression of apoE4[R142C] with lecithin cholesterol acyltransferase (LCAT) or lipoprotein lipase (LPL) in apoE^−/− mice partially corrected the apoE4[R142C]-induced dyslipidemia. High doses of C-terminally truncated apoE4[R142C]-202 partially cleared cholesterol in apoE^−/− mice and promoted formation of discoidal HDL. The findings establish that apoE4[R142C] causes accumulation of apoE in VLDL/IDL/LDL region and affects in vivo the activity of LCAT and LPL, the maturation of HDL, and the clearance of triglyceride-rich lipoproteins. The prevention of apoE4[R142C]-induced dyslipidemia by deletion of the 203-299 residues suggests that, in the full-length protein, the R142C substitution may have altered the conformation of apoE bound to VLDL/IDL/LDL in ways that prevent triglyceride hydrolysis, cholesterol esterification, and receptor-mediated clearance in vivo.     

Threading a database of protein cores

We present an analysis of 10 blind predictions prepared for a recent conference, “Critical Assessment of Techniques for Protein Structure Prediction.”¹ The sequences of these proteins are not detectably similar to those of any protein in the structure database then available, but we attempted, by a threading method, to recognize similarity to known domain folds. Four of the 10 proteins, as we subsequently learned, do indeed show significant similarity to then-known structures. For 2 of these proteins the predictions were accurate, in the sense that a similar structure was at or near the top of the list of threading scores, and the threading alignment agreed well with the corresponding structural alignment. For the best predicted model mean alignment error relative to the optimal structural alignment was 2.7 residues, arising entirely from small “register shifts” of strands or helices. In the analysis we attempt to identify factors responsible for these successes and failures. Since our threading method does not use gap penalties, we may readily distinguish between errors arising from our prior definition of the “cores” of known structures and errors arising from inherent limitations in the threading potential. It would appear from the results that successful substructure recognition depends most critically on accurate definition of the “fold” of a database protein. This definition must correctly delineate substructures that are, and are not, likely to be conserved during protein evolution. © 1995 Wiley-Liss, Inc.     

Protein structure prediction by threading methods: Evaluation of current techniques

This paper evaluates the results of a protein structure prediction contest. The predictions were made using threading procedures, which employ techniques for aligning sequences with 3D structures to select the correct fold of a given sequence from a set of alternatives. Nine different teams submitted 86 predictions, on a total of 21 target proteins with little or no sequence homology to proteins of known structure. The 3D structures of these proteins were newly determined by experimental methods, but not yet published or otherwise available to the predictors. The predictions, made from the amino acid sequence alone, thus represent a genuine test of the current performance of threading methods. Only a subset of all the predictions is evaluated here. It corresponds to the 44 predictions submitted for the 11 target proteins seen to adopt known folds. The predictions for the remaining 10 proteins were not analyzed, although weak similarities with known folds may also exist in these proteins. We find that threading methods are capable of identifying the correct fold in many cases, but not reliably enough as yet. Every team predicts correctly a different set of targets, with virtually all targets predicted correctly by at least one team. Also, common folds such as TIM barrels are recognized more readily than folds with only a few known examples. However, quite surprisingly, the quality of the sequence-structure alignments, corresponding to correctly recognized folds, is generally very poor, as judged by comparison with the corresponding 3D structure alignments. Thus, threading can presently not be relied upon to derive a detailed 3D model from the amino acid sequence. This raises a very intriguing question: how is fold recognition achieved? Our analysis suggests that it may be achieved because threading procedures maximize hydrophobic interactions in the protein core, and are reasonably good at recognizing local secondary structure. © 1995 Wiley-Liss, Inc.     

Protein acyl thioesterases (Review)

Many proteins are S-acylated, affecting their localization and function. Dynamic S-acylation in response to various stimuli has been seen for several proteins in vivo. The regulation of S-acylation is beginning to be elucidated. Proteins can autoacylate or be S-acylated by protein acyl transferases (PATs). Deacylation, on the other hand, is an enzymatic process catalyzed by protein thioesterases (APT1 and PPT1) but only APT1 appears to be involved in the regulation of the reversible S-acylation of cytoplasmic proteins seen in vivo. PPT1, on the other hand, is involved in the lysosomal degradation of S-acylated proteins and PPT1 deficiency causes the disease infant neuronal ceroid lipofuscinosis.     

Assays of plasma dehydrocholesteryl esters and oxysterols from Smith-Lemli-Opitz syndrome patients

Smith-Lemli-Opitz syndrome (SLOS) is caused by mutations in the gene encoding 3β-hydroxysterol-Δ⁷-reductase and as a result of this defect, 7-dehydrocholesterol (7-DHC) and 8-dehydrocholesterol (8-DHC) accumulate in the fluids and tissues of patients with this syndrome. Both 7- and 8-DHC are susceptible to peroxidation reactions, and several biologically active DHC oxysterols are found in cell and animal models of SLOS. Ex vivo oxidation of DHCs can be a confounding factor in the analysis of these sterols and their esters, and we developed HPLC/MS methods that permit the direct analysis of cholesterol, 7-DHC, 8-DHC, and their esters in human plasma, thus avoiding ex vivo oxidation. In addition, three oxysterols were classified as endogenously formed products by the use of an isotopically-labeled 7-DHC (d₇-7-DHC) added to the sample before workup, followed by MS analysis of products formed. Analysis of 17 SLOS plasma samples shows that 8-DHC linoleate correlates better with the SLOS severity score of the patients than other sterols or metabolites, including cholesterol and 7-DHC. Levels of 7-ketocholesterol also correlate with the SLOS severity score. 8-DHC esters should have utility as surrogate markers of severity in SLOS for prognostication and as endpoints in clinical trials.     

Decreased activity of lecithin:cholesterol acyltransferase and hepatic lipase in chronic hypothyroid rats: Implications for reverse cholesterol transport

Chronic hypothyroidism is frequently associated with atherosclerosis due to increased cholesterol plasma levels; nevertheless, the contribution of impaired reverse cholesterol transport (RCT) in this process has not been completely elucidated. The aim of this study was to evaluate the effect of thyroidectomy (Htx) upon the main stages of RCT in rats. Plasma lipid alterations induced by thyroidectomy showed a slight, but significant, reduction of total plasma triglycerides, a 300% increase of LDL-cholesterol and a 25% decrease in HDL-cholesterol compared to control rats. We evaluated the first stage of RCT determining ₃H-cholesterol efflux in Fu5AH cells. The capacity of HDL obtained from Htx rats to promote cholesterol efflux was similar to that of controls. Lecithin:cholesterol acyltransferase (LCAT) activity, the second stage and the driving force of RCT was 30% lower in Htx animals compared to controls, as determined by reconstituted HDL used as an external substrate. Lipoproteins are remodeled by hepatic lipase; the mean activity of this enzyme in postheparin plasma of Htx animals was reduced by 30% compared to controls, thus suggesting an impaired HDL remodeling by this enzyme in the hypothyroid status. In contrast, lipoprotein lipase activity in the Htx group was unchanged. In summary, this study demonstrates that chronic hypothyroidism in the rat induced an impaired RCT mainly at the cholesterol esterification, and HDL remodeling mediated by hepatic lipase. The latter probably results in an abnormal HDL structure, i.e. phospholipid enrichment, which contributes to decrease HDL-apo AI fractional catabolic rates.     

Effect of cigarette smoking on high density lipoprotein phospholipids

The effect of acute inhalation of cigarette smoke on high density lipoprotein (HDL) phospholipid composition in White Carneau pigeons was examined. Four treatments included: 1) Shelf Control birds fed a chow diet and retained in their cages; 2) Sham pigeons fed a cholesterol-saturated fat diet and exposed to fresh air by a smoking machine; 3) Low nicotine-low carbon monoxide (LoLo) animals also fed the cholesterol diet and exposed to low concentrations of these cigarette smoke products; and 4) High nicotine-high carbon monoxide (HiHi) birds fed the cholesterol diet and subjected to high concentrations of these inhalants. The cholesterol-fat diet caused an increase in the concentration of most HDL phospholipid classes. Exposure to the HiHi regimen resulted in an increase in the HDL cholesterol/phospholipid ratio and a reduction in the concentration of HDL phosphatidyl ethanolamine, phosphatidyl serine/inositol, sphingomyelin and lysophosphatidyl choline. Cigarette smoking may thus attenuate HDL's anti-atherogenic properties by altering surface phospholipid components.     

Evaluation of threading specificity and accuracy

Threading experiments with proteins from the globin family provide an indication of the nature of the structural similarity required for successful fold recognition and accurate sequence-structure alignment. Threading scores are found to rise above the noise of false positives whenever roughly 60% of residues from a sequence can be aligned with analogous sites in the structure of a remote homolog. Fold recognition specificity thus appears to be limited by the extent of structural similarity, regardless of the degree of sequence similarity. Threading alignment accuracy is found to depend more critically on the degree of structural similarity. Alignments are accurate, placing the majority of residues exactly as in structural alignment, only when superposition residuals are less than 2.5 Å. These criteria for successful recognition and sequence-structure alignment appear to be consistent with the successes and failures of threading methods in blind structure prediction. They also suggest a direct assay for improved threading methods: Potentials and alignment models should be tested for their ability to detect less extensive structural similarities, and to produce accurate alignments when superposition residuals for this conserved “core” fall in the range characteristic of remote homologs. © 1996 Wiley-Liss, Inc.

1 This article is a US Government work and, as such, is in the public domain in the United States of America.

     

In vitro modification of the chemical composition of human plasma low density lipoproteins: effects of morphology and thermal properties

The effects of enzymatic action on human low density lipoproteins (LDL) occurring during in vitro incubation of plasma have been studied by chemical analysis, analytical ultracentrifugation, negative stain electron microscopy and X-ray small angle scattering. Chemically, the action of cholesteryl ester exchange and transfer proteins(s) (CEPT) leads to a relative increase in trigylcerides at the expense of cholesteryl esters. Morphologically, the particles maintain their characteristic features detectable by X-ray small angel scattering. Additional action of lecithin/cholesterol acyl transferase (LCAT) causes mainly a decrease in polar lipid contents and a reduction in particle size. The associated changes in the thermotropic transition were found to be strongly correlated to the triglyceride/cholesteryl ester ratio.     

Membrane phospholipids and the dark side of vision

The key step in the visual pigment regeneration process is an enzyme-catalyzedtrans tocis retinoid isomerization reaction. This reaction is of substantial general interest, because it requires the input of metabolic energy. The energy is needed because the 11-cis-retinoid reaction products are approximately 4kcal/mol higher in energy than their all-trans congeners. In the retinal pigment epithelium a novel enzymatic system has been discovered which is capable of converting all-trans-retinol into all-trans retinyl esters, by means of a lecithin retinol acyl transferase (LRAT), followed by the direct processing of the ester into 11-cis-retinol. In this process the free energy of hydrolysis of a retinyl ester, estimated to be approximately –5kcal/mol, is coupled to the endothermic (+4kcal/mol) isomerization reaction, resulting in an overall exothermic process. The overall process is analogous to ATP-dependent group transfer reactions, but here the energy is provided by the membrane phospholipids. This process illustrates a new role for membranes: they can serve as an energy source.     

UV Light-Induced Crosslinking of the Strands of Poly(dA-dT) and Related Alternating Purine-Pyrimidine DNAs

Abstract

Alkaline agarose gel electrophoresis was used to detect UV-induced crosslinking of the strands of poly(dA-dT) and related alternating purine-pyrimidine DNAs in solutions stabilizing various polynucleotide conformations. Strands of the B-form and A-form of poly(dA-dT) were not crosslinked but a UV dose-dependent retarded species appeared in the denaturing gels in parallel with the polynucleotide isomerization into the unusual X-form. Most other polynucleotides adopting the X-form were crosslinked as well. The exceptions include the X-forms of poly(dA-butyl⁵dU) and poly(dA-pentyl⁵dU) whose strands do not crosslink because the long exocyclic substituents attached to uracil make the photodimerization impossible. Strands of poly (amino²dA-dT) and poly(dA, amino ²dA-dT), the latter polynucleotide containing roughly equal amounts of amino ²adenine and adenine, also do not crosslink upon UV irradiation because they isomerize into an A-like conformation which is different from the X- form of poly (dA-dT). In contrast, strands of the mixed copolymers of poly(dA, amino ²dA-dT) containing low amino ²adenine contents are crosslinked upon UV irradiation, in accordance with the observation that they isomerize into the X-form.     

Role of 1-acyl-2-lyso-phosphatidylcholine acyl transferase in the biosynthesis of pulmonary phosphatidylcholine.

The majority of pulmonary dipalmitoyl phosphatidylcholine, whose surface tension lowering properties are necessary for maintenance of alveolar structural integrity and lung function, is synthesized via a reacylation mechanism. V_max and K_m values were obtained with the 1-acyl-2-lyso-PC: acyl-CoA acyl transferase system in rabbit lung microsomes and long term cultures of rabbit lung cells derived from type ll pneumonocytes enriched fractions. The data, especially for V_max, can be interpreted to indicate that this reacylation system may be an important factor in the biosynthesis of lung dipalmitoyl phosphatidylcholine.