Mass spectral analyses of the two major apolipoproteins of great ape high density lipoproteins

The two major apolipoproteins associated with human and chimpanzee (Pan troglodytes) high density lipoproteins (HDL) are apoA-I and dimeric apoA-II. Although humans are closely related to great apes, apolipoprotein data do not exist for bonobos (Pan paniscus), western lowland gorillas (Gorilla gorilla gorilla) and the Sumatran orangutans (Pongo abelii). In the absence of any data, other great apes simply have been assumed to have dimeric apoA-II while other primates and most other mammals have been shown to have monomeric apoA-II. Using mass spectrometry, we have measured the molecular masses of apoA-I and apoA-II associated with the HDL of these great apes. Each was observed to have dimeric apoA-II. Being phylogenetically related, one would anticipate these apolipoproteins having a high percentage of invariant sequences when compared with human apolipoproteins. However, the orangutan, which diverged from the human lineage between 16 and 21 million years ago, had an apoA-II with the lowest monomeric mass, 8031.3 Da and the highest apoA-I value, 28,311.7 Da, currently reported for various mammals. Interestingly, the gorilla that diverged from the lineage leading to the human–chimpanzee branch after the orangutan had almost identical mass values to those reported for human apoA-I and apoA-II. But chimpanzee and the bonobo that diverged more recently had identical apoA-II mass values that were slightly larger than reported for the human apolipoprotein. The chimpanzee A-I mass values were very close to those of humans; however, the bonobo had values intermediate to the molecular masses of orangutan and the other great apes. With the already existing genomic data for chimpanzee and the recent entries for the orangutan and gorilla, we were able to demonstrate a close agreement between our mass spectral data and the calculated molecular weights determined from the predicted primary sequences of the respective apolipoproteins. Post-translational modification of these apolipoproteins, involving truncation and oxidation of methionine, are also reported.     

Analysis of apolipoproteins in high density lipoproteins by high performance liquid chromatography

A simple and rapid method for the analysis of apolipoproteins in high density lipoprotein (HDL) by high performance liquid chromatography (HPLC) has been developed (Kinoshita et al. (1983) J. Biochem. 94, 615-617). With this method, using a sodium phosphate buffer containing 0.1% sodium dodecyl sulfate (SDS) as an eluent, apolipoproteins can be analyzed from a very small amount of HDL fraction without delipidation using organic solvents. Separation profiles of apolipoproteins by this method were examined using several techniques. The elution pattern monitored by A280 can give precise quantitative as well as qualitative information about size-distribution of apolipoproteins, except for the apo C group. Moreover, separation of apo E from apo A-I was found to be improved by column elongation.     

Mass spectral study of polymorphism of the apolipoproteins of very low density lipoprotein

New isoforms of apolipoprotein (apo)C-I and apoC-III have been detected in delipidated fractions from very low density lipoprotein (VLDL) using matrix-assisted laser desorption (MALDI) and electrospray ionization (ESI) mass spectrometry (MS). The cleavage sites of truncated apoC-III isoforms have also been identified. The VLDL fractions were isolated by fixed-angle single-spin ultracentrifugation using a self-generating sucrose density gradient and delipidated using a newly developed C18 solid phase extraction protocol. Fifteen apoC isoforms and apoE were identified in the MALDI spectra and the existence of the more abundant species was verified by ESI-MS. The relative intensities of the apoCs are closely correlated in three normolipidemic subjects. A fourth subject with type V hyperlipidemia exhibited an elevated apoC-III level and a suppressed level of the newly discovered truncated apoC-I isoform. ApoC-II was found to be particularly sensitive to in vitro oxidation. The dynamic range and specificity of the MALDI assay shows that the complete apoC isoform profile and apoE phenotype can be obtained in a single measurement from the delipidated VLDL fraction.     

Synthesis, transport, and processing of apolipoproteins of high density lipoproteins

Cell biology methods have greatly influenced the elucidation of the biosynthetic pathways of apolipoproteins. In vitro and tissue culture systems allow the study, to a large extent, of the process of synthesis, intracellular processing, secretion, and extracellular processing of the major high density lipoprotein apoproteins apoA-I and A-II and also of a minor component, apoA-IV. Whereas the latter apoprotein is equipped only with a signal sequence, the primary translation products of apoA-I and apoA-II carry N-terminal extensions of preprosequence of 24 amino acids for apoA-I and 23 amino acid residues for apoA-II. The pro-form of apoA-I characterized by a hexapeptide extension is completely stable intracellularly and is secreted as such. The pro-form is further processed by a serum protease specific for an unusual -Gln-Gln-Asp-Glu-sequence site. Pro-apoA-II, a pentapeptide sequence, is partially processed intracellularly to its mature form and secreted together with the residual pro-form. The cleavage site of pro-apoA-II is characterized by two basic amino acid residues Arg-Arg, present also in other known pro-proteins. The biological function of the N-terminal pro-sequences and details of their final processing by the serum protease(s) have yet to be established.     

Surface exposure of apolipoproteins in high density lipoproteins. I. Reactivities with agarose-immobilized proteases.

The exposure of apolipoproteins at the surface of human plasma high density lipoproteins (HDL) was assessed by their accessibility to agarose-immobilized forms of trypsin and chymotrypsin. Proteolysis of lipid-free apolipoproteins and the lipoprotein subfractions HDL2 (d = 1.08--1.125 g/ml) and HDL3 (d = 1.125--1.195 g/ml) that differ in lipid-to-protein ratio was compared by polyacrylamide gel electrophoresis and isoelectric focusing of the apolipoproteins and peptide fragments and by quantitation of the various carboxyl-terminal groups formed. Gel filtration of the proteolyzed lipoproteins on Sephadex G-150 column indicated that more than 90% of the apolipoproteins and peptides remain associated with lipoprotein complexes. Proteolysis of lipoproteins occurred more slowly and with less fragmentation of the lipoproteins and apolipoproteins than proteolysis of thelipid-free apolipoproteins or the proteolysis of lipoproteins by soluble proteases reported by other investigators. The difference in lipid content of HDL2 and HDL3 made little difference in their proteolysis. Proteolysis of the lipoproteins by agarose-trypsin was more rapid at 37 degrees C than at 22 degrees C, but the proteolytic products were similar and differed from the products from the lipid free proteins. Peptide fragments from lipoproteins were larger than those from lipid-free proteins, which suggests masking of potentially cleavable groups by lipid. The amounts (mol/g protein) of new carboxyl-terminal tyrosine and phenylalanine released by agarose -chymotrypsin were much greater from the lipid-free proteins, but about 3/4 of the tryptophan residues were inacessible in both lipoproteins and lipid-free proteins. In agarose-trypsin digestion, lysine residues were slightly more masked than arginine in the absence of lipids and much more so in the lipoproteins. However, in the lipoproteins apoA-II, which contains lysine but no arginine, was cleaved more rapidly and extensively by agarose-trypsin than apoA-I.     

Secretion of apolipoproteins in very low density and high density lipoproteins by perfused rat liver

The incorporation of labeled amino acids into the peptides of very low density lipoproteins (VLDL) and high density lipoproteins (HDL) secreted by perfused rat liver was studied using a Ringer-albumin solution in the perfusate in place of serum to diminish exchange of peptides between VLDL and HDL. Among the lipoproteins, the greatest release of protein, greatest incorporation of amino acid, and highest specific activity were found in VLDL. After separation of the delipidated peptides by electrophoresis on polyacrylamide gel, the incorporation into VLDL peptides was found to be 5-10 times as great as into HDL peptides. There was virtually no incorporation into the peptides of low density lipoproteins (LDL). Approximately 25% of the radioactivity incorporated into perfusate VLDL failed to enter the 13% polyacrylamide gel. The remaining radioactivity was distributed primarily among three peptide bands; one, found in the upper portion of the gel, contained 45% of the total, most of the remainder being found in two rapidly migrating bands. These three peptides appear to approximate those of human apo-C in relative electrophoretic mobility. Most of the HDL peptide radioactivity entering the running gel was found in a band that migrates slightly faster than the main VLDL band. A portion of the radioactivity of this major HDL band did not enter the running gel unless beta-mercaptoethanol was present. Greater separation of these two bands by polyacrylamide gel electrophoresis for 24 hr confirmed that the major bands in VLDL and in HDL were different. The rapidly moving peptides of HDL were found to contain very little radioactivity. Determination of the intensity of staining of carrier-free perfusate VLDL and HDL peptides produced a pattern similar to the incorporation of labeled amino acids. It is concluded that the rapidly moving peptides, which may contain activators of lipoprotein lipase, are only secreted as part of the VLDL.     

Proteomic analysis of post-translational modifications

Post-translational modifications modulate the activity of most eukaryote proteins. Analysis of these modifications presents formidable challenges but their determination generates indispensable insight into biological function. Strategies developed to characterize individual proteins are now systematically applied to protein populations. The combination of function- or structure-based purification of modified 'subproteomes', such as phosphorylated proteins or modified membrane proteins, with mass spectrometry is proving particularly successful. To map modification sites in molecular detail, novel mass spectrometric peptide sequencing and analysis technologies hold tremendous potential. Finally, stable isotope labeling strategies in combination with mass spectrometry have been applied successfully to study the dynamics of modifications.     

Delicate analysis of post-translational modifications on Dishevelled 3

The Wnt/β-catenin signaling pathway plays a critical role in multiple developmental events during embryogenesis and adult tissue homeostasis. Dishevelled (Dvl) is an important component of Wnt/β-catenin signaling pathway, although the modification, especially phosphorylation, seems closely related to the activity and stability of Dvl, the overall modification status of Dvl is still poorly understood. In this study, we focused on low abundant Dvl3, one of the three Dvl isoforms. Using affinity purification of different sources of Dvl3, followed by digestion with both trypsin and chymotrypsin, we systematically analyzed the overall modification status of Dvl3 with liquid chromatography coupled LTQ-Orbitrap. Altogether, we confidently identified Dvl3 with more than 50% sequence coverage, including 6 phosphorylation, 4 methylation, and 1 dimethylation sites. Most of the identified modification sites were novel and located in the linker region between different motifs. Subsequently, the validity of modified peptides was confirmed by synthetic modified peptides. Finally, SRM analysis was performed to verify and quantify the successive change of one dimethylation site on Dvl3 in vivo during Wnt signaling. Taken together, our study elucidated the existence of a novel post-translational modification on Dvl3 and provided a delicate experimental procedure for analysis of modification on low abundant proteins.     

Interaction of free apolipoproteins with macrophages. Formation of high density lipoprotein-like lipoproteins and reduction of cellular cholesterol

Mouse peritoneal macrophages, loaded with cholesteryl ester by incubating with acetylated human low density lipoprotein containing [3H]cholesteryl oleate, were exposed to purified human apolipoproteins (apo) A-I, A-II, C-III, or E in aqueous solutions. Unesterified cholesterol was released into the medium in the presence of apoA-I, -A-II, or -E, accompanied by the decrease in intracellular cholesteryl ester. ApoC-III had no such effects. Apparent Km values of the cholesterol release were estimated as 0.11, 0.14, and 0.24 microM, and Vmax values 35, 11, and 14 micrograms of cholesterol/mg of cell protein/6 h, for apoA-I, -A-II, and -E, respectively. The products formed with apoA-I, -A-II, or -E in the media were analyzed by density gradient ultracentrifugation when the cells were preloaded with [3H]cholesteryl oleate-acetylated low density lipoproteins and [3H]choline. Free [3H]cholesterol, [3H]phosphatidylcholine, and [3H]sphingomyelin were detected coincidentally as a symmetric peak at the density of 1.1 in each case. In the complex of lipids and apoA-I or apoA-II, the weight ratios of apolipoprotein/cholesterol/phosphatidylcholine/sphingomyelin/lysophosphatidyl- choline were estimated as 2.2:1:0.6:0.2:0.07 and 4.0:1:0.5:0.3:0.07, respectively. Both of the products formed with apoA-I and -A-II migrated slower than plasma high density lipoprotein in electrophoresis on agarose gel. Because the Km values are as low as 1:340-400, 1:140-160, and 1:6-8 of plasma concentrations of apoA-I, -A-II, and -E, respectively, the results have physiological relevance for a function of the free apolipoproteins in interstitial fluid to form high density lipoprotein and to reduce cellular cholesterol.     

Mass spectrometry analysis of Arabidopsis histone H3 reveals distinct combinations of post-translational modifications

Chromatin is regulated at many different levels, from higher-order packing to individual nucleosome placement. Recent studies have shown that individual histone modifications, and combinations thereof, play a key role in modulating chromatin structure and gene activity. Reported here is an analysis of Arabidopsis histone H3 modifications by nanoflow-HPLC coupled to electrospray ionization on a hybrid linear ion trap-Fourier transform mass spectrometer (LTQ/FTMS). We find that the sites of acetylation and methylation, in general, correlate well with other plants and animals. Two well-studied modifications, dimethylation of Lys-9 (correlated with silencing) and acetylation of Lys-14 (correlated with active chromatin) while abundant by themselves were rarely found on the same histone H3 tail. In contrast, dimethylation at Lys-27 and monomethylation at Lys-36 were commonly found together. Interestingly, acetylation at Lys-9 was found only in a low percentage of histones while acetylation of Lys-14 was very abundant. The two histone H3 variants, H3.1 and H3.2, also differ in the abundance of silencing and activating marks confirming other studies showing that the replication-independent histone H3 is enriched in active chromatin.     

Effect of temperature and plasma on the exchange of apolipoproteins and phospholipids between rat plasma very low and high density lipoproteins.

The effect of temperature and plasma on the exchange of apoprotein C and phospholipids between VLDL and HDL was studied using 125I-labeled and 32P-labeled VLDL. Temperature affected the exchange of apoproteins and phospholipids similarly, and both were enhanced by increasing the temperature of incubation to 20 degrees C and higher. The exchange of apoC was almost complete within 5 minutes of incubation and was not influenced by the addition of plasma to the incubation mixture. The exchange of phospholipids occurred much more slowly and was enhanced 5- to 10-fold in the presence of plasma. These results indicate that the exchange of both phospholipids and apoC is dependent on the temperature of the incubation, but that they exchange independently, at least in part. It is suggested that the exchange of apoC occurs through dissociation of the apoprotein from the lipoprotein surface to the water phase, whereas the exchange of phospholipids is mediated mainly by a carrier molecule present in plasma and absent in lipoproteins.     

Mass spectrometry-based strategies for characterization of histones and their post-translational modifications

Due to the intimate interactions between histones and DNA, the characterization of histones has become the focus of great attention. A series of mass spectrometry-based technologies have been dedicated to the characterization and quantitation of different histone forms. This review focuses on the discussion of mass spectrometry-based strategies used for the characterization of histones and their post-translational modifications.     

The heterogeneity of rat high density lipoproteins.

Ubiquitin was first found in nuclei in protein A24 where its carboxyl terminal is covalently bound to histone 2A by an isopeptide linkage (Goldknopf, I. L. and Busch, H. (1977) Proc. Natl. Acad. Sci. USA $\text{74}$, 864–868). Two-dimensional polyacrylamide gel electrophoresis of the 0.4 N H₂SO₄ soluble proteins from fractionated rat liver chromatin showed that protein A24 and histones H1, H2A, H2B, H3 and H4 were present in fractions P1 and P2 and markedly diminished in relative amounts in fraction S2. Conversely, a spot designated Ub was found in fraction S2 along with an increased amount and number of non-histone proteins. The Ub spot was not found in chromatin fractions P1 and P2. Ub was identified as ubiquitin by migration on two-dimensional gels and after purification by preparative polyacrylamide gel electrophoresis by its methionine NH₂-terminal amino acid and its amino acid composition.     

Properties of rooster serum high density lipoproteins.

1. Holo-superoxide dismutase from bovine erythrocytes has been shown to undergo a reversible structural modification in the pH 3-5 range. 2. The spectral alterations observed on changing from neutrality to pH 2 were: a slight attenuation of the 680 nm absorbance; the loss of the 450 nm shoulder, apparent in the optical spectrum of the native protein; and a new band appeared at 330 nm. The circular dichroism at 600 nm was essentially lost while a weak negative band appeared at approx. 380 nm and a positive band at 310 nm. 3. The EPR spectrum was also modified on changing from the native to the low pH form: A parallel increased from approximately 130 to approximately 150 G, g parallel remained unchanged at approximately 2.27, and gm decreased from approximately 2.09 to approximately 2.08. The apparent linewidth remained essentially constant. 4. High resolution (220 MHz) PMR spectra of holo- and apoproteins revealed that the metals influence the three-dimensional structure of the protein. 5. PMR studies indicated that at pH 3 the apoprotein existed almost entirely in a random coil form and that it assumed a compact well-ordered structure on returning to neutral pH. The holoprotein maintained a compact, apparently dimeric, structure even at pH 3.     

Changes in the size of reconstituted high density lipoproteins during incubation with cholesteryl ester transfer protein: the role of apolipoproteins.

It has been reported previously that the particle size distribution of discoidal, reconstituted HDL (r-HDL) changes dramatically during incubation in vitro with cholesteryl ester transfer protein (CETP). The present study was undertaken in order to determine whether these changes are influenced by the apolipoprotein composition of the r-HDL. Two preparations of r-HDL that contained egg phosphatidylcholine (egg PC) and unesterified cholesterol (UC) but differed in their apolipoprotein composition were used for the study. One preparation contained apolipoprotein (apo) A-I only (A-I w/o A-II r-HDL) while the other contained apoA-I and apoA-II (A-I w A-II r-HDL). The Stokes' radius of the major population of particles in the (A-I w/o A-II) and (A-I w A-II) r-HDL was, respectively, 4.8 and 4.9 nm. When the (A-I w/o A-II) r-HDL were incubated with CETP, most of the particles of radius 4.8 nm were converted to populations of smaller and larger particles. The smaller particles had Stokes' radii of 4.3 and 3.9 nm. The radii of the larger particles ranged from 8.2 to 13.7 nm. When the (A-I w A-II) r-HDL were incubated with CETP larger particles (Stokes' radii = 8.4-11.0 nm) appeared but there was minimal conversion to smaller particles. In addition, a significant proportion of the original (A-I w A-II) r-HDL of radius 4.9 nm was still present at the end of the incubation. These results are consistent with apoA-II inhibiting the conversion of r-HDL to small particles. It is concluded that the apolipoprotein content of r-HDL is an important determinant of the sizes of the particles that are formed during incubation with CETP.     

Mass spectrometry-based strategies for characterization of histones and their post-translational modifications

Due to the intimate interactions between histones and DNA, the characterization of histones has become the focus of great attention. A series of mass spectrometry-based technologies have been dedicated to the characterization and quantitation of different histone forms. This review focuses on the discussion of mass spectrometry-based strategies used for the characterization of histones and their post-translational modifications.