We have developed a method for calculating the stability in water of protein structures, starting from their atomic coordinates. The contribution of each protein atom to the solvation free energy is estimated as the product of the accessibility of the atom to solvent and its atomic solvation parameter. Applications of the method include estimates of the relative stability of different protein conformations, estimates of the free energy of binding of ligands to proteins and atomic-level descriptions of hydrophobicity and amphiphilicity.

Solvation energy in protein folding and binding

http://www.bio21.bas.bg/ibf/PC_review.pdf

Phases and phase transitions of the phosphatidylcholines

Molecular and cellular aspects of thiol-disulfide exchange.

The human apoCs (ie, apoC1, apoC2, and apoC3) are often portrayed as members of 1 consistent protein family because of their similar distributions among lipoprotein classes, their low molecular weights, and coincident purification. The human apoCs are protein constituents of chylomicrons, VLDL, and HDL. In comparison with the intensely studied apoE, apoB, and apoA1, which play important roles in the development of hyperlipidemia and atherosclerosis, only modest attention has been paid so far to the roles of the apoCs in lipoprotein metabolism. Many of the studies regarding the functional properties of apoCs have been hampered by methodological problems dealing with purification, quantification, and their poorly understood association with hyperlipidemia and other lipoprotein disorders. In the past few years, however, new insights into the metabolic properties of apoCs have been provided, in particular by the technologies of transgenesis and gene targeting in mice.

Role of ApoCs in Lipoprotein Metabolism Functional Differences Between ApoC1, ApoC2, and ApoC3

The complete amino acid sequence of the Ca2+-dependent modulator protein (calmodulin) of bovine brain.

Lecithin: cholesterol acyltransferase. Functional regions and a structural model of the enzyme

Human lipoprotein[a] contains at least two high-molecular-weight, disulfide-linked apolipoproteins, apo[a] and apo B-100. Apo[a] is a highly glycosylated, hydrophilic apoprotein that somewhat resembles plasminogen by containing an extended kringle domain and a carboxyl-terminal serine protease domain. The apo[a] kringle domain is composed of 11 distinct kringle types. Ten of these display high sequence homology to plasminogen kringle 4 (PGK4). The crystallographic coordinates for PGK4 were used to generate three-dimensional molecular models of the apo[a] kringle types, and the lysine-binding region of PGK4 was used to compare the different potential receptor-ligand and ligand-binding sites contained in each different PGK4-like kringle of apo[a]. A receptor-ligand site can be proposed for each kringle type. Potential serine protease cleavage sites, containing arginine-threonine and threonine-arginine, are located on the surface of the kringles. The ligand-binding site of one apo[a] kringle model is almost identical to that of PGK4 and may be a lysine-binding site of apo[a]. Four other apo[a] kringle models appear to have structurally similar lysine-binding sites, but with differences that may influence ligand-polypeptide specificity. Five apo[a] kringle models have ligand-binding sites that probably do not bind lysine; one of these is the highly repeated kringle in the known apo[a] polymorph.

Comparison of ligand-binding sites of modeled apo[a] kringle-like sequences in human lipoprotein[a].

The effect of ApoC-III, a major apoprotein constituent of human very low density lipoproteins, on the physical properties of dimyristoylphosphatidylcholine (DMPC) vesicles has been studied by magnetic resonance and fluorescence techniques. The sharp gel-liquid crystalline transition usually observed at 23 C in DMPC is both broadened and elevated when ApoC-III is bound as determined (a) from measurements of microscopic viscosity by pyrene excimer fluorescence, (b) from the distribution of di-tert-butyl nitroxide between the bulk aqueous phase and the fluid lipid phase, and (c) from the motion of fatty acyl chains of spin-labeled phosphatdylcholine. Experiments involving the translocation of ascorbate and charged nitroxide ions and the movement of paramagnetic Eu 3+ ions indicate that when ApoC-III binds to DMPC vesicles, it increases their permeability or destroys their original bilayer structure. These two possibilities were distinguishable by gel filtration of the DMPC-ApoC-III complex (approximately 34 mol mol) that indicated that the product particles were significantly smaller than the original vesicles. Taken together, the data indicate that ApoC-III binding to DMPC not only decreases the acyl chain motion of individual lipid molecules, but also induces break-down of bilamellar vesicular structure to give significantly smaller complexes.

Structure of an apolipoprotein-phospholipid complex: apoC-III induced changes in the physical properties of dimyristoylphosphatidylcholine.

Chapter 4 – Structural Properties of Apo(a): A Major Apoprotein of Human Lipoprotein(a)

The apoproteins (apo) C-I, C-II, and C-III are low molecular weight amphiphilic proteins that are associated with the lipid surface of the plasma chylomicron, very low density lipoprotein (VLDL), and high-density lipoprotein (HDL) subfractions. Purified apoC-I spontaneously reassociates with VLDL, HDL, and single-bilayer vesicles (SBV) of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine. ApoC-I also transfers reversibly from VLDL to HDL and from VLDL and HDL to SBV. The kinetics of association of the individual apoC proteins with SBV are second order overall and first order with respect to lipid and protein concentrations. At 37 degrees C, the rates of association were 2.5 x 10(10), 4.0 x 10(10) and 3.8 x 10(10) M-1 s-1 for apoC-I, apoC-II, and apoC-III, respectively. Arrhenius plots of association rate vs temperature were linear and yielded activation energies of 11.0 (apoC-I), 9.0 (apoC-II), and 10.6 kcal/mol (apoC-III). The kinetics of vesicle to vesicle apoprotein transfer are biexponential for intermembrane transfer, indicating two concurrent transfer processes. Rate constants at 37 degrees C for the fast component of dissociation were 11.7, 9.5, and 9.9 s-1, while rate constants for the slow component were 1.3, 0.6, and 0.9 s-1 for apoC-I, apoC-II, and apoC-III, respectively. The dissociation constants, Kd, of apoC-I, apoC-II, and apoC-III bound to the surface monolayer of phospholipid-coated latex beads were 0.5, 1.4, and 0.5 microM, respectively. These studies show that the apoC proteins are in dynamic equilibrium among phospholipid surfaces on a time scale that is rapid compared to lipolysis, lipid transfer, and lipoprotein turnover.

Apolipoproteins C-I, C-II, and C-III: kinetics of association with model membranes and intermembrane transfer.

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