Non-polar interactions between cholesterol and phospholipids: a molecular dynamics simulation study

A 15-ns molecular dynamics simulation of the fully hydrated dimyristoylphosphatidylcholine-cholesterol (DMPC-Chol) bilayer containing approximately 22 mol% Chol was carried out. An 8-ns trajectory was analysed to investigate the effect of Chol on the chain packing in the bilayer core. While the packing of DMPC chains on the smooth alpha-face side of the Chol ring is similar to that in the pure DMPC bilayer, the packing on the rough beta-face side is less regular and less tight. Two methyl groups located on the Chol beta-face disturb the packing; in effect, van der Waals (vdW) interactions between Chol rings and DMPC chains are weaker than the ones between sole DMPC chains. VdW interactions between an alkyl chain of DMPC and an isooctyl tail of Chol are similarly strong as those between two DMPC chains.     

The fluorescent cholesterol analog dehydroergosterol induces liquid-ordered domains in model membranes

The fluorescent sterol dehydroergosterol (DHE) is often used as a marker for cholesterol in cellular studies. We show by vesicle fluctuation analysis that DHE has a lower ability than cholesterol to stiffen lipid bilayers suggesting less efficient packing with phospholipid acyl chains. Despite this difference, we found by fluorescence and atomic force microscopy, that DHE induces liquid-ordered/-disordered coexistent domains in giant unilamellar vesicles (GUVs) and supported bilayers made of dipalmitoylphosphatidylcholine (DPPC), dioleylphosphatidylcholine (DOPC) and DHE or cholesterol. DHE-induced phases have a height difference of 0.9-1 nm similar as known for cholesterol-containing domains. DHE not only promotes formation of liquid-liquid immiscibility but also shows strong partition preference for the liquid-ordered phase further supporting its suitability as cholesterol probe.     

A thermodynamic model for extended complexes of cholesterol and phospholipid

Studies of monolayer mixtures of certain phospholipids with cholesterol by epifluorescence microscopy and measurement of cholesterol desorption show evidence for the formation of "condensed complexes." A thermodynamic model of these complexes has been developed and has been shown to be generally consistent with observed phase diagrams, cholesterol desorption rates, and electric field susceptibility. Previous work has shown that complexes comprising 10-50 molecules provide good agreement with experimental results. The present study examines the calculated properties of complexes containing very large numbers of molecules and extends the condensed complex model to incorporate the formation of complexes of variable size. Trends in equilibrium composition are similar to those calculated for small complexes. Thermal transitions are continuous, with a strong composition dependence of the breadth of the transition. The average number of molecules in a large complex shows a pronounced dependence on the composition of the reaction mixture. Large complexes have properties of a separate thermodynamic phase.     

Translocation of phospholipids and dithionite permeability in liquid-ordered and liquid-disordered membranes

We present a detailed study of the translocation rate of two headgroup-labeled phospholipid derivatives, one with two acyl chains, NBD-DMPE, and the other with a single acyl chain, NBD-lysoMPE, in lipid bilayer membranes in the liquid-disordered state (POPC) and in the liquid-ordered states (POPC/cholesterol (Chol), molar ratio 1:1, and sphingomyelin (SpM)/Chol, molar ratio 6:4). The study was performed as a function of temperature and the thermodynamic parameters of the translocation process have been obtained. The most important findings are 1), the translocation of NBD-DMPE is significantly faster than the translocation of NBD-lysoMPE for all bilayer compositions and temperatures tested; and 2), for both phospholipid derivatives, the translocation in POPC bilayers is approximately 1 order of magnitude faster than in POPC/Chol (1:1) bilayers and approximately 2-3 orders of magnitude faster than in SpM/Chol (6:4) bilayers. The permeability of the lipid bilayers to dithionite has also been measured. In liquid disordered membranes, the permeability rate constant obtained is comparable to the translocation rate constant of NBD-DMPE. However, in liquid-ordered bilayers, the permeability of dithionite is significantly faster then the translocation of NBD-DMPE. The change in enthalpy and entropy associated with the formation of the activated state in the translocation and permeation processes has also been obtained.     

A thermodynamic model for Nap1-histone interactions

The yeast nucleosome assembly protein 1 (yNap1) plays a role in chromatin maintenance by facilitating histone exchange as well as nucleosome assembly and disassembly. It has been suggested that yNap1 carries out these functions by regulating the concentration of free histones. Therefore, a quantitative understanding of yNap1-histone interactions also provides information on the thermodynamics of chromatin. We have developed quantitative methods to study the affinity of yNap1 for histones. We show that yNap1 binds H2A/H2B and H3/H4 histone complexes with low nm affinity, and that each yNap1 dimer binds two histone fold dimers. The yNap1 tails contribute synergistically to histone binding while the histone tails have a slightly repressive effect on binding. The (H3/H4)(2) tetramer binds DNA with higher affinity than it binds yNap1.     

The liquid-ordered state comes of age

Biomembranes are unique states of soft matter that share some of their materials properties with the mesophases of liquid crystals. Although of genuinely fluid character, membranes can display ordered states under physiological conditions, and it appears that their lateral organization and the related functional properties are intimately coupled to states in-between order and disorder. Hence, the liquid-ordered state of membranes, which owes its existence to the unique ability of cholesterol to mediate between order and disorder, has moved center stage in the characterization of membranes in terms of domains or rafts.     

Investigation on the interactions between pirarubicin and phospholipids

Differential scanning calorimetry (DSC), Fourier transform infrared (FTIR) spectroscopy and quantum calculation based on molecular modeling were applied to investigate the interaction between pirarubicin (THP), an anthracycline antibiotic frequently used in chemotherapy, and zwitterionic distearoylphosphatidylcholine (DSPC) or anionic distearoylphosphatidylglycerol (DSPG). DSC and FTIR studies suggested that DSPG bilayers were less perturbed by THP than those of DSPC, and this might be due to the strong interactions between NH₃⁺ of THP and the phosphate (PO₂⁻) group in the polar head of DSPG, which limit the further access of THP into its bilayers. Quantum calculation results based on molecular modeling could further confirm the DSC and FTIR conclusions. Meanwhile, it could well translate the calorimetric and spectroscopic phenomena into the underlying physical knowledge. Interactions between THP and phospholipids can play a critical role in the liposomal drug delivery system, especially in the safety mechanism elucidation and rational formulation design.     

Building up of the liquid-ordered phase formed by sphingomyelin and cholesterol

The long-range and molecular orders and dynamics in codispersions of egg sphingomyelin-cholesterol have been investigated by synchrotron x-ray diffraction and electron spin resonance using phosphatidylcholine spin-labeled at several positions on the sn-2 chain. Mixtures containing 0, 17, 33, 41, 50 mol% cholesterol exhibited a single phase by x-ray diffraction methods. The temperature dependence of the d-spacing between 20 and 50 degrees C is attenuated with increasing proportions of cholesterol, becoming invariant for cholesterol contents of 41 and 50 mol% on completion of the liquid-ordered phase. Electron spin resonance revealed two sites for 17 and 33 mol% cholesterol. One site is highly ordered and the other is less ordered than the fluid phase of pure sphingomyelin as shown by the molecular and the intramolecular order parameters reflecting the segmental motions of the probe. The two-sites exchange rate indicates a mean lifetime of the sites of approximately 0.1 micros during which the lipid displacement is approximately 1 nm. The short lifetime of the sites probed by ESR and the single phase detected by x-ray diffraction support in this binary mixture, the building up of the Lo phase by a progressive accumulation of randomly distributed sphingomyelin-cholesterol condensed complexes rather than by diffusional exchange between extended domains.     

Characterization of the liquid-ordered state by proton MAS NMR

We investigated if magic angle spinning (MAS) 1H NMR can be used as a tool for detection of liquid-ordered domains (rafts) in membranes. In experiments with the lipids SOPC, DOPC, DPPC, and cholesterol we demonstrated that 1H MAS NMR spectra of liquid-ordered domains (lo) are distinctly different from liquid-disordered (ld) and solid-ordered (so) membrane regions. At a MAS frequency of 10 kHz the methylene proton resonance of hydrocarbon chains in the ld phase has a linewidth of 50 Hz. The corresponding linewidth is 1 kHz for the lo phase and several kHz for the so phase. According to results of 1H NMR dipolar echo spectroscopy, the broadening of MAS resonances in the lo phase results from an increase in effective strength of intramolecular proton dipolar interactions between adjacent methylene groups, most likely because of a lower probability of gauche/trans isomerization in lo. In spectra recorded as a function of temperature, the onset of lo domain (raft) formation is seen as a sudden onset of line broadening. Formation of small domains yielded homogenously broadened resonance lines, whereas large lo domains (diameter >0.3 microm) in an ld environment resulted in superposition of the narrow resonances of the ld phase and the much broader resonances of lo. 1H MAS NMR may be applied to detection of rafts in cell membranes.     

A thermodynamic study of the effects of cholesterol on the interaction between liposomes and ethanol

The association of ethanol with unilamellar dimyristoyl phosphatidylcholine (DMPC) liposomes of varying cholesterol content has been investigated by isothermal titration calorimetry over a wide temperature range (8-45 degrees C). The calorimetric data show that the interaction of ethanol with the lipid membranes is endothermic and strongly dependent on the phase behavior of the mixed lipid bilayer, specifically whether the lipid bilayer is in the solid ordered (so), liquid disordered (ld), or liquid ordered (lo) phase. In the low concentration regime (<10 mol%), cholesterol enhances the affinity of ethanol for the lipid bilayer compared to pure DMPC bilayers, whereas higher levels of cholesterol (>10 mol%) reduce affinity of ethanol for the lipid bilayer. Moreover, the experimental data reveal that the affinity of ethanol for the DMPC bilayers containing small amounts of cholesterol is enhanced in the region around the main phase transition. The results suggest the existence of a close relationship between the physical structure of the lipid bilayer and the association of ethanol with the bilayer. In particular, the existence of dynamically coexisting domains of gel and fluid lipids in the transition temperature region may play an important role for association of ethanol with the lipid bilayers. Finally, the relation between cholesterol content and the affinity of ethanol for the lipid bilayer provides some support for the in vivo observation that cholesterol acts as a natural antagonist against alcohol intoxication.     

Effects of cholesterol on the divalent cation-mediated interactions of vesicles containing amino and choline phospholipids

We have used assays of lipid probe mixing, contents mixing and contents leakage to monitor the divalent cation-mediated interactions between lipid vesicles containing phosphatidylserine (PS) as a minority component together with mixtures of phosphatidylethanolamine (PE), phosphatidylcholine (PC) or sphingomyelin, and cholesterol in varying proportions. The initial rates of calcium- and magnesium-induced lipid probe quenching between vesicles, which reflect primarily the rates of vesicle aggregation, are strongly reduced as progressively higher proportions of PC or sphingomyelin are incorporated into PE/PS vesicles. The initial rates of divalent cation-induced contents mixing and contents leakage for PE/PS vesicles are also strongly reduced when choline phospholipids are incorporated into the vesicles in even low molar proportions. Sphingomyelin has a more potent inhibitory effect on these processes than does PC at an equal level in the vesicle membranes. The inclusion of cholesterol in these vesicles, at levels up to 1:2 moles sterol/mole phospholipid, has little effect on the rates of calcium- or magnesium-induced vesicle aggregation. However, cholesterol significantly enhances the initial rates of vesicle contents mixing and contents leakage in the presence of divalent cations when the vesicles contain choline as well as amino phospholipids. This effect is substantial only when the level of cholesterol exceeds the level of choline phospholipids in the vesicles. These results may have significance for the fusion of certain cellular membranes in mammalian cells, whose cytoplasmic faces have lipid compositions very similar to those of the vesicles examined in this study.     

Phosphatidylcholine and cholesterol interactions in model membranes

Various phosphatidylcholines differing either in the stereochemistry around their chiral center or in the position of a cis double bond along the acyl chains were synthesized in order to study critical contact regions in the phospholipid molecule with adjacent cholesterol in model membranes. Microviscosities calculated from fluorescence depolarization of diphenylhexatriene and chain order from spin label studies were measured to monitor physical membrane properties. The enhancing effect of cholesterol on the microviscosity of membranes containing phosphatidylcholines with comparable acyl chain length was largest when the two acyl chains were saturated and smallest when both were unsaturated. Membranes prepared from phosphatidylcholines having a single cis double bond at different positions along the sn-2 acyl chain showed roughly the same changes of microviscosity or chain order upon incorporation of cholesterol. No discrimination was evident in the interaction between cholesterol and enantiomeric phosphatidylcholines or between the enantiomeric phosphatidylcholine molecules themselves. We conclude that the rigidifying effect of cholesterol in membranes does not depend on specific sites of interaction and that with respect to physical membrane properties phosphatidylcholine behaves as an achiral molecule.     

A simple physical model for the prediction and design of protein-DNA interactions

Protein-DNA interactions are crucial for many biological processes. Attempts to model these interactions have generally taken the form of amino acid-base recognition codes or purely sequence-based profile methods, which depend on the availability of extensive sequence and structural information for specific structural families, neglect side-chain conformational variability, and lack generality beyond the structural family used to train the model. Here, we take advantage of recent advances in rotamer-based protein design and the large number of structurally characterized protein-DNA complexes to develop and parameterize a simple physical model for protein-DNA interactions. The model shows considerable promise for redesigning amino acids at protein-DNA interfaces, as design calculations recover the amino acid residue identities and conformations at these interfaces with accuracies comparable to sequence recovery in globular proteins. The model shows promise also for predicting DNA-binding specificity for fixed protein sequences: native DNA sequences are selected correctly from pools of competing DNA substrates; however, incorporation of backbone movement will likely be required to improve performance in homology modeling applications. Interestingly, optimization of zinc finger protein amino acid sequences for high-affinity binding to specific DNA sequences results in proteins with little or no predicted specificity, suggesting that naturally occurring DNA-binding proteins are optimized for specificity rather than affinity. When combined with algorithms that optimize specificity directly, the simple computational model developed here should be useful for the engineering of proteins with novel DNA-binding specificities.     

A simple genetically structured model of trp repressor-operator interactions

A genetically structured mathematical model of the trp operon based on known molecular interactions of aporepressor, corepressor, and inducer is proposed. The model simulates, both qualitatively and quantitatively, the influence of these regulatory species on the extent of repression and expression of cloned gene products. It shows that at low aporepressor concentration, full repression is not possible even with high tryptophan levels, resulting in leaky expression. Calculations based on the model enabled predictions of optimum levels of aporepressor and tryptophan for effective repression and, concurrently, the beta-indoleacrylic acid concentrations required for induction for both low and high plasmid copy number clones. Using the model we attempted to provide explanations for seemingly anomalous and sometimes contradictory observations by researchers when working with the trp promoter. (c) 1993 John Wiley & Sons, Inc.     

A simple probabilistic model of multibody interactions in proteins

Protein structure prediction methods typically use statistical potentials, which rely on statistics derived from a database of know protein structures. In the vast majority of cases, these potentials involve pairwise distances or contacts between amino acids or atoms. Although some potentials beyond pairwise interactions have been described, the formulation of a general multibody potential is seen as intractable due to the perceived limited amount of data. In this article, we show that it is possible to formulate a probabilistic model of higher order interactions in proteins, without arbitrarily limiting the number of contacts. The success of this approach is based on replacing a naive table‐based approach with a simple hierarchical model involving suitable probability distributions and conditional independence assumptions. The model captures the joint probability distribution of an amino acid and its neighbors, local structure and solvent exposure. We show that this model can be used to approximate the conditional probability distribution of an amino acid sequence given a structure using a pseudo‐likelihood approach. We verify the model by decoy recognition and site‐specific amino acid predictions. Our coarse‐grained model is compared to state‐of‐art methods that use full atomic detail. This article illustrates how the use of simple probabilistic models can lead to new opportunities in the treatment of nonlocal interactions in knowledge‐based protein structure prediction and design. Proteins 2013; 81:1340–1350. © 2013 Wiley Periodicals, Inc.     

A simple chemical example of hierarchical thermodynamic interactions: the protonation equilibria of inorganic polyprotic acids

A general method for formulating complex thermodynamic systems in terms of hierarchical interactions has been developed, and has been applied in a previous analysis to hemoglobin oxygen binding data. Polyprotic acids can be considered a simple chemical model of thermodynamic interaction between ligand binding events. To further illustrate the hierarchical interaction approach it is applied to the analysis of the thermodynamic interactions between proton binding events in inorganic polyprotic acids. pK values for arsenate, carbonate, chromate, phosphate, phosphite, selenite, sulfide and sulfite were recast into hierarchical interaction terms. The intrinsic K(d,h) for protonation ranged from 8.8 x 10(-13) (M) for phosphate to 1.3 x 10(-6) (M) for chromate. Pairwise interactions (K(d,hh)) between protonation events ranged from 1.3 x 10(4) for phosphite to 9.4 x 10(5) for carbonate. Third order interactions (K(d,hhh)) were 0.91 and 0.51 for arsenate and phosphate, respectively, values relatively close to the no interaction value of 1. A principle feature of systems described by hierarchical interactions is that higher order interactions, representing more complex interactions, are less likely to be significant than lower order interactions, and this is further illustrated by these observations from polyprotic acids. The set of significant hierarchical interaction values can be used to predict values for as yet unobserved events, and projected pK values are made for all the polyprotic acids included in this study. Finally, application of this method to the protonation equilibria of water demonstrates a profound pairwise interaction between protonation events (K(d,hh) = 1.3 x 10(17)), which is attributed to oxygen's small size and lack of polarizability.     

A model of lipid and cholesterol interactions in hydrated phases: formation of linear cholesterol multimers

On the ground of Martin and Yeagle's model based on the possibility of formation of cholesterol dimers in the course of its interaction with lipids, the scheme of lipid cholesterol interaction is presented. Its essence is connected with possible formation of linear cholesterol multimers circled by unshared aliphatic chains.     

A simple theoretical model for the effects of cholesterol and polypeptides on lipid membranes

A simple theoretical model for the effects of impurities on biomembranes is proposed. The model accounts for the cholesterol-induced decrease of membrane phase transition temperature, membrane condensation above the gel to liquid crystalline phase transition, and increase in lateral compressibility. The model also predicts that addition of molecules such as cholesterol and polypeptides to membranes results in unmasking of a continuous phase transition. This results in a second broad peak in the calorimetric curves for melting of lipid-cholesterol mixtures, and the appearance of a second melting transition in membranes modified by the incorporation of polypeptides. The theory assumes that the membrane may be adequately described by a kink model, and that impurities are randomly distributed in the membrane. The difference in size and shape of impurity molecules, compared to membrane lipids, results in a spatial disordering in the membrane which in turn causes increased chain disorder and membrane condensation, as well as a decrease in the cooperativity of melting. The second transition results from a second expansion of the condensed, partially disordered membrane, which takes place over a several degree temperature range. This transition, although unmasked by boundary effects of non-lipid molecules, does not correspond to melting of a boundary annulus or phase separation.