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K Hristova

Publications and source records attributed to K Hristova.

13 recordsLinked to original sources
PubMed2001

Energetics, stability, and prediction of transmembrane helices.

We show that the peptide backbone of an alpha-helix places a severe thermodynamic constraint on transmembrane (TM) stability. Neglect of this constraint by commonly used hydrophobicity scales underlies the notorious uncertainty of TM helix prediction by sliding-window hydropathy plots of membrane protein (MP) amino acid sequences. We find that an experiment-based whole-residue hydropathy scale (WW scale), which includes the backbone constraint, identifies TM helices of membrane proteins with an accuracy greater than 99 %. Furthermore, it correctly predicts the minimum hydrophobicity required for stable single-helix TM insertion observed in Escherichia coli. In order to improve membrane protein topology prediction further, we introduce the augmented WW (aWW) scale, which accounts for the energetics of salt-bridge formation. An important issue for genomic analysis is the ability of the hydropathy plot method to distinguish membrane from soluble proteins. We find that the method falsely predicts 17 to 43 % of a set of soluble proteins to be MPs, depending upon the hydropathy scale used.

Bacteriorhodopsins↗
PubMed2001

Structure, location, and lipid perturbations of melittin at the membrane interface.

Melittin is arguably the most widely studied amphipathic, membrane-lytic alpha-helical peptide. Although several lines of evidence suggest an interfacial membrane location at low concentrations, melittin's exact position and depth of penetration into the hydrocarbon core are unknown. Furthermore, the structural basis for its lytic action remains largely a matter of conjecture. Using a novel x-ray absolute-scale refinement method, we have now determined the location, orientation, and likely conformation of monomeric melittin in oriented phosphocholine lipid multilayers. Its helical axis is aligned parallel to the bilayer plane at the depth of the glycerol groups, but its average conformation differs from the crystallographic structure. As observed earlier for another amphipathic alpha-helical peptide, the lipid perturbations induced by melittin are remarkably modest. Small bilayer perturbations thus appear to be a general feature of amphipathic helices at low concentrations. In contrast, a dimeric form of melittin causes larger structural perturbations under otherwise identical conditions. These results provide direct structural evidence that self-association of amphipathic helices may be the crucial initial step toward membrane lysis.

Animals↗
PubMed2001

MPtopo: A database of membrane protein topology.

The reliability of the transmembrane (TM) sequence assignments for membrane proteins (MPs) in standard sequence databases is uncertain because the vast majority are based on hydropathy plots. A database of MPs with dependable assignments is necessary for developing new computational tools for the prediction of MP structure. We have therefore created MPtopo, a database of MPs whose topologies have been verified experimentally by means of crystallography, gene fusion, and other methods. Tests using MPtopo strongly validated four existing MP topology-prediction algorithms. MPtopo is freely available over the internet and can be queried by means of an SQL-based search engine.

Algorithms↗
PubMed1999

An amphipathic alpha-helix at a membrane interface: a structural study using a novel X-ray diffraction method.

The amphipathic alpha-helix is a recurrent feature of membrane-active proteins, peptides, and toxins. Despite extensive biophysical studies, the structural details of its affinity for membrane interfaces remain rather vague. We report here the first results of an effort to obtain detailed structural information about alpha-helices in membranes by means of a novel X-ray diffraction method. Specifically, we determined the transbilayer position and orientation of an archetypal class A amphipathic helical peptide in oriented fluid-state dioleoylphosphatidylcholine (DOPC) bilayers. The peptide, Ac-18A-NH2(Ac-DWLKAFYDKVAEKLKEAF-NH2), is a model for class A amphipathic helices of apolipoprotein A-I and other exchangeable lipoproteins. The diffraction method relies upon experimental determinations of absolute scattering-length density profiles along the bilayer normal and the transbilayer distribution of the DOPC double bonds by means of specific bromination, and molecular modeling of the perturbed lipid bilayer (derived using the transbilayer distribution of the double bonds) and the peptide. The diffraction results showed that Ac-18A-NH2was located in the bilayer interface and that its transbilayer distribution could be described by a Gaussian function with a 1/e-halfwidth of 4.5(+/-0.3) A located 17.1(+/-0.3) A from the bilayer center, close to the glycerol moiety. Molecular modeling suggested that Ac-18A-NH2is helical and oriented generally parallel with the bilayer plane. The helicity and orientation were confirmed by oriented circular dichroism measurements. The width of the Gaussian distribution, a measure of the diameter of the helix, indicated that the Ac-18A-NH2helix penetrated the hydrocarbon core to about the level of the DOPC double bonds. Bilayer perturbations caused by Ac-18A-NH2were surprisingly modest, consisting of a slight decrease in bilayer thickness with a concomitant shift of the double-bond distribution toward the bilayer center, as expected from a small increase in lipid-specific area caused by the peptide.

Amino Acid Sequence↗
PubMed1998

Folding of beta-sheet membrane proteins: a hydrophobic hexapeptide model.

Beta-sheets, in the form of the beta-barrel folding motif, are found in several constitutive membrane proteins (porins) and in several microbial toxins that assemble on membranes to form oligomeric transmembrane channels. We report here a first step towards understanding the principles of beta-sheet formation in membranes. In particular, we describe the properties of a simple hydrophobic hexapeptide, acetyl-Trp-Leu5 (AcWL5), that assembles cooperatively into beta-sheet aggregates upon partitioning into lipid bilayer membranes from the aqueous phase where the peptide is strictly monomeric and random coil. The aggregates, containing 10 to 20 monomers, undergo a relatively sharp and reversible thermal unfolding at approximately 60 degreesC. No pores are formed by the aggregates, but they do induce graded leakage of vesicle contents at very high peptide to lipid ratios. Because beta-sheet structure is not observed when the peptide is dissolved in n-octanol, trifluoroethanol or sodium dodecyl sulfate micelles, aggregation into beta-sheets appears to be an exclusive property of the peptide in the bilayer membrane interface. This is an expected consequence of the hypothesis that a reduction in the free energy of partitioning of peptide bonds caused by hydrogen bonding drives secondary structure formation in membrane interfaces. But, other features of interfacial partitioning, such as side-chain interactions and reduction of dimensionality, must also contribute. We estimate from our partitioning data that the free energy reduction per residue for aggregation is about 0.5 kcal mol-1. Although modest, its aggregate effect on the free energy of assembling beta-sheet proteins can be huge. This surprising finding, that a simple hydrophobic hexapeptide readily assembles into oligomeric beta-sheets in membranes, reveals the potent ability of membranes to promote secondary structure in peptides, and shows that the formation of beta-sheets in membranes is more facile than expected. Furthermore, it provides a basis for understanding the observation that membranes promote self-association of beta-amyloid peptides. AcWL5 and related peptides thus provide a good starting point for designing peptide models for exploring the principles of beta-sheet formation in membranes.

Circular Dichroism↗
PubMed1998

Determination of the hydrocarbon core structure of fluid dioleoylphosphocholine (DOPC) bilayers by x-ray diffraction using specific bromination of the double-bonds: effect of hydration.

Changes in the structure of the hydrocarbon core (HC) of fluid lipid bilayers can reveal how bilayers respond to the partitioning of peptides and other solutes (Jacobs, R. E., and S. H. White. 1989. Biochemistry. 28:3421-3437). The structure of the HC of dioleoylphosphocholine (DOPC) bilayers can be determined from the transbilayer distribution of the double-bonds (Wiener, M. C., and S. H. White. 1992. Biophys. J. 61:434-447). This distribution, representing the time-averaged projection of the double-bond positions onto the bilayer normal (z), can be obtained by means of neutron diffraction and double-bond specific deuteration (Wiener, M. C., G. I. King, and S. H. White. 1991. Biophys. J. 60:568-576). For fully resolved bilayer profiles, a close approximation of the distribution could be obtained by x-ray diffraction and isomorphous bromine labeling at the double-bonds of the DOPC sn-2 acyl chain (Wiener, M. C., and S. H. White. 1991. Biochemistry. 30:6997-7008). We have modified the bromine-labeling approach in a manner that permits determination of the distribution in under-resolved bilayer profiles observed at high water contents. We used this new method to determine the transbilayer distribution of the double-bond bromine labels of DOPC over a hydration range of 5.4 to 16 waters per lipid, which reveals how the HC structure changes with hydration. We found that the transbilayer distributions of the bromines can be described by a pair of Gaussians of 1/e half-width A(Br) located at z = +Z(Br) relative to the bilayer center. For hydrations from 5.4 waters up to 9.4 waters per lipid, Z(Br) decreases from 7.97 +/- 0.27 A to 6.59 +/- 0.15 A, while A(Br) increased from 4.62 +/- 0.62 A to 5.92 +/- 0.37 A, consistent with the expected hydration-induced decrease in HC thickness and increase in area per lipid. After the phosphocholine hydration shell was filled at approximately 12 waters per lipid, we observed a shift in Z(Br) to approximately 7.3 A, indicative of a distinct structural change upon completion of the hydration shell. For hydrations of 12-16 waters per lipid, the bromine distribution remains constant at Z(Br) = 7.33 +/- 0.25 A and A(Br) = 5.35 +/- 0.5 A. The absolute-scale structure factors obtained in the experiments provided an opportunity to test the so-called fluid-minus method of structure-factor scaling. We found that the method is quite satisfactory for determining the phases of structure factors, but not their absolute values.

Absorption↗
PubMed1997

Critical role of lipid composition in membrane permeabilization by rabbit neutrophil defensins.

We have examined the interactions of the six known rabbit neutrophil defensin antimicrobial peptides with large unilamellar vesicles (LUV) made from various lipid mixtures based on the lipid composition of Escherichia coli membranes. We find that the permeabilization of LUV made from E. coli whole lipid extracts differs dramatically from that of single-component LUV made from palmitoyl-oleoyl-phosphatidylglycerol (POPG). Specifically, defensins NP-1, NP-2, NP-3A, NP-3B, and a natural mixture of the six defensins cause fast nonpreferential leakage of high molecular weight dextrans as well as the low molecular weight fluorophore/quencher pair 8-aminonapthalene-1,3,6 trisulfonic acid (ANTS)/p-xylene-bis-pyridinium bromide (DPX) from E. coli whole lipid LUV through large, transient membrane lesions. In contrast, release of ANTS/DPX from POPG LUV induced by the defensins is slow and graded with preference for DPX (Hristova, K., Selsted, M. E., and White, S. H. (1996) Biochemistry 35, 11888-11894). Interestingly, defensins NP-4 and NP-5 alone do not induce leakage from E. coli whole lipid LUV, whereas only NP-4 is ineffective with POPG LUV. Examination of the sequences of the six defensins suggests that the inactivity of NP-4 and NP-5 may be due to their lower net positive charge and/or the substitution of a Thr for the Arg or Lys that follows the fourth Cys residue. We found the presence of three major lipid components of E. coli whole lipid to be essential for creation of the large lesions observed in LUV: phosphatidylethanolamine, phosphatidylglycerol, and cardiolipin. Cardiolipin appears to play a key role because no leakage can be induced when only phosphatidylglycerol and phosphatidylethanolamine are present. These results indicate the importance of membrane lipid composition in the permeabilization of cell membranes by rabbit defensins.

Amino Acid Sequence↗
PubMed1996

Interactions of monomeric rabbit neutrophil defensins with bilayers: comparison with dimeric human defensin HNP-2.

Human antimicrobial neutrophil defensin HNP-2 has been shown to form large multimeric pores in pure 1-palmitoyl-2-oleoyl phosphatidylglycerol (POPG) bilayers that lead to all-or-none release of vesicle contents [Wimley et al. (1994) Protein Sci.3, 1362-1373]. Because human neutrophil defensins form natural dimers in solution, the question arises as to the role of dimerization in pore formation. However, the dimers are so stable that this question is not easily answered directly. Rabbit neutrophil defensins, whose three-dimensional structures are very similar to those of human defensins, are monomeric in aqueous solution and thus provide an opportunity to test the hypothesis that dimerization may play a role in multimeric pore formation. We therefore examined the interactions of the six known rabbit neutrophil defensins with large unilamellar vesicles (LUV) under the conditions known to lead to stable pore formation by HNP-2. We find that the rabbit defensins bind strongly to LUVs formed from pure POPG or mixtures of POPG with neutral (zwitterionic) phospholipid but induce leakage of vesicle contents only from pure POPG vesicles. Rabbit defensin NP-4 does not cause leakage under any conditions examined. The remaining defensins, NP-1, NP-2, NP-3A, NP-3B, and NP-5, cause graded release of the contents of pure POPG vesicles as does a mixture of the six defensins. The graded release indicates that the rabbit defensins do not form stable pores in the membrane. This result thus suggests that the structural features of human defensins that permit dimer formation in aqueous solution are likely to be important in the formation of multimeric pores.

Amino Acid Sequence↗
PubMed1995

Range and magnitude of the steric pressure between bilayers containing phospholipids with covalently attached poly(ethylene glycol).

The interactive properties of liposomes containing phospholipids with covalently attached poly(ethylene glycol) (PEG-lipids) are of interest because such liposomes are being developed as drug delivery vehicles and also are ideal model systems for measuring the properties of surface-grafted polymers. For bilayers containing PEG-lipids with PEG molecular weights of 350, 750, 2000, and 5000, pressure-distance relations have been measured by X-ray diffraction analysis of liposomes subjected to known applied osmotic pressures. The distance between apposing bilayers decreased monotonically with increasing applied pressure for each concentration of a given PEG-lipid. Although for bilayers containing PEG-350 and PEG-750 the contribution of electrostatic repulsion to interbilayer interactions was significant, for bilayers containing PEG-2000 and PEG-5000 the major repulsive pressure between bilayers was a steric pressure due to the attached PEG. The range and magnitude of this steric pressure increased both with increasing PEG-lipid concentration and PEG size, and the extension length of the PEG from the bilayer surface at maximum PEG-lipid concentration depended strongly on the size of the PEG, being less than 35 A for PEG-750, and about 65 A for PEG-2000 and 115 A for PEG-5000. The measured pressure-distance relations have been modeled in terms of current theories (deGennes, 1987; Milner et al., 1988b) for the steric pressure produced by surface-grafted polymers, as modified by us to take into account the effects of polymer polydispersity and the possibility that, at low grafting densities, polymers from apposing bilayers surfaces can interpenetrate or interdigitate. No one theoretical scheme is sufficient to account for all the experimental results. However, for a given pressure regime, PEG-lipid size, and PEG-lipid surface density, the appropriately modified theoretical treatment gives a reasonable fit to the pressure-distance data.

Kinetics↗
PubMed1993

Flexoelectric effects in model and native membranes containing ion channels.

An experimental study of flexoelectricity in model membranes containing ion pores and native membranes containing ion channels has been undertaken with the objective of determining the relationship, if any, between flexoelectricity and ion transport. Model membrane patches containing ion pores induced by a blue-green algal toxin, microcystin-LR, and locust muscle membrane patches containing potassium channels were studied using patch-clamp techniques. A correspondence was established between the presence of open channels and pores and the amplitude of the 1st harmonic of the total membrane current when the membranes or patches were subjected to pressure oscillations. The 2nd harmonic of the membrane current provided a measure of the amplitude of a membrane curvature induced by pressure, thus making it possible to determine the membrane flexoelectric coefficient. This study shows that flexoelectricity could be an effective driving force for ion transport through membrane pores and channels, thus further highlighting the possible biological significance of this mechano-electric phenomenon.

Cell Membrane↗