Solid-state NMR investigations of interaction contributions that determine the alignment of helical polypeptides in biological membranes

Helical peptides reconstituted into oriented phospholipid bilayers were studied by proton-decoupled 15N solid-state NMR spectroscopy. Whereas hydrophobic channel peptides, such as the N-terminal region of Vpu of HIV-1, adopt transmembrane orientations, amphipathic peptide antibiotics are oriented parallel to the bilayer surface. The interaction contributions that determine the alignment of helical peptides in lipid membranes were analysed using model sequences, and peptides that change their topology in a pH-dependent manner have been designed. The energy contributions of histidines, lysines, leucines and alanines as well as the alignment of peptides and phospholipids under conditions of hydrophobic mismatch have been investigated in considerable detail.     

Novel polymer substrates for SFM investigations of living cells, biological membranes, and proteins.

Extended studies were performed to prepare substrates for scanning force microscopy of biological samples with a surface roughness below 1 nm rms over an area of 500 x 500 nm2. The substrate smoothness and the lack of tip obscuring material are indispensable in order to visualize detailed structures of membrane surfaces, particularly when scanning the lamellipodia of mechanically sensitive goldfish glial cells where peripheral lamellipodia are only 20-30 nm in thickness. Appropriate substrates are poly(vinyl phenyl ketone) or furan polymers with corrugations of 0.3 and 0.15 nm rms, respectively, to which the growth-promoting protein laminin adsorbs directly with an acceptably increased roughness. Cells show normal growth behavior on these substrates and stick to the substrates in a stable fashion during several scans. Thus details of the membrane's surface may be resolved and are not obscured by the substrate texture. The uncoated furan polymer substrates are suitable for immobilization of membrane preparations such as purified membrane fragments containing bacteriorhodopsin or Na, K-ATPase and protein preparations such as antibodies.     

Fluorine-19 nuclear magnetic resonance studies of lipid phase transitions in model and biological membranes.

Fluorinated fatty acids of the general formula CH3(CH2)13-mCF2(CH2)m-2COOH are informative spectroscopic probes of the gel to liquid-crystalline phase transitions in phospholipid dispersions and in biological membranes. We present theoretical considerations to suggest that the 19F nuclear magnetic resonance line shapes are very different for frozen and fluid lipid regions. Our studies confirm this expectation for mixed phospholipid multilamellar dispersions containing a trace of difluoromyristate. The method correctly measures the onset and completion temperatures of the transition in the well-studied dimyristoylphosphaditylcholine distearoylphosphatidylcholine system and also describes the motional behavior of the solid and fluid phases within the transition. Lipids extracted from Escherichia coli membranes show similar motional phenomena through the transition-temperature range according to 19F nuclear magnetic resonance studies of difluoromyristate biosynthetically incorporated into the K1060B5 strain, an unsaturated fatty acid auxotroph. Intact cells or membrane vesicles show substantially different behavior from extracted lipids, indicating that membrane proteins significantly perturb the phase transition. Evidence presented in this paper also shows that the 19F resonance from Escherichia coli phospholipids is sensitive to various intramembrane interactions. There is a general decrease in restriction of motion due to neutral lipids and an opposite effect due to the architecture of the native membrane. Neither effect is temperature sensitive. However, there are interactions in the intact membrane, affecting the 19F resonance, that are temperature dependent both due to the phase-transition process and due to processes occurring at high temperatures.     

The dynamic properties of biological membranes.

Biological membranes must be viewed as highly dynamic, undergoing continuous structural fluctuations and changes in response to external perturbations. The study of liposomes by 31 P n.m.r. and fluorescence can reveal some of the motional characteristics of the different regions in a bilayer. Asymmetric lipid distribution and how this depends on the environment is also observed by n.m.r. The nature of the interaction of amine anaesthetics and of polypeptide antibodies with membranes is discussed in relation to their perturbing effect. The role of lipid mobility in modulating hormone-receptor interaction is discussed with reference to the binding of thyroid stimulating hormone.     

Alamethicin-induced pore formation in biological membranes.

The effects of alamethicin on the membrane barrier function of rabbit erythrocytes, human platelets and sarcoplasmic reticulum vesicles, as well as on that of brain microsomes and liver mitochondria of the rat were compared. An upset of the barrier function was observed for plasma membranes of brain microsomes as well as for erythrocyte and platelet membranes at alamethicin concentrations ranging between 25-80 micrograms/ml. The membrane barrier functions of sarcoplasmic reticulum vesicles, of endoplasmic reticulum vesicles of rat brain microsomes, and of liver mitochondria were disturbed at 3-7 micrograms/ml alamethicin. The different sensitivities of plasma and intracellular membranes to alamethicin were supposed to be due to the presence of considerable quantities of cholesterol in plasma membranes as well as to peculiarities of their protein compositions.     

Pareto-optimal alignment of biological sequences]

The problem of alignment of two symbol sequences is considered. The validity of the available algorithms for constructing optimal alignment depends on the weighting coefficients which are frequently difficult to choose. A new approach to the problem is proposed, which is based on the use of vector weighting functions (instead of tradionally used scalar ones) and Pareto-optimal alignment (an alignment that is optimal at any choice of weighting coefficient will always be Pareto-optimal). An efficient algorithm for constructing all Pareto-optimal alignments of two sequences is proposed. An approach to choosing a "biologically correct" alignment among all Pareto-optimal alignments is suggested.     

生物序列比对算法的研究现状

序列比对是生物信息学研究的一个重要工具,它在序列拼接、蛋白质结构预测、蛋白质结构功能分析、系统进化分析、数据库检索以及引物设计等问题的研究中被广泛使用。本文详细介绍了在生物信息学中常用的一些序列比对算法,比较了这些算法所需的计算复杂度,优缺点,讨论了各自的使用范围,并指出今后序列比对研究的发展方向。     

Estimation of surface charges in some biological membranes.

The resting membrane potential data existing in the literature for the giant axon of the squid, frog muscle and barnacle muscle have been analyzed from the standpoint of the theory of membrane potential due to Kobatake and co-workers. The average values derived for the effective charge density phi chi (where phi is a constant, 0 less than phi less than 1, and represents the fraction of counterions that are free, and chi is the stoichiometric charge density in the membrane) present on the different biomembranes existing in their normal ionic environment are 0.3, 0.325 and 0.17 M for the squid axon, frog and barnacle muscles, respectively. On the assumption that the values of phi are 0.4 and 0.2 for nerve and muscle membranes, respectively, values of 0.75, 1.62 and 0.85 M have been derived for the stoichiometric charge density (chi) present in the respective biological membranes. These correspond to 1 negative charge per 222, 103 and 195 A2 of the membrane area of the squid axon, frog and barnacle muscles, respectively.     

Electric fields induced in chicken eggs by 60-Hz magnetic fields and the dosimetric importance of biological membranes.

Chicken eggs are convenient models for observing the effects of inhomogeneities and variations, such as those found in biological membranes and in cellular conductivities, on the distribution of internal electric fields as induced by exposure to magnetic fields. The vitelline membrane separates the yolk, which has a conductivity of 0.26 S/m, from the white, which has a conductivity of 0.85 S/m. A miniaturized probe with 2.4-mm resolution was used to measure induced fields in eggs placed in a uniform, 1-mT magnetic field at 60 Hz. The E fields induced in eggs with homogenized contents agreed with expectations based on simple theory. Results were similar to intact eggs unless the probe moved the yolk off-center, which greatly perturbed the induced fields. A more reproducible arrangement, which consisted of saline-agar filled dishes with a hole cut for test samples, was developed to enhance definition of electrical parameters. With this test system, the vitelline membrane was found to be responsible for most of the perturbation of the induced field, because it electrically isolates the yolk from the surrounding white. From a theoretical viewpoint, this dosimetry for the macroscopic egg yolk is analogous to the interaction of fields with microscopic cells. These findings may have important implications for research on biological effects of ELF electromagnetic fields, especially for studies of avian embryonic development.     

Domains in biological membranes

Our current view on biological membranes has gradually evolved from the influential fluid mosaic model of the early 1970s to a distinctively more complex picture. Biological membranes are now assumed to encompass multiple membrane domains and a plethora of protein-lipid and protein-protein interactions that compartmentalize and temporarily order what has originally been envisioned to be mostly random. In this minireview, we will first highlight some structural principles that govern membrane domain formation and permit a classification of membrane domains. We will then focus on the still controversial issue of lipid-based membrane domains, or lipid rafts, and discuss recent advances in detecting these enigmatic structures in living cells. Finally we will evaluate biochemical approaches to characterize lipid rafts and discuss their contribution to the emerging topic of lipid raft diversity     

The organization of biological membranes

A nomenclature for the organization of biological membranes is proposed. The terms primary (composition), secondary (transverse and lateral distribution), tertiary (membrane stacking/unstacking), and quaternary (membrane-membrane, cell-cell interactions) levels of organization are used by analogy with protein structure, but at each level the membrane organization is more complex and dynamic than protein structure.