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Biomedical subjects

B P Gaber

Publications and source records attributed to B P Gaber.

At least 19 recordsLinked to original sources
PubMed1995

Thermodynamics of interaction of the fusion-inhibiting peptide Z-D-Phe-L-Phe-Gly with dioleoylphosphatidylcholine vesicles: direct calorimetric determination.

The binding of the fusion-inhibiting peptide Z-D-Phe-L-Phe-Gly to unilamellar lipid vesicles of dioleoylphosphatidylcholine (DOPC) was investigated by isothermal titration calorimetry (ITC). The peptide Z-D-Phe-L-Phe-Gly is known to inhibit fusion of myxo- and paramyxoviruses with cells as well as cell-cell and vesicle-vesicle fusion in model systems. Calorimetric titrations conducted over a range of temperatures permitted characterization of the thermodynamics of the interaction of Z-D-Phe-L-Phe-Gly with model DOPC lipid membranes. Simultaneous global analysis of 15 ITC binding curves acquired at four different temperatures allowed determination of the equilibrium site association constant (K), stoichiometry of binding (n), binding enthalpy change (delta H), and heat capacity change of binding (delta Cp) in a single set of experiments. The binding affinity and enthalpy change per mole of DOPC bound at 25 degrees C was log K = 2.463 +/- 0.075 and delta H = -1.07 +/- 0.12 kcal/mol DOPC while the binding heat capacity change per mole of DOPC bound was delta Cp = -20.3 +/- 2.8 cal/(K.mol DOPC) with a temperature dependence (from 10-45 degrees C) of d(delta Cp)/dT = 0.37 +/- 0.18 cal/(K2.mol DOPC). A temperature-independent binding stoichiometry was determined to be n = 5.56 +/- 0.33 DOPC molecules per Z-D-Phe-L-Phe-Gly. A comparison of these results with previous peptide-lipid binding studies is discussed as is their relevance to a current model of the interaction of fusion-inhibiting peptides with phospholipid membranes.

Antiviral Agents↗
PubMed1995

Expression of the Neurospora crassa metallothionein gene in Escherichia coli and its effect on heavy-metal uptake.

The gene coding for the Neurospora crassa metallothionein protein was chemically synthesized and cloned into the fusion expression vectors pMal-c and pMal-p. Cell-fractionation experiments demonstrated the proper localization of the pMal-c and pMal-p- expressed proteins to the cytosol and periplasm of the bacteria respectively. Control bacteria as well as the recombinant bacteria producing the metallothionein protein were incubated with solutions of 109Cd at concentrations of 0.2 microM, 1 microM, and 10 microM. The recombinant bacteria were able to accumulate significantly more 109Cd than control bacteria at all concentrations tested. Cadmium accumulation was rapid and highly selective. Maximum uptake was achieved at a pH of 7.0, with lower accumulation at lower or higher pH values. The pH-dependent uptake of cadmium by the recombinant bacteria was exploited to strip off the bound cadmium from the recombinant bacteria and to regenerate most of the cadmium-binding sites. These observations suggest the potential for using a metallothionein-based biosorbent for certain heavy-metal removal applications.

ATP-Binding Cassette Transporters↗
PubMed1995

Interaction of small peptides with lipid bilayers.

Molecular dynamics simulations of the tripeptide Ala-Phe-Ala-O-tert-butyl interacting with dimyristoylphosphatidylcholine lipid bilayers have been carried out. The lipid and aqueous environments of the peptide, the alkyl chain order, and the lipid and peptide dynamics have been investigated with use of density profiles, radial distribution functions, alkyl chain order parameter profiles, and time correlation functions. It appears that the alkyl chain region accommodates the peptides in the bilayer with minimal perturbation to this region. The peptide dynamics in the bilayer bound form has been compared with that of the free peptide in water. The peptide structure does not vary on the simulation time scale (of the order of hundreds of picoseconds) compared with the solution structure in which a random structure is observed.

Amino Acid Sequence↗
PubMed1994

NanoVision--molecular graphics for the Macintosh.

NanoVision is a molecular graphics program for the Apple Macintosh. The program follows accepted Macintosh design criteria, making it easy to learn by anyone familiar with the Macintosh. Molecules containing up to 32,000 atoms may be displayed. The program includes a range of molecular display options, including skeletal, ball-and-stick, and CPK. Images may be displayed using up to 240 colors. Color depth cuing is provided, as is Z-clipping. NanoVision images may be easily transferred (cut and paste) to drawing programs.

Carbonic Anhydrases↗
PubMed1994

Calcium ionophore, A23187 and its amino acid complexes: spectroscopic and molecular modeling studies.

The circular dichroism, fluorescence, Nuclear Magnetic Resonance and BLM conductance studies indicate that A23187 forms a stable complex with amino acids at low ionophore concentrations (< 10(-4)M). However, A23187 prefers to be in a dimeric structure with no significant binding to amino acids, at concentrations higher than 10(-4)M. It was also observed that at lower concentrations, at which the amino acids bind to the ionophore, the affinity for calcium ions was several orders of magnitude lower than that at higher ionophore concentrations. We have also conducted molecular modeling studies to examine the structure of the A23187 dimer and its amino acid complexes. The results of these modeling studies strongly support our experimental results and validate the formation of a hydrogen bonded and energetically stable A23187 dimer and its amino acid complexes.

Amino Acids↗
PubMed1992

Structure and dynamics of the dilauroylphosphatidylethanolamine lipid bilayer.

A 200-ps molecular dynamics (MD) simulation trajectory of a model dilauroylphosphatidylethanolamine (DLPE) bilayer in water at 315 K has been generated. Segmental order parameters, electron density profiles, and water pair distribution functions have been calculated. Comparison to experiment is made where possible. The dynamics of the system has been studied by analyzing the velocity autocorrelation functions (VAF) of both water and lipid atoms. Furthermore, the diffusive properties of water have been analyzed by computing the mean square displacement (MSD) and orientational correlation function (OCF) of water in two regions around the bilayer. The calculated order parameters show a behavior similar to the liquid crystalline phase of other bilayers, but the region around C1-C3 does not show the expected behavior. The electron density profile shows features that are characteristic of the liquid crystalline phase. The radial distribution functions suggest ordering of water near the charged head groups, which results in about 15 water molecules solvating each lipid molecule. We find from the VAF, MSD, and OCF calculation that the water molecules near the head groups of the lipid bilayer move more slowly than those further away. The VAF of the hydrocarbon chains have features of low-frequency motions that are probably cooperative nature in addition to the high-frequency motions associated with bond angle and torsional motions.

Lipid Bilayers↗
PubMed1992

A crystallographic molecular lattice builder applied to model lipid bilayers.

It is often desirable for noncrystallographers to generate graphical models of three-dimensional crystal structures based on published coordinates of the atoms that make up the crystallographic unit cells. This type of visualization is particularly important for small-molecule crystals, such as lipid crystals, where one may be interested in investigating interactions between the individual molecules in addition to their conformations. BILAYER BUILDER is a program that generates a portion of the entire crystal structure from the coordinates of the molecules in a single unit cell. It gives users of small desktop computers, such as the Apple Macintosh, the capability to generate and examine model crystal structures with a molecular graphics display program. BILAYER BUILDER stores the crystal coordinates in a Brookhaven Protein Data Bank file format for possible use in a variety of applications on many different computers. Initially, it was written for use with lipid crystals and bilayers but may be used for building an assortment of molecular crystals.

Computer Graphics↗
PubMed1992

Using a RIBBON program to illustrate lipid bilayer packing.

We describe the use of the Priestle RIBBON program suite for the illustration of lipid bilayer packing. The hydrocarbon chains of lecithin-like molecules are representable by beta-sheet arrows. The lateral packing, packing across the bilayer midline and any twisting, bowing, or curling of the polymethylene chain are readily detectable.

Computer Graphics↗
PubMed1992

Lipid conformational nomenclature: a general method.

We propose a conformational nomenclature for amphiphilic lipid molecules that is general and compatible with the stereospecific numbering scheme, in contrast to earlier methods in which discrepancies with the sn-scheme lead to contradictory assignments of the absolute configuration of the system. The present method can be rationally extended to different classes of lipids, both natural and synthetic. It is simple and provides a convenient framework for conformational studies on widely varying classes of lipids.

Lipids↗
PubMed1990

Insertion of bacteriorhodopsin into polymerized diacetylenic phosphatidylcholine bilayers.

We have developed a method to incorporate the membrane protein bacteriorhodopsin into polymerized bilayers composed of a diacetylenic phosphatidylcholine, 1,2-bis(tricosa-10,12-diynoyl)-sn-glycero-3-phosphocholine (DC8,9PC) and a non-polymerizable phospholipid, dinonanoylphosphatidylcholine (DNPC). The extent of DC8,9PC polymerization in the bilayer was significantly improved when 2:1 mole ratio DNPC-DC8,9PC was used. Octyl glucopyranoside-solubilized bacteriorhodopsin was inserted into the polymerized DNPC-DC8,9PC bilayers by overnight incubation at 4 degrees C followed by dialysis to remove the detergent. The protein was inserted into the membranes after photo-polymerization to avoid inactivation of the protein due to the UV irradiation. The insertion of bacteriorhodopsin into the polymerized DNPC-DC8,9PC membranes was confirmed by density gradient centrifugation, UV/visible spectroscopy, and freeze fracture electron microscopy. The polymerized DNPC-DC8,9PC membranes containing bacteriorhodopsin were about 10% protein by weight. These results suggest that mixed lipid systems such as the DNPC-DC8,9PC can be used to improve both the extent of polymerization and the efficiency of membrane protein incorporation in the polymerized bilayer.

Bacteriorhodopsins↗
PubMed1990

NRL-3D: a sequence-structure database derived from the protein data bank (PDB) and searchable within the PIR environment.

The protein identification resource (PIR) and the Brookhaven National Laboratory protein data bank (PDB) are well-known databases for primary sequences and three-dimensional structures of proteins, respectively. Lesk et al, have compared the primary sequences in these two databases and concluded that the sequences in them are not redundant. Moreover, PIR programs can not be used directly on PDB files to access primary sequences because the FORMATS of these two data bases are different. We have developed a sequence-structure database, called NRL-3D, from the sequences, chain identification and the residue numbers of proteins in the PDB. This new database is designed such that it can be used in conjunction with PIR programs to search and extract sequences of interest and the corresponding three-dimensional coordinates from the structures in PDB.

Amino Acid Sequence↗
PubMed1988

Stabilization of the bio-membrane by small molecules: interaction of trehalose with the phospholipid bilayer.

Anhydrobiotic organisms undergo periods of acute dehydration during their life cycle. It is of interest to understand how the biomembrane remains intact through such stress. A disaccharide, trehalose, which is metabolised during anhydrobiosis is found to prevent disruption of model membrane systems. Molecular modelling techniques are used to investigate the possible mode of interaction of trehalose with a model monolayer. The objective is to maximise hydrogen bonding between the two systems. A phospholipid matrix consisting of 1,2-dimyristoyl-sn-glycero-3-phosphatidylcholine (DMPC) is chosen to represent the monolayer. The crystal structure of DMPC reveals that there are two distinct conformers designated as A and B. An expansion of the monolayer, coplanar with its surface, results in the trehalose molecule being accommodated in a pocket formed by four B conformers. One glucose ring of the sugar rests on the hydrophobic patch provided by the choline methyls of an A conformer. Five hydrogen bonds are formed involving the phosphate oxygens of three of the surrounding B conformers. The model will be discussed with reference to relevant experimental data on the interaction.

Dimyristoylphosphatidylcholine↗