Search PubMed⌕ Search

Biomedical subjects

C M Deber

Publications and source records attributed to C M Deber.

At least 55 records · Page 3Linked to original sources
PubMed1992

Transmembrane region of wild-type and mutant M13 coat proteins. Conformational role of beta-branched residues.

Although transmembrane (TM) segments of integral membrane proteins are putatively alpha-helical in conformation, beta-sheet promoters (Val, Ile, Thr) often account for approximately 40% of TM residue composition. We are examining the conformational role(s) of these residues, using as a model system the major coat protein of the filamentous bacteriophage M13. This 50-residue protein, which is located at the Escherichia coli host membrane during phage reproduction, contains a prototypic 19-residue hydrophobic midregion (residues 21-39: YIGYAWAMVVVIVGATIGI). Using "Eckstein" site-directed mutagenesis, we have generated several viable M13 coat protein mutants with beta-branched amino acid substitutions within their TM region. Mutant coat proteins, including Ile32----Val (I32V) and Ala27----Thr (A27T), were obtained in milligram quantities by growing M13 mutant phages in liter preparations, confirming that these coat proteins are capable of assuming their normal biological function(s) in phage reproduction. Circular dichroism spectroscopy performed in the membrane-mimetic medium of deoxycholate micelles indicated comparable alpha-helical contents of mutants I32V and A27T to wild-type protein. 13C nuclear magnetic resonance experiments with mutant A27T demonstrated that the combination of additional beta-branched content and introduction of an -OH substituent induced chemical shift and temperature-dependent changes and influenced the local protein environment at sites up to 12 residues remote from the mutation site. In contrast, mutant I32V (of which a salient feature is a mid-TM pentavaline segment) behaved very similarly to wild-type coat. These findings are interpreted in terms of the range of TM secondary structure and stability which can be accommodated by viable M13 coat protein mutants.

Amino Acid Sequence↗
PubMed1992

Minimum energy conformations of proline-containing helices.

Proline occurs frequently in transmembrane alpha-helices of transport and receptor proteins even though statistical surveys demonstrate the overwhelming preference of this residue for a non-alpha-helical, hydrophilic environment. As a result, membrane-buried proline has been proposed to be functionally important, with function arising from structural discontinuity or destabilization of the helix. Destabilization may occur by Pro-mediated conformational transitions between discrete states, and may be manifested in membrane protein systems through reversible processes such as channel opening and closing or signal transduction. In this study, computer modeling of a model transmembrane alpha-helix, (Ala)8-Leu-Pro-Phe-(Ala)8, in a medium of low polarity (dielectric = 2), is used to examine the occurrence and energetic accessibility of Pro-mediated conformational interconversions. Leu psi and chi 1, Pro psi, and Phe phi and chi 1 torsion angles were assigned random values so that a data base of 200 conformations for each of the cis and trans states was generated. The conformations were minimized and low-energy structures organized into families. This analysis demonstrated that the most populated lowest energy family is the Trans-I conformation, corresponding to proline in a kinked alpha-helix. Two additional trans structures, Trans-II and Trans-III, as well as a cis conformation, Cis-I, are also energetically competitive. Interconversions between the trans states could thus be mediated by changes at a single torsion angle, accompanied by minor local hydrogen-bonding rearrangements. This work substantiates that membrane-buried proline can provide the basis for conformational transitions between discrete alpha-helix-based structures in a nonpolar environment.

Amino Acid Sequence↗
PubMed1991

Viable transmembrane region mutants of bacteriophage M13 coat protein prepared by site-directed mutagenesis.

Bacteriophage M13 coat protein - a 50-residue protein located at the E. coli host membrane during phage reproduction - is subjected to cytoplasmic, membrane-bound, and DNA-interactive environments during the phage life cycle. In research to examine the specific features of primary/secondary structure in the effective transmembrane (TM) region of the protein (residues 21-39: YIGYAWAMVVVIVGATIGI) which modulate its capacity to respond conformationally to the progressive influences of these varying environments, we have prepared over two dozen viable mutant phages with alterations in their coat protein TM regions. Mutants were obtained through use of site-directed mutagenesis techniques in combination with three "randomized" oligonucleotides which spanned the TM region. No subcloning was required. Among mutations observed were those in which each of the four TM Val residues was changed to Ala, and several with increased Ser or Thr content, including one double Ser mutant (G23S-A25S). Polar substitutions arising at Gly23 and Tyr24-including G23D, Y24H, Y24D and Y24N-suggested that this local segment resides external to the host membrane. Milligram quantities of mutant coat proteins are obtained by growing M13 mutant phages in liter preparations, with isotopic (e.g., 13C) labelling at desired sites, for subsequent characterization and conformational analysis in membrane-mimetic media.

Amino Acid Sequence↗
PubMed1991

Central nervous system myelin: structure, function, and pathology.

Multiple sclerosis (MS) and a number of related distinctive diseases are characterized by the active degradation of central nervous system (CNS) myelin, an axonal sheath comprised essentially of proteins and lipids. These demyelinating diseases appear to arise from complex interactions of genetic, immunological, infective, and biochemical mechanisms. While circumstances of MS etiology remain hypothetical, one persistent theme involves recognition by the immune system of myelin-specific antigens derived from myelin basic protein (MBP), the most abundant extrinsic myelin membrane protein, and/or another equally susceptible myelin protein or lipid component. Knowledge of the biochemical and physical-chemical properties of myelin proteins and lipids, particularly their composition, organization, structure, and accessibility with respect to the compacted myelin multilayers, thus becomes central to the understanding of how and why these antigens become selected during the development of MS. This review focuses on current understanding of the molecular basis underlying demyelinating disease as it may relate to the impact of the various protein and lipid components on myelin morphology; the precise molecular architecture of this membrane as dictated by protein-lipid and lipid-lipid interactions; and the relationship, if any, between the protein/lipid components and the destruction of myelin in pathological situations.

Amino Acid Sequence↗
PubMed1991

Conformations of neurotensin in solution and in membrane environments studied by 2-D NMR spectroscopy.

Two-dimensional HOHAHA and ROESY nuclear magnetic resonance techniques are used to obtain complete proton resonance assignments and to perform a conformational investigation of the neuropeptide neurotensin (pGlu-Leu-Tyr-Glu-Asn-Lys-Pro-Arg-Arg-Pro-Tyr-Ile-Leu) in aqueous solution, methanol, and membrane-mimetic [deuterated sodium dodecylsulfate (SDS)] environments. Results suggest the absence of discernible elements of secondary structure in water and methanol. ROESY spectra confirm that Lys-Pro and Arg-Pro peptide bonds are all-trans, but that a significant population of cis Arg-Pro bonds arises in aqueous solution, which increases in the environment of SDS micelles. The conformational ensemble of the peptide is observed to narrow as it becomes bound through its cationic mid-region to SDS micelles, with the accompanying advent of local extended structure. The overall results indicate the inherent conformational flexibility of neurotensin, and emphasize the environmental dependence of conformation in peptides of medium length.

Amino Acid Sequence↗
PubMed1990

Conformation of proline residues in bacteriorhodopsin.

Proline, noted as a hydrophilic residue with helix-breaking potential, nevertheless occurs widely in putatively alpha-helical transmembrane segments of many transport proteins. Ligand-activated or enzyme-assisted trans/cis isomerization of an X-proline peptide bond (where X = any amino acid)--a dynamic, reversible event which could alter the orientation of a transmembrane alpha-helix--may provide the molecular basis for a protein channel regulatory process. Further elucidation of such a function requires knowledge of the isomeric status of the X-Pro bonds in native conformations of membrane proteins. We have used 13C nuclear magnetic resonance (NMR) spectroscopy to examine the conformation of intramembranous X-Pro peptide bonds in biosynthetically-labelled samples of a model transport protein, bacteriorhodopsin (bR) (purple membrane). Spectra of 13C-Tyr-carbonyl labelled bR (in the solvent system CHCl3:CD3OD (1:1) + 0.1 M LiClO4) first established that all 11 bR Tyr residues were sufficiently mobile for their resonances to be detected and resolved, independent of their domain location within the bR sequence. By taking advantage of the known diagnostic chemical shifts of the isomers of Pro-C gamma carbon resonances, spectra of bR labelled with 13C gamma-Pro were then used to demonstrate that all 11 bR X-Pro peptide bonds--including those within the protein's membrane domain (Pro50, Pro91, Pro186)--are in the trans conformation in resting state bR.

Amino Acid Sequence↗
PubMed1990

Ligand-dependent quenching of tryptophan fluorescence in human erythrocyte hexose transport protein.

D-Glucose transport by the 492-residue human erythrocyte hexose transport protein may involve ligand-mediated conformational/positional changes. To examine this possibility, hydrophilic quencher molecules [potassium iodide and acrylamide (ACR)] were used to monitor the quenching of the total protein intrinsic fluorescence exhibited by the six protein tryptophan (Trp) residues in the presence and absence of substrate D-glucose, and in the presence of the inhibitors maltose and cytochalasin B. Protein fluorescence was found to be quenched under various conditions, ca. 14-24% by KI and ca. 25-33% by ACR, indicating that the bulk of the Trp residue population occurs in normally inaccessible hydrophobic regions of the erythrocyte membrane. However, in the presence of D-glucose, quenching by KI and ACR decreased an average of -3.4% and -4.4%, respectively; Stern-Volmer plots displayed decreased slopes in the presence of D-glucose, confirming the relatively reduced quenching. In contrast, quenching efficiency increased in the presence of maltose (+5.9%, +3.3%), while addition of cytochalasin B had no effect on fluorescence quenching. The overall results are interpreted in terms of ligand-activated movement of an initially aqueous-located protein segment containing a Trp residue into, or toward, the cellular membrane. Relocation of this segment, in effect, opens the D-glucose channel; maltose and cytochalasin B would thus inhibit transport by mechanisms which block this positional change. Conformational and hydropathy analyses suggested that the region surrounding Trp-388 is an optimal "dynamic segment" which, in response to ligand activation, could undergo the experimentally deduced aqueous/membrane domain transfer.

Acrylamides↗
PubMed1990

Conformations of proline residues in membrane environments.

Although noted as hydrophilic residues with helix-breaking potential, proline residues are observed in putatively alpha-helical transmembrane (TM) segments of many channel-forming integral membrane proteins. In addition to the recognized property of X-Pro peptide bonds (where X = any amino acid) to occur in cis as well as trans isomeric states, the tertiary amide character of the X-Pro bond confers increased propensity for involvement of its carbonyl group in specific H-bonded structures (e.g., beta- and gamma-turns) and/or liganding interactions with positively charged species. To examine this latter situation in further detail, we identified Leu-Pro-Phe as a consensus sequence triad based on actual occurrences of intramembranous Pro residues in transport protein TM segments. Accordingly, we have undertaken the synthesis of hydrophobic peptides with potential membrane affinity, of which t-butyloxycarbonyl-L-Ala-L-Ala-L-Ala-L-Leu-L-Pro-L-Phe-OH (t-Boc-AAALPF-OH) is an initial compound. Partitioning of this peptide into model membrane environments composed of lipid micelles induces specific conformation(s) for the membrane-bound hexapeptide, as monitored by 75-MHz 13C-nmr spectral behavior of 13C-enriched Leu and Pro carbonyl carbons, and by 300-MHz 1H-nmr spectra of peptide alpha, beta, and aromatic protons. Data are interpreted in terms of an intramolecularly H-bonded inverse gamma-turn conformation in the membrane environment involving the Leu-Pro-Phe triad. The inherent structural instability of a Pro-containing segment in a TM helix due to the multiplicity of possible local conformations is discussed as a functional aspect of membrane-buried prolines in transport proteins.

Carrier Proteins↗
PubMed1989

Bilayer-stabilizing properties of myelin basic protein in dioleoylphosphatidylethanolamine systems.

31P-NMR and X-ray diffraction techniques are used to study the comparative ability of myelin basic protein (MBP) vs. other basic proteins to convert hexagonal (HII) phases to stable lamellar (L alpha) structures. Pure dioleoylphosphatidylethanolamine (DOPE) at pH 9 and 7, and mixtures of DOPE/phosphatidylserine (PS) (95:5 and 80:20% w/w) at pH 7 were employed for this investigation. The polymorphic behavior of the lipid suspensions was evaluated in the presence and absence of several basic proteins (MBP, calf thymus histone, lysozyme, melittin) and the cationic polypeptide, polylysine (PL). Each of the proteins and PL was capable of binding the pure DOPE HII phase at pH 9 but with varying morphological consequences, i.e., lamellar stabilization (MBP, histone, PL), formation of new protein-DOPE HII phases (lysozyme) or lipid disordering/vesiculation (melittin). Reduction to pH 7 resulted in the dissociation of protein from DOPE - with the exception of melittin - and the reformation of a pure lipid HII phase. Additions of PS to DOPE at pH 7 facilitated protein binding, but among the proteins examined, only MBP was capable of converting the lipid suspension into a stable multilamellar form. Differences in the lipid morphology produced by each protein are discussed in terms of protein physicochemical characteristics. In addition, a possible relationship between MBP-lipid interactions and the stability of myelin sheath lipid multilayers is inferred from the significant bilayer-stabilizing capacity of MBP.

Calorimetry, Differential Scanning↗
PubMed1989

A lipid vesicle system for probing voltage-dependent peptide-lipid interactions: application to alamethicin channel formation.

A membrane potential is shown to be established in phosphatidylcholine/cholesterol unilamellar vesicles using valinomycin in conjunction with a potassium ion gradient; this potential is monitored using the externally added fluorescent dye Safranine O. In the same system, transmembrane calcium fluxes are then detected using the (internally trapped) fluorescent dye Quin-2. The calcium-transport behavior of the channel-forming peptide alamethicin is shown to be potential dependent in this system, in contrast to calcium transport by the ionophore Br-A23187, which is unaffected by the potential. The observation of this potential-dependent behavior for alamethicin suggests that this vesicle system may be suitable for direct spectroscopic observation of the voltage-gating process.

Alamethicin↗
PubMed1988

Transpeptidation reactions of porcine pepsin. Formation of tetrapeptides from dipeptide substrates.

Pepsin-catalyzed transpeptidation was studied by high resolution 75 MHz 13C nuclear magnetic resonance spectroscopy. Enrichment with 13C at the carbonyl carbons of the substrates Leu-Tyr-NH2 and Leu-Leu-NH2 facilitated detection and identification of the transpeptidation and hydrolysis products of enzymic action. Porcine pepsin was found in each case to synthesize and release the tetrapeptide Leu-Leu-Leu-Leu as the primary product of transpeptidation, the longest oligomeric product of transpeptidation observed to date. Productive binding of the dipeptide substrates into the active site groove of pepsin required an induction period of several minutes. Quenching experiments suggested the presence of strongly bound intermediate forms of Leu and Leu-Leu prior to observation of any enzyme-free products. The finding of the tetrapeptide as a primary product is discussed as an instance where transpeptidation of the tripeptide competes successfully with the action of pepsin subsite S3 as a trigger for product release.

Animals↗
PubMed1987

D-glucose binding increases secondary structure of human erythrocyte monosaccharide transport protein.

Purified hexose transport protein ("band 4.5") from human erythrocytes, reconstituted in vesicles of its endogenous lipids, displays minima in its circular dichroism (CD) spectrum at 222 and 207 nm, a pattern diagnostic for alpha-helical content of proteins. Upon addition of D-glucose, a saturable increment of +10-12% in negative ellipticity at 222 nm is observed stereospecifically and reproducibly. Addition of L-glucose had no effect on the CD spectrum of the transport protein. Addition of cytochalasin B (CB), a reversible inhibitor of hexose transport, had no effect itself on transporter CD spectra, but restored the spectrum at 222 nm to its original value when added in the presence of D-glucose. The observed D-glucose-induced increase in ordered secondary structure is proposed to result from incorporation into the membrane of a segment of the transport protein originally at a membrane-water interface.

Blood Glucose↗
PubMed1986

Spontaneous vesicularization of myelin lipids is counteracted by myelin basic protein.

Hand-vortexed dispersions of several lipids (cerebrosides, sulfatides, PC, PE, PS and sphingomyelin), mixed in the ratios found for these categories of lipids in myelin, exhibit 31P-NMR spectra which have contributions from both isotropic and lamellar resonances. Investigation of this system by freeze-fracture electron microscopy and X-ray diffraction revealed that this lipid mixture has spontaneously formed small unilamellar vesicles (SUVs) (diam. approximately 400 A) and large highly convoluted unilamellar vesicles (LUVs) (diam. approximately 1000 A), the latter possibly resulting from aggregation and fusion of the SUV structures. This vesicularization of the myelin lipids was reversed by the addition of myelin basic protein: only large multilamellar aggregates were formed in the presence of protein, as shown by all three experimental methods. Although no rigorous physical-chemical explanation for these phenomena is yet available, the possibility is suggested that the high concentration of cerebrosides and/or phosphatidylethanolamine in this particular mixture of myelin lipids play pivotal roles in the formation of these unusual vesicles. Spontaneous vesicularization of myelin lipids is discussed as a potential pathway toward destabilization of the myelin sheath.

Centrifugation, Density Gradient↗
PubMed1986

Amino acid composition of the membrane and aqueous domains of integral membrane proteins.

To identify residues which might impart transport capability to the intramembranous regions of transport proteins, we surveyed available data for the 9991 amino acids contained in the aqueous and intramembranous regions of 24 integral membrane proteins: 10 transport (T) proteins and 14 nontransport (NT) proteins. Statistical comparison of percentage occurrence of each amino acid within T and NT samples provided a measure of "typical" composition of T and NT membrane-spanning regions, and showed that the residues partition into membrane and aqueous domains largely in accord with expectation from hydropathy indices. Comparison of aqueous and membrane domain composition between protein categories revealed a statistically similar distribution of residues in aqueous domains, but significant differences in membrane domains: seven residues (Asn, Asp, Gln, Glu, Phe, Pro, Tyr) were preferred in membrane regions of T proteins, and one (Val) was selectively excluded. Chemical and structural considerations suggested that three of these residues--Asn, Tyr, and Pro--are the most likely functional participants in transport processes.

Amino Acid Sequence↗
PubMed1986

The modulation of bovine milk D-galactosyltransferase by various phosphatidylethanolamines.

To investigate the possible role of nonbilayer phases in the modulation of glycosyltransferase activity, bovine milk D-galactosyltransferase has been studied in phosphatidylethanolamine (PE) membranes, including soybean PE, egg PE, PE prepared by transphosphatidylation of egg PC, bovine brain PE, plasmalogen PE, and DPPE. The gel-to-liquid crystalline transition (TC) and the lamellar-to-hexagonal transitions (TH) are known for most of the PE compounds. The lower the TC (or TH) value, the greater the stimulation of galactosyltransferase activity in both the lactose- and N-acetyllactosamine-synthetase reactions. No correlation was found between either TC or TH value and the break in the Arrhenius plots for the N-acetyllactosamine synthetase. In membranes consisting of mixtures of PE with PC, the dominant effect was that of PC. The stimulation of activity in the mixed-lipid systems was never greater than that produced by PC alone, therefore the enzyme showed a definite preference for PC in the mixtures.

Animals↗