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M Caffrey

Publications and source records attributed to M Caffrey.

At least 55 records · Page 3Linked to original sources
PubMed1995

1H and 13C NMR assignment and secondary structure of Chlorobium limicola f. thiosulfatophilum ferrocytochrome c555.

The 1H resonances of the ferrocytochrome c555 from the anaerobic green sulfur bacterium Chlorobium limicola f thio-sulfatophilum (strain Tassajara) have been assigned. Identification of spin systems and sequential assignment of 1H was accomplished by automated assignment computer programs followed by manual verification. In addition, 13C resonances have been extensively assigned by HSQC experiments at natural abundance. As determined by short-range NOE connectivities, 13C alpha chemical shifts, and HN exchange experiments, the secondary structure consists of 3 helices ranging from residues 3-13, 43-53 and 70-86. Interestingly, the second helix is significantly longer than observed by X-ray crystallography [1977, Proc. Natl. Acad. Sci. USA 74, 5244-5247]. A topological model of the cytochrome c555 is presented based on a small number of long-range NOE contacts. The helices are shown to pack onto the heme according to the pattern common to all class I cytochromes c.

Amino Acid Sequence↗
PubMed1995

NMR assignment of Rhodobacter capsulatus ferricytochrome c', a 28 kDa paramagnetic heme protein.

The cytochromes c' are paramagnetic heme proteins generally consisting of two identical 14 kDa subunits. The 1H and 15N resonances of the ferricytochrome c' from the purple phototrophic bacterium Rhodobacter capsulatus have been extensively assigned by the TOCSY-HSQC, NOESY-HSQC, HSQC-NOESY-HSQC, and HNHA 3D heteronuclear experiments performed on an 8 mM sample labeled with 15N. In addition, the 13C alpha and 13CO resonances were assigned by the HNCA and multiple-quantum HNCOCA 3D experiments performed on a 0.5 mM sample labeled with 13C and 15N. The assignment of the backbone 13C resonances was used to confirm the 1H and 15N assignments and to better define secondary structure. On the basis of medium-range NOEs, 3JHN alpha coupling constants, and backbone 13C chemical shifts, the secondary structure consists of four helices: helix-1 (3-29), helix-2 (33-49), helix-3 (78-97), and helix-4 (103-117). On the basis of long-range NOE contacts, the Rb. capsulatus ferricytochrome c' is a four-helix bundle protein in which consecutive helices are antiparallel with respect to one another.

Amino Acid Sequence↗
PubMed1995

Phases and phase transitions of the sphingolipids.

LIPIDAT is a computerized database providing access to the wealth of information scattered throughout the literature concerning synthetic and biologically derived polar lipid polymorphic and mesomorphic phase behavior. Herein, we present a review of the LIPIDAT data subset referring to sphingolipids together with an analysis of these data. It includes data collected over a 40-year period and consists of 867 records obtained from 112 articles in 25 different journals. An analysis of these data has allowed us to identify trends in hydrated sphingolipid phase behavior reflecting differences in fatty acyl chain length, saturation and hydroxylation, head group type, and sphingoid base identity. Information on the mesomorphism of biologically-derived and dry sphingolipids is also presented. This review includes 161 references.

Animals↗
PubMed1995

Kinetics of lipid phase changes.

In the past two years, the kinetics of transitions involving the assorted lamellar and inverted hexagonal and cubic phases in bulk hydrated lipid systems have been established using a variety of physical techniques. In several cases, the kinetic data have lead to a transition mechanisms being deciphered.

Crystallization↗
PubMed1995

Polymorphism, mesomorphism, and metastability of monoelaidin in excess water.

The polymorphic and metastable phase behavior of monoelaidin dry and in excess water was studied by using high-sensitivity differential scanning calorimetry and time-resolved x-ray diffraction in the temperature range of 4 degrees C to 60 degrees C. To overcome problems associated with a pronounced thermal history-dependent phase behavior, simultaneous calorimetry and time-resolved x-ray diffraction measurements were performed on individual samples. Monoelaidin/water samples were prepared at room temperature and stored at 4 degrees C for up to 1 week before measurement. The initial heating scan from 4 degrees C to 60 degrees C showed complex phase behavior with the sample in the lamellar crystalline (Lc0) and cubic (Im3m, Q229) phases at low and high temperatures, respectively. The Lc0 phase transforms to the lamellar liquid crystalline (L alpha) phase at 38 degrees C. At 45 degrees C, multiple unresolved lines appeared that coexisted with those from the L alpha phase in the low-angle region of the diffraction pattern that have been assigned previously to the so-called X phase (Caffrey, 1987, 1989). With further heating the X phase converts to the Im3m cubic phase. Regardless of previous thermal history, cooling calorimetric scans revealed a single exotherm at 22 degrees C, which was assigned to an L alpha+cubic (Im3m, Q229)-to-lamellar gel (L beta) phase transition. The response of the sample to a cooling followed by a reheating or isothermal protocol depended on the length of time the sample was incubated at 4 degrees C. A model is proposed that reconciles the complex polymorphic, mesomorphic, and metastability interrelationships observed with this lipid/water system. Dry monoelaidin exists in the lamellar crystalline (beta) phase in the 4 degrees C to 45 degrees C range. The beta phase transforms to a second lamellar crystalline polymorph identified as beta* at 45 degrees C that subsequently melts at 57 degrees C. The beta phase observed with dry monoelaidin is identical to the LcO phase formed by monoelaidin that was dispersed in excess water and that had not been previously heated.

Biophysical Phenomena↗
PubMed1995

Membrane-structure studies using X-ray standing waves.

The principle and unique features of X-ray standing waves as a means for investigating membrane structure are described in this review. Thus far, X-ray standing waves have been used in structural studies of Langmuir-Blodgett and self-assembled monomolecular lipid films. Most recently, the method has been used in studies of supported membranes hosting the peripheral membrane protein, cytochrome c. Structural rearrangements occurring in membranes and at surfaces driven by temperature and composition changes have been monitored as well. Finally, ion distribution in the diffuse-double layer next to a charged membrane has been determined using this approach. The review addresses the manner in which these and related measurements were made. What is not covered in the review is a critical appraisal of the limitations of the X-ray standing wave method. Such limitations (which are pronounced and introduce significant mensuration ambiguities at short distances on silver mirrors as used in the membrane protein topology study) have just recently come to our attention and will be reported on separately (S Kirchner, Z Yin, J Wang & M Caffrey, in preparation).

Cytochrome c Group↗
PubMed1994

Assignment of the 13C and 13CO resonances for Rhodobacter capsulatus ferrocytochrome c2 using double-resonance and triple-resonance NMR spectroscopy.

Rhodobacter capsulatus cytochrome c2 uniformly labelled with 13C/15N has been prepared. The 13C resonances of the reduced state, including those of the carbonyl and heme 13C, have been assigned using a combination of various two- and three-dimensional correlated NMR experiments. Assignment of the sidechain 13C resonances facilitated correction of a small number of previously misassigned sidechain 1H and led to the additional assignment of 32 1H. It was found that 13C alpha and 13CO secondary shifts were better indicators of secondary structure than 1H alpha and 13C beta secondary shifts. Moreover, it was demonstrated that, despite the significant ring current effects present in heme proteins, 13C alpha and 13CO secondary shifts can be employed to accurately identify secondary structure in heme proteins, independently of NOE experiments.

Carbon Isotopes↗
PubMed1994

Structure characterization of membrane bound and surface adsorbed protein.

X-ray standing waves (XSW) have been used to study the topology of the protein cytochrome c, bound to a negatively charged model membrane and adsorbed at a metal surface. At the metal surface, cytochrome c forms an hexagonally close-packed monolayer. A similar packing arrangement is observed at the surface of a self-assembled lipid film on silver. The data suggest that cytochrome c maintains its native globular structure upon surface binding and subsequent storage for an extended period. Further, the data are consistent with a protein docking mechanism wherein the heme plane is oriented perpendicular to and with its exposed edge facing the surface. This study demonstrates the utility of XSW as a new and powerful structural tool for investigating membrane- and surface-protein interactions.

Adsorption↗
PubMed1994

The curvature elastic-energy function of the lipid-water cubic mesophase.

Cell and lipid membranes are able to bend, as manifested during membrane fusion and the formation of non-lamellar lyotropic mesophases in water. But there is an energy cost to bending of lipid layers, called the curvature elastic energy. Although the functional form of this energy is known, a complete quantitative knowledge of the curvature elastic energy, which is central to predicting the relative stability of the large number of phases that lipid membranes can adopt, has been lacking. Here we use X-ray synchrotron diffraction measurements of the variation of lattice parameter with pressure and temperature for the periodic Ia3d (Q230) cubic phase of hydrated monoolein to calculate the complete curvature elastic-energy function for the lipid cubic mesophase. This allows us to predict the stabilities of different cubic and lamellar phases for this system as a function of composition.

Glycerides↗
PubMed1994

Phases and phase transitions of the glycoglycerolipids.

LIPIDAT is a computerized database providing access to the wealth of information scattered throughout the literature concerning synthetic and biologically derived polar lipid polymorphic and mesomorphic phase behavior. The database is considered comprehensive for glycerophospholipids, glycoglycerolipids, sphingolipids and natural membrane extracts. Here, a review of the LIPIDAT data subset referring to glycoglycerolipids is presented together with an analysis of these data. The glycoglycerolipids subset represents 4% of all LIPIDAT records. It includes data collected over a 20-year period and consists of 419 records obtained from 37 articles in 13 journals. An analysis of the data in the subset has allowed us to identify trends in hydrated glycoglycerolipids phase behavior reflecting differences in hydrocarbon chain length, chain branching, chain-glycerol linkage type (ether vs. ester), sugar headgroup-glycerol linkage type (alpha vs. beta) and sugar headgroup identity. Included is a summary of the data concerning the effect of pH and of stereochemical purity on glycoglycerolipid phase behavior. Information on the mesomorphism of biologically derived and dry glycoglycerolipids is also presented. This review includes 92 references.

Carbohydrate Sequence↗
PubMed1994

Phases and phase transitions of the hydrated phosphatidylethanolamines.

LIPIDAT is a computerized database providing access to the wealth of information scattered throughout the literature concerning synthetic and biologically derived polar lipid polymorphic and mesomorphic phase behavior. Here, a review of the LIPIDAT data subset referring to hydrated phosphatidylethanolamines (PE) is presented together with an analysis of these data. The PE subset represents 14% of all LIPIDAT records. It includes data collected over a 38-year period and consists of 1511 records obtained from 203 articles in 35 different journals. An analysis of the data in the subset has allowed us to identify trends in synthetic PE phase behavior reflecting changes in lipid chain length, chain unsaturation (number, isomeric type and position of double bonds), chain asymmetry and branching, type of chain-glycerol linkage (ether vs. ester) and headgroup modification. Also included is a summary of the data concerning the effect of pH, stereochemical purity, and different additives such as salts, saccharides, alcohols, amino adds and alkanes on PE phase behavior. Information on the phase behavior of biologically derived PE is also presented. This review includes 236 references.

Chemical Phenomena↗
PubMed1994

Kinetics and mechanism of the barotropic lamellar gel/lamellar liquid crystal phase transition in fully hydrated dihexadecylphosphatidylethanolamine: a time-resolved x-ray diffraction study using pressure jump.

The kinetics and mechanism of the barotropic lamellar gel (L beta')/lamellar liquid crystal (L alpha) phase transition in fully hydrated 1,2-dihexadecyl-sn-glycero-3-phosphoethanolamine (DHPE) has been studied using time-resolved x-ray diffraction (TRXRD). The phase transition was induced by pressure jumps of varying amplitudes in both the pressurization and depressurization directions at controlled temperature (78 degrees C). Both low- and wide-angle diffracted x rays were recorded simultaneously in live time using an x-ray-sensitive image intensifier coupled to a CCD camera and Super-VHS videotape recorder. Such an arrangement allowed for the direct and quantitative characterization of the long- (lamellar repeat spacing) and short-range order (chain packing) during a kinetic experiment. The image-processed live-time x-ray diffraction data were fitted using a nonlinear least-squares model, and the parameters of the fits were monitored continuously throughout the transition. The pressure-induced transitions from the L alpha to the L beta' phase and from the L beta' to the L alpha phase was two-state (no formation of intermediates apparent during the transition) to within the sensitivity limits of the method. The corresponding transit time (the time during which both phases coexist) associated with the long- and short-range order of the pressurization-induced L alpha-to-L beta' phase transition decreased to a limiting value of approximately 50 ms with increasing pressure jump amplitude. This limiting value was close to the response time of the detector/recording system. Thus, the intrinsic transit time of this transition in fully hydrated DHPE at 78 degrees C was less than or equal to 50 ms. In contrast, the depressurization-induced L beta'-to-L alpha phase transition was slower, taking approximately 1 s to complete, and occurred with no obvious dependence of the transit time on pressure jump amplitude. In the depressurization jump experiment, the lipid responded rapidly to the pressure jump in the L beta' phase up to the rate-determining L beta'-to-L alpha transition. Such behavior was examined carefully, as it could complicate the interpretation of phase transition kinetic measurements.

Crystallization↗
PubMed1994

The temperature-composition phase diagram and mesophase structure characterization of monopentadecenoin in water.

The temperature-composition phase diagram of monopentadecenoin, a monoacylglycerol with a cis monounsaturated fatty acid 15 carbon atoms long (C15:1c10) in water was constructed using x-ray diffraction. Low- and wide-angle diffraction patterns were collected from samples of fixed hydration as a function of temperature in the heating direction on x-ray-sensitive film. The temperature and hydration ranges investigated were 0-104 degrees C and 0-60% (w/w) water, respectively. The phases identified in the system include the lamellar crystalline phase, the lamellar liquid crystalline phase, the fluid isotropic phase, and two inverted cubic phases belonging to space groups la3d (Q230) and Pn3m (Q244). Particular attention has been devoted to the issues of phase equilibrium, phase boundary verification, and structure characterization. The phase diagrams of monopentadecenoin, monomyristolein (C14:1c9), and monoolein (C18:1c9) are compared, and the impact of molecular structure on mesophase stability and structure is discussed.

Fatty Acids, Monounsaturated↗
PubMed1994

The neutral area surface of the cubic mesophase: location and properties.

A neutral area surface can be defined as one whose area remains fixed upon bending. It is assumed that such a surface exists within the amphiphilic monolayers that constitute the bicontinuous cubic mesophases and that it parallels approximately the highly convoluted polar/apolar interface in such systems. Here, we report on how the neutral area surface in the cubic phase (space group Ia3d) of the hydrated monoacylglycerol, monoolein, was determined. It is located at a distance of approximately 8.8 A from the methyl terminus of the acyl chain. At 25 degrees C, the surface area per lipid molecule at the neutral area surface is 35.1 +/- 0.2 A2, which is remarkably similar to the mean cross-sectional area of hydrated monoolein in the lamellar liquid crystalline phase at this same temperature.

Biophysical Phenomena↗
PubMed1994

The temperature-composition phase diagram of monomyristolein in water: equilibrium and metastability aspects.

The temperature-composition phase diagram of monomyristolein in water was constructed using x-ray diffraction. Low- and wide-angle diffraction patterns were collected from samples of fixed hydration as a function of temperature in the heating direction on x-ray-sensitive film and/or image plates. The phases identified in the system include the lamellar crystalline phase, the lamellar liquid crystalline phase, the fluid isotropic phase, and two inverted cubic phases. Particular attention has been devoted to the issues of phase equilibrium and phase boundary verification. Cubic phase undercooling was examined by adjusting the temperature of several samples in the cubic phase to a value where the lamellar liquid crystalline phase represents equilibrium behavior. Cooling-induced structure and phase changes were monitored continuously over a 30-min period by recording low-angle diffraction patterns from the samples using a streak camera. The cubic-to-lamellar transition rate decreased with increasing sample hydration. Additionally, the transition proceeded more rapidly at an incubation temperature of 25 degrees C compared to that at 0 degrees C. A mechanism is proposed that accounts for the hydration and temperature sensitivity of the phase transition under nonequilibrium conditions.

Biophysical Phenomena↗
PubMed1993

Observation of inter-subunit nuclear Overhauser effects in a dimeric protein. Application to the Arc repressor.

For the structure determination of symmetric protein dimers it is necessary to distinguish between intra- and inter-subunit NOEs. A method is presented to measure selectively the inter-subunit NOEs using uniform 15N and 13C isotope labelling. This is accomplished by double filtered 2D NOE experiments on mixtures of native protein with isotope-labeled protein. The method has been applied to the Arc repressor and allows the characterization of virtually all proton-proton NOEs in terms of their intra- or inter-subunit nature.

Bacterial Proteins↗
PubMed1993

X-rays destroy the lamellar structure of model membranes.

Lipid membranes undergo a dramatic lamellar-to-non-lamellar phase transformation upon being irradiated with X-rays. The structure change was evidenced by chemical breakdown of the lipid and by a change in the X-ray diffraction properties of the model membrane indicating complete disruption of lamellar stacking. Considering the importance of X-ray diffraction as a structure probe the problem of radiation damage to biological materials must be duly recognized. Because X-ray damage has been shown to be free radical-mediated these results suggest a means by which free radicals accumulating in cells during aging might compromise membrane integrity and contribute to cell death.

Chromatography, Thin Layer↗