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D W Urry

Publications and source records attributed to D W Urry.

At least 55 records · Page 3Linked to original sources
PubMed1989

A mismatch between the length of gramicidin and the lipid acyl chains is a prerequisite for HII phase formation in phosphatidylcholine model membranes.

Previously it was shown that gramicidin can induce HII phase formation in diacylphosphatidylcholine model membranes only when the lipid acyl chain length exceeds 16 carbon atoms (Van Echteld, C.J.A., De Kruijff, B., Verkleij, A.J., Leunissen-Bijvelt, J. and De Gier, J. (1982) Biochim. Biophys. Acta 692, 126-138). Using 31P-NMR and small angle X-ray diffraction we now demonstrate that upon increasing the length of gramicidin, the peptide loses its ability to induce HII phase formation in di-C18:1c-PC but not in the longer chained di-C22:1c-PC. It is concluded that a mismatch in length between gramicidin and the lipid acyl chains, when the latter would provide excess bilayer thickness, is a prerequisite for HII phase formation in phosphatidylcholine model membranes.

Gramicidin↗
PubMed1989

Two-dimensional proton NMR studies on poly(VPGVG) and its cyclic conformational correlate, cyclo(VPGVG)3.

Two-dimensional nuclear Overhauser enhancement (2D NOESY) data are reported for the polypentapeptide of elastin, poly(VPGVG), and the cyclopentadecapeptide, cyclo(VPGVG)3. In both, the repeating type II Pro2-Gly3 beta-turn can be derived from the NOE data, providing confirmation of many previous studies. In addition, other through-space connectivities are detailed that also compare favorably with previously determined crystal and solution structures for cyclo(VPGVG)3. Also, near identical data for the cyclopentadecapeptide and the polypentapeptide demonstrate the cyclic conformation-linear (helical) conformational correlate relationship between the two molecules. The 2D NOESY experiment is seen to be an effective means of establishing the presence or absence of a conformational relationship between a cyclic repeating sequence and its higher molecular weight linear counterpart. This is an approach of substantial practical value when developing the conformation of sequential polypeptides and when attempting to identify the presence of the conformation of a repeating peptide sequence within a more complex primary structure. Having established the basic conformational relationship between a cyclic conformation and its linear helical counterpart, cross peaks present in the linear helical structure that are not present in the cyclic conformational correlate can provide information on the interactions between adjacent turns of the helix. In this connection, a Val gamma CH3 in equilibrium Pro beta CH2 interaction is reported that can be the basis for determining the number of pentamers per turn of helix once it is determined whether it is dominantly the Val1 or Val4 gamma CH3 that is interacting with the Pro2 beta CH2.

Elastin↗
PubMed1989

Elastin repeat peptides as chemoattractants for bovine aortic endothelial cells.

Cultured bovine aortic endothelial cells migrate toward a concentration gradient of repeating elastin peptides, specifically the repeating nonamers Gly-Phe-Gly-Val-Gly-Ala-Gly-Val-Pro and Gly-Leu-Gly-Val-Gly-Ala-Gly-Val-Pro and the repeating hexamer Val-Gly-Val-Ala-Pro-Gly. Dose-response experiments demonstrate that the peak of activity occurs at 8 x 10(-8) M for the nonapeptides and 1 x 10(-8) M for the hexapeptide. Checkerboard assays establish that the movement is chemotaxis and not chemokinesis. Because of the concentration difference in the responsiveness between the nonapeptide and the hexapeptide, the cells can differentiate between the two types of repeats. The positive control for the chemotaxis studies was fibronectin.

Amino Acid Sequence↗
PubMed1989

Synthesis of 4% Glu-containing Val1 and Ile1-polypentapeptides: model protein systems for demonstrating mechanochemical coupling.

The synthesis of 4% Glu-polypentapeptide (PPP) (i.e., 4 Glu residues per 100 amino acid residues) and 4% Glu-Ile1-PPP, in which Val1 is substituted by a more hydrophobic Ile residue, is carried out by copolymerizing the p-nitrophenyl-active esters of GE(OMe)GVP and GE(OMe)GIP with their parent pentamers GVGVP and GVGIP in 1:4 ratios, respectively. After removal of the methyl ester on the side chain of Glu, these polymers exhibited a remarkable pH dependence of the temperature for their inverse temperature transitions, which are followed as turbidity development at 300 nm. On gamma-irradiation crosslinking, the elastomeric bands obtained exhibited a pH-mediated contraction and relaxation. Thus, for the first time, mechanochemical coupling is demonstrated in a synthetic polypeptide system. That the basic mechanism involves the hydrophobic effect (chemical modulation of an inverse temperature transition) and not ion-ion electrostatic repulsion is also discussed.

Glutamates↗
PubMed1989

Nuclear Overhauser effect and computational characterization of the beta-spiral of the polypentapeptide of elastin.

The structure of the elastin polypentapeptide, poly(VPGVG), was studied by nuclear Overhauser effect experiments using perdeuterated Val1 and Val4 samples under the condition where intermolecular interactions are absent. More extensive interaction was found between the Val1 gamma CH and Pro2 beta CH protons than between the Val4 gamma CH and Pro2 beta CH protons. The Val1 gamma CH3-Pro2 beta CH interaction does not occur within the same pentamer as previously shown experimentally and as expected from steric considerations. The results are incompatible with the presence of a random chain network in poly(VPGVG) at room temperature but are readily explicable in terms of interturn interactions in a beta-spiral structure. More specifically, the results indicate that the beta-spiral conformation with 2.9 pentamers/turn is more prevalent than that with 2.7 pentamers/turn. Using conformations developed by molecular mechanics calculations, molecular dynamics simulations were carried out to compare the relative energies of these two variants of this class of beta-spiral structures. It was found in vacuo that the structure with 2.9 pentamers/turn is indeed more stable than that of 2.7 pentamers/turn by approximately 1 kcal/mole-pentamer.

Crystallography↗
PubMed1988

Nucleation and accretion of bioelastomeric fibers at biological temperatures and low concentrations.

Quasi-elastic light scattering (QELS) studies are reported, which address the early stages of aggregation of the polypentamer poly(VPGVG). This reflects the major primary structural feature of native elastin. The study is focused on the region of the phase diagram which in both its temperature and concentration range is closest to the state of affairs occurring in the course of bioelastogenesis by progressive synthesis of the precursor protein. Results here reported allow for the first time a self-consistent view of the physics of elastogenesis, and specify the role of the region of metastability and of that of instability of the phase diagram in the non-chaotic, orderly formation of elastomeric fibers.

Biopolymers↗
PubMed1988

Conformation of gramicidin in relation to its ability to form bilayers with lysophosphatidylcholine.

The ability of gramicidin to induce bilayer formation in lysophosphatidylcholine (LPC) systems was investigated as a function of the conformation of the peptide. The conformation was varied by using different solvents to cosolubilize gramicidin and lipid. Using circular dichroism (CD), it was found that when codissolved in trifluoroethanol (TFE), after drying and subsequent hydration, gramicidin is mainly present in the single-stranded beta 6.3-helical configuration, whereas when using chloroform/methanol or ethanol as the solvent, it is proposed that the dominant conformation of gramicidin in the membrane is that of the double-stranded antiparallel dimer. Employing 31P NMR, the stoichiometry for bilayer formation was found to be 6 to 7 lipid molecules per gramicidin monomer, when samples were prepared from TFE, whereas a stoichiometry of 4 was found when chloroform/methanol or ethanol was the solvent. Upon heating the latter samples, a conversion was observed in the CD pattern toward that indicative of the beta 6.3-helical configuration. This change was accompanied by an increase in the extent of bilayer formation. Next, it was investigated whether the conformation of gramicidin and its ability to induce bilayer formation were dependent on the lipid acyl chain length. CD measurements of samples prepared from TFE indicated that gramicidin, independent of acyl chain length, was present in the beta 6.3-helical configuration but the intensity of the ellipticities at 218 nm increased with the length of the acyl chain. The extent of bilayer formation in these samples was found to be largely chain length independent.(ABSTRACT TRUNCATED AT 250 WORDS)

Cell Membrane↗
PubMed1988

The membrane as an environment of minimal interconversion. A circular dichroism study on the solvent dependence of the conformational behavior of gramicidin in diacylphosphatidylcholine model membranes.

The conformation of gramicidin in diacylphosphatidylcholine model membranes was investigated as a function of the solvent in which peptide and lipid are initially codissolved. By use of circular dichroism it is demonstrated that, upon removal of the solvent and hydration of the mixed gramicidin/lipid film, it is the conformational behavior of the peptide in the organic solvent that determines its final conformation in dimyristoylphosphatidylcholine model membranes. As a consequence, parameters that influence the conformation of the peptide in the solvent also play an essential role, such as the gramicidin concentration and the rate of interconversion between different conformations. Of the various solvents investigated, only with trifluoroethanol is it possible directly to incorporate gramicidin entirely in the beta 6.3-helical (channel) configuration. It is also shown that the conformation of gramicidin in the membrane varies with the peptide/lipid ratio, most likely as a result of intermolecular gramicidin-gramicidin interactions at higher peptide/lipid ratios, and that heat incubation leads to a conformational change in the direction of the beta 6.3-helical conformation. Using lipids with an acyl chain length varying from 12 carbon atoms in dilauroylphosphatidylcholine to 22 carbon atoms in dierucoylphosphatidylcholine, it was possible to investigate the acyl chain length dependence of the gramicidin conformation in model membranes prepared from these lipids with the use of different solvent systems. It is demonstrated for each solvent system that the distribution between different conformations is relatively independent of the acyl chain length but that the rate at which the conformation converts toward the beta 6.3-helical configuration upon heating of the samples is affected by the length of the acyl chain.(ABSTRACT TRUNCATED AT 250 WORDS)

Circular Dichroism↗
PubMed1988

pK shift of functional group in mechanochemical coupling due to hydrophobic effect: evidence for an apolar-polar repulsion free energy in water.

In the sequential polypeptide poly[4(VPGVG),(VPGEG)] and its more hydrophobic analog poly[4(IPGVG),(IPGEG)] when the material is gamma-irradiation cross-linked to form an elastomeric matrix, mechanochemical coupling occurs on changing the pH, that is, motion and mechanical work are achieved by a change in proton chemical potential. The temperature dependence of aggregation at different pH values in phosphate buffered saline demonstrates the pK to be shifted approximately one pH unit higher for the more hydrophobic sequential polypeptide. The pH dependence of contraction or relaxation for each elastomer shows a similar shift. Data are reviewed and 2D-NMR data are presented which argue that the pK shift is not due to different conformations of the polypentapeptides. Specifically it is proposed that there exist a competition between carboxylates and hydrophobic side chains for mutually incompatible water structures; this results in an apolar-polar repulsion free energy in water with the difference in free energy reflecting the difference in the lle and Val hydrophobicities.

Elastin↗
PubMed1988

A method for fixation of elastin demonstrated by stress/strain characterization.

In the process of examining the effects of oxidants on the mechanical properties of purified ligamentum nuchae elastin, it was found that sodium hypochlorite as constituted in Clorox will fix elastin at any preset extension. The treatments were carried out at a 1 to 5 dilution and at 0, 20 and 40% extensions. In each case, the new resting length was near the preset length and the elastic modulus increased remarkably, for example, from 1 to 5 x 10(7) dynes/cm2 for the sample preset at 20% extension. As reflected in the increased elastic modulus, the fixation was achieved by the formation of irreversible cross-links. Due to the near absence of side chains containing chemically reactive groups suitable for contributing to the formation of additional cross-links required in fixation, this is the first method whereby irreversible fixation of elastin has been achieved. The absence of a suitable fixative for elastic tissues such as lung, arteries, etc. has limited the microscopic characterization of functional extended states of these tissues.

Animals↗
PubMed1988

Chemotaxis of fibroblasts toward nonapeptide of elastin.

Bovine ligamentum fibroblasts, which produce elastin, migrate towards a positive chemical gradient of human platelet-derived growth factor and of the tropoelastin repeat hexapeptide Val-Gly-Val-Ala-Pro-Gly, as previously shown. They are also responsive to two permutations of a nonapeptide that repeats in tropoelastin, i.e., Ala-Gly-Val-Pro-Gly-Phe-Gly-Val-Gly and Gly-Phe-Gly-Val-Gly-Ala-Gly-Val-Pro. Concentration curves and checkerboard assays prove that the nonapeptides are chemoattractants. The component pentapeptide, Gly-Phe-Gly-Val-Gly, is chemotactic, while the component tetrapeptide Ala-Gly-Val-Pro is not. The hexapeptide competitively suppresses the nonapeptide chemotaxis suggesting the involvement of a common cell receptor. The results support the concept that elastin has multiple cell recognition sites as measured by the chemotactic response and that among the hydrophobic repeating sequences of elastin chemotacticity is selectively and multiply localized.

Animals↗
PubMed1988

Entropic elastic processes in protein mechanisms. II. Simple (passive) and coupled (active) development of elastic forces.

The first part of this review on entropic elastic processes in protein mechanisms (Urry, 1988) demonstrated with the polypentapeptide of elastin (Val1-Pro2-Gly3-Val4-Gly5)n that elastic structure develops as the result of an inverse temperature transition and that entropic elasticity is due to internal chain dynamics in a regular nonrandom structure. This demonstration is contrary to the pervasive perspective of entropic protein elasticity of the past three decades wherein a network of random chains has been considered the necessary structural consequence of the occurrence of dominantly entropic elastomeric force. That this is not the case provides a new opportunity for understanding the occurrence and role of entropic elastic processes in protein mechanisms. Entropic elastic processes are considered in two classes: passive and active. The development of elastomeric force on deformation is class I (passive) and the development of elastomeric force as the result of a chemical process shifting the temperature of a transition is class II (active). Examples of class I are elastin, the elastic filament of muscle, elastic force changes in enzyme catalysis resulting from binding processes and resulting in the straining of a scissile bond, and in the turning on and off of channels due to changes in transmembrane potential. Demonstration of the consequences of elastomeric force developing as the result of an inverse temperature transition are seen in elastin, where elastic recoil is lost on oxidation, i.e., on decreasing the hydrophobicity of the chain and shifting the temperature for the development of elastomeric force to temperatures greater than physiological. This is relevant in general to loss of elasticity on aging and more specifically to the development of pulmonary emphysema. Since random chain networks are not the products of inverse temperature transitions and the temperature at which an inverse temperature transition occurs depends on the hydrophobicity of the polypeptide chain, it now becomes possible to consider chemical processes for turning elastomeric force on and off by reversibly changing the hydrophobicity of the polypeptide chain. This is herein called mechanochemical coupling of the first kind; this is the chemical modulation of the temperature for the transition from a less-ordered less elastic state to a more-ordered more elastic state. In the usual considerations to date, development of elastomeric force is the result of a standard transition from a more-ordered less elastic state to a less-ordered more elastic state.(ABSTRACT TRUNCATED AT 400 WORDS)

Amino Acid Sequence↗
PubMed1988

Entropic elastic processes in protein mechanisms. I. Elastic structure due to an inverse temperature transition and elasticity due to internal chain dynamics.

Numerous physical characterizations clearly demonstrate that the polypentapeptide of elastin (Val1-Pro2-Gly3-Val4-Gly5)n in water undergoes an inverse temperature transition. Increase in order occurs both intermolecularly and intramolecularly on raising the temperature from 20 to 40 degrees C. The physical characterizations used to demonstrate the inverse temperature transition include microscopy, light scattering, circular dichroism, the nuclear Overhauser effect, temperature dependence of composition, nuclear magnetic resonance (NMR) relaxation, dielectric relaxation, and temperature dependence of elastomer length. At fixed extension of the cross-linked polypentapeptide elastomer, the development of elastomeric force is seen to correlate with increase in intramolecular order, that is, with the inverse temperature transition. Reversible thermal denaturation of the ordered polypentapeptide is observed with composition and circular dichroism studies, and thermal denaturation of the crosslinked elastomer is also observed with loss of elastomeric force and elastic modulus. Thus, elastomeric force is lost when the polypeptide chains are randomized due to heating at high temperature. Clearly, elastomeric force is due to nonrandom polypeptide structure. In spite of this, elastomeric force is demonstrated to be dominantly entropic in origin. The source of the entropic elastomeric force is demonstrated to be the result of internal chain dynamics, and the mechanism is called the librational entropy mechanism of elasticity. There is significant application to the finding that elastomeric force develops due to an inverse temperature transition. By changing the hydrophobicity of the polypeptide, the temperature range for the inverse temperature transition can be changed in a predictable way, and the temperature range for the development of elastomeric force follows. Thus, elastomers have been prepared where the development of elastomeric force is shifted over a 40 degrees C temperature range from a midpoint temperature of 30 degrees C for the polypentapeptide to 10 degrees C by increasing hydrophobicity with addition of a single CH2 moiety per pentamer and to 50 degrees C by decreasing hydrophobicity.(ABSTRACT TRUNCATED AT 400 WORDS)

Chemical Phenomena↗
PubMed1988

A synthetic polypentapeptide of elastin for initiating calcification.

A polypentapeptide (PPP) of tropoelastin having a repeating amino acid sequence of (Val-Pro-Gly-Val-Gly)n was evaluated for its potential to initiate in vivo calcification and to enhance bone formation in nonhealing calvarial wounds (8.0 mm) in 396 adult Walter Reed rats. There were four configurations of the PPP (molecular weight range of 50-100K dalton) consisting of 1-dry PPP; 2-coacervate PPP; 3-gamma irradiated, cross-linked PPP; 4-calcified, gamma irradiated, cross-linked PPP. These four iterations plus a control group of animals constituted the five treatment classes that were evaluated at days 1, 3, 7, 21, 42, and 147. Seventy two rats were used for each treatment and 36 rats for the control. Following euthanatization, specimens were placed into 70% ethanol, embedded in polymethyl methacrylate, sectioned at 3.5 micrometers, and alternating sections were stained with Masson-Goldner trichrome and von Kossa stains. Histomorphometric analysis was accomplished using a Zeiss Universal microscope (250 X) and Videoplan Image Analysis System to evaluate five random histologic fields from margin to margin of the craniotomy. Trabecular bony volume and area of calcification islands were quantitated. A Student's t test for unpaired data to determine treatment differences (within the same temporal groups) revealed that there was no significant difference between treatments and control for trabecular bony volume; however, there was a significant difference between experimentals and control for calcification islands (P less than 0.05) such that calcifications islands for the experimentals were greater than the control. There was not a significant difference between experimental treatments.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗
PubMed1988

Mechanochemical coupling in synthetic polypeptides by modulation of an inverse temperature transition.

For the polypentapeptide of elastin, (L-Val-L-Pro-Gly-L-Val-Gly)n, and appropriate analogs when suitably cross-linked, it has been previously demonstrated that development of elastomeric force at fixed length and length changes at fixed load occur as the result of an inverse temperature transition, with the temperature of the transition being inversely dependent on the hydrophobicity of the polypeptide. This suggests that at fixed temperature a chemical means of reversibly changing the hydrophobicity could be used for mechanochemical coupling. Evidence for this mechanism of mechanochemical coupling is given here with a 4%-Glu-polypentapeptide, in which the valine in position 4 is replaced in 1 out of 5 pentamers by a glutamic acid residue. Before cross-linking, the temperature for aggregation of 4%-Glu-polypentapeptide is remarkably sensitive to pH, shifting from 25 degrees C at pH 2 to 70 degrees C at pH 7.4 in phosphate-buffered saline (PBS). At 37 degrees C, the cross-linked 4%-Glu-polypentapeptide matrix in PBS undergoes a pH-modulated contraction and relaxation with a change from pH 4.3 to 3.3 and back. The mean distance between carboxylates at pH 4.3 in the elastomeric matrix is greater than 40 A, twice the mean distance between negatively charged species in PBS. Accordingly, charge-charge repulsion is expected to make little or no contribution to the coupling. Mechanochemical coupling is demonstrated at fixed load by monitoring pH dependence of length and at constant length by monitoring pH dependence of force. To our knowledge, this is the first demonstration of mechanochemical coupling in a synthetic polypeptide and the first system to provide a test of the recent proposal that chemical modulation of an inverse temperature transition can be a mechanism for mechanochemical coupling. It is suggested that phosphorylation and dephosphorylation may modulate structure and forces in proteins by locally shifting the temperatures of inverse temperature transitions.

Amino Acid Sequence↗