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D W Urry

Publications and source records attributed to D W Urry.

At least 19 recordsLinked to original sources
PubMed1995

Ion pair binding of Ca2+ and Cl- ions in micellar-packaged gramicidin A.

The two independent NMR experiments were performed to investigate the interaction between CaCl2 and the gramicidin A (GA) ion transport channel, using 13C-enriched GA and GA molecules incorporated into dodecylphosphocholine (DPC) micelles. The chemical shifts of C-13 labeled carbonyl carbons vs. CaCl2 concentration demonstrate that Ca2+ and Cl- ions interact as an ion pair within the GA structure with the Cl- ion located near the position of the carbonyl group of the Trp11 residue some 5.5 A from the mouth of the GA helix, and the Ca2+ ion bound at the position of the carbonyl group of the Trp15 residue some 2.5 A from the entrance to the helical pore. The measurements of the 35Cl line-widths and transverse relaxation times illustrate that the interaction occurs between Cl- ions and GA in DPC when in CaCl2 solution, that no interaction is detected between Cl- ions and GA in DPC when in NaCl solution, and that the interaction between Cl- ions and GA in DPC when in MgCl2 solution is much weaker than in CaCl2 solution. In short, a Cl- ion can enter the GA when it is paired with a divalent Ca2+ ion; and Ca2+ and Cl- ions as a pair exchange rapidly with sites of the GA dimer.

Amino Acid Sequence↗
PubMed1995

The determination of binding constants of micellar-packaged gramicidin A by 13C-and 23Na-NMR.

Based on the malonyl gramicidin A structure of a single-stranded head-to-head hydrogen bonded right-handed, beta 6.3-helix in dodecyl phosphocholine (DPC) lipid micelles (Jing et al. (1994) Biophys. J. 66, A353), the determination of cation binding sites for gramicidin A (GA) in DPC micelles becomes a significant step in the study of ion transport through the model channel. First, the investigation of cation binding sites in DPC micellar packaged gramicidin A was achieved by 13C-NMR experiments at 30 degrees C using four C-13 labeled GA samples. Then, the analyses based on two different equations, one for single and one for double occupancy, were employed to evaluate the correct occupancy model for GA in DPC micelles. The results clearly indicate double occupancy to be correct for Na+ ion as well as for K+, Rb+, Cs+, and Tl+ ions. Finally, the binding constants for Na+ ion were also estimated by the measurement of the longitudinal relaxation time (T1) using 23Na-NMR of the same sample at the same ffmperature as used for the 13C-NMR study. The binding constants obtained from 23Na-NMR are essentially equivalent to those determined from the 13C-chemical shifts.

Amino Acid Sequence↗
PubMed1992

Reduction-driven polypeptide folding by the delta Tt mechanism.

Poly(Gly-Val-Gly-Val-Pro), i.e., poly(GVGVP), exhibits composition and solute dependence of Tt, the temperature of the inverse temperature transition at which hydrophobic folding and assembly occur on raising the temperature. Importantly, a means whereby the value of Tt is lowered from above to below the working temperature becomes an isothermal means of driving folding and assembly, i.e., of achieving free energy transduction. Using poly[0.73(GVGVP),0.27(GK[NMeN]GVP)] where [NMeN] indicates N-methyl nicotinamide attached to the epsilon-NH2 of the Lys(K) residue, chemical and electrochemical reductions are found to remarkably lower the value of Tt; reduction can drive hydrophobic folding and assembly as effectively as decreasing ionization. Changing the redox state of a protein becomes yet another means of achieving free energy transduction by the delta Tt mechanism.

Amino Acid Sequence↗
PubMed1992

Hydrophobicity-induced pK shifts in elastin protein-based polymers.

Three polypentapeptides--poly[0.8(GVGVP), 0.2(GEGVP)], poly[0.8(GVGIP), 0.2(GEGIP)], and poly[0.75(GFGVP), 0.25(GEGVP)]--all analogues of the polypentapeptide of elastin--(Val1-Pro2-Gly3-Val4-Gly5)n or poly(VPGVG)--have been prepared to determine the effect of changing the hydrophobicity, i.e., Val1----Ile1 (I) and Val4----Phe4 (F), on the pKa and the temperature dependence of pKa of the Glu (E) residue. Shifts in pKa as large as 1.7 units are observed and the temperature dependence is much steeper for the structure-dependent proximity of the more hydrophobic Ile1 residues to the Glu4 residue. Even though this system is dominated by the inverse temperature transition of hydrophobically driven folding on raising the temperature, the effect of adding 0.15 N NaCl is to suppress the hydrophobicity-induced pKa shift.

Amino Acid Sequence↗
PubMed1992

Hydrophobicity scale for proteins based on inverse temperature transitions.

In general, proteins fold with hydrophobic residues buried, away from water. Reversible protein folding due to hydrophobic interactions results from inverse temperature transitions where folding occurs on raising the temperature. Because homoiothermic animals constitute an infinite heat reservoir, it is the transition temperature, Tt, not the endothermic heat of the transition, that determines the hydrophobically folded state of polypeptides at body temperature. Reported here is a new hydrophobicity scale based on the values of Tt for each amino acid residue as a guest in a natural repeating peptide sequence, the high polymers of which exhibit reversible inverse temperature transitions. Significantly, a number of ways have been demonstrated for changing Tt such that reversibly lowering Tt from above to below physiological temperature becomes a means of isothermally and reversibly driving hydrophobic folding. Accordingly, controlling Tt becomes a mechanism whereby proteins can be induced to carry out isothermal free energy transduction.

Amino Acid Sequence↗
PubMed1992

Hydrophobicity of amino acid residues: differential scanning calorimetry and synthesis of the aromatic analogues of the polypentapeptide of elastin.

Relative hydrophobicities of aromatic amino acid residues are investigated by using differential scanning calorimetry (DSC) on 10 synthetic copolypentapeptides of poly(VPGVG) of elastin. Utilizing the hydrophobic-driven process of the inverse temperature transition exhibited by these polypentapeptides in aqueous solution, the relative hydrophobicities of Phe, Trp, and Tyr residues are determined by the critical temperature and heat of the transition. The DSC data for the aromatic residue containing copolypentapeptide aqueous solution indicate that tryptophan is the most hydrophobic amino acid residue, phenylalanine the third most hydrophobic on basis of transition temperature and the second on basis of transition heat. For tyrosine, significant differences are observed between the phenolic and the phenoxide anionic states. At pH 7, where tyrosine is protonated, it is found to be the second most hydrophobic amino acid residue on the basis of the transition temperature, whereas on the basis of the heat of transition, it is less hydrophobic than both tryptophan and phenylalanine. Changing the pH from pH 7 to pH 12, for example, for poly[0.8(VPGVG), 0.2(VPGYG)] in aqueous solution shifts the transition temperature from 7 to 49 degrees C with a dramatically reduced heat. On the basis of both the transition temperature scale and the heat of transition, the hydroxylated tyrosine appears less hydrophobic than glycine.

Amino Acid Sequence↗
PubMed1992

Cell adhesion and growth on synthetic elastomeric matrices containing Arg-Gly-Asp-Ser-3.

Synthetic elastomeric polypeptide matrices based on the repeating amino acid sequences of elastin have biophysical and biological properties which are favorable for prosthetic materials. An important requirement envisaged for some applications is the ability to support cell adhesion and growth. The X20-poly-(GVGVP), the gamma-irradiation cross-linked elastomeric matrix based on the repeating pentamer Val-Pro-Gly-Val-Gly, and X20-poly[n(GVGVP), (GRGDSP)] containing the covalently incorporated cell adhesion sequence Arg-Gly-Asp-Ser (RGDS) were synthesized. These matrices were tested for their ability to support the adhesion and growth of bovine aortic endothelial cells and of bovine ligamentum nuchae fibroblasts. Adhesion experiments carried out in albumin-containing media showed that matrices containing 60:1, 40:1, and 20:1 ratios of (GVGVP):(GRGDSP) supported maximal cell attachment, that matrices containing 100:1 exhibited an intermediate level of attachment and that matrices composed of 500:1 and (GVGVP) alone were very poor supports for cell attachment. Serum in the media promoted submaximal cell attachment to X20-poly(GVGVP) but did not permit substantial cell growth. Cell growth was supported by matrices having high ratios of (GRGDSP). Ratios of 60:1, 40:1, and 20:1 supported three population doublings of endothelial cells over 3 days resulting in confluent matrix-adherent monolayers. Ratios of 40:1 and 20:1 similarly supported the growth of fibroblasts.

Amino Acid Sequence↗
PubMed1991

Phosphorylation and dephosphorylation modulation of an inverse temperature transition.

Poly[15(IPGVG),(RGYSLG)], where RGYSLG is a protein kinase site, was synthesized. On raising the temperature of a 5 mg/ml solution, this polypeptide undergoes an inverse temperature transition at 18 degrees C in which it folds into a contracted state by optimizing intramolecular hydrophobic interactions. Averaging the data of five experiments, phosphorylation by means of a 3':5' cyclic AMP dependent protein kinase to the extent of one phosphate in 360 residues raises the temperature of the folding transition to 32 degrees C. The shift is completely reversed on dephosphorylation by alkaline phosphatase. Phosphorylation is hereby shown to be the most potent chemical perturbation known for shifting the temperature of an inverse temperature transition, which has been shown to be an efficient mechanism for achieving chemomechanical transduction (mechanochemical coupling).

Alkaline Phosphatase↗
PubMed1991

Differential scanning calorimetry studies of NaCl effect on the inverse temperature transition of some elastin-based polytetra-, polypenta-, and polynonapeptides.

Differential scanning calorimetry studies of the effect of NaCl on protein-based polymer self-assembly has been carried out on six elastin-based synthetic sequential polypeptides--i.e., the polypentapeptide (L-Val1-L-Pro2-Gly3-L-Val4-Gly5)n and its more hydrophobic analogues (L-Leu1-L-Pro2-Gly3-L-Val4-Gly5)n and (L-Val1-L-Pro2-L-Ala3-L-Val4-Gly5)n; the polytetrapeptide (L-Val1-L-Pro2-Gly3-Gly4)n and its more hydrophobic analogue (L-Ile1-L-Pro2-Gly3-Gly4)n; and the polynonapeptide (a pentatetra hybrid), (L-Val1-L-Pro2-Gly3-L-Val4-Gly5-L-Val6-L-Pro7-Gly8-Gly9++ +)n. Previous physical characterizations of the polypentapeptides have demonstrated the occurrence of an inverse temperature transition since increase in order of the polypentapeptide, as the temperature is raised from below to above that of the transition, has been repeatedly observed using different physical characterizations. In the present experiments, it is observed that the transition temperatures of the polypeptides studied are linearly dependent on NaCl concentration. The molar effectiveness of NaCl in shifting the transition temperature delta Tm/[N], is about 14 degrees C/[N], with the dependence on peptide hydrophobicity being fairly small. Interestingly, however, the delta delta Q/[N] does depend on the hydrophobicity of a polypeptide.

Amino Acid Sequence↗
PubMed1990

Differential scanning calorimetry studies of the inverse temperature transition of the polypentapeptide of elastin and its analogues.

Differential scanning calorimetry studies have been carried out on the sequential polypeptide of elastin, (L-Val1-L-Pro2-Gly3-L-Val4-Gly5)n, abbreviated as PPP, and its more hydrophobic analogues (L-Leu1-L-Pro2-Gly3-L-Val4-Gly5)n, referred to as Leu1-PPP, and (L-Ile1-L-Pro2-Gly3-L-Val4-Gly5)n, referred to as Ile1-PPP Consistent with inverse temperature transitions, the temperatures of the transitions for which maximum heat absorption occurs are inversely proportional to the hydrophobicities of the polypentapeptides (31 degrees C for PPP, 16 degrees C for Leu1-PPP, and 12 degrees C for Ile1-PPP), and the endothermic heats of the transitions are small and increase with increasing hydrophobicity, i.e., 1.2, 2.9, and 3.0 kcal/mol pentamer for PPP, Leu1-PPP, and Ile1-PPP, respectively. Previous physical characterizations of the polypentapeptides have demonstrated the occurrence of an inverse temperature transition since increase in order, as the temperature is raised above that of the transition, has been repeatedly observed using different physical characterizations. Furthermore, the studies demonstrated identical conformations for PPP and Il21-PPP above and below the transition. Both heats and temperatures of the transitions vary with hydrophobicity, but not in simple proportionality.

Amino Acid Sequence↗
PubMed1990

Conformation of a cyclic decapeptide analog of a repeat pentapeptide sequence of elastin: cyclo-bis(valyl-prolyl-alanyl-valyl-glycyl).

The conformation of a cyclic decapeptide analog of a repeat sequence of elastin has been determined in the crystalline state using X-ray crystallographic techniques. Tetragonal crystals were grown from a solution of the decapeptide in water; space group P4(2)2(1)2, a = 19.439(2) & c = 13.602(1) A, with four formula units (C40H66N10O10.4H2O) per unit cell. The cyclic decapeptide in the crystal exhibits exact twofold symmetry. The asymmetric unit contains one pentapeptide and two water molecules for a total of 32 nonhydrogen atoms. The structure has been determined by the application of direct methods and refined by full-matrix least squares to an R index of 0.053 for 2272 reflections with intensities greater than 2 sigma(I). The backbone conformation of the asymmetric pentapeptide can be described as consisting of a double beta bend of Type III-I. The Type III turn has Pro (phi = -59.3 degrees, psi = -26.8 degrees) and Ala (phi = -65.9 degrees, psi = -23.1 degrees) at the corners while Type I turn has Ala (phi = -65.9 degrees, psi = -23.1 degrees) and Val (phi = -98.9 degrees, psi = 8.3 degrees) as the corner residues. The cyclic decapeptide has two such double bends linked together by Gly-Val bridges.

Amino Acid Sequence↗
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↗