Dan Urry - Academia.edu (original) (raw)

Papers by Dan Urry

Proceedings of the National Academy of Sciences, 1971

A series of helical structures for gramicidin A, with alternating L and D residues, are character... more A series of helical structures for gramicidin A, with alternating L and D residues, are characterized as to number of residues per turn, atoms in hydrogenbonded rings, and dihedral angles. Because of alternating peptide C-O directions, these helices are capable of forming head-to-head hydrogen-bonded dimers with the capacity of functioning as transmembrane channels. The dimers are characterized as to channel length, pore size, and expected ion selectivity. In a test of the proposed head-to-head association for channel formation, the malonyl dimer [N,N'-(dideformyl gramicidin A)-malonamide] was synthesized. The chemical and conformational integrity of the product was verified by nuclear magnetic resonance; in lipid bilayer studies, the dimer was found to be a potent mediator of ion conductance with the predicted concentration dependence.Thus, the results on malonyl gramicidin A prove head-to-head association in formation of the transmembrane channel, and the results are consistent with the specific geometrical configuration involved in head-to-head dimerization of pi((L,D)) helices. At this stage, the action of gramicidin A on membranes with lipid-layer thicknesses of 30 A or less can best be understood in terms of the pi((L,D)) helix with 6.3 residues per turn.

Journal of the American Chemical Society, 1972

... David F. Mayers and Dan W. Urry* Contribution from the Division of Molecular Biophysics, Labo... more ... David F. Mayers and Dan W. Urry* Contribution from the Division of Molecular Biophysics, Laboratory of Molecular Biology, University of Alabama ... structure has been characterized as a series of p turns.lObll An interesting representation of the backbone con-formation is given ...

Journal of the American Chemical Society, 1970

ChemInform

Bioelastic materials are elastomeric polypeptides composed of repeating sequences. They are a rel... more Bioelastic materials are elastomeric polypeptides composed of repeating sequences. They are a relatively new class of polymers that may also be called elastic protein-based polymers, having their origins in repeating sequences found in the mammalian elastic protein, elastin. The most striking and longest sequence between cross-links in pig and cow is the polypentapeptide-(PPP), poly(VPGVG) or (Val1-Pro2-Gly3-Val4-Gly5)n, where n is 11 (Sandberg et al., 1985; Yeh et al, 1987). Another repeat first found in porcine elastin is a polytetrapeptide-(PTP), poly(VPGG) or (Val1-Pro2-Gly3-Gly4)n, but this repeat has not been found to occur with n greater than 2 without substitution (Sandberg et al., 1981). The next most common recurring sequence in mammalian elastin is a polyhexapeptide-(PHP), poly(APGVGV) or (Ala1-Pro2-Gly3-Val4-Gly5-Val6)n where, with but a couple of isomorphous hydrophobic residue replacements such as Val by He or Leu, n is 8 in man (Indik et al., 1987). The monomers, olig...

Controlled Drug Delivery: Challenges and Strategies: ACS Professional Reference Books. Park K, ed... more Controlled Drug Delivery: Challenges and Strategies: ACS Professional Reference Books. Park K, editor. ACS Press; 1997. p. 405-437.

CLASS Polypeptides and proteins REPRESENTATIVE STRUCTURES Elastomer Poly(G�G�P) Plastic Poly(AVGV... more CLASS Polypeptides and proteins REPRESENTATIVE STRUCTURES Elastomer Poly(G�G�P) Plastic Poly(AVGVP) Hydrogel Poly(GGAP) MAJOR APPLICATIONS Medical: soft tissue augmentation; cell attachment to elastic matrices; prevention of post-surgical adhesions; tissue reconstruction; coatings on catheters, leads, and tubings; drug delivery; biosensors. Nonmedical: controlled release of herbicides, pesticides, fertilizers, and growth factors; food product additives; material coating; transducers (sensors/actuators); molecular machines; biodegradable plastics; controllable super absorbents. PROPERTIES OF SPECIAL INTEREST Water soluble below a critical temperature. Hydrophobic folding and assembly (inverse temperature transition). Biocompatible. Biodegradable (chemical clocks enabling proteolytic degradation). Relatively low cost when microbially produced. To perform free energy transduction involving the intensive variables of mechanical force, temperature, pressure, chemical potential, electroc...

http://www.knovel.com/web/portal/browse/display?\_EXT\_KNOVEL\_DISPLAY\_bookid=2620

Protein-Based Materials, 1996

ABSTRACT The term protein-based polymer has its origin in a symposium containing that name organi... more ABSTRACT The term protein-based polymer has its origin in a symposium containing that name organized by D.L. Kaplan, M.T. Marron, and D.A. Tirrell (1990). As the term is used here, it refers to polymers comprised of repeating peptide sequences in which the repeats may be as few as two residues or as many as hundreds of residues. In the latter case, properties of protein-based polymers and globular proteins naturally merge. For the former case, there are now known many examples of repeating peptide sequences in proteins. These occur most commonly in proteins that fill structural roles as opposed to the frequently discussed catalytic, transport, or transductional roles of globular proteins. http://link.springer.com/chapter/10.1007%2F978-1-4612-4094-5_5#

Biochimica et Biophysica Acta (BBA) - Protein Structure, 1973

a-Elastin in the coacervated state has been studied by electron microscopy utilizing the techniqu... more a-Elastin in the coacervated state has been studied by electron microscopy utilizing the technique of negative staining. This purified and solubilized protein was found to undergo reconstitution to filamentous structures at the elevated temperature required for coacervation. This observation suggests that hydrophobic interactions are responsible for the phase transition (i.e. coacervation) of a-elastin with increase in temperature, and for the formation of fibrous structures with dimensions similar to those observed for the elastin fiber in the native state.

Current Topics in Membranes and Transport, 1988

ABSTRACT This chapter illustrates the capacity to determine meaningful rate constants by means of... more ABSTRACT This chapter illustrates the capacity to determine meaningful rate constants by means of NMR relaxation studies of spin 7/2 cesium- 133 and allow these approaches to be considered for spin 7/2 calcium-43. Background NMR data are presented for calcium-43, e.g., CaCI2 concentration dependence and temperature dependence of the longitudinal relaxation time, TI, in D,O, in the presence of phosphatidylcholine lipid and in the presence of phosphatidylcholine lipid plus gramicidin A channels and the transverse relaxation time, T2 for 100 mM and 1 M CaCI2, in the presence and absence of channels. These data allow determination of the off-rate constant for calcium ions leaving the channel binding site to be of the order of 5 x 107/sec. With the binding constant demonstrated here to be about l/M for the site at the mouth of the gramicidin A channel and with the experimental off-rate constant, it becomes apparent that the lack of a calcium ion current is due to a high central barrier arising from the large repulsive image force which occurs when a divalent charge is separated from the lipid dielectric constant by no more than a single layer of polypeptide backbone.

$Research paper thumbnail of Optical diffraction of tropelastin and α-elastin coacervates$

Biochimica et Biophysica Acta (BBA) - Protein Structure, 1976

Optical diffraction applied to micrographs of coacervated tropoelastin and a-elastin show an equa... more Optical diffraction applied to micrographs of coacervated tropoelastin and a-elastin show an equatorial repeat around 50 •. This confirms a 50 A center-to-center distance of parallel aligned filaments to be a fundamental property of the tropoelastin and a-elastin coacervates. This periodicity is similar to that of mature cross-linked elastin. These results allow the conclusion that hydrophobic association is the predominant driving force for formation of filamentous elastin in vitro. It is suggested that the coacervate is a model for relaxed fibrous elastin.

Protein expression and purification, 1996

By constructing a basic gene unit encoding (GVGVP)10, it was possible to build concatemer genes w... more By constructing a basic gene unit encoding (GVGVP)10, it was possible to build concatemer genes with as many as 25 repeats of the monomer unit encoding a protein-based polymer with a molecular weight of greater than 100,000 Da. This employed the use of terminal cloning adaptor oligonucleotides as chain terminators to enhance the desired polymer gene size distribution. These genes have been expressed in Escherichia coli and the products have been purified from the culture lysates using a simple centrifugation method which relies upon the inverse temperature transitional properties of these elastomeric protein-based polymers. At 4 degrees C, the polymers are soluble; on raising the temperature above 26 degrees C, the onset temperature (Tt) for the (GVGVP)251 inverse temperature transition, the polymer separates out as the more dense phase. Upon shifting the temperature between 4 and 37 degrees C, the recombinant elastomeric protein-based polymers undergo reversible phase transitions f...

Ciba Foundation symposium, 1995

Owing to the presence of the recurring sequence XPGX' (where X and X' are hydrophobic res... more Owing to the presence of the recurring sequence XPGX' (where X and X' are hydrophobic residues), the molecular structure of the sequences between cross-links in elastin is viewed primarily as a series of beta-turns which become helically ordered by hydrophobic folding into beta-spirals, which in turn assemble hydrophobically into twisted filaments. Both hydrophobic folding and assembly occur when the temperature is raised above Tt, the onset of an inverse temperature transition. Using poly[fv(VPGVG),fx(VPGXG)] (where fv and fx are mole fractions with fv + fx = 1 and X is now any of the naturally occurring amino acid residues), plots of fx versus Tt result in a new hydrophobicity scale based directly on the hydrophobic folding and assembly processes of interest. With the reference values chosen at fx = 1, the most hydrophobic residues of elastin, Tyr (Y) and Phe (F), have low values of Tt, -55 and -30 degrees C, respectively, and the most hydrophilic residues, Glu (E-), Asp (...

Biochimica et biophysica acta, Jan 18, 1974

... Biophys. Acta 310, 481--486 8 Cox, BA, Starcher, BC and Urry, DW (1973) Biochim. Biophys. Act... more ... Biophys. Acta 310, 481--486 8 Cox, BA, Starcher, BC and Urry, DW (1973) Biochim. Biophys. Acta 317, 209--213 9 Cox, BA, Starcher, BC and Urry, DW (1974) J. Biol. Chem. ... Biol. Med., Autumn issue 20 Urry, DW, Mitchell, I,.W. and Ohnishi, T. (1974) Proc. Natl. Acad. Sci. ...

International journal of peptide and protein research, 1985

The coupling of Boc-Val-OH to either H-Pro-OBzl or H-Pro-Gly-Val-Gly-OBzl by the mixed anhydride ... more The coupling of Boc-Val-OH to either H-Pro-OBzl or H-Pro-Gly-Val-Gly-OBzl by the mixed anhydride method leads to the formation of a urethane by-product in yields of 40-60%. This side reaction can be suppressed by the addition of HOBt to the reaction mixture before the amino component is added. This results in a substantially increased yield of the desired peptide.

Self-Assembling Peptide Systems in Biology, Medicine and Engineering, 2002

Protein-based polymers can be designed in which self-assembly occurs as the temperature is raised... more Protein-based polymers can be designed in which self-assembly occurs as the temperature is raised above the onset temperature, Tt, of an inverse temperature transition for hydrophobic folding and assembly. Instead of changing the temperature, however, by many means the value of Tt can be lowered from above to below an operating temperature to drive hydrophobic folding and assembly. This is

International Journal of Peptide and Protein Research, 1986

High molecular weight polytetrapeptide of elastin, (L.Val1-L.Pro2-Gly3-Gly4)n, was synthesized us... more High molecular weight polytetrapeptide of elastin, (L.Val1-L.Pro2-Gly3-Gly4)n, was synthesized using activation of the (GGVP) permutation for polymerization. The temperature-dependence of aggregation was characterized as a function of concentration and the circular dichroism spectra were obtained in the 20 degrees to 70 degrees C temperature range. The latter showed an inverse temperature transition centered near 50 degrees C in which polypeptide order increased on raising the temperature. A concentration of 0.6 g of polytetrapeptide in 1 g of water was gamma irradiation cross-linked (20 Mrad) to form an elastomeric matrix. A study of the temperature-dependence of elastomeric force demonstrated a transition toward increased force on raising the temperature with a midpoint of the transition near 50 degrees C. Thus, there is a correlation between increase in intramolecular order and elastomeric force development. These results are compared to previous results on the polypentapeptide of elastin, (VPGVG)n and on an analog, (IPGVG)n, to demonstrate that the temperature of the transition is proportional to the hydrophobicity of the repeating unit. The point is noted that the elastomeric force development correlates better with intramolecular ordering than with intermolecular processes.

International Journal of Peptide and Protein Research, 1982

ABSTRACT The 13C-D-Leu12,14 gramicidin A was synthesized by the solid phase method incorporating ... more ABSTRACT The 13C-D-Leu12,14 gramicidin A was synthesized by the solid phase method incorporating 13C-D-leucine in positions 12 and 14 with about 25 and 50% enrichment, respectively. The pentadecapeptide was removed from the resin by ethanolamine treatment, with the N-protecting group (Boc) still on. After removal of the protecting group, the peptide was formylated and purified by preparative t.l.c. to obtain 13C-D-Leu12,14 gramicidin A in a very pure state in an overall yield of about 12.5%. The peptide was then thoroughly characterized by HPLC which gave one single peak with the same retention time as that of Val1-gramicidin A of the natural gramicidin mixture. The CD spectra of the synthetic and the HPLC purified natural Val1 -GA were obtained and found to be identical, indicating the optical purity of the sample. The synthetic GA was characterized by 13C n.m.r. spectrum and compared with that of natural GA. Single channel conductance parameters of the synthetic GA were determined and found to be indistinguishable from those of natural Val1-GA in lipid bilayer membranes and the mean channel lifetime was found to be as reported earlier by others.

MRS Proceedings, 1992

... Res. 26, 393-413 (1992). 10. DW Urry, DC Gowda, C. Harris, RD Harris and BA Cox, Polym. Prepr... more ... Res. 26, 393-413 (1992). 10. DW Urry, DC Gowda, C. Harris, RD Harris and BA Cox, Polym. Preprints, Div. Polym. Chem., Am. Chem. Soc. 33 (2) 84-85 (1992). 11. DT McPherson, C. Morrow, DS Minehan, J. Wu, E. Hunter and DW Urry, Biotechnol. Prog. 8, 347-352 (1992). 12. ...