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D A Tirrell

Publications and source records attributed to D A Tirrell.

At least 19 recordsLinked to original sources
PubMed2002

Confinement-induced order of tethered alkyl chains at the water/vapor interface.

Packing of tethered alkyl chains in Langmuir monolayers of a hairy-rod polypeptide poly[gamma-4-(n-hexadecyloxy)benzyl alpha,L-glutamate] on water has been studied by x-ray scattering measurements at room temperature. The rods lie parallel to the surface while the alkyl side chains segregate toward the vapor. Results indicate that the herringbone order of the alkyl chains is established initially by one-dimensionally confined chains between aligned rods and grows laterally with compression.

Journal Article↗
PubMed2001

Protein-based materials, toward a new level of structural control.

Through billions of years of evolution nature has created and refined structural proteins for a wide variety of specific purposes. Amino acid sequences and their associated folding patterns combine to create elastic, rigid or tough materials. In many respects, nature's intricately designed products provide challenging examples for materials scientists, but translation of natural structural concepts into bio-inspired materials requires a level of control of macromolecular architecture far higher than that afforded by conventional polymerization processes. An increasingly important approach to this problem has been to use biological systems for production of materials. Through protein engineering, artificial genes can be developed that encode protein-based materials with desired features. Structural elements found in nature, such as beta-sheets and alpha-helices, can be combined with great flexibility, and can be outfitted with functional elements such as cell binding sites or enzymatic domains. The possibility of incorporating non-natural amino acids increases the versatility of protein engineering still further. It is expected that such methods will have large impact in the field of materials science, and especially in biomedical materials science, in the future.

Animals↗
PubMed2001

Self-association and membrane-binding behavior of melittins containing trifluoroleucine.

We have investigated the effect of trifluoroleucine substitution on the membrane-binding and tetramerization behavior of melittin. Analogues were synthesized in which Leu 9, Leu 13, and all four intrinsic leucine residues of melittin were replaced by 5,5,5-trifluoroleucine. Both the mono- and tetra-substituted melittins were found to exhibit stronger self-association and enhanced affinity for lipid bilayer membranes, compared to the wild-type peptide. The extent of the observed effects depends on the site of introduction of trifluoroleucine and, in the case of substitution at position 13, on the stereochemistry of the trifluoroleucine side chain. Analysis of the membrane association isotherms is consistent with aggregation of fluorinated melittins within the lipid bilayer. These results suggest that fluorocarbon-hydrocarbon separation, in addition to an increase in hydrophobic character, contributes to enhanced membrane binding.

Amino Acid Sequence↗
PubMed2001

Identification of an expanded set of translationally active methionine analogues in Escherichia coli.

Amino acid incorporation into proteins in vivo is controlled most stringently by the aminoacyl-tRNA synthetases. Here we report the incorporation of several new methionine analogues into protein by increasing the rate of their activation by the methionyl-tRNA synthetase (MetRS) of Escherichia coli. cis-Crotylglycine (4), 2-aminoheptanoic acid (7), norvaline (8), 2-butynylglycine (11), and allylglycine (12) will each support protein synthesis in methionine-depleted cultures of E. coli when MetRS is overexpressed and the medium is supplemented with the analogue at millimolar concentrations. These investigations suggest important opportunities for protein engineering, as expansion of the translational apparatus toward other amino acid analogues by similar strategies should also be possible.

Escherichia coli↗
PubMed2001

Stabilization of coiled-coil peptide domains by introduction of trifluoroleucine.

Substitution of leucine residues by 5,5,5-trifluoroleucine at the d-positions of the leucine zipper peptide GCN4-p1d increases the thermal stability of the coiled-coil structure. The midpoint thermal unfolding temperature of the fluorinated peptide is elevated by 13 degrees C at 30 microM peptide concentration. The modified peptide is more resistant to chaotropic denaturants, and the free energy of folding of the fluorinated peptide is 0.5-1.2 kcal/mol larger than that of the hydrogenated form. A similarly fluorinated form of the DNA-binding peptide GCN4-bZip binds to target DNA sequences with affinity and specificity identical to those of the hydrogenated form, while demonstrating enhanced thermal stability. Molecular dynamics simulation on the fluorinated GCN4-p1d peptide using the Surface Generalized Born implicit solvation model revealed that the coiled-coil binding energy is 55% more favorable upon fluorination. These results suggest that fluorination of hydrophobic substructures in peptides and proteins may provide new means of increasing protein stability, enhancing protein assembly, and strengthening receptor-ligand interactions.

Amino Acid Sequence↗
PubMed2000

Efficient introduction of aryl bromide functionality into proteins in vivo.

Artificial proteins can be engineered to exhibit interesting solid state, liquid crystal or interfacial properties and may ultimately serve as important alternatives to conventional polymeric materials. The utility of protein-based materials is limited, however, by the availability of just the 20 amino acids that are normally recognized and utilized by biological systems; many desirable functional groups cannot be incorporated directly into proteins by biosynthetic means. In this study, we incorporate para-bromophenylalanine (p-Br-phe) into a model target protein, mouse dihydrofolate reductase (DHFR), by using a bacterial phenylalanyl-tRNA synthetase (PheRS) variant with relaxed substrate specificity. Coexpression of the mutant PheRS and DHFR in a phenylalanine auxotrophic Escherichia coli host strain grown in p-Br-phe-supplemented minimal medium resulted in 88% replacement of phenylalanine residues by p-Br-phe; variation in the relative amounts of phe and p-Br-phe in the medium allows control of the degree of substitution by the analog. Protein expression yields of 20-25 mg/l were obtained from cultures supplemented with p-Br-phe; this corresponds to about two-thirds of the expression levels characteristic of cultures supplemented with phe. The aryl bromide function is stable under the conditions used to purify DHFR and creates new opportunities for post-translational derivatization of brominated proteins via metal-catalyzed coupling reactions. In addition, bromination may be useful in X-ray studies of proteins via the multiwavelength anomalous diffraction (MAD) technique.

Amino Acid Substitution↗
PubMed2000

Thermal and structural properties of biologically derived monodisperse hairy-rod polymers.

Monodisperse derivatives of poly(gamma-4-(hexadecyloxy)benzyl alpha,L-glutamate) (PHBG-X, X = 3 or 4) with backbone sequence GluAsp(Glu17Asp)xGluGlu were prepared by reaction of 4-(hexadecyloxy)phenyldiazomethane with the corresponding monodisperse poly(alpha,L-glutamate) (PLGA) derivatives (PLGA-X, X = 3 or 4). PHBG-3 and -4 exhibited strong endotherms near 45 degrees C and weak endotherms near 86 degrees C when analyzed by differential scanning calorimetry. X-ray diffraction suggested that these polymers aggregate to form layerlike solid structures at room temperature, with extended alkyl side chains forming paraffinlike crystallites. Most of the side chain order disappears at the first melting transition; however, the layerlike structure remains. Both polymers are isotropic above the second melting transition; no ordered melts were observed at higher temperatures, possibly due to the small aspect ratios of PHBG-3 and -4. In contrast, polydisperse poly(gamma-4-(hexadecyloxy)benzyl alpha,L-glutamate) (PDI = 1.2, DP = 98) (PHBG-P1), prepared from commercial PLGA, formed liquid crystalline (LC) phases between 97 and 105 degrees C.

Calorimetry, Differential Scanning↗
PubMed2000

Engineering the extracellular matrix: a novel approach to polymeric biomaterials. I. Control of the physical properties of artificial protein matrices designed to support adhesion of vascular endothelial cells.

Methods of genetic engineering were applied to the design and biosynthesis of three extracellular matrix protein analogues constructed from identical elastin- and fibronectin-derived repeating units but characterized by different molecular weights in the range of 14,000 to 59,000. Expression levels were enhanced by the serendipitous choice of an N-terminal fusion sequence such that gram-scale syntheses were achieved for each protein. Purification protocols were developed that resulted in proteins of high purity and correct sequence, as determined by amino acid analysis, NMR spectroscopy, and lower critical solution temperature (LCST). Glutaraldehyde was shown to insolubilize the otherwise soluble proteins in a concentration-dependent manner. Tensile moduli of cross-linked protein films were measured and found to be inversely related to the molecular weights of the engineered proteins, which in each case corresponds to the theoretical molecular weight between cross-links. At the highest cross-link density (lowest molecular weight) the elastic modulus was similar to that of native elastin.

Amino Acid Sequence↗
PubMed2000

Effects of temperature and pressure on the aggregation properties of an engineered elastin model polypeptide in aqueous solution.

The pressure and temperature dependence of the cloud point transition of an aqueous solution of an elastin-like polypeptide (MGLDGSMG(VPGIG)40VPLE), prepared by bacterial expression of the corresponding artificial gene, was measured. A temperature-pressure diagram was constructed over a wide range of conditions. The (VPGIG)40 solution exhibited a well-defined pressure-induced cloudpoint (Pc), as well as a temperature-induced transition (Tc). From near atmospheric pressure up to 100 MPa, Tc increased with increasing pressure, but decreased with further increases in pressure above 200 MPa. The maximum Tc was reached at 100-200 MPa. Between 10 and 25 degrees C, the Pc decreased with increasing temperature, and a broad maximum in Pc was observed in the range -10 to 0 degree C. These results are compared with our previous results on synthetic thermoresponsive vinyl polymers.

Calorimetry↗
PubMed1999

The design and synthesis of polymers for eukaryotic membrane disruption.

The intracellular trafficking of drugs is critical to the efficacy of drugs that are susceptible to attack by lysosomal enzymes. It is therefore an important goal to design and synthesize molecules which can enhance the transport of endocytosed drugs from the endosomal compartments to the cytoplasm. The pH of an endosome is lower than that of the cytosol by one to two pH units, depending on the stage of endosomal development. This pH gradient is a key factor in the design of membrane-disruptive polymers which could enhance the endosomal release of drugs. Such polymers should disrupt lipid bilayer membranes at pH 6.5 and below, but should be non-lytic at pH 7.4. We have designed and synthesized pH-sensitive synthetic polymers which efficiently disrupt red blood cells within a sharply defined pH range. One of these polymers, poly(ethyl acrylic acid) (PEAAc) has been previously shown to disrupt synthetic vesicles in a pH-dependent fashion [6]. PEAAc hemolyzes red blood cells with an activity of 10(7) molecules per red blood cell, which is as efficient on a molar basis as the peptide melittin. The mechanism of RBC hemolysis by PEAAc is consistent with the colloid osmotic mechanism. PEAAc's hemolytic activity rises rapidly as the pH decreases from 6.3 to 5.0, and there is no hemolytic activity at pH 7.4. A related polymer, poly(propyl acrylic acid) (PPAAc), was synthesized to test whether making the pendant alkyl group more hydrophobic by adding one methylene group would increase the hemolytic activity. PPAAc was found to disrupt red blood cells 15 times more efficiently than PEAAc at pH 6.1. PPAAc was also not active at pH 7.4 and displayed a pH-dependent hemolysis that was shifted toward higher pH's. Random 1:1 copolymers of ethyl acrylate (EA) and acrylic acid (AAc) (which contain random -COOH and -C(2)H(5) groups that are present and regularly repeat in PEAAc) also displayed significant hemolytic activity, with an efficiency close to PEAAc. These results demonstrate that pH-sensitive synthetic polymers can be molecularly engineered to efficiently disrupt eukaryotic membranes within defined and narrow pH ranges. Thus, these polymers might serve as endosomal disruptive agents with specificities for early or late endosomes.

Cell Membrane↗
PubMed1998

Reversible hydrogels from self-assembling artificial proteins.

Recombinant DNA methods were used to create artificial proteins that undergo reversible gelation in response to changes in pH or temperature. The proteins consist of terminal leucine zipper domains flanking a central, flexible, water-soluble polyelectrolyte segment. Formation of coiled-coil aggregates of the terminal domains in near-neutral aqueous solutions triggers formation of a three-dimensional polymer network, with the polyelectrolyte segment retaining solvent and preventing precipitation of the chain. Dissociation of the coiled-coil aggregates through elevation of pH or temperature causes dissolution of the gel and a return to the viscous behavior that is characteristic of polymer solutions. The mild conditions under which gel formation can be controlled (near-neutral pH and near-ambient temperature) suggest that these materials have potential in bioengineering applications requiring encapsulation or controlled release of molecular and cellular species.

Amino Acid Sequence↗
PubMed1998

Efficient introduction of alkene functionality into proteins in vivo.

The methionine analogue 2-amino-5-hexenoic acid (homoallylglycine, Hag) can be utilized by Escherichia coli in the initiation and elongation steps of protein biosynthesis. Use of an E. coli methionine auxotroph and Hag-supplemented medium resulted in replacement of ca. 85% of the methionine residues in mouse dihydrofolate reductase expressed under control of a bacteriophage T5 promoter. N-terminal sequencing indicated 92+/-5% occupancy of the initiator site by Hag. The vinyl function of Hag remains intact in the purified protein and suggests new chemistries for modification of natural and artificial proteins prepared in bacterial hosts.

Alkenes↗
PubMed1998

Effect of local sequence inversions on the crystalline antiparallel beta-sheet lamellar structures of periodic polypeptides: implications for chain-folding.

The crystal structure and texture of the monodisperse periodic polypeptide [(AG)3EG(GA)3EG]10 (poly(+/-AG)3EG: A=alanine, G=glycine, E=glutamic acid) were analyzed by X-ray diffraction, Fourier transform infrared spectroscopy, and electron microscopy. Structure determination was aided by comparison with the recently described structure for the related periodic polypeptide [(AG)3EG]36 by Krejchi et al. (Macromolecules 1997;30:5012). Texture-oriented samples of poly(+/-AG)3EG were obtained by crystallization of the polymer from aqueous formic acid solution. The evidence supports an antiparallel (ap) beta-sheet protein structure and the X-ray diffraction signals index on an orthorhombic unit cell with parameters: a=0.950 nm (hydrogen-bond direction), b=1.052 nm (apbeta-sheet stacking direction), c=6.95 nm (chain direction). The absence of the (010) diffraction signal, a prominent signal in the poly(AG)3EG diffraction pattern, implies that the apbeta-sheets are 'apolar', i.e. both surfaces are equally populated with alanyl methyl groups. Selective line broadening of wide-angle diffraction signals with l not equal to 0 gives an estimated crystal size of approximately/= 4 nm in the chain direction. This observation, coupled with the appearance of low-angle particle interference peaks, indicates a crystal thickness considerably less than the chain length and suggests an adjacent-re-entry chain-folded lamellar structure incorporating the apbeta-sheet architecture. The polypeptide folds through gamma-turns, in-phase with the pseudo-octapeptide repeat; the glutamic acid residues occur on the lamellar surfaces. These results and those from the crystalline lamellae of poly(AG)3EG suggest that beta-turns are not compatible with these repetitively stacked apbeta-sheet structures. This implies that intersheet interactions of alanyl methyl groups and glycyl alpha-protons are not sufficiently strong to dictate the folding geometry in these structures.

Crystallization↗
PubMed1997

Smectic ordering in solutions and films of a rod-like polymer owing to monodispersity of chain length.

Solutions and melts of stiff ('rod-like') macromolecules often exhibit nematic liquid crystalline phases characterized by orientational, but not positional, molecular order. Smectic phases, in which macromolecular rods are organized into layers roughly perpendicular to the direction of molecular orientation, are rare, owing at least in part to the polydisperse nature (distribution of chain lengths) of polymers prepared by conventional polymerization processes. Bacterial methods for polypeptide synthesis, in which artificial genes encoding the polymer are expressed in bacterial vectors, offer the opportunity to make macromolecules with very well defined chain lengths. Here we show that a monodisperse derivative of poly(gamma-benzyl alpha,L-glutamate) prepared in this way shows smectic ordering in solution and in films. This result suggests that methods for preparing monodisperse polymers might provide access to new smectic phases with layer spacings that are susceptible to precise control on the scale of tens of nanometres.

Biofilms↗
PubMed1997

Effects of amino acid side-chain volume on chain packing in genetically engineered periodic polypeptides.

The fidelity of bacterial protein synthesis allows the production of architecturally well-defined polymeric materials through precise control of chain length, sequence, stereochemistry, and interchain interactions. In the present paper, we examine the relation between amino acid residue volume and crystalline unit cell dimensions, in a set of periodic protein polymers of repeating unit sequence -(AlaGly)3-X-Gly-, where X is Asn, Phe, Ser, Val, or Tyr. The proteins were overexpressed in Escherichia coli, purified by simple procedures based on acid/ethanol precipitation or insolubility in aqueous sodium dodecyl sulfate, and processed to form oriented crystalline mats by precipitation from formic acid under mechanical shear. X-ray diffraction analyses revealed that the basic structures of the -(AlaGly)3-X-Gly- polymers are identical to that previously reported for [(AlaGly)3-GluGly]36, [Krejchi, M.T., Atkins, E.D.T., Waddon, A.J., Fournier, M.J., Mason, T.L., and Tirrell, D.A. (1994) Science 265, 1427-1432], with the oligoalanylglycine segments forming antiparallel beta-sheets and the substituted amino acids occurring within three-residue folds at the lamellar surfaces. The X-ray diffraction signals for each member of the family index on an orthorhombic unit cell; the a-axis (hydrogen bond direction) and c-axis (chain direction) spacings remain invariant but the b-axis (sheet stacking direction) spacing increases with increasing volume of the substituted amino acid. The results obtained from a variant with alternating Glu and Lys substitution at the X position, together with the results previously reported for poly(L-alanylglycine) [Panitch, A., Matsuki, K., Cantor, E.J., Cooper, S.J., Atkins, E.D.T., Fournier, M.J., Mason, T.L., and Tirrell, D.A. (1997) Macromolecules 30, 42-49] are included for comparison. The average intersheet stacking distance (b/2) increases linearly with the volume of the amino acid inserted at position X. Because the chain-folded lamellar architecture adopted by these periodic polypeptides accommodates a wide range of residues differing in charge, steric bulk, and hydrophobicity, these results illustrate a new approach to the engineering of intermolecular interactions in polymeric solids.

Amino Acids↗
PubMed1996

Kinetics of membrane micellization by the hydrophobic polyelectrolyte poly(2-ethylacrylic acid).

Rates of pH-dependent micellization of multilamellar vesicles by the hydrophobic polyelectrolyte poly(2-ethylacrylic acid) (PEAA) have been measured turbidometrically. This polymer shows a strong ph-dependence in its affinity for phospholipid membranes, binding in increasing amounts as pH is lowered and ultimately solubilizing membranes to form mixed micelles (Tirrell, Takigawa and Seki (1985) Ann. N.Y. Acad. Sci. 446, 237). The rate of solubilization of dipalmitoylphosphatidylcholine (DPPC) vesicle suspensions by PEAA increases approximately linearly with reductions in pH below a threshold at pH 6.55. Interestingly, negatively-charged dipalmitoylphosphatidylglycerol membranes showed qualitatively similar behavior in the presence of PEAA, and incorporation of 10% or 20% dipalmitoylphosphatidic acid in DPPC membranes did not affect solubilization rates, demonstrating that membrane charge is not an important factor in determining micellization kinetics. Micellization of DPPC and dimyristoylphosphatidylcholine membranes occurs most rapidly at their respective gel-liquid crystalline transition temperatures (Tm); the rate enhancement is correlated with a peak in the temperature-dependent binding of a fluorescently-modified PEAA in slightly alkaline solutions in which no micellization is observed. The lateral compressibility of the membrane, which has a similar peak at Tm, is proposed to be an important determinant of the rate and extent of polymer adsorption, and consequently of the rate of micellization.

1,2-Dipalmitoylphosphatidylcholine↗