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Sample records for alanine-alpha

  1. Beta-alanine/alpha-ketoglutarate aminotransferase for 3-hydroxypropionic acid production

    Energy Technology Data Exchange (ETDEWEB)

    Jessen, Holly Jean; Liao, Hans H; Gort, Steven John; Selifonova, Olga V

    2014-11-18

    The present disclosure provides novel beta-alanine/alpha ketoglutarate aminotransferase nucleic acid and protein sequences having increased biological activity. Also provided are cells containing such enzymes, as well as methods of their use, for example to produce malonyl semialdehyde and downstream products thereof, such as 3-hydroxypropionic acid and derivatives thereof.

  2. Beta-alanine/alpha-ketoglutarate aminotransferase for 3-hydroxypropionic acid production

    Energy Technology Data Exchange (ETDEWEB)

    Jessen, Holly Jean [Chanhassen, MN; Liao, Hans H [Eden Prairie, MN; Gort, Steven John [Apple Valley, MN; Selifonova, Olga V [Plymouth, MN

    2011-10-04

    The present disclosure provides novel beta-alanine/alpha ketoglutarate aminotransferase nucleic acid and protein sequences having increased biological activity. Also provided are cells containing such enzymes, as well as methods of their use, for example to produce malonyl semialdehyde and downstream products thereof, such as 3-hydroxypropionic acid and derivatives thereof.

  3. Effect of pH, urea, peptide length, and neighboring amino acids on alanine alpha-proton random coil chemical shifts.

    Science.gov (United States)

    Carlisle, Elizabeth A; Holder, Jessica L; Maranda, Abby M; de Alwis, Adamberage R; Selkie, Ellen L; McKay, Sonya L

    2007-01-01

    Accurate random coil alpha-proton chemical shift values are essential for precise protein structure analysis using chemical shift index (CSI) calculations. The current study determines the chemical shift effects of pH, urea, peptide length and neighboring amino acids on the alpha-proton of Ala using model peptides of the general sequence GnXaaAYaaGn, where Xaa and Yaa are Leu, Val, Phe, Tyr, His, Trp or Pro, and n = 1-3. Changes in pH (2-6), urea (0-1M), and peptide length (n = 1-3) had no effect on Ala alpha-proton chemical shifts. Denaturing concentrations of urea (8M) caused significant downfield shifts (0.10 +/- 0.01 ppm) relative to an external DSS reference. Neighboring aliphatic residues (Leu, Val) had no effect, whereas aromatic amino acids (Phe, Tyr, His and Trp) and Pro caused significant shifts in the alanine alpha-proton, with the extent of the shifts dependent on the nature and position of the amino acid. Smaller aromatic residues (Phe, Tyr, His) caused larger shift effects when present in the C-terminal position (approximately 0.10 vs. 0.05 ppm N-terminal), and the larger aromatic tryptophan caused greater effects in the N-terminal position (0.15 ppm vs. 0.10 C-terminal). Proline affected both significant upfield (0.06 ppm, N-terminal) and downfield (0.25 ppm, C-terminal) chemical shifts. These new Ala correction factors detail the magnitude and range of variation in environmental chemical shift effects, in addition to providing insight into the molecular level interactions that govern protein folding.

  4. Non-specific esterases and esterproteases in masticatory muscles from the muscular dystrophic mouse

    DEFF Research Database (Denmark)

    Kirkeby, S; Moe, D; Vilmann, H

    1989-01-01

    With the aid of histochemical and electrophoretic techniques activities for esterase and esterprotease were investigated in the digastric and masseter muscles from normal and dystrophic mice. The substrates used were alpha-naphthyl acetate and N-acetyl-L-alanine alpha-naphthyl ester. According to...

  5. Gaussian and finite-element Coulomb method for the fast evaluation of Coulomb integrals.

    Science.gov (United States)

    Kurashige, Yuki; Nakajima, Takahito; Hirao, Kimihiko

    2007-04-14

    The authors propose a new linear-scaling method for the fast evaluation of Coulomb integrals with Gaussian basis functions called the Gaussian and finite-element Coulomb (GFC) method. In this method, the Coulomb potential is expanded in a basis of mixed Gaussian and finite-element auxiliary functions that express the core and smooth Coulomb potentials, respectively. Coulomb integrals can be evaluated by three-center one-electron overlap integrals among two Gaussian basis functions and one mixed auxiliary function. Thus, the computational cost and scaling for large molecules are drastically reduced. Several applications to molecular systems show that the GFC method is more efficient than the analytical integration approach that requires four-center two-electron repulsion integrals. The GFC method realizes a near linear scaling for both one-dimensional alanine alpha-helix chains and three-dimensional diamond pieces.

  6. Infrared and vibrational CD spectra of partially solvated alpha-helices: DFT-based simulations with explicit solvent.

    Science.gov (United States)

    Turner, David R; Kubelka, Jan

    2007-02-22

    Theoretical simulations are used to investigate the effects of aqueous solvent on the vibrational spectra of model alpha-helices, which are only partly exposed to solvent to mimic alpha-helices in proteins. Infrared absorption (IR) and vibrational circular dichroism (VCD) amide I' spectra for 15-amide alanine alpha-helices are simulated using density functional theory (DFT) calculations combined with the property transfer method. The solvent is modeled by explicit water molecules hydrogen bonded to the solvated amide groups. Simulated spectra for two partially solvated model alpha-helices, one corresponding to a more exposed and the other to a more buried structure, are compared to the fully solvated and unsolvated (gas phase) simulations. The dependence of the amide I spectra on the orientation of the partially solvated helix with respect to the solvent and effects of solvation on the amide I' of 13C isotopically substituted alpha-helices are also investigated. The partial exposure to solvent causes significant broadening of the amide I' bands due to differences in the vibrational frequencies of the explicitly solvated and unsolvated amide groups. The different degree of partial solvation is reflected primarily in the frequency shifts of the unsolvated (buried) amide group vibrations. Depending on which side of the alpha-helix is exposed to solvent, the simulated IR band-shapes exhibit significant changes, from broad and relatively featureless to distinctly split into two maxima. The simulated amide I' VCD band-shapes for the partially solvated alpha-helices parallel the broadening of the IR and exhibit more sign variation, but generally preserve the sign pattern characteristic of the alpha-helical structures and are much less dependent on the alpha-helix orientation with respect to the solvent. The simulated amide I' IR spectra for the model peptides with explicitly hydrogen-bonded water are consistent with the experimental data for small alpha-helical proteins

  7. Interaction of some hydrophobic amino acids, peptides, and protein with aqueous 3-chloro-1,2-propanediol and 3-chloro-1-propanol: Biophysical studies

    Energy Technology Data Exchange (ETDEWEB)

    Keswani, Neelam [Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400 076 (India); Kishore, Nand, E-mail: nandk@chem.iitb.ac.i [Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400 076 (India)

    2011-04-15

    Research highlights: Thermodynamic properties of amino acids, peptides and protein determined in solution. The solvents chosen were 3-chloropropan-1-ol and 3-chloropropan-1,2-diol. {yields}The results enabled understanding the interactions quantitatively in these systems affecting the protein stability. Fine details of interactions provided in-depth analysis. - Abstract: The apparent molar volume V{sub 2,{phi},} apparent molar isentropic compressibility K{sub S,2,{phi},} and heat of dilution (q) of aqueous glycine, alanine, {alpha}-amino butyric acid, valine, leucine, diglycine, triglycine, and hen egg white lysozyme have been determined in aqueous solutions of 3-chloropropano-1-ol and 3-chloropropan-1,2-diol solutions at T = 298.15 K. These data have been used to calculate the infinite dilution standard partial molar volume V{sub 2,m}{sup 0}, partial molar isentropic compressibility K{sub S,2,m}{sup 0}, and enthalpy of dilution {Delta}{sub dil}H{sup o} of the amino acids and peptides in aqueous 3-chloropropano-1-ol and 3-chloropropan-1,2-diol, and the standard partial molar quantities of transfer of the amino acids and peptides to the aqueous alcohol and diol solutions. The linear correlation of V{sub 2,m}{sup 0} for a homologous series of amino acids has been utilized to calculate the contribution of the charged end groups (NH{sub 3}{sup +},COO{sup -}), CH{sub 2} group and other alkyl chains of the amino acids to the values of V{sub 2,m}{sup 0}. The results on the standard partial molar volumes of transfer, compressibility and enthalpy of dilution from water to aqueous alcohol and diol solutions have been correlated and interpreted in terms of ion-polar, ion-hydrophobic, and hydrophobic-hydrophobic group interactions. The heat of dilution of these amino acids, peptides, and hen egg white lysozyme measured in aqueous solutions of 3-chloropropano-1-ol and 3-chloropropan-1,2-diol by using isothermal titration calorimetry along with the volumetric, compressibility