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Amino Acid Amides (amino + acid_amide)
Selected AbstractsDetermination of isokinetic ratios necessary for equimolar incorporation of carboxylic acids in the solid-phase synthesis of mixture-based combinatorial librariesBIOPOLYMERS, Issue 1 2002Achyuta N. Acharya Abstract The methods used to study the relative reaction rates of 45 different aliphatic and aromatic carboxylic acids when coupled to resin-bound amino acid amides is described. Competition experiments involving the coupling of incoming carboxylic acids to resin-bound amino acid amides were performed. The relative composition of each N-acylated amino acid amide in the resulting mixtures was compared to controls prepared by physically mixing equal aliquots of individual compounds in order to study the relative reaction rates of the incoming carboxylic acids. The ratios of the incoming carboxylic acids were then iteratively adjusted to yield as close to equimolar products as possible. As expected, the steric and electronic nature of the incoming carboxylic acids was found to influence their relative reaction rates. The steric hindrance of the resin-bound amino acid appears to have a proportional effect on the reaction rates of the incoming carboxylic acids. N-acylated amino acid amides in the final mixtures, prepared using the final isokinetic ratios, were found to be approximately equimolar. © 2002 Wiley Periodicals, Inc. Biopolymers 65: 32,39, 2002 [source] CE with electrochemical detection for investigation of label-free recognition of amino acid amides by guanine-rich DNA aptamersELECTROPHORESIS, Issue 17 2007Tao Li Abstract In this work, we report a simple and effective investigation into adaptive interactions between guanine-rich DNA aptamers and amino acid amides by CE with electrochemical (EC) detection. Argininamide (Arm) and tyrosinamide (Tym) were chosen as model molecules. On a copper electrode, Arm generated a good EC signal in 60 mM NaOH at 0.7 V (vs Ag/AgCl), while Tym was detected well on a platinum electrode at 1.3 V in 20 mM phosphate of pH 7.0. Based on their EC properties, the ligands themselves were used as indicators for the adaptive interactions investigated by CE-EC, making any step of labeling and/or modification of aptamers with indicators exempted. Hydrophilic ionic liquid was used as an additive in running buffer of CE to improve the sensitivity of Arm detection, whereas the additive was not used for Tym detection due to its negative effect. Two guanine-rich DNA aptamers were used for molecular recognition of Arm and Tym. When the aptamers were incubated with ligands, they bound the model molecules with high affinity and specificity, reflected by obvious decreases in the signals of ligands but no changes in those of the control molecules. However, the ligands were hardly affected by the control ssDNAs after incubation. The results revealed the specific recognition of Arm and Tym by the aptamers. The mechanisms for binding model molecules by aptamers were discussed. Not as expected, these aptamers were not to form the G-quartets, which were generally responsible for binding the ligands when the guanine-rich aptamers were used. [source] Extended application of a chiral stationary phase based on (+)-(18-crown-6)-2,3,11,12-tetracarboxylic acid to the resolution of N -(substituted benzoyl)-,-amino acid amidesJOURNAL OF SEPARATION SCIENCE, JSS, Issue 10 2006Guanghui Tan Abstract A chiral stationary phase (CSP 1) based on (+)-(18-crown-6)-2,3,11,12-tetracarboxylic acid was applied to the resolution of N -(substituted benzoyl)-,-amino acid amides and esters. N -(Substituted benzoyl)-,-amino acid amides were well resolved using a mixture of acetic acid-triethylamine-acetonitrile (0.01 : 0.05 : 100, v/v/v) as an optimum mobile phase while N -(substituted benzoyl)-,-amino acid esters were not resolved at all. In contrast, both N -(substituted benzoyl)-,-amino acid amides and esters were not resolved at all or resolved very poorly on another CSP (CSP 2), which lacks the two N,H hydrogens of the amide tethers of CSP 1. Among the substituents on the benzoyl group of analytes, the nitro group was the best for good resolution of analytes on CSP 1. From these results, the two N,H hydrogens of the amide tethers of CSP 1, the carbonyl oxygen of the amide group of analytes, and the nitro group on the benzoyl group of analytes were concluded to play significant roles in chiral recognition. In addition, various N -(3,5-dinitrobenzoyl)leucine amides with different lengths of N -alkylamide chains were resolved on CSP 1 and N -(3,5-dinitrobenzoyl)leucine N -propylamide was found to show the best chiral recognition in terms of the separation (, = 1.30) and the resolution factor (RS = 3.17). [source] Deduced catalytic mechanism of d -amino acid amidase from Ochrobactrum anthropi SV3JOURNAL OF SYNCHROTRON RADIATION, Issue 3 2008Seiji Okazaki d -Amino acid amidase (DAA) from Ochrobactrum anthropi SV3 catalyzes d -stereospecific hydrolysis of amino acid amides. DAA has attracted attention as a catalyst for the stereospecific production of d -amino acids, although the mechanism that drives the reaction has not been clear. Previously, the structure of DAA was classified into two types, a substrate-bound state with an ordered , loop, and a ground state with a disordered , loop. Because the binding of the substrate facilitates ordering, this transition was regarded to be induced fit motion. The angles and distances of hydrogen bonds at Tyr149 O,, Ser60 O, and Lys63 N, revealed that Tyr149 O, donates an H atom to a water molecule in the substrate-bound state, and that Tyr149 O, donates an H atom to Ser60 O, or Lys63 N, in the ground state. Taking into consideration the locations of the H atoms of Tyr149 O,, Ser60 O, and Lys63 N,, a catalytic mechanism of DAA activity is presented, wherein a shift of an H atom at Tyr149 O, in the substrate-bound versus the ground state plays a significant role in the reaction. This mechanism explains well why acylation proceeds and deacylation does not proceed in the substrate-bound state. [source] Urea interactions with protein groups: A volumetric study,BIOPOLYMERS, Issue 10 2010Soyoung Lee Abstract We determined the partial molar volumes and adiabatic compressibilities of N -acetyl amino acid amides, N -acetyl amino acid methylamides, N -acetyl amino acids, and short oligoglycines as a function of urea concentration. We analyze these data within the framework of a statistical thermodynamic formalism to determine the association constants for the reaction in which urea binds to the glycyl unit and each of the naturally occurring amino acid side chains replacing two waters of hydration. Our determined association constants, k, range from 0.04 to 0.39M. We derive a general equation that links k with changes in free energy, ,Gtr, accompanying the transfer of functional groups from water to urea. In this equation, ,Gtr is the sum of a change in the free energy of cavity formation, ,,GC, and the differential free energy of solute,solvent interactions, ,,GI, in urea and water. The observed range of affinity coefficients, k, corresponds to the values of ,,GI ranging from highly favorable to slightly unfavorable. Taken together, our data support a direct interaction model in which urea denatures a protein by concerted action via favorable interactions with a wide range of protein groups. Our derived equation linking k to ,Gtr suggests that ,,GI and, hence, the net transfer free energy, ,Gtr, are both strongly influenced by the concentration of a solute used in the experiment. We emphasize the need to exercise caution when two solutes differing in solubility are compared to determine the ,Gtr contribution of a particular functional group. © 2010 Wiley Periodicals, Inc. Biopolymers 93: 866,879, 2010. [source] Determination of isokinetic ratios necessary for equimolar incorporation of carboxylic acids in the solid-phase synthesis of mixture-based combinatorial librariesBIOPOLYMERS, Issue 1 2002Achyuta N. Acharya Abstract The methods used to study the relative reaction rates of 45 different aliphatic and aromatic carboxylic acids when coupled to resin-bound amino acid amides is described. Competition experiments involving the coupling of incoming carboxylic acids to resin-bound amino acid amides were performed. The relative composition of each N-acylated amino acid amide in the resulting mixtures was compared to controls prepared by physically mixing equal aliquots of individual compounds in order to study the relative reaction rates of the incoming carboxylic acids. The ratios of the incoming carboxylic acids were then iteratively adjusted to yield as close to equimolar products as possible. As expected, the steric and electronic nature of the incoming carboxylic acids was found to influence their relative reaction rates. The steric hindrance of the resin-bound amino acid appears to have a proportional effect on the reaction rates of the incoming carboxylic acids. N-acylated amino acid amides in the final mixtures, prepared using the final isokinetic ratios, were found to be approximately equimolar. © 2002 Wiley Periodicals, Inc. Biopolymers 65: 32,39, 2002 [source] | ||||||||||