Chiral interaction and stochastic kinetics in stirred crystallization of amino acids

A study of chirally selective interaction in the stirred crystallization of glutamic acid and lysine is presented. The crystallization of S-glutamic acid is influenced by the presence of S-lysine but not R-lysine. Crystal nuclei in stirred systems are produced due to secondary nucleation. Secondary nucleation is an autocatalytic process in which a crystal produces secondary nuclei due to fluid motion, and due to crystal stirrer and crystal-crystal collisions. As a result of this autocatalysis, small fluctuations in the nucleation rates are amplified and the kinetics show a marked stochastic behavior. We investigate the stochastic behavior in detail and propose a kinetic mechanism that explains both the increase and the statistical distribution of the crystallization times of S-glutamic acid due to the presence of S-Lysine. Chirality 10:238–245, 1998. © 1998 Wiley-Liss, Inc.     

The role of polymorphic amino acids of the MHC molecule in the selection of the T cell repertoire

Allelic variants of MHC molecules expressed on cells of the thymus affect the selection and the specificity of the T cell repertoire. The selection is based on either the direct recognition by the TCR of the MHC molecules, or the recognition of a complex determinant formed by self-peptides bound to MHC molecules. In an analysis of the T cell repertoire in bone marrow chimeras that express allelic forms of MHC class II molecules in the thymus epithelium, we find that amino acid substitutions that are predicted to affect peptide binding influence the selection of the T cell repertoire during thymic selection.     

A similarity ring for amino acids based on their evolutionary substitution rates

A similarity ring for amino acids is obtained by reordering the rows and columns of their substitution probability matrix so as to minimize the variance of the matric elements about the main diagonal.     

Comparison of amino acids interaction with gold nanoparticle

The study of nanomaterial/biomolecule interface is an important emerging field in bionanoscience, and additionally in many biological processes such as hard-tissue growth and cell-surface adhesion. To have a deeper understanding of the amino acids/gold nanoparticle assemblies, the adsorption of these amino acids on the gold nanoparticles (GNPs) has been investigated via molecular dynamics simulation. In these simulations, all the constituent atoms of the nanoparticles were considered to be dynamic. The geometries of amino acids, when adsorbed on the nanoparticle, were studied and their flexibilities were compared with one another. The interaction of each of 20 amino acids was considered with 3 and 8 nm gold GNPs.     

pH-Dependent interaction of cytochrome c with mitochondrial mimetic membranes: the role of an array of positively charged amino acids

The interaction of cytochrome c (cyt c) with mitochondrial mimetic vesicles of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine, 1,2-dipalmitoyl-sn-glycero-3-phosphoethanolamine, and heart cardiolipin (PCPECL) was investigated over the 7.4-6.2 pH range by means of turbidimetry and photon correlation spectroscopy. In the presence of cyt c, the decrease of pH induced an increase in vesicle turbidity and mean diameter resulting from vesicle fusion as determined by a rapid decrease in the excimer/monomer ratio of 2-(10-(1-pyrene)-decanoyl)-phosphatidylcholine (PyPC). N-acetylated cyt c and protamine, a positively charged protein, increased vesicle turbidity in a pH-independent manner, whereas albumin did not affect PCPECL vesicle turbidity. pH-dependent turbidity kinetics revealed a role for cyt c-ionizable groups with a pK(a)((app)) of approximately 7.0. The carbethoxylation of these groups by diethylpyrocarbonate prevented cyt c-induced vesicle fusion, although cyt c association to vesicles remained unaffected. Matrix-assisted laser desorption ionization time-of-flight analysis revealed that Lys-22, Lys-27, His-33, and Lys-87 cyt c residues were the main targets for carbethoxylation performed at low pH values (<7.5). In fact, these amino acid residues belong to clusters of positively charged amino acids that lower the pK(a). Thus, at low pH, protonation of these invariant and highly conserved amino acid residues produced a second positively charged region opposite to the Lys-72 and Lys-73 region in the cyt c structure. These two opposing sites allowed two vesicles to be brought together by the same cyt c molecule for fusion. Therefore, a novel pH-dependent site associating cyt c to mitochondrial mimetic membranes was established in this study.     

The kinetics of diastereomeric amino acids with o-phthaldialdehyde.

The kinetics of the reaction of the amino acid epimers L-isoleucine, D-allo-isoleucine, L-threonine, and D-allo-threonine with o-phthaldialdehyde and mercaptoethanol were determined at 25 degrees C. L-Isoleucine reacts faster than its D-epimer whereas L-threonine reacts slightly slower than its D-epimer. In the case of isoleucine, the consequence can be an allo/iso ratio which in the worst case is 25% too low if these amino acids are quantified by liquid chromatography and o-phthaldialdehyde fluorescence detection. The effect on dating of fossils by amino acid racemization is discussed.     

POCKET: A computer graphies method for identifying and displaying protein cavities and their surrounding amino acids

A new interactive graphics program is described that provides a quick and simple procedure for identifying, displaying, and manipulating the indentations, cavities, or holes in a known protein structure. These regions are defined as, e.g., the X₀, y₀, Z₀ values at which a test sphere of radius r can be placed without touching the centers of any protein atoms, subject to the condition that there is some x < x₀ and some x > x₀ where the sphere does touch the protein atoms. The surfaces of these pockets are modeled using a modification of the marching cubes algorithm. This modification provides identification of each closed surface so that by “clicking” on any line of the surface, the entire surface can be selected. The surface can be displayed either as a line grid or as a solid surface. After the desired “pocket” has been selected, the amino acid residues and atoms that surround this pocket can be selected and displayed. The protein database that is input can have more than one protein “segment,” allowing identification of the pockets at the interface between proteins. The use of the program is illustrated with several specific examples. The program is written in C and requires Silicon Graphics graphics routines.     

Biphasic kinetics in the reaction between amino acids or glutathione and the chromium acetate cluster, [Cr3O(OAc)6]+

Kinetics for the breakdown of the trinuclear chromium acetate cluster with a series of monoprotic and diprotic amino acid ligands and with glutathione in aqueous media have been investigated spectrophotometrically at pH 3.5-5.5 and in a temperature range of 45-60 degrees C. Under pseudo-first-order conditions, reactions with these ligands exhibited biphasic kinetic behavior that can be accounted for by a consecutive two-step reaction, A-->B-->C, where A is assumed to be a forced ion pair, B an intermediate and C is the product; experimental data fit to a biexponential equation for the transformation. Rates for k(short), k(long), and k(obs) were determined by manual extrapolation of absorbance data or curve-fitting routines; associated activation parameters for each step of the reaction were calculated using the Eyring equation. Rates for the first and second steps of the reaction are on the order of approximately 10(-4) and approximately 10(-5)s(-1), respectively. The large negative values of DeltaS++ and smaller DeltaH++ in the first step indicate an associative step, while high positive values of DeltaS(double dagger) in the second step indicate dissociation. To account for the results mechanistically, the results are interpreted to be a first step of ligand exchange with a pseudo-axial aqua ligand, followed by a dissociative step involving acetate or oxo ligand displacement. The dissociative step is the rate determining step, with k(obs) approximately k(long). The results demonstrate reaction pathways that are available to the Cr(III) metal centers that may be physiologically relevant in the ligand-rich environment of biological systems. Under general conditions Cr(III) clusters may be expected to be broken down, unless some unique biological environment stabilizes the cluster. The present study has application to the processes related to Cr(III) transport and excretion, to potential mechanisms of Cr(III) action in a biological setting, and to the pharmacokinetics of Cr(III) supplements for animal and human consumption.     

Effect of amino acids on acrylamide formation and elimination kinetics

The effect of amino acids other than asparagine on acrylamide (AA) formation/elimination kinetics was studied in an asparagine-glucose model system (0.01 M, pH 6) heated at temperatures between 140 and 200 degrees C. Addition of cysteine or lysine to the model significantly lowered the AA yield, whereas addition of glutamine had a strong promoting effect and of alanine a rather neutral effect on the AA formation. This was also reflected by AA formation/elimination kinetics, which for all model systems studied could be modeled by two consecutive first-order reactions. The ratio of the elimination to the formation rate constant increased from the systems to which glutamine or alanine was added, over the control model system, to the model systems that contained lysine or cysteine.     

Factors, determining the effectiveness of tryptophanase interaction with amino acids

Inhibition of tryptophanase-catalyzed decomposition of S-(o-nitrophenyl)-L-cysteine by a variety of amino acids has been investigated. For amino acids similar to the natural substrate and for those having minimal steric requirements for the side chain, the linear correlation exists between-RTlnKi and side chain hydrophobicity. L-ornithine and L-arginine are anomalously potent inhibitors taking into account low hydrophobicity of their side chains. This can be explained by an interaction between a positively charged group of the side chain of L-arginine or L-ornithine and a nucleophilic group of the active site. The comparison of affinity of tryptophanase for L-phenylalanine and L-homophenylalanine indicates that there is a special locus in the active site where aromatic groups are bound and oriented approximately parallel to the cofactor plane experiencing no steric hindrance. For a large number of amino acids the rates of the enzymic alpha-proton exchange in 2H2O are comparable with the rate of the reaction with L-tryptophan. Very low rate of alpha-proton exchange observed with L-alanine is an exception.     

Recognition of amino acids in solution: The role of the hydrophobic forces

Theoretical results for molecular structures and solvation clusters have been used for an interpretation of the experimental observations on the selectivity of an amino acid-sensitive cell in the adult Colorado beetle. As a consequence, it is postulated that strong polar interactions (involving the charged groups-NH ₃ ⁺ and -COO^–), given the appropriate steric conditions, make the determining contribution toward the anchoring of the substrate to the receptor, while the hydrophobic forces are responsible for the specificity.     

Relationship between bound and free amino acids in the brain of growing rats]

Total pool of glutamate, glutamine and GABA in the hemispheres increases during postnatal life of rats, the increase being due to that in free and bound forms of amino acids. In the cerebellum of 1-day rats, the content of free and bound glu, gln asp, GABA, bound ala and free gly is lower, whereas the level of free glu and ala, bound gly is higher than in mature animals. To the end of the 1st week, total amino acid content decreases, except GABA, which is increased. Aminon acid content begins to increase at the 21th and 28th days of postnatal life.     

Transport of amino acids through the placenta and their role

Amino acids are transported across the human placenta mediated by transporter proteins that differ in structure, mechanism and substrate specificity. Some of them are Na⁺-dependent systems, whereas others are Na⁺-independent. Among these there are transporters composed of a heavy chain, a glycoprotein, and a light chain. Moreover, they can be differently distributed in the two membranes forming the syncytiotrophoblast. The transport mechanisms involved and their regulation are only partially known. In the placenta itself, part of the amino acids is metabolized to form other compounds important for the fetus. This occurs for instance for arginine, which gives rise to polyamines and to NO. Interconversion occurs among few other amino acids Transport is altered in pregnancy complications, such as restricted fetal growth.