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Experimental and theoretical infrared spectra for tryptophan-[water.sub.n] complexes where n=1-6 are described. The evidence for a gradual transition to zwitterionic structures comes from tryptophan-methanol complexes up to n=9 and starting from n=5, the infrared spectra show increasing intensity in the diagnostic asymmetric CO[O.sup.-] stretch and in the weaker N[H.sup.>sub.3] bending modes as the cluster size increases.

A range of amino acids are used to construct diverse gelators by using structures in which Boc-protected amino acids are attached to either end of an aliphatic diamine space chain. The choice of amino acid can be used for finding whether nanoscale self-assembly controls the properties of the resultant materials, while the function of the amino acid is translated into the self-assembled nanostructured gel.

Two novel series of polyfluorinated amino acids (PFAs) were conceptualized and synthesized as per a very short and scalable synthetic sequence. Results reveal that a short peptide that represents the amino acid sequence of a protein that is recognized by another protein could be tagged with one of the novel PFAs.

The isothermal titration calorimetry and equilibrium adsorption thermodynamics were used to determine the role of the basic amino acids in the hydroxyapatite adsorption thermodynamics. Results state that none of the individual basic amino acids of statherin are crucial for the binding of the protein to hydroxyapatite crystals.

Three hydrophilic residues in the active-site cavity of human carbonic anhydrase isozyme (HCA II) are replaced with residues of approximately equivalent size but with hydrophobic characteristics to determine their effects on proton transfer. It is confirmed that the efficient proton transfer is due to a combination of three features.

The study employs the umbrella-sampling molecular dynamics simulations in explicit water as functions of distance and orientation to calculate and parameterize the potentials of mean force of identical hydrophobic side chains of amino acid. The analysis of the positions and depths of the contact minima and the positions and heights of the desolvation maxima proves and confirms the application of such potentials in coarse-grain protein-folding simulations.

Classical molecular dynamics simulations are used to investigate a martensitic-type transformation in crystals of the amino acid DL-norleucine (2-aminohexanoic acid, C[H.sub.3][(C[H.sub.2]).sub.3]CH(H[H.sub.2])COOH). Concerted molecular displacements are considered to be a significant feature of all displacive transformations.

The study about the relative contributions of a secondary structure and side chains was carried out to understand the interaction between core peptide (CP) and the CD3/T-cell receptor (TCR) by introducing two D-amino acids in the positions of the two positive residues (2D-CP). The results indicate that the 2D-CP that could interfere in vivo with T-cell activation in a sequence specific manner is independent of the secondary structure of the peptide.

The selective forces acting on amino acid substitutions may be different in the two phases of molecular evolution: polymorphism and fixation. Negative selection and genetic drift may dominate the first phase, whereas positive selection may become much more significant in the second phase. However, the conventional dichotomy of synonymous vs. nonsynonymous changes does not offer the resolution needed to study the dynamics of these two phases. Following previously published methods, we separated amino acid changes into 75 elementary types (1-bp substitution between their respective codons). The likelihood of each type of amino acid change becoming polymorphic (PI, which stands for 'polymorphic index'), relative to synonymous changes, can then be calculated. Similarly, the likelihood of fixation (FI, for 'fixation index'), conditional on common polymorphisms, is also calculated. Using Perlegen and HapMap data on human polymorphisms and the chimpanzee sequences as the outgroup, we compared the evolutionary dynamics of the 75 elementary changes in the two phases. We found a strong 'L-shaped' negative correlation (P < 0.001) between FI and PI. Only those changes with low PIs show FI > 1, which is often a signature of adaptive evolution. These patterns suggest that negative and positive selection operate more effectively on the same set of amino acid changes and that [approximately equal to] 10-13% of amino acid substitutions between humans and chimpanzee may be adaptive. amino acid substitution | deleterious mutation | positive selection | selective constraint

The density functional theory is employed to study and explain the various effects of the hydrogen-bonding and stacking interactions with amino acids on the acidity of uracil, which depends on the nature of amino acid and binding orientation. The results show that such interactions decrease the gas-phase acidity of uracil, which also varies with the nature of the molecule bound, as well as the binding orientations and strengths.

A large number of structural and functional studies are employed to show that pita acts as an acetyltransferase (gene PA4866) from pseudomonas aeruginosa using L-methionine sulfoximine instead of the commonly thought to be used phosphinothricin. The results prove that pita plays a vital role in protecting the glutamine synthetase from inhibiton, as L-methionine sulfoximine leads to a growth of strain Depp4 in the absence of glutamine.

Asymmetric reduction of ketimines with trichlorosilane, which could be catalyzed by N-methylvaline-derived Lewis-basic formamides, is described. The results reveal that appending a fluorous tag simplifies the isolation procedure, while preserving high enantioselectivity.

One-electron oxidation of a methionine model peptide (N-acetylmethionine amide) is examined by using density function theory calculations in order to elucidate amino acid oxidation mechanism. The results have revealed the contribution of protonated species to the peptide oxidation, suggesting that DFT methodology has great potential in examining amino acid oxidation mechanism.

Two-photon circular dichroism spectra calculated within the density functional theory approximation in the absorption region, where the lowest electronic states are seen are described for the essential amino acids in the gas phase. The contributions of the electric dipole, magnetic dipole and electric quadrupole transitions to the rotational strengths are analyzed and the fingerprinting capabilities of the two-photon circular dichroism spectroscopy are highlighted.

Solid-state chlorine-35/37 NMR for L-tryptophan hydrochloride and DL-arginine hydrochloride monohydrate have helped in understanding the trends in the spans of the chlorine chemical shift tensors in amino acid hydrochlorides. The inference indicates the application of chlorine NMR interaction tensors in the refinement of proton positions in structurally similar compounds like chlorine ion channels, for which neutron diffraction data is not available.

The study of molecular recognition using solid-state supramolecular [beta]-cyclodextrin complexes is conducted by analyzing the crystal structure of a triclinic 2:2 inclusion complex of [beta]-cyclodextrin with N-acetyl-L-phenylalanine methyl ester at various temperatures between 298 and 20 K. The kinetic energy dependent changes in guest molecule conformations, orientations, and positions in the binding pocket presented by the crystal lattice are revealed.

The binding energies are calculated for hydrogen-bonded complexes of six cyclic ethers having four to six C and O ring atoms, with five hydrogen-bond donor molecules mimicking amino acid side chains, with and without counterpoise correction throughout the structure optimizations. This study is the first step toward the development of an affordable computational level for estimating the binding energies of natural product, fused ring ether systems to the human estrogen receptor.

Mass spectrometry is used to observe and analyze the formation of homochiral serine clusters on spontaneous assembly of amino acids into vapor phase, which is a result of the thermal heating of solid compounds in air. The results show that the sublimation of serine under relatively mild conditions leads to the formation of chirally enriched serine octamers, while on the other hand, several cluster-forming chemical reactions can be used to transfer the chiral preference of the starting serine to various other compounds.

The interface between 3-(3,4-dihydroxyphenyl)-L-alanine (L-DOPA) and a single-crystalline Au(110) model surface is investigated in order to understand the fundamentals about the surface bonding of this amino acid and its role in mussel adhesion. The results have shown that the aromatic ring system of L-DOPA functions as a surface anchor and also that the catechol ring supports adhesion of mussel proteins through two independent functions.

Characterization of stable conformers of gaseous arginine, both the canonical and zwitterionic tautomers, is performed using extensive ab initio calculations. The lowest energies of the canonical and zwitterionic structures are found to be lower than the existing values by 2.0 and 2.3 kcal/mol, respectively.

Full-length pentameric WT-phospholamban (PLB) and its phosphorylated form (P-PLB) were employed to compare the structural changes in the acyl chains of 1-palmitoyl-2-oleoyl-sn-glycero-phosphocholine (POPC) multilamellar vesicles (MLVs) upon the insertion of both proteins utilizing A [super 31]P, [super 2]H, and [super 13]C solid-state NMR spectroscopy. Results reveal that a direct interaction takes place between both proteins and the phospholipid head groups, but the interaction of P-PLB with POPC bilayers was less significant compared with that of PLB.

The nucleocapsid protein of HIV-1 is 55 amino acids in lengths and possesses two CCHC-type zinc fingers where finger one (N-terminal) contributes significantly more to helix destabilizing activity than finger two (C-terminal). Study is presented in an attempt to determine at the amino acid level the reason for the apparent distinction between the zinc fingers. Results indicate that amino acid differences at positions 24 and 27 contribute significantly to finger one's helix destabilizing activity.

Sorcin-annexin VII interaction was studied directly by Western blot and surface plasmon resonance experiments and the interaction of sorcin with ryanodine receptor (RyR2) was monitored by measuring [Ca.sup.2} spark activity in isolated rabbit heart cells. Results provide experimental support to the proposal that the interaction network around the D helix is central to the [Ca.sup.2}-induced activation mechanism of sorcin.

Two Ozma problems are defined which might be solved by bate decay or atomic optical activity. Atomic and molecular sum frequency generation is chosen, as it supplies rich methods of effecting 'gedanken' solutions to the Ozma problems.

The creation of first broad substrate range, nicotinamide cofactor dependent, and highly D-enantio-selective amino acid dehydrogenase is reported. The findings show significant activity toward synthesis of a number of straight, branched and cyclic aliphatic and aromatic D-amino acids.

The location of multiple amino acids within the native replication protein A three-dimensional structure was studied using reactivity of these amino acids toward proteolytic and chemical modification reagents. This showed that the reactivity analysis approach is capable of critically evaluating structure models and could be used as a basis for selecting the most important amongst alternate models of a protein structure.

The coupling of stepwise mobile phase gradient elution and flow programming is proposed as an integrated approach to the general elution problem in reversed-phase liquid chromatography. A model is developed to describe the above separation process performed under simultaneous programming of two separation parameters by extending our previous work on the rigorous derivation of the fundamental equation governing the concentration gradient of organic modifier in the mobile phase, that is, a single gradient elution mode (Anal. Chem. 2005, 77, 5670-5677). The theory was tested in the retention prediction and separation optimization of 18 o-phthal-aldehyde derivatives of amino acids in eluting systems modified by acetonitrile or methanol. The retention prediction obtained for all solutes under all dual-mode gradient conditions was excellent. In addition, it has been shown that the combination of mobile phase and flow rate programming modes is particularly favorable, whereas the separations among the analytes were considerably improved by using the acetonitrile eluting system, as compared to those obtained by the methanol system.

The quantitative analysis of amino acids by terahertz (THz) time-domain absorption spectroscopy is demonstrated. The optical densities of the amino acids were found to be linearly proportional to the concentration. The molar absorption coefficients of L-glutamic acid (L-Glu), L-glutamic acid sodium salt (Na-L-Glu), L-glutamic acid hydrochloric salt (HCl-L-Glu), L-cysteine (L-Cys), and L-histidine (L-His) were calculated by averaging the THz spectra of the amino acids at several different concentrations in approximately the 0.2-1.0 mol [L.sup.-1] range. The concentrations of L-Glu, L-Cys, and L-His mixed samples were successfully calculated with errors of less than 11% and 20% when their concentrations were higher than 0.45 and 0.22 mol [L.sup.-1], respectively, by using the obtained molar absorption coefficient.

The presented work proposes a new methodology based on proteomics techniques to identify proteins in old art paintings. The main challenging tasks of this work were (i) to find appropriate conditions for extracting proteins from the binding media without protein hydrolysis in amino acids and (ii) to develop analytical methods adapted to the small sample quantity available. Starting from microsamples of painting models (ovalbumin-based, which is the major egg white protein, and egg-based paintings), multiple extraction solutions (HCI, HCOOH, N[H.sub.3], NaOH) and conditions (ultrasonic bath, mortar and pestle, grinding resin) were evaluated. The best results were obtained using a commercial kit including a synthetic resin, mortar and pestle to grind the sample in an aqueous solution acidified with trifluoroacetic acid at 1% with additional multiple steps of ultrasonic baths. The resulting supernatant was analyzed by MALDI-TOF in linear mode to verify the efficiency of the extraction solution. An enzymatic hydrolysis step was also performed for protein identification; the peptide mixture was analyzed by nanoLC/ nanoESI/Q-q-TOF MS/MS with an adapted chromatographic run for the low sample quantity. Finally, the developed methodology was successfully applied to Renaissance art painting microsamples of ~10 [micro]g from Benedetto Bonfigli's triptych, The Virgin and Child, St. John the Baptist, St. Sebastian (XVth century), and Niccolo di Pietro Gerini's painting, The Virgin and Child (XIVth century), identifying, for the first time and without ambiguity, the presence of whole egg proteins (egg yolk and egg white) in a painting binder.

In this work, we investigate the slow dynamics of 1-butyl-3-methylimidazolium hexafluorophosphate, a very popular room-temperature ionic solvent. Our study predicts the existence of heterogeneity in the liquid and shows that this heterogeneity is the underlying microscopic cause for the recently reported 'red-edge effect' (REE) observed in the study of fluorescence of the organic probe 2-amino-7-nitrofluorene. This theoretical work explains in microscopic terms the relation between REE and dynamic heterogeneity in a room-temperature ionic liquid (IL). The REE is typical of micellar or colloidal systems, which are characterized by microscopic environments that are structurally very different. In contrast, in the case of this room-temperature IL, the REE occurs because of the long period during which molecules are trapped in quasistatic local solvent cages. This trapping time, which is longer than the lifetime of the excited-state probe, together with the inability of the surroundings to adiabatically relax, induces a set of site-specific spectroscopic responses. Subensembles of fluorescent molecules associated with particular local environments absorb and emit at different frequencies. We describe in detail the absorption wavelength-dependent emission spectra of 2-amino-7-nitrofluorene and show that this dependence on [[lambda].sub.ex] is characteristic of the IL and, as is to be expected, is absent in the case of a normal solvent such as methanol. dynamic heterogeneity | excitation wavelength-dependent fluorescence

A new technique is described for specific recognition of protein analytes by observing protein-induced changes in the drying/crystallization patterns (DCP) of an array of microdroplets containing solutions of different reporter substances. Recognition is based on a difference in interaction of the protein analyte crystalline elements (planes, edges, defects, etc.) in the growing reporter crystals. Using a set of natural L-amino acids as reporters and denoting the amino acid solutions displaying substantial protein-induced changes in the DCP as '1' and those that show no or small changes as '0', a digital binary code was determined for several proteins at multiple concentrations. It was demonstrated that globular proteins can be reliably identified using this code as a 'signature' when only 2-100 ng of protein was added to amino acid microdroplets.

Random mutagenesis and phage display selection are used to evolve proteins with a high degree of sequence identity but different tertiary structures (homologous heteromorphs) to understand better how amino acid sequences specify unique tertiary folds. A thermodynamic analysis of the folding reactions and the binding reactions of a pair of homologous heteromorphs is presented and the thermodynamic linkage is used to evaluate the tendency of one sequence to adopt unique folds.

A 2D layered spin crossover complex, [Fe(super II)H3L(super Me)]Cl.I3, is synthesized from the reaction of Fe(super III)Cl3, a tripod ligand (H3L(super ME) = tris[2-(((2-methylimidazoyl-4-yl)methylidene)amino)ethyl]amine), and Nal in methanol. The compound has shown an abrupt spin transition between the HS (s = 2) and LS (S = 0) states at T(sub 1/2) = 110 K without hysteresis.

Competitive experiments with isotopically labeled chorismate derivates have provided direct information about the nature of the transition state of the chorismate mutase reaction both in solution and at the active sites of evolutionarily unrelated enzymes. The competing reaction of chorismate leading to 4-hydroxybenzoate, an intermediate in ubiquinone biosynthesis, likewise appears to occur via an asynchronous concerted mechanism.

The biochemical characterization and crystallographic structure of a 149 amino acid protein, hDim2, which shares 38% sequence identity with hDim1 is reported. The structural investigations suggested that in higher eukaryotes, although both hDim1 and hDim2 are involved in pre-mRNA splicing, the two properties are likely to participate in different multisubunit complexes and biological processes.

The calculation of (super 13)C, (super 14)N, (super 15)N, (super 17)O and (super 35)Cl NMR parameters, chemical shift tensors and quadrupolar tensors for (super 14)N, (super 17)O and (super 35)Cl for the crystalline forms of various amino acids is discussed. The isotropic chemical shift value of (super 17)O is markedly affected by small differences in the experimental structure whereas the values of (super 13)C and (super 15)N are relatively insensitive to the differences.

A study on the evaluation of free amino acids (FAAs) in tarhana during fermentation and storage was performed. The FAAs in tarhana were determined by RP-HPLC with a fluorescence detector following extraction from the sample and derivatization with dansyl chloride. The amount of FAAs increased significantly (p < 0.01) during fermentation and storage. The increase in the content of total free amino acids (TFAAs) and total free essential amino acids (TFEAAs) of fermented tarhana, which was used with yogurt bacteria and baker's yeast, was 57% and 93%, respectively. The amino acids primarily responsible for the increase were valine and tryptophan followed by methionine, alanine, isoleucine+leucine, phenylalanine, arginine, proline, and lysine. The TFAA content of tarhana at the end of fermentation was found to be 8% of total protein (16.8%). The ratio of TFEAAs/TFAAs was initially 0.46 and increased to 0.57 at the end of fermentation. The TFAA content of wet tarhanas was higher than that of the dry counterpart. It was found that the TFAA content of dry tarhana was 25% lower than the fresh wet tarhana (FWT), at the end of fermentation. It was concluded that the decrease in FAAs in dry tarhana was due to the Maillard reaction and partial degradation of FAAs during dehydration. Keywords: Fermentation, storage, free amino acids, tarhana

Twenty five amino acids within the 'N', 'P', and 'A' domains of Calcium(super 2+) ATPase(SERCA1) headpiece were subjected to site directed mutagenesis, taking advantage of high yield expression system. Functional and conformational effects of mutations were interpreted systematically in the light of the high resolution WT(wild type) structure.

Abstract: This research integrated the Revised Universal Soil Loss Equation (RUSLE) and the soil statistical analysis with RS and GIS techniques to quantify soil and nutrients loss risk. The Letianxi [...]

Two new families of orthogonally protected cyclic homooligomers with two to four sugar units are synthesized from pyranoid sugar amino acids. Cyclic oligomers composed of amide-linked sugar amino acids are prepared by cyclization of linear oligomers of the novel orthogonally protected pyranoid sugar amino acid using a solution-phase coupling method.

A complete and systematic analysis of the relationship between side chain structure and the 14-helicity of a well-studied class of foldamers, beta(super 3)-peptides, in water is reported. The 14-helix propensities of beta(super 3)-amino acids differ starkly from the Alpha-helix propensities of analogous Alpha-amino acids.

Bacteriocins produced by latic acid bacteria are potent antimicrobial compounds that are active against closely related bacteria. The NMR solution structure of the 111-amino acid immunity protein for carnobacteriocin B2 (ImB2) is reported.

The diversity of mechanisms for enantiodiscrimination and of bond types that can be formed makes Pd-catalyzed asymmetric allylic alkylation, a powerful step for simplification of synthetic strategy to complex molecular targets. A wide range of different classes of compounds including chromanes, polyhydrofurans and amino acids are used and novel synthetic strategies emerge, which provide short efficient asymmetric syntheses.

The ground- and excited-state interactions of N-(2-ethanoic acid)-1,8-naphthalimide (NI-ala), along with tryptophan and tyrosine-substituted 1,8-naphthalimide derivatives (NI-trp and NI-tyr), with amino acids and native proteins are investigated in aqueous buffered solution. Results suggest that the studies have identified the potential oxidative targets in native proteins and demonstrate the utility of naphthalimide derivatives to photomodify native proteins.

Chiral L-amino acids bearing sulfonamide side chains is synthesized, with the tetrahedral sulfonamide groups designed to target bridging coordination interactions with the binuclear manganese cluster in the arginase active site. The results demonstrate that the sulfonamide group is an excellent ligand for the displacement of a hydroxide ion bound to either a single metal ion or a binuclear metal cluster.

A systematic study of aryl radical additions to azomethines that validates the expectation that use of C-N bond would provide a base-free aryl amination method, which is expected to be relatively insensitive to electronic effects, is reported. A more efficient synthetically useful process is the direct addition of aryl radicals to the nitrogen of an azomethine.

An artificial anion receptor is presented, in which two cyclohexapeptide subunits containing l-proline and 6-aminopicolinic acid subunits in an alternating sequence are connected via an adipinic acid spacer. Covalently linking two cyclopeptide molecules derived from 6-aminopicolinic acid subunits with a suitable spacer, an artificial receptor is accessible that strongly binds anions in 50% water/methanol.

The structures and energetics of interactions between aromatic and basic amino acids in alpha-helices are investigated. The results clearly show that each of the five pairs interact favorably when placed i, i + 4 in a helix, with a preference for the aromatic-polar orientation.

A different approach to amino acids based on an expeditious route to enantiopure allylic amines is reported. This is an efficient and general method toward both the L and D configuration of this class of alpha-substituted glycines, as demonstrated by the synthesis of N-protected L and D (1-adamantyl)-glycines.