An experimental and theoretical investigation of the chemical shielding tensors of (13)C(alpha) of alanine, valine, and leucine residues in solid peptides and in proteins in solution

We have carried out a solid-state magic-angle sample-spinning (MAS) nuclear magnetic resonance (NMR) spectroscopic investigation of the (13)C(alpha) chemical shielding tensors of alanine, valine, and leucine residues in a series of crystalline peptides of known structure. For alanine and leucine, which are not branched at the beta-carbon, the experimental chemical shift anisotropy (CSA) spans (Omega) are large, about 30 ppm, independent of whether the residues adopt helical or sheet geometries, and are in generally good accord with Omega values calculated by using ab initio Hartree-Fock quantum chemical methods. The experimental Omegas for valine C(alpha) in two peptides (in sheet geometries) are also large and in good agreement with theoretical predictions. In contrast, the "CSAs" (Deltasigma) obtained from solution NMR data for alanine, valine, and leucine residues in proteins show major differences, with helical residues having Deltasigma values of approximately 6 ppm while sheet residues have Deltasigma approximately 27 ppm. The origins of these differences are shown to be due to the different definitions of the CSA. When defined in terms of the solution NMR CSA, the solid-state results also show small helical but large sheet CSA values. These results are of interest since they lead to the idea that only the beta-branched amino acids threonine, valine, and isoleucine can have small (static) tensor spans, Omega (in helical geometries), and that the small helical "CSAs" seen in solution NMR are overwhelmingly dominated by changes in tensor orientation, from sheet to helix. These results have important implications for solid-state NMR structural studies which utilize the CSA span, Omega, to differentiate between helical and sheet residues. Specifically, there will be only a small degree of spectral editing possible in solid proteins since the spans, Omega, for the dominant nonbranched amino acids are quite similar. Editing on the basis of Omega will, however, be very effective for many Thr, Val, and Ileu residues, which frequently have small ( approximately 15-20 ppm) helical CSA (Omega) spans.     

Capillary gas chromatography of tert-butyldimethlysilylamino acids with PTV injection

The programmable temperature vaporizing injector (PTV) has been used to study the effects of injection temperature and initial heating period on the FID response factors of TBDMS derivatives of 17 protein amino acids. The relative response factors were calculated for injection temperatures of 50°C, 90°C, 160°C, 220°C, and 260°C with different initial heating periods (1 s, 5 s, and 10 s) and the results compared with the values obtained for the calculated response factors obtained under classical split injection conditions (300°C, continuous). Except for expected peak broadening effects, the initial heating period does not seem to have significative effects on relative peak areas. The response to the derivatives of alanine, glycine, α-aminobutyric acid, valine, proline, methionine, cysteine, phenylalanine, asparagine, and arginine was only slightly affected by increasing the injection temperature whereas the response factors for the derivatives of serine, threonine, glutamic acid, lysine, histidine, tyrosine, and tryptophan were strongly dependent upon initial injection temperatures, decreasing rapidly at temperatures above 160°C. The cold split-splitless injection is clearly advantageous over the classical hot injection techniques for the analysis of this type of aminoacid derivative.     

A thermodynamic study of the complexation reaction for some amino acids with cerium(III) and yttrium(III)

The thermodynamic parameters for the complexation reaction of leucine, valine, proline and hydroxyproline with cerium(III) and yttrium(III) were determined potentiometrical1y in aqueous solution at 25, 35 °C and μ=0.1. The values for the formation constants have been reported. The values of enthalpy changes (ΔS) and entropy changes (ΔS) are positive for all systems. The chelation effect is believed to be essentially an entropy effect.     

Stereoselective Formation of Ternary Copper(II) Complexes of (S)-amino-acid amides and (R)- or (S)-amino acids in aqueous solution

Formation constants of ternary complexes of Cu^II with (S)-amino-acid amides (phenylalaninamide, prolinamide, and tryptophanamide) and (R)- or (S)-amino acids (valine, phenylalanine, proline, and tryptophan) were determined potentiometrically at 25° and I = 0.1M (KC1). Significant stereoselectivity was found for the systems (S)-tryptophanamide/proline, (S)-prolinamide/tryptophan, and (S)-phenylalaninamide/proline, the diastereoisomeric complexes with ‘homochiral’ (SS) being more stable than with ‘heterochiral’ (SR) ligands. The stereoselectivity observed may be explained on the basis of repulsive interactions between the ligand side-chain residues. The present data on the stability of mixed complexes in solution allow to draw some conclusions on the mechanism of chiral discrimination of amino acids in HPLC (reversed-phase) using Cu^II complexes of (S)-amino-acid amides as selectors for ligand-exchange chromatography (LEC).     

Helix forming tendency of valine substituted poly-alanine: a molecular dynamics investigation

In this study, classical molecular dynamics simulations have been carried out on the valine (guest) substituted poly alanine (host) using the host-guest peptide approach to understand the role of valine in the formation and stabilization of helix. Valine has been substituted in the host peptide starting from N terminal to C terminal. Various structural parameters have been obtained from the molecular dynamics simulation to understand the tolerance of helical motif to valine. Depending on the position of valine in the host peptide, it stabilizes (or destabilizes) the formation of the helical structure. The substitution of valine in the poly alanine at some positions has no effect on the helix formation (deformation). It is interesting to observe the coexistence of 3 10 and alpha-helix in the peptides due to the dynamical nature of the hydrogen bonding interaction and sterical interactions.     

FORMATION EQUILIBRIA OF COPPER(II) TERNARY COMPLEXES WITH (S)-LEUCINEHYDROXAMIC ACID AND (R)- OR (S)-AMINO ACIDS IN AQUEOUS SOLUTION

Abstract

Solution equilibria of binary copper(II) complexes with (S)-leucinehydroxamic acid and of ternary complexes with (R)- or (S)-amino acids (valine, proline, phenylalanine, tryptophan) were studied by potentiometry and electronic spectrophotometry at T=25°C and I= 0.5moldm^?3 (KCl). The mixed species [CuLA] and [CuLH-^IA]^? (L^?=leucinehydroxamate, A^?= aminoacidate), do not present stereoselectivity, but are strongly stabilized with respect to their parent binary complexes. Possible structures of the ternary complexes are proposed.     

Effect of proline and glycine residues on dynamics and barriers of loop formation in polypeptide chains

Glycine and proline residues are frequently found in turn and loop structures of proteins and are believed to play an important role during chain compaction early in folding. We investigated their effect on the dynamics of intrachain loop formation in various unstructured polypeptide chains. Loop formation is significantly slower around trans prolyl peptide bonds and faster around glycine residues compared to any other amino acid. However, short loops are formed fastest around cis prolyl bonds with a time constant of 6 ns for end-to-end contact formation in a four-residue loop. Formation of short loops encounters activation energies in the range of 15 to 30 kJ/mol. The altered dynamics around glycine and trans prolyl bonds can be mainly ascribed to their effects on the activation energy. The fast dynamics around cis prolyl bonds, in contrast, originate in a higher Arrhenius pre-exponential factor, which compensates for an increased activation energy for loop formation compared to trans isomers. All-atom simulations of proline-containing peptides indicate that the conformational space for cis prolyl isomers is largely restricted compared to trans isomers. This leads to decreased average end-to-end distances and to a smaller loss in conformational entropy upon loop formation in cis isomers. The results further show that glycine and proline residues only influence formation of short loops containing between 2 and 10 residues, which is the typical loop size in native proteins. Formation of larger loops is not affected by the presence of a single glycine or proline residue.     

TLC separation and derivative spectrophotometry of some amino acids

Chromatographic systems for the separation of amino acid mixtures on RP-18 as a stationary phase have been elaborated. The best results were obtained using methanol-water (1:1, v/v; 1:3, v/v; 1:5, v/v) as a mobile phase. The following amino acids have been examined: asparagine, arginine monohydrochloride, cystine, cysteine chloride, glycine, histidine monohydrochloride, hydroxyproline, isoleucine, leucine, lysine monochloride, methionine, ornithine monohydrochloride, phenylalanine, proline, threonine, tryptophan, tyrosine, serine, valine. Histidine (as monohydrochloride) and methionine were determined by first-, second- and third-derivative spectrophotometry in a mixture of several amino acids.     

Polyamide Layer Chromatography. Identification of Amino Acids in Angelica acutiloba Kitagawa via DNP Derivative

Eighteen amino acids; proline, alanine, valine, leucine, isoleucine, hydroxyproline, phenylalanine, ornithine, glycine, serine, aspartic acid, glutamic acid, threonine, asparagine, lysine, tyrosine, tryptophan, and arginine were identified by polyamide layer chromatography via DNP (dinitrophenly) derivatives in Angelica acutiloba Kitagawa (Tang-Kwei)     

Phosphorylation and ATP-binding induced conformational changes in the PrkC,Ser/Thr kinase from <Emphasis Type="Italic">B. subtilis</Emphasis>

Recent studies on the PrkC, serine-threonine kinase show that that the enzyme is located at the inner membrane of endospores and is responsible for triggering spore germination. The activity of the protein increases considerably after phosphorylation of four threonine residues placed on the activation loop and one serine placed in the C-terminal lobe of the PrkC. The molecular relationship between phosphorylation of these residues and enzyme activity is not known. In this work molecular dynamics simulation is performed on four forms of the protein kinase PrkC from B. subtilis—phosphorylated or unphosphorylated; with or without ATP bound—in order to gain insight into phosphorylation and ATP binding on the conformational changes and functions of the protein kinase. Our results show how phosphorylation, as well as the presence of ATP, is important for the activity of the enzyme through its molecular interaction with the catalytic core residues. Three of four threonine residues were found to be involved in the interactions with conservative motifs important for the enzyme activity. Two of the threonine residues (T167 and T165) are involved in ionic interactions with an arginine cluster from αC-helix. The third residue (T163) plays a crucial role, interacting with His-Arg-Asp triad (HRD). Last of the threonine residues (T162), as well as the serine (S214), were indicated to play a role in the substrate recognition or dimerization of the enzyme. The presence of ATP in the unphosphorylated model induced conformational instability of the activation loop and Asp-Phe-Gly motif (DFG). Based on our calculations we put forward a hypothesis suggesting that the ATP binds after phosphorylation of the activation loop to create a fully active conformation in the closed position.