Conformational characterization

The catalytic cycle of the Na+/K+-ATPase can be described by juxtaposition of distinct reaction sequences that are associated with two different conformational states termed Ei and E2 [1]. In the first step, the Ei conformation is that the enzyme binds Na+ and ATP with very high affinity (KD values of 0.19-0.26 mM and 0.1-0.2 pM, respectively) (Fig. 1A, Step 1). After autophosphorylation by ATP at the aspartic acid within the sequence DKTGS/T the enzyme occludes the 3 Na+ ions (Ei-P(3Na+) Fig. la, Step 2) and releases them into the extracellular space after attaining the E2-P 3Na+ conformation characterized by low affinity for Na+ (Kq5 = 14 mM) (Fig. la, Step 3). The following E2-P conformation binds 2 K+ ions with high affinity (KD approx. 0.1 mM Fig. la, Step 4). The binding of K+ to the enzyme induces a spontaneous dephosphorylation of the E2-P conformation and leads to the occlusion of 2 K+ ions (E2(2K+) Fig. la, Step 5). Intracellular ATP increases the extent of the release of K+ from the E2(2K+) conformation (Fig. la, Step 6) and thereby also the return of the E2(2K+) conformation to the EiATPNa conformation. The affinity ofthe E2(2K+) conformation for ATP, with a K0.5 value of 0.45 mM, is very low. 

Garcia de la Torre J., Carrasco B. 1999. Universal size-independent quantities for the conformational characterization of rigid and flexible macromolecules. Progress in Colloid Polymers Science 113, 81-86. 

Figure 2 Effect of branch frequency on glucan conformation. Conformational characterization of glucans was carried out as described in the experimental section. Curdlan is a linear p(l-3)linked glucan Yeast glucan has a 30% P(l-6) branch frequency and PGG-R glucan has a 50% p(l-6) branch frequency. The Congo Red-single/triple helix complex absorption maxima are indicated.

Asakura, T., Suzuki, H., and Watanabe, Y. (1983). Conformational characterization of silk fibroin in intact Bombyx mod and Philosamia cynthia ricini silkworms by 13C NMR spectroscopy. Macromolecules 16, 1024—1026. 

The cyclohexyl ring adopts a chair conformation characterized by the near-coplanarity of the atoms C(2), C(3), C(4) and C(6). Neither of the nitro groups deviate significantly from planarity. 

Stabilization of a P-hairpin structure can be achieved in two ways, promoting a stable (or restricted) turn structure (as done with mimetics) or linking the two arms either chemically, or, more naturally, by hydrophobic interactions. In an approach to utilizing both methods, a D-Pro-Gly linkage was used to stabilize a left-handed turn (type I or II ) and various charged and hydrophobic residues were used to stabilize the molecule and enhance the interaction between arms. I252"254 Examples of these peptides studied in nonaqueous solution by IR, VCD and NMR spectroscopy exhibit characteristics of well-formed hairpins. 255 Alternatively, in aqueous solution, IR, VCD, and ECD results for related peptides agree with the NMR interpretation of conformations characterized as hairpins stabilized at the turn and frayed at the ends. 256 These latter results also have a qualitative match with theoretical simulations. Recently, examples of hydrophobically stabilized hairpins studied by NMR spectroscopy have avoided use of a nonnatural amino acid. 257,258 ... 

Baublis, A.J. and Berber-Jimenez, M.D., Structural and conformational characterization of stable anthocyanin from Tradescantiapallida, J. Agric. Food Chem., 43, 640, 1995. 

C CP/MAS NMR SPECTRAL ANALYSIS AND CONFORMATIONAL CHARACTERIZATION OF HOMOPOLYPEPTIDES AND THEIR .ENDS... 

In order to elucidate the conformational characterization of PLA/PLV blend samples obtained by using the four methods as mentioned above, solid-state 13C NMR measurements are made on the blend samples. 

We are concerned with the conformational characterization of a PDA/PLV blend sample. The observed 13C CP/MAS NMR spectrum for the PDA/PLV (50/50) blend sample is shown in Fig. 12 (b). In the 13C CP/MAS spectrum, a new peak for the Ca carbon of PDA appears clearly at 48.9 ppm. This peak can be assigned to the Ca carbon of PDA in the p-sheet form. In order to clarify in detail the appearance of this new peak, the carbonyl-carbon region and the Ca, Cp and Cy carbon regions in the spectrum of the PDA/PLV (50/50) blend sample were expanded as shown in Fig. 13. By computer-fitting the observed spectrum was decomposed, and then the fractions of the a-helix and p-sheet forms for PDA and PLV were determined. Another new peak of the Cp carbon of PDA appears at about 20.9 ppm, in addition to an intense peak assigned to the a-helix form (15.7 ppm), and this can be assigned to the p-sheet form (20.9 ppm). These results show that the a-helix form of PDA in the PDA/PLV blends is partially transformed. 

Hjerde, T., Smidsrad, O., Christensen, B.E. (1998b). Acid hydrolysis of k- and i-carra-geenan in the disordered and ordered conformations characterization of partially hydrolyzed samples and single-stranded oligomers released from the ordered structures. Macromolecules, 31, 1842-1851. 

It is interesting to compare the fluctuation rate vn for mobile conformations characterized by two or more positions with the molecular dislocations taking place in the... 

Assembled states interconvert between different conformers characterized by differently bound states of monomers that themselves remain inert ... 

The Xc values below 230 m/i could, in all of the foregoing cases, be reconciled with the relatively small native levorotations by the presence of some /3-conformation characterized by positive rotations and a positive bo. Numerical assessment of Eq. (27) (Section III, C, 1) shows that Xc is linearly related to ratios of bo to Oo that can be negative as well as positive and that this ratio can be as low as —0.2 for rotations in the visible and near ultraviolet spectrum. Thus a positive slope and a negative intercept furnished by simple mixtures of /3-form and random coil will lead to Xc values lower than 212 m/i. It is possible to have a more complex mixture of disordered regions... 

The synthesis and conformational characterization of the m ,m -bis(isodiCp) dichloro titanium compound shown in Scheme 477 has been described. Dynamic NMR spectroscopy suggests a chiral -symmetric structure in solution... 

Folding Equilibrium Studies. E. coli RTEM p-lactamase is a monomeric protein. Its amino acid sequence has been determined (79). It has one disulfide bond between the residues Cys S and Cys. The presence of four tyrosines and four tryptophans allows the use of spectroscopic method for the conformational characterization of the enzyme. In this study, the effect of denaturants on the unfolding of p-lactamase was determined from activity measurements, difference spectroscopy and fluorescence intensity measurements. 

Conformational characterization of these samples was made on the basis of conformation-dependent C chemical shifts determined from CP-MAS NMR, the characteristic bands in IR and far-IR spectra and X-ray diffraction data. Synthetic conditions and characteristics of these samples are summarized in Table 3. 

A well-defined monodisperse penta(L-alanine)- -butylamide H-[Ala]5-NHBu was synthesized by an activated ester method " and other natural abundant polypeptides, [Ala]n-5, [Leu]n-1 and [Leu]n-2, were synthesized by the N-carboxy a-amino-acid anhydride (NCA) method.Fully N-labelled homopolypeptides, [Ala ]n (99 at.% of N purity MASSTRACE, Inc.) and [Leu ]n (99 at.% of N purity MASSTRACE, Inc.), which show characteristic differences in conformation such as the a-helix and /3-sheet forms, were prepared by the heterogeneous polymerization of the corresponding NCAs in acetonitrile with -butylamine as an initiator. Conformational characterization of these samples was made on the basis of the conformation-dependent C and chemical shifts determined from the CP-MAS NMR method and from the characteristic bands in the IR and far-IR spectra. Figs. 38 and 39 show the 75.5 MHz C and 30.4 MHz N CP-MAS NMR spectra respectively of these fully N-labelled (99 at.% purity of N) homopolypeptides adopting the a-helical and /3-sheet forms (A) [Ala ]n-2 (a-helix), (B) [Ala ]n-1 (/3-sheet), (C) [Leu ]n-2 (a-helix), (D) [Leu ]n-1 (/3-sheet) in the solid state. Synthetic conditions and conformational characteristics of these samples are summarized... 

Hounsell, E. F. (1987). Structural and conformational characterization of carbohydrate differentiation antigens. Chem. Soc. Rev. 16, 161-185. 

From the standpoint of switchable properties it would be desirable to build a rotaxane capable of more sharply defined on-off conversions. Before switching, rotaxane 24+ presents two translational conformers, characterized by either benzidine or biphenol occupation by the bead. Although benzidine occupation is heavily favored (84% vs. 16%), the fraction of systems that show biphenol occupation are conceptually equivalent to a leak in the switching device. The selectivity of the bead for one of the two donor stations can be accomplished by one of two approaches ... 

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