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At least 343 records · Page 19Linked to original sources
PubMed2004

Hydrogen bonding in mimics of Watson-Crick base pairs involving C-H proton donor and F proton acceptor groups: a theoretical study.

We have theoretically analyzed mimics of Watson-Crick adenine-thymine (AT) and guanine-cytosine (GC) base pairs in which N-H...O and N...H-N hydrogen bonds are replaced by N-H...F and N...H-C, respectively, by using the generalized gradient approximation of density functional theory at BP86/TZ2P. The general effect of the above substitutions is an elongation and weakening of the hydrogen bonds that hold together the base pairs. However, the precise effects depend on how many and, in particular, on which hydrogen bonds are substituted in AT and GC. Another purpose of this work is to clarify the relative importance of electrostatic attraction versus orbital interaction in the weak hydrogen bonds involved in the mimics, by using a quantitative bond-energy decomposition scheme. At variance with widespread believe, the orbital interaction component in these weak hydrogen bonds is found to contribute 34-42% of the attractive interactions and is thus of the same order of magnitude as the electrostatic component, which provides the remaining attraction component.

Base Pairing↗
PubMed1989

Chloroplast thylakoid proteins associated with sequestered proton-buffering domains. Plastocyanin contributes buffering groups to localized proton domains.

Thylakoid membrane proteins are organized so as to shield 30-50 nmol H+ (mg Chl)-1 from freely equilibrating with either the external or the lumen aqueous phases. Amine groups provide binding sites for this metastable buffering array and can be quantitatively measured by acetylation using [3H]acetic anhydride. The principle of the assay is that a metastable acidic domain will have relatively less of the reactive neutral form of the amine compared to the amount present after addition of an uncoupler. The extent of the acetylation reaction is strongly influenced by whether the lumen pH comes to complete equilibrium with the external pH prior to adding the acetic anhydride. Determination of the lumen pH by [14C]methylamine distribution after the standard 3 or 5 min equilibration in pH 8.6 buffer indicated that the lumen may have been 0.2 to 0.3 pH more acidic than the external phase. This effect was taken into account by determining the pH dependence, in the pH 8.2-8.6 range, of acetylation of the membrane proteins studied, and the labeling data were conservatively corrected for this possible contribution. Experiments were carried out to identify the thylakoid proteins that contribute such metastable domain amine groups, using the above conservative correction. Surprisingly, plastocyanin contributes buried amine groups, but cytochrome f did not give evidence for such a contribution, if the conservative correction in the labeling was applied. If the correction was too conservative, cytochrome f may contribute amines to the sequestered domains. The new methodology verified earlier results suggesting that three Tris-releasable photosystem II-associated proteins also contribute significantly to the sequestered amine-buffering array.

Acetic Anhydrides↗
PubMed2000

Flexible coupling between light-dependent electron and vectorial proton transport in illuminated leaves of C3 plants. Role of photosystem I-dependent proton pumping.

The role of cyclic electron transport has been re-examined in leaves of C3 plants because the bioenergetics of chloroplasts (H +/e = 3 in the presence of a Q-cycle; H+/ATP = 4 of ATP synthesis) had suggested that cyclic electron flow has no function in C3 photosynthesis. After light activation of pea leaves, the dark reduction of P700 (the donor pigment of PSI) following far-red oxidation was much accelerated. This corresponded to loss of sensitivity of P700 to oxidation by farred light and a large increase in the number of electrons available to reduce P700+ in the dark. At low CO2 and O2 molar ratios, far-red light was capable of decreasing the activity of photosystem II (measured as the ratio of variable to maximal chlorophyll fluorescence, Fv/Fm) and of increasing light scattering at 535 nm and zeaxanthin synthesis, indicating formation of a trans-thylakoid pH gradient. Both the light-induced increase in the number of electrons capable of reducing far-redoxidised P700 and the decline in Fv/Fm brought about by far-red in leaves were prevented by methyl viologen. Antimycin A inhibited CO2-dependent O2 evolution of pea leaves at saturating but not under limiting light; in its presence, far-red light failed to decrease Fv/Fm. The results indicate that cyclic electron flow regulates the quantum yield of photosystem II by decreasing the intrathylakoid pH when there is a reduction in the availability of electron acceptors at the PSI level (e.g. during drought or cold stresses). It also provides ATP for the carbon-reduction cycle under high light. Under these conditions, the Q-cycle is not able to maintain a H+/e ratio of 3 for ATP synthesis: we suggest that the ratio is flexible, not obligatory.

Carbon Dioxide↗
PubMed1981

Combined use of proton-proton Overhauser enhancements and a distance geometry algorithm for determination of polypeptide conformations. Application to micelle-bound glucagon.

In a new approach for the determination of polypeptide conformation, experimental data on intramolecular distances between pairs of hydrogen atoms obtained from nuclear Overhauser enhancement studies are used as input for a distance geometry algorithm. The algorithm determines the limits of the conformation space occupied by the polypeptide chain. The experimental data are used in such a way that the real conformation should in all cases be within these limits. Two important features of the method are that the results do not depend critically on the accuracy of the distance measurements by nuclear Overhauser enhancement studies and that internal mobility of the polypeptide conformation is explicitly taken into consideration. The use of this new procedure is illustrated with a structural study of the region 19-27 of glucagon bound to perdeuterated dodecylphosphocholine micelles.

Amino Acid Sequence↗
PubMed1985

Calculation of protein conformations by proton-proton distance constraints. A new efficient algorithm.

We have developed a method to determine the three-dimensional structure of a protein molecule from such a set of distance constraints as can be determined by nuclear magnetic resonance studies. The currently popular methods for distance geometry based on the use of the metric matrix are applicable only to small systems. The method developed here is applicable to large molecules, such as proteins, with all atoms treated explicitly. This method works in the space of variable dihedral angles and determines a three-dimensional structure by minimization of a target function. We avoid difficulties hitherto inherent in this type of approach by two new devices: the use of variable target functions; and a method of rapid calculation of the gradient of the target functions. The method is applied to the determination of the structures of a small globular protein, bovine pancreatic trypsin inhibitor, from several artificial sets of distance constraints extracted from the X-ray crystal structure of this molecule. When a good set of constraints was available for both short- and long-range distances, the crystal structure was regenerated nearly exactly. When some ambiguities, such as those expected in experimental information, are allowed, the protein conformation can be determined up to a few local deformations. These ambiguities are mainly associated with the low resolving power of the short-range information.

Aprotinin↗