Hydrogen bonding in globular proteins.

A global census of the hydrogen bonds in 42 X-ray-elucidated proteins was taken and the following demographic trends identified: (1) Most hydrogen bonds are local, i.e. between partners that are close in sequence, the primary exception being hydrogen-bonded ion pairs. (2) Most hydrogen bonds are between backbone atoms in the protein, an average of 68%. (3) All proteins studied have extensive hydrogen-bonded secondary structure, an average of 82%. (4) Almost all backbone hydrogen bonds are within single elements of secondary structure. An approximate rule of thirds applies: slightly more than one-third (37%) form i----i--3 hydrogen bonds, almost one-third (32%) form i----i--4 hydrogen bonds, and slightly less than one-third (26%) reside in paired strands of beta-sheet. The remaining 5% are not wholly within an individual helix, turn or sheet. (5) Side-chain to backbone hydrogen bonds are clustered at helix-capping positions. (6) An extensive network of hydrogen bonds is present in helices. (7) To a close approximation, the total number of hydrogen bonds is a simple function of a protein's helix and sheet content. (8) A unique quantity, termed the reduced number of hydrogen bonds, is defined as the maximum number of hydrogen bonds possible when every donor:acceptor pair is constrained to be 1:1. This quantity scales linearly with chain length, with 0.71 reduced hydrogen bond per residue. Implications of these results for pathways of protein folding are discussed.     

Hydrogen bonding stabilizes globular proteins.

It is clear that intramolecular hydrogen bonds are essential to the structure and stability of globular proteins. It is not clear, however, whether they make a net favorable contribution to this stability. Experimental and theoretical studies are at odds over this important question. Measurements of the change in conformational stability, delta (delta G), for the mutation of a hydrogen bonded residue to one incapable of hydrogen bonding suggest a stabilization of 1.0 kcal/mol per hydrogen bond. If the delta (delta G) values are corrected for differences in side-chain hydrophobicity and conformational entropy, then the estimated stabilization becomes 2.2 kcal/mol per hydrogen bond. These and other experimental studies discussed here are consistent and compelling: hydrogen bonding stabilizes globular proteins.     

Hydrogen ion binding properties of tuna haemoglobins.

Tunas are very active fish with a high aerobic capacity, but they also regularly perform burst swimming with massive production of lactic acid. The present study examines whether H(+) buffering by tuna haemoglobin (Hb) is elevated to cope with metabolic acidoses (by analogy with the high buffer capacity of tuna white musculature) or whether the Hb-H(+) binding properties resemble other teleosts that have low buffer values and high Haldane effects. H(+) titration of oxygenated and deoxygenated composite Hb from yellowfin tuna, skipjack tuna and bigeye tuna in 0.1 M KCl revealed low Hb-specific buffer values in all three tunas. Values at physiological pH were comparable to those reported in less active species such as carp and eel. The fixed acid Haldane effect was large (maximal uptakes of close to 4 mol H(+) per mol Hb tetramer upon deoxygenation). Thus, the Hb-H(+) binding properties of very active tuna species correspond to other teleosts. Low Hb buffer values may be a pre-requisite for the regulation of red blood cell pH via Na(+)/H(+) exchange. Approximately nine "neutral" groups were titratable in tuna Hbs, suggesting that two alpha-amino groups and seven histidine residues are titrated within each tetramer.     

Hydrogen exchange study of membrane-bound rhodopsin. I. Protein structure.

Structural parameters of rhodopsin in disc membrane preparations from frog and cattle were studied by hydrogen exchange methods. The method measures the exchange of protein amide hydrogens with water and can distinguish protons which are internally bonded from those which are hydrogen-bonded to water. The results show that about 70% of rhodopsin's peptide group protons are exposed to water. The identification of these groups as free peptides was made initially on the usual basis of the identity of their exchange rate with the well characterized free peptide rate; other experiments specifically excluded contributions from lipids, protein side chains, adventitious mucopolysaccharides, and intradisc water. In contrast to rhodopsin, other proteins generally have only 20 to 40% free peptide groups. Apparently rhodopsin has some unusual structural feature. Our results together with available information on rhodopsin suggest that a considerable length of its polypeptide chain is arranged at the surface of a channel of water penetrating into the membrane. Physicochemical considerations indicate that such a channel would have to be quite wide, 10 to 12 A or more, to explain the hydrogen exchange results.     

Hydrogen bonding in DNA base complexes.

Experimental intermolecular frequencies in the DNA base complexes 1-methylthymine (1-MT) and cytosine monohydrate (CMH) are analyzed in terms of simple analytic interatomic potentials. Calculations with two different values for the constants of the nonbonded interactions are considered, and the hydrogen bond potentials are determined for each of these models. The observed frequencies in 1-MT are reasonably well described, although corresponding potentials are very different in the two models. The observed frequencies in CMH are less well described, although corresponding hydrogen bond potentials are similar in the two models. Hydration interactions are found to be important in CMH and the role of the water molecule is discussed. Possible reasons for the shortcomings of this simple analysis are considered.     

Hydrogen production. Green algae as a source of energy.

Hydrogen gas is thought to be the ideal fuel for a world in which air pollution has been alleviated, global warming has been arrested, and the environment has been protected in an economically sustainable manner. Hydrogen and electricity could team to provide attractive options in transportation and power generation. Interconversion between these two forms of energy suggests on-site utilization of hydrogen to generate electricity, with the electrical power grid serving in energy transportation, distribution utilization, and hydrogen regeneration as needed. A challenging problem in establishing H(2) as a source of energy for the future is the renewable and environmentally friendly generation of large quantities of H(2) gas. Thus, processes that are presently conceptual in nature, or at a developmental stage in the laboratory, need to be encouraged, tested for feasibility, and otherwise applied toward commercialization.     

Hydrogen bonding of iron-coordinated histidine in heme proteins.

The hydrogen-bonding motifs of the proton on the N delta atom of iron-coordinated histidine residues in heme proteins have been classified into three categories: (1) Those in which the hydrogen-bond acceptor is either an amino acid residue (serine) directly adjacent to the histidine or a carbonyl group of the polypeptide chain less than five residues away from the histidine; (2) those in which the hydrogen-bonding acceptor is a carbonyl group of the polypeptide backbone associated with an amino acid residue 8 to 17 residues away from the histidine; and (3) those in which the hydrogen-bonding acceptor is an exogenous water molecule or an amino acid residue located far from the histidine in the amino acid sequence. Some biological functions are defined by this classification, whereas others span all classes.     

Hydrogen bonds involving sulfur atoms in proteins.

Intrachain hydrogen bonds are a hallmark of globular proteins. Traditionally, these involve oxygen and nitrogen atoms. The electronic structure of sulfur is compatible with hydrogen bond formation as well. We surveyed a set of 85 high-resolution protein structures in order to evaluate the prevalence and geometry of sulfur-containing hydrogen bonds. This information should be of interest to experimentalists and theoreticians interested in protein structure and protein engineering.     

Hydrogen production by nitrogen-starved cultures of Anabaena cylindrica.

Nitrogen-starved cultures of the alga Anabaena cylindrica 629 produced hydrogen and oxygen continuously for 7 to 19 days. Hydrogen production attained a maximum level after 1 to 2 days of starvation and was followed by a slow decline. The maximum rates were 30 ml of H2 evolved per liter of culture per h or 32 mul of H2 per mg of dry weight per h. In 5 to 7 days the rate of H2 evolution by the more productive cultures fell to one-half its maximum value. The addition of 10(-4) to 5 X 10(-4) M ammonium increased the rate of oxygen evolution and the total hydrogen production of the cultures. H2-O2 ratios were 4:1 under conditions of complete nitrogen starvation and about 1.7:1 after the addition of ammonium. Thus, oxygen evolution was affected by the extent of the nitrogen starvation. Thermodynamic efficiencies of converting incident light energy to free energy of hydrogen via algal photosynthesis were 0.4%. Possible factors limiting hydrogen production were decline of reductant supply and filament breakage. Hydrogen production by filamentous, heterocystous blue-green algae could be used for development of a biophotolysis system.     

Hydrogen production by nitrogen-starved cultures of Anabaena cylindrica.

Nitrogen-starved cultures of the alga Anabaena cylindrica 629 produced hydrogen and oxygen continuously for 7 to 19 days. Hydrogen production attained a maximum level after 1 to 2 days of starvation and was followed by a slow decline. The maximum rates were 30 ml of H2 evolved per liter of culture per h or 32 mul of H2 per mg of dry weight per h. In 5 to 7 days the rate of H2 evolution by the more productive cultures fell to one-half its maximum value. The addition of 10(-4) to 5 X 10(-4) M ammonium increased the rate of oxygen evolution and the total hydrogen production of the cultures. H2-O2 ratios were 4:1 under conditions of complete nitrogen starvation and about 1.7:1 after the addition of ammonium. Thus, oxygen evolution was affected by the extent of the nitrogen starvation. Thermodynamic efficiencies of converting incident light energy to free energy of hydrogen via algal photosynthesis were 0.4%. Possible factors limiting hydrogen production were decline of reductant supply and filament breakage. Hydrogen production by filamentous, heterocystous blue-green algae could be used for development of a biophotolysis system.     

Hydrogen ion titration of horse heart ferricytochrome c.

Continuous hydrogen ion titration curves of deionized solutions of horse heart ferricytochrome c have been obtained at 25 degrees C. at a constant ionic strength of 0.10 from pH 3.0 to 11.0. Titration of the oxidized protein in KCl required 28.4 equiv over that pH range, and a small hysteresis between the forward and reverse limbs was displayed. The Linderstrom-Lang approximation, which takes into account electrostatic interactions between charged groups on the protein surface, was used in a computer simulation program to analyze the forward and reverse limbs of the titration curve separately. The results indicated 1 alpha-, 12 beta- and gamma-, and 1 heme propionic carboxylic, 1 imidazole, 1 phenolic, and 18 epsilon-amino residues appear to titrate normally. Variations in the electrostatic interaction factor omega suggest conformational changes in the protein at the extremes of pH, although the relationship of the variations in omega to the magnitude of the conformational changes does not appear to be strictly quantitative for cytochrome c. These results show the acid-base behavior of cytochrome c to be complex in nature, and suggest that the Lindenstrom-Lang model may not be adequate for cytochrome c.     

Hydrogen peroxide evolution during V-UV photolysis of water.

Hydrogen peroxide evolution during the vacuum-ultraviolet (V-UV, 172 nm) photolysis of water is considerably affected by the presence of oxalic acid (employed as a model water pollutant) and striking differences are observed in the absence and in the presence of dioxygen.     

Hydrogen utilization by clostridia in sewage sludge.

A sporeformer morphologically different but physiologically similar to Clostridium aceticum Wieringa was isolated from sewage sludge. It used large amounts of H2 and CO2, converting them chiefly to acetic acid. Growth occurs anaerobically on yeast extract alone, but after the nutrients in yeast extract are used, growth continues at a reduced rate, supported by the conversion of the gases to acetate.