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Energy considerations show that low-barrier hydrogen bonds do not offer a catalytic advantage over ordinary hydrogen bonds.

ABSTRACT: Low-barrier hydrogen bonds have recently been proposed as a major factor in enzyme catalysis. Here we evaluate the feasibility of transition state (TS) stabilization by low-barrier hydrogen bonds in enzymes. Our analysis focuses on the facts that (i) a low-barrier hydrogen bond is less stable than a regular hydrogen bond in water, (ii) TSs are more stable in the enzyme active sites than in water, and (iii) a nonpolar active site would destabilize the TS relative to its energy in water. Combining these points and other experimental and theoretical facts in a physically consistent frame-work shows that a low-barrier hydrogen bond cannot stabilize the TS more than an ordinary hydrogen bond. The reason for the large catalytic effect of active site hydrogen bonds is that their formation entails a lower reorganization energy than their solution counterparts, due to the preorganized enzyme environment.

SUBMITTER: Warshel A

PROVIDER: S-EPMC19385 | biostudies-other | 1996 Nov

REPOSITORIES: biostudies-other

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Project description:Background and aimsCluster roots (CRs) constitute a special root adaptation that enables plants to take up nutrients, especially phosphorus (P), from soils with low nutrient availability, including recent volcanic deposits. It is unclear, however, how CR species interact with non-cluster root-bearing (NCR) species, and how substrates' fertility modulates potential interactions.MethodsWe experimentally assessed the net interaction between CR and NCR species using two substrates of contrasting fertility: nutrient-rich nursery mix and tephra (low P availability). We planted seedlings of two southern South American (SSA) Proteaceae, CR species and two NCR Nothofagus species in pairs (conspecifics and heterospecifics) and as singles. We analysed the effect of seedling neighbours on survival, growth performance (e.g. total biomass and leaf area) and leaf and substrate nutrient concentrations (including manganese, a proxy for P-acquisition efficiency through CR activity) using the relative interaction index.Key resultsAfter three growing seasons, we found that (1) Proteaceae species had fewer CRs and lower CR biomass and grew less in the tephra than in the nursery substrate; (2) Nothofagus species did not improve their survival and growth in the presence of Proteaceae species in any substrate; (3) contrary to Nothofagus, Proteaceae species improved their growth more when planted with any neighbour (including conspecifics) than when planted alone, which was accompanied by a significant accretion of leaf P; and (4) the presence of a neighbour increased the final nitrogen and P concentrations in the nursery substrate, regardless of species identity.ConclusionsCRs provide Proteaceae a competitive advantage over NCR species at the seedling stage, which may have important consequences for species coexistence and community structuring. The investigated SSA Proteaceae, which have not evolved in nutrient-impoverished soils, as have their relatives in south-western Australia and South Africa, improve their growth when cultivated in pairs, especially in nutrient-rich substrates.

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Energy considerations show that low-barrier hydrogen bonds do not offer a catalytic advantage over ordinary hydrogen bonds.

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