The glucose analog, 2-deoxy-D-glucose (2DG), has been used widely for studying the initial steps in the metabolism of glucose by radio-isotope tracer methods and by 31P NMR. In the rat heart perfused with acetate/2DG (both 5 mM) plus insulin, trapping of phosphorus by 2-deoxy-D-glucose-6-phosphate (2DG6P) results in a steady state exhibiting high 2DG6P (55 mM) and low ATP concentrations but near-normal function, as observed in an earlier 31P NMR study. In order to understand how the 2DG6P concentration is stabilized, we studied the inhibition of a mammalian hexokinase by 2DG6P in vitro by a 31P NMR technique. Inhibition, previously unobserved, was found. It is similar to inhibition by G6P in that it is competitive with ATP and not competitive with 2DG, but the inhibition constant (1.4 mM) is much larger. The experimental protocol includes provisions for enzymatic destruction of stray inhibitors such as G6P. The results show that the high 2DG6P and low ATP concentrations found in the steady state of the perfused heart should strongly reduce the rate of phosphorylation of sugars by hexokinase.

Animals↗

PubMedDate not supplied

The distance of manganese to phosphorus atoms of polynucleotides, and dynamics of binding.

The structure of manganese - polynucleotide complexes is studied by phosphorous NMR. An average value for the phosphorus-manganese distance is derived from the longitudinal relaxation rate. It is larger than the distance for direct coordination and decreases as a function of temperature. An inner-sphere/outer sphere equilibrium is proposed. The outer-sphere dominates in the doublestranded polynucleotides, whereas the inner-sphere contribution is important in single-stranded species. The kinetic parameters of the model are derived from the transverse relaxation time. The similar properties of DNA fragments and tRNA argue strongly against entrapment of of manganese in special sites of tRNA.

Chemical Phenomena↗

PubMedDate not supplied

Polyelectrolyte theory of charged-ligand binding to nucleic acids.

The Poisson-Boltzmann framework provides simple and sound formulae for evaluation of the interactions of polynucleotides with charged ligands. The theory is based on the observation that shape-dependent effects are small. Hence the results for the charged plane may be used as a first approximation for polyelectrolytes. The counterion distribution and the extent of counterion or ligand binding is derived on the basis of a sum-rule for counterion concentrations, combined with the mass-action law. Calculations require no more than a pocket calculator even in the case of mixed-salt solutions. Significant qualitative results are given, and applied to the problems of site-binding and of repressor-DNA interaction.

Binding Sites↗

PubMedDate not supplied

A single mode of DNA base-pair opening drives imino proton exchange.

The opening of base pairs of double-stranded DNA is an important process, being a prerequisite for replication and transcription and possibly a factor in the recognition, flexibility and structure of DNA. The kinetics of base-pair opening have, however, been controversial. Base-pair opening can be studied by following the exchange of protons from imino groups with water, a process that seems only to occur from open base pairs. We have recently demonstrated catalysis by proton acceptors of imino proton exchange in nucleic acids. This has enabled us to determine the base-pair lifetimes, which are in the region of 10 ms at room temperature. In earlier reports it had been considered that proton exchange is limited by the rate of base-pair opening, which had led to estimates of base-pair lifetimes that were larger by one or two orders of magnitude. There are also important discrepancies between recent and early estimates of the base-pair dissociation constant. Earlier estimates of base-pair lifetimes correspond in fact to the time required for proton exchange in the absence of added catalyst (AAC exchange). This could be a distinct mode of base-pair opening with a very long open lifetime, different from the mode revealed by the effect of catalyst. The evidence reported here suggests on the contrary that there is only a single mode of here suggests on the contrary that there is only a single mode of base-pair opening and that proton exchange in the absence of added catalyst is in fact catalysed by a proton acceptor intrinsic to the nucleic acid, most probably the other base of the open pair.

Adenosine↗

PubMedDate not supplied

[Application of nuclear magnetic resonance for the determination of the structure of proteins in solution].

Knowledge of three-dimensional structure is a key factor in protein engineering. It is useful, for example, in predicting and understanding the functional consequences of specific substitution of one or more amino acids of the polypeptide chain. It is also necessary for the design of new effectors or analogs of the substrates of enzymes and receptors. X-ray diffraction by crystals of the biomolecule was for a long time the only method of determining three-dimensional structures. In the last 5 years, it has been joined by a new technique, two-dimensional nuclear magnetic resonance (2D NMR), which can resolve the structure of middle-sized proteins (less than 10 kilodaltons). The technique is applied on solutions whose pH, ionic strength, and temperature can be chosen and changed. The two basic measurements, COSY and NOESY, detect respectively the systems of hydrogen nuclei, or protons, coupled through covalent bonds, and those in which the interproton distances are less than 0.5 nm. A systematic strategy leads from resonance assignments of the two-dimensional spectrum to molecular modeling with constraints and finally to the determination of the molecular structure in the solution. Much sophistication is needed even today for the first task, the assignment of the resonances. Each of the COSY and NOESY spectra is a two-dimensional map, where the diagonal line is the one-dimensional spectrum, and the off-diagonal peaks indicate connectives between protons. Peak assignment to a specific type of amino acid is based on the pattern of scalar couplings observed in the COSY spectrum. Next, the amino acids are positioned in the primary sequence, using the spatial proximities of polypeptide chain protons, as observed in the NOESY spectrum. The principal secondary structures (alpha helix, beta sheets, etc.) are then identified by their specific connectivities. The tertiary structure is detected by NOESY connectivities between protons of different amino acids which are far apart in the primary sequence. The distance constraints from the NOESY connectivities also provide the starting point for modeling the tertiary structure. This is then refined using distance geometry and molecular dynamics algorithms. The resolution of the structures obtained with the help of recent algorithmic developments may be comparable to that provided by X-ray diffraction. The COSY measurement can be completed or substituted by other measurements, useful albeit more complex. For example, the HOHAHA experiment, currently in wide use, gives the correlations through multiple covalent bonds. Multiquanta experiments, which select systems of a given number of coupled spins, provide spectral simplification.(ABSTRACT TRUNCATED AT 400 WORDS)

Amino Acids↗

PubMedDate not supplied

Enhanced selectivity of enzymes by kinetic proofreading.

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Adenosine Triphosphate↗