The allosteric properties of hemoglobins, especially their responses to ligands other than oxygen, vary widely in different classes of vertebrates. Knowing the stereochemistry of the cooperative effects in human hemoglobin, one can infer the stereochemical basis of these variations from the changes in amino acid sequence. The results indicate that the tertiary and quaternary structures of deoxy- and oxyhemoglobin have remained almost invariant during vertebrate evolution and that most of the amino acid replacements between species are functionally neutral. Adaptations leading to responses to new chemical stimuli have evolved by only a few (one to five) amino acid substitutions in key positions. Once such a response has become superfluous, it may be inactivated, not necessarily by a reversal of one of the original substitutions but by any other that happens to inhibit it.

Species adaptation in a protein molecule.

Tautomerism and protonation of guanine and cytosine in the gas phase and in aqueous solution have been examined by theoretical methods. High level ab initio calculations with inclusion of correlation effects at the Moller−Plesset level have been used to study these processes in the gas phase. The influence of solvent has been examined using self-consistent reaction field and Monte Carlo free energy perturbation simulations. The results provide a complete and accurate picture of tautomerism and protonation of these nucleic acid bases. Comparison with the available experimental data gives confidence in the quality of the results derived from theoretical computations. Inspection of the most stable tautomeric forms for the neutral and protonated nucleic acid bases allows rationalization of the formation of unusual DNA structures like the triple helix.

Tautomerism and protonation of guanine and cytosine. implications in the formation of hydrogen-bonded complexes

The results of an ab initio post Hartree−Fock study of the molecular structures, relative stabilities, and mechanisms of intermolecular proton transfer in isolated, mono- and dihydrated guanine complexes are reported. The geometries of the local minima and transition states were optimized without symmetry restrictions by the gradient procedure at the HF and the MP2 levels of theory and were verified by energy second derivative calculations. The standard 6-31G(d) basis set was used. The single point calculations have been performed at the MP4(SDQ)/6-31G(d)//MP2/6-31G(d) and the MP2/6-311++G(d,p)//MP2/6-31G(d) approximations. All values of total energies have been corrected for zero point energy contributions scaled by a factor of 0.9. The post Hartree−Fock ab initio theory predicts the height of the proton transfer barrier for monohydrated guanine complexes to be approximately two times lower for the tautomeric oxo−hydroxo reactions and approximately three times lower for the reverse hydroxo−oxo reactions ...

Intramolecular Proton Transfer in Mono- and Dihydrated Tautomers of Guanine: An ab Initio Post Hartree−Fock Study

Publisher Summary This chapter discusses cytophysiology of fish chromatophores, with emphasis on the chromatophores of class Osteichthyes. The chromatophores are responsible not only for the generation of color but also for changes in coloration of the surface coat. The beautiful colors and patterns and the spectacular changes in coloration is considered an important phenomena as it provides protection and assist in the survival of species in their habitats. Many poikilothermic aquatic animals, including fishes, use chromatic changes as a means of visual communication. The chapter highlights “physiological color changes,” which are the rapid changes caused by the motile activities of chromatophores. The absorption of light by the pigment in poikilothermic vertebrates is achieved by the light absorbing chromatophores, which include the melanophores, the erythrophores, and the xanthophores and also by the scattering and the reflection of light by intracellular structures, in the absence of colored materials, dependent on the presence in the skin of the light-reflecting chromatophores—namely, the leucophores and the iridophores. In the integument of fishes, pigment cells are found mostly in the dermis, where all the varieties of chromatophores can be located.

Cytophysiology of fish chromatophores

The base-stacking patterns in over 70 published crystal structures of nucleic acid constituents and polynucleotides were examined. Several recurring stacking patterns were found. Base stacking in the solid state apparently is very specific, with particular modes of interaction persisting in various crystalline environments. The vertical stacking of purities and pyrimidines in polynucleotides is similar to that observed in crystals of nucleic acid constituents. Only partial base overlap was found in the majority of the structures examined. Usually, the base overlap is accomplished by positioning polar substituents over the ring system of an adjacent base. The stacking interactions are similar to those found in the crystal structures of other polar aromatic compounds, but are considerably different from the ring–ring interactions in nonpolar aromatic compounds. Apparently, dipole-induced dipole forces are largely responsible for solid-state base stacking. It is found that halogen substituents affect base-stacking patterns. In general, the presence of a halogen substituent results in a stacking pattern which permits intimate contact between the halogen atom and adjacent purine or pyrimidine rings. Considering differences in the stacking patterns found for halogenated and nonhalogenated pyrimidines, a model is proposed to account for the mutagenic effects of halogenated pyrimidines.

Stereochemistry of Nucleic Acids and Their Constituents. X. * Solid-state Base-Stacking Patterns in Nucleic Acid Constituents and Polynucleotides

Crystals of the dihydrates of guanosine (C_(10)H_(13)N_5O_5) and inosine (C_(10)H_(12)N_4O_5) are nearly isostructural. They are monoclinic, space group P2_1, with cell dimensions ɑ = 17·518, b = 11 ·502, c = 6·658 A, β = 98·17° (guanosine) and ɑ = 17·573, b =11·278, c=6-654 A, β = 98·23° (inosine). There are two nucleoside
molecules and four water molecules per asymmetric unit. Data were collected on an automated diffractometer; the structures were solved by Patterson and trial-and-error methods and refined to R indices of about 0·035. The structure features hydrogen bonding between purine bases to form ribbons parallel to b and parallel stacking of purine bases along c; the separation between adjacent rings within
a stack is 3·3 A. The conformations about the glycosidic C-N bond and the puckerings of the sugar rings arc quite different for the two molecules in the asymmetric unit.

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The crystal structure of guanosine dihydrate and inosine dihydrate

The crystal structure of guanine monohydrate

Effects of halogen substituents on base stacking in nucleic acid components: the crystal structure of 8-bromoguanosine.

DL-μ-Hydroxo-di-μ-nitro-bis(triamminecobalt)(3 + )-trichloride hydrate, [(NH_3)_3Co(OH)(N0_2hCo(NH_3)_3]Cl_3. H_20, crystallizes in the monoclinic space group P2_1/c with ɑ = 9·70, b = 6-73, c = 24·57 A and β = 104·3°; there are four formula units in the cell. The structure was determined by the heavy-atom method and refined by three-dimensional least-squares calculations. The
final R index for 1397 observed reflections of non-zero weight is 0·067.

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Ulf Thewalt

Papers

The crystal structure of guanosine dihydrate and inosine dihydrate

The crystal structure of guanine monohydrate

Effects of halogen substituents on base stacking in nucleic acid components: the crystal structure of 8-bromoguanosine.

Die Struktur von dl‐μ‐hydroxo‐di‐μ‐nitro‐bis(triamminkobalt)(3+)‐trichlorid‐hydrat