Secondary structure affecting

Isotactic macromolecules derived from achiral monomers have no preference for right- or left-handed screw senses, and the two are perfectly balanc at inter-and intramolecular level. However, distribution of left- and right-handed helical secondary structures affects markedly the free energy of the system, alternation of the two senses in the same chain being favored for entropic reasons [4,5]. If this last situation takes place, conformational optical activity cannot be obtained... 

Finally we investigated the Cu complexes of a- and 3-cyclodextrin and also of the monomeric model compound VII. Since the same ORD and CD curves are obtained each time, we conclude that neither DP nor the secondary structure affect the Cotton effects. The CD of the Cu complex of a water soluble salepmannan is completely different. Obviously in this case a complex with another chirality is formed. 

Figure 11.3 The secondary structures affect the characteristics of the translocation events, (a) Comparison between poly dC and poly C, under identical experimental conditions. (From Akeson, M. et al., Biophys. J., 77, 3227, 1999. With permission.) (b) Comparison between poly dA and polydC. (Adapted from Meller, A. et al., Proc. Natl. Acad. Sci. USA, 97, 1079, 2000.)...

Such differences in the secondary structure behavior with respect to temperature can be explained by suggesting that molecular close packing of proteins in the film is the main parameter responsible for the thermal stability. In fact, as in the case of BR, we have close packing of molecules even in the solution (membrane fragments) there are practically no differences in the CD spectra of BR solution at least tiU 75°C (denaturation takes place only for the sample heated to 90°C). RC in solution begins to be affected even at 50°C and is completely denatured at 75°C, for the solution contains separated molecules. 

Recently, Tse et al. [73] and Orlowski et al. [74] have cloned a third isoform of Na /H exchanger (named NHE-3). The inferred 832-amino acid sequence of rabbit NHE-3 is 41% identical with NHE-1, 44% identical with NHE-2, and has a similar secondary structure. In contrast to NHE-1 and NHE-2, NHE-3 is only expressed in epithelia in intestine and kidney. Moreover, administration of glucocorticoids, which stimulates transport activity of the apical Na /H" exchanger in rabbit intestine, increased levels of NHE-3 transcripts but did not affect NHE-1 or NHE-2 [75]. Taken together, these results suggest that NHE-3 may encode a resistant-type Na /H exchanger of epithelia. A fourth Na /H exchanger isoform (NHE-4) is preferentially expressed in stomach [74]. 

Molecular dynamics simulations are capable of addressing the self-assembly process at a rudimentary, but often impressive, level. These calculations can be used to study the secondary structure (and some tertiary structure) of large complex molecules. Present computers and codes can handle massive calculations but cannot eliminate concerns that boundary conditions may affect the result. Eventually, continued improvements in computer hardware will provide this added capacity in serial computers development of parallel computer codes is likely to accomplish the goal more quickly. In addition, the development of realistic, time-efficient potentials will accelerate the useful application of dynamic simulation to the self-assembly process. In addition, principles are needed to guide the selec-... 

Fig. 3. The hepatitis delta virus ribozyme. A Secondary structure of the genomic HDV ribo-zyme RNA used for the determination of the crystal structure [37]. The color code is reflected In the three dimensional structure B of this ribozyme. PI to P4 indicate the base-paired regions. Nucleotides in small letters indicate the U1 A binding site that was engineered into the ribozyme without affecting the overall tertiary structure. The yellow region indicates close contacts between the RNA and the U1 A protein...

In RPC separation of peptides, the fundamental structural properties of the amino adds within the sequence and the relative accessibility of the nonpolar amino add residues to a large measure determine the overall selectivity that can be achieved with a defined RPC systemJ20-23 As a consequence, peptides typically elute from RPC sorbents in the order of their relative hydrophobicities, for a pre-selected mobile-phase composition, pH, and temperature. However, the relative hydrophobicities of different peptides are also conditional on the solvation environment in which they are placed. The exposure or greater accessibility of previously sequestered polar or hydrophobic amino acid side chains in polypeptides with well-developed secondary structures will thus significantly affect the relative binding affinities of these peptides to hydrocarbonaceous-bonded phase surfaces. 

The secondary structure of poly(iV-alkynylamides) is influenced by the position of the chiral center and amide group.The position of the chiral center mainly affects the helical pitch, which becomes short when the chiral center is positioned away from the main chain. The stability of the helical structure is also influenced by the position of the amide group. Based on molecular orbital study, it is concluded that poly(iV-propargylamides) with right-handed helical structure display a plus Cotton effect around 390 nm. This is also confirmed by the exciton chirality method using porphyrin as a chromophore. ... 

Our objective is to understand how the noncovalent interactions responsible for nucleic acid secondary structure (i.e. base stacking and base pairing) affect the photophysics of these multichromophoric systems. Here we describe initial experimental results that demonstrate dramatic differences in excited-state dynamics of nucleic acid polymers compared to their constituent monomers. Although ultrafast internal conversion is the dominant relaxation pathway for single bases, electronic energy relaxation in single-stranded polynucleotides... 

The protein concentration should be as high as possible, consistent with the absorbance in the cell not exceeding 1.0 to 1.5, and must be accurately determined by UV absorbance. Values of mean residue ellipticity and secondary structure content results are both affected by uncertainties in protein concentration. 

The effect of pH and ions on acid DNase activity has been investigated in several laboratories, and rather different results have been reported. It appears now that many discrepancies result from a rather poor understanding of the complexity of pH and ion effects. In fact, it has been shown (34) that electrolytes and pH modify the acid DNase activity not only by affecting the enzyme itself but also by stabilizing or destabilizing the secondary structure of native DNA. Since the enzyme has a quite different affinity for the native vs. the denatured structure... 

The basic monomers of nucleic acids are nucleotides which are made up of heterocyclic nitrogen-containing compounds, purines and pyrimidines, linked to pentose sugars. There are two types of nucleic acids and these can be distinguished on the basis of the sugar moiety of the molecule, Ribonucleic acids (RNA) contain ribose, while deoxyribonucleic acid (DNA) contains deoxyribose. The bases cytosine (C) adenine (A) and guanine (G) are common in both RNA and DNA. However, RNA molecules contain a unique base, uracil (U), while the unique DNA base is thymidine (T). These differences in the base structure markedly affect the secondary structures of these polymers. The structures of DNA and RNA are outlined in Appendix 5.2. 

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