摘要:

AbstractA simplified scheme for treating the spatial configurations of polynucleotide chains is developed using the rotational isomeric state approximation and statistical methods applicable to linear systems of interacting subunits. As a consequence of geometric constraints imposed by the skeletal structure and of the severity of certain steric interactions, it is possible to represent the repeat unit comprising six skeletal bonds by two virtual bonds of fixed length. The configuration of the polynucleotide chain as a whole may be conveniently described by an alternating succession of these two virtual bonds. Moreover, analysis of steric interactions suggests that bond rotations governing the mutual orientation of a given pair of successive virtual bonds should be sensibly independent of the rotations affecting the mutual orientation of other pairs. The statistical mechanical treatment of configuration‐dependent properties is much simplified in consequence of this mutual independence. Mean‐square dimensions calculated by giving equal weights to all sterically allowed conformations are much smaller than values determined by Felsenfeld and co‐workers. The calculated dimensions are markedly increased, however, by placing certain arbitrary restrictions on the rotations about selected pairs of skeletal bonds. It is thus demonstrated that steric interactions alone are insufficient to account for the spatial characteristics of polynucleotide chains. The dimensions are also found to be sensitive to the conformation of the ribose ring of each nucleotide unit, but, insofar as the influences of steric interactions are concerned, the dimensions do not depend on the heterocyclic base attached to the ribose

ISSN:0006-3525    

DOI:10.1002/bip.1972.360110102

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1972

数据来源: WILEY

摘要:

AbstractConformational energies are calculated for pairs of successive bond rotations within an internal residue of a polyribonucleotide chain. Contributions to these energies include bond torsional strain, van der Waals repulsions, London attractions, electrostatic interactions, and inductive interactions between nonbonded atoms in the nucleotide repeat unit. The average dimensions of unperturbed random‐coil polyribonucleotide chains are then evaluated on the basis of energies thus estimated, using for this purpose the previously developed virtual bond treatment. The characteristic ratio\documentclass{article}\pagestyle{empty}\begin{document}$ C_\infty = \mathop {{\rm lim}}\limits_{n \to \infty } (\langle r^2 \rangle_0/nl^2) $\end{document}of the mean‐square end‐to‐end distance calculated for polyribonucleotide chains in which all pentose rings are fixed in a C3′‐endo conformation is ≈9; for chains consisting exclusively ofC2′‐endo units it is ≈25. These values are considerably greater than those obtained by giving equal weight to all conformations judged to be sterically allowed. Satisfactory agreement between the calculations here and experimental values from viscosity and light‐scattering studies is achieved by treating the chain as a random copolymer of C3′‐endo and C2′‐endo conformational isomers. The critical dependence of the characteristic ratio on the rotation about bond C3′–O3′in the C2′‐endo chain, however, obscures the interpretation of chain dimensions. The chain is also treated in higher approximation as a sequence of independent repeat units, each of which consists of six chemical bonds. The characteristic ratio obtained in this manner is 6.5 for the C3′‐endo chain and 18.5 for the C2′‐endo chain. Finally, the effects of partially stacked conformations in polyribonucleotides are investigated using the virtual bond treatment. Chain dimensions are calculated for random coil poly rA chains in which stacking is introduced b

ISSN:0006-3525    

DOI:10.1002/bip.1972.360110103

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1972

数据来源: WILEY

摘要:

AbstractThe virtual bond scheme set forth in preceding papers for treating the average properties of polyriboadenylic acid (poly rA) is here applied to the calculation of the unperturbed mean‐square end‐to‐end distance of polydeoxyriboadenylic acid (poly dA). The modifications in structure and in charge distribution resulting from the replacement of the hydroxyl group at C2′in the ribose residue by hydrogen in deoxyribose produce only minor modifications in the conformational energies associated with the poly dA chain as compared to those found for poly rA. The main difference is manifested in the energy associated with rotations about the C3′–O3′bond of the deoxyribose residue in the C2′‐endo conformation; accessible rotations are confined to the range between 0° and 30° relative to thetransconformation, whereas in the ribose unit the accessible regions comprise two ranges centered at approximately 35° and 85°. The characteristic ratio 〈r2〉0/nl2calculated on the basis of the conformational energy estimates is ≈9 for the poly dA chain with all deoxyribose residues in the C3′‐endo conformation and ≈21 with all residues in the C2′‐endo form. Satisfactory agreement is achieved between the theoretical values and experimental results on apurinic acid by treating the poly dA chain as a random copolymer of C3′‐endo and C2′‐endo conform

ISSN:0006-3525    

DOI:10.1002/bip.1972.360110104

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1972

数据来源: WILEY

摘要:

AbstractTheN‐carboxyanhydride of δ‐benzylL‐α‐aminoadipate polymerizes when initiated by strong base through an “active monomer” mechanism. This is shown by the isolation of 6‐oxo‐L‐pipecolic acid from the product mixture, since this byproduct could only arise from an “active monomer” pathway. This study also specifies conditions for preparing high molecular weight poly(δ‐benzylL‐

ISSN:0006-3525    

DOI:10.1002/bip.1972.360110105

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1972

数据来源: WILEY

摘要:

AbstractBy means of x‐ray fiber diffraction, it has been found that xylan diacetate crystallizes with two chains or four residues in a monoclinic cell (space groupP21):a= 7.64,b= 12.44,c(fiber axis) = 10.31 Å, and γ = 85°. Pairs of residues are related by a twofold screw axis in thecdirection. Based on the observed fiber repeat and chain symmetry, the probable conformation of a pair of xylose diacetate residues joined via a β‐1,4′ linkage has been obtained by energy minimization methods. The conformations corresponding to a threefold screw axis and a twofold screw axis along the chain have been compared and the reason why xylan diacetate assumes a twofold screw axis seems to be due to intermolecular packing effects rather than intramolecular non‐bonded i

ISSN:0006-3525    

DOI:10.1002/bip.1972.360110106

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1972

数据来源: WILEY

摘要:

AbstractCounterion activity of poly‐S‐carboxyethyl‐L‐cysteine in salt‐free solutions neutralized to various degrees with sodium hydroxide was determined either directly from the e.m.f measurements of concentration cells formed across a Na–glass electrode, or from the potentiometric titrations at different sodium chloride concentrations assuming the additivity rule.From e.m.f. measurements, the activity coefficient of counterions was confirmed to display the β‐structure random coil transition of the polymer.For random coil state, both methods gave identical results. Observed values of the activity coefficient was generally smaller than those for other randomly coiled polypeptides. The activity coefficient was found to decrease with the increase of the polymer concentration.The activity coefficient of counterions for β‐structure was extremely small as compared with that for random coil at the same degree of neutralization. The activity coefficient obtained from titrations was almost independent of degree of neutralization and increased with the increase of the poly

ISSN:0006-3525    

DOI:10.1002/bip.1972.360110107

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1972

数据来源: WILEY

摘要:

AbstractThe sumEof the packing and conformation energies of the crystals ofDL‐acetylleucineN‐methylamide (ALNMA) andDL‐acetyl‐α‐amino‐n‐butyric acidN‐methylamide (ABAMA) is calculated as a function of the crystallographic parameters and the conformational angles. The intermolecular energy is assumed to be the pairwise sum of nonbonded and electrostatic atomic interactions, while both these terms and intrinsic terms describing barriers of internal rotation contribute to the intramolecular energy. For ALNMAEis minimized with respect to 18 parameters: the minimum found when starting from the experimental structure agrees with this within 0.07 Å and 3°, except for one angle which deviates by 6° the average deviations of the atomic coordinates are\documentclass{article}\pagestyle{empty}\begin{document}$ |\overline {\Delta x|} = 0.02,|\overline {\Delta y|} = 0.07,|\overline {\Delta z|} = 0.08 $\end{document}Å. Another minimum with about the same energy shows slightly worse agreement. A comparison between different sets of nonbonded functions is made. The prediction of conformation and intermolecular packing of ABAMA is attempted on the basis of the knowledge of the unit cell and the space group. In agreement with available experimental data it is found that only one‐di‐mensional arrays of molecules linked by pairs of hydrogen bonds are compatible with the unit cell. The more stable of two possible conformations of the main chain agrees approximately with the experimental conformation. The calculation is not conclusive with regard to the side‐chain conformation and the packing of non

ISSN:0006-3525    

DOI:10.1002/bip.1972.360110108

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1972

数据来源: WILEY

摘要:

AbstractA theory is presented concerning the possible arrangements of protomers in tetrameric molecules. Isoenzymes may exist even in the case of homotetramers if the asymmetry of the identical protomers is detectable. The number of tetrahedral isoenzymes that can be isolated depends on the nature of the intersubunit bonds and on the level of the asymmetry of the protomers. Five isoenzymes can be distinguished only if two different types of protomers form tetrahedral tetramers and the asymmetry of protomers is not detectable with the method used. If the two types of protomers can bind each other by any pairs of binding sets and the asymmetry of both protomer types reaches the level of detection with the method used, we obtain 117 isoenzymes: 15 individual ones, and 51 stereoisomeric pairs.

ISSN:0006-3525    

DOI:10.1002/bip.1972.360110109

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1972

数据来源: WILEY

摘要:

AbstractWe prepared helices with noncomplementary bases byN1‐oxidation of poly A, followed by reaction with poly U. Mixing curves indicate that doubly and triply helical structures form, with only the unmodified adenines involved in base pair formation. Circular dichroism spectra were examined particularly at the absorbance maximum of the adenineN1‐oxide (A*). In the single strand poly (A,A*), there is a relatively strong pair of positive and negative CD bands from the A*. These are greatly reduced in the double helix, and abolished in the triple helix. We conclude that A* stacks in a conventional manner with A in the single strand, but is rotated out of the double and triple helix. In the double helix the A* probably maintains a preferred orientation with respect to the helix, but rotates randomly in the triple he

ISSN:0006-3525    

DOI:10.1002/bip.1972.360110110

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1972

数据来源: WILEY

摘要:

AbstractThe potentiometric titration curves of carboxymethylcellulose, which has a relatively stiff backbone, and also of poly(D‐glutamic acid) in the helical region are compared with the theoretical curves calculated assuming that the polyions are rods and have smeared charges on their surfaces. For carboxymethylcellulose good agreement is observed when its charge density is high, whereas as the charge density decreases the calculated curves deviate from the observed ones. The main reason for the disagreement at low charge densities may be attributed to the flexibility of the polymer backbone. For helical poly(D‐glutamic acid) satisfactory agreement between calculated and observed curves is found if a radius thicker than the realistic radius is employed. The reason for the excessively large radius may be attributed to the inapplicability of the smeared charge mo

ISSN:0006-3525    

DOI:10.1002/bip.1972.360110111

出版商:Wiley Subscription Services, Inc., A Wiley Company    

年代:1972

数据来源: WILEY