摘要:

AbstractThe normal modes have been calculated for β‐turns of types I, II, III, I′, II′, and III′. The complete set of frequencies is given for the first three structures; only the amide I, II, and III modes are given for the latter three structures. Calculations have been done for structures with standard dihedral angles, as well as for structures whose dihedral angles differ from these by amounts found in protein structures. The force field was that refined in our previous work on polypeptides. Transition dipole coupling was included, and is crucial to predicting frequency splittings in the amide I and amide II modes. The results show that in the amide I region, β‐turn frequencies can overlap with those of the α‐helix and β‐sheet structures, and therefore caution must be exercised in the interpretation of protein bands in this region. The amide III modes of β‐turns are predicted at significantly higher frequencies than those of α‐helix and β‐sheet structures, and this region therefore provides the best possibility of identifying β‐turn structures. Amide V frequencies of β‐turns may also be

ISSN:0006-3525    

DOI:10.1002/bip.1980.360190102

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

年代:1980

数据来源: WILEY

摘要:

AbstractThe normal modes have been calculated for structures having the dihedral angles of the four β‐turns of insulin. Frequencies are predicted in the amide I region near 1652 and 1680 cm−1. The former overlaps the α‐helix band at 1658 cm−1in the Raman spectrum, while the latter accounts for the hitherto unassignable band at 1681 cm−1. Calculated amide III frequencies extend above 1300 cm−1, providing a compelling assignment of the 1303‐cm−1band in insulin and similar bands in other

ISSN:0006-3525    

DOI:10.1002/bip.1980.360190103

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

年代:1980

数据来源: WILEY

摘要:

AbstractA thermodynamic analysis of the bending free energy of DNA, initiated previously, is extended. It was demonstrated that the ionic‐strength dependence of the persistence length of DNA in aqueous NaCl can be understood by postulating (1) a rigid‐rod 60 base‐pair unit and (2) a negative contribution from nonelectrostatic sources to the bending free energy of this unit. On electrostatic neutralization of the phosphate charge, the latter term alone survives, and bending becomes a spontaneous process. In this paper it is demonstrated from a theoretical analysis of the ionic‐strength dependence of the rate of denaturation of DNA that the above statements are restricted in their validity to radii of curvature greater than 170 Å; beyond this limit, the steeply rising repulsive energy of tightly packed atoms dominates the bending free energy. Therefore, spontaneous bending on charge neutralization proceeds up to, but not beyond, this barrier to curvature. It is noted that doughnut forms of DNA induced by binding of cationic spermidine, or mixtures of Mg2+and polyamines are observed to possess maximum curvatures, corresponding to the radius of the “hole in the middle,” in the range 1

ISSN:0006-3525    

DOI:10.1002/bip.1980.360190104

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

年代:1980

数据来源: WILEY

摘要:

AbstractAn explicit analytic formula accurately describing the melting of a natural DNA is derived. For phage ϕX‐174 and virus SV‐40, the nucleotide sequences of which are known, the formula fits experimental data for the differential melting curve almost within the experimental accu

ISSN:0006-3525    

DOI:10.1002/bip.1980.360190105

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

年代:1980

数据来源: WILEY

摘要:

AbstractAn explicit analytical theory of DNA melting is constructed. It accounts for the loop entropy and the elasticity of DNA strands. Explicit analytical formulas are presented for the melting curves of natural DNA and periodic polymers. The nature of the DNA helix–coil transition is investigated, and it is found to crucially depend on the nucleotide sequenc

ISSN:0006-3525    

DOI:10.1002/bip.1980.360190106

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

年代:1980

数据来源: WILEY

摘要:

AbstractWe show that the fine oscillatory structure of the DNA melting curve can be used to determine explicitly the nucleotide composition and the order of certain domains within the DNA. If DNA is specifically fragmented, the order of fragments can be learned directly from a comparison of the differential melting curves of the nonfragmented and fragmented DNA. The indicated information may complement exact methods of DNA sequencing. The proposed analysis is applied to bacteriophage ϕX‐174, whose melting curve is known. Compared to the known ϕX‐174 DNA sequence, the results of the analysis are found to be very acc

ISSN:0006-3525    

DOI:10.1002/bip.1980.360190107

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

年代:1980

数据来源: WILEY

摘要:

AbstractWe studied the temperature‐dependent effects of intramolecular interactions on the mutual diffusion coefficient of normal human oxygenated hemoglobin in salt solution. We used photon correlation spectroscopy to observe this temperature dependence of the mutual diffusion coefficient of two protein concentrations (1.25 and 17.0 g %) between 13 and 37°C. This coefficient was our probe for monitoring temperature‐dependent structural changes of hydrated hemoglobin in solution. Comparison of our measured diffusion coefficient with that predicted by the Stokes‐Einstein relationship in terms of solvent or solution viscosity showed a clear transition in the conformation of hemoglobin at approximately 22°C, independent of the hemoglobin concentration. We postulated that at this physiological temperature, a considerable quaternary rearrangement of the hemoglobin chains takes place. We believe this rearrangement changes the effective volume and the hydration sphere of the hemoglobin macrom

ISSN:0006-3525    

DOI:10.1002/bip.1980.360190108

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

年代:1980

数据来源: WILEY

摘要:

AbstractThe theory presented in Part I [Iwata, K. (1979)J. Chem. Phys.71, 931–943] is applied to calculation of complex viscosities of the following three models which are designed to simulate various motions of polypeptides in helicogenic solvents. Model I is composed of identical spheres which are arranged regularly along a Kratky‐Porod chain and is adopted for describing flexural deformation of polypeptide helices. Model II is composed of two kinds of spheres, mobile and immobile, which are arranged in a pillar form with a multilayer structure and is adopted for estimating sidegroup motion of polypeptide helices. The mobile spheres are assumed movable in their individual intramolecular potential field under the influences of hydrodynamic resistance by solvent and of “internal friction” caused by other spheres in the same molecule. When the mobile and immobile spheres are arranged alternatively in a mosaic form (model IIa), the model exhibits a local motion of the side groups. When all the spheres are mobile (model IIb), their motions are correlated with each other through the internal friction.The complex viscosities of these models are computed and compared with those measured by Ookubo et al. [(1976)Biopolymers15, 929–949] for poly(γ‐benzyl‐L‐glutamate)‐[Glu(OBzl)]ninm‐cresol. The results are as follows: (1) The dynamic viscosity [η′] of [Glu(OBzl)]nwith molecular weight 75,000 is explained well not by model IIa or IIb, but by model I, and the relaxational modeBobserved at 760 kHz is assigned to the flexural deformation of the [Glu(OBzl)]nhelix. (2) [η′] of [Glu(OBzl)]nwith molecular weight 120,000 deviates largely from that predicted by model I; it is therefore deduced that the interruption of the helix becomes predominant betweenMr75,000 andMr120,000. (3) The persistence length of [Glu(OBzl)]ninm‐cresol is estimated to be 1600 Å and the flexural rigidity of the helix to be 6.7 × 10−19dyn cm2from the relaxation time of modeB. The present estimate of the persistence length is larger than the previous ones (700–1100 Å), which were obtained by neglecting th

ISSN:0006-3525    

DOI:10.1002/bip.1980.360190109

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

年代:1980

数据来源: WILEY

摘要:

AbstractOptical rotation and density studies have been performed as a function of time on solutions of a single‐strand gelatin in salt‐free solutions and in solutions containing sodium bromide, tetramethyl and tetrabutylammonium bromide. The reversion to the collagen fold is shown to be first order in all cases but undergoes a change in magnitude as a function of an aggregation process which occurs at a concentration of approximately 0.1% w/v. The structuring effects of the electrolytes on the solvent are shown to relate to the extent of helix regeneration by the protein, in the presence of the electrolyte. The extent of helix regeneration is also shown to relate to the thickness of the electric double layer surrounding the protein molec

ISSN:0006-3525    

DOI:10.1002/bip.1980.360190110

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

年代:1980

数据来源: WILEY

摘要:

AbstractThe lone‐pair orbital interactions arising in a phosphodiester are incorporated into semiempirical conformational energy calculations using a unifold “torsional potential” around the virtual bond linking the ester oxygen atoms. The results explain the observed experimental data better than other me

ISSN:0006-3525    

DOI:10.1002/bip.1980.360190111

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

年代:1980

数据来源: WILEY