摘要:

AbstractRecently, it was suggested that parallel β‐sheets have a significant dipole moment, in contrast to antiparallel sheets.Ab initiomolecular‐orbital (MO) calculations on parallel and antiparallel β‐strands of tetra(Gly) show that they have very similar charge distributions. Interaction energies between two and three strands of tetra(Gly), obtained using the direct reaction field Hamiltonian, show that a particular choice of point charges is probably not crucial for calculating interactionswithinβ‐sheets, but that it might be for calculating interactions between these sheets and other parts of a protein, in particular, α‐helices. The point‐charge representation of our MO‐SCF results will probably reduce the hazard of introducing artefacts in electrostatic calculations of protein conformational energies, provided the short‐range interactions are treated in a more realistic way, i.e., such that intra‐ and interchain induction

ISSN:0006-3525    

DOI:10.1002/bip.360240502

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

年代:1985

数据来源: WILEY

摘要:

AbstractProton 2D‐NOE spectroscopy has been used to investigate the three‐dimensional conformations of several sonicated polydeoxynucleotides in solution. The observed pattern of cross peaks indicate that poly(dA‐dT) · poly(dA‐dT) in all salt concentrations studied (up to 6.6MCsF), and poly(dG‐m5dC) · poly(dG‐m5dC) in low salt (0.1MNaCl) are righthanded B‐structures. Poly(dG‐m5dC) · poly(dG‐m5dC) in Mg2+(3 mM) solution exhibits a pattern characteristic of the left‐handed Z‐form. These results for poly(dA‐dT) · poly(dA‐dT) are in contrast to suggestions that this copolymer exists as a left‐handed form, either in low or high salt. We present pure absorption‐mode 2D‐NOE spectra that enable us to compare several distances and define the conformations of the

ISSN:0006-3525    

DOI:10.1002/bip.360240503

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

年代:1985

数据来源: WILEY

摘要:

AbstractThe pH and ionic strength dependence of conformation of the COOH‐terminal fragment 206–316 (fragment FII) of thermolysin was monitored by far‐uv CD and difference absorption measurements. This fragment was shown previously to possess the properties of a protein domain, i.e., able to refold into a stable nativelike structure [Fontana, A., Vita, C.&Chaiken, I. M. (1983)Biopolymers22, 69–78]. Analysis of the CD spectra in the pH range of 1–12 indicated that near pH 1, the conformation of fragment FII appears to be in an intermediate state (H) between the fully unfolded one (U) [the guanidine hydrochloride (Gdn · HCl)‐induced unfolded state]and the nativelike state (N—that attained at neutral pH). Quantitative analysis of secondary structure from CD spectra revealed that state H at 4°C is characterized by some 30% α‐helical structure, compared to 47% for state N. The heat‐ and Gdn · HCl‐mediated unfolding transitions of state H were fully reversible and characterized by little cooperativity, which is taken as an indication that state H corresponds to several species possessing different, and low, conformational stabilities. The midpoint transition from state H to N occurs near pH 2.5, implying that the acid transition results from the titration of carboxyl groups of the fragment with anomalously low pK, as would be expected for groups involved in specific salt bridges. Fragment FII at pH 1 (state H) may be induced to exhibit nearly the same degree of helicity of state N simply by increasing the ionic strength of the solution, thus reducing the repulsive interactions between positive charges within the highly charged fragment at pH 1. The results obtained emphasize the role of electrostatic interactions in the folding and stability of fragment FII and suggest a mechanism of folding of the fragment from U to N involving an intermediate state characterized by an assembly o

ISSN:0006-3525    

DOI:10.1002/bip.360240504

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

年代:1985

数据来源: WILEY

摘要:

AbstractCircular intensity differential scattering (CIDS) patterns have been calculated for two general types of chiral arrangements. The calculations were done using the second Born approximation. The geometries considered are (a) a linear array of anisotropic scattering groups with a spiraling orientation (a twisted ladder) and (b) a helical array of scattering groups with arbitrary anisotropy and orientation. The CIDS expressions for the first of these models (twisted ladder) reduces to a simple analytical form and clearly illustrates many properties of CIDS patterns. The second geometry (helix) is more general. Calculations were done for oriented scatterers and for rotationally averaged scatterers as would be found in solution.

ISSN:0006-3525    

DOI:10.1002/bip.360240505

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

年代:1985

数据来源: WILEY

摘要:

AbstractVibrational CD (VCD) spectra have been obtained in the amide I region of poly(γ‐benzyl‐L‐glutamate), using a Fourier transform ir VCD spectrometer operating at 4‐cm−1resolution. These results reveal a new negative VCD band at 1650 cm−1in addition to the previously observed negative positive VCD couplet centered at 1660 cm−1. Fourier self‐deconvolution (FSD) of the VCD spectrum reveals three strong VCD component bands, rather than just two, as originally supposed. FSD also resolves the absorbance spectrum into two components corresponding to the parallel polarized A mode at lower frequency, and an unresolved perpendicular polarized E1mode at higher frequency. The VCD spectrum is reassigned on the basis of this new spectral data and the FSD‐VCD results are analyzed for the Moffitt contribution and the so‐called helical contribution. Comparison with theory shows the VCD to be more intense than expected, particularly for the helical term. Charge flow between subunits is suggested as an additional source of VCD intensity that is presently not included in theoretical exciton descriptions. The splitting of the E1mode and the large VCD contribution attributed to the helical term implies a deviation of the polypeptide structure from perfect helical symmetry and, as a result, a mixing of the A and

ISSN:0006-3525    

DOI:10.1002/bip.360240506

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

年代:1985

数据来源: WILEY

摘要:

AbstractElementary but general statistical‐mechanical relations are derived that relate the thermodynamic properties of the dissolution process to those of the pure solvent. A number of conclusions are drawn from qualitative arguments that these relations suggest. These include the following: (1) The low solubility of nonpolar solutes in water arises not from the fact that water molecules can form hydrogen bonds, but rather from the fact that they are small in size. (2) The large entropy decrease attending the transfer of an inert solute from a nonaqueous solvent to water is largely due to the decrease in entropy of the nonaqueous solvent as the solvent–solvent interaction is restored on removal of the solute from it. (3) It is improper to use values of thermodynamic quantities obtained from small‐molecule transfer studies for those that involve macromolecular folding and intera

ISSN:0006-3525    

DOI:10.1002/bip.360240507

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

年代:1985

数据来源: WILEY

摘要:

AbstractWe have measured the CD, isotropic absorption, and LD of poly[d(A)]–poly[d(T)]and poly[d(AT)]–poly[d(AT)]in the vacuum‐uv spectral region. The reduced dichroism (LD divided by isotropic absorption) varied as a function of wavelength and was independent of shear gradient. Thus, the bases are not perpendicular to the helix axis in solution. Since the directions of the transition dipoles are known, the orientations of the bases in the polymers can be calculated from the reduced dichroism spectra. The results show that the base normals are tilted at angles greater than 25°, with respect to the helix axis, and thymine is tilted more than adenine for both polymers. The tilt axes of adenine and thymine are not parallel, indicating a large propeller twist. Space‐filling models of poly[d(A)]–poly[d(T)]and poly[(AT)]–poly[d(AT)]are built based on our results, and the conformations of the two (A + T) polymers in solution a

ISSN:0006-3525    

DOI:10.1002/bip.360240508

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

年代:1985

数据来源: WILEY

摘要:

AbstractThe stochastic boundary molecular‐dynamics approach for studying chemical events in liquids is extended to proteins. A method for simulating the localized dynamics of a portion of a protein is developed and illustrated by an application to the bovine pancreatic trypsin inhibitor (BPTI). The dynamics of the aromatic ring atoms of Tyr 21 of BPTI are targeted as the “active site,” and the results from several different localized models are compared with those from a simulation of the entire molecule. The most consistent results are obtained with a model that consists of a buffer region composed of harmonically constrained Langevin atoms surrounding the active site region whose atoms are treated by molecular dynamics. Possible applications of the model are disc

ISSN:0006-3525    

DOI:10.1002/bip.360240509

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

年代:1985

数据来源: WILEY

摘要:

AbstractDNA supercoiling is both an interesting problem from the theoretical point of view and an important phenomenon affecting DNA functionsin vivo. Experimentally, however, hardly more than the overall hydrodynamic shape, superhelical density, and enzymic or chemical reactivity of the parameters that are in some way related to DNA secondary and tertiary structure in the superhelical state can be determined. Consequently, it is highly desirable to build up models of DNA supercoiling that, on the one hand, match the above type of global data and, on the other, take advantage of the knowledge about DNA structure at lower levels of complexity, i.e., with linear DNA molecules and its synthetic models. One possible approach, presented here, deals with an extension of Fuller's and Benham's general ideas concerning an elastomechanical model of DNA supercoiling. We extend their model with an algorithm suitable for numerical calculations and construct a fast computer program,ROPASE, that displays the rod shapes as dependent on its elastic properties and applied stress. Development of this program made inevitable a detailed analysis of the input parameters found to be degenerate in the sense that not all of them should be considered variable to generate the whole set of possible solutions of the model. Many calculations were performed using ROPASE to test its properties and the properties of the elastomechanical model. Representative DNA shapes are presented.

ISSN:0006-3525    

DOI:10.1002/bip.360240510

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

年代:1985

数据来源: WILEY

摘要:

AbstractThe thermotropic behavior of lipid vesicles prepared from dimyristoylphosphatidylcholine in the presence of cytochrome c oxidase has been studied by highly sensitive differential scanning microcalorimetry. This protein has a remarkable effect on the gel–liquid crystalline transition of dimyristoylphosphatidylcholine. In the presence of cytochrome c oxidase, the thermogram of the lipid vesicles exhibits a second endothermic peak, which is adjacent to the main lipid phase‐transition peak and appears at a higher temperature. As the concentration of added protein increases, the two endothermic peaks become further separated, and the transition temperatures and the heats of transition corresponding to both endothermic peaks decrease. A greater decrease in the transition temperature at the lower‐temperature peak with added protein suggests that the lower‐temperature peak is more perturbed than the higher‐temperature peak. The higher‐temperature peak is not thermally reversible. Treatment of sample well above the transition temperature results in a reduction of the magnitude of the higher‐temperature peak. The lipid–protein interaction contributing to the higher‐temperature

ISSN:0006-3525    

DOI:10.1002/bip.360240511

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

年代:1985

数据来源: WILEY