ISSN:0006-3525    

DOI:10.1002/bip.360250502

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

年代:1986

数据来源: WILEY

摘要:

AbstractConformational energy calculations oncyclo(glycyl‐L‐phenylalanyl),c(Gly‐Phe), were carried out by means of the semiempirical MO CNDO/2 method. They corroborated earlier experimental findings that inc(Gly‐Phe) the conformations with an aromatic side‐chain ring folded over the dioxopiperazine (DOP) ring contribute significantly to the overall equilibrium, provided that the empirical optimization of the DOP ring geometry, extracted from x‐ray data, rather than that of the CNDO/2‐derived data is used throughout the computations. Following these studies, more detailed calculations, based partly on CNDO/2‐derived data and partly on experimental data, were carried out to clarify the question, which are the forces responsible for this ring‐ring stacking? In contrast to early suggestions, it was found that the quadrupole‐quadrupole and dispersion interactions mainly contribute to folded conformations ofc(Gly‐Phe). Some implications of this finding on devising force fields for molecular‐mechanics calculations of peptid

ISSN:0006-3525    

DOI:10.1002/bip.360250503

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

年代:1986

数据来源: WILEY

摘要:

AbstractThe thermally elicited structural and conformational transitions of the polynucleotide analog, poly(‐)‐2‐[2‐(thymin‐1‐yl)propanamido]propenoic acid, P(‐)TDHA, have been studied using differential scanning calorimetry (DSC), differential thermal analysis (DTA), and thermogravmetric analysis (TGA). The differential scanning calorimetry curves obtained on solid P(‐)TDHA samples exhibited five distinct transitions. The transition occurring at 50°C is attributed to a disruption of interactions involving thymine–thymine stacking. In contrast the transition observed at 83°C is attributed to a hydrogen‐bonding interaction involving the thymine residues, whereas the transition occurring at 110°C is assigned to hydrogen bonding of the carboxylic acid side‐chain groups. The transitions observed at 50, 83, and 110°C are reversible if the heated and quenched sample is allowed to equilibrate in an atmosphere of high humidity. The transition occurring at 127°C is viewed as a structural rearrangement of the polymer backbone that does not involve the participation of water molecules. The transition observed at a temperature above 197°C is attributed to a structural modification of the polymer resulting from decomposition. Solutions of P(‐)TDHA in 0.1Mphosphate buffer at pH 7.05 showed only a single transition at 50°C, which is in accord with an observed transition in the solid state assigned to the disruption of base‐stacking interactions. The average enthalpy for the transition at 50°C was 0.92 cal/g in the solid state and 1.08 cal/g for the solution, which provides addi

ISSN:0006-3525    

DOI:10.1002/bip.360250504

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

年代:1986

数据来源: WILEY

摘要:

AbstractConformational energy calculations, aimed at verification of the suitability of the semiempirical molecular orbital CNDO/2 method for conformational elucidations in cyclic dipeptides formed from amino acids with aliphatic side chains, have been carried out. The results obtained for four dioxopiperazines [DOP;cyclo(Glycyl‐L‐Alanyl),cyclo(Glycyl‐L‐Valyl), and both epimers ofcyclo‐di‐(Alanyl)] point out very good agreement with experimental premises. The latter include (1) the preference of thecis‐peptide bonds for being nonplanar, which results in twisted‐boat conformations of the DOP ring; (2) greater stability of conformers with a side chain oriented axially over those with a side chain oriented equatorially; (3) the preference ofcyclo(Gly‐Val) for assuming a folded conformation with one of the side chain γ‐methyl groups sticki

ISSN:0006-3525    

DOI:10.1002/bip.360250505

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

年代:1986

数据来源: WILEY

摘要:

AbstractThe effective diffusion rate of a tracer molecule through a polymer network can be influenced by nonspecific binding. If such binding occurs, the local density fluctuations (segmental diffusion) of the network molecules will contribute to the net displacements of tracer molecules. If the network is strongly interconnected by entanglement or cross‐linking, these local motions will only carry the tracer molecules over a small region, and effective transport would require dissociation and reassociation of the tracer molecule to another part of the network. Alternatively, tracer molecules could be transferred directly (intersegment transfer) between different parts of the network whenever they are brought sufficiently close by the density fluctuations. A wormlike‐chain model for the segmental diffusion of a polymer is used to describe the network motions and to derive the effective diffusion rate for a tracer molecule as a function of network density and binding constant with or without intersegment transfer contributing. It is found that the density dependence for the effective diffusion of ethidium bromide through dense DNA solutions studied by photobleaching recovery [R. D. Icenogle and E. L. Elson (1983)Biopolymers22, 1949–1966] agrees with an intersegment‐transfer mechanism limited by the segmental DNA motions. The calculations are also applied to a model for the intracellular diffusion of molecules loosely bound to the cytomatrix. If intersegment transfer dominates it can account for the observed size independence for the intracellular diffusion rates of various injected macromo

ISSN:0006-3525    

DOI:10.1002/bip.360250506

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

年代:1986

数据来源: WILEY

摘要:

Abstract31P‐ and1H‐nmr and laser Raman spectra have been obtained for poly[d(G‐T)]·[d(C‐A)]and poly[d(A‐T)] as a function of both temperature and salt. The31P spectrum of poly[d(G‐T)]·[d(C‐A)]appears as a quadruplet whose resonances undergo separation upon addition of CsCl to 5.5M.1H‐nmr measurements are assigned and reported as a function of temperature and CsCl concentration. One dimensional nuclear Overhauser effect (NOE) difference spectra are also reported for poly[d(G‐T)]·[d(C‐A)]at low salt. NOE enhancements between the H8 protons of the purines and the C5 protons of the pyrimidines, (H and CH3) and between the base and H‐2′,2″ protons indicate a right‐handed B‐DNA conformation for this polymer. The NOE patterns for the TH3 and GH1 protons in H2O indicate a Watson–Crick hydrogen‐bonding scheme. At high CsCl concentrations there are upfield shifts for selected sugar protons and the AH2 proton. In addition, laser Raman spectra for poly[d(A‐T)] and poly[d(G‐T)]·[d(C‐A)] indicate B‐type conformations in low and high CsCl, with predominantly C2′‐endosugar conformations for both polymers. Also, changes in base‐ring vibrations indicate that Cs+binds to O2 of thymine and possibly N3 of adenine in poly[d(G‐T)]·[d(C‐A)]but not in poly[d(A‐T)]. Further,1H measurements are reported for poly[d(A‐T)] as a function of temperature in high CsCl concentrations. On going to high CsCl there are selective upfield shifts, with the most dramatic being observed for TH1′. At high temperature some of the protons undergo severe changes in linewidths. Those protons that undergo the largest upfield shifts also undergo the most dramatic changes in linewidths. In particular TH1′, TCH3, AH1′, AH2, and TH6 all undergo large changes in linewidths, whereas AH8 and all the H‐2′,2″ protons remain essentially constant. The maximum linewidth occurs at the same temperature for all protons (65°C). This transition does not occur for d(G‐T)·d(C‐A) at 65°C or at any other temperature studied. These changes are cooperative in nature and can be rationalized as a temperature‐induced equilibrium between bound and unbound Cs+, with duplex and single‐stranded DNA. NOE measurements for poly[d(A‐T)] indicate that at high Cs+the polymer is in a right‐handed B‐conformation. Assignments and NOE effects for the low‐salt1H spectra of poly[d(A‐T)] agree with those of Assa‐Munt and Kearns [(1984)Biochemistry23, 791–796] and provide a basis for analysis of the high Cs+spectra. These results indicate that both polymers adopt a B‐type conformation in both low and high salt. However, a significant variation is the ability of the phosphate backbone to adopt a repeat dependent upon the base sequence. This feature is common to poly[d(G‐T)]·[d(C‐A)], poly[d(A‐T)], and some other pyr–pu

ISSN:0006-3525    

DOI:10.1002/bip.360250507

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

年代:1986

数据来源: WILEY

摘要:

AbstractX‐ray diffraction diagrams of 80 specimens, mainly from woody plants, were recorded and resolved into characteristic reflections of cellulose I. Significant differences were observed ind‐spacings and integrated intensity ratios between softwoods and hardwoods. Of the lattice parameters, the monoclinic angle was found to be correlated with plant taxonomy and tended towards the right angle in the more advanced taxonomic groups. We have therefore demonstrated that the crystal structure of natural cellulose shows some variations related to the source of the cellul

ISSN:0006-3525    

DOI:10.1002/bip.360250508

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

年代:1986

数据来源: WILEY

摘要:

AbstractA method, molecular cartography, is introduced as a way to quantitate the topographic structure of a protein surface. The method is applied to the problem of antigenic determinants, and it is used to examine local and global topography of reported antigenic regions on the surface of myoglobin and lysozyme. In nine antigenic sites taken from the literature and studied in detail, no local property was found in sites that was not also found in remaining regions of the surface. However, a strong correlation was found between antigenic sites and regions of the surface that are globally exposed. This finding suggests that global exposure of the protein surface may play a primary role in determining the antigenic structure of the protein. Molecular cartography may be useful in other instances of protein–protein interactions such as those between proteolytic enzymes and their substrate

ISSN:0006-3525    

DOI:10.1002/bip.360250509

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

年代:1986

数据来源: WILEY

摘要:

AbstractValues of the apparent intrinsic dichroism of the 260‐nm transition of duplex poly(dG‐dC) and poly(dG‐m5dC) in both B‐ and Z‐conformations are determined from electric dichroism (ED) measurements by extrapolation of the data at high field strengths. These values are compared to each other and to values of the intrinsic dichroism calculated for the Z‐ and B‐forms generated respectively from the crystal structure coordinates [(1981) A. H. J. Wang, G. J. Quigley, F. J. Kolpak, G. Van der Marel, T. H. Van Boom&A. Rich,Science211, 171–176.] of the d(CpGpCpGpCpGp) hexamer and from the coordinates [(1982) A. V. Fratini, M. L. Kopka, H. R. Drew&R. E. Dickerson,J. Biol. Chem.257, 14686–14707.]. of the terminal CpGpCpGp base pairs of the crystal of straight B‐form dodecamer d(CpGpCpGpApApTpTpCpGpCpGp). Direct association of the dichroism with the orientation of the optical transition moments with respect to the helix axis of poly(dG‐dC) implies that the average tilt of the bases is much different than the values calculated from the structural coordinates. The experimental values for both the B‐ and Z‐forms are, however, almost identical to those observed with fragments of “random” sequence B‐form DNA ofthe same molecular length. It is argued that this descrepancy and other anomalies reported in the literature are due to the theoretically predicted unusual high field behavior associated with diffuse ion atmosphere polarization. Unlike either permanent dipoles or induced moments based on bond polarizabilities, the orienting dipole energy from the polarization of the counterions surrounding DNA approaches a finite limiting value, dependent on DNA length, at very high field strengths. This can result in extrapolated dichroisms that do not reflect structure at perfect orientation, but rather structure at some limiting orientation. Consequently, we believe, the conclusiondrawn from ED measurementson short fragments of DNA that the bases are highly tilted from the perpendicular to the helix axis by propeller t

ISSN:0006-3525    

DOI:10.1002/bip.360250510

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

年代:1986

数据来源: WILEY

摘要:

AbstractBy combining measurements of the enzymatic release of fibrinopeptide A (FPA) with measurements of intensity and linewidth of Rayleigh scattering from fibrin polymer solutions prior to gelation, we have systematically tested a variety of predictions that can be made on the basis of a simple geometrical abstraction of fibrin polymerization. The experimental investigations include FPA content of fibrin polymers, aggregation of fibrin with fibrinogen, enzyme kinetics, shift of the chemical equilibrium by adding Gly‐Pro‐Arg‐Pro or fibrinogen to the polymer solution, evolution of the polymerization, and influence of fibrinopeptide B release. Among the considered geometrical abstractions there is only one that survives the experimental tests and at the same time is compatible with the electron micrographs by other authors. The main conclusions that can be drawn are (1) the location of binding sites A must be taken from the structure of the fibrinogen molecule proposed by Hoeprich and Doolittle [Biochemistry(1983)22, 2049–2055], (2) The fibrinogen monomer is basically centrosymmetric, (3) the state of polymerization is reversible and corresponds to a chemical equilibrium, and (4) Michaelis–Menten enzyme kinetics can b

ISSN:0006-3525    

DOI:10.1002/bip.360250511

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

年代:1986

数据来源: WILEY