摘要:

AbstractEnergy embedding has been shown recently to be a useful extension of the distance geometry approach to conformational calculations in the case of very small molecules and simple energy functions. This paper tests the ability of energy embedding to locate low energy conformations satisfying both weak and strong geometric constraints when the molecule is the small protein, bovine pancreatic trypsin inhibitor, and the energy function is the complicated Oobatake‐Crippen residue–residue potential. Using the potential function alone, the algorithm reaches a structure with energy lower than that of the native conformation, but with little resemblance to it. Aided by numerous geometric constraints, such as preformed secondary structure segments, the algorithm again finds a local minimum with energy better than that of the native, and with only 3.3 Å rms deviation from it. This is significantly closer to the native value than can be obtained using standard distance geometry and the geometric constraints alone. Thus, energy embedding using the Oobatake‐Crippen potential function is a significant help in finding native conformations of proteins. However, additional trials on a hairpin bend fragment of trypsin inhibitor demonstrate the potential's shortcomings in encouraging proper secondary str

ISSN:0006-3525    

DOI:10.1002/bip.360211002

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

年代:1982

数据来源: WILEY

摘要:

AbstractMolecular‐mechanical studies of the left‐handed Z‐DNA polymers have been carried out and the results compared with similar calculations on B‐DNA polymers. We have studied d(CGCGCG)2, d(GCGCGC)2(and their 5‐methyl cytosine analogs), dG6·dC6, d(ATATAT)2, and d(TATATA)2in both B‐ and Z‐forms. For the left‐handed Z helices, we considered the ZIand ZIImodel of Quigley and co‐workers [Wang, A. H., Quigley, G. J., Kolpak, F. J., Crawford, J. L., van Boom, J. H., van der Marel, G.&Rich, A. (1979)Nature (London)282, 680–686], the actual “Z spermidine” and “Z spermine” structures of Quigley and the model‐built structure of Chandresekharan et al. [Arnott, S., Chandresekharan, R., Bindsall, D. L., Leslie, A. G. W.&Ratliff, R. L. (1980)Nature283, 743–745]. The major conclusions of this study are as follows. (1) The stabilization of Z‐DNA relative to B‐DNA occurs as one increases the “effective” dielectric constant or adds counterions, consistent with observations of Z‐DNA only under high salt conditions. (2) The ZIIpolymer is calculated to be more stable than the ZIpolymer. It is not yet clear whether the greater stability of ZIIthan ZIis a real effect or an artifact caused by the lack of inclusion of specific solvation effects in these calculations. (3) The greater tendency of the 5‐methyl cytosine analog of poly(dG‐dC)·poly(dG‐dC) to undergo the B → Z transition is found in our calculations and is due to destabilizing base–base and base–phosphate interactions, which are greater in the B‐ than in the Z‐form of the 5‐methyl cytosine polymer. (4) There are no large sequence‐dependent effects on the relative stabilities, and the AT polymers are calculated to be as likely to form Z‐helices as the GC polymers. In addition, the relative stability of a nonalternating sequence in the conformatio

ISSN:0006-3525    

DOI:10.1002/bip.360211003

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

年代:1982

数据来源: WILEY

摘要:

AbstractThe crystal structure of the title compound, a model for the glycosyl linkage between the asparagine side chain andN‐acetyl glucosamine in glycoproteins, has been determined and compared to other model structures. The pyranose ring in the crystal is in the4C1chair conformation and the amide functions at C1and at C2are both oriented such that the amide protons are nearlytransto their respective sugar‐ring protons. Coupling constants determined from the fully assigned proton nmr spectrum in aqueous solution are consistent with the conformation in the crys

ISSN:0006-3525    

DOI:10.1002/bip.360211004

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

年代:1982

数据来源: WILEY

摘要:

AbstractThe atomic position distributions obtained from a 32‐ps molecular‐dynamics simulation of tuna ferrocytochrome c at 297 K are analyzed in terms of their second, third, and fourth moments. Non‐Gaussian relations among these moments are found for the majority of atoms in the molecule, indicating anharmonicity in the effective potential functions for the atomic motions. Many atoms exhibit only slightly anharmonic mobility during the 32‐ps period, but about half of the atoms exhibit sizeable anharmonicity. For a typical atom, the anharmonic effects are largest for motions in the direction along which the largest displacements occur. Two classes of significantly anharmonic atoms are apparent: those whose effective potentials are distorted toward a square‐well shape and those whose effective potentials have secondary minima corresponding to conformational

ISSN:0006-3525    

DOI:10.1002/bip.360211005

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

年代:1982

数据来源: WILEY

摘要:

AbstractFlow linear dichroic studies have been conducted on phage T4B in its fast and slow forms. The behavior of the phages is well represented by an equivalent ellipsoid model using the Peterlin‐Stuart theory. The measurements permit the evaluation of the optical factor of the DNA in the phage and the rotary diffusion coefficient of the phage particle. Both these quantities change during the slow–fast conversion. The rotary diffusion results are in good agreement with those obtained by other workers with other methods. The optical factor is negative, indicating a net alignment of DNA helices parallel to the phage axis. The results exclude certain simplified models for the packaged DNA but do not lead to a unique structural conclusion. The flow dichroism experiment and its interpretation are described, and a simple method of calculating optical factors for complicated but cylindrically symmetric structures is presen

ISSN:0006-3525    

DOI:10.1002/bip.360211006

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

年代:1982

数据来源: WILEY

摘要:

AbstractThe flow linear dichroism of bacteriophage λ and its deletion mutants, λb2and λb221, was determined. The hydrodynamic behavior of the three phages differed slightly, but the magnitude of the dichroism was substantially the same with 〈cos2θμp〉 = 0.364, 0.368, and 0.372, respectively. The dichroism of intercalating dyes combined with bacteriophage was used as a further probe of phage structure. The reduced dichroism from proflavin with T4 showed no change with time during the reaction, but the interpretation of the ligand dichroism is complicated by an alteration of the hydrodynamic behavior of the phage–dye complex relative to the phage alone. Ethidium with λ also produced a stable reduced dichroism, but the signal indicated an average orientation of intercalated dye that is different from the average base orientation. The reduced dichroism of ethidium changes with time as it penetrates λb2, eventually approaching the dichroism of the nucleotide bases. The implication of these findings on the plausibility of various simple DNA packing models

ISSN:0006-3525    

DOI:10.1002/bip.360211007

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

年代:1982

数据来源: WILEY

摘要:

AbstractIt has recently been proposed that the repeating backbone nucleotide may be regarded as consisting of two blocks of equal magnitude representable by two virtual bonds. Implicit consideration of the nucleotide (ψ,ψ) and internucleotide (ω′,ω) geometry that generate variety in polynucleotide conformations, and of the constancy of the repeating structural moieties (P‐C4′ and C4′‐P) independent of the above rotations, has enabled us to utilize this scheme in the study of ordered structures such as di‐, oligonucleotides and, most significantly, tRNA. The polynucleotide folding dictated by short‐, intermediate‐, and long‐range interactions in the monoclinic and orthorhombic forms is described and compared through circular plots depicting the virtual bond torsions and distance plots constructed independently for backbone as well as bases. The torsions and the bond angles associated with the virtual bonds afford a clear distinction between ordered helical segments from loops and bends of tRNA. Lower virtual bond torsions (−60° to 60°) concomitant with higher values of virtual bond angles characterize various bend regions, while torsions around 160°–210° typify ordered helical strands. The distance plot elucidates the type of interaction associated with various sub‐structures (helix–helix, helix–loop, and loop–loop) that form the constituents of different structural domains. Several other features such as the manifestation of the P10loop and the approximate twofold symmetry in the tRNA molecule

ISSN:0006-3525    

DOI:10.1002/bip.360211008

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

年代:1982

数据来源: WILEY

摘要:

AbstractWe have studied the temperature dependence of the tracer diffusion coefficient of carbonmonoxy hemoglobin A (HbA‐CO) by means of pulsed‐field gradient nmr (PFG‐nmr). Measurements were made over the temperature range from 15 to 35°C for samples having concentrations 7.4 and 16.7 g/dL. No significant deviations were found from the predictions of the Stokes‐Einstein relation. Thus, this work does not corroborate the recently proposed conformational change in hemoglobin at 22°C. The advantages of PFG‐nmr for the study of hemoglobin ar

ISSN:0006-3525    

DOI:10.1002/bip.360211009

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

年代:1982

数据来源: WILEY

摘要:

AbstractThe complex piezoelectric constant (d=d′ −id″), elastic constant (c=c′ +ic″), and dielectric constant (ε = ε′ −iε″) were measured at a frequency of 10 Hz over the temperature range from −150 to 50°C and for a range of hydration up to 0.26 g/g for decalcified bone and up to 0.084 g/g for bone. For decalcified bone, ε′ and ε″ increased with increasing hydration with a deflection at the critical hydrationhc= 0.08 g/g;d′ at −150°C increased belowhcbut decreased abovehcwith increasing hydration;c′ increased below −60°C but decreased above −60°C with increasing hydration; and the peak temperatures of ε″,d″, andc″ below −50°C agree with each other and decreased with increasing hydration with a deflection athc. For bone, similar hydration and temperature dependences were observed for ε andc. However, the dependence ofdon hydration and temperature was different from that of decalcified bone, reflecting a two‐phase structure consisting of collagen fibers and mineral hydroxy

ISSN:0006-3525    

DOI:10.1002/bip.360211010

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

年代:1982

数据来源: WILEY

摘要:

AbstractThe probability of DNA base‐pair opening was calculated at temperatures below the denaturation region. The helix–coil transition theory, modified to include different nearest‐neighbor interactions, was employed. Predictions of base‐pair opening employing DNA melting‐curve parameters differed considerably from predictions based on parameters evaluated from synthetic RNA oligomer data of Gralla and Crothers (G‐C) and formaldehyde–DNA binding experiments of McGhee and von Hippel (M‐vH). Calculations based on the latter parameters indicate a base‐pair‐opening probability of 10−2–10−3at 35°C in 0.1MNaCl. DNA melting‐curve parameters predict values about 103smaller. At a temperature 10°C below the transition midpoint of a specific DNA sequence, DNA melting parameters predict base‐pair opening of about 10−3, whereas the G‐C and M‐vH parameters predict that ≳0.16 of the DNA is melted. Experiments and theoretical assumptions relevant to the calculations are analyzed. Evidence suggests that DNA melting parameters are valid when the average loop size exceeds some minimum value, whereas the G‐C and M‐vH parameters appear more valid for single base‐pair loops. A reconciliation of the two sets of predictions can be made if interactions extending beyond neighboring base pairs are considered. Such interactions will make the parameters of the nearest‐neighbor model appear to change with the average loop size. Experiments that may provide further

ISSN:0006-3525    

DOI:10.1002/bip.360211011

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

年代:1982

数据来源: WILEY