摘要:

AbstractThe partial molar volumes of various compounds that model protein constituent groups, such as tripeptides (Gly‐X‐Gly, where X = Gly, Ala, Val, Leu, Ile, Pro, Met, His, Ser), homopeptides (Glyn,n= 3, 4, 5), and simple organic analogues of amino acid side chains (methanol, acetamide, propanamide, acetic acid, propanoic acid,n‐butanamine,n‐butanamine nitrate,n‐propylguanidine nitrate, 4‐methylphenol), have been determined in aqueous solution with a vibrational densimeter in the temperature range of 5–85°C. The partial molar volumes of amino acid side chains and the peptide unit were estimated from the data obtained. Assuming additivity of component groups, the partial molar volumes of polypeptide chains of several proteins over a broad temperature range were calculated. The partial molar volume functions of four proteins (myoglobin, cytochrome C, ribonuclease A, lysozyme) were compared with those determined experimentally for the unfolded and native forms of these proteins. It has been shown that the average deviation of the calculated functions from the experimental ones does not exceed 3% over the temperature

ISSN:0006-3525    

DOI:10.1002/bip.360301102

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

年代:1990

数据来源: WILEY

摘要:

AbstractA systematic Conformational search has been performed for the 14‐membered ring in model compounds for disulfide‐containing enkephalin analogues. The model compounds examined are , and the corresponding compounds withL‐amino acids at the C‐terminus. About 100 starting conformations were generated for each compound with the RNGCFM program and energy minimized with the AMBER program. Between 21 and 38 conformers within 3 kcal/mole of the apparent global minimum were found for each compound. There appeared to be fewer possible conformations of the disulfide‐containing side chain than of the main chain. , whose parent compound is selective for opioid δ receptors, was found to prefer conformers with a positive dihedral angle of the disulfide bond, which is consistent with the previous proposal that δ‐receptor selectivity may be associated with this conformational preference. Additional calculations were performed on the complete structure of (DPDPE) with various possible conformations of the tyrosine and phenylalanine side chains. Conformational free energies and entropies were computed for these conformers from the molecular vibrations obtained from a normal mode analysis. As was found previously, conformers with low energies tended to have lower entropies, which resulted in a narrowing of the free energy differences between conformers. A conformer is identified that has the lowest energy hitherto found for DPDPE. It is suggested that DPDPE may be a useful compound for evaluating conformational search strategies because of its relatively small size and the number of conformers that have already been identified. Conformational energy calculations are also reported for naltrindole using the MM2(87) program. Naltrindole, which incorporates two aromatic 6‐membered rings in a rigid structure, is a highly selective and potent opioid δ‐receptor antagonist and may be an important clue regarding the biologically active conformer of DPDPE. Various conformers of DPDPE have been superimposed quantitatively onto the structure of naltrindole using the SUPER program and those conformers of DPDPE that are the best fit to naltri

ISSN:0006-3525    

DOI:10.1002/bip.360301103

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

年代:1990

数据来源: WILEY

摘要:

AbstractMacromolecules in solution can have large effects on the properties of other solutes through nonideal excluded‐volume (crowding) interactions. Minton [(1983)Mol. Cell. Biochem.55, 119–140] has calculated such effects by treating the macromolecules as a hard‐sphere fluid in a background of an inert structureless solvent. In the present paper these calculations are extended by including the primary solvent as a separate component in a hard‐sphere mixture. The results are in good agreement with experimental data. However, some predictions of this model differ drastically from those based on Minton's approach. Thus, much smaller effects from macromolecular crowding, particularly by smaller molecules, are expected. The present results also predict a much larger dependence on the shape of the molecules under study; notably for a dimerization reaction, it is found that the excluded‐volume effects actually can destabilize side‐by‐side binding of two spherical molecules, while a dimerization to a spherical complex is stabilized. Therefore there will exist intermediate shapes of complexes whose stability is insensitive to crowded‐volume effects. The consequences for crowding effects inside the living cell are

ISSN:0006-3525    

DOI:10.1002/bip.360301104

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

年代:1990

数据来源: WILEY

摘要:

AbstractThe role of the amino acid proline in influencing the secondary and tertiary structure of proteins and polypeptides has been an area of active study for many years. We have investigated this problem by incorporating the four‐membered ring amino acid, azetidine‐2‐carboxylic acid, into some proline polypeptides. An adjunct to the synthesis of the peptides was the synthesis of azetidine‐2‐carboxylic acid and its resolution. We developed an improved synthesis of N‐benzhydryl‐2‐carbobenzyloxy azetidine, an essential intermediate required for the synthesis ofLazetidine‐2‐carboxylic acid. This amino acid was subsequently obtained via the partial hydrogenation of the N‐benzhydryl compound, under mild conditions. Our ability to isolate the intermediate N‐benzhydryl‐2‐carboxylic acid demonstrated that the rate of cleavage of theO‐benzyl ester group in this molecule is faster than the cleavage of the N‐benzhydryl group.The tetrapeptides, Boc‐(LPro)3‐LAze‐Opcp, and Boc‐(LAze‐LPro)2‐Opcp (Boc:t‐butoxycarbonyl; Pro: praline; Aze: azetidine‐2‐carboxyl acid; Opcp: pentachlorophenyl), were prepared using traditional solution peptide synthesis. They were characterized by direct chemical ionization‐mass spectrometry, CD spectra, and13C‐ and1H‐nmr spectroscopy. The assessment of the secondary structure assessment of the two peptides using the methods noted above has led us to conclude that the compound Boc‐(L‐Aze‐LPro)2‐Opcp, in trifluoroethanol, has an all‐cispeptide bond conformation with ϕ and ψ torsion angles compatible with a left‐handed helix. The secondary structure assessment of the peptide Boc‐(LPro)3‐LAze‐Opcp, in chloroform or trifluoroethanol, leads to an assignment of bothcisandtranspeptide bonds as being present in the peptide. We have interpreted this latter finding as indicating that the introduction of the azetidine group into a peptide containing three consecutive praline residues in a linear sequence p

ISSN:0006-3525    

DOI:10.1002/bip.360301105

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

年代:1990

数据来源: WILEY

摘要:

AbstractConditions for the occurrence of one, two, and even three helix–coil transitions are summarized and further delineated in terms of thermodynamic parameters in simple modifications of a 2 × 2 matrix of statistical weights for amino acid residues in the coiled and helical conformations. Solvent interaction with segments in both the exposed, coiled and compact, helical conformations is worked into the model. Theoretical expressions for the temperature dependence of helical fractions, maximum attained degrees of helicity, and the compositional dependence of transition temperatures are compared with experimental data for two synthetic polypeptides that exhibit multiple helix–coil transit

ISSN:0006-3525    

DOI:10.1002/bip.360301106

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

年代:1990

数据来源: WILEY

摘要:

AbstractThis paper reports the chiroptical properties of thionated N‐acyl amino acid and N‐acyl dipeptide N′‐methylamide models. It was found that the optical activity of the thioamide chromophore is dominated by the chiral contribution of perturbants attached to Cαat the N‐H side of the thioamide group. The appearance of a strong negative ππ* band near 270 nm is indicative of the semiextended conformation of this residue. The ϕ ∼ −70°, ψ ⩾ 120° set of torsion angles is compatible with a type II βt‐turn or a γt‐turn conformation with the perturbing N‐H side residue in thei+ 1 position of the turn. (The subscript t or tt denotes that one or both of the H‐bonded moieties is thioamide.) Earlier data show that both βt‐ and γt‐turns may be fixed by CS ⃛H‐N(CO) intramolecular H bonds. The appearance of one or two weaknπ* bands and a positive ππ* band at about 270 nm is characteristic of type II βt‐turns containing the H‐bonded thioamide group attached to the glycine residue in positioni+ 2. The extended conformation (ϕ ∼ −140°, ψ ∼ 140°) of a residue after the thioamide group gives rise to a negativenπ* and a positive ππ* band of comparable magnitude. Peptid1e sequences with alternating thioamide–amide–thioamide backbone tend to adopt 1t⇆ 4tH‐bonded βttconformations. CD studies show that type II βtt‐turns have unique chiroptical properties: the ππ* region is dominated by an exceedingly strong negative band near

ISSN:0006-3525    

DOI:10.1002/bip.360301107

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

年代:1990

数据来源: WILEY

摘要:

AbstractA recently developed theory of the light scattering by random coils undergoing random scission is applied to the digestion of hyaluronate by hyaluronidase. The time dependence of the scattered light from solutions undergoing digestion was monitored. Working at a high angle with high molecular weight hyaluronate allowed the use of a powerful approximation for determining initial velocities and the Henri–Michaelis–Menten coefficients, without explicit knowledge of the hyaluronate molecular weight, radius of gyration, second virial coefficient, or polydispersity. Effects due to a molecular weight dependent second virial coefficient and to non‐Gaussian behavior are briefly considered. Assays were performed over nearly two orders of magnitude in substrate concentration. The initial velocities are compared with those obtained by a standard reducing sugar assay, which was performed on identical samples. The main advantages of the light scattering assay procedure over the more traditional assays are that many relatively high‐precision data points can be quickly and automatically collected with simple apparatus, and that the technique is most sensitive for the initial period of digestion, where the other assays are least sensitive. The shapes of the scattering curves also provide evidence that hyaluronate in these solutions is not a stable double strand and that the hyaluronidase cleaves bonds randomly. The curves also indicate that enzyme deactivation occurs, which accounts for the lower velocities yielded by the slower reductimetric assay, which is measured over longer initial

ISSN:0006-3525    

DOI:10.1002/bip.360301108

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

年代:1990

数据来源: WILEY

摘要:

AbstractMolecular dynamics simulations on the transmembrane antibiotic peptide alamethicin have been performed in the NVT ensamble (i.e., the number of particlesN, the volumeV, and the temperatureTof the system are kept constant). Results on the structure and conformational flexibility of this molecule are discussed and compared with previous experimental CD, x‐ray, nmr data and theoretical computations on fragments analogues.An extensive study of structural and dynamic properties from H‐bonding pattern analysis is presented. Evidences for a largely α‐helix structure with some extent of freedom in the C‐terminal region are found.Further, a partition of the molecule into three regions on the base of structural features and dynamic behavior has been proposed, and the correlation among the motions of the three regions is d

ISSN:0006-3525    

DOI:10.1002/bip.360301109

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

年代:1990

数据来源: WILEY

摘要:

AbstractHigh purity, high molecular weight hyaluronate from bacteria and rooster comb exhibited clear polyelectrolyte properties, as observed by static and dynamic light scattering. The scattered intensity of hyaluronate solutions increased markedly with ionic strength, while the radii of gyration decreased. Apparent persistence lengths within the wormlike chain model in the coil limit were estimated as a function of ionic strength. The total apparent persistence length varied from about 87 Å in the high ionic strength limit to nearly 400 Å at 1 mMadded NaCl. The apparent electrostatic persistence length varied approximately as the inverse square root of the ionic strength. Deviations from the theoretically predicted inverse ionic strength dependence were investigated in terms of excluded volume effects. Dynamic light scattering yielded “ordinary phase” diffusion coefficients whose dependence on polymer and salt concentration agreed reasonably well with hydrodynamic coupled mode theory in the linear limit. Extrapolations to infinite polymer dilution at fixed salts yielded, surprisingly, a constant diffusion coefficient. Thus, there was no evidence of either polyion expansion or electrolyte friction effects in the infinite dilution diffusion coefficients. Since clear evidence for polyion expansion was seen in the static scattering, it is thought that the relative stiffness and consequent openness of the hyaluronate coils lead to partial free draining behavior. There was no evidence for an “extraordinary phase” under no added salt and low added salt conditions. The overall results are contrasted with the very different behavior previously reported for medium purity hyaluronate from anima

ISSN:0006-3525    

DOI:10.1002/bip.360301110

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

年代:1990

数据来源: WILEY

摘要:

AbstractThe binding ofn‐mer ligands to a one‐dimensional lattice involving many ligand species and complex multiple‐binding mechanisms is studied. We show that, when derived using the sequence‐generating function method of Lifson, the secular equation of any binding system with a finite number of “elementary units” can be expressed in a matrix determinant form that is very symmetric and easy to construct. In other words, for any binding system whose elementary units are known, the secular equation of the system can be obtained readily without going through the formal derivation of the equation. We also show that the “determinant” secular equation obtained using the present procedure can be employed directly to the calculation of bi

ISSN:0006-3525    

DOI:10.1002/bip.360301111

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

年代:1990

数据来源: WILEY