摘要:

AbstractThe structure and activity of a protein molecule are strongly influenced by the extent of hydration of its cavities. This is, in turn, related to the free energy change on transfer of a water molecule from bulk solvent into a cavity. Such free energy changes have been calculated for two cavities in a sulfate‐binding protein. One of these cavities contains a crystallo graphically observed water molecule while the other does not. Thermodynamic integration and perturbation methods were used to calculate free energies of hydration for each of the cavities from molecular dynamics simulations of two separate events: the removal of a water molecule from pure water, and the introduction of a water molecule into each protein cavity. From the simulations for the pure water system, the excess chemical potential of water was computed to be −6.4 ± 0.4 kcal/mol, in accord with experiment and with other recent theoretical calculations. For the protein cavity containing an experimentally observed water molecule, the free energy change on hydrating it with one water molecule was calculated as −10.0 ± 1.3 kcal/mol, indicating the high probability that this cavity is occupied by a water molecule. By contrast, for the cavity in which no water molecules were experimentally observed, the free energy change on hydrating it with one water molecule was calculated as 0.2 ± 1.5 kcal/mol, indicating its low occupancy by water. The agreement of these results with experiment suggests that thermodynamic simulation methods may become useful for the prediction and analysis of internal hydration in

ISSN:0006-3525    

DOI:10.1002/bip.360310802

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

年代:1991

数据来源: WILEY

摘要:

AbstractHigh‐resolution solid‐state13C‐nmr spectra of (1 → 3) ‐β‐D‐xylan fromBryopsis maximaandCaulerpa brachypuswere recorded for various preparations from intact through dried frond to anhydrous and hydrated xylan, to gain insight into their secondary structures as compared with those of (1 → 3)‐β‐D‐glucans. It turned out that13C‐nmr peaks of intact or dried frond were mainly ascribed to the peaks from (1 → 3)‐β‐D‐linked xylose residue, although some peaks were seen at the carbonyl and aliphatic regions. Dehydration of frond by either air drying or ethanol, and extraction of xylan with acid, did not result in substantial spectral change, although extraction with saturated ZnCl2solution caused appreciable displacements of the C‐3 as well as C‐2 and C‐5 peaks. This means that no major conformational change was induced during the above‐mentioned processes of the dehydration and the extraction with acid. The extraction with ZnCl2solution, however, induced major conformational change. Thus, we found that the above‐mentioned three distinct conformations–triple helix, single helix, and single chain–are also present in (1 → 3)‐β‐D‐xylan, as judged from the conformation‐dependent displacements of13C chemical shifts, hydration/dehydration‐induced spectral change, and the x‐ray diffraction data onPenicillus dumetosusby Atkins et al. In particular, we found that all the preparations except for the extraction with ZnCl2solution retain the triple helix form, whereas the anhydrous and hydrate samples of the latter preparations take the single‐chain and single‐helix form, respectively. Further, we measured the13C spin‐lattice relaxation times of laboratory frame of the xylan to gain insight into better understanding of the role of the hydroxy

ISSN:0006-3525    

DOI:10.1002/bip.360310803

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

年代:1991

数据来源: WILEY

摘要:

AbstractThe conformational possibilities of three different δ‐selective opioid peptides, which are DPDPE, and DRE (Tyr‐D‐Met‐Phe‐His‐Leu‐Met‐Asp‐NH2, dermenkephalin), were explored using energy calculations. Sets of low‐energy conformers were obtained for each of these peptides. The sets consisted of 61 structures for DPDPE, 32 for DCFPE, and 38 for DRE, including various types of rotamers of the Tyr and Phe side‐chain groups. Comparison of the geometrical shapes of the conformers was performed for these sets using topographical considerations, i.e., examination of the mutual spatial arrangement of the N‐terminal α‐amino group, and of the Tyr and Phe side‐chain groups. The results obtained suggest a model for the δ‐receptor‐bound conformer(s) for opioid peptides. The model suggests the placement of the Phe side chain in a definite position in space corresponding to theg−rotamer of Phe for peptides containing Phe4and to thetrotamer for peptides containing Phe.3The position of the Tyr1side chain cannot be specified so precisely. The proposed model is in a good agreement with the results of biological testing of β‐Me‐Phe4‐substituted DPDPE analogues that were not cons

ISSN:0006-3525    

DOI:10.1002/bip.360310804

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

年代:1991

数据来源: WILEY

摘要:

AbstractMeasurements are presented on the time course of chain exchange among two‐chain α‐helical coiled coils of rabbit tropomyosin. All experiments are in a regime (temperature, protein concentration) in which coiled‐coil dimers are the predominant species. Self‐exchange in αα‐tropomyosin was investigated by mixing αα species with α*α*, the asterisk designating an α‐chain whose lone sulfhydryl (C190) has been blocked by carboxyamidomethylation. The overall process αα + α*α* ⇄ 2αα* is followed by measurement of the fraction (h) of αα* species as a function of time. Similarly, self‐exchange in ββ‐tropomyosin is examined by measurements of the overall process: ββ + β*β* ⇄ 2ββ*, in which β* signifies a β‐chain blocked at both sulfhydryls (C36 and C190). The observed time course for both chains is well fit by the first‐order equation:h(t) =h(∞)(1 − e −k 1t), withh(∞) ≃ 0.5. This long‐time limit is as expected for self‐exchange, and agrees with experiments that attain equilibrium after slow cooling of thermally dissociated and unfolded chains. The simplest consonant mechanism is chain exchange by rate‐limiting dissociation of dimers followed by random reassociation. Kinetic analysis showsk1to be the rate constant for the chain dissociation step, a quantity not previously measured for any coiled coil. This rate constant for ββ species is about an order of magnitude greater than for αα. In both, the activation enthalpy and entropy are very large, suggesting that activation to an extensively (>50%) unfolded species necessarily precedes dissociation. Experiments are also reported for overall processes: αα + β*β* ⇄ 2αβ* and α*α* + ββ ⇄ 2α*β. Results are independent of which chain is blocked. Againh(∞) ≃ 0.5, in agreement with equilibrium experiments, and the time course is first order.

ISSN:0006-3525    

DOI:10.1002/bip.360310805

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

年代:1991

数据来源: WILEY

摘要:

Abstract13C‐nmr measurements are reported for samples of poly (L‐lysine) both static and spinning at the magic angle in the β‐sheet form as a function of water content. The addition of water decreases the side‐chain line widths considerably. Measurements of the cross‐polarization time constants indicate that hydration by either H2O or D2O increases the time constant. Measurements of spin–lattice relaxation times in the laboratory frame and the rotating frame indicate that hydration does not change the dynamics of the backbone carbon atoms in the β‐sheet structure appreciably, but the side‐chain atoms experience considerable increase in local mobility with increasing hydration. Deuteration of the exchangeable protons or the water has only small effects on the carbon relaxation times indicating that relaxation is driven by intramolecular dipole–

ISSN:0006-3525    

DOI:10.1002/bip.360310806

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

年代:1991

数据来源: WILEY

摘要:

AbstractSample peptides Boc‐Leu4‐Aib‐Leu4‐OBzl and Boc‐(Leu4‐Aib)2‐OBzl, were crystallized by the solvent‐evaporation method. Both crystals are monoclinic, with space group of P21andZ= 2. The cell parameters area= 16.580(7),b= 21.105(7),c= 11.583(4) Å, and β = 104.90(3)° (Boc‐Leu4‐Aib‐Leu4‐OBzl), anda= 15.247(9),b= 19.04(l),c= 16.311(9) Å, and β = 117.10(1)° [Boc‐(Leu4‐Aib)2‐OBzl]. Crystal structures were solved by the direct method and refined toRvalues of 0.096 (the former peptide) and 0.112 (the latter). Peptide backbones fold into a right‐handed α‐helix, except for the C‐terminal Aib residue in Boc‐(Leu4‐Aib)2‐OBzl. Both peptide molecules are stabilized by six (the former) or seven (the latter) intramolecular (5 → 1) hydrogen bonds, and arranged in the head‐to‐tail fashion, which makes an infinite column. In this column, one (the former) or two (the latter) intermolecular hydrogen bonds link the neighboring molecules. In the case of Boc‐Leu4‐Aib‐Leu4‐OBzl, the solvent molecule N, N‐dimethylformamide was found in the difference Fourier map. There was a hydrogen bond between peptide and solvent molecule. Along the lateral direction, only hydro

ISSN:0006-3525    

DOI:10.1002/bip.360310807

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

年代:1991

数据来源: WILEY

摘要:

AbstractThe peptide N‐Ac‐dehydro‐Phe‐L‐Val‐L‐Val‐OCH3(C22H31N3O5) was synthesized by the usual workup procedure and finally by coupling the N‐Ac‐dehydro‐Phe‐L‐Val‐OH to valine methyl ester. It was crystallized from its solution in acetonitrile‐water mixture at 4°C. The crystals belong to the space group P1 witha= 8.900(3) Å,b= 11.135(2) Å,c= 12.918(2) Å, α = 90.36(1)°, β = 110.14(3)°, γ = 90.10(3)°,V= 1207.7(6) Å,3Z= 2,dm= 1.156(5) Mgm−3,dc= 1.148(5) Mgm−3. The structure was determined by direct methods using SHELXS86. The structure was refined by full‐matrix least‐squares procedure to anRvalue of 0.077 for 3916 observed reflections. The molecular dimensions and conformations of the two crystallographically independent molecules are in good agreement. In the dehydro residues, the average Cα–Cβdistance is 1.31(2) Å whereas the bond angle Cα–Cβ–Cγis 132(1)°. The average backbone torsion angles are ω0= 169(1)°, ϕ1= −40(1)°, ψ1= −50(1)°, ω1= −177(1)°, ϕ2= 54(1)°, ψ2= 46(1)°, ω2= −174(l)°, ϕ3= 103(1)°, ψ 3T= −139(1)°, and θ 3T= −176(1)°. The acetyl group is in the trans conformation, while the backbone adopts a right‐handed and left‐handed helical conformation alternatingly. The two crystallographically independent molecules are held together by three hydrogen bonds: N21–H21–O′12= 2.911(12) Å, N22–H22–O′11= 2.941(12) Å and N23–H23–O11= 3.005 (9) Å. The crystal structure is stabilized by van der Waals force

ISSN:0006-3525    

DOI:10.1002/bip.360310808

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

年代:1991

数据来源: WILEY

摘要:

AbstractThe experimental thermodynamic data for the dissolution of five simple hydrocarbon molecules in water were combined with the solute–solvent interaction energy from a computer simulation study to yield data on the enthalpy change of solvent reorganization. Similar data were generated for dissolving these same solute molecules in their respective neat solvents using the equilibrium vapor pressure and the heat of vaporization data for the pure liquid. The enthalpy and the free energy changes upon cavity formation were also estimated using the temperature dependence of the solute–solvent interaction energy. Both the enthalpy andTΔSfor cavity formation rapidly increase with temperature in both solvent types, and the free energy of cavity formation can be reproduced accurately by the scaled particle theory over the entire temperature range in all cases. These results indicate that the characteristic structure formation around an inert solute molecule in water produces compensating changes in enthalpy and entropy, and that the hydrophobicity arises mainly from the difference in the excluded volume ef

ISSN:0006-3525    

DOI:10.1002/bip.360310809

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

年代:1991

数据来源: WILEY

摘要:

AbstractChanges in conformation, length, and mobility of individual DNA molecules during agarose gel electrophbresis were measured using video micrographs obtained by epifluorescence microscopy. Globular, V‐shaped, and linear conformations of DNA are found. The mobility, upon transformation from the globular to the V‐shaped conformation, decreases, suggesting a collision with a gel fiber. The duration of interaction between DNA and gel fiber is proportional to the length of DNA. Hypothetically, this proportionality underlies the size separation of DNA by agarose gel electrophoresis.DNA release from the gel fiber appears to involve the movement of the arms of the V‐shaped molecule around the gel fiber. Concomitant with this movement is a length reduction the degree of which is constant for DNA of various lengths in a particular buffer milieu. The luminant densitometric profiles of DNA molecules in the V conformation show maxima at the ends and apex of the V. The unequal distribution of nucleotides along the DNA chain appears to provide the driving force for the molecular movement around the gel

ISSN:0006-3525    

DOI:10.1002/bip.360310810

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

年代:1991

数据来源: WILEY

摘要:

AbstractThe conformation of cyclolinopeptide A [c‐(Pro‐Pro‐Phe‐Phe‐Leu‐Ile‐Ile‐Leu‐Val)], a naturally occurring peptide with remarkable cytoprotective activity, has been investigated by means of molecular dynamics simulations in various molecular environments. Structural and dynamical properties have been analyzed and compared with those experimentally determined. A detailed analysis of hydrogen

ISSN:0006-3525    

DOI:10.1002/bip.360310811

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

年代:1991

数据来源: WILEY