摘要:

AbstractWe employ a mean field, modified, self‐consistent phonon theory to evaluate the single base‐pair opening rate and the probability of a base pair in the amino proton exchangeable state for the homopolymer poly(dA) · poly(dT) at temperatures below the helix–coil transition region. Our calculated premelting single base‐pair opening probabilities are in general agreement with several available experimental estimates from imino proton exchange and formaldehyde‐induced DNA melting measurements. These calculated opening probabilities, however, are in disagreement with the prediction of the helix–coil transition theory. Possible reasons for the differences are discussed, especially the possible different definition of a meaningful open state in the premelting region. The premelting open state of the modified self‐consistent phonon approximation theory seems to be appropriate to describe a solvent‐accessible open configuration that is sufficient to facilitate important chemical reactions such as imino proton exchange and formaldehyde reaction with the bases. This can be compared with the completely unstacked open state of the helix–coil transition theory originally defined in the helix–coil transition region. We propose that the amino proton exchangeable state is different from the open state associated with melting and only involves the breaking of the amino interbase H bond. The agreement between the calculated and experimentally estimated probability of a base pair in the amino proton exchangeable state seems to sup

ISSN:0006-3525    

DOI:10.1002/bip.360310202

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

年代:1991

数据来源: WILEY

摘要:

AbstractTwo low structure‐resolution methods are proposed for prediction of rotational diffusion parameters. The indirect procedure is based on the structure of a molecule in solution or in crystal, and uses the structure parameters of radius of gyration, and low‐resolution molecular surface and volume, determined from measured or theoretically calculated small‐angle x‐ray scattering intensities, to estimate a frictional equivalent ellipsoid of revolution. The direct method starts mainly from the crystallographic structure of a molecule and calculates the triaxial inertia equivalent ellipsoid, experimentally calibrated by translation diffusion data, to simulate the frictional behavior. The predicted harmonic mean of the rotational correlation times of compact globular macromolecules with molar masses of 14,000–65,000 g/mol agree with experimental results within the error limits. The prediction method is recommended for expert systems in structure research and for detection of internal protein flexibility or marker mobility by nmr and electron paramagnetic resonance ex

ISSN:0006-3525    

DOI:10.1002/bip.360310203

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

年代:1991

数据来源: WILEY

摘要:

AbstractThe temperature dependence of the apparent expansibility of lysozyme and ovalbumin in Solution has been measured as a function of pH. This temperature dependence is explained in terms of suppressed fluctuations in bound water due to the protein. It is shown that the thermal expansion coefficient of bound water is different from bulk water. The pH dependence can be explained by increased hydration of side chains at lower pH. The amount in volume of hydration water in a typical protein–water system varies from 0.16 to 0.7. How the intrinsic thermal expansion coefficient of proteins can be derived from the apparent quantity is discussed. Intrinsic values of the thermal expansion coefficient for lysozyme at room temperature are between 1.7 and 4.4 × 10−4K−1for a 10% so

ISSN:0006-3525    

DOI:10.1002/bip.360310204

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

年代:1991

数据来源: WILEY

摘要:

AbstractResults of free electrophoresis and free sedimentation of charged rods are introduced to allow for electrical double‐layer effects in the gel electrophoresis of DNA, modeled as a Random flight sequence of rodlike Kuhn chain elements. The kinetics of DNA is shown to depend strongly on the orientation of the chain elements with respect to the external field and with respect to the direction of their velocity. The new theory gives approximate agreement between the DNA charge derived from electrophoresis of free and tethered DNA (close to 1.0e per DNA phosphate in both cases), compared with the earlier discrepancy of a factor 10 or 20 for the theory without shielding by salt. As part of a realistic force field for macromolecular dynamics simulation, the small ion effects are included in an expression for the gel forces restraining the DNA in gel electrophoresis from moving as in free electrophoresi

ISSN:0006-3525    

DOI:10.1002/bip.360310205

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

年代:1991

数据来源: WILEY

摘要:

AbstractA high directional Monte Carlo procedure that predicts the topology of the energy hyper‐surface before it walks, is developed as a method to obtain a global energy minimum structure of polypeptides and proteins. It calculates its covariance matrix, which controls the individual trial step distribution of the next set of steps, from the second moment of the actual walk segment in the previous set. The method is successfully applied to the pentapeptide Metenkephalin system. And it is shown that some initial heating process, which provides the more flexible molecule, is necessary in order to overcome the energy barriers that can be overestimated by some biases in the empirical description of the system. The sampling efficiency, traced by an average conformational changes, is found to be at least 20 times greater than the one in the conventional Metropolis Monte Carlo methods, and it is expected that this increases in efficiency will be more prominent when the system is large

ISSN:0006-3525    

DOI:10.1002/bip.360310206

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

年代:1991

数据来源: WILEY

摘要:

AbstractThe tripeptideL‐alanyl‐L‐alanyl‐L‐alanine has been crystallized from a water/dimethyl‐formamide solution in an unhydrated form, with cell dimensionsa= 11.849,b= 10.004,c= 9.862 Å, β = 101.30°, monoclinic space group P21, with 4 molecules per cell (2 independent molecules in the asymmetric unit). The Structure was determined by direct methods and refined to a discrepancy indexR= 0.057. The tri‐L‐alanine molecules are packed in a parallel pleated sheet arrangement with unusually long amide nitrogen‐carbonyl oxygen contacts within sheets. Comparisons are made with the antiparallel pleated sheet structure of tri‐L‐alanine hemihydrate, previously crystallized from

ISSN:0006-3525    

DOI:10.1002/bip.360310207

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

年代:1991

数据来源: WILEY

摘要:

AbstractWe have found that tri‐L‐alanine (Ala3) can crystallize in a parallel‐chain β structure in addition to the previously known antiparallel‐chain β structure. Although the chain conformations in each structure are essentially similar, their and Raman spectra are distinctively different. We have calculated the normal modes of each structure, and can account in significant detail for these differences. This demonstrates the essential validity of our empirically refined force fields, as well as showing that deeper insights into polypeptide and protein structure can be achieved through the rigorous analyses of normal mode cal

ISSN:0006-3525    

DOI:10.1002/bip.360310208

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

年代:1991

数据来源: WILEY

摘要:

AbstractThe effect of G · T mispair incorporation into a double‐helical environment was examined by molecular dynamics simulation. The 60‐ps simulations performed on the two hexanucleotide duplexes d (G3C3)2and d (G3TC2)2included 10 Na+counterions and first hydration shell waters. The resulting backbone torsional angle trajectories were analyzed to select time spans representative of conformational domains. The average backbone angles and helical parameters of the last time span for both duplexes are reported. During the simulation the hexamers retained B‐type DNA structures that differed from typical A‐ or B‐DNA forms. The overall helical structures for the two duplexes are vary similar. The presence of G · T mispairs did not alter the overall helical structure of the oligonucleotide duplex. Large propeller twist and buckle angles were obtained for both duplexes. The purine/pyrimidine crossover step showed a large decrease in propeller twist in the normal duplex but not in the mismatch duplex. Upon the formation of wobble mispairs in the mismatched duplex, the guanines moved into the minor groove and the thymines moved into the major groove. This helped prevent purine/purine clash and created a deformation in the relative orientation of the glycosidic bonds. It also exposed the free O4 of the thymines in the major groove and N2 of the guanines in the minor groove to interactions with solvent and counterions. These factors seemed to contribute to the apparently higher rigidity of the mismatched duplex during the

ISSN:0006-3525    

DOI:10.1002/bip.360310209

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

年代:1991

数据来源: WILEY

摘要:

AbstractSalmon calcitonin, a 32‐residue peptide with a 1–7 disulfide bridge, was synthesized by standard solid‐phase techniques, and studied by CD and two‐dimensional NMR experiments. The peptide was dissolved in pure trifluoroethanol (TFE) and in aqueous solutions containing various amounts of TFE. CD studies in pure TFE indicated the presence of an α‐helical structure comprising 40% of the constituent amino acids. This was fully confirmed by nmr. A detailed analysis was performed with the peptide in a 9 : 1 deuterated TFE/H2O mixture. A total of 365 nuclear Overhauser enhancements (154 intraresidual, 112 sequential and 99 long range) were compiled from the nuclear Overhauser enhancement spectroscopy spectra and used in the distance geometry calculations. The core of the peptide between residues 8 and 22 assumes an α‐helix like structure. The Cys 1–Cys 7 ring is well defined and in close association with the helix, while the C‐terminal decapeptide folds back toward the core, for

ISSN:0006-3525    

DOI:10.1002/bip.360310210

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

年代:1991

数据来源: WILEY

摘要:

AbstractThe Raman spectra of highly concentrated solutions of 5′‐GMP at neutral and acid pH were recorded in order to better characterize the structure of the self‐aggregates formed in these solutions and their melting behavior. Vibrational coupling of the CO stretching vibrations in tetrameric units at neutral pH is shown to yield a characteristic pattern of two Raman bands atca.1730 and 1680 cm−1(1708 and 1664 cm−1in D2O), and an iractive mode at 1678 cm−1in D2O. From the intensity of the 1730‐cm−1band, proportional to tetramer concentration, and that at 1485 cm−1, which reflects the stacking of the bases, the thermal stability of the self‐associates formed at neutral pH is shown to be higher for stacked tetramers. At acid pH, the melting of the helical aggregates responsible for the formation of a gel is preceded by the freeing of the hydrogen‐bonded phosphate groups, accompanied by a change of conformation from C3′‐endoto C2′‐endoin some of the associated ribose units. Previous spectroscopic results suggesting the formation of tetramers as an intermediate step in the melting of the gel we

ISSN:0006-3525    

DOI:10.1002/bip.360310211

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

年代:1991

数据来源: WILEY