摘要:

AbstractMonte Carlo computer simulations were performed to elucidate the dynamic aspects of the folding and unfolding transitions of island‐model protein. Five different types of model proteins were designed, according to characteristics of backbone structure. The computer simulations clearly show that the unfolding and folding transitions are all‐or‐none processes between the N‐and U‐states. They are typical Poisson processes. From the Arrhenius plots of rate constants, the activation enthalpies of folding and unfolding were determined. In addition, the folding pathways were determined along the reaction coordinate. Formations of several local structures along a polypeptide chain are almost simultaneous, but the most probable time sequence of events exists at the moment of transition. That is the most probable folding pathway. The unfolding pathway was found to be just the reverse process of the most probable folding pathway. The relationship between the fluctuations in each equilibrium state and the transition process was considered. In contrast to the theory of absolute reaction rate, the transient states are widely distributed along the reaction coordinate. From analysis of the “transient process,” we tried to determine the critical states from which the transient process starts. As a result, we found that the unfolding transition occurs at the stage near the N‐state. During the U‐state, large joined blocks rarely appear, but they appear in the transient process towards the N‐state. However, the “branch point” between the N‐ and U‐states lies near the N‐state, and joined blocks tend to unfold prior to passing over the branch point. We concluded that the stability of later folding intermediates is important for selection of the folding pathway, while preferential selection of an early folding intermediate is important in acceleration of the folding rate. The effects of intrachain cross‐linking and peptide fragment binding on the rate constants were examined by using computer simulations of model proteins. In general, a small‐sized loop formed by cross‐linking accelerates the folding rate and a large‐sized loop contributes much to the stabilization of the native conformation. We also found that peptide fragment binding contributes little to the acceleration of the

ISSN:0006-3525    

DOI:10.1002/bip.360251002

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

年代:1986

数据来源: WILEY

摘要:

AbstractInteractions of meso‐tetra(4‐N‐methylpyridyl)porphyrin [TMpyP(4)], meso‐tetra(2‐N‐methylpyridyl)porphyrin [TMpyP(2)], and meso‐tetra(para‐N‐trimethylanilinium)porphyrin (TMAP) with several native and synthetic DNAs were studied by a variety of physical techniques: nmr (31P and1H), absorption spectroscopy, viscosity, and flow dichroism (FD). Of the three porphyrins studied, only the interaction of TMpyP(4) with poly [d(G‐C)2] was fully consistent with intercalation. In particular, a large increase in viscosity, a downfield31P‐nmr signal (ca. ‐1 ppm), and upfield imino proton signals (11 to 12 ppm range) were observed. Comparison of the effects of TMpyP(4) on DNAs of different GC contents revealed larger changes in solution viscosity with increased GC content. However, the characteristic changes in31P‐ and1H‐nmr spectra were not observed. The viscosity increases observed in studies with poly[d(A‐C)(G‐T)] andC. Perf.DNA were much lower than with poly[d(G‐C)2],M. Lys.DNA, and calf thymus DNA. Thus, GC sequence and content are clearly important. The principal change in the31P‐nmr signal of native DNA is the appearance of a very broad shoulder centered at ca. ‐2.0 ppm, which is larger inM. Lys.DNA than inC. Perf.DNA. FD studies indicate highly ordered TMpyP(4) cations arranged perpendicular to the DNA axis of calf thymus DNA. Together, these results suggest the major effects of TMpyP(4) on DNA properties are due to strong GC‐binding interactions that influence DNA structure. The data are consistent with combined intercalative and outside binding interactions of TMpyP(4) with GC regions of DNA. In contrast, similar studies with TMAP suggest that it influences AT regions of DNA by an outside binding mode. On the other hand, TMpyP(2) effects on DNA properties are consi

ISSN:0006-3525    

DOI:10.1002/bip.360251003

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

年代:1986

数据来源: WILEY

摘要:

AbstractThe overall dynamics of the Pf1 filamentous bacteriophage particle in solution are characterized by nmr experiments. The chemical‐shift anisotropy powder‐pattern lineshapes from both DNA and protein backbone sites of the virus are motionally averaged in the same way, indicating that the entire particle undergoes rapid (<104Hz) reorientation about the long axis of the filament when the virus is in solution at high pH. In contrast, the virus particles in samples at low pH are immobile on this time sc

ISSN:0006-3525    

DOI:10.1002/bip.360251004

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

年代:1986

数据来源: WILEY

摘要:

AbstractPositron annihilation measurements are reported for hydrated DNA as a function of water content and as a function of temperature (20 to −180°C) for samples containing 10 and 50% wt of water. Theortho‐positronium mean lifetime and its intensity show distinct variations with the degree of hydration and with temperature for the 50% sample. The 10% water sample was relatively insensitive to temperature variation. The results indicate that hydrated DNA containing up to 10% water behaves as a rigid crystalline solid but that the rigidity markedly decreases with a further increase in water content until, for approximately 50% water, its properties resemble more those of a highly viscous f

ISSN:0006-3525    

DOI:10.1002/bip.360251005

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

年代:1986

数据来源: WILEY

摘要:

AbstractThe heat denaturation of pepsinized bovine nonfibrillar and fibrillar collagen was studied by differential scanning calorimetry. For fibrillar preparations that had been rapidly precipitated with stirring at low ionic strength, then resuspended at physiological ionic strength, multiple denaturational transitions were observed. At heating rates of 10°C/min, melting endotherms occurred at about 44, 50, 53, and 57°C. Fibrillar collagen that was slowly gelled without stirring at physiological ionic strength exhibited a similar series of endotherms, but the lower melting transitions were less conspicuous. In contrast, nonfibrillar bovine collagen in acidic solution showed only a single denaturational transition at 40°C. Nonfibrillar solutions at pH 7, to which inhibitors of fibrillogenesis were added, showed a major endotherm as high as 46°C. These results suggest that reconstituted fibrillar collagen contains a heterogeneous fibril population, possibly including molecules in a nonfibrillar state. It was proposed that the multiple melting endotherms of such preparations were due to sequential melting of molecular and fibril classes, each with a distinct melting temperature. The fibrillar classes may represent three or more types of banded and nonbanded species that differ from each other in packing order, collagen concentration, and possibly also in fibril width and level of cross‐li

ISSN:0006-3525    

DOI:10.1002/bip.360251006

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

年代:1986

数据来源: WILEY

摘要:

AbstractThe peptide hormone, somatostatin, has been studied by nmr at 500 MHz in a methanol solution and at low temperature (263 K) in order to investigate a possible similarity with conformationally restricted biologically active analogs. The more pronounced predominancy of one conformer already present in a water solution is demonstrated. No evidence has been shown for interactions between Phe11and other Phes in the molecule.

ISSN:0006-3525    

DOI:10.1002/bip.360251007

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

年代:1986

数据来源: WILEY

摘要:

AbstractThe structure and internal motions of the protein hen egg white lysozyme are studied by analysis of simulation and experimental data. A molecular dynamics simulation and an energy minimization of the protein in vacuum have been made and the results compared with high‐resolution structures and temperature factors of hen egg white lysozyme in two different crystal forms and of the homologous protein human lysozyme. The structures obtained from molecular dynamics and energy minimization have root‐mean‐square deviations for backbone atoms of 2.3 Å and 1.1–1.3 Å, respectively, relative to the crystal structures; the different crystal structures have root‐mean‐square deviations of 0.73–0.81 Å for the backbone atoms. In comparing the backbone dihedral angles, the difference between the dynamics and the crystal structure on which it is based is the same as that between any two crystal structures. The internal fluctuations of atomic positions calculated from the molecular dynamics trajectory agree well with the temperature factors from the three structures. Simulation and crystal results both show that there are large motions for residues involved in exposed turns of the backbone chain, relatively smaller motions for residues involved in the middle of helices or β‐sheet structures, and relatively small motions of residues near disulfide bridges. Also, both the simulation and crystal data show that side‐chain atoms have larger fluctuations than main‐chain atoms. Moreover, the regions that have large deviations among the x‐ray crystal structures, which indicates flexibility, are found to have large fluct

ISSN:0006-3525    

DOI:10.1002/bip.360251008

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

年代:1986

数据来源: WILEY

摘要:

AbstractThe Ile1analog of the polypentapeptide of elastin, (L · Ile1‐L · Pro2‐Gly3‐L · Val4‐Gly5)n, abbreviated as Ile1‐PPP, was synthesized withn>100 to determine the effect of the increased hydrophobicity of the pentamer resulting from Val1replacement by Ile1on the previously characterized inverse temperature transition of the polypentapeptide of elastin (PPP). Ile1‐PPP, dissolved in water at 4°C, was found to aggregate, forming a viscoelastic coacervate on raising the temperature. The onset of aggregation was 8°C for Ile1‐PPP, as compared to 24°C for PPP. Characterization by CD demonstrated an increase in intramolecular order on raising the temperature from 8°C to 25°C, and demonstrated similar conformations for PPP and Ile1‐PPP before and after their respective transitions. The CD‐characterized transition also occurred at a temperature some 15°C lower than that of PPP. By means of 20‐Mrad γ‐irradiation cross‐linking of the Ile1‐PPP coacervate, an elastomeric matrix was formed with an elastic modulus, similar to that of 20‐Mrad cross‐linked PPP. The temperature dependence of elastomeric force of cross‐linked Ile1‐PPP showed an abrupt increase from essentially zero at 8°C to three‐quarters of full force at 10°C and essentially full force by 20–25°C. This development of elastomeric force for the more hydrophobic Ile1‐PPP matrix, which parallels the increase in intramolecular order characterized by the CD studies, also occurs at a temperature some 15°C lower than that for the PPP matrix. Thus, in these elastomeric polypeptides, development of elastomeric force is coupled to an inverse temperature transition, the temperature of which depends inversely on the hydrophobicity of the constituent pentamer. It appears that a series of elastomeric polypeptide biomaterials are possible in which the temperatur

ISSN:0006-3525    

DOI:10.1002/bip.360251009

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

年代:1986

数据来源: WILEY

摘要:

AbstractHydrolysis of (1 → 6)‐α‐DL‐glucopyranan (syntheticDL‐dextran) by anendo‐dextranase from aPenicilliumspecies was examined in an acetate buffer solution (pH 5.3) at 37°C. Three samples of different tacticities (isotactic dyad content, 55, 63, and 72%) were employed with a clinical dextran for comparison. Colorimetric determination of the reducing end units of the saccharides produced during hydrolysis showed that the maximum degrees of hydrolysis based on the D‐glucose units, (D.H.)D, for theDL‐dextrans were 21.4, 27.8, and 33.0% in the order of increasing isotacitic dyad content, whereas the (D.H.)Dvalue for the clinical dextran was 51.9%. A statistical treatment of the enzymatic hydrolysis is proposed to interpret the exp

ISSN:0006-3525    

DOI:10.1002/bip.360251010

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

年代:1986

数据来源: WILEY

摘要:

AbstractSorption isotherms of water vapor by solid biopolymers are necessary for the determination of thermodynamic quantities for water–biopolymer interactions. Such isotherms are generally irreversible, so equilibrium thermodynamics may not be applicable. General relationships are derived for thermodynamic quantities of sorption when the sorbent is a single uniform phase. In general, use of the Clausius–Clapeyron equation allows correct determination of differential entropies of sorption. However, calorimetric data are also necessary for the correct determination of other thermodynamic quantities. The single uniform phase model appears more useful than a domain model in explaining the hysteresis seen in water–biopolymer sorption isot

ISSN:0006-3525    

DOI:10.1002/bip.360251011

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

年代:1986

数据来源: WILEY