摘要:

AbstractIn the past, two important objections against McClare's idea of biological molecular energy 4 machines were raised. One of the criticisms was concerned with the origin of energy gained in ATP cleavage and with an interpretation of McClare's “excited vibrational state.” The former argument reveals a failure of the critics to comprehend McClare's approach. As to the excited vibrational state, it can be identified with nonequilibrium conformational states of the unit rather than with a single vibrational mode. The other criticism based on Brillouin's energy cost of measurement argued that reversible operation of biological molecular energy machines would be virtually impossible. Using propagation velocities of deformations of the unit's structure (instead of velocity of light), the objections against reversibility are invalidated even in the framework of the critic's approach. McClare's idea and relevant definitions are thus physically corr

ISSN:0006-3525    

DOI:10.1002/bip.360320502

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

年代:1992

数据来源: WILEY

摘要:

AbstractA qualitative picture of operation modes of biological molecular energy machines is presented. It is suggested that there is mutual control between the flow of molecular energy stored in a biological molecular energy machine and the sequence of nonequilibrium conformational states through which the machine passes in doing work. If the structure of the conformational space is favorable, the set of trajectories in this space decomposes into two families, each of which accomplishes another task. This divergence of trajectories enables to distinguish molecular objects according to differences in interaction between the machine and the object, i.e., to perform a measurement on a molecular object and process the object according to the result of that measurement.

ISSN:0006-3525    

DOI:10.1002/bip.360320503

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

年代:1992

数据来源: WILEY

摘要:

AbstractThe interhelical interfaces have been examined in seven high‐resolution globin chains. The profiles of hydrophobic contact, as measured by the residue solvent‐accessible area loss upon folding, have been calculated. The seven globins studied differ in their overall loss of solvent‐accessible area upon packing of their helices, the order being 1MBD>1LH1>1ECD>2MHBB>2HHBB>2HHBA>2MHBA, which gives a measure of the difference in stability due to the hydrophobic interaction. The five helix‐pair packings (AH, BE, BG, FH and GH) examined in detail have qualitative similarities. There are, however, substantial quantitative differences both at the equivalent residue level and at the level of overall helix–helix contact, which has significance in some models of folding. The AH pair has the most uniform area loss over the seven globins and the largest variation in accessible area loss on packing among the five helix pairs is the GH pair. The set of residues required to produce the globin fold has been deduced from the residue ar

ISSN:0006-3525    

DOI:10.1002/bip.360320504

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

年代:1992

数据来源: WILEY

摘要:

AbstractRandom copolymers of lysine and alanine, 2 : 1 and 1 : 1, were trimethylated on the lysine. amino groups to quaternary ammonium groups. Methylated and unmethylated polymers were prepared with Cl−or ClO 4−as the counterion. CD spectra were measured for increasing concentration of peptide without added salt, and at constant peptide concentration in increasing NaCl or NaClO4. Unmethylated peptides, as the chloride, form α‐helix more readily than do the methylated peptides. The opposite occurs with ClO 4−as counterion. The helix‐promoting effect of methylated lysine residues (ClO 4−counterion) is diminished by the presence of alanine, as compared with effects when lysine is the only type of residue. The effect of methylation of proteins on helix formation may depend on the types of anionic groups with which the prote

ISSN:0006-3525    

DOI:10.1002/bip.360320505

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

年代:1992

数据来源: WILEY

摘要:

AbstractA method was developed for computing the free energy (ΔFi) of aggregates of type I collagen. The method was based on a treatment of Matheson and Flory describing phase equilibria of rigid rod polymers. It included a polymer–solvent interaction term that depended on near neighbor transfer energies. Extrahelical portions of the molecule were assigned local interaction energies differing from that assigned to the helix. Free energies of reaction for successive steps along assembly pathways (ΔFi–i+1) were computed. When allowance was made for specific pairing between extrahelical and helical domains, the so‐called D‐staggered (D = 670 Å) alignment of molecules was preferred, as opposed to a nonstaggered, or nematic, alignment. Based on ΔFi–i+1alone, it appeared that 1D‐staggered oligomers arise first in assembly, followed later by addition of molecules in 4D alignment.Neither 4D dimers nor 4D‐8D trimers were predicted to be major intermediates in assembly. This result is contrary to previous hypotheses. When energies of activation were included in the analysis, the prediction was less certain, and specific circumstances were identified in which 4D dimers and 4D‐8D trimers were the earliest aggregated

ISSN:0006-3525    

DOI:10.1002/bip.360320506

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

年代:1992

数据来源: WILEY

摘要:

AbstractA procedure commonly used to transform native adult human hemoglobin (Hb) into a physiological oxygen carrier consists of a pyridoxylation of the protein to lower its oxygen affinity, followed by its polymerization in the presence of glutaraldehyde, with or without further reduction, to increase its circulating half‐life. This series of reactions yields derivatives presenting a great molecular heterogeneity that have to be fractionated for use in vivo. Hemoglobin derivatives with low oxygen affinity and a narrow distribution of molecular weights were obtained by linking a dextran polyaldehydic derivative to deoxyhemoglobin at pH 8. From oxygen‐binding measurements carried out in the presence of inositolhexaphosphate, a strong effector of hemoglobin, it appeared that the allosteric site of hemoglobin was blocked, probably by crosslinking bonds, which stabilizes its deoxy structure. On the other hand, when the reaction was performed in the presence of inositolhexaphosphate, the resulting conjugates exhibited an oxygen affinity identical to that of unmodified hemoglobin. After treatment with NaBH4, the polymer–hemoglobin derivatives were stable and possessed a reversible oxygen‐carrying capacity similar to that of blood. The conjugates prepared from oxyhemoglobin all possessed a lowerP50than native hemoglobin whatever the reaction con

ISSN:0006-3525    

DOI:10.1002/bip.360320507

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

年代:1992

数据来源: WILEY

摘要:

AbstractThe rate constant for the transition between the equatorial and axial conformations ofN‐acetylalanyl‐N′‐methylamide has been determined from Langevin dynamics (LD) simulations with no explicit solvent. The isomerization rate is maximum at collision frequency γ = 2 ps−1, shows diffusive character for γ ≥ 10 ps−1, but does not approach zero even at γ = 0.01 ps−1. This behavior differs from that found for a one‐dimensional bistable potential and indicates that both collisional energy transfer with solvent and vibrational energy transfer between internal modes are important in the dynamics of barrier crossing for this system. It is suggested that conformational searches of peptides be carried out using LD with a collision frequency that maximizes the isomerization rate (i.e., γ ≈ 2 ps−1). This method is expected to be more efficient than either molecular dynamicsin vacuo(which corresponds to LD with γ = 0) or molecular dynamics in solvent (where dyna

ISSN:0006-3525    

DOI:10.1002/bip.360320508

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

年代:1992

数据来源: WILEY

摘要:

AbstractThe partial molar volumes of some amino acid side‐chains were determined in two recent studies [Makhatadzes, G. I., et al. (1990)Biopolymers30, 1001, and Reading, J. F.&Hedwig, G. R. (1990)J. Chem. Soc. Faraday Trans.86, 3117] using partial molar volume data,V 20, in aqueous solution at 25°C for some peptides of sequence Gly‐X‐Gly, whereXis an amino acid. These side‐chain partial molar volumes are critically compared with those obtained usingV 20data for amino acids. It is concluded that side‐chain partial molar volumes calculated usingV 20data for the tripeptides are better estimates of side‐chain partial molar volumes in proteins than are those determined usingV 20

ISSN:0006-3525    

DOI:10.1002/bip.360320509

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

年代:1992

数据来源: WILEY

摘要:

AbstractA previously developed theory for the delocalized binding of ions to polyelectrolytes was restricted to point ions and a structurally rigid polyelectrolyte. For the binding of substances like oligolysines and polyamines to DNA, the restriction to point ions would appear not to be realistic. For the binding of ions to flexible chains like single‐stranded polynucleotides, the restriction to a rigid polyelectrolyte may not be realistic. In this article, we assess the effect of relaxation of these two restrictions. Excluded volume among bound ions is modeled by a hard‐rod potential in the context of the theory of a one‐dimensional fluid. The possibility that a flexible chain folds in some manner in the immediate vicinity of a bound ion is modeled by allowing the mean spacing between charged groups on the polymer to become smaller as the number of bound ions increases. We compare our results with recent data on the binding of a series of oligolysines to single‐stranded polynucleotides, which conflict with the predictions of the original theory of delocalized binding of point ions to rigid polyelectrolytes. Inclusion of excluded volume among bound ions does not significantly improve agreement with the data. Substantial improvement in the level of agreement is obtained when the polyion chain is assumed to be flexible. One of our conclusions is that the excluded‐site description of anticooperativity, which was designed for the binding of ligands to discrete sites on a polymer chain, and which does not include the effect of ionic forces, should not be used in cases of delocalized bindin

ISSN:0006-3525    

DOI:10.1002/bip.360320510

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

年代:1992

数据来源: WILEY

摘要:

AbstractA computer program SAINT has been developed for the investigation of the structure and for the prediction of minimum‐energy structure of polysaccharide–polysaccharide complexes. The energy minimization is carried out on internal geometrical parameters—namely bond angles, torsional angles, and five parameters describing the mutual orientations of polysaccharide chains. For this purpose, the nonderivative method of conjugated directions is used. This procedure was applied to computer modeling of an idealized model of the binary gelling κ‐carrageenan and galactomannan system. It is shown that the interaction between two chains influences the structure of the individual polysaccharide molecule and that in the minimum‐energy structures of the complex, the conformation of the chains does not correspond to the low

ISSN:0006-3525    

DOI:10.1002/bip.360320511

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

年代:1992

数据来源: WILEY