摘要:

AbstractStatistical mechanical calculations for one‐dimensional interacting units have undergone great development in many fields of macromolecular science. The partition function is the most rigorous description of an ensemble of molecules in equilibrium. Specific methodological formulations and algorithms were developed to handle numerically the inclusion of long‐range effects (as compared to usual nearest neighbor Ising models) and known sequence‐dependent heterogeneities of biological macromolecules. The most successful approach in formulating these problems in a very general and tractable framework was the so‐called matrix method. Despite several improvements, it was claimed that in practical applications this approach had fundamental limitations inherent to any “matrix” formulation. We show here that a new conceptual formulation allows us to overcome these limitations completely. We propose a general iterative procedure that combines the theoretical advantages of the matrix method with the possibility of highly optimized and efficient numerical

ISSN:0006-3525    

DOI:10.1002/bip.360300502

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

年代:1990

数据来源: WILEY

摘要:

AbstractIt is possible to construct fragments of protein structures by using the known values for the fixed bond lengths, bond angles, and torsion angles, and “dialing” in the dihedral angles ϕ and ψ. By choosing these angles in different ways, it is possible to create different populations of fragments and to investigate their properties. We analyzed the following populations:Real fragmentstaken randomly from known structures.Reconstructed fragments, which are constructed, using the “fixed geometry” assumption, from a set of consecutive pairs of dihedral angles drawn from known structures.Random fragmentsthat are constructed from a random set of dihedral angles from known structures, anddoublet‐preserving fragments, which are constructed from a set of dihedral angles drawn at random from known structures in a way such that the distribution of two consecutive pairs of dihedral angles in this population is similar to that distribution in the known structures. We examine the fixed geometry assumption and demonstrate that even reconstructed fragments contain many atomic collisions. We show that random fragments have only slightly more interatomic collisions than the reconstructed fragments. Nevertheless, the population of random fragments is structurally different from the population of reconstructed fragments. On the other hand, we show that the doublet‐preserving fragments exhibit properties that are similar to the real population. Thus the doublet preserving random population can be used to simulate the structure of short

ISSN:0006-3525    

DOI:10.1002/bip.360300503

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

年代:1990

数据来源: WILEY

摘要:

AbstractThe solid state conformational analysis of the ionophoric homodetic bicyclic cyclo(Glu‐Leu‐Pro‐Gly‐Lys‐Leu‐Pro‐Gly)cyclo(1γ‐5ϵ)Gly (BCP3) has been carried out by x‐ray diffraction. It crystallizes with 4.5 molecules of water per peptide molecule in the monoclinic system, space group P21, witha= 11.425 Å,b= 16.616 Å,c= 13.931 Å, β = 109.24°, andZ= 2. The structure has been determined by direct methods and refined to anRfactor of 0.061 for 2448 observed reflections. The structure characterized by alltranspeptide bonds is stabilized by three intramolecular hydrogen bonds: a type II β‐turn, a mixed type I‐type III β‐turn, and a pseudo γ‐turn, which involves the side chain CO and the main‐chain NH groups of the Glu1residue. The resulting globular molecule presents a rather hydrophilic surface with most of the CO groups available to hydration of the solvent molecules, which are linked through hydrogen bonds of the NH … O or OH … O types in a complicated H‐bonding scheme. The conformation observed in the solid state is rather different from the conformation proposed in solution f

ISSN:0006-3525    

DOI:10.1002/bip.360300504

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

年代:1990

数据来源: WILEY

摘要:

AbstractThe formation of triple‐stranded nucleic acid helices is studied by molecular mechanics and molecular dynamics calculations. Using standard TAT and CGG homopolymers, single, triple, and quintuple molecular replacements are made. Some of these replacements are expected to form Hoogsteen bonds and some are not. While the electrostatic and total energetic differences for base triplet mismatches were dependent on the electrostatic model chosen, clear trends in the local geometric distortions were apparent. Relationships between these model‐built strand geometries and chemical probe experiments are discus

ISSN:0006-3525    

DOI:10.1002/bip.360300505

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

年代:1990

数据来源: WILEY

摘要:

AbstractEnergy calculations have been performed on right‐handed helical structures ofL‐alanine and α‐methylalanine oligomers. A new ′3.610′‐helix is described for α‐methylalanine peptides. The dependence of the relative stability of the α, 310, and 3.610structural forms on helix length, dielectric, and force‐field, in the gas phase, has been studied. Potential energy surfaces for the interconversion of helices have been generated. The 310‐helix in α‐methylalanine oligomers exhibits a degree of enthalpic and entropic stabilization not observed for alanine. The relevance of the results to the formation of voltage‐sensitive

ISSN:0006-3525    

DOI:10.1002/bip.360300506

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

年代:1990

数据来源: WILEY

摘要:

AbstractA simple bead model is proposed for the antibody molecule immunoglobulin IgG1. The partial flexibility of the hinge is represented by a quadratic potential associated to the angles between arms. Conformational and hydrodynamic properties are calculated using Monte Carlo (rigid‐body) and Brownian dynamics simulations. Comparison of experimental and calculated values for some overall properties allows the assignment of dimensions and other model parameters. The Brownian dynamics technique is used next to simulate a rotational correlation function that is comparable with the decay of fluorescence emission anisotropy. This is done with varying flexibility at the hinge. The longest relaxation time shows a threefold decrease when going from the rigid Y‐shaped conformation to the completely flexible case. The calculations are in good agreement with the decay times observed for IgG1. A flexibility analysis of the latter indicates that a variability of ±55° (standard deviation) in the angle between the Fab

ISSN:0006-3525    

DOI:10.1002/bip.360300507

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

年代:1990

数据来源: WILEY

摘要:

AbstractA previous model for acoustic mode vibrations of a DNA molecule in water is extended to the case of an array of many DNA molecules, as occurs in the fibers studied in most experimental work on DNA. The acoustic modes of this system are found to consist of coupled modes of water sound vibrations and DNA acoustic modes. This model is used to study the electrostatic coupling of acoustic vibrations to the relaxational modes of the orientational degrees of freedom of the water molecules. It is found that the long‐range or macroscopic electric field generated by the acoustic mode vibrations of the water‐DNA system gives too small a damping and frequency shift of the acoustic modes to account for the observations on DNA fibers. Therefore, the observed damping and frequency shifts are most likely due to either friction between the surrounding water and the vibrating DNA, or coupling to the water orientation degrees of freedom resulting from the short range (i.e., screened) Coulomb interaction. The latter explanation (which is most likely the correct one) implies that the relaxation time of the hydration shell water is longer than the observed relaxation time by a factor of the static dielectric constant of the hydration wa

ISSN:0006-3525    

DOI:10.1002/bip.360300508

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

年代:1990

数据来源: WILEY

摘要:

AbstractMonte Carlo simulations [(N, V, T)‐ensemble] were performed for the hydration shell of poly(dA‐dT)·poly(dA‐dT) in canonical B form and for the hydration shell of poly(dA) ·poly(dT) in canonical B conformation and in a conformation with narrow minor groove, highly inclined bases, but with a nearly zero‐inclined base pair plane (B′ conformation). We introduced helical periodic boundary conditions with a rather small unit cell and a limited number of water molecules to reduce the dimensionality of the configuration space. The coordinates of local maxima of water density and the properties of one‐ and two‐membered water bridges between polar groups of the DNA were obtained.The AT‐alternating duplex hydration mirrors the dyad symmetry of polar group distribution. At the dApdT step, a water bridge between the two carbonyl oxygens O2 of thymines is formed as in the central base‐pair step of Dickerson's dodecamer. In the major groove, 5‐membered water chains along the tetranucleotide pattern d (TATA) · d (TATA) are observed.The hydration geometry of poly (dA) · poly(dT) in canonical B conformation is distinguished by autonomous primary hydration of the base‐pair edges in both grooves. When this polymer adopts a conformation with highly inclined bases and narrow minor groove, the water density distribution in the minor groove is in excellent agreement with Dickerson's spine model. One local maximum per base pair of the first layer is located near the dyad axis between adjacent base pairs, and one local maximum per base pair in the second shell lies near the dyad axis of the base pair itself. The water bridge between the two strands formed within the first layer was observed with high probability. But the water molecules of the second layer do not have a statistically favored orientation necessary for bridging first layer waters. In the major groove, the hydration geometry of the (A · T) base‐pair edge resembles the main features of the AT‐pair hydration derived from other sequences for the canonical B form. The preference of the B′ conformation for oligo(dA) · oligo(dT) tracts may express the tendency to common hydration of base‐pair edges of successive base pairs in the grooves of B‐type DNA.The mean potential energy of hydration of canonical B‐DNA was estimated to be −60 to −80 kJ/mole nucleotides in dependence on the (G · C) contents. Because of the small

ISSN:0006-3525    

DOI:10.1002/bip.360300509

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

年代:1990

数据来源: WILEY

摘要:

AbstractCyclopeptides I and II containing anortho‐ ormeta‐aminobenzoic acid residue are comparatively analysed by1H‐ and13C‐nmr. The1H‐nmr results, i.e., the temperature coefficients ΔδNH/ΔT, the exchange rates of the amide protons, and nuclear Overhauser effects, suggest a predominant conformation for cyclopeptides I. Themetaanalogues II present a greater conformational mobility. This observation is related to the greater reactivity of peptides II toward enzymatic hydrolysis, compared to theirorth

ISSN:0006-3525    

DOI:10.1002/bip.360300510

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

年代:1990

数据来源: WILEY

摘要:

AbstractRaman spectra of series of aqueous solutions of peptides containing two amino acids, glycine‐X, alanine‐X, and serine‐X, where X is an uncharged amino acid, show that the amide III band shifts systematically to lower frequencies as the side chain of the X amino acid becomes larger. The range of this shift is about 20cm−1, starting at 1275cm−1for alanine‐glycine and moving to 1251 cm−1for alanine‐tryptophan, with a correlation coefficient of 0.93 with the mass of the X amino acid side chain for 10 peptides. The amide I frequencies remain constant as the X amino acid is changed. This shift may result from a change in the average conformational preference of the peptide, a change in vibrational coupling of the amide III modes with the X amino acid side chain, a change in molecular force constants, or a combination of these. These results present a test for comput

ISSN:0006-3525    

DOI:10.1002/bip.360300511

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

年代:1990

数据来源: WILEY