A recent study of crystal structures of protein-ligand complexes has shown that bioactive conformations tend to be more extended than random ones (Diller and Merz, J. Comput. Aid. Mol. Des. 2002, 16, 105-112). Existing conformational sampling techniques produce molecular conformations with a distribution of geometric sizes that may not cover that of the bioactive conformations. Here, we describe a simple heuristic for biasing the conformational search toward more extended or compact conformations, while maintaining excellent sampling. The method uses a boosting strategy to generate a series of conformations, each of which is at least as extended (or compact) as the previous one. We demonstrate that this method significantly expands the range of geometric sizes generated during the search and thus increases the efficiency of sampling bioactive conformations. 相似文献
A new model for concentration dependence of polymer chain dimensions over the wholeconcentration range was proposed. The hydrodynamic volume of a solvated macromoleculewas found to be a universal function of the degree of coil overlapping (c/c~*). The radiusof gyration (R_g) and the expansion coefficient (α) of polymer in solution or in bulk. pre-dicted by this model are much better in agreement with the experimental data of small angleX-ray scattering and neutron scattering from literature, than with the values predicted byother models and theories. 相似文献
Abstract The determination of the radius of gyration and intrinsic viscosity as function of molecular weight for xanthan polysaccharide allows for a better understanding of the conformation of this polymer in solution. The native ordered conformation of xanthan, which corresponds to that obtained during its biosynthesis appears to be a single chain characterized by a persistence length of approximately 400 Å. In contrast, the renatured ordered conformation restored after the first denaturation of the native conformation exhibits behavior suggesting doublestranded conformation as described previously in the literature. In fact, this conformation seems to correspond to a folded xanthan chain. 相似文献
Summary: The conformational behavior of a polymer in a critical binary solvent confined in a porous medium is studied. The size of the polymer in bulk, which is mainly governed by the correlation length of the solvent density fluctuations, depends on the proximity to the critical point of the binary mixture. We find that in contrast to the bulk behavior, the conformational properties of the polymer in a porous medium depends strongly on the pore size. The latter controls the correlation length of the solvent density fluctuations and thus determines the polymer size. 相似文献
Small angle neutron scattering measurements have been carried out on the tetramethylammonium salt of the polystyrenesulfonic acid withDPw=310 and 1060 in water solution with tetramethylammonium chloride with ionic strength between 0.02 M and 1.0 M. The scattering curves in the scattering vector range 0.05 nm–1Q1.8nm–1 have been fitted using the form factor of a worm-like chain of finite thickness. The conformational parameters mean square radius of gyration, statistic chain element, mass per unit length and mean square radius of the cross-section have been determined experimentally and used for describing the conformation of the coils. By these molecular weights and ionic strengths, excluded volume is not necessary to explain the conformation changes depending on the salt content of the solutions; relatively short coil molecules can be described in their unperturbed dimensions even in a thermodynamically good solvent: a change in the stiffness of the chain according to Odijk's theory succeeds in describing the conformation of the polyions. Together with a slow decrease of the coil dimension by increasing salt content, a transition at ionic strength 0.1–0.5 M between two different conformations has been observed. The conformation at lower ionic strength is characterized by higher stiffness of the chain and lower mass per unit length than the form at higher salt concentration. 相似文献
A general kinetic approach allowing the prediction of the molecular architecture of non-linear polymers is applied to the study of the copolymerization of methyl methacrylate (MMA) with ethylene glycol dimethacrylate (EGDMA). Dynamic predictions of molecular weight distributions, sequence length distributions and mean square radius of gyration are possible before and after gelation. A set of experiments concerning the copolymerization of MMA and EGDMA was carried out in toluene solution at 60 °C for which classic radical kinetics is a good approximation. The time evolution of key polymer properties was followed using a SEC system with a refractive index detector coupled with MALLS allowing the determination of absolute weight average molecular weight and apparent molecular size distributions as well as z-average radius of gyration. Special focus was given to assess the influence of the initial amount of cross-linker on the dynamics of the non-linear structure build-up of these products. A kinetic scheme comprising 23 different chemical species and 76 chemical reactions was used in the modeling studies of this chemical system. Most of the kinetic parameters used in the simulations have been collected from previous studies. For experiments at low monomer conversion (up to about 0.5) a good agreement between predictions and experimental measurements is observed for molecular weights and z-average radius of gyration by fitting a small number of parameters describing gel effect (with a conversion dependent but chain length independent termination rate parameter) and the relative propagation on pendant double bonds. However, predicted values of weight-average molecular weights and z-average radius of gyration before gelation are too low at higher monomer conversions with non-linear systems. The likely cause is the presence of intramolecular reactions which should not be neglected in these circumstances. 相似文献
Conformational Memories (CM) is a simulated annealing/Monte Carlo method that explores peptide and protein dihedral conformational space completely and efficiently, independent of the original conformation. Here we extend the CM method to include the variation of a randomly chosen bond angle, in addition to the standard variation of two or three randomly chosen dihedral angles, in each Monte Carlo trial of the CM exploratory and biased phases. We test the hypothesis that the inclusion of variable bond angles in CM leads to an improved sampling of conformational space. We compare the results with variable bond angles to CM with no bond angle variation for the following systems: (1) the pentapeptide Met-enkephalin, which is a standard test case for conformational search methods; (2) the proline ring pucker in a 17mer model peptide, (Ala)(8)Pro(Ala)(8); and (3) the conformations of the Ser 7.39 chi(1) in transmembrane helix 7 (TMH7) of the cannabinoid CB1 receptor, a 25-residue system. In each case, analysis of the CM results shows that the inclusion of variable bond angles results in sampling of regions of conformational space that are inaccessible to CM calculations with only variable dihedral angles, and/or a shift in conformational populations from those calculated when variable bond angles are not included. The incorporation of variable bond angles leads to an improved sampling of conformational space without loss of efficiency. Our examples show that this improved sampling leads to better exploration of biologically relevant conformations that have been experimentally validated. 相似文献
Three-dimensional molecular structure is fundamental in chemical function identification and computer-aided drug design. The enumeration of a small number of feasible conformations provides a rigorous way to determine the optimal or a few acceptable conformations. Our contribution concerns a heuristic enhancement of a method based on distance geometry, typically in relation with experiments of the NMR type. Distance geometry has been approached by different viewpoints; ours is expected to help in several subtasks arising in the process that determines 3D structure from distance information. More precisely, the input to our algorithm consists of a set of approximate distances of varying precision; some are specified by the covalent structure and others by Nuclear Magnetic Resonance (NMR) experiments (or X-ray crystallography which, however, requires crystallization). The output is a valid tertiary structure in a specified neighborhood of the input. Our approach should help in detecting outliers of the NMR experiments, and handles inputs with partial information. Moreover, our technique is able to bound the number of degrees of freedom of the conformation manifold. We have used numerical linear algebra algorithms for reasons of speed, and because they are well-implemented, fully documented and widely available. Our main tools include, besides distance matrices, structure-preserving matrix perturbations for minimizing singular values. Our MATLAB (or SCILAB) implementation is described and illustrated.AMS subject Classification: 92E10 Molecular structure, 92C40 Biochemistry, molecular biology, 65F15 Eigenvalues, eigenvectors, 15A18 Eigenvalues, singular values, and eigenvectors 相似文献
Summary: This work reports experimental and modeling studies concerning the conventional (FRP) and atom transfer radical polymerization (ATRP) of acrylate/diacrylate monomers. In the framework of a recently developed general approach, kinetic models including crosslinking reactions and branching by chain transfer to polymer are discussed for FRP and ATRP polymerization systems. Besides molecular weight distribution (MWD), fairly good predictions of the z-average radius of gyration could be obtained for these non-linear polymers. A set of experiments was performed at 1 L scale in a batch reactor using n-butyl acrylate (BA) or methyl acrylate (MA) as monovinyl monomers and 1,6-Hexanediol diacrylate (HDDA) or bisphenol A ethoxylate diacrylate (BEDA) as crosslinkers. In FRP experiments, AIBN was used as initiator and ATRP polymerizations were initiated by ethyl 2-bromopropionate (EBrP) and mediated by CuBr using PMDETA (N,N,N′,N″,N″-pentamethyldiethylenetriamine) as ligant. Polymerizations were carried out in solution at 60 °C with different dilutions using toluene and DMF as solvents. Products formed at different polymerization times were analyzed by SEC/RI/MALLS yielding average MW, MWD, z-average radius of gyration and monomer conversion. Important differences in the molecular architecture of the synthesized FRP and ATRP highly branched polyacrylates have been identified. Comparisons of experimental results with predictions have put into evidence the important effect of intramolecular cyclizations at all dilutions, even with ATRP polymerizations. 相似文献
The ratio of the radius of gyration, obtained by static light scattering, and the hydrodynamic radius, obtained by dynamic light scattering, are routine experimental techniques for the assessment of nanoparticle shape. The potential effect of particle nonuniformity is mostly not considered. In this communication, we demonstrate that, even with medium particle nonuniformities, it is advisable to apply appropriate corrections. The values of the correction factors are offered in a diagram for various particle shapes, and two types of particle-size distributions and their widths. 相似文献
Chains containing side groups were generated with up to 102 bonds in the backbone for both iso- and syndiotactic arrangements. The mean-square end-to-end distance <h2>, the mean-square radius of gyration <r2> and the ratios <li2
>/<l12
> of the axes of inertia were investigated. It could be shown that the mean size and shape of such chains are not influenced by the kind of stereoregularity.Dedicated to Prof. Dr. K. Ueberreiter on the occasion of his 70th birthday. 相似文献
Summary: The evolution of the various structural units incorporated into hyperbranched polymers formed from the copolymerization of AB2 and AB monomers has been derived by the kinetic scheme. The degree of branching was calculated with a new definition given in this work. The degree of branching monotonously increased with increasing A group conversion (x) and the maximum value could reach 2r/(1 + r)2, where r is the initial fraction of AB2 monomers in the total. Like the average degree of polymerization, the mean‐square radius of gyration of the hyperbranched polymers increased moderately with A group conversion in the range x < 0.9 and displayed an abrupt rise when the copolymerization neared completion. The characteristic ratio of the mean‐square radius of gyration remained constant for the linear polymers. However, the hyperbranched polymers did not possess this character. In comparison with the linear polymerization, the weight average and z‐average degree of polymerization increased due to the addition of the branched monomer units AB2 and the mean‐square radius of gyration decreased quickly for the products of copolymerization.