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101.
López-Mejías V Knight JL Brooks CL Matzger AJ 《Langmuir : the ACS journal of surfaces and colloids》2011,27(12):7575-7579
The phase-selective crystallization of acetaminophen (ACM) using insoluble polymers as heteronuclei was investigated in a combined experimental and computational effort to elucidate the mechanism of polymer-induced heteronucleation (PIHn). ACM heteronucleates from supersaturated aqueous solution in its most thermodynamically stable monoclinic form on poly(n-butyl methacrylate), whereas the metastable orthorhombic form is observed on poly(methyl methacrylate). When ACM crystals were grown through vapor deposition, only the monoclinic polymorph was observed on each polymer. Each crystallization condition leads to a unique powder X-ray diffraction pattern with the major preferred orientation corresponding to the crystallographic faces in which these crystal phases nucleate from surfaces of the polymers. The molecular recognition events leading to these outcomes are elucidated with the aid of computed polymer-crystal binding energies using docking simulations. This investigation illuminates the mechanism by which phase selection occurs during the crystallization of ACM using polymers as heteronuclei, paving the way for the improvement of methods for polymorph selection and discovery based on heterogeneous nucleation promoters. 相似文献
102.
HdeA protein is a small, ATP-independent, acid stress chaperone that undergoes a dimer-to-monomer transition in acidic environments. The HdeA monomer binds a broad range of proteins to prevent their acid-induced aggregation. To understand better HdeA's function and mechanism, we perform constant-pH molecular dynamics simulations (CPHMD) to elucidate the details of the HdeA dimer dissociation process. First the pK(a) values of all the acidic titratable groups in HdeA are obtained and reveal a large pK(a) shift only for Glu(37). However, the pH-dependent monomer charge exhibits a large shift from -4 at pH > 6 to +6 at pH = 2.5, suggesting that the dramatic change in charge on each monomer may drive dissociation. By combining the CPHMD approach with umbrella sampling, we demonstrate a significant stability decrease of the HdeA dimer when the environmental pH changes from 4.0 to 3.5 and identify the key acidic residue-lysine interactions responsible for the observed pH sensing in HdeA chaperon activity function. 相似文献
103.
The self-guided Langevin dynamics (SGLD) is a method to accelerate conformational searching. This method is unique in the way that it selectively enhances and suppresses molecular motions based on their frequency to accelerate conformational searching without modifying energy surfaces or raising temperatures. It has been applied to studies of many long time scale events, such as protein folding. Recent progress in the understanding of the conformational distribution in SGLD simulations makes SGLD also an accurate method for quantitative studies. The SGLD partition function provides a way to convert the SGLD conformational distribution to the canonical ensemble distribution and to calculate ensemble average properties through reweighting. Based on the SGLD partition function, this work presents a force-momentum-based self-guided Langevin dynamics (SGLDfp) simulation method to directly sample the canonical ensemble. This method includes interaction forces in its guiding force to compensate the perturbation caused by the momentum-based guiding force so that it can approximately sample the canonical ensemble. Using several example systems, we demonstrate that SGLDfp simulations can approximately maintain the canonical ensemble distribution and significantly accelerate conformational searching. With optimal parameters, SGLDfp and SGLD simulations can cross energy barriers of more than 15 kT and 20 kT, respectively, at similar rates for LD simulations to cross energy barriers of 10 kT. The SGLDfp method is size extensive and works well for large systems. For studies where preserving accessible conformational space is critical, such as free energy calculations and protein folding studies, SGLDfp is an efficient approach to search and sample the conformational space. 相似文献
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A. Plionis D. Haas S. Landsberger G. Brooks 《Journal of Radioanalytical and Nuclear Chemistry》2008,276(2):369-373
Several methods for the electrodeposition of actinides for alpha-spectrometry analysis have been developed over the past few
decades, but none have been specifically designed to facilitate rapid analysis in a field situation. This paper describes
the development of an electrodeposition procedure that is specifically adapted for use in a mobile lab. Using these techniques
one would be able to obtain preliminary results in the event of a radiological incident. Quantitative yields with associated
uncertainties have been determined for the procedure. It has also been shown that short deposition times can provide quantitative
results. 相似文献
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A. Brooks Harris 《Zeitschrift für Physik B Condensed Matter》1983,49(4):347-349
The properties of self-avoiding walks on dilute lattices are studied, both directly and using the replica formalism. It is shown that dilution does not affect the exponents and careful use of the Haris criterion also leads to this conclusion. 相似文献