The configurational properties of tail-like polymer chains with one end attached to a flat surface are studied by using dynamic Monte Carlo technique. We find that the probability distribution of the free end in z direction P(R(z)) and the density profile rho(z) can be scaled approximately by a factor beta to be a length independent function for both random walking (RW) and self-avoiding walking (SAW) tail-like chains, where the factor beta is related to the mean square end-to-end distance . The scaled P(R(z)) of the SAW chain roughly overlaps that of the RW chain, but the scaled rho(z) of the SAW chain locates at smaller betaz than that of the RW chain.
Computer Simulation ; Models, Chemical ; Models, Molecular ; Models, Statistical ; Molecular Conformation ; Molecular Structure ; Monte Carlo Method ; Polymers ; chemistry ; Statistical Distributions

AIMIn order to find a way to prognosticate the region-selectivity in the O-methylation reaction of erythromycin and its derivatives, conformation search model of Hyperchem Pro 6.0 used in personal computer was used to establish it.

METHODSThe results of O-methylation reaction of compound 1, 2 and 3 showed the difference between 6-OH and 11-OH. Using the conformational search model of hyperchem, 1,000 conformations of compound 4, 5 and 6 were found with the parameter of dihedral angle. The 14-membered lactone ring was defined as a "plane". The position of carbonyl of 1- or 9- and hydroxyl of 6- or 11- is different, either "up-plane" or "down-plane". A statistic analysis of low-energy conformation clusters was used to sort these clusters by the parameter of the dihedral angle. The data is in accord with the results of the experiments.

RESULTSConformation numbers, energy minimum, energy average and position of the active groups of compounds 4, 5 and 6, the simplified structures of compound 1, 2 and 3, were given in Table 1. by sorting the dihedral angle.

CONCLUSIONThe interaction of the hydroxyl and carbonyl were analysed and found that O-methylation reactions of erythromycin and its derivatives were impacted by the space factor. The clusters of energy minimum, maximum number and "outside" were discussed. The selectivity of the O-methylation reaction of erythromycin and its derivatives can be prognosticated by analysing the parameter of the dihedral angle.

The relation between the critical radius and the particle size distribution for generalized Ostwald type ripening processes whereby the mass transfer coefficient is modelled by a power law was derived. The critical radius is determined by the growth rate, the mass transfer coefficient and the mass balance, and is independent of whether the limiting stationary growth regime has been obtained.
Computer Simulation ; Crystallization ; methods ; Macromolecular Substances ; analysis ; chemistry ; Models, Chemical ; Models, Molecular ; Molecular Conformation ; Particle Size

Huntington's disease (HD) is a late-onset and progressive neurodegenerative disorder that is caused by aggregation of mutant huntingtin protein which contains expanded-polyglutamine. The molecular chaperones modulate the aggregation in early stage and known for the most potent protector of neurodegeneration in animal models of HD. Over the past decades, a number of studies have demonstrated molecular chaperones alleviate the pathogenic symptoms by polyQ-mediated toxicity. Moreover, chaperone-inducible drugs and anti-aggregation drugs have beneficial effects on symptoms of disease. Here, we focus on the function of molecular chaperone in animal models of HD, and review the recent therapeutic approaches to modulate expression and turn-over of molecular chaperone and to develop anti-aggregation drugs.
Huntington Disease* ; Models, Animal ; Molecular Chaperones ; Neurodegenerative Diseases

In the process of new drug discovery, the application of virtual screening can enrich active compounds, reduce the cost of drug screening, and increase the feasibility of drug screening. Therefore virtual screening technology has become an important approach for new drug discovery. As virtual screening and bioactivity screening possess different advantages, their combination can effectively promote new drug discovery. In the present paper, the application and the trend of removal of non-drug compounds, removal of false positive compounds, pharmacophore searching, molecular docking, and molecular similarity in the process of drug discovery are introduced in order to obtain more benefit from virtual screening strategy for new drug discovery.
Drug Design ; Drug Discovery ; Drug Evaluation, Preclinical ; Models, Molecular

In this symposium, we reviewed the principle and development of time-resolved fluorescence anisotropy measurement. Its method of measurement, characteristics and applications in the research of biomacromolecule, configuration and molecular structure have been discussed. Its potential applications are also illustrated.
Fluorescence Polarization ; methods ; Macromolecular Substances ; Mathematics ; Models, Molecular ; Time Factors

This paper proposes a method based on quaternion for characterization a helix of proteins. The method defines the parameter called Quaternion Helix Axis Spherical Distance (QHASD) on the basis of mapping protein Cα frames' helical axis onto a unit sphere, and uses QHASD to characterize the a helix of the protein secondary structure. Application of this method has been verified based on the PDBselect database, with an a helix characterization accuracy of 91.7%. This method possesses significant advantages of high detection accuracy, low computation and clear geometric significance.
Algorithms ; Databases, Protein ; Models, Molecular ; Protein Structure, Secondary ; Proteins ; chemistry

Optically-triggered phase-transition droplets have been introduced as a promising contrast agent for photoacoustic and ultrasound imaging that not only provide significantly enhanced contrast but also have potential as photoacoustic theranostic molecular probes incorporated with targeting molecules and therapeutics. For further understanding the dynamics of optical droplet vaporization process, an innovative, methodical analysis by concurrent acoustical and ultrafast optical recordings, comparing with a theoretical model has been employed. In addition, the repeatability of the droplet vaporization-recondensation process, which enables continuous photoacoustic imaging has been studied through the same approach. Further understanding the underlying physics of the optical droplet vaporization and associated dynamics may guide the optimal design of the droplets. Some innovative approaches in preclinical studies have been recently demonstrated, including sono-photoacoustic imaging, dual-modality of photoacoustic and ultrasound imaging, and super-resolution photoacoustic imaging. In this review, current development of optically triggered phase-transition droplets and understanding on the vaporization dynamics, their applications are introduced and future directions are discussed.
Methods ; Models, Theoretical ; Molecular Probes ; Theranostic Nanomedicine ; Ultrasonography ; Volatilization

Coronavirus ; chemistry ; ultrastructure ; Microscopy, Electron ; Models, Molecular ; Ribonucleoproteins ; chemistry ; ultrastructure

OBJECTIVE: To construct a three-dimensional structural model for the selectivity filter in the transient receptor pontential melastatin 8 (TRPM8) ion channel. METHODS: In the Rosetta computational structural biology suite, multiple rounds of modeling with the kinematic loop closure algorithm were performed. RESULTS: After nine rounds of computational modeling, we obtained the models of the selectivity filter within the TRPM8 channel with the lowest energy and high convergence. The model showed that the sidechain of D918 points were away from the central ion permeation pathway, while the sidechains of Q914, D920 and T923 pointed towards it. The glycosylation site N934 was located outside the pore region and its side chain directed to the extracellular water environment. CONCLUSIONS A three-dimensional structural model for the selectivity filter in the TRPM8 ion channel was constructed, which provides reliable structural information for exploring the mechanism of ion selectivity.
Algorithms ; Ion Channel Gating ; Models, Molecular ; TRPM Cation Channels ; chemistry