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Molecular dynamics and principal components of potassium binding with human telomeric intra-molecular G-quadruplex

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Protein & Cell 2015年第6期6卷 423-433页

作者： Zhiguo Wang Ruping Chen Ling Hou Jianfeng Li Jun-Ping Liu Institute of Aging Research School of Medicine Hangzhou Normal University Hangzhou 311121 China School of Medicine Shandong University Jinan 250100 China Department of Immunology Central Eastern Clinical School Monash University Melbourne VIC 3004 Australia Center for Cancer Research Monash Institute of Medical Research Clayton VIC 3168 Australia

Telomere assumes intra-molecular G-quadruplex that is a significant drug target for inhibiting telomerase main- tenance of telomeres in cancer. Metal cations have been recognized as playing important roles in stabilizing G-quadruplex, but their binding processes to human telomeric G-quadruplex remain uncharacterized. To in- vestigate the detailed binding procedures, molecular dynamics simulations were conducted on the hybrid [3 ＋ 1] form-one human telomeric intra-molecular G-quadruplex. We show here that the binding of a potas- sium ion to a G-tetrad core is mediated by two alternative pathways. Principal component analysis illustrated the dominant concerted motions of G-quadruplex occurred at the loop domains. MM-PBSA calculations revealed that binding was energetically favorable and driven by the electrostatic interactions. The lower binding site was found more constructive favorable for binding. Our data provide useful information on a potassium-mediated stable structure of human telomeric intra-molecular G-quadruplex, implicating in ion disorder associated conformationa｜ changes and targeted drug design.

关键词： G-quadruplex potassium ion moleculardynamics principal component analysis MM-PBSA

Binding and conformation of dendrimer-based drug delivery systems:a molecular dynamics study

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Advances in Manufacturing 2015年第3期3卷 221-231页

作者： Fa-Da Zhang Yi Liu Jing-Cheng Xu Sheng-Juan Li Xiu-Nan Wang Yue Sun Xin-Luo Zhao Department of Physics and Materials Genome Institute Shanghai University School of Materials Science and Engineering University of Shanghai for Science and Technology School of Energy & Power Engineering University of Shanghai for Science and Technology

All atomistic molecular dynamics simulations were performed on poly （amidoamine）（PAMAM） dendrimers that compound non-covalently with anticancer drug molecules including DOX, MTX, CE6, and SN38. The binding energies as well as their associated interaction energies and deformation energies were combined to evaluate the relative binding strength among drug, PAMAM, and PEG chains. We find that the deformation of dendrimers due to drug loading plays a crucial role in the drug binding. It is energetically favorable for the drug molecules to bind with PAMAM while the drugs bind with PEG metastable chains via kinetic confinement. Surface PEGylation helps dendrimers to accommodate more drug molecules with greater strength without inducing too much expansion. This work indicates that tuning the functionalized terminal groups of dendrimers is critical to design efficient dendrimer-based drug delivery systems.

关键词： Dendrimer PAMAM - PEGylation-Anticancer drug Drug delivery systems moleculardynamics

EFFECT OF TEMPERATURE ON DISLOCATION EMISSION FROM CRACK TIP FOR BCC METAL MO

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Acta Mechanica Solida Sinica 1998年第3期11卷 189-198页

作者： Tang Qiheng Wang Tzuchiang Chinese Acad Sci Inst Mech LNM Beijing 100080 Peoples R China

The effect of thermally activated energy on the dislocationemission from a crack tip in BCC metal Mo is simulated in this *** on the correlative reference model on which the flexi- bledisplacement boundary scheme is introduced naturally, the simulationshows that as temperature in creases the critical stress intensityfactor for the first dislocation emission will decrease and the totalnumber of emitted dislocations increase for the same external *** dislocation velocity and exten- sive distance among partialdislocations are not sensitive to temperature.

关键词： correlative reference model flexible displacement boundary moleculardynamics