Abstract:
:A large amount of experimental evidence is available on the effect of magnesium ions on the structure and stability of DNA double helix. Less is known, however, on how these ions affect the stability and dynamics of the molecule. The static time average pictures from X-ray structures or the quantum chemical energy minimized structures lack understanding of the dynamic DNA-ion interaction. The present work addresses these questions by molecular dynamics simulation studies on two DNA duplexes and their interaction with magnesium ions. Results show typical B-DNA character with occasional excursions to deviated states. We detected expected stability of the duplexes in terms of backbone conformations and base pair parameter by the CHARMM-27 force field. Ion environment analysis shows that Mg²⁺ retains the coordination sphere throughout the simulation with a preference for major groove over minor. An extensive analysis of the influence of the Mg²⁺ ion shows no evidence of the popular predictions of groove width narrowing by dipositive metal ion. The major groove atoms show higher occupancy and residence time compared to minor groove for magnesium, where no such distinction is found for the charge neutralizing Na⁺ ions. The determining factor of Mg²⁺ ion's choice in DNA binding site evolves as the steric hindrance faced by the bulky hexahydrated cation where wider major groove gets the preference. We have shown that in case of binding of Mg²⁺ to DNA non electrostatic contributions play a major role. An animated Interactive 3D Complement (I3DC) is available in Proteopedia at http://proteopedia.org/w/Journal:JBSD:5.
journal_name
J Biomol Struct Dynjournal_title
Journal of biomolecular structure & dynamicsauthors
Mukherjee S,Bhattacharyya Ddoi
10.1080/07391102.2012.713780subject
Has Abstractpub_date
2013-01-01 00:00:00pages
896-912issue
8eissn
0739-1102issn
1538-0254journal_volume
31pub_type
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journal_title:Journal of biomolecular structure & dynamics
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doi:10.1080/07391102.1998.10508266
更新日期:1998-12-01 00:00:00
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journal_title:Journal of biomolecular structure & dynamics
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更新日期:2020-08-01 00:00:00
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pub_type: 杂志文章
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更新日期:1992-02-01 00:00:00
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更新日期:2020-11-17 00:00:00
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更新日期:2020-07-08 00:00:00
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journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2016.1163294
更新日期:2017-03-01 00:00:00
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journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2017.1326320
更新日期:2018-05-01 00:00:00
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journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
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更新日期:1984-08-01 00:00:00
abstract::Alkylamine-substituted naphthalene imides and diimides bind DNA by intercalation and have applications as anticancer agents. The unique structures of these imides in which two adjacent carbonyl groups lie coplanar to an extended aromatic ring system allow the possibility of sequence-selective interactions between the ...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
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更新日期:1996-12-01 00:00:00
abstract::Hydroxylated polybrominated diphenyl ethers (OH-PBDEs) are a class of toxic environmental pollutants that are persistent, bioaccumulative, and difficult to degrade. Their structure is very similar to the thyroid hormone (T4) and uses the body's thyroid transporter (TTR) binding to interfere with the endocrine balance,...
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journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.1992.10508637
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journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章,评审
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abstract::An ab initio quantum-chemical study of stacked and hydrogen-bonded protonated cytosine dimer has been carried out. The calculations were made using the second-order Moller-Plesset perturbational method (MP2) with a medium-sized polarized set of atomic orbitals. H-bonded as well as stacked protonated base pairs are mor...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
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journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
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abstract::PPARα and PPARγ play important roles in regulating glucose and lipid metabolism. In recent years, the development of dual PPAR agonists has become a hot topic in the field of anti-diabetic medicinal chemistry. The dual PPARα/γ agonists can both improve metabolism and reduce side effects caused by single drugs, and has...
journal_title:Journal of biomolecular structure & dynamics
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journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2020.1792988
更新日期:2020-07-16 00:00:00
abstract::The aim of the present study focuses on the molecular docking approach to screen alternative drug that can regulate the hyperglycemia by down-regulating α-glucosidase and α-amylase activity using phenolic compounds: tannic acid (L1), catechin (L2), gallic acid (L3), quercetin (L5) and epicatechin (L6). L1 gives the be...
journal_title:Journal of biomolecular structure & dynamics
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journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2016.1145143
更新日期:2017-02-01 00:00:00
abstract::Inhibition of normal cellular apoptosis or programed cell death is the hallmark of all cancers. Apoptotic dysregulation can result in numerous pathological conditions, such as cancers, autoimmune disorders, and neurodegeneration. Members of the BCL-2 family of proteins regulate the process of apoptosis by its promotio...
journal_title:Journal of biomolecular structure & dynamics
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doi:10.1080/07391102.2018.1508371
更新日期:2019-08-01 00:00:00
abstract::Computations on the energy profiles for Na+ in the gramicidin A (GA) channel have been extended by introducing the effect, previously neglected, of the amino acid side chains of GA, fixed in their most stable conformations. The calculations have been performed in two approximations: 1) with the ethanolamine tail fixed...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.1985.10507605
更新日期:1985-02-01 00:00:00
abstract::Apoptosis is a fundamental biological phenomenon, in which anti- or proapoptotic proteins of the Bcl-2 family regulate a committed step. Overexpression of Bcl-2, the prototypical antiapoptotic protein in this family, is associated with therapy resistance in various human cancers. Accordingly, Bcl-2 inhibitors intended...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2018.1491424
更新日期:2019-07-01 00:00:00