Abstract:
:A useful property of DMSO solvent has been exploited to reveal a new catalytic route for cytidine amino proton exchange, relevant to exchange in the macromolecular state, but hidden in aqueous solution. Additional exchange mechanisms in aqueous monomeric cytidine (and adenosine) are obscured by the formation of a fast-exchanging endocyclic-protonated intermediate, which dominates the kinetics. Endocyclic nucleobase protonation could be circumvented in the presence of buffer conjugate acid by the use of DMSO/water solvent, permitting the first unequivocal observation buffer acid-catalyzed exchange from the neutral, unprotonated nucleobase, i.e., general acid catalysis. Because buffer ionization is greatly reduced in DMSO through anion desolvation, nucleobase protonation is suppressed in the presence of buffer acid. Evidence is presented to describe this catalytic route as one involving hydrogen bond formation between the buffer acid and the endocyclic protonation site, C(N-3). Since this same configuration is found in Watson-Crick hydrogen bonding, experiments are presented to demonstrate faster cytidine amino proton exchange with the formation of the G-C base pair in DMSO. The importance of this mechanism in past aqueous monomer studies and in the interpretation of macromolecular (DNA) hydrogen exchange is discussed.
journal_name
J Biomol Struct Dynjournal_title
Journal of biomolecular structure & dynamicsauthors
McConnell Bdoi
10.1080/07391102.1986.10506359subject
Has Abstractpub_date
1986-12-01 00:00:00pages
419-36issue
3eissn
0739-1102issn
1538-0254journal_volume
4pub_type
杂志文章abstract::Alzheimer's disease (AD) is the most common progressive neurodegenerative brain disorder. It is characterized by the presence of extracellular aggregated fibrillary form of amyloid beta (Aβ) peptide and intraneuronal neurofibrillary tangles caused by the hyperphosphorylation of tau protein. Monomeric form of Aβ peptid...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
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更新日期:2020-03-02 00:00:00
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journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
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journal_title:Journal of biomolecular structure & dynamics
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更新日期:2020-11-19 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:2020-04-01 00:00:00
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journal_title:Journal of biomolecular structure & dynamics
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journal_title:Journal of biomolecular structure & dynamics
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更新日期:2014-01-01 00:00:00
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journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/073911012010525025
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journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2015.1075158
更新日期:2016-06-01 00:00:00
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journal_title:Journal of biomolecular structure & dynamics
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更新日期:2020-06-09 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:2020-04-15 00:00:00
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journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2016.1160257
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
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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:2015-01-01 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:2020-05-01 00:00:00
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journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.1989.10507761
更新日期:1989-08-01 00:00:00
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journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2021.1872418
更新日期:2021-01-21 00:00:00
abstract::Drug efflux pumps (EP) like Mmr in Mycobacterium transported drugs out of cell, a main reason for drug resistance developing in Mycobacterium tuberculosis. In this in silico study, mainly analysed EP inhibitory potential of a plant-derived flavonoid, quercetin, through docking analysis. Mmr present in Mycobacterium sm...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2014.974211
更新日期:2015-01-01 00:00:00
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journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.1992.10507962
更新日期:1992-04-01 00:00:00
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journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
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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
doi:10.1080/07391102.2018.1552895
更新日期:2019-10-01 00:00:00
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journal_title:Journal of biomolecular structure & dynamics
pub_type: 历史文章,杂志文章
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更新日期:2004-08-01 00:00:00
abstract::The mechanism by which peptides bind to micelles is believed to be a two-phase process, involving (i). initial electrostatic interactions between the peptide and micelle surface, followed by (ii). hydrophobic interactions between peptide side chains and the micelle core. To better characterize the electrostatic portio...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2004.10506949
更新日期:2004-02-01 00:00:00
abstract::HIV protease inhibitors (PIs) approved by the FDA (US Food and Drug Administration) are a major class of antiretroviral. HIV-2 protease (PR2) is naturally resistant to most of them as PIs were designed for HIV-1 protease (PR1). In this study, we explored the impact of amino-acid substitutions between PR1 and PR2 on th...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2019.1704877
更新日期:2020-10-01 00:00:00
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journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2020.1718553
更新日期:2020-02-10 00:00:00
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journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.1996.10508872
更新日期:1996-02-01 00:00:00
abstract::Low sampling efficiency in conformational space is the well-known problem for conventional molecular dynamics. It greatly increases the difficulty for molecules to find the transition path to native state, and costs amount of CPU time. To accelerate the sampling, in this paper, we re-couple the critical degrees of fre...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2012.698244
更新日期:2013-01-01 00:00:00
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journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2020.1738960
更新日期:2020-03-18 00:00:00
abstract::A stably-bound external binding site for ethidium cation in the major groove of B-form DNA is proposed. This complex is stabilized by hydrogen bonding between this ligand and the nucleophilic centers O6 and N7 of guanine, both of which are accessible via the major groove. This binding site is not the same as the well-...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2007.10507160
更新日期:2007-10-01 00:00:00
abstract::Human male germ cell-associated kinase (hMAK) is an androgen-inducible gene in prostate epithelial cells, and it acts as a coactivator of androgen receptor signaling in prostate cancer. The 3D structure of the hMAK kinase was modeled based on the crystal structure of CDK2 kinase using comparative modeling methods, and...
journal_title:Journal of biomolecular structure & dynamics
pub_type: 杂志文章
doi:10.1080/07391102.2014.968622
更新日期:2015-01-01 00:00:00