Abstract：
:Chlamydia trachomatis (C.t) is a Gram-negative obligate intracellular bacteria and is a major causative of infectious blindness and sexually transmitted diseases. Among the varied serovars of this organism, A, B and C are reported as prominent ocular pathogens. Genomic studies of these strains shall aid in deciphering potential drug targets and genomic influence on pathogenesis. Hence, in this study we performed deep statistical profiling of codon usage in these serovars. The overall base composition analysis reveals that these serovars are over biased to AU than GC. Similarly, relative synonymous codon usage also showed preference towards A/U ending codons. Parity Rule 2 analysis inferred unequal distribution of AT and GC, indicative of other unknown factors acting along with mutational pressure to influence codon usage bias (CUB). Moreover, absolute quantification of CUB also revealed lower bias across these serovars. The effect of natural selection on CUB was also confirmed by neutrality plot, reinforcing natural selection under mutational pressure turned to be a pivotal role in shaping the CUB in the strains studied. Correspondence analysis (COA) clarified that, C.t C/TW-3 to show a unique trend in codon usage variation. Host influence analysis on shaping the codon usage pattern also inferred some speculative relativity. In a nutshell, our finding suggests that mutational pressure is the dominating factor in shaping CUB in the strains studied, followed by natural selection. We also propose potential drug targets based on cumulative analysis of strand bias, CUB and human non-homologue screening.
journal_name
J Biomol Struct Dynjournal_title
Journal of biomolecular structure & dynamicsauthors
Sadhasivam A,Vetrivel Udoi
10.1080/07391102.2017.1343685subject
Has Abstractpub_date
2018-06-01 00:00:00pages
1979-2003issue
8eissn
0739-1102issn
1538-0254journal_volume
36pub_type
杂志文章abstract：:Osmium tetroxide complexes with nitrogen ligands (Os,L) have been widely used as probes of the DNA structure. A monoclonal antibody OsBP7H8 against DNA adducts with Os,L was produced in mice. OsBP7H8 does not bind to proteins or total yeast RNA modified with Os,2,2'-bipyridine (bipy) nor to the unmodified nucleic acid...
journal_title：Journal of biomolecular structure & dynamics
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doi：10.1080/07391102.1999.10508339
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journal_title：Journal of biomolecular structure & dynamics
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doi：10.1080/07391102.2015.1100551
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journal_title：Journal of biomolecular structure & dynamics
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doi：10.1080/07391102.2000.10506667
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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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journal_title：Journal of biomolecular structure & dynamics
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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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doi：10.1080/07391102.2018.1426044
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journal_title：Journal of biomolecular structure & dynamics
pub_type： 杂志文章
doi：10.1080/07391102.1985.10506322
更新日期：1985-02-01 00:00:00
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journal_title：Journal of biomolecular structure & dynamics
pub_type： 杂志文章
doi：10.1080/07391102.2012.762724
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journal_title：Journal of biomolecular structure & dynamics
pub_type： 杂志文章
doi：10.1080/07391102.1985.10506327
更新日期：1985-02-01 00:00:00
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journal_title：Journal of biomolecular structure & dynamics
pub_type： 杂志文章
doi：10.1080/07391102.2020.1760135
更新日期：2020-05-06 00:00:00
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journal_title：Journal of biomolecular structure & dynamics
pub_type： 杂志文章
doi：10.1080/07391102.2019.1664324
更新日期：2020-08-01 00:00:00
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journal_title：Journal of biomolecular structure & dynamics
pub_type： 杂志文章
doi：10.1080/07391102.1998.10508209
更新日期：1998-04-01 00:00:00
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journal_title：Journal of biomolecular structure & dynamics
pub_type： 杂志文章
doi：10.1080/07391102.2020.1820381
更新日期：2020-09-15 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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journal_title：Journal of biomolecular structure & dynamics
pub_type： 杂志文章
doi：10.1080/07391102.1987.10507683
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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
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doi：10.1080/07391102.2019.1633409
更新日期：2020-05-01 00:00:00
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journal_title：Journal of biomolecular structure & dynamics
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doi：10.1080/07391102.2020.1841028
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abstract：:Actinomycin D (ActD) is a DNA-binding antitumor antibiotic that appears to act in vivo by inhibiting RNA polymerase. The mechanism of DNA binding of ActD has attracted much attention because of its strong preference for 5'-dGpdC-3' sequences. Binding is thought to involve intercalation of the tricyclic aromatic phenox...
journal_title：Journal of biomolecular structure & dynamics
pub_type： 杂志文章
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更新日期：1989-12-01 00:00:00
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journal_title：Journal of biomolecular structure & dynamics
pub_type： 杂志文章
doi：10.1080/07391102.1984.10507572
更新日期：1984-10-01 00:00:00
abstract：:Molecular modeling and molecular dynamics were performed to investigate the interaction of norfloxacin with the DNA oligonucleotide 5'-d(ATACGTAT)(2). Eight quinolone-DNA binding structures were built by molecular modeling on the basis of experimental results. A 100ps molecular dynamics calculation was carried out on ...
journal_title：Journal of biomolecular structure & dynamics
pub_type： 杂志文章
doi：10.1080/07391102.2002.10506811
更新日期：2002-06-01 00:00:00
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journal_title：Journal of biomolecular structure & dynamics
pub_type： 杂志文章
doi：10.1080/07391102.2020.1802342
更新日期：2020-08-07 00:00:00
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journal_title：Journal of biomolecular structure & dynamics
pub_type： 杂志文章,评审
doi：10.1080/07391102.1984.10507565
更新日期：1984-10-01 00:00:00
abstract：:The novel method allowing identification of protein structure elements responsible for catalytic activity manifestation is proposed. Structural organization of various hydrolases was studied using the ANIS (ANalysis of Informational Structure) method. ANIS allows to reveal a hierarchy of the ELements of Information St...
journal_title：Journal of biomolecular structure & dynamics
pub_type： 杂志文章
doi：10.1080/07391102.2008.10507202
更新日期：2008-04-01 00:00:00
abstract：:It is well known that the biological activity of gallated proanthocyanidins (PAs) is highly structure-dependent. Polymerization degree (DP) and linkage types affect their biological activity greatly. Positions and orientations of gallated PAs in lipid bilayer reveal their structure-function activity at the molecular l...
journal_title：Journal of biomolecular structure & dynamics
pub_type： 杂志文章
doi：10.1080/07391102.2017.1369163
更新日期：2018-08-01 00:00:00
