Abstract：
:The Transformer2 (Tra2) proteins in humans are homologues of the Drosophila Tra2 protein. One of the two RNA-binding paralogs, Tra2β, has been very well-studied over the past decade, but not much is known about Tra2α. It was very recently shown that the two proteins demonstrate the phenomenon of paralog compensation. Here, we provide a structural basis for this genetic backup circuit, using molecular modelling and dynamics studies. We show that the two proteins display similar binding specificities, but differential affinities to a short GAA-rich RNA stretch. Starting from the 6-nucleotide RNA in the solution structure, close to 4000 virtual mutations were modelled on RNA and the domain-RNA interactions were studied after energy minimisation to convergence. Separately, another known 13-nucleotide stretch was docked and the domain-RNA interactions were observed through a 100-ns dynamics trajectory. We have also demonstrated the 'compensatory' mechanism at the level of domains in one of the domain repeat-containing RNA-binding proteins.
journal_name
J Biomol Struct Dynjournal_title
Journal of biomolecular structure & dynamicsauthors
Ghosh P,Grellscheid SN,Sowdhamini Rdoi
10.1080/07391102.2015.1100551subject
Has Abstractpub_date
2016-09-01 00:00:00pages
1979-86issue
9eissn
0739-1102issn
1538-0254journal_volume
34pub_type
杂志文章abstract：:The conformation of a complex of a 41 mer/31 mer DNA fragment and the Klenow fragment of DNA polymerase I of Escherichia coli was studied by scanning tunnelling microscopy (STM). The results shows that near two turns of double helix of this DNA fragment was outside of enzyme while another part containing more than one...
journal_title：Journal of biomolecular structure & dynamics
pub_type： 杂志文章
doi：10.1080/07391102.1991.10507909
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journal_title：Journal of biomolecular structure & dynamics
pub_type： 杂志文章
doi：10.1080/07391102.1989.10506524
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journal_title：Journal of biomolecular structure & dynamics
pub_type： 杂志文章
doi：10.1080/07391102.1995.10508820
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journal_title：Journal of biomolecular structure & dynamics
pub_type： 杂志文章
doi：10.1080/07391102.2009.10507266
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journal_title：Journal of biomolecular structure & dynamics
pub_type： 杂志文章
doi：10.1080/07391102.2020.1796809
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journal_title：Journal of biomolecular structure & dynamics
pub_type： 杂志文章
doi：10.1080/07391102.2006.10507075
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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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doi：10.1080/07391102.2013.788983
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journal_title：Journal of biomolecular structure & dynamics
pub_type： 杂志文章
doi：10.1080/07391102.2015.1135823
更新日期：2017-01-01 00:00:00
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journal_title：Journal of biomolecular structure & dynamics
pub_type： 杂志文章
doi：10.1080/07391102.2013.832384
更新日期：2014-01-01 00:00:00
abstract：:The model of locally accurate conformation for the HIV-Thailand principal neutralizing determinant (PND) located within the V3 loop of the virus envelope protein gp120 was built in terms of NMR spectroscopy data. To this end, the NMR-based conformational analysis of synthetic molecule representing the peptide copy of ...
journal_title：Journal of biomolecular structure & dynamics
pub_type： 杂志文章
doi：10.1080/07391102.2002.10506801
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：10.1080/07391102.1996.10508927
更新日期：1996-08-01 00:00:00
abstract：:All major suggestions about the nucleosome positioning sequence pattern(s) are overviewed. Two basic binary periodical patterns are well established: in purine/pyrimidine alphabet - YRRRRRYYYYYR and in strong/weak alphabet -SWWWWWSSSSSW. Their merger in four-letter alphabet sequence coincides with first ever complete ...
journal_title：Journal of biomolecular structure & dynamics
pub_type： 杂志文章
doi：10.1080/073911010010524944
更新日期：2010-06-01 00:00:00
abstract：:The effect of two widely used polyphenols, curcumin and EGCG was investigated on the amyloid fibrillogenesis of the well-characterized model protein human lysozyme (HuL), associated with non-neuropathic systemic amyloidosis, towards exploring their efficacy as modulators of HuL amyloid aggregation and toxicity and unr...
journal_title：Journal of biomolecular structure & dynamics
pub_type： 杂志文章
doi：10.1080/07391102.2020.1860824
更新日期：2020-12-17 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 number of tandemly repeated DNA sequences have the ability to form hairpin structures by forming non-standard base pairs. When (GCC)15 and (GGC)15 strands are annealed together, the expected duplex is the only product. However, when (GCC)15 is annealed with (GCC)10, depending on the relative concentrations, up to fi...
journal_title：Journal of biomolecular structure & dynamics
pub_type： 杂志文章
doi：10.1080/07391102.1996.10508113
更新日期：1996-10-01 00:00:00
abstract：:Glycation and oxidation induce structural alterations in the proteins in an interdependent manner with consequent pathological implications. The published literature presents wide range of modifications in conformational characteristics of proteins by glycation and oxidation; however, there is little data that could e...
journal_title：Journal of biomolecular structure & dynamics
pub_type： 杂志文章
doi：10.1080/07391102.2017.1365770
更新日期：2018-08-01 00:00:00
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journal_title：Journal of biomolecular structure & dynamics
pub_type： 杂志文章
doi：10.1080/07391102.2011.10508616
更新日期：2011-06-01 00:00:00
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journal_title：Journal of biomolecular structure & dynamics
pub_type： 杂志文章
doi：10.1080/07391102.1993.10508711
更新日期：1993-08-01 00:00:00
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journal_title：Journal of biomolecular structure & dynamics
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更新日期：2020-03-01 00:00:00
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journal_title：Journal of biomolecular structure & dynamics
pub_type： 杂志文章
doi：10.1080/07391102.2019.1680435
更新日期：2020-08-01 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
pub_type： 杂志文章
doi：10.1080/07391102.2018.1508371
更新日期：2019-08-01 00:00:00
abstract：:The ongoing outbreak of Coronavirus disease 2019 (COVID-19) is a matter of great concern. Although the mortality rate caused by this virus is less than that of SARS and MERS, it is showing higher efficacy in terms of human-to-human transmission. Several strategies have been taken by scientists and researchers worldwid...
journal_title：Journal of biomolecular structure & dynamics
pub_type： 杂志文章
doi：10.1080/07391102.2020.1850528
更新日期：2020-11-23 00:00:00
abstract：:Seven new quinoline-based bioorganic compounds were prepared by solvent-free synthesis and characterized using spectral techniques. The binding of these compounds with human serum albumin (HSA) was investigated by multi-spectroscopic methods. The quenching of Trp fluorescence upon addition of these compounds to HSA co...
journal_title：Journal of biomolecular structure & dynamics
pub_type： 杂志文章
doi：10.1080/07391102.2018.1496141
更新日期：2019-07-01 00:00:00
abstract：:Catalytic mechanism of orotidine 5'-monophosphate decarboxylase (OMPDC), one of the nature most proficient enzymes which provides large rate enhancement, has not been fully understood yet. A series of 30 ns molecular dynamics (MD) simulations were run on X-ray structure of the OMPDC from Saccharomyces cerevisiae in it...
journal_title：Journal of biomolecular structure & dynamics
pub_type： 杂志文章
doi：10.1080/07391102.2014.881303
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journal_title：Journal of biomolecular structure & dynamics
pub_type： 杂志文章
doi：10.1080/07391102.2015.1110835
更新日期：2016-10-01 00:00:00
abstract：:The hypothetical protection of genes from oxidative damage provided by the G-rich telomeric overhangs located at the end of chromosomes, which consist, in humans, of single strands of TTAGGG sequence repeats, is investigated here. First principle Moller-Plesset perturbation theory calculations reveal that the TTAGGG h...
journal_title：Journal of biomolecular structure & dynamics
pub_type： 杂志文章
doi：10.1080/07391102.2011.10507405
更新日期：2011-12-01 00:00:00
abstract：:The structural and thermodynamic characters of alpha-syn12 peptide in aqueous solution at different pH and temperatures have been investigated through temperature replica exchange molecular dynamics (T-REMD) simulations with GROMOS 43A1 force field. The two independent T-REMD simulations were completed at pH = 7.0 and...
journal_title：Journal of biomolecular structure & dynamics
pub_type： 杂志文章
doi：10.1080/07391102.2010.10507364
更新日期：2010-12-01 00:00:00
abstract：:Infections by Candida albicans in immune compromised patients cause significant morbidity and mortality. In the search for potential molecular targets for drug development, the family of agglutinin-like proteins (Als) in C. albicans have been identified due to numerous attributes associated with high virulence, most p...
journal_title：Journal of biomolecular structure & dynamics
pub_type： 杂志文章
doi：10.1080/07391102.2017.1417159
更新日期：2018-12-01 00:00:00
abstract：:Plasma membrane of each micro-organism has a unique set of lipid composition as a consequence of the environmental adaptation or a response to exposure to antimicrobial peptides (AMPs) as antibiotic agents. Understanding the relationship between lipid composition and action of antimicrobial peptides or considering how...
journal_title：Journal of biomolecular structure & dynamics
pub_type： 杂志文章
doi：10.1080/07391102.2012.737295
更新日期：2013-12-01 00:00:00
