RNA–LIM: A novel procedure for analyzing protein/single-stranded RNA propensity data with concomitant estimation of interface structure

Hall, Damien; Li, Songling; Yamashita, Kazuo; Azuma, Ryuzo; Carver, John A.; Standley, Daron M.

doi:10.1016/j.ab.2014.11.004

Cited by 10 publications

(12 citation statements)

References 35 publications

(100 reference statements)

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“…To the best of our knowledge, essentially all current methods are limited to structured RNA. Only the RNA-lim method [ 25 ] has attempted to predict protein-ssRNA structures based on fragments. The authors dock and assemble ultra-coarse-grained nucleotides (one bead per nucleotide) in a pre-defined binding site.…”

Section: Resultsmentioning

confidence: 99%

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Binding Site Identification and Flexible Docking of Single Stranded RNA to Proteins Using a Fragment-Based Approach

2016

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Protein-RNA docking is hampered by the high flexibility of RNA, and particularly single-stranded RNA (ssRNA). Yet, ssRNA regions typically carry the specificity of protein recognition. The lack of methodology for modeling such regions limits the accuracy of current protein-RNA docking methods. We developed a fragment-based approach to model protein-bound ssRNA, based on the structure of the protein and the sequence of the RNA, without any prior knowledge of the RNA binding site or the RNA structure. The conformational diversity of each fragment is sampled by an exhaustive RNA fragment library that was created from all the existing experimental structures of protein-ssRNA complexes. A systematic and detailed analysis of fragment-based ssRNA docking was performed which constitutes a proof-of-principle for the fragment-based approach. The method was tested on two 8-homo-nucleotide ssRNA-protein complexes and was able to identify the binding site on the protein within 10 Å. Moreover, a structure of each bound ssRNA could be generated in close agreement with the crystal structure with a mean deviation of ~1.5 Å except for a terminal nucleotide. This is the first time a bound ssRNA could be modeled from sequence with high precision.

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Section: Resultsmentioning

confidence: 99%

“…A first attempt to model protein-bound ssRNA has recently been made by the RNA-Lim method [ 25 ]. Tested on one 6-nucleotide ssRNA–protein complex, and restricting the search on the known binding site, RNA-Lim achieved only limited success, with a 5 Å precision on the nucleotide placement in ~ 10% of the proposed solutions.…”

Section: Introductionmentioning

confidence: 99%

Binding Site Identification and Flexible Docking of Single Stranded RNA to Proteins Using a Fragment-Based Approach

2016

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“…The consensus sequence was segregated as fragments in such a way that six nucleotides at a stretch were taken per fragment ( Figure 4A) for analog library construction. Resulted library sequences were later utilized for binding studies with the target by RNA-Lim method and recognized the various conformations of fragments bound in the active sites of the protein (Hall et al, 2015). Fragments which bound on active sites are selected to design the high précised aptamer model.…”

Section: Nucleotide Fragment Library Constructionmentioning

confidence: 99%

Protein Network Studies on PCOS Biomarkers With S100A8, Druggability Assessment, and RNA Aptamer Designing to Control Its Cyst Migration Effect

Manibalan

Shobana

Kiruthika

et al. 2020

Front. Bioeng. Biotechnol.

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The prevalence of polycystic ovary syndrome (PCOS) has been gradually increasing among adult females worldwide. Laparoscopy drilling on ovary is the only available temporary solution with a high incidence of reoccurrence. S100A8 with S100A9 complex is believed to facilitate the cyst migration in PCOS condition. The high evident protein interaction network studies between PCOS biomarkers, cancer invasion markers, and the interactors of S100A8 confirm that this protein has strong interaction with other selective PCOS biomarkers, which may be associative in the immature cyst invasion process. Through the network studies, intensive structural and pathway analysis, S100A8 is identified as a targetable protein. In this research, the non-SELEX in silico method is adapted to construct RNA Library based on the consensus DNA sequence of Glucocorticoid Response Element (GRE) and screened the best nucleotide fragments which are bound within the active sites of the target protein. Selected sequences are joined as a single strand and screened the one which competitively binds with minimal energy. In vitro follow-up of this computational research, the designed RNA aptamer was used to infect the MCF7 cell line through Lipofectamine 2000 mediated delivery to study the anti-cell migration effect. Wound Scratch assay confirms that the synthesized 18-mer oligo has significant inhibition activity toward tumor cell migration at the cellular level.

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“…The consensus sequence was segregated as fragments in such a way that six nucleotides at a stretch was considered for RNA analog library construction. This was later utilized for binding with target by RNA-Lim method to recognize the various conformations exhibited in protein (22). This is modelled to achieve highly précised sequences.…”

Section: Construction Of Fragment Librarymentioning

confidence: 99%

Identification of target candidate in Polycystic ovarian syndrome and invitro evaluation of therapeutic activity of the designed RNA Aptamer

Subramanian¹,

Ayyachamy²,

Manickam³

et al. 2019

Preprint

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Prevalence of poly cystic ovary syndrome has been gradually increasing among adult females and Laparoscopy drilling on the ovary is only available temporary solution with high incidence of reoccurrence. Confidential gene disease association studies combined with various graph theory analysis on the biological protein interaction network of this syndrome has resulted, the 15 genes are overexpressed as central nodes among 434 proteins of disease specific proteome network. Through the Intensive Structural and functional prioritization analysis we have identified S100A8, calprotectin is the ideal drug target protein. In this research, we have constructed RNA library of consensus DNA sequence of Glucocorticoid Response Element (GRE) and screened the best RNA Aptamer fragment which competitively binds with minimal energy to inhibit the cell migration activity of S100A8. In order to prove this computational research, Lipofectamine mediated RNA aptamer delivered and Wound scrap assay in cell lines confirms that the synthesized 18mer oligo has significant molecular level inhibition activity toward cyst formation and spreading in poly cystic condition in ovary.

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RNA–LIM: A novel procedure for analyzing protein/single-stranded RNA propensity data with concomitant estimation of interface structure

Cited by 10 publications

References 35 publications

Binding Site Identification and Flexible Docking of Single Stranded RNA to Proteins Using a Fragment-Based Approach

Binding Site Identification and Flexible Docking of Single Stranded RNA to Proteins Using a Fragment-Based Approach

Protein Network Studies on PCOS Biomarkers With S100A8, Druggability Assessment, and RNA Aptamer Designing to Control Its Cyst Migration Effect

Identification of target candidate in Polycystic ovarian syndrome and invitro evaluation of therapeutic activity of the designed RNA Aptamer

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