Therapeutic Potential of Aptamer–Protein Interactions
AS Shraim, BA Abdel Majeed… - ACS Pharmacology & …, 2022 - ACS Publications
Aptamers are single-stranded oligonucleotides (RNA or DNA) with a typical length between
25 and 100 nucleotides which fold into three-dimensional structures capable of binding to …
25 and 100 nucleotides which fold into three-dimensional structures capable of binding to …
Intrinsic regulatory role of RNA structural arrangement in alternative splicing control
K Taylor, K Sobczak - International journal of molecular sciences, 2020 - mdpi.com
Alternative splicing is a highly sophisticated process, playing a significant role in
posttranscriptional gene expression and underlying the diversity and complexity of …
posttranscriptional gene expression and underlying the diversity and complexity of …
Discovery of key physicochemical, structural, and spatial properties of RNA‐targeted bioactive ligands
While a myriad non‐coding RNAs are known to be essential in cellular processes and
misregulated in diseases, the development of RNA‐targeted small molecule probes has met …
misregulated in diseases, the development of RNA‐targeted small molecule probes has met …
Assessing the performance of MM/PBSA and MM/GBSA methods. 8. Predicting binding free energies and poses of protein–RNA complexes
Molecular docking provides a computationally efficient way to predict the atomic structural
details of protein–RNA interactions (PRI), but accurate prediction of the three-dimensional …
details of protein–RNA interactions (PRI), but accurate prediction of the three-dimensional …
Can we execute stable microsecond-scale atomistic simulations of protein–RNA complexes?
We report over 30 μs of unrestrained molecular dynamics simulations of six protein–RNA
complexes in explicit solvent. We utilize the AMBER ff99bsc0χOL3 RNA force field combined …
complexes in explicit solvent. We utilize the AMBER ff99bsc0χOL3 RNA force field combined …
Sampling native-like structures of RNA-protein complexes through Rosetta folding and docking
RNA-protein complexes underlie numerous cellular processes including translation,
splicing, and posttranscriptional regulation of gene expression. The structures of these …
splicing, and posttranscriptional regulation of gene expression. The structures of these …
A novel protocol for three-dimensional structure prediction of RNA-protein complexes
Three-dimensional structures of RNA-protein complexes are crucial for understanding their
diverse functions. However, the number of the RNA-protein complex structures solved by …
diverse functions. However, the number of the RNA-protein complex structures solved by …
Molecular dynamics simulations of protein RNA complexes by using an advanced electrostatic model
Protein–RNA interactions are integral to the biological functions of RNA. It is well recognized
that molecular dynamics (MD) simulations of protein–RNA complexes are more challenging …
that molecular dynamics (MD) simulations of protein–RNA complexes are more challenging …
Evidence of direct complementary interactions between messenger RNAs and their cognate proteins
AA Polyansky, B Zagrovic - Nucleic acids research, 2013 - academic.oup.com
Recently, the ability to interact with messenger RNA (mRNA) has been reported for a
number of known RNA-binding proteins, but surprisingly also for different proteins without …
number of known RNA-binding proteins, but surprisingly also for different proteins without …
Molecular architecture of protein-RNA recognition sites
The molecular architecture of protein-RNA interfaces are analyzed using a non-redundant
dataset of 152 protein-RNA complexes. We find that an average protein-RNA interface is …
dataset of 152 protein-RNA complexes. We find that an average protein-RNA interface is …