Protein-RNA interactions: a structural analysis.

By S. Jones, D. Daley, Nicholas M. Luscombe, Helen M. Berman, Janet M. Thornton. Nucleic Acids Research, 2001

741 citations recorded by the source corpus.

Subfields: Materials Chemistry, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/fe116d616a382ea77e0f417167a71f149116da3f

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Citations in the corpus

Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 a resolution. (2002, background): “Those which are, have on average 12 water molecules located in positions mediating protein–DNA interactions.(14) In contrast, the NCP147 structure reveals ten times this number of water molecules at the protein–DNA interface.”
An overview of the structures of protein-DNA complexes (2000, neutral): “A2(103-160), B1(5-75), B2(102-161) 1oct C1(5-75) Oct-1 POU domain H.”
3D-DART: a DNA structure modelling server (2009, background): “The structures of double-stranded DNA in complex with various ligands often show considerable conformational changes compared to their unbound counterparts (9–12).”
BindN: a web-based tool for efficient prediction of DNA and RNA binding sites in amino acid sequences (2006, background): “At the atomic level, the interactions involve a complex combination of hydrogen bonds, van der Waals contacts and water-mediated bonds between amino acid residues and nucleotide bases (4,5).”
How RNA binding proteins interact with RNA: molecules and mechanisms (2020, background): “VdW interactions generally share the same preferences for amino acids that are observed for hydrogen bonds (Ellis et al., 2007; Han and Nepal, 2007; Jones et al., 2001; Treger and Westhof, 2001).”
Aptamers as therapeutics (2010, background): “Although this is true for biological nucleic acids [1] [2] [3] [4] , it was only recently that a series of technological advances allowed the development of in vitro evolutionary methods for the discovery of additional, non-biological oligonucleotides that can bind to protein targets.”
ASEdb: a database of alanine mutations and their effects on the free energy of binding in protein interactions (2001, background): “Protein interactions with other proteins and with nucleic acids have been widely studied from both structural and energetic perspectives (Janin, 1995, 1997; Jones and Thornton, 1996; Jones et al., 1999; Larsen et al., 1998; McCoy et al., 1997; Nadassy et al., 1999).”
Protein–protein interaction and quaternary structure (2008, background): “…to protein–protein recognition, and use results of the transverse studies of protein–DNA complexes by Jones et al. (1999), Nadassy et al. (1999) and Sarai & Kono (2005), and of protein–RNA complexes by Jones et al. (2001), Treger & Westhof (2001), Ellis et al. (2007) and Bahadur et al. (2008).”
Amino acid?base interactions: a three-dimensional analysis of protein?DNA interactions at an atomic level (2001, background): “Although tyrosine and tryptophan should be capable of similar interactions, few contacts are produced as they are not frequently found in DNA-binding sites (23).”