Anatomy of noncovalent interactions between the nucleobases or ribose and π-containing amino acids in RNA–protein complexes

The CH-π interaction in protein - carbohydrate binding: Bioinformatics and in vitro quantification

(2020) Josef Houser et al.   CHEMISTRY-A EUROPEAN JOURNAL

Crystal structure of the plant symporter STP10 illuminates sugar uptake mechanism in monosaccharide transporter superfamily

(2019) Peter Aasted Paulsen et al.   Nature Communications

Crystal structure of a Y-box binding protein 1 (YB-1)–RNA complex reveals key features and residues interacting with RNA

(2019) Xiao-Juan Yang et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Dissecting macromolecular recognition sites in ribosome: implication to its self-assembly

(2019) Smita P. Pilla et al.   RNA Biology

Impact of Aromatic Stacking on Glycoside Reactivity: Balancing CH/π and Cation/π Interactions for the Stabilization of Glycosyl-Oxocarbenium Ions

(2019) Laura Montalvillo-Jiménez et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

RNA 5-Methylcytosine Facilitates the Maternal-to-Zygotic Transition by Preventing Maternal mRNA Decay

(2019) Ying Yang et al.   MOLECULAR CELL

HNRNPH1-dependent splicing of a fusion oncogene reveals a targetable RNA G-quadruplex interaction

(2019) Carla Neckles et al.   RNA

Functions, mechanisms and regulation of Pumilio/Puf family RNA binding proteins: a comprehensive review

(2019) M. J. Nishanth et al.   MOLECULAR BIOLOGY REPORTS

Structural basis for mRNA recognition by human RBM38

(2019) Kaiyue Qian et al.   BIOCHEMICAL JOURNAL

Experimental and theoretical study of the role of CH/π interactions in the aminolysis reaction of acetyl galactoside

(2019) Fabián Cuétara-Guadarrama et al.   CARBOHYDRATE RESEARCH

Computational investigation reveals Picrasidine C as selective PPARα lead: binding pattern, selectivity mechanism and ADME/tox profile

(2019) Fangfei Li et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Lone pair···π interactions on the stabilization of intra and intermolecular arrangements of coordination compounds with 2-methyl imidazole and benzimidazole derivatives

(2018) Guillermo Durán-Solares et al.   JOURNAL OF COORDINATION CHEMISTRY

Expanding RNA binding specificity and affinity of engineered PUF domains

(2018) Yang-Yang Zhao et al.   NUCLEIC ACIDS RESEARCH

Anion-π Interactions in Computer-Aided Drug Design: Modeling the Inhibition of Malate Synthase by Phenyl-Diketo Acids

(2018) Jill F. Ellenbarger et al.   Journal of Chemical Information and Modeling

Revealing the mechanism for covalent inhibition of glycoside hydrolases by carbasugars at an atomic level

(2018) Weiwu Ren et al.   Nature Communications

YB-1, an abundant core mRNA-binding protein, has the capacity to form an RNA nucleoprotein filament: a structural analysis

(2018) Dmitry A Kretov et al.   NUCLEIC ACIDS RESEARCH

Protein engineering strategies for improving the selective methylation of target CpG sites by a dCas9-directed cytosine methyltransferase in bacteria

(2018) Tina Xiong et al.   PLoS One

Occurrence and stability of lone pair–π stacking interactions between ribose and nucleobases in functional RNAs

(2017) Mohit Chawla et al.   NUCLEIC ACIDS RESEARCH

Combining crystallographic and quantum chemical data to understand DNA-protein π-interactions in nature

(2017) Katie A. Wilson et al.   STRUCTURAL CHEMISTRY

CD72 negatively regulates B lymphocyte responses to the lupus-related endogenous toll-like receptor 7 ligand Sm/RNP

(2016) Chizuru Akatsu et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Topology of RNA–protein nucleobase–amino acid π–π interactions and comparison to analogous DNA–protein π–π contacts

(2016) Katie A. Wilson et al.   RNA

Molecular architecture of protein-RNA recognition sites

(2015) Amita Barik et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Landscape ofπ–πand sugar–πcontacts in DNA–protein interactions

(2015) Katie A. Wilson et al.   JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS

Carbohydrate–Aromatic Interactions in Proteins

(2015) Kieran L. Hudson et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

DNA–protein π-interactions in nature: abundance, structure, composition and strength of contacts between aromatic amino acids and DNA nucleobases or deoxyribose sugar

(2014) Katie A. Wilson et al.   NUCLEIC ACIDS RESEARCH

Absolute binding-free energies between standard RNA/DNA nucleobases and amino-acid sidechain analogs in different environments

(2014) Anita de Ruiter et al.   NUCLEIC ACIDS RESEARCH

Engineering RNA-binding proteins for biology

(2013) Yu Chen et al.   FEBS Journal

Significant Strength of Charged DNA–Protein π–π Interactions: A Preliminary Study of Cytosine

(2013) Rachael A. Wells et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Examination of Tyrosine/Adenine Stacking Interactions in Protein Complexes

(2013) Kari L. Copeland et al.   JOURNAL OF PHYSICAL CHEMISTRY B

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

How an exonuclease decides where to stop in trimming of nucleic acids: crystal structures of RNase T–product complexes

(2012) Yu-Yuan Hsiao et al.   NUCLEIC ACIDS RESEARCH

Evaluating How Discrete Water Molecules Affect Protein–DNA π–π and π+–π Stacking and T-Shaped Interactions: The Case of Histidine-Adenine Dimers

(2011) Fern M. V. Leavens et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Regulation by Small RNAs in Bacteria: Expanding Frontiers

(2011) Gisela Storz et al.   MOLECULAR CELL

Structural basis for RNA trimming by RNase T in stable RNA 3′-end maturation

(2011) Yu-Yuan Hsiao et al.   Nature Chemical Biology

A Preliminary Investigation of the Additivity of π−π or π+−π Stacking and T-Shaped Interactions between Natural or Damaged DNA Nucleobases and Histidine

(2010) Lesley R. Rutledge et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Evolution and Functions of Long Noncoding RNAs

(2009) Chris P. Ponting et al.   CELL

Noncovalent Interactions Involving Histidine: The Effect of Charge on π−π Stacking and T-Shaped Interactions with the DNA Nucleobases

(2009) Cassandra D. M. Churchill et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Mercury CSD 2.0– new features for the visualization and investigation of crystal structures

(2008) Clare F. Macrae et al.   JOURNAL OF APPLIED CRYSTALLOGRAPHY

Probing Phenylalanine/Adenine π-Stacking Interactions in Protein Complexes with Explicitly Correlated and CCSD(T) Computations

(2008) Kari L. Copeland et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Dissecting protein–RNA recognition sites

(2008) Ranjit Prasad Bahadur et al.   NUCLEIC ACIDS RESEARCH