4.8 Article

Structural study of the Fox-1 RRM protein hydration reveals a role for key water molecules in RRM-RNA recognition

Related references

Note: Only part of the references are listed.
Article Biochemistry & Molecular Biology

Probing binding hot spots at protein-RNA recognition sites

Amita Barik et al.

NUCLEIC ACIDS RESEARCH (2016)

Review Biochemistry & Molecular Biology

Hydration of proteins and nucleic acids: Advances in experiment and theory. A review

Lada Biedermannova et al.

BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS (2016)

Article Chemistry, Physical

Can We Execute Stable Microsecond-Scale Atomistic Simulations of Protein-RNA Complexes?

M. Krepl et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2015)

Article Chemistry, Physical

ff14SB: Improving the Accuracy of Protein Side Chain and Backbone Parameters from ff99SB

James A. Maier et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2015)

Article Biochemistry & Molecular Biology

The First Crystal Structure of the UP1 Domain of hnRNP A1 Bound to RNA Reveals a New Look for an Old RNA Binding Protein

Christopher E. Morgan et al.

JOURNAL OF MOLECULAR BIOLOGY (2015)

Article Chemistry, Physical

Are Waters around RNA More than Just a Solvent? - An Insight from Molecular Dynamics Simulations

Petra Kuehrova et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2014)

Article Chemistry, Physical

Building Water Models: A Different Approach

Saeed Izadi et al.

JOURNAL OF PHYSICAL CHEMISTRY LETTERS (2014)

Article Chemistry, Physical

Molecular Dynamics Simulations of Nucleic Acids. From Tetranucleotides to the Ribosome

Jiri Sponer et al.

JOURNAL OF PHYSICAL CHEMISTRY LETTERS (2014)

Article Biochemistry & Molecular Biology

Characterization of the RNA recognition mode of hnRNP G extends its role in SMN2 splicing regulation

Ahmed Moursy et al.

NUCLEIC ACIDS RESEARCH (2014)

Article Biochemistry & Molecular Biology

Hydration of protein-RNA recognition sites

Amita Barik et al.

NUCLEIC ACIDS RESEARCH (2014)

Article Biochemical Research Methods

The structure of the ARE-binding domains of Hu antigen R (HuR) undergoes conformational changes during RNA binding

Hong Wang et al.

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY (2013)

Article Biochemistry & Molecular Biology

RRM-RNA recognition: NMR or crystallography ... and new findings

Gerrit M. Daubner et al.

CURRENT OPINION IN STRUCTURAL BIOLOGY (2013)

Article Chemistry, Physical

PTRAJ and CPPTRAJ: Software for Processing and Analysis of Molecular Dynamics Trajectory Data

Daniel R. Roe et al.

JOURNAL OF CHEMICAL THEORY AND COMPUTATION (2013)

Article Biochemical Research Methods

Towards automated crystallographic structure refinement with phenix.refine

Pavel V. Afonine et al.

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY (2012)

Article Chemistry, Physical

Simulations of A-RNA Duplexes. The Effect of Sequence, Solute Force Field, Water Model, and Salt Concentration

Ivana Besseova et al.

JOURNAL OF PHYSICAL CHEMISTRY B (2012)

Article Chemistry, Multidisciplinary

Quantitation of Affinity, Avidity, and Binding Kinetics of Protein Analytes with a Dynamically Switchable Biosurface

Jelena Knezevic et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2012)

Article Biochemistry & Molecular Biology

Interdomain Allostery Promotes Assembly of the Poly(A) mRNA Complex with PABP and eIF4G

Nozhat Safaee et al.

MOLECULAR CELL (2012)

Article Chemistry, Medicinal

Modeling of the Water Network at Protein-RNA Interfaces

Yiyu Li et al.

JOURNAL OF CHEMICAL INFORMATION AND MODELING (2011)

Article Chemistry, Multidisciplinary

Soft-Core Potentials in Thermodynamic Integration: Comparing One- and Two-Step Transformations

Thomas Steinbrecher et al.

JOURNAL OF COMPUTATIONAL CHEMISTRY (2011)

Article Biochemistry & Molecular Biology

Structural basis for the dual RNA-recognition modes of human Tra2-β RRM

Kengo Tsuda et al.

NUCLEIC ACIDS RESEARCH (2011)

Review Chemistry, Physical

Structure determination and dynamics of protein-RNA complexes by NMR spectroscopy

Cyril Dominguez et al.

PROGRESS IN NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY (2011)

Review Chemistry, Multidisciplinary

Molecular Dynamics and Quantum Mechanics of RNA: Conformational and Chemical Change We Can Believe In

Mark A. Ditzler et al.

ACCOUNTS OF CHEMICAL RESEARCH (2010)

Article Biochemical Research Methods

XDS

Wolfgang Kabsch

ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY (2010)

Article Biochemical Research Methods

Features and development of Coot

P. Emsley et al.

ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY (2010)

Article Biochemistry & Molecular Biology

Structural Insights into RNA Recognition by the Alternate-Splicing Regulator CUG-Binding Protein 1

Marianna Teplova et al.

STRUCTURE (2010)

Review Biochemical Research Methods

A short guide for molecular dynamics simulations of RNA systems

Yaser Hashem et al.

METHODS (2009)

Article Biochemistry & Molecular Biology

Structural basis for the sequence-specific RNA-recognition mechanism of human CUG-BP1 RRM3

Kengo Tsuda et al.

NUCLEIC ACIDS RESEARCH (2009)

Review Biochemistry & Molecular Biology

Molecular dynamics guided study of salt bridge length dependence in both fluorinated and non-fluorinated parallel dimeric coiled-coils

Scott S. Pendley et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2009)

Review Chemistry, Multidisciplinary

Water as an active constituent in cell biology

Philip Ball

CHEMICAL REVIEWS (2008)

Review Biochemistry & Molecular Biology

RNA recognition motifs:: boring?: Not quite

Antoine Clery et al.

CURRENT OPINION IN STRUCTURAL BIOLOGY (2008)

Article Chemistry, Physical

Nonlinear scaling schemes for Lennard-Jones interactions in free energy calculations

Thomas Steinbrecher et al.

JOURNAL OF CHEMICAL PHYSICS (2007)

Article Biochemistry & Molecular Biology

Structural and functional analysis of RNA and TAP binding to SF2/ASF

Aura M. Tintaru et al.

EMBO REPORTS (2007)

Article Biochemistry & Molecular Biology

MolProbity: all-atom contacts and structure validation for proteins and nucleic acids

Ian W. Davis et al.

NUCLEIC ACIDS RESEARCH (2007)

Article Biochemistry & Molecular Biology

Nucleic acid solvation: from outside to insight

Pascal Auffinger et al.

CURRENT OPINION IN STRUCTURAL BIOLOGY (2007)

Article Biochemistry & Molecular Biology

Comparison of multiple amber force fields and development of improved protein backbone parameters

Viktor Hornak et al.

PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS (2006)

Article Multidisciplinary Sciences

Trapped water molecules are essential to structural dynamics and function of a ribozyme

Maria M. Rhodes et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2006)

Article Biochemistry & Molecular Biology

RNA kink-turns as molecular elbows:: Hydration, cation binding, and large-scale dynamics

Filip Razga et al.

STRUCTURE (2006)

Article Biochemistry & Molecular Biology

Molecular basis of RNA recognition by the human alternative splicing factor Fox-1

SD Auweter et al.

EMBO JOURNAL (2006)

Article Biochemistry & Molecular Biology

Homologues of the Caenorhabditis elegans Fox-1 protein are neuronal splicing regulators in mammals

JG Underwood et al.

MOLECULAR AND CELLULAR BIOLOGY (2005)

Article Biochemistry & Molecular Biology

Tissue-dependent isoforms of mammalian Fox-1 homologs are associated with tissue-specific splicing activities

S Nakahata et al.

NUCLEIC ACIDS RESEARCH (2005)

Article Biochemistry & Molecular Biology

Protein and drug interactions in the minor groove of DNA

Z Moravek et al.

NUCLEIC ACIDS RESEARCH (2002)

Article Biochemistry & Molecular Biology

Computational analysis of candidate intron regulatory elements for tissue-specific alternative pre-mRNA splicing

M Brudno et al.

NUCLEIC ACIDS RESEARCH (2001)

Article Biochemical Research Methods

Checking nucleic acid crystal structures

U Das et al.

ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY (2001)

Article Biochemistry & Molecular Biology

Molecular dynamics simulation reveals conformational switching of water-mediated uracil-cytosine base-pairs in an RNA duplex

C Schneider et al.

JOURNAL OF MOLECULAR BIOLOGY (2001)

Article Chemistry, Multidisciplinary

Nanosecond molecular dynamics of zipper-like DNA duplex structures containing sheared G•A mismatch pairs

N Spacková et al.

JOURNAL OF THE AMERICAN CHEMICAL SOCIETY (2000)

Review Biochemistry & Molecular Biology

Water and ion binding around RNA and DNA (C,G) oligomers

P Auffinger et al.

JOURNAL OF MOLECULAR BIOLOGY (2000)