A binding mechanism in protein-nucleotide interactions: implication for U1A RNA binding (Q30350329)

30 September 2017

A binding mechanism in protein-nucleotide interactions: implication for U1A RNA binding (English)

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30 September 2017

1

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30 September 2017

Kenneth W Borrelli

2

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PMC publication ID

554833

30 September 2017

language of work or name

English

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publication date

7 March 2005

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Proceedings of the National Academy of Sciences of the United States of America

30 September 2017

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30 September 2017

102

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30 September 2017

11

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30 September 2017

3954-3959

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Atomic snapshots of an RNA packaging motor reveal conformational changes linking ATP hydrolysis to RNA translocation

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=554833

A hierarchical approach to all-atom protein loop prediction

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=554833

Computational modeling of the catalytic reaction in triosephosphate isomerase.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=554833

High-resolution structure of the E.coli RecQ helicase catalytic core

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=554833

Substitution of an essential adenine in the U1A-RNA complex with a non-polar isostere

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=554833

Estimates of the ab initio limit for pi-pi interactions: the benzene dimer

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=554833

On the molecular discrimination between adenine and guanine by proteins

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=554833

Two functionally distinct steps mediate high affinity binding of U1A protein to U1 hairpin II RNA

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=554833

Protein-RNA interactions: a structural analysis

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=554833

Induced fit in RNA-protein recognition

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=554833

The NMR structure of the 38 kDa U1A protein - PIE RNA complex reveals the basis of cooperativity in regulation of polyadenylation by human U1A protein

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=554833

Investigating the binding specificity of U1A-RNA by computational mutagenesis

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=554833

Molecular dynamics simulations of the complex between human U1A protein and hairpin II of U1 small nuclear RNA and of free RNA in solution

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=554833

Structural basis for recognition of the tra mRNA precursor by the Sex-lethal protein

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=554833

Molecular dynamics studies of U1A-RNA complexes

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=554833

Structural basis of the RNA-binding specificity of human U1A protein

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=554833

Contribution of the C-terminal tail of U1A RBD1 to RNA recognition and protein stability.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=554833

Contribution of the tyrosines to the structure and function of the human U1A N-terminal RNA binding domain

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=554833

Solution structure of the N-terminal RNP domain of U1A protein: the role of C-terminal residues in structure stability and RNA binding

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=554833

Analysis of the RNA-recognition motif and RS and RGG domains: conservation in metazoan pre-mRNA splicing factors

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=554833

Crystal structure at 1.92 A resolution of the RNA-binding domain of the U1A spliceosomal protein complexed with an RNA hairpin

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=554833

Crosslinking of an iodo-uridine-RNA hairpin to a single site on the human U1A N-terminal RNA binding domain

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=554833

Identification of the RNA binding segment of human U1 A protein and definition of its binding site on U1 snRNA.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=554833

Escherichia coli RecQ protein is a DNA helicase

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=554833

Crystal structure of the RNA-binding domain of the U1 small nuclear ribonucleoprotein A

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=554833

Identification of molecular contacts between the U1 A small nuclear ribonucleoprotein and U1 RNA

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=554833

Interaction of N-terminal domain of U1A protein with an RNA stem/loop

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=554833

Altering the RNA-binding mode of the U1A RBD1 protein

3 June 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0500888102

Molecular dynamics and thermodynamics of protein-RNA interactions: mutation of a conserved aromatic residue modifies stacking interactions and structural adaptation in the U1A-stem loop 2 RNA complex

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0500888102

Toward true DNA base-stacking energies: MP2, CCSD(T), and complete basis set calculations

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0500888102

Free-energy calculations of protein-ligand cation-pi and amino-pi interactions: from vacuum to proteinlike environments

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0500888102

Multiple Intermolecular Interaction Modes of Positively Charged Residues with Adenine in ATP-Binding Proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0500888102

Amino/aromatic interactions in proteins: is the evidence stacked against hydrogen bonding?

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0500888102

Force Field Validation Using Protein Side Chain Prediction

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0500888102

Molecular Interactions of Nucleic Acid Bases. A Review of Quantum-Chemical Studies

21 January 2018

1 reference

https://api.crossref.org/works/10.1073%2FPNAS.0500888102

RNA binding mediates the local cooperativity between the beta-sheet and the C-terminal tail of the human U1A RBD1 protein

21 January 2018

1 reference

12 December 2020

Determination of the NMR structure of the complex between U1A protein and its RNA polyadenylation inhibition element

1 reference

12 December 2020

Interaction of RNA hairpins with the human U1A N-terminal RNA binding domain

1 reference

12 December 2020

RNA recognition by the human U1A protein is mediated by a network of local cooperative interactions that create the optimal binding surface

1 reference

12 December 2020

Changes in side-chain and backbone dynamics identify determinants of specificity in RNA recognition by human U1A protein

1 reference

12 December 2020

Changes in sidechain and backbone dynamics identify determinants of specificity in RNA recognition by human U1A protein

1 reference

12 December 2020

Identifiers

DOI

10.1073/PNAS.0500888102

1 reference

30 September 2017

0 references

1 reference

PMC publication ID

554833

30 September 2017

PubMed publication ID

15753311

1 reference

PMC publication ID

554833