Transcription-factor binding and sliding on DNA studied using micro- and macroscopic models (Q37377471)

20 August 2017

Transcription-factor binding and sliding on DNA studied using micro- and macroscopic models (English)

1 reference

20 August 2017

7

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20 August 2017

5

David van der Spoel

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Erik G Marklund

object named as

Erik G Marklund

1

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author name string

Anel Mahmutovic

2

1 reference

20 August 2017

Otto G Berg

3

1 reference

20 August 2017

Petter Hammar

4

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20 August 2017

David Fange

6

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20 August 2017

language of work or name

English

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publication date

12 November 2013

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20 August 2017

6

1 reference

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

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published in

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20 August 2017

110

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20 August 2017

49

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20 August 2017

19796-19801

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GROMACS 4: Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation

20 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3856812

Fast flexible modeling of RNA structure using internal coordinates.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3856812

Stochastic reaction-diffusion kinetics in the microscopic limit

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3856812

Improved side-chain torsion potentials for the Amber ff99SB protein force field

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3856812

Nonspecifically bound proteins spin while diffusing along DNA.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3856812

Probing transcription factor dynamics at the single-molecule level in a living cell

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3856812

Canonical sampling through velocity rescaling

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3856812

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

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3856812

How proteins search for their specific sites on DNA: the role of DNA conformation

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3856812

GROMACS: fast, flexible, and free

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3856812

H++: a server for estimating pKas and adding missing hydrogens to macromolecules

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3856812

How do site-specific DNA-binding proteins find their targets?

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3856812

Energetic and structural considerations for the mechanism of protein sliding along DNA in the nonspecific BamHI-DNA complex.

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3856812

A closer view of the conformation of the Lac repressor bound to operator

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3856812

Crystal structure of the lactose operon repressor and its complexes with DNA and inducer

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3856812

The lac repressor-operator interaction. 3. Kinetic studies

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3856812

Lac repressor binding to synthetic DNAs of defined nucleotide sequence

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3856812

Diffusion controlled reaction rates in spheroidal geometry. Application to repressor--operator association and membrane bound enzymes

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3856812

Diffusion in a rough potential

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3856812

The three operators of the lac operon cooperate in repression

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3856812

Direct measurement of association constants for the binding of Escherichia coli lac repressor to non-operator DNA

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3856812

Kinetics of protein-DNA interaction: facilitated target location in sequence-dependent potential

6 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3856812

High-throughput gene expression analysis at the level of single proteins using a microfluidic turbidostat and automated cell tracking

14 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3856812

Diffusion-driven mechanisms of protein translocation on nucleic acids. 3. The Escherichia coli lac repressor--operator interaction: kinetic measurements and conclusions.

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3856812

Nonspecific interaction of lac repressor with DNA: an association reaction driven by counterion release.

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3856812

The lac repressor displays facilitated diffusion in living cells.

26 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3856812

Insights into the sliding movement of the lac repressor nonspecifically bound to DNA.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3856812

Structure and flexibility adaptation in nonspecific and specific protein-DNA complexes.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3856812

Biochemistry. Completing the view of transcriptional regulation.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3856812

Diffusion-driven mechanisms of protein translocation on nucleic acids. 1. Models and theory.

2 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3856812

Comparison of simple potential functions for simulating liquid water

2 September 2018

1 reference

Crossref

https://api.crossref.org/works/10.1073%2FPNAS.1307905110

Molecular dynamics with coupling to an external bath

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1073%2FPNAS.1307905110

Uptake of monoaromatic hydrocarbons during biodegradation by FadL channel-mediated lateral diffusion

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1073%2FPNAS.1307905110

Interaction of lac repressor with alternating poly d (A-T) and poly d (G-C). Circular dichroism studies

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24222688

12 December 2020

inferred from PubMed ID database lookup

Facilitated diffusion on mobile DNA: configurational traps and sequence heterogeneity

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24222688

12 December 2020

inferred from PubMed ID database lookup

Protein sliding along DNA: dynamics and structural characterization

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/24222688

12 December 2020

inferred from PubMed ID database lookup

Identifiers

DOI

10.1073/PNAS.1307905110

1 reference

20 August 2017

0 references

1 reference

20 August 2017

PubMed publication ID

24222688

1 reference