| Title |
Opening mechanism of adenylate kinase can vary according to selected molecular dynamics force field
|
|---|---|
| Published in |
Perspectives in Drug Discovery and Design, May 2015
|
| DOI | 10.1007/s10822-015-9849-0 |
| Pubmed ID | |
| Authors |
Hulya Unan, Ahmet Yildirim, Mustafa Tekpinar |
| Abstract |
Adenylate kinase is a widely used test case for many conformational transition studies. It performs a large conformational transition between closed and open conformations while performing its catalytic function. To understand conformational transition mechanism and impact of force field choice on E. Coli adenylate kinase, we performed all-atom explicit solvent classical molecular dynamics simulations starting from the closed conformation with four commonly used force fields, namely, Amber99, Charmm27, Gromos53a6, Opls-aa. We carried out 40 simulations, each one 200 ns. We analyzed completely 12 of them that show full conformational transition from the closed state to the open one. Our study shows that different force fields can have a bias toward different transition pathways. Transition time scales, frequency of conformational transitions, order of domain motions and free energy landscapes of each force field may also vary. In general, Amber99 and Charmm27 behave similarly while Gromos53a6 results have a resemblance to the Opls-aa force field results. |
X Demographics
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Geographical breakdown
| Country | Count | As % |
|---|---|---|
| Unknown | 1 | 100% |
Demographic breakdown
| Type | Count | As % |
|---|---|---|
| Members of the public | 1 | 100% |
Mendeley readers
The data shown below were compiled from readership statistics for 13 Mendeley readers of this research output. Click here to see the associated Mendeley record.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| United Kingdom | 1 | 8% |
| Unknown | 12 | 92% |
Demographic breakdown
| Readers by professional status | Count | As % |
|---|---|---|
| Student > Ph. D. Student | 5 | 38% |
| Lecturer | 2 | 15% |
| Researcher | 2 | 15% |
| Student > Bachelor | 1 | 8% |
| Student > Master | 1 | 8% |
| Other | 1 | 8% |
| Unknown | 1 | 8% |
| Readers by discipline | Count | As % |
|---|---|---|
| Chemistry | 5 | 38% |
| Biochemistry, Genetics and Molecular Biology | 3 | 23% |
| Computer Science | 2 | 15% |
| Engineering | 1 | 8% |
| Unknown | 2 | 15% |
Attention Score in Context
This research output has an Altmetric Attention Score of 1. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 21 April 2016.
All research outputs
#22,834,739
of 25,461,852 outputs
Outputs from Perspectives in Drug Discovery and Design
#868
of 949 outputs
Outputs of similar age
#239,512
of 280,565 outputs
Outputs of similar age from Perspectives in Drug Discovery and Design
#4
of 5 outputs
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