• Je něco špatně v tomto záznamu ?

On the Use of Molecular Dynamics Simulations for Probing Allostery through DNA

T. Dršata, M. Zgarbová, P. Jurečka, J. Šponer, F. Lankaš,

. 2016 ; 110 (4) : 874-6. [pub] 20160127

Jazyk angličtina Země Spojené státy americké

Typ dokumentu časopisecké články, práce podpořená grantem

Perzistentní odkaz   https://www.medvik.cz/link/bmc17000549
E-zdroje Online Plný text

NLK Cell Press Free Archives od 1960-01-01 do Před 1 rokem
Free Medical Journals od 1960 do Před 1 rokem
Freely Accessible Science Journals od 1960 do Před 12 měsíci
PubMed Central od 1960 do Před 1 rokem
Europe PubMed Central od 1960 do Před 1 rokem
Open Access Digital Library od 1960-09-01
Elsevier Open Access Journals od 1960-09-01 do 2018-02-06
Elsevier Open Archive Journals od 1960-09-01 do Před 1 rokem

Odkazy

PubMed 26827073
DOI 10.1016/j.bpj.2015.12.039
Knihovny.cz E-zdroje

A recent study described an allosteric effect in which the binding of a protein to DNA is influenced by another protein bound nearby. The effect shows a periodicity of ∼10 basepairs and decays with increasing protein-protein distance. As a mechanistic explanation, the authors reported a similar periodic, decaying pattern of the correlation coefficient between major groove widths inferred from a shorter molecular dynamics simulation. Here we show that in a state-of-the-art, microsecond-long simulation of the same DNA sequence, the periodicity of the correlation coefficient is not observed. To study the problem further, we extend an earlier mechanical model of DNA allostery based on constrained minimization of effective quadratic deformation energy of the DNA. We demonstrate that, if the constraints mimicking the bound proteins are properly applied, the periodicity in the binding energy is indeed recovered.

Citace poskytuje Crossref.org

000      
00000naa a2200000 a 4500
001      
bmc17000549
003      
CZ-PrNML
005      
20170113114401.0
007      
ta
008      
170103s2016 xxu f 000 0|eng||
009      
AR
024    7_
$a 10.1016/j.bpj.2015.12.039 $2 doi
024    7_
$a 10.1016/j.bpj.2015.12.039 $2 doi
035    __
$a (PubMed)26827073
040    __
$a ABA008 $b cze $d ABA008 $e AACR2
041    0_
$a eng
044    __
$a xxu
100    1_
$a Dršata, Tomáš $u Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic; Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic.
245    10
$a On the Use of Molecular Dynamics Simulations for Probing Allostery through DNA / $c T. Dršata, M. Zgarbová, P. Jurečka, J. Šponer, F. Lankaš,
520    9_
$a A recent study described an allosteric effect in which the binding of a protein to DNA is influenced by another protein bound nearby. The effect shows a periodicity of ∼10 basepairs and decays with increasing protein-protein distance. As a mechanistic explanation, the authors reported a similar periodic, decaying pattern of the correlation coefficient between major groove widths inferred from a shorter molecular dynamics simulation. Here we show that in a state-of-the-art, microsecond-long simulation of the same DNA sequence, the periodicity of the correlation coefficient is not observed. To study the problem further, we extend an earlier mechanical model of DNA allostery based on constrained minimization of effective quadratic deformation energy of the DNA. We demonstrate that, if the constraints mimicking the bound proteins are properly applied, the periodicity in the binding energy is indeed recovered.
650    _2
$a alosterická regulace $7 D000494
650    _2
$a DNA $x chemie $7 D004247
650    12
$a simulace molekulární dynamiky $7 D056004
650    12
$a konformace nukleové kyseliny $7 D009690
655    _2
$a časopisecké články $7 D016428
655    _2
$a práce podpořená grantem $7 D013485
700    1_
$a Zgarbová, Marie $u Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University, Olomouc, Czech Republic.
700    1_
$a Jurečka, Petr $u Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University, Olomouc, Czech Republic.
700    1_
$a Šponer, Jiří $u Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno, Czech Republic; Central European Institute of Technology, Campus Bohunice, Brno, Czech Republic.
700    1_
$a Lankaš, Filip $u Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic; Laboratory of Informatics and Chemistry, University of Chemistry and Technology Prague, Prague, Czech Republic. Electronic address: lankasf@vscht.cz.
773    0_
$w MED00000774 $t Biophysical journal $x 1542-0086 $g Roč. 110, č. 4 (2016), s. 874-6
856    41
$u https://pubmed.ncbi.nlm.nih.gov/26827073 $y Pubmed
910    __
$a ABA008 $b sig $c sign $y a $z 0
990    __
$a 20170103 $b ABA008
991    __
$a 20170113114502 $b ABA008
999    __
$a ok $b bmc $g 1179689 $s 961116
BAS    __
$a 3
BAS    __
$a PreBMC
BMC    __
$a 2016 $b 110 $c 4 $d 874-6 $e 20160127 $i 1542-0086 $m Biophysical journal $n Biophys J $x MED00000774
LZP    __
$a Pubmed-20170103

Najít záznam

Citační ukazatele

Možnosti archivace