Molecular dynamics study of the opening mechanism for DNA polymerase I.
Molecular dynamics study of the opening mechanism for DNA polymerase I.
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DOI：
10.1371/journal.pcbi.1003961
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发表时间：
2014-12
影响因子：
4.3
通讯作者：
Wu EY
中科院分区：
文献类型：
--
作者：
Miller BR 3rd;Parish CA;Wu EY
During DNA replication, DNA polymerases follow an induced fit mechanism in order to rapidly distinguish between correct and incorrect dNTP substrates. The dynamics of this process are crucial to the overall effectiveness of catalysis. Although X-ray crystal structures of DNA polymerase I with substrate dNTPs have revealed key structural states along the catalytic pathway, solution fluorescence studies indicate that those key states are populated in the absence of substrate. Herein, we report the first atomistic simulations showing the conformational changes between the closed, open, and ajar conformations of DNA polymerase I in the binary (enzyme∶DNA) state to better understand its dynamics. We have applied long time-scale, unbiased molecular dynamics to investigate the opening process of the fingers domain in the absence of substrate for B. stearothermophilis DNA polymerase in silico. These simulations are biologically and/or physiologically relevant as they shed light on the transitions between states in this important enzyme. All closed and ajar simulations successfully transitioned into the fully open conformation, which is known to be the dominant binary enzyme-DNA conformation from solution and crystallographic studies. Furthermore, we have detailed the key stages in the opening process starting from the open and ajar crystal structures, including the observation of a previously unknown key intermediate structure. Four backbone dihedrals were identified as important during the opening process, and their movements provide insight into the recognition of dNTP substrate molecules by the polymerase binary state. In addition to revealing the opening mechanism, this study also demonstrates our ability to study biological events of DNA polymerase using current computational methods without biasing the dynamics. All organisms are dependent on the proper replication of their DNA for survival. DNA polymerase is the enzyme responsible for copying our DNA during cell division. We have performed computational simulations on DNA polymerase to understand the fundamental dynamics of the enzyme. Our simulations provide new information about the way polymerase moves in solution that is not obtainable through traditional experimental techniques. In particular, we investigated the dynamics of DNA polymerase “opening” in the binary state (enzyme+DNA with no nucleotide substrate) starting from three different conformations. The results are consistent with available experimental data on the relative conformations of DNA polymerase in the binary state. Furthermore, we identified a novel intermediate species that we hypothesize plays a role in the dynamics of nucleotide substrate binding. Additionally, we determined the previously unknown ordering of events in the opening mechanism, and suggest new details about how the polymerase may interact with an incoming nucleotide substrate. Lastly, this research serves as a proof of principle that we can use our methodology to perform long-time scale computational simulations on DNA polymerase to explain currently unknown phenomena surrounding DNA replication.
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影响因子：
3.3
作者：
Florián, J;Warshel, A;Goodman, MF
通讯作者：
Goodman, MF
影响因子：
6.8
作者：
Klepeis, John L.;Lindorff-Larsen, Kresten;Shaw, David E.
通讯作者：
Shaw, David E.
影响因子：
15
作者：
Berezhna, Svitlana Y.;Gill, Joshua P.;Lamichhane, Rajan;Millar, David P.
通讯作者：
Millar, David P.
DOI：
10.1073/pnas.0508452103
发表时间：
2006-01-24
影响因子：
11.1
作者：
Hornak, V;Okur, A;Simmerling, C
通讯作者：
Simmerling, C
影响因子：
56.9
作者：
DERBYSHIRE, V;FREEMONT, PS;STEITZ, TA
通讯作者：
STEITZ, TA