Conformational ensemble of an intrinsically flexible loop in mitochondrial import protein Tim21 studied by modeling and molecular dynamics simulations

Tim21, a subunit of a highly dynamic translocase of the inner mitochondrial membrane (TIM23) complex, translocates proteins by interacting with subunits in the translocase of the outer membrane (TOM) complex and Tim23 channel in the TIM23 complex. A loop segment in Tim21, which is in close proximity...

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Vydáno v:	Biochimica et biophysica acta. General subjects Ročník 1864; číslo 2; s. 129417
Hlavní autoři:	Srivastava, Arpita, Bala, Siqin, Motomura, Hajime, Kohda, Daisuke, Tama, Florence, Miyashita, Osamu
Médium:	Journal Article
Jazyk:	angličtina
Vydáno:	Netherlands Elsevier B.V 01.02.2020
Témata:	binding sites computational methodology Crystal contact-free space crystal structure energy enzymes Gibbs free energy Loop modeling mitochondrial membrane Molecular dynamics multidimensional scaling nuclear magnetic resonance spectroscopy physiological transport proteins simulation models Tim21 X-radiation MD_NMR Tim21 L2 Molecular dynamics mdm1-mdm10 RMSF Loop modeling RMSD m1-m10 IMS clus1-clus10 Crystal contact-free space NMR CCFS MD_CCFS MD MD_Xray MBP Xray MDS
ISSN:	0304-4165, 1872-8006, 1872-8006
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Abstract	Tim21, a subunit of a highly dynamic translocase of the inner mitochondrial membrane (TIM23) complex, translocates proteins by interacting with subunits in the translocase of the outer membrane (TOM) complex and Tim23 channel in the TIM23 complex. A loop segment in Tim21, which is in close proximity of the binding site of Tim23, has different conformations in X-ray, NMR and new crystal contact-free space (CCFS) structures. MD simulations can provide information on the structure and dynamics of the loop in solution. The conformational ensemble of the loop was characterized using loop modeling and molecular dynamics (MD) simulations. MD simulations confirmed mobility of the loop. Multidimensional scaling and clustering were used to characterize the dynamic conformational ensemble of the loop. Free energy landscape showed that the CCFS crystal structure occupied a low energy region as compared to the conventional X-ray crystal structure. Analysis of crystal packing indicates that the CCFS provides larger conformational space for the motions of the loop. Our work reported the conformational ensemble of the loop in solution, which is in agreement with the structure obtained from CCFS approach. The combination of the experimental techniques and computational methods is beneficial for studying highly flexible regions of proteins. Computational methods, such as loop modeling and MD simulations, have proved to be useful for studying conformational flexibility of proteins. These methods in integration with experimental techniques such as CCFS has the potential to transform the studies on flexible regions of proteins. •Loop modeling was used to generate multiple conformations of a loop segment.•MD simulations confirmed highly dynamic nature of the flexible loop.•CCFS is a crystal contact-free space formed in designed MBP-Tim21 fusion crystals.•CCFS structure is consistent with solution conformational ensemble of the loop.•CCFS approach provides sufficient space for flexible loops to allow their motions.
AbstractList	Tim21, a subunit of a highly dynamic translocase of the inner mitochondrial membrane (TIM23) complex, translocates proteins by interacting with subunits in the translocase of the outer membrane (TOM) complex and Tim23 channel in the TIM23 complex. A loop segment in Tim21, which is in close proximity of the binding site of Tim23, has different conformations in X-ray, NMR and new crystal contact-free space (CCFS) structures. MD simulations can provide information on the structure and dynamics of the loop in solution. The conformational ensemble of the loop was characterized using loop modeling and molecular dynamics (MD) simulations. MD simulations confirmed mobility of the loop. Multidimensional scaling and clustering were used to characterize the dynamic conformational ensemble of the loop. Free energy landscape showed that the CCFS crystal structure occupied a low energy region as compared to the conventional X-ray crystal structure. Analysis of crystal packing indicates that the CCFS provides larger conformational space for the motions of the loop. Our work reported the conformational ensemble of the loop in solution, which is in agreement with the structure obtained from CCFS approach. The combination of the experimental techniques and computational methods is beneficial for studying highly flexible regions of proteins. Computational methods, such as loop modeling and MD simulations, have proved to be useful for studying conformational flexibility of proteins. These methods in integration with experimental techniques such as CCFS has the potential to transform the studies on flexible regions of proteins. •Loop modeling was used to generate multiple conformations of a loop segment.•MD simulations confirmed highly dynamic nature of the flexible loop.•CCFS is a crystal contact-free space formed in designed MBP-Tim21 fusion crystals.•CCFS structure is consistent with solution conformational ensemble of the loop.•CCFS approach provides sufficient space for flexible loops to allow their motions. Tim21, a subunit of a highly dynamic translocase of the inner mitochondrial membrane (TIM23) complex, translocates proteins by interacting with subunits in the translocase of the outer membrane (TOM) complex and Tim23 channel in the TIM23 complex. A loop segment in Tim21, which is in close proximity of the binding site of Tim23, has different conformations in X-ray, NMR and new crystal contact-free space (CCFS) structures. MD simulations can provide information on the structure and dynamics of the loop in solution. The conformational ensemble of the loop was characterized using loop modeling and molecular dynamics (MD) simulations. MD simulations confirmed mobility of the loop. Multidimensional scaling and clustering were used to characterize the dynamic conformational ensemble of the loop. Free energy landscape showed that the CCFS crystal structure occupied a low energy region as compared to the conventional X-ray crystal structure. Analysis of crystal packing indicates that the CCFS provides larger conformational space for the motions of the loop. Our work reported the conformational ensemble of the loop in solution, which is in agreement with the structure obtained from CCFS approach. The combination of the experimental techniques and computational methods is beneficial for studying highly flexible regions of proteins. Computational methods, such as loop modeling and MD simulations, have proved to be useful for studying conformational flexibility of proteins. These methods in integration with experimental techniques such as CCFS has the potential to transform the studies on flexible regions of proteins. Tim21, a subunit of a highly dynamic translocase of the inner mitochondrial membrane (TIM23) complex, translocates proteins by interacting with subunits in the translocase of the outer membrane (TOM) complex and Tim23 channel in the TIM23 complex. A loop segment in Tim21, which is in close proximity of the binding site of Tim23, has different conformations in X-ray, NMR and new crystal contact-free space (CCFS) structures. MD simulations can provide information on the structure and dynamics of the loop in solution.The conformational ensemble of the loop was characterized using loop modeling and molecular dynamics (MD) simulations.MD simulations confirmed mobility of the loop. Multidimensional scaling and clustering were used to characterize the dynamic conformational ensemble of the loop. Free energy landscape showed that the CCFS crystal structure occupied a low energy region as compared to the conventional X-ray crystal structure. Analysis of crystal packing indicates that the CCFS provides larger conformational space for the motions of the loop.Our work reported the conformational ensemble of the loop in solution, which is in agreement with the structure obtained from CCFS approach. The combination of the experimental techniques and computational methods is beneficial for studying highly flexible regions of proteins.Computational methods, such as loop modeling and MD simulations, have proved to be useful for studying conformational flexibility of proteins. These methods in integration with experimental techniques such as CCFS has the potential to transform the studies on flexible regions of proteins. Tim21, a subunit of a highly dynamic translocase of the inner mitochondrial membrane (TIM23) complex, translocates proteins by interacting with subunits in the translocase of the outer membrane (TOM) complex and Tim23 channel in the TIM23 complex. A loop segment in Tim21, which is in close proximity of the binding site of Tim23, has different conformations in X-ray, NMR and new crystal contact-free space (CCFS) structures. MD simulations can provide information on the structure and dynamics of the loop in solution.BACKGROUNDTim21, a subunit of a highly dynamic translocase of the inner mitochondrial membrane (TIM23) complex, translocates proteins by interacting with subunits in the translocase of the outer membrane (TOM) complex and Tim23 channel in the TIM23 complex. A loop segment in Tim21, which is in close proximity of the binding site of Tim23, has different conformations in X-ray, NMR and new crystal contact-free space (CCFS) structures. MD simulations can provide information on the structure and dynamics of the loop in solution.The conformational ensemble of the loop was characterized using loop modeling and molecular dynamics (MD) simulations.METHODSThe conformational ensemble of the loop was characterized using loop modeling and molecular dynamics (MD) simulations.MD simulations confirmed mobility of the loop. Multidimensional scaling and clustering were used to characterize the dynamic conformational ensemble of the loop. Free energy landscape showed that the CCFS crystal structure occupied a low energy region as compared to the conventional X-ray crystal structure. Analysis of crystal packing indicates that the CCFS provides larger conformational space for the motions of the loop.RESULTSMD simulations confirmed mobility of the loop. Multidimensional scaling and clustering were used to characterize the dynamic conformational ensemble of the loop. Free energy landscape showed that the CCFS crystal structure occupied a low energy region as compared to the conventional X-ray crystal structure. Analysis of crystal packing indicates that the CCFS provides larger conformational space for the motions of the loop.Our work reported the conformational ensemble of the loop in solution, which is in agreement with the structure obtained from CCFS approach. The combination of the experimental techniques and computational methods is beneficial for studying highly flexible regions of proteins.CONCLUSIONSOur work reported the conformational ensemble of the loop in solution, which is in agreement with the structure obtained from CCFS approach. The combination of the experimental techniques and computational methods is beneficial for studying highly flexible regions of proteins.Computational methods, such as loop modeling and MD simulations, have proved to be useful for studying conformational flexibility of proteins. These methods in integration with experimental techniques such as CCFS has the potential to transform the studies on flexible regions of proteins.GENERAL SIGNIFICANCEComputational methods, such as loop modeling and MD simulations, have proved to be useful for studying conformational flexibility of proteins. These methods in integration with experimental techniques such as CCFS has the potential to transform the studies on flexible regions of proteins.
ArticleNumber	129417
Author	Kohda, Daisuke Miyashita, Osamu Bala, Siqin Srivastava, Arpita Motomura, Hajime Tama, Florence
Author_xml	– sequence: 1 givenname: Arpita surname: Srivastava fullname: Srivastava, Arpita email: srivastava.arpita@g.mbox.nagoya-u.ac.jp organization: Department of Physics, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan – sequence: 2 givenname: Siqin surname: Bala fullname: Bala, Siqin email: siqin@bioreg.kyushu-u.ac.jp organization: Division of Structural Biology, Medical Institute of Bioregulation, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka 812-8582, Japan – sequence: 3 givenname: Hajime surname: Motomura fullname: Motomura, Hajime email: h-motomura@bioreg.kyushu-u.ac.jp organization: Division of Structural Biology, Medical Institute of Bioregulation, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka 812-8582, Japan – sequence: 4 givenname: Daisuke surname: Kohda fullname: Kohda, Daisuke email: kohda@bioreg.kyushu-u.ac.jp organization: Division of Structural Biology, Medical Institute of Bioregulation, Kyushu University, Maidashi 3-1-1, Higashi-ku, Fukuoka 812-8582, Japan – sequence: 5 givenname: Florence surname: Tama fullname: Tama, Florence email: florence.tama@nagoua-u.jp organization: Department of Physics, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8602, Japan – sequence: 6 givenname: Osamu surname: Miyashita fullname: Miyashita, Osamu email: osamu.miyashita@riken.jp organization: Center for Computational Science, RIKEN, 6-7-1 Minatojima-minami-machi, Chuo-ku, Kobe, Hyogo 650-0047, Japan
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Keywords	MD_NMR Tim21 L2 Molecular dynamics mdm1-mdm10 RMSF Loop modeling RMSD m1-m10 IMS clus1-clus10 Crystal contact-free space NMR CCFS MD_CCFS MD MD_Xray MBP Xray MDS
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Snippet	Tim21, a subunit of a highly dynamic translocase of the inner mitochondrial membrane (TIM23) complex, translocates proteins by interacting with subunits in the...
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SubjectTerms	binding sites computational methodology Crystal contact-free space crystal structure energy enzymes Gibbs free energy Loop modeling mitochondrial membrane Molecular dynamics multidimensional scaling nuclear magnetic resonance spectroscopy physiological transport proteins simulation models Tim21 X-radiation
Title	Conformational ensemble of an intrinsically flexible loop in mitochondrial import protein Tim21 studied by modeling and molecular dynamics simulations
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