Brownian dynamics simulations of the interactions between lactate dehydrogenase (LDH) and G- or F-Actin. Part I: Muscle and heart homo-isoforms
Glycolytic enzymes may compartment in cells by binding to cytoskeletal structures. One potentially important step in compartmentation is the binding of the cytoskeletal protein F-actin by lactate dehydrogenase (LDH). Brownian dynamics (BD) simulations of LDH interacting with G- or F-actin provided f...
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| Published in | Scientific African Vol. 9; p. e00510 |
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| Language | English |
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| Abstract | Glycolytic enzymes may compartment in cells by binding to cytoskeletal structures. One potentially important step in compartmentation is the binding of the cytoskeletal protein F-actin by lactate dehydrogenase (LDH). Brownian dynamics (BD) simulations of LDH interacting with G- or F-actin provided first-encounter snapshots and relative binding free energies. Models of muscle (LDH-M4) and heart (LDH-H4) isoforms of lactate dehydrogenase for four species (rabbit, human, rat and pig) were examined. Strong electrostatic interactions were observed between both monomeric and polymerized actin for LDH-M4, but not LDH-H4. These electrostatic field potentials were examined in detail and explained the differences in complex formations between LDH-M4 and LDH-H4 with G- and F-actin. Complexes formed between LDH-M4 and G-actin involved residues found in the surface grooves between the A/D and B/C subunits. Several binding modes occurred between LDH-M4 and F-actin, the most frequent of which involved two subunits of actin interacting with two subunits of LDH-M4. LDH-M4 interactions with F-actin relied on 10 residues, nine of which were conserved between species. All of these residues except two were located in the positive grooves between A/D and B/C subunits, where the protein's electrostatic potential is enhanced by its quaternary structure. LDH-H4, however, does not show unique binding modes nor does it have a favorable relative binding free energy compared to LDH-M4. Thus, BD supports experimental findings [Ehmann, J. D.; Hultin, H. O. Arch. Biochem. Biophys.1973, 154, 471], that LDH-M4 binds actin, but LDH-H4 does not. |
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| AbstractList | Glycolytic enzymes may compartment in cells by binding to cytoskeletal structures. One potentially important step in compartmentation is the binding of the cytoskeletal protein F-actin by lactate dehydrogenase (LDH). Brownian dynamics (BD) simulations of LDH interacting with G- or F-actin provided first-encounter snapshots and relative binding free energies. Models of muscle (LDH-M4) and heart (LDH-H4) isoforms of lactate dehydrogenase for four species (rabbit, human, rat and pig) were examined. Strong electrostatic interactions were observed between both monomeric and polymerized actin for LDH-M4, but not LDH-H4. These electrostatic field potentials were examined in detail and explained the differences in complex formations between LDH-M4 and LDH-H4 with G- and F-actin. Complexes formed between LDH-M4 and G-actin involved residues found in the surface grooves between the A/D and B/C subunits. Several binding modes occurred between LDH-M4 and F-actin, the most frequent of which involved two subunits of actin interacting with two subunits of LDH-M4. LDH-M4 interactions with F-actin relied on 10 residues, nine of which were conserved between species. All of these residues except two were located in the positive grooves between A/D and B/C subunits, where the protein's electrostatic potential is enhanced by its quaternary structure. LDH-H4, however, does not show unique binding modes nor does it have a favorable relative binding free energy compared to LDH-M4. Thus, BD supports experimental findings [Ehmann, J. D.; Hultin, H. O. Arch. Biochem. Biophys. 1973, 154, 471], that LDH-M4 binds actin, but LDH-H4 does not. |
| ArticleNumber | e00510 |
| Author | Patouossa, Issofa Njabon, Eric N. Carlson, Kristine L. Forlemu, Neville Y. Lowe, Stephen L. Thomasson, Kathryn A. |
| Author_xml | – sequence: 1 givenname: Eric N. surname: Njabon fullname: Njabon, Eric N. email: enn232@mun.ca organization: Faculty of Science, Laboratory of Physical and Theoretical Chemistry University of Yaoundé., P.O Box 812, Yaoundé I, Cameroon – sequence: 2 givenname: Issofa surname: Patouossa fullname: Patouossa, Issofa email: patouossa12@yahoo.fr organization: Faculty of Science, Laboratory of Physical and Theoretical Chemistry University of Yaoundé., P.O Box 812, Yaoundé I, Cameroon – sequence: 3 givenname: Kristine L. surname: Carlson fullname: Carlson, Kristine L. organization: University of North Dakota, Department of Chemistry, Abbott Hall Room 236, 151 Cornell St, Stop 9024, Grand Forks, ND, 58202-9024 USA – sequence: 4 givenname: Stephen L. surname: Lowe fullname: Lowe, Stephen L. email: steve.lowe@und.edu organization: University of North Dakota, Department of Chemistry, Abbott Hall Room 236, 151 Cornell St, Stop 9024, Grand Forks, ND, 58202-9024 USA – sequence: 5 givenname: Neville Y. surname: Forlemu fullname: Forlemu, Neville Y. email: nforlemu@ggc.edu organization: University of North Dakota, Department of Chemistry, Abbott Hall Room 236, 151 Cornell St, Stop 9024, Grand Forks, ND, 58202-9024 USA – sequence: 6 givenname: Kathryn A. surname: Thomasson fullname: Thomasson, Kathryn A. email: kathryn.thomasson@und.edu organization: University of North Dakota, Department of Chemistry, Abbott Hall Room 236, 151 Cornell St, Stop 9024, Grand Forks, ND, 58202-9024 USA |
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| Cites_doi | 10.1002/1097-0134(20010501)43:2<175::AID-PROT1029>3.0.CO;2-# 10.1093/nar/gkg095 10.1098/rstb.1991.0047 10.1016/S0006-3495(99)77174-2 10.1139/o81-069 10.1080/14756360310001623309 10.1006/jmbi.1993.1135 10.1016/0003-9861(73)90080-5 10.1002/jmr.599 10.1007/BF00219393 10.1016/0167-4838(86)90198-6 10.1111/j.1471-4159.1980.tb04646.x 10.1073/pnas.91.20.9392 10.1016/S0021-9258(18)32327-5 10.1016/S0006-3495(01)76224-8 10.1016/S0021-9258(18)55120-6 10.1111/j.1432-1033.1971.tb01522.x 10.1093/nar/30.1.245 10.1016/0065-2571(86)90020-8 10.1038/347044a0 10.1002/bip.20611 10.1042/bj2570921 10.1016/S0021-9258(19)84964-5 10.1016/j.neuron.2016.03.011 10.1016/0022-2836(82)90505-8 10.1016/0304-4165(75)90187-7 10.1111/j.1432-1033.1990.tb15479.x 10.1093/nar/13.3.711 10.1002/bip.10560 10.1002/prot.340010109 10.1016/0047-6374(85)90027-2 |
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| Keywords | BD Brownian dynamics LDH-H4 PMF Electrostatic interactions LDH-M4 EP COMs Free energy Protein-protein interactions LDH aldolase GAPDH Glycolytic enzymes |
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| Title | Brownian dynamics simulations of the interactions between lactate dehydrogenase (LDH) and G- or F-Actin. Part I: Muscle and heart homo-isoforms |
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