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Exploring the conformational transitions of biomolecular systems using a simple two-state anisotropic network model.

Das A, Gur M, Cheng MH, Jo S, Bahar I, Roux B - PLoS Comput. Biol. (2014)

Bottom Line: Application to several systems of broad biological interest such as adenylate kinase, ATP-driven calcium pump SERCA, leucine transporter and glutamate transporter shows that ANMPathway yields results in good agreement with those from other similar methods and with data obtained from all-atom molecular dynamics simulations, in support of the utility of this simple and efficient approach.Notably the method provides experimentally testable predictions, including the formation of non-native contacts during the transition which we were able to detect in two of the systems we studied.An open-access web server has been created to deliver ANMPathway results.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry and Molecular Biology, Gordon Center for Integrative Science, University of Chicago, Chicago, Illinois, United States of America.

ABSTRACT
Biomolecular conformational transitions are essential to biological functions. Most experimental methods report on the long-lived functional states of biomolecules, but information about the transition pathways between these stable states is generally scarce. Such transitions involve short-lived conformational states that are difficult to detect experimentally. For this reason, computational methods are needed to produce plausible hypothetical transition pathways that can then be probed experimentally. Here we propose a simple and computationally efficient method, called ANMPathway, for constructing a physically reasonable pathway between two endpoints of a conformational transition. We adopt a coarse-grained representation of the protein and construct a two-state potential by combining two elastic network models (ENMs) representative of the experimental structures resolved for the endpoints. The two-state potential has a cusp hypersurface in the configuration space where the energies from both the ENMs are equal. We first search for the minimum energy structure on the cusp hypersurface and then treat it as the transition state. The continuous pathway is subsequently constructed by following the steepest descent energy minimization trajectories starting from the transition state on each side of the cusp hypersurface. Application to several systems of broad biological interest such as adenylate kinase, ATP-driven calcium pump SERCA, leucine transporter and glutamate transporter shows that ANMPathway yields results in good agreement with those from other similar methods and with data obtained from all-atom molecular dynamics simulations, in support of the utility of this simple and efficient approach. Notably the method provides experimentally testable predictions, including the formation of non-native contacts during the transition which we were able to detect in two of the systems we studied. An open-access web server has been created to deliver ANMPathway results.

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Occurrence of outward-facing occluded/closed (OFc) state along the computed transition pathway between outward-facing open (OFo) and inward-facing open (IFo) states of LeuT.A. Relative orientations of TM1, TM6 and TM10 of LeuT in the OFo (orange), OFc (yellow) and IFo (cyan) crystal structures. The OFo crystal structure is shown in transparent cartoon. Inward tilting of the TM1b and TM6a segments contributes to the closure of the extracellular vestibule, indicating the decreased distances of TM1b-TM10 and TM6a-TM10. Outward tilting of TM1a dominates the opening of the intracellular vestibule, resulting in the increased distance between TM1a andTM6b. B. Variation of the center of mass (COM) distances of TM1a-TM10 (red+), TM6b-TM10 (blue+), and TM1a-TM6b (gray+) as the LeuT undergoes transition from the OFo to IFo states. For COM distance calculations, TM1a (R11 to A22), TM1b (L25 to A35), TM6a (G242 to L255), TM6b (F259 to Y268), and TM10 (K398 to V412)  atoms are taken from ANMPathway calculations of LeuT from IFo to OFo. Yellow arrows point to the values found in the OFc crystal structure. Clearly, occluded intermediates are identified by ANMPathway calculations (highlighted by the horizontal blue arrow).
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pcbi-1003521-g005: Occurrence of outward-facing occluded/closed (OFc) state along the computed transition pathway between outward-facing open (OFo) and inward-facing open (IFo) states of LeuT.A. Relative orientations of TM1, TM6 and TM10 of LeuT in the OFo (orange), OFc (yellow) and IFo (cyan) crystal structures. The OFo crystal structure is shown in transparent cartoon. Inward tilting of the TM1b and TM6a segments contributes to the closure of the extracellular vestibule, indicating the decreased distances of TM1b-TM10 and TM6a-TM10. Outward tilting of TM1a dominates the opening of the intracellular vestibule, resulting in the increased distance between TM1a andTM6b. B. Variation of the center of mass (COM) distances of TM1a-TM10 (red+), TM6b-TM10 (blue+), and TM1a-TM6b (gray+) as the LeuT undergoes transition from the OFo to IFo states. For COM distance calculations, TM1a (R11 to A22), TM1b (L25 to A35), TM6a (G242 to L255), TM6b (F259 to Y268), and TM10 (K398 to V412) atoms are taken from ANMPathway calculations of LeuT from IFo to OFo. Yellow arrows point to the values found in the OFc crystal structure. Clearly, occluded intermediates are identified by ANMPathway calculations (highlighted by the horizontal blue arrow).

Mentions: There is another crystal structure of LeuT which models the outward-facing open state (PDB ID: 3TT1 [74]). The sequence of functional states in the reaction cycle is: OF open (PDB ID: 3TT1)OF occluded (PDB ID: 2A65)IF open (PDB ID: 3TT3). There are important differences in the helical orientations of several TM helices between the OF open and OF occluded structures (Fig. (5A)) even though their overall architectures are quite similar. It is natural to ask whether the ANMPathway could predict the existence of OF closed state along a transition pathway calculated between OF open and IF open states. We indeed found a conformer which is very close to the OF closed state (RMSD from 2A65: ∼1.0 Å) along the pathway between the crystal structures of OF open and IF open states. The detection of the occluded intermediate is studied by monitoring order parameters that describe the instantaneous conformations of the TM helices responsible for gating and binding of ions. The order parameters are the center of mass (COM) distances between the pairs of helices TM1a-TM10, TM6b-TM10 and TM1a-TM6b. The results are shown in Fig. (5B). In all three distance profiles the intermediate is detected as indicated by the yellow arrows. Given the simplicity of the potential energy function, it is quite remarkable that the method is capable of detecting a functionally relevant and experimentally observed intermediate state. This fact highlights the usefulness of the method as well as significance of global modes of motion in facilitating the conformational transition of transporters.


Exploring the conformational transitions of biomolecular systems using a simple two-state anisotropic network model.

Das A, Gur M, Cheng MH, Jo S, Bahar I, Roux B - PLoS Comput. Biol. (2014)

Occurrence of outward-facing occluded/closed (OFc) state along the computed transition pathway between outward-facing open (OFo) and inward-facing open (IFo) states of LeuT.A. Relative orientations of TM1, TM6 and TM10 of LeuT in the OFo (orange), OFc (yellow) and IFo (cyan) crystal structures. The OFo crystal structure is shown in transparent cartoon. Inward tilting of the TM1b and TM6a segments contributes to the closure of the extracellular vestibule, indicating the decreased distances of TM1b-TM10 and TM6a-TM10. Outward tilting of TM1a dominates the opening of the intracellular vestibule, resulting in the increased distance between TM1a andTM6b. B. Variation of the center of mass (COM) distances of TM1a-TM10 (red+), TM6b-TM10 (blue+), and TM1a-TM6b (gray+) as the LeuT undergoes transition from the OFo to IFo states. For COM distance calculations, TM1a (R11 to A22), TM1b (L25 to A35), TM6a (G242 to L255), TM6b (F259 to Y268), and TM10 (K398 to V412)  atoms are taken from ANMPathway calculations of LeuT from IFo to OFo. Yellow arrows point to the values found in the OFc crystal structure. Clearly, occluded intermediates are identified by ANMPathway calculations (highlighted by the horizontal blue arrow).
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3974643&req=5

pcbi-1003521-g005: Occurrence of outward-facing occluded/closed (OFc) state along the computed transition pathway between outward-facing open (OFo) and inward-facing open (IFo) states of LeuT.A. Relative orientations of TM1, TM6 and TM10 of LeuT in the OFo (orange), OFc (yellow) and IFo (cyan) crystal structures. The OFo crystal structure is shown in transparent cartoon. Inward tilting of the TM1b and TM6a segments contributes to the closure of the extracellular vestibule, indicating the decreased distances of TM1b-TM10 and TM6a-TM10. Outward tilting of TM1a dominates the opening of the intracellular vestibule, resulting in the increased distance between TM1a andTM6b. B. Variation of the center of mass (COM) distances of TM1a-TM10 (red+), TM6b-TM10 (blue+), and TM1a-TM6b (gray+) as the LeuT undergoes transition from the OFo to IFo states. For COM distance calculations, TM1a (R11 to A22), TM1b (L25 to A35), TM6a (G242 to L255), TM6b (F259 to Y268), and TM10 (K398 to V412) atoms are taken from ANMPathway calculations of LeuT from IFo to OFo. Yellow arrows point to the values found in the OFc crystal structure. Clearly, occluded intermediates are identified by ANMPathway calculations (highlighted by the horizontal blue arrow).
Mentions: There is another crystal structure of LeuT which models the outward-facing open state (PDB ID: 3TT1 [74]). The sequence of functional states in the reaction cycle is: OF open (PDB ID: 3TT1)OF occluded (PDB ID: 2A65)IF open (PDB ID: 3TT3). There are important differences in the helical orientations of several TM helices between the OF open and OF occluded structures (Fig. (5A)) even though their overall architectures are quite similar. It is natural to ask whether the ANMPathway could predict the existence of OF closed state along a transition pathway calculated between OF open and IF open states. We indeed found a conformer which is very close to the OF closed state (RMSD from 2A65: ∼1.0 Å) along the pathway between the crystal structures of OF open and IF open states. The detection of the occluded intermediate is studied by monitoring order parameters that describe the instantaneous conformations of the TM helices responsible for gating and binding of ions. The order parameters are the center of mass (COM) distances between the pairs of helices TM1a-TM10, TM6b-TM10 and TM1a-TM6b. The results are shown in Fig. (5B). In all three distance profiles the intermediate is detected as indicated by the yellow arrows. Given the simplicity of the potential energy function, it is quite remarkable that the method is capable of detecting a functionally relevant and experimentally observed intermediate state. This fact highlights the usefulness of the method as well as significance of global modes of motion in facilitating the conformational transition of transporters.

Bottom Line: Application to several systems of broad biological interest such as adenylate kinase, ATP-driven calcium pump SERCA, leucine transporter and glutamate transporter shows that ANMPathway yields results in good agreement with those from other similar methods and with data obtained from all-atom molecular dynamics simulations, in support of the utility of this simple and efficient approach.Notably the method provides experimentally testable predictions, including the formation of non-native contacts during the transition which we were able to detect in two of the systems we studied.An open-access web server has been created to deliver ANMPathway results.

View Article: PubMed Central - PubMed

Affiliation: Department of Biochemistry and Molecular Biology, Gordon Center for Integrative Science, University of Chicago, Chicago, Illinois, United States of America.

ABSTRACT
Biomolecular conformational transitions are essential to biological functions. Most experimental methods report on the long-lived functional states of biomolecules, but information about the transition pathways between these stable states is generally scarce. Such transitions involve short-lived conformational states that are difficult to detect experimentally. For this reason, computational methods are needed to produce plausible hypothetical transition pathways that can then be probed experimentally. Here we propose a simple and computationally efficient method, called ANMPathway, for constructing a physically reasonable pathway between two endpoints of a conformational transition. We adopt a coarse-grained representation of the protein and construct a two-state potential by combining two elastic network models (ENMs) representative of the experimental structures resolved for the endpoints. The two-state potential has a cusp hypersurface in the configuration space where the energies from both the ENMs are equal. We first search for the minimum energy structure on the cusp hypersurface and then treat it as the transition state. The continuous pathway is subsequently constructed by following the steepest descent energy minimization trajectories starting from the transition state on each side of the cusp hypersurface. Application to several systems of broad biological interest such as adenylate kinase, ATP-driven calcium pump SERCA, leucine transporter and glutamate transporter shows that ANMPathway yields results in good agreement with those from other similar methods and with data obtained from all-atom molecular dynamics simulations, in support of the utility of this simple and efficient approach. Notably the method provides experimentally testable predictions, including the formation of non-native contacts during the transition which we were able to detect in two of the systems we studied. An open-access web server has been created to deliver ANMPathway results.

Show MeSH