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Conformational dynamics and ligand binding in the multi-domain protein PDC109.

Kim HJ, Choi MY, Kim HJ, Llinás M - PLoS ONE (2010)

Bottom Line: The effective PDC109-PhC association constant of 28 M(-1), estimated from their potential of mean force is consistent with the experimental result.Principal component analysis of the long timescale MD simulations was compared to the significantly less expensive normal mode analysis of minimized structures.The present study illustrates the use of detailed MD simulations to clarify the energetics of specific ligand-domain interactions revealed by a static crystallographic model, as well as their influence on relative domain motions in a multi-domain protein.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America.

ABSTRACT
PDC109 is a modular multi-domain protein with two fibronectin type II (Fn2) repeats joined by a linker. It plays a major role in bull sperm binding to the oviductal epithelium through its interactions with phosphorylcholines (PhCs), a head group of sperm cell membrane lipids. The crystal structure of the PDC109-PhC complex shows that each PhC binds to the corresponding Fn2 domain, while the two domains are on the same face of the protein. Long timescale explicit solvent molecular dynamics (MD) simulations of PDC109, in the presence and absence of PhC, suggest that PhC binding strongly correlates with the relative orientation of choline-phospholipid binding sites of the two Fn2 domains; unless the two domains tightly bind PhCs, they tend to change their relative orientation by deforming the flexible linker. The effective PDC109-PhC association constant of 28 M(-1), estimated from their potential of mean force is consistent with the experimental result. Principal component analysis of the long timescale MD simulations was compared to the significantly less expensive normal mode analysis of minimized structures. The comparison indicates that difference between relative domain motions of PDC109 with bound and unbound PhC is captured by the first principal component in the principal component analysis as well as the three lowest normal modes in the normal mode analysis. The present study illustrates the use of detailed MD simulations to clarify the energetics of specific ligand-domain interactions revealed by a static crystallographic model, as well as their influence on relative domain motions in a multi-domain protein.

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RMSDs for (A) PDC109/a, (B) PDC109/b, (C) linker, and (D) the entire protein.The time series for ligand-bound and free PDC109 is shown in blue and red, respectively.
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pone-0009180-g010: RMSDs for (A) PDC109/a, (B) PDC109/b, (C) linker, and (D) the entire protein.The time series for ligand-bound and free PDC109 is shown in blue and red, respectively.

Mentions: Root Mean Square Deviation (RMSD) of the segmental backbone atoms of PDC109 was calculated relative to the crystal structure conformation of the protein complexed with PhC. As shown in Fig. 10 A and B, the RMSD values in the time series for individual domains PDC109/a (C24–C61) and PDC109/b (C69–C109) remain less than 1.5 Å, whether in the presence or absence of PhC. The long duration of the MD simulations indicates that the CHARMM force field [57], [58] is able to maintain the stability of the domains’ global folds in the absence of imposed experimental or ad hoc harmonic restraints. For the linker region, the RMSDs are less than 2.0 Å regardless of PhC binding, while for the PhC-bound PDC109 protein the RMSD increases and fluctuates around 3.5 Å during the last 100 ns (Fig. 10 C). This suggests that most of the conformational variability of PDC109 results from the internal conformational changes of the linker as it contracts and extends (Fig. 8). In particular, the large RMSD value of the linker segment during the last 100 ns reflects structural deformation of the linker relative to the X-ray structure (Fig. 8 blue). Fig. 10 D shows that the RMSD values markedly increase for the entire PDC109 protein, with or without bound PhC. The RMSDs increase from 2 Å to 10 Å at 20 ns for the ligand-free protein and at 60 ns for the PhC-bound PDC109. After 250 ns, the RMSD of the entire PhC-bound PDC109 gradually decreases and remains 5.0 Å. This variation in the RMSD suggests that the relative orientation of the two domains drifts away from the crystal structure orientation in the absence of ligand (Fig. 8 green and Fig. 8 B); however, they can also return to the crystallographic conformation in the presence of ligand (Fig. 8 blue).


Conformational dynamics and ligand binding in the multi-domain protein PDC109.

Kim HJ, Choi MY, Kim HJ, Llinás M - PLoS ONE (2010)

RMSDs for (A) PDC109/a, (B) PDC109/b, (C) linker, and (D) the entire protein.The time series for ligand-bound and free PDC109 is shown in blue and red, respectively.
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC2823774&req=5

pone-0009180-g010: RMSDs for (A) PDC109/a, (B) PDC109/b, (C) linker, and (D) the entire protein.The time series for ligand-bound and free PDC109 is shown in blue and red, respectively.
Mentions: Root Mean Square Deviation (RMSD) of the segmental backbone atoms of PDC109 was calculated relative to the crystal structure conformation of the protein complexed with PhC. As shown in Fig. 10 A and B, the RMSD values in the time series for individual domains PDC109/a (C24–C61) and PDC109/b (C69–C109) remain less than 1.5 Å, whether in the presence or absence of PhC. The long duration of the MD simulations indicates that the CHARMM force field [57], [58] is able to maintain the stability of the domains’ global folds in the absence of imposed experimental or ad hoc harmonic restraints. For the linker region, the RMSDs are less than 2.0 Å regardless of PhC binding, while for the PhC-bound PDC109 protein the RMSD increases and fluctuates around 3.5 Å during the last 100 ns (Fig. 10 C). This suggests that most of the conformational variability of PDC109 results from the internal conformational changes of the linker as it contracts and extends (Fig. 8). In particular, the large RMSD value of the linker segment during the last 100 ns reflects structural deformation of the linker relative to the X-ray structure (Fig. 8 blue). Fig. 10 D shows that the RMSD values markedly increase for the entire PDC109 protein, with or without bound PhC. The RMSDs increase from 2 Å to 10 Å at 20 ns for the ligand-free protein and at 60 ns for the PhC-bound PDC109. After 250 ns, the RMSD of the entire PhC-bound PDC109 gradually decreases and remains 5.0 Å. This variation in the RMSD suggests that the relative orientation of the two domains drifts away from the crystal structure orientation in the absence of ligand (Fig. 8 green and Fig. 8 B); however, they can also return to the crystallographic conformation in the presence of ligand (Fig. 8 blue).

Bottom Line: The effective PDC109-PhC association constant of 28 M(-1), estimated from their potential of mean force is consistent with the experimental result.Principal component analysis of the long timescale MD simulations was compared to the significantly less expensive normal mode analysis of minimized structures.The present study illustrates the use of detailed MD simulations to clarify the energetics of specific ligand-domain interactions revealed by a static crystallographic model, as well as their influence on relative domain motions in a multi-domain protein.

View Article: PubMed Central - PubMed

Affiliation: Department of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania, United States of America.

ABSTRACT
PDC109 is a modular multi-domain protein with two fibronectin type II (Fn2) repeats joined by a linker. It plays a major role in bull sperm binding to the oviductal epithelium through its interactions with phosphorylcholines (PhCs), a head group of sperm cell membrane lipids. The crystal structure of the PDC109-PhC complex shows that each PhC binds to the corresponding Fn2 domain, while the two domains are on the same face of the protein. Long timescale explicit solvent molecular dynamics (MD) simulations of PDC109, in the presence and absence of PhC, suggest that PhC binding strongly correlates with the relative orientation of choline-phospholipid binding sites of the two Fn2 domains; unless the two domains tightly bind PhCs, they tend to change their relative orientation by deforming the flexible linker. The effective PDC109-PhC association constant of 28 M(-1), estimated from their potential of mean force is consistent with the experimental result. Principal component analysis of the long timescale MD simulations was compared to the significantly less expensive normal mode analysis of minimized structures. The comparison indicates that difference between relative domain motions of PDC109 with bound and unbound PhC is captured by the first principal component in the principal component analysis as well as the three lowest normal modes in the normal mode analysis. The present study illustrates the use of detailed MD simulations to clarify the energetics of specific ligand-domain interactions revealed by a static crystallographic model, as well as their influence on relative domain motions in a multi-domain protein.

Show MeSH
Related in: MedlinePlus