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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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Relative orientation and distance of the two domains of PDC109. is the angle between two vectors, V and V in (A) [74], defined as displacements of C atom between W47 and W58 of PDC109/a and between W93 and W106 of PDC109/b, respectively. Fluctuations of  are shown for ligand-free PDC109 in red (B) and for PDC109 complexed with PhC in blue (C). Fluctuations of center-to-center distance  between two domains of PDC109 are in red (D) and of PhC-bound PDC109 are in blue (E).
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pone-0009180-g009: Relative orientation and distance of the two domains of PDC109. is the angle between two vectors, V and V in (A) [74], defined as displacements of C atom between W47 and W58 of PDC109/a and between W93 and W106 of PDC109/b, respectively. Fluctuations of are shown for ligand-free PDC109 in red (B) and for PDC109 complexed with PhC in blue (C). Fluctuations of center-to-center distance between two domains of PDC109 are in red (D) and of PhC-bound PDC109 are in blue (E).

Mentions: The global variation of the relative arrangement of Fn2 domains in PDC109 was monitored by tracking , as defined by:(2)where V1 and V2 represent vectors connecting the atoms of residues W47 and W58 in PDC109/a and residues W93 and W106 in PDC109/b (Fig. 9 A). These residues were chosen owing to their location within the binding site and because they exhibited, by reflecting the crystal structure, less mobility during the MD simulations. The value calculated from the crystal structure is 0.8, corresponding to 37. Fig. 9 B and C illustrates the time course of for PDC109 in the absence and presence of PhC, respectively. The values fluctuate for both systems during the first 160 ns, with less stability seen in the values for the PhC bound protein. In the absence of ligand, the two vectors mostly remain close to perpendicular (0). However, in the presence of PhC, the vectors approach anti-parallel (−1) orientation around 160 ns and parallel (1) orientation around 300 ns. The conformational changes of the protein lead the ligand dissociation and association around 240 ns and 334 ns, respectively (Fig. 3). Interestingly, this implies that the PhC binding affinity to PDC109 varies with the relative orientation of the two domains.


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

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

Relative orientation and distance of the two domains of PDC109. is the angle between two vectors, V and V in (A) [74], defined as displacements of C atom between W47 and W58 of PDC109/a and between W93 and W106 of PDC109/b, respectively. Fluctuations of  are shown for ligand-free PDC109 in red (B) and for PDC109 complexed with PhC in blue (C). Fluctuations of center-to-center distance  between two domains of PDC109 are in red (D) and of PhC-bound PDC109 are in blue (E).
© Copyright Policy
Related In: Results  -  Collection

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

pone-0009180-g009: Relative orientation and distance of the two domains of PDC109. is the angle between two vectors, V and V in (A) [74], defined as displacements of C atom between W47 and W58 of PDC109/a and between W93 and W106 of PDC109/b, respectively. Fluctuations of are shown for ligand-free PDC109 in red (B) and for PDC109 complexed with PhC in blue (C). Fluctuations of center-to-center distance between two domains of PDC109 are in red (D) and of PhC-bound PDC109 are in blue (E).
Mentions: The global variation of the relative arrangement of Fn2 domains in PDC109 was monitored by tracking , as defined by:(2)where V1 and V2 represent vectors connecting the atoms of residues W47 and W58 in PDC109/a and residues W93 and W106 in PDC109/b (Fig. 9 A). These residues were chosen owing to their location within the binding site and because they exhibited, by reflecting the crystal structure, less mobility during the MD simulations. The value calculated from the crystal structure is 0.8, corresponding to 37. Fig. 9 B and C illustrates the time course of for PDC109 in the absence and presence of PhC, respectively. The values fluctuate for both systems during the first 160 ns, with less stability seen in the values for the PhC bound protein. In the absence of ligand, the two vectors mostly remain close to perpendicular (0). However, in the presence of PhC, the vectors approach anti-parallel (−1) orientation around 160 ns and parallel (1) orientation around 300 ns. The conformational changes of the protein lead the ligand dissociation and association around 240 ns and 334 ns, respectively (Fig. 3). Interestingly, this implies that the PhC binding affinity to PDC109 varies with the relative orientation of the two domains.

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