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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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X-ray structure of BSP-A1.(A) Sequence and associated secondary structure organization of PDC109. Cystine bridges are indicated by black lines. (B) Crystal structure of PDC109 [24]. The N-terminal Fn2 domain (PDC109/a, residues 24–61) and the C-terminal Fn2 domain (PDC109/b, residues 69–109) are connected by a linker peptide (residues 62–68) shown in blue. The net charges are 1, 1, and 2 for PDC109/a, linker, and PDC109/b, respectively. Loop 1 (H41-L44) between 2 and 3 strands in PDC109/a and loop 2 (G87-M91) between the 2 and 3 strands in PDC109/b are denoted by green arrows [74].
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pone-0009180-g001: X-ray structure of BSP-A1.(A) Sequence and associated secondary structure organization of PDC109. Cystine bridges are indicated by black lines. (B) Crystal structure of PDC109 [24]. The N-terminal Fn2 domain (PDC109/a, residues 24–61) and the C-terminal Fn2 domain (PDC109/b, residues 69–109) are connected by a linker peptide (residues 62–68) shown in blue. The net charges are 1, 1, and 2 for PDC109/a, linker, and PDC109/b, respectively. Loop 1 (H41-L44) between 2 and 3 strands in PDC109/a and loop 2 (G87-M91) between the 2 and 3 strands in PDC109/b are denoted by green arrows [74].

Mentions: The structure of the complex of PDC109 with PhC [24] has been solved as a homodimer using X-ray crystallography (Figs. 1 and 2). The dimer is composed of two protomers, BSP-A1 and BSP-A2, which only differ in the extent of glycosylation [26], [27]. PDC109 refers to a mixture of BSP-A1 and BSP-A2. It is composed of 109 amino acids with an N-terminal O-glycosylated acidic extension followed by two fibronectin type II (Fn2) repeats, where each has the capability to bind to one PhC molecule [24]. For the sake of simplicity, the N-terminal (residues 24–61) and C-terminal (residues 69–109) Fn2 domains of PDC109 are denoted as PDC109/a and PDC109/b, respectively.


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

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

X-ray structure of BSP-A1.(A) Sequence and associated secondary structure organization of PDC109. Cystine bridges are indicated by black lines. (B) Crystal structure of PDC109 [24]. The N-terminal Fn2 domain (PDC109/a, residues 24–61) and the C-terminal Fn2 domain (PDC109/b, residues 69–109) are connected by a linker peptide (residues 62–68) shown in blue. The net charges are 1, 1, and 2 for PDC109/a, linker, and PDC109/b, respectively. Loop 1 (H41-L44) between 2 and 3 strands in PDC109/a and loop 2 (G87-M91) between the 2 and 3 strands in PDC109/b are denoted by green arrows [74].
© Copyright Policy
Related In: Results  -  Collection

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

pone-0009180-g001: X-ray structure of BSP-A1.(A) Sequence and associated secondary structure organization of PDC109. Cystine bridges are indicated by black lines. (B) Crystal structure of PDC109 [24]. The N-terminal Fn2 domain (PDC109/a, residues 24–61) and the C-terminal Fn2 domain (PDC109/b, residues 69–109) are connected by a linker peptide (residues 62–68) shown in blue. The net charges are 1, 1, and 2 for PDC109/a, linker, and PDC109/b, respectively. Loop 1 (H41-L44) between 2 and 3 strands in PDC109/a and loop 2 (G87-M91) between the 2 and 3 strands in PDC109/b are denoted by green arrows [74].
Mentions: The structure of the complex of PDC109 with PhC [24] has been solved as a homodimer using X-ray crystallography (Figs. 1 and 2). The dimer is composed of two protomers, BSP-A1 and BSP-A2, which only differ in the extent of glycosylation [26], [27]. PDC109 refers to a mixture of BSP-A1 and BSP-A2. It is composed of 109 amino acids with an N-terminal O-glycosylated acidic extension followed by two fibronectin type II (Fn2) repeats, where each has the capability to bind to one PhC molecule [24]. For the sake of simplicity, the N-terminal (residues 24–61) and C-terminal (residues 69–109) Fn2 domains of PDC109 are denoted as PDC109/a and PDC109/b, respectively.

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