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Capturing spontaneous partitioning of peripheral proteins using a biphasic membrane-mimetic model.

Arcario MJ, Ohkubo YZ, Tajkhorshid E - J Phys Chem B (2011)

Bottom Line: Furthermore, in many cases, the nature of the membrane "anchor", i.e., the part of the protein that inserts into the membrane, is also unknown.In addition to efficiently and consistently identifying the "keel" region as the hydrophobic membrane anchor, within a few nanoseconds each configuration simulated showed a convergent height (2.20 ± 1.04 Å) and angle with respect to the interface normal (23.37 ± 12.48°).We demonstrate that the model can produce the same results as those obtained from a full representation of a membrane, in terms of both the depth of penetration and the orientation of the protein in the final membrane-bound form with an order of magnitude decrease in the required computational time compared to previous models, allowing for a more exhaustive search for the correct membrane-bound configuration.

View Article: PubMed Central - PubMed

Affiliation: Center for Biophysics and Computational Biology, Department of Biochemistry, College of Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.

ABSTRACT
Membrane binding of peripheral proteins, mediated by specialized anchoring domains, is a crucial step for their biological function. Computational studies of membrane insertion, however, have proven challenging and largely inaccessible, due to the time scales required for the complete description of the process, mainly caused by the slow diffusion of the lipid molecules composing the membrane. Furthermore, in many cases, the nature of the membrane "anchor", i.e., the part of the protein that inserts into the membrane, is also unknown. Here, we address some of these issues by developing and employing a simplified representation of the membrane by a biphasic solvent model which we demonstrate can be used efficiently to capture and describe the process of hydrophobic insertion of membrane anchoring domains in all-atom molecular dynamics simulations. Applying the model, we have studied the insertion of the anchoring domain of a coagulation protein (the GLA domain of human protein C), starting from multiple initial configurations varying with regard to the initial orientation and height of the protein with respect to the membrane. In addition to efficiently and consistently identifying the "keel" region as the hydrophobic membrane anchor, within a few nanoseconds each configuration simulated showed a convergent height (2.20 ± 1.04 Å) and angle with respect to the interface normal (23.37 ± 12.48°). We demonstrate that the model can produce the same results as those obtained from a full representation of a membrane, in terms of both the depth of penetration and the orientation of the protein in the final membrane-bound form with an order of magnitude decrease in the required computational time compared to previous models, allowing for a more exhaustive search for the correct membrane-bound configuration.

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Structure of human protein C. (A) A general representation of hPrC showing the relative positions of the GLA anchoring domain, the two EGF-like domains, and the catalytic serine protease (SP) domain. (B) The GLA domain of hPrC. The backbone is shown in gray while the seven bound Ca2+ ions are shown as yellow spheres and numbered according to the crystal structure of the GLA domain of FVIIa.(69) The nine Gla residues of hPrC-GLA are colored in cyan, and the hydrophobic residues of the keel are shown in red. The arrow represents the vector connecting Ca2+-4 and the Cα of Phe40 which was used to represent the GLA domain’s axis in subsequent angle calculations. This structure is the starting point for all the simulations in the biphasic solvent system.
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fig1: Structure of human protein C. (A) A general representation of hPrC showing the relative positions of the GLA anchoring domain, the two EGF-like domains, and the catalytic serine protease (SP) domain. (B) The GLA domain of hPrC. The backbone is shown in gray while the seven bound Ca2+ ions are shown as yellow spheres and numbered according to the crystal structure of the GLA domain of FVIIa.(69) The nine Gla residues of hPrC-GLA are colored in cyan, and the hydrophobic residues of the keel are shown in red. The arrow represents the vector connecting Ca2+-4 and the Cα of Phe40 which was used to represent the GLA domain’s axis in subsequent angle calculations. This structure is the starting point for all the simulations in the biphasic solvent system.

Mentions: In this study we have utilized the GLA domain of human protein C (hPrC) as a representative membrane anchoring domain to test the effectiveness and efficiency of a simple biphasic solvent, membrane-mimetic model in characterizing the nature of the membrane anchoring domain and in capturing and describing the process of hydrophobic insertion of membrane anchoring domains. During the coagulation cascade, activated protein C (APC) acts as an anticoagulant(40) helping to stop clot formation. hPrC has a similar overall structure to other vitamin K-dependent coagulation proteins (Figure 1A) containing a serine protease (SP) catalytic domain, two EGF-like domains and the membrane-anchoring GLA domain.(41) The structure of the hPrC GLA domain is very similar to the GLA domains of other vitamin K-dependent hemostatic proteins such as factor VIIa (FVIIa) and prothrombin,(42) containing seven bound Ca2+ ions coordinated by nine Gla residues (Figure 1B). Binding of these Ca2+ ions is necessary for the formation of an active tertiary structure, as this causes the conformational change necessary to expose the 11-residue hydrophobic ω-loop and prepare the anchoring domain for insertion into the plasma membrane.21,43−46 Recent studies have also demonstrated that membrane insertion involves mainly the ω-loop and the bound Ca2+ ions, with the hydrophobic triad known as the keel forming the penetrating surface.21,47,48


Capturing spontaneous partitioning of peripheral proteins using a biphasic membrane-mimetic model.

Arcario MJ, Ohkubo YZ, Tajkhorshid E - J Phys Chem B (2011)

Structure of human protein C. (A) A general representation of hPrC showing the relative positions of the GLA anchoring domain, the two EGF-like domains, and the catalytic serine protease (SP) domain. (B) The GLA domain of hPrC. The backbone is shown in gray while the seven bound Ca2+ ions are shown as yellow spheres and numbered according to the crystal structure of the GLA domain of FVIIa.(69) The nine Gla residues of hPrC-GLA are colored in cyan, and the hydrophobic residues of the keel are shown in red. The arrow represents the vector connecting Ca2+-4 and the Cα of Phe40 which was used to represent the GLA domain’s axis in subsequent angle calculations. This structure is the starting point for all the simulations in the biphasic solvent system.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3102442&req=5

fig1: Structure of human protein C. (A) A general representation of hPrC showing the relative positions of the GLA anchoring domain, the two EGF-like domains, and the catalytic serine protease (SP) domain. (B) The GLA domain of hPrC. The backbone is shown in gray while the seven bound Ca2+ ions are shown as yellow spheres and numbered according to the crystal structure of the GLA domain of FVIIa.(69) The nine Gla residues of hPrC-GLA are colored in cyan, and the hydrophobic residues of the keel are shown in red. The arrow represents the vector connecting Ca2+-4 and the Cα of Phe40 which was used to represent the GLA domain’s axis in subsequent angle calculations. This structure is the starting point for all the simulations in the biphasic solvent system.
Mentions: In this study we have utilized the GLA domain of human protein C (hPrC) as a representative membrane anchoring domain to test the effectiveness and efficiency of a simple biphasic solvent, membrane-mimetic model in characterizing the nature of the membrane anchoring domain and in capturing and describing the process of hydrophobic insertion of membrane anchoring domains. During the coagulation cascade, activated protein C (APC) acts as an anticoagulant(40) helping to stop clot formation. hPrC has a similar overall structure to other vitamin K-dependent coagulation proteins (Figure 1A) containing a serine protease (SP) catalytic domain, two EGF-like domains and the membrane-anchoring GLA domain.(41) The structure of the hPrC GLA domain is very similar to the GLA domains of other vitamin K-dependent hemostatic proteins such as factor VIIa (FVIIa) and prothrombin,(42) containing seven bound Ca2+ ions coordinated by nine Gla residues (Figure 1B). Binding of these Ca2+ ions is necessary for the formation of an active tertiary structure, as this causes the conformational change necessary to expose the 11-residue hydrophobic ω-loop and prepare the anchoring domain for insertion into the plasma membrane.21,43−46 Recent studies have also demonstrated that membrane insertion involves mainly the ω-loop and the bound Ca2+ ions, with the hydrophobic triad known as the keel forming the penetrating surface.21,47,48

Bottom Line: Furthermore, in many cases, the nature of the membrane "anchor", i.e., the part of the protein that inserts into the membrane, is also unknown.In addition to efficiently and consistently identifying the "keel" region as the hydrophobic membrane anchor, within a few nanoseconds each configuration simulated showed a convergent height (2.20 ± 1.04 Å) and angle with respect to the interface normal (23.37 ± 12.48°).We demonstrate that the model can produce the same results as those obtained from a full representation of a membrane, in terms of both the depth of penetration and the orientation of the protein in the final membrane-bound form with an order of magnitude decrease in the required computational time compared to previous models, allowing for a more exhaustive search for the correct membrane-bound configuration.

View Article: PubMed Central - PubMed

Affiliation: Center for Biophysics and Computational Biology, Department of Biochemistry, College of Medicine, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States.

ABSTRACT
Membrane binding of peripheral proteins, mediated by specialized anchoring domains, is a crucial step for their biological function. Computational studies of membrane insertion, however, have proven challenging and largely inaccessible, due to the time scales required for the complete description of the process, mainly caused by the slow diffusion of the lipid molecules composing the membrane. Furthermore, in many cases, the nature of the membrane "anchor", i.e., the part of the protein that inserts into the membrane, is also unknown. Here, we address some of these issues by developing and employing a simplified representation of the membrane by a biphasic solvent model which we demonstrate can be used efficiently to capture and describe the process of hydrophobic insertion of membrane anchoring domains in all-atom molecular dynamics simulations. Applying the model, we have studied the insertion of the anchoring domain of a coagulation protein (the GLA domain of human protein C), starting from multiple initial configurations varying with regard to the initial orientation and height of the protein with respect to the membrane. In addition to efficiently and consistently identifying the "keel" region as the hydrophobic membrane anchor, within a few nanoseconds each configuration simulated showed a convergent height (2.20 ± 1.04 Å) and angle with respect to the interface normal (23.37 ± 12.48°). We demonstrate that the model can produce the same results as those obtained from a full representation of a membrane, in terms of both the depth of penetration and the orientation of the protein in the final membrane-bound form with an order of magnitude decrease in the required computational time compared to previous models, allowing for a more exhaustive search for the correct membrane-bound configuration.

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