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Molecular dynamics simulation of human LOX-1 provides an explanation for the lack of OxLDL binding to the Trp150Ala mutant.

Falconi M, Biocca S, Novelli G, Desideri A - BMC Struct. Biol. (2007)

Bottom Line: In vivo assays revealed that in LOX-1 the basic spine arginine residues are important for binding, which is lost upon mutation of Trp150 with alanine.Molecular dynamics simulations of the wild-type LOX-1 and of the Trp150Ala mutant C-type lectin-like domains, have been carried out to gain insight into the severe inactivating effect.The symmetrical motion of monomers is completely damped by the structural rearrangement caused by the Trp150Ala mutation.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biology and Center of Biostatistics and Bioinformatics, University of Rome Tor Vergata, Via della Ricerca Scientifica, Rome, Italy, 00133. falconi@uniroma2.it

ABSTRACT

Background: Dimeric lectin-like oxidized low-density lipoprotein receptor-1 LOX-1 is the target receptor for oxidized low density lipoprotein in endothelial cells. In vivo assays revealed that in LOX-1 the basic spine arginine residues are important for binding, which is lost upon mutation of Trp150 with alanine. Molecular dynamics simulations of the wild-type LOX-1 and of the Trp150Ala mutant C-type lectin-like domains, have been carried out to gain insight into the severe inactivating effect.

Results: The mutation does not alter the dimer stability, but a different dynamical behaviour differentiates the two proteins. As described by the residues fluctuation, the dynamic cross correlation map and the principal component analysis in the wild-type the two monomers display a symmetrical motion that is not observed in the mutant.

Conclusion: The symmetrical motion of monomers is completely damped by the structural rearrangement caused by the Trp150Ala mutation. An improper dynamical coupling of the monomers and different fluctuations of the basic spine residues are observed, with a consequent altered binding affinity.

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Per residue RMSF of the two subunits of the LOX-1 wild-type (A) and Trp150Ala (B) proteins. Each residue is indicated by a filled circle. Subunit A is shown by a black line and subunit B by a blue line. The black (subunit A) and blue (subunit B) dotted lines shows the corresponding experimental B-factors as converted to RMSF values from the PDB file 1YPQ (see Eq. 2 in Methods). On the X-axis residues that in the X-ray starting structure are in α-helix and β-strand are indicated by the red and green bars, respectively.
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Figure 3: Per residue RMSF of the two subunits of the LOX-1 wild-type (A) and Trp150Ala (B) proteins. Each residue is indicated by a filled circle. Subunit A is shown by a black line and subunit B by a blue line. The black (subunit A) and blue (subunit B) dotted lines shows the corresponding experimental B-factors as converted to RMSF values from the PDB file 1YPQ (see Eq. 2 in Methods). On the X-axis residues that in the X-ray starting structure are in α-helix and β-strand are indicated by the red and green bars, respectively.

Mentions: The main chain root mean square fluctuations (RMSFs) calculated over the trajectories and averaged over each residue for the wild-type and the Trp150Ala (Fig. 3A and 3B), indicate that a large part of residues is characterized by fluctuations not higher than 2.0 Å, apart from the random coil regions of the C-terminal tails which reach values around 3.5 Å. The N-terminal tails are less flexible due to the presence of the inter-subunit disulfide bridge (Cys140.A-Cys140.B) and do not exceed 1.8 Å. A relatively highly fluctuating region in both proteins (values between 1.6 and 2.3 Å) is localized between Arg209 and Gly241, including the loops L1, L2 and L3 and the two small β-strands β2a and β2b.


Molecular dynamics simulation of human LOX-1 provides an explanation for the lack of OxLDL binding to the Trp150Ala mutant.

Falconi M, Biocca S, Novelli G, Desideri A - BMC Struct. Biol. (2007)

Per residue RMSF of the two subunits of the LOX-1 wild-type (A) and Trp150Ala (B) proteins. Each residue is indicated by a filled circle. Subunit A is shown by a black line and subunit B by a blue line. The black (subunit A) and blue (subunit B) dotted lines shows the corresponding experimental B-factors as converted to RMSF values from the PDB file 1YPQ (see Eq. 2 in Methods). On the X-axis residues that in the X-ray starting structure are in α-helix and β-strand are indicated by the red and green bars, respectively.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2194713&req=5

Figure 3: Per residue RMSF of the two subunits of the LOX-1 wild-type (A) and Trp150Ala (B) proteins. Each residue is indicated by a filled circle. Subunit A is shown by a black line and subunit B by a blue line. The black (subunit A) and blue (subunit B) dotted lines shows the corresponding experimental B-factors as converted to RMSF values from the PDB file 1YPQ (see Eq. 2 in Methods). On the X-axis residues that in the X-ray starting structure are in α-helix and β-strand are indicated by the red and green bars, respectively.
Mentions: The main chain root mean square fluctuations (RMSFs) calculated over the trajectories and averaged over each residue for the wild-type and the Trp150Ala (Fig. 3A and 3B), indicate that a large part of residues is characterized by fluctuations not higher than 2.0 Å, apart from the random coil regions of the C-terminal tails which reach values around 3.5 Å. The N-terminal tails are less flexible due to the presence of the inter-subunit disulfide bridge (Cys140.A-Cys140.B) and do not exceed 1.8 Å. A relatively highly fluctuating region in both proteins (values between 1.6 and 2.3 Å) is localized between Arg209 and Gly241, including the loops L1, L2 and L3 and the two small β-strands β2a and β2b.

Bottom Line: In vivo assays revealed that in LOX-1 the basic spine arginine residues are important for binding, which is lost upon mutation of Trp150 with alanine.Molecular dynamics simulations of the wild-type LOX-1 and of the Trp150Ala mutant C-type lectin-like domains, have been carried out to gain insight into the severe inactivating effect.The symmetrical motion of monomers is completely damped by the structural rearrangement caused by the Trp150Ala mutation.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biology and Center of Biostatistics and Bioinformatics, University of Rome Tor Vergata, Via della Ricerca Scientifica, Rome, Italy, 00133. falconi@uniroma2.it

ABSTRACT

Background: Dimeric lectin-like oxidized low-density lipoprotein receptor-1 LOX-1 is the target receptor for oxidized low density lipoprotein in endothelial cells. In vivo assays revealed that in LOX-1 the basic spine arginine residues are important for binding, which is lost upon mutation of Trp150 with alanine. Molecular dynamics simulations of the wild-type LOX-1 and of the Trp150Ala mutant C-type lectin-like domains, have been carried out to gain insight into the severe inactivating effect.

Results: The mutation does not alter the dimer stability, but a different dynamical behaviour differentiates the two proteins. As described by the residues fluctuation, the dynamic cross correlation map and the principal component analysis in the wild-type the two monomers display a symmetrical motion that is not observed in the mutant.

Conclusion: The symmetrical motion of monomers is completely damped by the structural rearrangement caused by the Trp150Ala mutation. An improper dynamical coupling of the monomers and different fluctuations of the basic spine residues are observed, with a consequent altered binding affinity.

Show MeSH
Related in: MedlinePlus