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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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Related in: MedlinePlus

Dynamic cross-correlation maps calculated for the wild-type and the mutant LOX-1 proteins. Panels A and C reports the intra-subunit motion correlations in the wild-type, while panels B and D the intra-subunit motion correlations in the mutant. The black and grey squares represent the Cα motion correlations with /cij/ ≥ 0.5 and /cij/ < 0.5, respectively (cij is defined in Eq. 1 of Methods).
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Figure 5: Dynamic cross-correlation maps calculated for the wild-type and the mutant LOX-1 proteins. Panels A and C reports the intra-subunit motion correlations in the wild-type, while panels B and D the intra-subunit motion correlations in the mutant. The black and grey squares represent the Cα motion correlations with /cij/ ≥ 0.5 and /cij/ < 0.5, respectively (cij is defined in Eq. 1 of Methods).

Mentions: Interesting results concerning the relative flexibility and communication of the two proteins can be obtained by looking at the correlated motion between different regions of the protein as described by the dynamic cross correlation (DCC) map calculated on the Cα atoms [19]. Such plots are reported in Fig. 5, where a black spot represents a correlation between two Cα greater than 0.5 in absolute value. The panels indicate that both the native (panels A and C) and the mutant LOX-1 (panels B and D) have a low degree of correlation. The native protein displays a symmetric behaviour, with the correlation maps being almost identical for the two subunits (panels A and C). In particular, in the wild-type protein the correlation spots present in the two subunits involve the segment including strand β1, helix α1 and strand β1a that is correlated with strand β5; strand β2 that is correlated with strand β3 and β5; and strand β2b that is correlated with strand β4. In contrast the symmetric correlation is lost in the mutant. In this case the maps of the two subunits are different (panels B and D), and an higher degree of correlations is observed between residues adjacent along the sequence (black spots grouped on the diagonal) when compared to the wild-type.


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)

Dynamic cross-correlation maps calculated for the wild-type and the mutant LOX-1 proteins. Panels A and C reports the intra-subunit motion correlations in the wild-type, while panels B and D the intra-subunit motion correlations in the mutant. The black and grey squares represent the Cα motion correlations with /cij/ ≥ 0.5 and /cij/ < 0.5, respectively (cij is defined in Eq. 1 of Methods).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 5: Dynamic cross-correlation maps calculated for the wild-type and the mutant LOX-1 proteins. Panels A and C reports the intra-subunit motion correlations in the wild-type, while panels B and D the intra-subunit motion correlations in the mutant. The black and grey squares represent the Cα motion correlations with /cij/ ≥ 0.5 and /cij/ < 0.5, respectively (cij is defined in Eq. 1 of Methods).
Mentions: Interesting results concerning the relative flexibility and communication of the two proteins can be obtained by looking at the correlated motion between different regions of the protein as described by the dynamic cross correlation (DCC) map calculated on the Cα atoms [19]. Such plots are reported in Fig. 5, where a black spot represents a correlation between two Cα greater than 0.5 in absolute value. The panels indicate that both the native (panels A and C) and the mutant LOX-1 (panels B and D) have a low degree of correlation. The native protein displays a symmetric behaviour, with the correlation maps being almost identical for the two subunits (panels A and C). In particular, in the wild-type protein the correlation spots present in the two subunits involve the segment including strand β1, helix α1 and strand β1a that is correlated with strand β5; strand β2 that is correlated with strand β3 and β5; and strand β2b that is correlated with strand β4. In contrast the symmetric correlation is lost in the mutant. In this case the maps of the two subunits are different (panels B and D), and an higher degree of correlations is observed between residues adjacent along the sequence (black spots grouped on the diagonal) when compared to the wild-type.

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