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Taming molecular flexibility to tackle rare diseases.

Cubellis MV, Baaden M, Andreotti G - Biochimie (2015)

Bottom Line: These mutations are associated to a milder phenotype and are potentially curable with a pharmacological therapy either with chaperones or with drugs that modulate proteostasis.We found that mutations occurring at flexible sites are likely to retain activity in vivo.The usefulness of molecular dynamics for diagnostic purposes is not limited to lysosomal galactosidase because destabilizing mutations are widely encountered in other proteins, too, and represent a large share of all the ones associated to human diseases.

View Article: PubMed Central - PubMed

Affiliation: Dipartimento di Biologia, Università Federico II, 80126 Napoli, Italy. Electronic address: cubellis@unina.it.

No MeSH data available.


Related in: MedlinePlus

Correlation of residual AGAL activity measured in cells with the RMSF per residue obtained from running molecular dynamics on the 3GXT structure. Flexible residues that once mutated have activity lower than expected are shown (red circles).
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fig3: Correlation of residual AGAL activity measured in cells with the RMSF per residue obtained from running molecular dynamics on the 3GXT structure. Flexible residues that once mutated have activity lower than expected are shown (red circles).

Mentions: As shown in Fig. 3 the correlation is medium (Pearson correlation coefficient R 0.50; p < 0.0001), but the trend is clear. When looking at this figure it should be born in mind that the experimental data come from several labs [22–28], who applied different methods and no attempt was made to exclude a priori those mutants that are known to have reduced kcat or higher KM. Mutations occurring at flexible sites tend to be less severe. It is interesting to analyze the outliers, i.e. flexible residues that once mutated, have lower activity than expected (red in Fig. 3). Most of the outliers are residues for which abnormal kinetic parameters were determined (E59K or R112H) [29], residues lining the active site pocket (Y207) [31] or intrinsically flexible glycine residues (G35, G183, G258, G260, G261, G325, G360, G395) which can adopt unusual dihedral angles. Due to the correlation between flexibility and accessibility, it is not surprising that mutations occurring at exposed sites tend to retain residual activity. However it is not possible to find a molecular-level explanation to justify the numerous exceptions observed among buried as well as exposed sites (data not shown).


Taming molecular flexibility to tackle rare diseases.

Cubellis MV, Baaden M, Andreotti G - Biochimie (2015)

Correlation of residual AGAL activity measured in cells with the RMSF per residue obtained from running molecular dynamics on the 3GXT structure. Flexible residues that once mutated have activity lower than expected are shown (red circles).
© Copyright Policy - CC BY
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4441037&req=5

fig3: Correlation of residual AGAL activity measured in cells with the RMSF per residue obtained from running molecular dynamics on the 3GXT structure. Flexible residues that once mutated have activity lower than expected are shown (red circles).
Mentions: As shown in Fig. 3 the correlation is medium (Pearson correlation coefficient R 0.50; p < 0.0001), but the trend is clear. When looking at this figure it should be born in mind that the experimental data come from several labs [22–28], who applied different methods and no attempt was made to exclude a priori those mutants that are known to have reduced kcat or higher KM. Mutations occurring at flexible sites tend to be less severe. It is interesting to analyze the outliers, i.e. flexible residues that once mutated, have lower activity than expected (red in Fig. 3). Most of the outliers are residues for which abnormal kinetic parameters were determined (E59K or R112H) [29], residues lining the active site pocket (Y207) [31] or intrinsically flexible glycine residues (G35, G183, G258, G260, G261, G325, G360, G395) which can adopt unusual dihedral angles. Due to the correlation between flexibility and accessibility, it is not surprising that mutations occurring at exposed sites tend to retain residual activity. However it is not possible to find a molecular-level explanation to justify the numerous exceptions observed among buried as well as exposed sites (data not shown).

Bottom Line: These mutations are associated to a milder phenotype and are potentially curable with a pharmacological therapy either with chaperones or with drugs that modulate proteostasis.We found that mutations occurring at flexible sites are likely to retain activity in vivo.The usefulness of molecular dynamics for diagnostic purposes is not limited to lysosomal galactosidase because destabilizing mutations are widely encountered in other proteins, too, and represent a large share of all the ones associated to human diseases.

View Article: PubMed Central - PubMed

Affiliation: Dipartimento di Biologia, Università Federico II, 80126 Napoli, Italy. Electronic address: cubellis@unina.it.

No MeSH data available.


Related in: MedlinePlus