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Multivariate Analysis of the Sequence Dependence of Asparagine Deamidation Rates in Peptides

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Abstract

Purpose

To develop a quantitative scheme to describe and predict asparagine deamidation in polypeptides using chemometric models employing reduced physicochemical property scales of amino acids.

Methods

Deamidation rates for 306 pentapeptides, Gly-(n−1)-Asn-(n+1)-Gly, with the residues n−1 and n+1 varying over the naturally occurring amino acids, were obtained from literature. A multivariate regression technique, called projection to latent structures (PLS), was used to establish mathematical relationships between the physicochemical properties and the deamidation half-lives of the amino acid sequences. Three reduced physicochemical property scales, amide hydrogen exchange rates (to describe the relative acidity of the amide protons) and flexibility parameters for the sequences were evaluated for their predictive capacity.

Results

The most effective descriptors of the deamidation half-lives were reduced-property parameters for amino acids called zz-scores. The PLS models with the reduced property scales, combined with the hydrogen exchange rates and/or flexibility parameters, explained more than 95% of the sequence-dependent variation in the deamidation half-lives. The amide hydrogen exchange rate (i.e., amide proton acidity), hydrophilicity, polarizability, and size of amino acids in position n+1 were found to be the principal factors governing the rate of deamidation. The effect of amino acids in position n−1 was found to be negligible.

Conclusions

Chemometric analysis employing reduced physicochemical parameters can provide an accurate prediction of chemical instability in peptides and proteins. The relative importance of these various factors could also be determined.

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Abbreviations

3loc:

Flexibility parameter of the n+1 residue

Asn:

Asparagine

HX:

Amide hydrogen exchange

ln(HX):

Natural logarithm of the n+1 residue amide proton half-lives

ln(t1/2):

Natural logarithm of the deamidation half-lives

PC:

Principle component

PCA:

Principle component analysis

PLS:

Projection to latent structures or partial least squares

RMSEP:

Root mean squared error of prediction

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ACKNOWLEDGMENTS

The authors thank Amgen Incorporated for sponsoring this project and Art and Noah Robinson for permission to reproduce their table of deamidation half-times.

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Authors and Affiliations

  1. Genentech, Inc., 1 DNA Way, South San Francisco, CA, 94010, USA

    Andrew A. Kosky

  2. Amgen Inc., Thousand Oaks, California, 91320, USA

    Vasumathi Dharmavaram & Gayathri Ratnaswamy

  3. Legacy BioDesign LLC, Johnstown, Colorado, 80534, USA

    Mark Cornell Manning

Authors
  1. Andrew A. Kosky
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  2. Vasumathi Dharmavaram
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  3. Gayathri Ratnaswamy
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  4. Mark Cornell Manning
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Correspondence to Andrew A. Kosky.

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Kosky, A.A., Dharmavaram, V., Ratnaswamy, G. et al. Multivariate Analysis of the Sequence Dependence of Asparagine Deamidation Rates in Peptides. Pharm Res 26, 2417–2428 (2009). https://doi.org/10.1007/s11095-009-9953-8

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  • DOI: https://doi.org/10.1007/s11095-009-9953-8

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