Zou, J;
Song, B;
Simmerling, C;
Raleigh, D;
(2016)
Experimental and Computational Analysis of Protein Stabilization by Gly-to-D-Ala Substitution: A Convolution of Native State and Unfolded State Effects.
Journal of the American Chemical Society
, 138
(48)
pp. 15682-15689.
10.1021/jacs.6b09511.
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Abstract
The rational and predictable enhancement of protein stability is an important goal in protein design. Most efforts target the folded state, however stability is the free energy difference between the folded and unfolded states thus both are suitable targets. Strategies directed at the unfolded state usually seek to decrease chain entropy by introducing cross-links or by replacing glycines. Cross-linking has led to mixed results. Replacement of glycine with an l-amino acid, while reducing the entropy of the unfolded state, can introduce unfavorable steric interactions in the folded state, since glycine is often found in conformations that require a positive φ angle such as helical C-capping motifs or type I′ and II″ β-turns. l-Amino acids are strongly disfavored in these conformations, but d-amino acids are not. However, there are few reported examples and conflicting results have been obtained when glycines are replaced with d-Ala. We critically examine the effect of Gly-to-d-Ala substitutions on protein stability using experimental approaches together with molecular dynamics simulations and free energy calculations. The data, together with a survey of high resolution structures, show that the vast majority of proteins can be stabilized by substitution of C-capping glycines with d-Ala. Sites suitable for substitutions can be identified via sequence alignment with a high degree of success. Steric clashes in the native state due to the new side chain are rarely observed, but are likely responsible for the destabilizing or null effect observed for the small subset of Gly-to-d-Ala substitutions which are not stabilizing. Changes in backbone solvation play less of a role. Favorable candidates for d-Ala substitution can be identified using a rapid algorithm based on molecular mechanics.
| Type: | Article |
|---|---|
| Title: | Experimental and Computational Analysis of Protein Stabilization by Gly-to-D-Ala Substitution: A Convolution of Native State and Unfolded State Effects |
| Open access status: | An open access version is available from UCL Discovery |
| DOI: | 10.1021/jacs.6b09511 |
| Publisher version: | https://doi.org/10.1021/jacs.6b09511 |
| Language: | English |
| Additional information: | This version is the author accepted manuscript. For information on re-use, please refer to the publisher’s terms and conditions. |
| Keywords: | Science & Technology, Physical Sciences, Chemistry, Multidisciplinary, Chemistry, DEHYDROGENASE MULTIENZYME COMPLEX, SUBUNIT-BINDING DOMAIN, ENGINEERED DISULFIDE BONDS, ULTRAFAST FOLDING PROTEIN, CONFORMATIONAL ENTROPY, BACILLUS-STEAROTHERMOPHILUS, ENGRAILED HOMEODOMAIN, SEQUENCE STATISTICS, SIDE-CHAINS, STABILITY |
| UCL classification: | UCL UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Life Sciences > Div of Biosciences > Structural and Molecular Biology |
| URI: | https://discovery.ucl.ac.uk/id/eprint/10055849 |
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