Dataset Information

Deposition for: Mild and Chemoselective, Light-Driven Post-translational Editing Allows Installation of Reactive Side-Chains into Proteins

ABSTRACT: MS/MS characterisation data of the publication: Mild anChemoselective, Light-Driven Post-Translational Editing Allows Installation of Reactive Side Chains into Proteins.

INSTRUMENT(S): LTQ Orbitrap Elite, Q Exactive

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Simon Nadal

LAB HEAD: Shabaz Mohammed

PROVIDER: PXD019565 | Pride | 2020-09-24

REPOSITORIES: Pride

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Dataset's files

Source:

			Action	DRS
	MSMS_photoluche_all_samples_v2.xlsx	Xlsx
	Qex01_SFN_190801_05090A_BJ28927_H3K9Pr_06.pep.xml	Pepxml
	Qex01_SFN_190801_05090A_BJ28927_H3K9Pr_06.raw	Raw
	Qex01_SFN_190801_05090B_BJ25318b_H3K9But_07.pep.xml	Pepxml
	Qex01_SFN_190801_05090B_BJ25318b_H3K9But_07.raw	Raw

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Publications

Light-driven post-translational installation of reactive protein side chains.

Josephson Brian B Fehl Charlie C Isenegger Patrick G PG Nadal Simon S Wright Tom H TH Poh Adeline W J AWJ Bower Ben J BJ Giltrap Andrew M AM Chen Lifu L Batchelor-McAuley Christopher C Roper Grace G Arisa Oluwatobi O Sap Jeroen B I JBI Kawamura Akane A Baldwin Andrew J AJ Mohammed Shabaz S Compton Richard G RG Gouverneur Veronique V Davis Benjamin G BG

Nature 20200923 7826

Post-translational modifications (PTMs) greatly expand the structures and functions of proteins in nature1,2. Although synthetic protein functionalization strategies allow mimicry of PTMs3,4, as well as formation of unnatural protein variants with diverse potential functions, including drug carrying5, tracking, imaging6 and partner crosslinking7, the range of functional groups that can be introduced remains limited. Here we describe the visi ...[more]

PMID: 32968259

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Project description:Amino acid side-chain conformational properties influence the overall structural and dynamic properties of proteins and, therefore, their biological functions. In this study, quantum mechanical (QM) potential energy surfaces for the rotation of side-chain χ(1) and χ(2) torsions in dipeptides in the alphaR, beta, and alphaL backbone conformations were calculated. The QM energy surfaces provide a broad view of the intrinsic conformational properties of each amino acid side-chain. The extent to which intrinsic energetics dictates side-chain orientation was studied through comparisons of the QM energy surfaces with χ(1) and χ(2) free energy surfaces from probability distributions obtained from a survey of high resolution crystal structures. In general, the survey probability maxima are centered in minima of the QM surfaces as expected for sp(3) (or sp(2) for χ(2) of Asn, Phe, Trp, and Tyr) atom centers with strong variations between amino acids occurring in the energies of the minima indicating intrinsic differences in rotamer preferences. High correlations between the QM and survey data were found for hydrophobic side-chains except Met, suggesting minimal influence of the protein and solution environments on their conformational distributions. Conversely, low correlations for polar or charged side-chains indicate a dominant role of the environment in stabilizing conformations that are not intrinsically favored. Data also link the presence of off-rotamers in His and Trp to favorable interactions with the backbone. Results also suggest that the intrinsic energetics of the side-chains of Phe and Tyr may play important roles in protein folding and stability. Analyses on whether intrinsic side-chain energetics can influence backbone preference identified a strong correlation for residues in the alphaL backbone conformation. It is suggested that this correlation reflects the intrinsic instability of the alphaL backbone such that assumption of this backbone conformation is facilitated by intrinsically favorable side-chain conformations. Together our results offer a broad overview of the conformational properties of amino acid side-chains and the QM data may be used as target data for force field optimization.