Reconciling ASPP-p53 binding mode discrepancies through an ensemble binding framework that bridges crystallography and NMR data

Te Liu; Sichao Huang; Qian Zhang; Yu Xia; Manjie Zhang; Bin Sun

doi:10.1371/journal.pcbi.1011519

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Peer-reviewed

Research Article

Reconciling ASPP-p53 binding mode discrepancies through an ensemble binding framework that bridges crystallography and NMR data

Te Liu,

Roles Data curation, Formal analysis, Investigation, Writing – original draft

Affiliation Research Center for Pharmacoinformatics, College of Pharmacy, Harbin Medical University, Harbin, China

https://orcid.org/0009-0002-3205-0988

⨯
Sichao Huang,

Roles Data curation, Methodology, Software

Affiliation Research Center for Pharmacoinformatics, College of Pharmacy, Harbin Medical University, Harbin, China
⨯
Qian Zhang,

Roles Methodology, Resources, Software

Affiliation Research Center for Pharmacoinformatics, College of Pharmacy, Harbin Medical University, Harbin, China
⨯
Yu Xia,

Roles Methodology, Software

Affiliation Research Center for Pharmacoinformatics, College of Pharmacy, Harbin Medical University, Harbin, China
⨯
Manjie Zhang ,

Roles Conceptualization, Funding acquisition, Project administration, Supervision, Writing – review & editing

* E-mail: zhangmj454@nenu.edu.cn (MZ); binsun@hrbmu.edu.cn (BS)

Affiliation Research Center for Pharmacoinformatics, College of Pharmacy, Harbin Medical University, Harbin, China
⨯
Bin Sun

Roles Conceptualization, Funding acquisition, Investigation, Methodology, Project administration, Supervision, Validation, Writing – original draft, Writing – review & editing

* E-mail: zhangmj454@nenu.edu.cn (MZ); binsun@hrbmu.edu.cn (BS)

Affiliation Research Center for Pharmacoinformatics, College of Pharmacy, Harbin Medical University, Harbin, China

https://orcid.org/0000-0003-2583-4493

⨯

Reconciling ASPP-p53 binding mode discrepancies through an ensemble binding framework that bridges crystallography and NMR data

Te Liu,
Sichao Huang,
Qian Zhang,
Yu Xia,
Manjie Zhang,
Bin Sun

Published: February 7, 2024
https://doi.org/10.1371/journal.pcbi.1011519

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Confused statement regarding NMR structure determination.

Posted by shyberts on 09 Feb 2024 at 17:11 GMT

The authors state: :In contrast, solution NMR captures protein motion in an aqueous environment and is therefore more functionally related. However, it suffers from inaccuracies in chemical shift assignments and cannot directly provide atomistic structures; instead, it serves as constraints to derive structures that satisfy the observed chemical shifts."
Whereas it is true that no one has been able to exactly derive chemical shifts from a structure or an ensemble of structure, the chemical shifts are used very little or not at all in structure determination more than pinpoint chemical information (primary structure information). Instead through bond coupling constants (J couplings) and especially through space distance information via the nuclear Overhouser effect (noe:s) are used. The latter are crucial even though there may be inaccuracies in converting the strength to distance.

No competing interests declared.

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Reconciling ASPP-p53 binding mode discrepancies through an ensemble binding framework that bridges crystallography and NMR data

Reconciling ASPP-p53 binding mode discrepancies through an ensemble binding framework that bridges crystallography and NMR data

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Confused statement regarding NMR structure determination.

Posted by shyberts on 09 Feb 2024 at 17:11 GMT