3D-BioInfo Webinar: Nucleic Acids Structural Bioinformatics

Programme

Improving validation of nucleic acid structures

Prof. Bohdan Schneider (Institute of Biotechnology of the Czech Academy of Sciences, 252 50
Vestec, Czech Republic)

The community of structural biologists and bioinformaticians benefit from the culture of data sharing and generally well-functioning publicly accessible archive, the PDB. Despite this generally positive situation there remain quality problems. The problems are more serious for nucleic acid than for protein structures because there are many fewer high-quality nucleic acid structures; in addition, the evolutionary alignments are limited just to a few RNA functional classes [1]. The problems with nucleic acid geometry can be divided into three groups:

1. Inconsistently set and applied target values of bond distances and angles for nucleotides
2. Poorly refined backbone geometries
3. Incompletely and often incorrectly assigned base pairing topologies.

In the talk, I introduce web-based tools that address these problems and offer solution to some. The tools are available from our web application dnatco.datmos.org [2]. The web leads you from the Annotation TAB, which offers an overview of the analyzed structures accessible for a non-expert. The Validation TAB enables an in-depth analysis of nucleic acid structures and expert-level judgement of their quality. This TAB
provides a detailed analysis of NA conformation at the level of dinucleotide based on our original system of the dinucleotide NtC classes [3]. This TAB also offers validation of the valence geometry.

Soon, we will also provide an integrated tool to analyze base pairs detected in the analyzed structure. Now the web basepairs.datmos.org provides an overview of base pairs in the PDB structures. The TAB Refine offers tools to modify structures during the process of their refinement. The last TAB, Browse, allows the user to view NA structures from various perspectives. Results of most analyses are available for download in several formats.

This research was funded by Czech Academy of Sciences, grant RVO86652036 and by grant LM2023055 to ELIXIR CZ from MEYS Czech Republic.

[1] Bohdan Schneider, Blake Alexander Sweeney, Alex Bateman, Jiří Černý, Tomasz Zok, & Marta Szachniuk: When will RNA get its AphaFold moment? Nucleic Acids Research. 51(18): 9522-9532 (2023). doi: 10.1093/nar/gkad726.
[2] Jiří Černý, Paulína Božíková, Michal Malý, Michal Tykač, Lada Biedermannová & Bohdan Schneider: Structural alphabets for conformational analysis of nucleic acids available at dnatco.datmos.org. Acta Crystallographica D76: 805-813 (2020). doi: 10.1107/S2059798320009389.
[3] Jiří Černý, Paulína Božíková, Jakub Svoboda & Bohdan Schneider: A unified dinucleotide alphabet describing both RNA and DNA structures. Nucleic Acids Research. 48(11): 6367-6381 (2020). doi: 10.1093/nar/gkaa383.

Structural insight into the mechanism of the SorC protein family

Markéta Šoltysová (Institute of Organic Chemistry and Biochemistry of Czech Academy of Sciences, Prague, Czech Republic)

Proteins of the SorC family are bacterial transcription regulators involved in carbohydrate metabolism and quorum-sensing control [1, 2]. They consist of a DNA‑binding domain (DBD) and an effector‑binding domain (EBD), though which the protomers oligomerize. Based on the sequence similarity of DBDs, the family is divided into two subfamilies, SorC/DeoR and SorC/CggR. Prior to our research, there was no structural information on their complex with the cognate DNA (operator) and thus neither knowledge of how the proteins recognize their operator targets [3-8].
In my talk, I will present our integrative approach combining Xray crystallography and cryogenic electron microscopy (cryoEM) to structurally characterize two SorC prototypes in the complex with their operators, DeoR and CggR from Bacillus subtilis. Xray and cryoEM studies of the fulllength repressorDNA complexes provided lowresolution information revealing the general mechanism of binding. We further complemented these models with  highresolution crystal structures of DeoR and CggR DBDs in complex with halfoperator duplexes. By integrating all this information, we propose the SorC protein family mechanism
of the function, which might be used for further basic and applied research.
Supported by project 8J23FR035 from Ministry of Education, Youth and Sports of the Czech Republic.

[1] Fillinger S et al. J Biol Chem. (2000), 275, 14031-7.
[2] Taga ME et al. Mol Microbiol. (2001), 42, 777-93.
[3] Řezáčová P et al. Mol Microbiol. (2008), 69, 895-910.
[4] Škerlová J et al. FEBS J. (2014), 281, 4280-92.
[5] de Sanctis D et al. J Mol Biol. (2009), 387, 759-70.
[6] Ha JH et al. J Am Chem Soc. (2013), 135, 15526-35.
[7] Šoltysová M et al. Acta Cryst (2021), D77, 1411-1424.
[8] Šoltysová M et al. Nucleic Acids Res (2024), 52, 7305-7320.

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