Searching for New Z-DNA/Z-RNA Binding Proteins Based on Structural Similarity to Experimentally Validated Zα Domain

Z-DNA and Z-RNA are functionally important left-handed structures of nucleic acids, which play a significant role in several molecular and biological processes including DNA replication, gene expression regulation and viral nucleic acid sensing. Most proteins that have been proven to interact with Z-DNA/Z-RNA contain the so-called Zα domain, which is structurally well conserved. To date, only eight proteins with Zα domain have been described within a few organisms (including human, mouse, Danio rerio, Trypanosoma brucei and some viruses). Therefore, this paper aimed to search for new Z-DNA/Z-RNA binding proteins in the complete PDB structures database and from the AlphaFold2 protein models. A structure-based similarity search found 14 proteins with highly similar Zα domain structure in experimentally-defined proteins and 185 proteins with a putative Zα domain using the AlphaFold2 models. Structure-based alignment and molecular docking confirmed high functional conservation of amino acids involved in Z-DNA/Z-RNA, suggesting that Z-DNA/Z-RNA recognition may play an important role in a variety of cellular processes.

Short-Range Imbalances in the AMBER Lennard-Jones Potential for (Deoxy)Ribose…Nucleobase Lone-pair…π Contacts in Nucleic Acids.

The lone-pair…π (lp…π) (deoxy)ribose…nucleobase stacking is a recurring structural motif in Z DNA and RNAs that is characterized by sub-van der Waals lp…π contacts (<3.0 Å). It is part of the structural signature of the CpG Z-steps in Z-DNA and r(UNCG) tetraloops. These nucleic acid structures are poorly behaving in molecular dynamics (MD) simulations. Although the exact origin of these issues remains unclear, a significant part of the problem might be due to an imbalanced description of non-bonded interactions including the characteristic lp…π stacking. To gain insights into the links between lp…π stacking and MD issues, we present an in-depth comparison between accurate large-basis-set double-hybrid Kohn-Sham density functional theory calculations DSD-BLYP-D3/ma-def2-QZVPP (DHDF-D3) and data obtained with the non-bonded potential of the AMBER force field (AFF) for NpN Z-steps (N = G, A, C, U). Among other differences, we found that the AFF overestimates the DHDF D3 lp…π distances by ~0.1-0.2 Å while the deviation between the DHDF-D3 and AFF descriptions sharply increases in the short-range region of the interaction. Based on atom-in-molecule (AIM) polarizabilities and SAPT analysis, we inferred that the DHDF-D3 vs. AFF differences partly originate in the Lennard-Jones (LJ) parameters that are identical for nucleobase carbon atoms despite the presence/absence of connected electron withdrawing groups that lead to different effective volumes or vdW radii. Thus, to precisely model the very short CpG lp…π contact distances, we recommend revision of the nucleobase atom LJ parameters. Additionally, we suggest that the large discrepancy between DHDF-D3 and AFF short-range repulsive part of the interaction energy potential may significantly contribute to the poor performances of MD simulations of nucleic acid systems containing Z-steps. Understanding where, and if possible why, the point-charge-type effective potentials reach their limits is vital for developing next-generation FFs and for addressing specific issues in contemporary MD simulations.

The Binding of Monoclonal and Polyclonal Anti-Z-DNA Antibodies to DNA of Various Species Origin

DNA is a polymeric macromolecule that can display a variety of backbone conformations. While the classical B-DNA is a right-handed double helix, Z-DNA is a left-handed helix with a zig-zag orientation. The Z conformation depends upon the base sequence, base modification and supercoiling and is considered to be transient. To determine whether the presence of Z-DNA can be detected immunochemically, the binding of monoclonal and polyclonal anti-Z-DNA antibodies to a panel of natural DNA antigens was assessed by an ELISA using brominated poly(dG-dC) as a control for Z-DNA. As these studies showed, among natural DNA tested (Micrococcus luteus, calf thymus, Escherichiacoli, salmon sperm, lambda phage), micrococcal (MC) DNA showed the highest binding with both anti-Z-DNA preparations, and E. coli DNA showed binding with the monoclonal anti-DNA preparation. The specificity for Z-DNA conformation in MC DNA was demonstrated by an inhibition binding assay. An algorithm to identify propensity to form Z-DNA indicated that DNA from Mycobacterium tuberculosis could form Z-DNA, a prediction confirmed by immunoassay. Together, these findings indicate that anti-Z-DNA antibodies can serve as probes for the presence of Z-DNA in DNA of various species origin and that the content of Z-DNA varies significantly among DNA sources.

Special Issue: A, B and Z: The Structure, Function and Genetics of Z-DNA and Z-RNA

It is now difficult to believe that a biological function for the left-handed Z-DNA and Z-RNA conformations was once controversial. The papers in this Special Issue, “Z-DNA and Z-RNA: from Physical Structure to Biological Function”, are based on presentations at the ABZ2021 meeting that was held virtually on 19 May 2021 and provide evidence for several biological functions of these structures. The first of its kind, this international conference gathered over 200 scientists from many disciplines to specifically address progress in research involving Z-DNA and Z-RNA. These high-energy left-handed conformers of B-DNA and A-RNA are associated with biological functions and disease outcomes, as evidenced from both mouse and human genetic studies. These alternative structures, referred to as “flipons”, form under physiological conditions, regulate type I interferon responses and induce necroptosis during viral infection. They can also stimulate genetic instability, resulting in adaptive evolution and diseases such as cancer. The meeting featured cutting-edge science that was, for the most part, unpublished. We plan for the ABZ meeting to reconvene in 2022.

Z-DNA as a Touchstone for Additive Empirical Force Fields and a Refinement of the Alpha/Gamma DNA torsions for AMBER

Although current AMBER force fields are relatively accurate for canonical B-DNA, many non-canonical structures are still described incorrectly. As non-canonical motifs are attracting increasing attention due to the role they play in living organisms, further improvement is desirable. Here, we have chosen Z-DNA molecule, can be considered a touchstone of the universality of empirical force fields, since the non-canonical α and γ backbone conformations native to Z-DNA are also found in protein-DNA complexes, i-motif DNA and other non-canonical DNAs. We show that spurious α/γ conformations occurring in simulations with current AMBER force fields, OL15 and bsc1, are largely due to inaccurate α/γ parameterization. Moreover, stabilization of native Z-DNA substates involving γ = trans conformations appears to be in conflict with the correct description of the canonical B-DNA structure. Because the balance of the native and spurious conformations is influenced by non-additive effects, this is a difficult case for an additive dihedral energy scheme such as AMBER. We propose new α/γ parameters, denoted OL21, and show that they improve the stability of native α/γ Z-DNA substates while keeping the canonical DNA description virtually unchanged, and thus represent a reasonable compromise within the additive force field framework. Although further extensive testing is needed, the new modification appears to be a promising step towards a more reliable description of non-canonical DNA motifs and provides the best performance for Z-DNA molecules among current AMBER force fields.

Roszczenia restytucyjne z zakresu podwodnego dziedzictwa kultury – sprawa Brązu Getty’ego

W artykule przytoczone skomplikowane dzieje antycznej rzeźby znanej jako Brąz Getty’ego (Atleta z Fano, Zwycięski Młodzieniec), datowanej na IV wiek p.n.e. i wydobytej przeszło 50 lat temu z dna Adriatyku u wybrzeży Włoch, a obecnie znajdującej się w Muzeum Getty’ego w Kalifornii. Spór Muzeum z Republiką Włoską trwa od lat; niedawny wyrok włoskiego Sądu Najwyższego utrzymał w mocy nakaz wydania rzeźby „gdziekolwiek się ona znajduje”. Czy nakaz taki może być wykonany za granicą i czy zabytek powróci do Włoch? W artykule poddano analizie prawo właściwe dla nielegalnie wywiezionych dóbr kultury i wskazano przy tym na nieadekwatność zasady lex rei sitae do rozwiązywania sporów windykacyjnych, których przedmiotem są rzeczy będące częścią dziedzictwa kultury całego kraju. Poruszono także zagadnienia wykonania za granicą krajowych nakazów wydania rzeczy i zaproponowano alternatywne rozwiązanie zadawnionego sporu.