Luca Grisanti

Despite its essential role in pre-mRNA splicing, the structure and functional significance of the intrinsically disordered N-terminal domain (NTD) of SF3B1, a core component of the SF3b spliceosome complex, remain poorly understood. Here, we combine nuclear magnetic resonance (NMR) spectroscopy, small-angle X-ray scattering (SAXS), biochemistry, bioinformatics approaches, with molecular dynamics simulations to characterize the conformational landscape of the SF3B1-NTD and its phosphorylation-dependent remodelling. Specifically, we focus on the 186–341 region ( ^186–341 SF3B1), which contains at least four regulatory phosphorylation sites. We reveal that ^186–341 SF3B1 is highly dynamic, lacking a stable secondary structure, and that phosphorylation of T211, T235, T313, and T328 induces a shift toward more compact states driven by the formation of intramolecular interactions. Additionally, we unveil that ^186–341 SF3B1 interacts with RNA primarily via the arginine residues flaking one of the conserved tryptophan-centred motifs present within SF3B1-NTD. These interactions are transient and heterogeneous, reflecting a nonspecific yet sequence-dependent recognition mechanism. Collectively, this study provides a comprehensive description of the conformational landscape and functional features of the SF3B1-NTD, and expands the portfolio of its possible interactors, thus broadening our understanding of how intrinsic disorder, post-translational modifications, and sequence-encoded motifs cooperate to regulate pre-mRNA splicing. Highlights: SAXS and NMR experiments reveal that SF3B1-NTD is intrinsically disordered Phosphorylation compacts the SF3B1 intrinsically disordered region SF3B1 intrinsically disordered region interacts with RNA at W200-centred motif

I-motifs are noncanonical DNA secondary structures stabilized by hemiprotonated C⁺:C base pairs. Their intrinsic flexibility, conformational heterogeneity, and sensitivity to environmental conditions often hinder structural characterization. Here, all-atom simulations, combined with biophysical experiments, were used to characterize the structure of the i-motif monomer formed by the HRAS gene promoter (iHRAS), a member of the RAS proto-oncogene family. Our results reveal that iHRAS exhibits intricate conformational behavior characterized by multiple interconverting states. The core i-motif is stabilized by a protective G:G cap, a recurrent i-motif-stabilizing factor, on one side, while the C⁺:C base pairs content on the other side is variable. Structural heterogeneity is most pronounced in loops, which sample several base-exposed states aided by K⁺ ion binding. These findings contribute to a deeper understanding of the i-motif structure and dynamics.

Introns are removed from mRNAs by the spliceosome, a type of protein-RNA machinery enriched with intrinsically disordered regions (IDRs). Lacking stable 3D structures, IDRs can adopt diverse conformations interlacing protein and RNA components of the spliceosome and regulating splicing. In this work, we performed a comprehensive bioinformatics analysis of the human spliceosome proteome, revealing that many proteins contain more than 40% disordered residues. Spliceosome IDRs are mainly driven by compositional bias due to an excess of charged and RS-like sequences, with the nature and extent of this disorder being broadly conserved evolutionarily. Additionally, these IDRs are frequent targets of post-translational modifications, especially phosphorylation, and are hot spots for cancer-associated mutations, which have been implicated in different types of cancer. Our results collectively underscore the central role of IDRs in splicing regulation and disease.

The dielectric response of amorphous organic solids at the timescale of atomic motion has broad implications for their photophysics, governing spectroscopic properties and excited-state relaxation, among other phenomena. We present an original approach to the calculation of the vibrational contribution to the frequency-dependent dielectric permittivity. Our methodology, combining molecular dynamics simulations, density functional theory calculations, and linear response theory, is applied to a set of amorphous carbazole-based small-molecule matrices, widely used as host materials in organic light-emitting diodes. Our analysis reveals the crucial role of hindered molecular rotations (librations) in the solid-state matrices of dipolar compounds. These modes manifest in the very-low frequency ( < 100 cm − 1 ) region of the dielectric function, accounting for up to one-third of the total vibrational contribution to the static dielectric constant in a dipolar compound like 3,3'-di(carbazol-9-yl)-5-cyano-1,1'-biphenyl. This low-frequency contribution is found to be crucial for determining the variations in the static dielectric constant across various materials.

Introns are removed from messenger RNAs by the spliceosome, a protein-RNA machinery enriched with intrinsically disordered regions (IDRs). Lacking stable 3D structures, IDRs can adopt diverse conformations interlacing proteins and RNAs components of the spliceosome and regulating splicing. Here we performed a comprehensive bioinformatics analysis of the human spliceosome proteome revealing that many proteins contain over 40% of disordered residues. Spliceosome IDRs are mainly driven by compositional bias due to an excess of charged and RS-like sequences, with both the nature and extent of this disorder being broadly conserved evolutionarily. Additionally, these IDRs are frequent targets of post-translational modifications, especially phosphorylation, and are hotspots for cancer-associated mutations, implicated in different cancer types. Our results collectively underscore central role of IDRs in splicing regulation and disease. TOC Graphic:

The evolution of the optical properties of a molecule from solution to a crystalline phase is nontrivial, as it results from a complex interplay of several interactions, including electrostatic and charge-transfer intermolecular interactions and the coupling with molecular vibrations. In order to address the crystallochromism observed in quinacridone (QA), a hybrid modeling strategy is presented that successfully describes the optical properties (absorption and emission) of the βQA and γQA crystalline phases. The proposed protocol relies on the parametrization of the Frenkel-Holstein Hamiltonian against quantum chemical calculations. Periodic density functional theory (DFT) is adopted to optimize the crystallographic geometry and to extract effective atomic charges. Time-dependent DFT (TD-DFT) results on the isolated molecule are exploited to parametrize the Holstein coupling, while TD-DFT results on the embedded molecules and on embedded clusters of increasing size are finally exploited to extract the exciton model parameters. For safe validation, the missing optical spectra of the two polymorphs were measured. The approach is general and paves the way for the rationalization of crystallochromism of molecular condensed phases.

The photodynamics of nucleobase–water clusters was investigated using a pragmatic computational protocol that accounts for molecular flexibility and quantum distributions of initial conditions.

In chiral assemblies, the transition dipole moments of the individual molecules are arranged obliquely, leading to the appearance of two absorption bands and a bisignation in the circular dichroism (CD) spectra. However, the influence of the handedness of the self-assembled systems and their interaction energy on the sign of the CD bisignation and circularly polarized luminescence remains enigmatic. These aspects are explored using α- and β-dicyanostilbenes appended with R- and S-isomers of chiral groups, which spontaneously self-assemble in a THF-H₂O mixture. The β-dicyanostilbene aggregates, with predominantly H-type character, show positive interchromophoric interaction energy, confirming the exciton chirality rule; i.e., a bisignate CD signal with a positive Cotton effect for right-handed chiral arrangement and vice versa. Conversely, α-dicyanostilbene aggregates with predominantly J-type character exhibit negative interaction energy, displaying a bisignate CD signal with a negative Cotton effect for a right-handed chiral arrangement, which reverses for the left-handed system.

Nucleobases possess a tendency to establish hydrogen bonds and stacking interactions. What is the thermodynamics of these intermolecular interactions of nucleobases in water?