RNA-Dependent Structures of the RNA-Binding Loop in the Flavivirus NS3 Helicase

Computational study of the HLTF ATPase remodeling domain suggests its activity on dsDNA and implications in damage tolerance

The Helicase-Like Transcription Factor (HLTF) is member of the SWI/SNF-family of ATP dependent chromatin remodellers known primarily for maintaining genome stability. Biochemical and cellular assays support its multiple roles in DNA Damage Tolerance. However, the lack of sufficient structural data limits the comprehension of the molecular basis of its modes of action. In this work we have modelled and characterized the HLTF ATPase remodeling domain by using bioinformatic tools and all-atoms molecular dynamics simulations. In-silico results suggested that its binding to dsDNA is mainly mediated by the positively charged residues Arg563 and Lys913, found conserved in HLTF homologs, and Arg620 and Lys999, found only in HLTF. Interestingly, these residues are mutated in cancer cells. During translocation on dsDNA, HLTF remains persistently bound through the N-terminal ATPase subunit. However, DNA advancement occurs only in the presence of the synergic-anticorrelated action of both motor lobes. In contrast, the C-terminal facilitates substrate remodeling through DNA deformation and generation of bulges according to a wave-model. Finally, the large conformational change suggested between the two motor-remodeling subunits might be activated upon the release of PARP1 on stalled fork and be responsible for the intervention of HLTF-HIRAN in the formation of D-loop and 4-way junction DNA structures.

Dynamics and Function of sRNA/mRNAs Under the Scrutiny of Computational Simulation Methods

Molecular dynamics simulations have proved extremely useful in investigating the functioning of proteins with atomic-scale resolution. Many applications to the study of RNA also exist, and their number increases by the day. However, implementing MD simulations for RNA molecules in solution faces challenges that the MD practitioner must be aware of for the appropriate use of this tool. In this chapter, we present the fundamentals of MD simulations, in general, and the peculiarities of RNA simulations, in particular. We discuss the strengths and limitations of the technique and provide examples of its application to elucidate small RNA's performance.

Nucleo-Cytoplasmic Transport of ZIKV Non-Structural 3 Protein Is Mediated by Importin-α/β and Exportin CRM-1

Flaviviruses have a cytoplasmic replicative cycle, and crucial events, such as genome translation and replication, occur in the endoplasmic reticulum. However, some viral proteins, such as C, NS1, and NS5 from Zika virus (ZIKV) containing nuclear localization signals (NLSs) and nuclear export signals (NESs), are also located in the nucleus of Vero cells. The NS2A, NS3, and NS4A proteins from dengue virus (DENV) have also been reported to be in the nucleus of A549 cells, and our group recently reported that the NS3 protein is also located in the nucleus of Huh7 and C636 cells during DENV infection. However, the NS3 protease-helicase from ZIKV locates in the perinuclear region of infected cells and alters the morphology of the nuclear lamina, a component of the nuclear envelope. Furthermore, ZIKV NS3 has been reported to accumulate on the concave face of altered kidney-shaped nuclei and may be responsible for modifying other elements of the nuclear envelope. However, nuclear localization of NS3 from ZIKV has not been substantially investigated in human host cells. Our group has recently reported that DENV and ZIKV NS3 alter the nuclear pore complex (NPC) by cleaving some nucleoporins. Here, we demonstrate the presence of ZIKV NS3 in the nucleus of Huh7 cells early in infection and in the cytoplasm at later times postinfection. In addition, we found that ZIKV NS3 contains an NLS and a putative NES and uses the classic import (importin-α/β) and export pathway via CRM-1 to be transported between the cytoplasm and the nucleus. IMPORTANCE Flaviviruses have a cytoplasmic replication cycle, but recent evidence indicates that nuclear elements play a role in their viral replication. Viral proteins, such as NS5 and C, are imported into the nucleus, and blocking their import prevents replication. Because of the importance of the nucleus in viral replication and the role of NS3 in the modification of nuclear components, we investigated whether NS3 can be localized in the nucleus during ZIKV infection. We found that NS3 is imported into the nucleus via the importin pathway and exported to the cytoplasm via CRM-1. The significance of viral protein nuclear import and export and its relationship with infection establishment is highlighted, emphasizing the development of new host-directed antiviral therapeutic strategies.