Computational Molecular Biology 2024, Vol.14, No.5, 182-190 http://bioscipublisher.com/index.php/cmb 185 3.4 Viral and pathogen interactions Biophysical methods have significantly advanced our understanding of host-pathogen interactions, Techniques such as cryo-electron microscopy (cryo-EM) and X-ray crystallography have provided high-resolution structures of viral proteins and their complexes with host proteins, shedding light on the mechanisms of viral entry, replication, and immune evasion (Dobson, 2019). Computational approaches, including MD simulations and machine learning models, have further enhanced our ability to predict and analyze these interactions, offering new avenues for therapeutic intervention (Chen et al., 2018). These methods have been particularly useful in studying the structural principles of host-pathogen protein-protein interactions, providing insights into the design of novel antiviral and antibacterial agents. 4 Advancements and Innovations in Biophysical Techniques 4.1 Technological innovations in biophysics 4.1.1 Advances in imaging technologies Recent advancements in imaging technologies have significantly enhanced our ability to visualize and understand complex biological systems at the molecular level. Single-molecule imaging techniques, such as convex lens-induced confinement (CLiC) microscopy, have enabled researchers to observe molecular interactions with high precision and control under cell-like conditions, eliminating the biases associated with tethering molecules (Zhang, 2024). Additionally, the integration of super-resolution microscopy with other techniques, such as atomic force microscopy (AFM), has provided transformative insights into the dynamic processes of biomolecules, allowing for the investigation of molecular interactions closer to their native physiological states (Figure 2) (Haghizadeh et al., 2023). Figure 2 Understanding various DNA–protein interactions using correlated optical tweezers fluorescence microscopy (Adopted from Haghizadeh et al., 2023) Image caption: (a) Gene editing: a DNA molecule tethered between two optically trapped beads. (b) DNA organization: the left side depicts a cohesin bridge between two DNA molecules formed during the incubation of two DNA tethers in cohesin, ATP, and SCC2/4. (c) DNA replication: Schematic of DNA unwinding mechanism by BLM helicase. (d) DNA repair: an experimental schematic where an optical tweezers-based single-molecule technique was used to resolve individual RAD-51 filament growth and measure their growth rates in replacing RPA-covered resected DNA in the HR repair mechanism (Adopted from Haghizadeh et al., 2023)
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