Ghost in the Cell

Code is being updated.  Here we're looking at one of the best resolved polyQ regions in the Huntingtin protein. The resolution of small beta structures was made possible by histidine inserts. Beta turns contribute to nucleation in Huntington's disease, enabling the formation of larger beta structures, and downstream aggregation and propagation. Further analysis of the paper methodology would be updated in this same post. This is a test-drive of bio3d 2.3-0 in R studio. Since 4FE8 contains multiple copies of HTT in various conformations, I first got familiar with the 3D structure in Samson, and then deleted non-relevant duplicate chains. You can also use the  pdbsplit function if you're familiar with the structure.  Although 4FE8 consists of 410 amino acids, the first 370 amino acids are actually from the maltose binding protein (MBP), which aids in solubility and crystallisation of the structure. The MBP is fused to the N-terminal of HTT. Therefore, the HTT protei...

CPD Photolyase was the flagship model for Zhong’s pioneering femtobiology studies in the 2000s. This DNA repair mechanism is remarkable for its ultra-fast, light-mediated process. Previously, I briefly introduced CPD photolyase (CPDphr) .  6 Jan 2026 edits : clarified pump laser activation mechanisms.   Here I will discuss the most recent visualization studies via TR SFX. These were two complementary papers by independent teams published in the same issue of  Science  in November/December 2023. Maestre Reyna et al., 2023 covered the entire catalytic process from 100ps to 200 µs, while Christou et al., 2023 focused on early events from 3ps to 100ps, though also briefly covered the entire catalytic cycle. I will compare these 2 studies briefly, starting with Maestre-Reyna et al., 2023.  Visualization studies of CPDphr can be divided into 3 eras.   Static Era 1990s to 2000s: X-ray crystallography Park et al. 1995 ( Science ) Crystal structure of DNA photolyas...

G-quadruplexes can form in ssDNA, dsDNA or 4 stranded DNA. The basic unit is a G4 region – where 4 guanines form a tetrad connected to a central K+ ion. Here you can see an experimental model 1XAV whereby ssDNA was placed in K+ solution to form a G-quadruplex. I removed the hydrogens in this NMR model. K+ is sandwiched between 2 tetrad layers, connecting to 8 oxygen atoms in two layers of G4. This is the most stable configuration. Contrast this with Na+, which is small enough to slip inside the tetrad plane, reducing the sandwich effect, and creating more unstable topologies. In this way, stable G-quadruplexes act as a potassium sensor. Less stable G-quadruplex configurations indicate a change in normal intracellular ion balance. Normally, K+ is high, and Na+ is low in the intracellular environment. Now let’s look at the formula for G4. In 1XAV, the sequence is:  5′‑TGA G G G T G G G TA G G G T G G G TAA‑3′ The formula is [3G + (1 or 2)N] X 4 . Each consecutive G forms a n...

Before I learned Samson, I used Sketchup to do a geometric model of the electrostatic bridge in the PAM-interacting domain of SpCas9, based on PDB 4UN3. The point was to showcase how the spatial arrangement, and how mutations in this region relaxes the PAM specificity for NGG. Sketchup is quite useful for a geometric simplification, but you'll have to simplify a lot of the complex structures for a quick model. Sketchup now charges a fee for its license, while Samson is free for students. Samson is infinitely more powerful, but needs a gaming laptop to run smoothly. Sketchup is mainly used in the architecture/ interior design field for conceptual modelling. Much easier to learn and more fun than AutoCAD. There is a key triad in the PAM-interacting (PI) domain of Cas9. The triad forms an electrostatic bridge : Arg1333, Arg 1335 and Glu 1219. R1333, R1335 and E1219. Arginine is positively charged, and directly interacts with G1 and G2 of the NGG PAM site on target DNA. Arginine is a c...