CONCEPTUALLY DENSE WORDS

#1

if u find the right conceptually dense words, you can describe MUCH MORE with less [including rough “isomorphisms” between different kinds of common allosteric modifications], though biology is still messy enough that attempts may still have ROI only as high as that of the entire protein folding/molecular dynamics field…

mutation at a single position can result in significant drops in binding activities, known as activity cliffs

distance-dependent synaptic coupling

tortuosity
all the cell parameters anne carpenter uses [eg zerneike polynomials which can detect some cancer cells…]

“oversmoothing” [cf michael bronstein, taco cohen]

LRTCs, criticality
AR(p), viscoelasticity (jude phillip)

(high/low) (specificity/sensitivity)
(necessary vs sufficient vs facilitative conditions)
F-scores

https://meetings.ashg.org/event/ASHG25/sessions/SESQBKS9G9M4BWZ9R

#2

Reviewing some of RNA’s underlying physical characteristics is worthwhile for understanding RNA structure. Within an RNA strand, the negatively charged ribose–phosphate chain—which makes up two-thirds of the mass of a nucleotide—creates steric and electrostatic constraints on the backbone conformation. Bases, which account for the remaining third of mass, comprise planar aromatic rings decorated with partially charged hydrogen-bond donors and acceptors. Thus, each monomeric nucleotide unit contains charged, polar, and aromatic groups, which can make diverse types of interactions with water, ions, amino acids, small molecules, and other nucleotides. In other words, in their normal aqueous environment RNA nucleotides are highly social—they are made to interact with one another (7, 8).

The realization that every nucleotide in an RNA chain can favorably interact with every other nucleotide is critical for thinking about RNA structure and how it differs from protein structure. In proteins, distinct side-chain characteristics mean some of the 20 amino acids more favorably interact with one another; some are more readily accommodated on the inside of a fold (like phenylalanine due to its aromatic ring), while others are on the solvent interacting surface (like the charged amino acids). Biochemists regularly experience how the type and distribution of amino acids affect the solubility of a given protein. In contrast, although RNA contains a planar aromatic base at every link in its chain, RNA is soluble in salty water. This seeming paradox is resolved because noncovalent interactions drive RNA bases to stack on each other, exposing their charged exocyclic groups to the water molecules and ions in the aqueous environment, leading to RNA “solvation” (9, 10).