Molecular Regulation & Cellular Information

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Abstractions about biological information encoded and regulated across genes, proteins, lipids, pathways, and cell states. They include epigenetic and post-transcriptional control, molecular motifs and folds, signaling and secretion, sequence variation, metabolic cycles, and cellular division.

23 abstractions in this family — domain-specific abstractions that sit near one another in structural-signature space (k-means over structural-signature embeddings). Each is shown with its short description.

• Amphipathic lipid packing sensor motifs — Use a short, compositionally biased amphipathic sequence that folds into an alpha helix on loosely packed membranes, inserting bulky hydrophobes into lipid defects and thereby sensing curvature-dependent packing.
• Biological pathway — An ordered, branching or cyclic network of molecular interactions that converts a cellular input or state into a biochemical product, signal or phenotypic response.
• Citric acid cycle — A cyclic metabolic pathway that oxidizes acetyl units, regenerates oxaloacetate and transfers reducing equivalents for cellular energy metabolism.
• Contact order — A normalized measure of how far apart along a protein sequence the residues forming native-state contacts tend to be.
• Epigenetics — The study and mechanisms of persistent regulation of gene activity and cellular state that do not depend on changing the underlying DNA sequence, often mediated by chromatin, DNA modification and regulatory inheritance.
• Fim switch — An invertible bacterial promoter element whose orientation phase-varies expression of type-1 pili.
• Genetic code — The rule system mapping nucleotide codons in messenger RNA to amino acids or translation-stop signals.
• Histone fold — A conserved three-helix, two-loop protein motif that mediates histone-pair assembly and organizes DNA-associated multiprotein complexes.
• Immunome — The complete declared set of genes, proteins, peptides, receptors or interactions constituting an organism’s immune-system repertoire under a stated definition.
• Intracellular pH — The negative logarithmic measure of hydrogen-ion activity inside a cell or specified intracellular compartment.
• Ka/Ks ratio — Compare nonsynonymous substitutions per nonsynonymous site with synonymous substitutions per synonymous site to summarize selective constraint or episodic positive selection under an explicit codon-evolution model.
• Lipid — A broad class of hydrophobic or amphipathic biological molecules grouped by solubility and biosynthetic structure, including fatty acyls, glycerolipids, phospholipids, sphingolipids, sterols, and related families.
• Mitosis — Segregate a replicated eukaryotic chromosome complement through spindle-mediated attachment, alignment, sister separation, and daughter-nucleus reconstitution.
• Nuclear export signal — A short sequence or structural motif on a macromolecule that recruits nuclear-export machinery and biases transport from the nucleus to the cytoplasm.
• Post-transcriptional modification — Processing that chemically or structurally alters a primary RNA transcript into a mature or regulated RNA molecule.
• Protein fragment library — A curated collection of short backbone conformations indexed by sequence or structural context to reduce the search space in protein-structure modeling.
• Protein quinary structure — Evolutionarily shaped, transient and weak protein-surface interactions that arise in crowded cellular environments and influence diffusion, encounter selection, stability and function beyond isolated tertiary or stable quaternary structure.
• Pseudoprotease — A protease-family pseudoenzyme that retains the ancestral fold but lacks one or more catalytic requirements, often serving regulatory, binding, assembly or substrate-presentation roles.
• RAN translation — Repeat-associated non-AUG translation initiated within expanded nucleotide repeats without a conventional AUG start codon.
• Regulation of gene expression — The control of when, where and how strongly genetic information is converted into functional RNA or protein products.
• Secretory Protein — A functional protein class whose normal biosynthetic itinerary includes selective cellular export to extracellular space or a recipient-cell destination through a conventional or unconventional secretion route.
• Sequence feature variant type — A typed annotation describing how a protein sequence variation alters a defined structural or functional sequence feature.
• Single-strand conformation polymorphism — Sequence-dependent folding differences among equal-length single-stranded nucleic-acid fragments that alter electrophoretic mobility and can reveal small sequence variants.