Cathepsin S and other proteases {cysteine protease} can cleave proteins to activate pathways. Cysteine proteases have poor regulation in some diseases. Cathepsin S activates antigen receptor MHC-II, which initiates T-cell immune responses. Eph receptor kinases and ephrins affect cardiovascular function, nerve regeneration, and cancer.
Nuclear acidic proteins can bind to histones to unblock DNA reading {derepression}.
Techniques {DNA footprinting} can measure protein binding to DNA without measuring gene expression or protein synthesis. Protein binding to DNA sites prevents DNAase enzyme from cutting DNA. If protein binds to DNA, protein-DNA complex moves more slowly in gels than DNA with no protein {mobility-shift assay}, so slower moving fragments have bound proteins.
Myxobacterium S. cellulosum epothilone A, epothilone B, and epothilone D polyketides {epothilone} stabilize microtubules and interfere with cell division. They are like Taxol but more water-soluble.
Factors {hepatic nuclear factor-1-alpha} {HNF-1-alpha} can have dimerization domains, which have mini-zipper four-helix-bundle (4HBs) superfamilies. Low transcription factor affects glucose-metabolism regulation, because dimers bind anti-parallel to coactivator protein {DCoH protein} to start insulin secretion in response to glucose.
Basic proteins {histone}| can bind to DNA to make chromosome chromatin structure. Histones can methylate to regulate DNA expression.
Enzymes {ligase} can join slightly-separated DNA-fragment ends already hydrogen-bonded to other strands, using other strands as templates to add missing bases.
Proteins {mutS protein} can find imperfect DNA helices and uses mutH and mutL proteins to correct them.
Proteins {nuclear acidic protein}| can bind to histones to unblock DNA reading for derepression.
Regulators {P300 protein} can add acetyl groups to histones.
Histones surround chromosomal DNA and block polymerase DNA reading {repression, DNA}| {DNA repression}.
Enzymes {RNase} can cut RNA. RNase A cuts hybridized DNA-RNA at mismatched bases.
Regulatory proteins or ribonucleic acids {transcription factor}| bind before and after genes. Transcription factors and DNA regions differ for different genes. Typically, genes have several regions, for transcription-factor sets. Eukaryote DNA has transcription-factor recognition sites at gene 5' and 3' ends.
Fos
C-fos genes make Fos protein transcription factors.
TATAA
TATAA sites are at 5' ends, just before mRNA transcription-start sites.
GC box
GC boxes are at 5' ends, just before mRNA transcription-start sites.
CCAAT
CCAAT sites are at 5' ends, just before mRNA transcription-start sites.
mRNA enhancer
50-base to 150-base mRNA-enhancer sites can be at 3' ends, 5' ends, or anywhere. They have redundant regions. They react to signal molecules, heat, metal ions, growth factors, or hormones. They contain regions that suppress other-cell-type transcription.
AAUAAA
AAUAAA sites at 3' ends act as signals to cut mRNA 10 to 30 bases away and then add polyA tails.
zinc finger
RNA-polymerase-III 50-base internal-control regions have two regions that bind zinc.
transcription factors: classes
Eukaryotes have transcription-factor classes that bind to DNA-regulatory-region sites: RNA polymerase II promoter, homeodomain, zinc finger, leucine zipper, and helix-loop-helix.
transcription factors: RNA polymerase II promoters
Eukaryotes have transcription factors that bind to RNA polymerase II promoters. Eukaryote promoters have DNA-binding sites and transcriptional-activation sites. Transcription factors help RNA polymerase bind to promoters or change reaction rates. TFIID binds to TATAA sites. TFIIA binds before TATAA sites. TFIIB works with RNA polymerase II. TFIIE binds after RNA polymerase II sites.
transcription factors: homeodomain binding proteins
Homeodomain binding proteins have one helix lying in DNA major groove and another helix lying across DNA to contact other proteins. Fruitfly homeotic genes control body development and contain 180-base homeobox control regions that have helix-turn-helix homeodomain found in most development genes. Vertebrate Hox genes are similar.
400 million years ago, Hox Ubx regulatory-gene mutations caused sea-dwelling arthropods with limbs on all body segments to evolve into terrestrial six-legged insects. Ubx regulates many other genes to prevent fruitfly (Drosophila) thorax-limb development, allow some brine-shrimp (Artemia) thorax-limb development, and allow other-crustacean thorax limbs.
transcription factors: zinc finger
Zinc-finger binding proteins {Kruppel protein} have repeated cysteines and histidines involved with zinc, as in SV40 early-gene GC-box Sp1, steroid-receptor proteins, and gap-gene proteins.
transcription factors: leucine zipper
Leucine-zipper binding proteins, such as FOS oncogene and JUN oncogene proteins, have four or five leucines, seven amino acids apart and just after arginine and lysine regions, that make dimers that bind to DNA.
transcription factors: helix-loop-helix
Helix-loop-helix binding proteins have regions, with arginine and lysine, that bind to DNA and make dimers, as in MyoD-gene and Myc-gene proteins.
Outline of Knowledge Database Home Page
Description of Outline of Knowledge Database
Date Modified: 2022.0225