Chemistry of Life

Molecular genetics, biochemistry

regulatory proteins

Genetic regulatory proteins bind to segments of DNA and bring about gene regulation. Non-genetic classes of regulatory proteins include those target, effector proteins that are involved in special cellular functions such as signaling as receptor proteins and pumps, adhesion, chemotaxis, cellular transport and active transport, and metabolic regulation, including enzymatic action and protein degradation.

Repressors and other regulatory proteins probably search for target sequences by binding to DNA and scanning its major groove. Most regulatory proteins recognize DNA because they can slide along it while searching for a specific target sequence. Such a search would be much slower for a protein that cannot bind DNA. [s]

Tables  Regulatory Proteins Sequences  Gene Regulation in E.coli  Second Messengers  Cell signaling  Cell Adhesion Molecules  Enzymes Function Krebs Cycle  Enzymes Cofactors of Krebs Cycle

Most gene regulation proteins are single proteins, often homodimers or homotetramers, which bind to two ligands: a. a metabolic intermediate, and b. a cis-acting gene regulation element.

Most of the known phosphorylated response regulators employ the two-component system to stimulate or repress the transcription of specific targetted genes.

Allosteric regulatory proteins bring about the alteration of metabolic pathways by utilizing end product repression, enzyme induction, and catabolite repression. Like allosteric enzymes, these proteins alter their levels of activity in response to ligand-binding-induced conformational (shape) changes. The allosteric or effector ligand is a small molecule that affects the active site by binding to the allosteric site. In the case of allosteric regulatory proteins, the active site is a DNA binding site, which binds, only when active, to a specific sequence of DNA. By binding to specific DNA sequences, the allosteric regulatory protein impacts levels of gene expression.

Items allosteric enzymesanabolism and catabolismControl of prokaryotic gene expressiongene regulationInteractions in BacteriaphosphorylationPhosphorylation switches in bacteriaphosphotransfer-mediated signaling pathwaysProtein Kinase Signaling Networkssignaling gradientssignal transductiontwo-component systems ••
Tables  Regulatory Proteins Sequences  Gene Regulation in E.coli  Cell signaling  Receptor Tyrosine Kinases(RTK)  Second Messengers  Phosphate-handling Enzymes  Second Messengers
 Cell signaling  Immune Cytokines  Electron Transport Chain vs Oxidative Phosphorylation  Enzymes Function Krebs Cycle  Enzymes Cofactors of Krebs Cycle  Phosphate-handling enzymes

Specific Enzymes/Types : ·· A · adenylyl (adenylate) cyclase · allosteric enzymes · AP endonuclease (Ape1) ·· C · cAMP-dependent protein kinase · cyclin-dependent kinases ·· D · DAGKs · diacyl glycerol kinases · DNA glycosylase · DNA ligase · DNA Ligase I · DNA polymerases · DNA polymerase I · DNA polymerase beta · DNase IV · · E · exonuclease 1 · exosome ·· F · focal adhesion kinases (FAKs) · Fen1 · Flap Endonuclease FEN-1 · G · guanylate cyclases · guanyl cyclase ·· H · hOGG1 · hOGG1 oxoG repair ·· I · inducible transcription factors ·· L · LigIII · · M · MAP kinase · mitogen activated protein kinases · Msh2-Msh3 · MutS, MutL, and MutH ·· O · 8-oxoguanine glycosylase · oxoG repair hOGG1 ·· P · PCNA · phosphatases · phosphodiesterases · phospolipases · phospholipase C-gamma · PLC-G · protein kinase A · protein kinase C · protein tyrosine kinases (PTKs) · receptor tyrosine kinases · R · RNA polymerase · Replication factor C · reverse transcriptase · ribozymes · RNA polymerase II · RTKs ·· S · serine/threonine kinases · spliceosomal-mediated RNA trans-splicing · SMaRT ·· T · trans-splicing ribozymes ·· U · UvrD ·· X · XRCC1 ·

Specific proteins/types : ·· C · cAMP receptor binding protein · cofactor · core histones H2A, H2B, H3, and H4 · CRE-binding protein CREB · cytokines ·· E · elongation factor EF ·· G · general transcription factors ·· H · helicases : Helicase II · heterochromatin · histone · HP1 · I · inducible transcription factors · L · · LexA repressor ·· M · mCAT2 receptor · motor proteins ·· N · nucleosome ·· P · PcG proteins · PCNA · Polycomb group · proteome ·· R · RecA · regulatory proteins · repressor proteins · Receptor Tyrosine Kinases (RTKs) · ribosomes · RPA ·· S · serine rich (SR) splicing factors · silencers · Ski7p · small nuclear ribonucleoproteins (snRNPs) · spliceosome · SR (serine rich) splicing factors ·· T · TATA binding protein · TBP · trans-acting factors · trithorax group (trxG) ·· U · ubiquitin (Ub) · UPF1 UPF2 · upstream transcription factors ·

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. . . transcription begun 10/06/06