Structure and DNA binding

Calamai, P Guerri, A., Messori, L Orioli, P. and Speroni, G.P. (1999) Structure and DNA binding properties of the gold(III) complex [AuCl2(esal)]. Inorganica Chimica Acta, 285, 309. 

Mechanism. LexA protein normally blocks the expression of fifteen or more genes involved in DNA repair. RecA protein spedfidally binds to the singlestrands produced by physical or chemical damage to DNA (see RecomUnation for details of recA structure and DNA binding). The single-strand DNA-... 

Tarushi A, Psomas G, Raptopoulou C, Psycharis V, Kessissoglou D (2009) Structure and DNA-binding properties of bis(quinolonato)bis(pyridine)zinc(II) complexes. Polyhedron 28 3272-3278... 

Antitumor activity. X-ray crystal structure, and DNA binding properties of thiocoraline A, a natural bisintercalating tiiiodepsi-peptide./. Med. Chem., 50, 3322—3333. 

Pabo, C.O., Lewis, M. The operator-binding domain of X repressor structure and DNA recognition. Nature 298 443-447, 1982. 

E. and Randaccio, L. (1992) Gold(III) glycyl-L-histidine dipeptide complexes. Preparation and x-ray structures of monomeric and cyclic tetrameric species. Inorganic Chemistry, 31, 1983 (b) Carotti, S., Marcon, G., Marussich, M., Mazzei, T., Messori, L., Mini, E. and Orioli, P. (2000) Cytotoxicity and DNA binding properties... 

P-sheet structures as DNA-binding motifs are found in pro- and eucaryotic DNA-binding proteins. As an example, the structure of the MetJ repressor from E. coli is shown in Fig. 1.9. The DNA is contacted in the major groove by the protruding P-strands. 

Structure of the Recognition Sequence and Quarternary Structure of DNA-binding Proteins... 

Fig. 1.18. Structure and symmetry of DNA recognition elements and the ohgomeric structure of DNA-binding proteins, sequence and binding protein plays an important role in the specific binding process. If, for example, a mutation inactivates one half of the recognition sequence, the other intact site often no longer suffices to provide for a tight binding. The protein can then only bind weakly and the mutated DNA element is often inactive in the in vivo situation.

The effects of DNA-binding transactivators on Pol II are mediated by coactivator protein complexes such as TFIID or mediator. The modular structures of the transactivators have distinct activation and DNA-binding domains. Other protein complexes, including histone acetyltransferases such as GCN5-ADA2-ADA3 and ATP-dependent complexes such as SWI/SNF and NURF, reversibly remodel chromatin structure. 

Proteins are folded in many ways. We have already considered several simple patterns the antiparallel P cylinder (Fig. 2-16), the 2-helix coiled coil (Fig. 2-21) and the 3- and 4-helix bundles (Fig. 2-22). Another simple motif that has been found repeatedly is the helix-turn -helix or helix-loop-helix in which two helices at variable angles, one to another and with a turn or short loop between them, form a structural emit. DNA-binding repressors and transcription factors (see Fig. 2-21 and also Chapter 5) often contain this motif as do many Ca2+-binding proteins. Proteins containing 3-6 helical segments, often fold into a roughly polyhedral shape.258 259 An example is myoglobin (Fig. 2-19B). 

Transcription factors that increase the rate of transcription usually have at least two domains of protein structure, a DNA-binding domain that recognizes the specific DNA control element to bind to, and an activation domain that interacts with other transcription factors or the RNA polymerase. Many transcription factors operate as dimers (homodimers or heterodimers) held together via dimerization domains. Some transcription factors interact with small ligands via a ligand-binding domain. 

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