From 2007.igem.org

Protein Design

Design proteins with high selectivity for a board of different processes would be of tremendous practical interest for both science and the industry [1].Computational design is well concerned as its sufficiency and convenience. Redesign Protein-DNA complexes are so important that be concerned at the beginning of active sites redesign . Some keystones have been reported[2-5]. Here we are trying to construct several artificial repressor-operator pairs to serve as the connecting wires of our system.

There are several steps in protein design[6] . First , generate a random structure with random sequence .Second , optimize the sidechain structure for each random sequence .Third , score each random sequence and select the sequence with best score . In almost all the conditions , the number of sequence candidates is unconsiderable .It will be 2020 candidates if redesign 20 positions . So a great efforts have been done to decrease the computation complexity[1,7-14]: Using several discrete conformation , rotamer , to represent the status of sidechain ; Employing pair-wise energy function to score the sequence ; searching with Monte Carlo , Genetic Algorithm and etc. And another key here is the score function . Up to now , no method in silico has been given to exam the design results . One way to exam is to express the sequences designed in real system .

Lac Repressor

The lac repressor is a DNA-binding protein which inhibits the expression of genes coding for proteins involved in the metabolism of lactose in bacteria[15].There are three distinct regions in the protein . The headpiece ,which is a fragment with about 51 amino acids from its N-terminal and consists a helix-turn-helix motif , is the only region working for binding DNA . Figure 1 shows the NMR structure of the complex with two headpieces of lac repressor and its nature operator[16]. A series of expriments have shown that the mutation on the 7th , 9th site on the operator can sharply decrease the stability of the complex[15-17]. Figure 2 shows the structure of DNA sequence on site 7,8,9 and the residues interaction with them. From the structure , we can get that residue 17,18 ,which are YQ in native repressor sequence , take charge in recognizing the specific DNA sequence .The binding specificity may be adapted by changing the two positions.