Specific and nonspecific DNA binding complexes of lac repressor. (A) Schematic models of the specific (RO) and nonspecific (RD) complexes. Small arrows denote specific hydrogen bond donor and acceptor groups of amino acid residues in the protein binding site. Plus signs (+) denote basic side chains located in and around the same site. In the "down" position these groups are in "interactive contact" with the underlying dsDNA, and in the "up" position these contacts are broken. In the RO complex, there are seven hydrogen bond donor and acceptor "recognition" contacts with the base pairs of the DNA operator site, and only six electrostatic interactions with the charged DNA backbones. In the RD complex, there are 11 charge-charge interactions with the dsDNA backbone, but all the specific interactions with the DNA base pairs have been "withdrawn." As indicated by the double arrows, these conformations are dynamic and interconvert with rate constants kRO and kRD. The lower diagram shows the RD complex engaged in one-dimensional diffusion-driven sliding along dsDNA. Condensed monovalent salt cations are displaced from the backbone "ahead" of the sliding complex, and rebind "behind." Because this "relaxation" of the ion atmosphere is much faster than the sliding rate of the repressor, this sliding represents a true one-dimensional diffusion. [Reprinted from (17) with permission] (B) Structures of R, RD, and RO forms of lac repressor. Note the bending of the complex and the repositioning of the protein helices that occur in the RD to RO interconversion, as well as the dehydration of the protein-DNA interface. [Reprinted from (2)] (C) Base pair-specific and -nonspecific (backbone) contacts of a single lac repressor head-group in RO (left) (bases that are specifically defined by these contacts are colored yellow) and with the DNA of a representative nonspecific DNA binding site (right) (these contacts involve only sugar-phosphate backbone positions). [Reprinted from (2)]
有关转录调控的假说中，最为经典的应该是Jacob, Monod和他们的合作者提出的大肠杆菌的乳糖（lac）操纵子模型，它包括结构基因（Z、Y和A基因）、操纵基因（operator）和启动基因（又称启动子，promoter）。当lac阻遏物（repressor）结合在操纵基因上时阻止该操纵子的转录，阻遏物同操纵基因的结合由于诱导物别乳糖同阻遏蛋白的结合而解除其抑制作用。
在7月16日出版的Science上，350-352页，Peter H. von Hippel首先回顾了一下转录调控研究的历史，紧接着又对Kalodimos等人的最新工作进行了评述。386-389页，刊出了 Kalodimos的研究报告。
Rutger-Newark的化学教授Babis Kalodimos及其同事利用核磁共振（NMR）波谱来确定蛋白质如何在双螺旋结构的DNA长链上滑动并到达它们的靶位点—— 一段特异的DNA序列。更重要的是，他们提供了lac阻遏物（repressor）与非特异DNA作用的结构，并详细地叙述了蛋白质如何从成百万的DNA中挑选出他们的“搭档”DNA的过程。
Structure and Flexibility Adaptation in Nonspecific and Specific Protein-DNA Complexes
Interaction of regulatory DNA binding proteins with their target sites is usually preceded by binding to nonspecific DNA. This speeds up the search for the target site by several orders of magnitude. We report the solution structure and dynamics of the complex of a dimeric lac repressor DNA binding domain with nonspecific DNA. The same set of residues can switch roles from a purely electrostatic interaction with the DNA backbone in the nonspecific complex to a highly specific binding mode with the base pairs of the cognate operator sequence. The protein-DNA interface of the nonspecific complex is flexible on biologically relevant time scales that may assist in the rapid and efficient finding of the target site.
Fig. 1. Structure of the dimeric lac DBD complexed to a palindromic nonspecific DNA. (A) Ensemble of the final 20 structural conformers. The C terminus (residues 50 to 62) of each of the dimers is unstructured. Protein backbone is depicted in red, whereas the DNA heavy atoms are depicted in blue. The thin red lines depict the unstructured C-terminal region (51 to 62). The final structures have been deposited in the PDB (accession code 1OSL
Fig. 2. Comparison of specific with nonspecific binding mode and interactions. In (A) and (B), the left sites of the specific O1 and nonspecific complexes are overlaid on their DNA backbone so that the protein position with respect to the DNA can be compared. The proteins in the specific and nonspecific complexes are colored yellow and red, respectively. (A) The protein in the nonspecific complex is rotated 25°, relative to the DNA, compared to the protein in the specific complex. In (B), the four most important residues for conferring specificity are shown and their conformation is compared. (C) Schematic summary of the protein-DNA contacts in the specific and nonspecific complex (25). The bases that are specifically recognized by lac repressor are colored yellow. The solid and dashed lines indicate interactions in the major and minor grooves, respectively. Red, green, and dashed blue lines indicate hydrogen bonding and hydrophobic and electrostatic contacts, respectively. (D) Salt concentration dependence of specific and nonspecific binding for wild-type (wt) and Y17F repressors.
Fig. 3. Structural pathway of protein-DNA recognition. The hinge region (residues 50 to 62), which is colored red, remains unstructured in both the free state and the nonspecific complex, whereas it folds up to an 
helix in the specific complex with the natural operator O1. In the nonspecific complex, the DNA adopts a canonical B-DNA conformation, whereas in the specific complex it is bent by 
36°.
Fig. 4. Dynamic and H-D exchange rates analysis of the dimeric lac DBD-DNA interaction. (A) Exchange values, Rex, indicating motions on the micro- to millisecond time regime plotted as a function of residue number of the lac DBD. Values for the free state, nonspecific, and specific O1 complex are shown in red, green, and blue, respectively. Only residues with significant Rex values (>1 Hz) are displayed. (B) Color-coded representation of the conformational exchange dynamics alteration along the protein-DNA recognition pathway. (C) Protection factors of the dimeric lac DBD plotted as a function of residue number. Values for the free state, nonspecific, natural operators O3 and O1, and SymL complexes are shown in red, green, blue, cyan, and orange, respectively. Protection factors were calculated from the rate ratio kint/kobs and are displayed as a logarithmic scale.
