Crystallization mutants

We thank Joan Wozniak and Sheila Snow for help with purifying and crystallizing mutant lysozymes. We are also grateful to Drs. Ingrid Vetter, Eric Anderson, Dale Tronrud and Larry Weaver for helpful advice. This work was supported in part by National Institutes of Health grant GM21967 to B.W.M. 

WA Lim, A Hodel, RT Sauer, FM Richards. The crystal structure of a mutant protein with altered but improved hydrophobic core packing. Proc Natl Acad Sci USA 91 423-427, 1994. PB Harbury, B Tidor, PS Kim. Repacking proteins cores with backbone freedom Structure prediction for coiled coils. Pi oc Natl Acad Sci USA 92 8408-8412, 1995. 

FIR Faber, BW Matthews. A mutant T4 lysozyme displays five different crystal conformations. Nature 348 263-266, 1990. 

A second example is that of an Ala-to-Cys mutation, which causes the fonnation of a rare SH S hydrogen bond between the cysteine and a redox site sulfur and a 50 mV decrease in redox potential (and vice versa) in the bacterial ferredoxins [73]. Here, the side chain contribution of the cysteine is significant however, a backbone shift can also contribute depending on whether the nearby residues allow it to happen. Site-specific mutants have confirmed the redox potential shift [76,77] and the side chain conformation of cysteine but not the backbone shift in the case with crystal structures of both the native and mutant species [78] the latter can be attributed to the specific sequence of the ferre-doxin studied [73]. 

The elegant genetic studies by the group of Charles Yanofsky at Stanford University, conducted before the crystal structure was known, confirm this mechanism. The side chain of Ala 77, which is in the loop region of the helix-turn-helix motif, faces the cavity where tryptophan binds. When this side chain is replaced by the bulkier side chain of Val, the mutant repressor does not require tryptophan to be able to bind specifically to the operator DNA. The presence of a bulkier valine side chain at position 77 maintains the heads in an active conformation even in the absence of bound tryptophan. The crystal structure of this mutant repressor, in the absence of tryptophan, is basically the same as that of the wild-type repressor with tryptophan. This is an excellent example of how ligand-induced conformational changes can be mimicked by amino acid substitutions in the protein. 

Figure 17.14 Model of evolved mutant from cephalosphorinase shuffling. The sequence of the most active cephalosporinase mutant was modeled using the crystal structure of the class C cephalosporinase from Enterobacter cloacae. The mutant and wild-type proteins were 63% identical. This chimeric protein contained portions from three of the starting genes, including Enterobacter (blue), Klebsiella (yellow), and Citrobacter (green), as well as 33 point mutations (red). (Courtesy of A. Crameri.)...

Deng et al. (2004a,b) prepared the crystals of the spent obelin (W92F mutant from O. longissima) that had been luminesced with Ca2+, and successfully obtained the X-ray structure of apoobelin as an important information in elucidating the mechanism of the luminescence reaction. 

The lipase (PAL) used in these studies is a hydrolase having the usual catalytic triad composed of aspartate, histidine, and serine [42] (Figure 2.6). Stereoselectivity is determined in the first step, which involves the formation of the oxyanion. Unfortunately, X-ray structural characterization of the (S)- and (J )-selective mutants are not available. However, consideration of the crystal structure of the WT lipase [42] is in itself illuminating. Surprisingly, it turned out that many of the mutants have amino acid exchanges remote from the active site [8,22,40]. 

The ANEH-mutant displaying enhanced enantioselectivity ( =10.8) was sequenced and shown to be characterized by three mutations, A217V near the active site and K332E and A390E both at remote positions [58]. The X-ray crystal structure of the WT ANEH had been analyzed earlier [61], revealing a dimer comprising identical... 

Isomorphous replacement is where the phases from a previous sample are used directly for a protein that has crystallized in exactly the same space group as before. This is usually applicable to determining the structure of many protein-ligand complexes or protein mutants. 

While wild-type PAMO was unable to convert 2-phenylcyclohexanone efficiently, all deletion mutants readily accepted this ketone as substrate. All mutants also displayed a similar thermostability when compared with the parent enzyme. The most active mutant (deletion of S441 and A442) was used for examining its enantioselective properties. It was found that the mutant preferably formed the (/ )-enantiomer of the corresponding lactone E = 100). While CHMO also shows a similar enantioselective behavior, this PAMO deletion mutant is a better candidate for future applications due to its superior stability. This clearly demonstrates that PAMO can be used as parent enzyme to design thermostable BVMO variants. It also illustrates that the available crystal structure of PAMO will be of great help for BVMO redesign efforts. ... 

Both enzymes belong to the family of a,p-hydrolases." The active site of MeHNL is located inside the protein and connected to the outside through a small channel, which is covered by the bulky amino acid tryptophane 128." It was possible to obtain the crystal structure of the complex with the natural substrate acetone cyanohydrin with the mutant SerSOAla of MeHNL. This complex allowed the determination of the mode of substrate binding in the active site." A summary of 3D structures of known HNLs was published recently." " ... 

TKase is a homodimeric protein with a subunit of about 70kDa. The X-ray structures of TKase of E. colif S. cerevisiaeX Leishmania mexicana and mize have been solved. In addition, the crystal structures of a number of site-directed mutants have been determined. Schneider and co-workers have reported a series of studies in which they have mutated important residues of active site of TKase to elucidate the reaction mechanism and explain the origin of the stereospecificity of the C—C bond-forming process (Table The conserved... 

G. F. Maley, P. Van Roey 2001, (Crystal structure of a deletion mutant of human thymidylate synthase Delta(7-29) and its ternary complex with Tomudex and dUMP), Protein Sci. 10(5), 988. 

Protein crystallography often requires special constructs or mutants to facilitate crystallization it also requires large quantities of highly purified protein. Thus to move forward in a timely fashion, it is important that an industrial structural biology group employ molecular biologists and individuals with expertise in protein purification. 

This approach is not restricted to bacterial or viral cells. Mammalian cells under highly proliferating conditions can be cultured at increasing exposure to a compound in attempts to create resistant mutants. Alternatively, one can sometimes use a structural biology approach to predict amino acid changes that would abrogate inhibitor affinity from study of enzyme-inhibitor complex crystal structures. If the recombinant mutant enzyme displays the diminished inhibitor potency expected, one can then devise ways of expressing the mutant enzyme in a cell type of interest and look to see if the cellular phenotype is likewise abolished by the mutation. 

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