Crystal structures protein

The stereochemistry of liganding of metal ions in proteins is now known for several proteins (see Armstrong, 1988). Some selected examples follow with data derived from the Protein Data Bank (Bernstein et al., 1977). In the cases in which two different metals are bound, information can be obtained on preferential sites for each metal in the presence of the other. 

The blue, or type 1, copper proteins, azurin from Pseudomonas aeruginosa (Adman et ai, 1978 Adman and Jensen, 1981) and from Al-caligenes denitrificans (Norris et al., 1983, 1986) and poplar plastocyanin (Guss and Freeman, 1983 Guss et al., 1986), have been studied by X-ray diffraction. These involve a Cu(I)/Cu(II) redox system. Cu(I) d ) is 

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Traditionally, least-squares methods have been used to refine protein crystal structures. In this method, a set of simultaneous equations is set up whose solutions correspond to a minimum of the R factor with respect to each of the atomic coordinates. Least-squares refinement requires an N x N matrix to be inverted, where N is the number of parameters. It is usually necessary to examine an evolving model visually every few cycles of the refinement to check that the structure looks reasonable. During visual examination it may be necessary to alter a model to give a better fit to the electron density and prevent the refinement falling into an incorrect local minimum. X-ray refinement is time consuming, requires substantial human involvement and is a skill which usually takes several years to acquire. 

A3) Bond lengths and bond angles vary in protein crystal structures. 

I Pontius, I Richelle, SI Wodak. Deviations from standard atomic volumes as a quality measure for protein crystal structures. I Mol Biol 264 121-136, 1996. 

Yu N, Yennawar H, Merz KM Jr (2005) Refinement of protein crystal structures using energy restraints derived from linear-scaling quantum mechanics. Acta Crystallogr D Biol Crystallogr 61 322-332... 

Ryde U, Nilsson K (2003) Quantum chemistry can locally improve protein crystal structures. J Am Chem Soc 125(47) 14232-14233... 

Yu N et al (2006) Critical assessment of quantum mechanics based energy restraints in protein crystal structure refinement. Protein Sci 15(12) 2773-2784... 

Membrane-integrated proteins were always hard to express in cell-based systems in sufficient quantity for structural analysis. In cell-free systems, they can be produced on a milligrams per milliliter scale, which, combined with labeling with stable isotopes, is also very amenable forNMR spectroscopy [157-161]. Possible applications of in vitro expression systems also include incorporation of selenomethionine (Se-Met) into proteins for multiwavelength anomalous diffraction phasing of protein crystal structures [162], Se-Met-containing proteins are usually toxic for cellular systems [163]. Consequently, rational design of more efficient biocatalysts is facilitated by quick access to structural information about the enzyme. 

Fig. 7.14 Nomenclature for characteristic regions of peptide c >,t /-space taken from Karplus (1996). The frequencies of observed peptide conformations in protein crystal structures decrease from areas enclosed by a heavy solid line to regions enclosed by a plain solid line, to dashed outlines. Areas outside the dashed lines are disallowed in peptide conformational space. The lines are an approximate rendering of the exact contours given by Karplus (1996).

A growing number of protein crystal structures has provided solid evidence that in many phosphoesterase enzymes, two and sometimes even three, di- or trivalent metal ions are involved in substrate transformation. Consequently, the high catalytic efficiency is, in part, the result of a perfectly coordinated catalytic cooperation of the metal ions. Dinu-clear phosphoiyl transfer enzymes have been discussed thoroughly in recent reviews [1-3]. Therefore, this chapter (Section 2) only gives a brief description of enzymes for which two-metal promotion of phos-phoester hydrolysis was proposed on the basis of detailed mechanistic or crystallographic studies (Table 1). 

Alberts, I. L., Nadassy, K., and Wodak, S. J. (1998) Analysis of zinc binding sites in protein crystal structures. Protein. Sci. 7,1700-1716. 

Steinbacher, S., Miller, S., Baxa, U., Budisa, N., Weintraub, A., Seckler, R., and Huber, R. (1997). Phage P22 tailspike protein Crystal structure of the head-binding domain at 2.3 A, fully refined structure of the endorhamnosidase at 1.56 A resolution, and the molecular basis of O-antigen recognition and cleavage. J. Mol. Biol. 267, 865-880. 

Rao-Naik, C., delaCruz, W., Laplaza, J. M., Tan, S., Callis, J., and Fisher, A. J. The rub family of ubiquitin-like proteins. Crystal structure of Arabidopsis rubl and expression of multiple rubs in Arabidopsis, J Biol Chem 1998, 273, 34976-34982. 

For protein crystallography, the repository of most protein crystal structures is the PDB hosted at http // www.rcsb.org/pdb/ (Berman et al., 2000). This database contains the 3-D coordinates (and sometimes the structure factor files) for almost all protein crystal structures. Most journals currently require deposition of the coordinates when pubhshing stmcture papers. Each structure is given a unique identification code that will be listed in the paper (see Figure 22-1 for examples of PDB codes). Structures can be accessed using this code, or using various other search criteria. The PDB also contains structural information for NMR structures. 

Burling, F. T. and Brunger, A. T. (1994) Thermal motion and conformational disorder in protein crystal structures. Isr. J. Chem. 34,165-175. 

Pellegrini, M., Gronbech-Jensen, N., Kelly J. A., Pfluegl, G., and Yeates, T. O. (1997) Highly constrained multiple-copy refinement of protein crystal structures. Proteins 29, 426-432. 

Holton, J. and Alber, T. (2004). Automated protein crystal structure determination using ELVES. Proc. Natl. Acad. Sci. USA 101,1537-1542. 

Zwart, P H., Langer, G. G. and Lamzin, V. S. (2004). ModelUng bound hgands in protein crystal structures. Acta Crystallogr. D 60,2230-2239. 

Badger, J. and Hendle, J. (2002). ReUable quality-control methods for protein crystal structures. Acta Crystulhgr. 0 58,284-291. 

Table 17.1 Marketed drugs designed using knowledge of protein crystal structures...

Table 17.1 lists a number of successful drugs on the market that were designed using knowledge and analysis of protein crystal structures. Note that the list is dominated by HIV protease inhibitors, drugs for the treatment of AIDS. The speed by which these... 

An analysis of metal binding to peptide carbonyl groups (Chakrabarti, 1990), mainly calcium ions in protein crystal structures, shows that the cations tend to lie in the peptide plane near the C=0 bond direction. Generally, this binding occurs in turns in proteins or in regions with no regular secondary structures. Ca---0 distances range from 2.2 to 2.5 A, and metal ions do not deviate by more than 35° from the peptide plane. Thus, metal ions in proteins do not, Chakrabarti observed, bind in lone-pair directions. 

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