Chemistry, protein crystallization

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

Freely suspended liquid droplets are characterized by their shape determined by surface tension leading to ideally spherical shape and smooth surface at the subnanometer scale. These properties suggest liquid droplets as optical resonators with extremely high quality factors, limited by material absorption. Liquid microdroplets have found a wide range of applications for cavity-enhanced spectroscopy and in analytical chemistry, where small volumes and a container-free environment is required for example for protein crystallization investigations. This chapter reviews the basic physics and technical implementations of light-matter interactions in liquid-droplet optical cavities. 

Petsko, G. A., Phillips, D. C., Williams, R. J. P. and Wilson, I. A. (1978). On the protein crystal chemistry of chloroplatinite ions general principles and interactions with triose phosphate isomerase. /. Mol. Biol. 120, 345-359. 

Deszczynski, M., Harding, S.E., Winzor, D.J. (2006). Negative second virial coefficients as predictors of protein crystal growth evidence from sedimentation equilibrium studies that refutes the designation of those light scattering parameters as osmotic virial coefficients. Biophysical Chemistry, 120, 106-113. 

In view of its application to fuel cell development, research into hydrogen activation remains a forefront area for chemists, physicists, and biologists (7). A rekindling of opportunity and excitement in this field of chemistry has come from the delineation of simple catalytic sites of hydrogenase enzymes as displayed by protein crystal structures published within the last decade (2 10). These active sites hold out promise of using complexes comprised of base metals such as iron or... 

Since the introduction of combinatorial chemistry techniques, the emphasis has shifted from the design of large diverse libraries towards smaller more focused libraries. Indeed, as the number of protein crystal structures that are available has increased, so too has the interest in using this structural knowledge for combinatorial library design, compound acquisition programmes and virtual screening. This trend is likely to continue in the near future. 

Finney JL (1979) The organisation and function of water in protein crystals. In Franks F (ed) The physics and chemistry of water. A comprehensive treatise, vol. 6. Plenum Press, New York, pp 47-122... 

A brief look at the contents page of any recent issue of the Journal of Molecular Biology (founded by John Kendrew, protein crystal-lographer and winner of the Nobel prize for Chemistry together with Max Perutz for the 3-dimensional structures of myoglobin and haemoglobin) will clearly establish that this is not so ... 

The nse of X-ray crystallography in FBDD has become more prevalent, fostered by the development of techniques to more rapidly find conditions for protein crystallization and robotic methods for obtaining crystal structures. Having a ligand-protein crystal structure provides structural information abont the mode of binding and gives considerable insight into the chemistry optimization process. ... 

Protein chemistry provides again an illustrative example of the new light cast on conventional H-bonds. Baker and coworkers [32, 33] have used the geometric characteristics of H-bonds in a dataset of 698 high-resolution protein crystal structures to develop an orientation-dependent hydrogen bonding potential. Upon analyzing more than 100,000 H-bonds (most of them N-H- - -O backbone-backbone links), these authors concluded that quantum effects are utterly essential to explain the spatial orientation of these H-bonds [32] and even stated explicitly their partial covalent nature [33]. 

The chemical preparation step in which the protein is isolated, purified, and crystallized is critical in that the protein preparation must be chemically homogeneous otherwise, the resulting disorder will muddle the electron-density map. The preparation of isomorphous derivatives by soaking native protein crystals in various mercury, platinum, lead, uranium, etc., solutions also is critical since several crystals of each derivative are required for x-ray data collection (because of irradiation damage) and all the crystals should have the same heavy-atom distribution and concentration. The protein structure documentation should provide evidence that the preparative protein chemistry is sound. 

Table 4 shows some applications that have been realized on the centrifugal microfluidic platform. At the top of the applications section, sample preparation modules (plasma separation, DNA extraction) are shown. This is followed by assays based on the detection of proteins, nucleic acids and small molecules (clinical chemistry). Two additional applications are presented at the end of the table, demonstrating chromatography and protein crystallization. Some instmctive examples are discussed in more detail below. 

Thus, during the last decade, the method of cryoradiolytic reduction has emerged as a new tool to investigate critical intermediates of redox systems. X-ray-induced radiation chemistry is also increasingly recognized both as a potential source of misinterpretations due to measurement-induced changes of the sample, and as a new, important tool in X-ray crystallography, where the irradiation of protein crystals may be used to deliberately alter the redox state of metals, flavins, disulfides, and other cofactors - The... 

Much of this handbook is concerned with the how and why of crystallization and crystallizer design. This chapter will focus on the crystallization of one particular class of chemical compounds, namely the proteins. In the timeline of crystallization, protein crystallization is a newcomer. The first mention of protein crystal formation, roughly 150 years ago, involved crystallizing hemoglobin from the blood of various species (Lehman 1853 Reichert and Brown 1909 Debru 1983 McPherson 1991). This work was followed by the crystallization of a variety of proteins from plants to egg white (Sumner 1926). These early studies were pivotal in establishing that enzymes are proteins (Dounce and Allen 1988). The use of protein crystallization in purification and classification of biological chemicals resulted in the Nobel Prize for Chemistry being awarded to Sumner, Nothrop, and Stanley in 1946. 

A protein crystal structure has been reported for a form of the R. capsulatus DMSO reductase generated by addition of DMS to crystals of the enzyme." " The DMS binds to the 0x0 group, apparently producing DMSO bound to the reduced molybdenum center. This is depicted in Figure 5 as a des-oxo species, as formed by the addition of DMS to the mono-oxo center shown in Figure 4. The structures of the oxidized and reduced forms of the catalytic centers of the molybdenum DMSO reductases have stimulated an extensive range of coordination chemistry, directed at the production of their chemical analogues with some considerable success. ... 

Galactose oxidase (GO) catalyses the two-electron oxidation of primary alcohols to aldehydes. It contains a single type II copper centre. The enzyme employs the metal and a protein radical cofactor to effect the chemistry. The crystal structure shows a square pyramidal five-coordinate copper site with the metal coordinated by two histidines, two tyrosines and a water or acetate ligand. The equatorial tyrosine, Tyr272, has an interesting crosslink to a cysteine group ortho to the tyrosine oxygen. 

Based on the DLS measurements it is possible to find particle size distributions of polymers and proteins, particle aggregation phenomena, micellar systems and their stability, micro-emulsion technology, colloid behaviour, nucleation processes and protein crystallization. DLS is a non-destructive and convenient method and so it can find application in various branches of science. In chemistry it finds application in topics of colloids, polymers, emulsions, suspensions, nanoparticles, and in physics, applications such as in astrophysics and atmosphere physics and in biology it involves biophysics and biomedicine applications. 

EAN has many potential apphcations in protein chemistry [87] because of its hydrophobic and ionic characters and the ability to form hydrogen bonds. It may be used as an additive, a detergent, a precipitating agent, or to deliver ligands into protein crystals. EAN has been used to enhance the recovery of denatured-reduced hen egg white lysozyme (HEWL). EAN has the abihty to prevent aggregation of the denatured protein [88]. 

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