Properties of protein crystals

As the term X-ray crystallography implies, the sample being examined is in the crystalline state. Crystals of many proteins and other biomolecules have been obtained and analyzed in the X-ray beam. A few macromolecular crystals are shown in Fig. 3.1. 

In these photographs, the crystals appear much like inorganic materials such as sodium chloride. But there are several important differences between protein crystals and ionic solids. 

Whereas inorganic crystals can often be grown to dimensions of several centimeters or larger, it is frequently impossible to grow protein crystals as large as 1 mm in their shortest dimension. In addition, larger crystals are often twinned (two or more crystals grown into each other at different orientations) 

In efforts to obtain crystals, or to find optimal conditions for crystal growth, crystallographers sometimes obtain a protein or other macromolecule in more than one crystalline form. Compare, for instance, Figs. 3.1a and 3.le, which 

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In protein crystals, due to the large size of the molecule, the empty space can have cross sections of 10-15 A or greater. The empty space between the protein molecules is occupied by mother liquor. This property of protein crystals, shared by nucleic acids and viruses, is otherwise unique among the crystal structures. In fact, the values of the packing coefficient of protein crystals range from 0.7 to 0.2, but the solvent molecules occupy the empty space so that the total packing coefficient is close to 1 [37]. Nevertheless, a detailed theoretical study has been carried out to examine the models of DNA-DNA molecular interactions on the basis of hard-sphere contact criteria. The hard-sphere computations are insufficient for qualitative interpretation of the packing of DNA helices in the solid state, but... 

Another useful physical property of the crystal is its density, which can be used to determine several useful microscopic properties, including the protein molecular weight, the proteinlwater ratio in the crystal, and the number of protein molecules in each asymmetric unit (defined later). Molecular weights from crystal density are more accurate than those from electrophoresis or most other methods (except mass spectrometry) and are not affected by dissociation or aggregation of protein molecules. The proteinlwater ratio is used to clarify electron-density maps prior to interpretation (Chapter 7). If the unit cell is symmetric (Chapter 4), it can be subdivided into two or more equivalent parts called asymmetric units (the simplest unit cell contains, or in fact is, one asymmetric unit). For interpreting electron-density maps, it is helpful to know the number of protein molecules per asymmetric unit. 

The crude molecular image seen in the F0 map, which is obtained from the original indexed intensity data (IFobsI) and the first phase estimates (a calc), serves now as a model of the desired structure. A crude electron density function is devised to describe the unit-cell contents as well as they can be observed in the first map. Then the function is modified to make it more realistic in the light of known properties of proteins and water in crystals. This process is called, depending on the exact details of procedure, density modification, solvent leveling, or solvent flattening. 

Galli Marxer, C., Collaud Coen, M., and Schlapbach, L. (2003). Study of adsorption and viscoelastic properties of proteins with a quartz crystal microbalance by measuring the oscillation amplitude. J. Colloid Interface Sci., 261, 291-298. 

While the most obvious advantage of microfluidics is the enormous reduction in sample consumption, the growth of protein crystals can also be fundamentally improved by taking advantage of the physical properties of fluid flow at the mi-... 

An important feature of protein crystal growth experiments is the need to carry out crystallization trials with very small quantities of scarce and expensive materials. When experiments are carried out in such small volumes (typically, 5—100 ju.1), it becomes difficult to define and control solution properties. The situation becomes particularly complicated when vapor diffusion or other nonequilibrium approaches to crystal growth are used, as these produce different and changing conditions throughout the small volumes involved. 

The protein properties include (1) motions of several proteins monitored by ESR spin labels (Belonogova et al., 1978, 1979 Likhtenshtein, 1976 Steinhoff et al., 1989) and Mossbauer labels (Belonogova et al., 1979 Likhtenshtein, 1976) (2) temperature dependence of neutron scattering for myoglobin (Cusack, 1989 Doster et al., 1989) (3) Mossbauer spectra (Parak et al., 1988) and RSMR spectra (Goldanskii and Krupyanskii, 1989) of myoglobin and (4) mechanical properties of lysozyme crystals (Morozov and Gevorkyan, 1985 Morozov et al., 1988). 

The perplexing difficulties that arise in the crystallization of macromolecules, in comparison with conventional small molecules, stem from the greater complexity, lability, and dynamic properties of proteins and nucleic acids. The description offered above of labile and metastable regions of supersaturation are still applicable to macromolecules, but it must now be borne in mind that as conditions are adjusted to transport the solution away from equilibrium by alteration of its physical and chemical properties, the very nature of the solute molecules is changing as well. As temperature, pH, pressure, or solvation are changed, so may be the conformation, charge state, or size of the solute macromolecules. 

As with pH, proteins may vary in solubility as a function of temperature, and some are quite sensitive. One can take advantage of this property with both bulk and microtechniques (Jacoby, 1968 McPherson, 1999). Many of the earliest examples of protein crystallization were based on the formation of concentrated solutions at elevated temperatures followed by slow cooling. Osborne in 1892 successfully crystallized over 20 plant seed globulins by cooling relatively crude extracts from 60°C to room temperature in the presence of varying concentrations of sodium chloride. 

The methods of protein crystallography are subject to the same limitations and errors as are encountered with small structures. Because other factors may be dominant when dealing with proteins, some of these errors become inconsequential. However, there are errors associated with the special techniques that have been developed in protein crystallography, and these must be considered as well as the special properties of the crystals. To evaluate the methods and gain some idea of how errors affect the confidence that can be attached to the results, I will first treat briefly the nature of protein crystals and diffraction from them and then consider some of the special experimental and computational techniques. 

Synthetic polypeptides consist of a repeating sequence of certain amino acids and their primary structures are not as complicated as those in proteins. The polypeptides are very important polymers in both polymer and protein science. The characteristic properties related to the structure lead to possible expansion for research in the field of polymer science, to provide very different moplecules from conventional synthetic polymers. For example, the concept of the liquid crystal is expanded by revealing the variety of structures and properties of liquid crystals. Furthermore, the polypeptides are sometimes used as biomimic materials. On the other hand, synthetic polypeptides are sometimes used as model biomolecules for proteins because they take the a-helix, /3-sheet, o)-helix structure, and so on, under appropriate conditions. From such situations, it can be said that synthetic polypeptides are interdisplinary macromolecules and are very important for research work in both polymer and protein science. 

Curcio, E., Fontananova, E., Di Rrofio, G. and DrioU, E. 2006. Influence of the structural properties of poly(vinyhdene fluoride) membranes on the heterogeneous nucleation rate of protein crystals. 110 12438-12445. 

Liu, Y.X., Wang, X.J., Lu, J. and Ching, C.B. 2007. Influence of the roughness, topography, and physicochemical properties of chemically modified surfaces on the heterogeneous nucleation of protein crystals. J. Phvs. Chem. B 111 13971-13978. 

Self-assembly of matter (or the formation of superstructures by means of non-covalent bonds) is a fascinating field of research. The formation of crystals and liquid crystals by atoms or molecules is just one example. Also within a larger molecule with a lot of conformational freedom, such as a polyamide chain or a protein, certain conformations are stabilized by secondary interactions, such as hydrogen bonds, which is essential for their properties (eg, mechanical properties of polyamides and functional properties of proteins). Secondary interactions in supramolecular structures play an important role for many processes in living cells (1). Various aspects of self-assembly have been presented in books (2-4) and in a recent review (5). This article deals with the self-assembly (or self-organization) of synthetic macromolecules, namely block copolymers, principally teming triblocks (see Block Copolymers). 

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