Academic literature on the topic 'X-ray crystal structures; Amine complexes'

Crystallography provides the most direct way of forming images of molecules. Using crystallography, three-dimensional images have been made of thousands of macromolecules, especially proteins and nucleic acids. These give detailed information about their activity, their mechanism for recognizing and binding substrates and effectors, and the conformational changes which they may undergo. The three-dimensional structures show graphically the evolutionary relationships between molecules from widely separated systems. They give a wide view of the resemblances between different proteins, showing strong links in three-dimensional structure where the relationship between amino-acid sequences has dwindled to insignificance. The aim of this book is to tell the ordinary biologist enough about the methods of crystallography and the results that it gives, to allow results to be considered critically, to give insight into the limits of interpretation which are possible, and to identify the causes of the limitation in a particular case. Although the basic ideas are simple, the structural results are complicated, and based on huge numbers of measurements. The challenge for the teacher is to find a way through the simple basic ideas, without getting lost in detail. The main text is purely descriptive, and can be read from start to finish without any detailed mathematical knowledge. The explanations are backed up by numerous illustrations. For the reader who wants more detail, ‘boxes’ are supplied with more complete information, which can offer a deeper level of understanding, using some clearly presented mathematics. The book is not intended to teach the reader how to do practical crystallography. There are many other excellent books for this purpose. It is intended, rather, to give an overview which will allow any biochemist or molecular biologist to read structural papers with a critical awareness. In the first part of the book (Chapters 1–5), the general principles underlying the use of X-rays, crystals and diffraction are presented, using illustrations to make many of the ideas more graphic. In the second part (Chapters 6–13), the steps that need to be followed in the course of structure determination of a crystal are considered in more detail, again with many illustrations.

The formation of a solid, and especially an oxide, from soluble metal complexes is usually called “precipitation.” This term is a generic name that includes a set of complex and intricate phenomena. The process is governed by thermodynamic, structural, and kinetic contingencies, which should be examined in detail to understand the role of synthesis conditions and their influence on the solid obtained. The chemistry of the process involves a condensation reaction, olation or oxolation, between uncharged hydroxylated complexes. It forms particles of widely variable size over the nano- to micrometric range. These particles are portions of a solid identifiable in using techniques such as X-ray diffraction, absorption, and diffusion, electron microscopy, light-scattering, and various spectroscopies. Of course, these particles have the properties typical of the corresponding bulky solid, but they may be modulated because of the size effect, especially in the nanometric range (Chap. 1). Because of their small size, these objects have a large surface area highlighting their surface physicochemistry, such as ability to disperse in aqueous or nonaqueous medium, to aggregate, and to fix various species from solution, that allows the surface energy to be controlled to adjust the shape and size of these objects (Chap. 5). The crystal structure of polymorphic solids can also be controlled by the choice of the pathway of their formation. Thus, knowledge of the processes involved allows us to exploit the large versatility of the nanostructures synthesized in solution. This chapter has two main objectives. The first is to show that the crystalline structure of the solid may in many cases be anticipated from the characteristics of the precursor in solution, such as functionality, geometry, reactivity, and elec­tron configuration. This point concerns the structural aspect of the formation of the solid. The second objective is to understand why precipitation forms small particles, generally of nano- or micrometric size, and how the crystallization mechanism influences their morphology. These questions concern the kinetics and dynamics of the precipitation phenomenon.

The trp repressor from Escherichia coli is a DNA binding protein, which in the presence of the ami no acid tryptophan inhibits the transcription of at least five operons: trpEDCBA, trpR, aroH, mtr, and aroL (Zubay et al., 1972; Rose et al., 1973; Zurawski et al., 1981; Heatwole and Somerville, 1991, 1992). The ligand-free form (aporepressor) shows only weak binding (KD ~ 106 - 107 M) to DNA, independent of the nucleotide sequence (Carey, 1988; Hurlburt and Yanofsky, 1990). The tryptophan containing form (holorepressor) binds preferentially to specific operator sequences with a much higher binding constant (KD ~ 1010 - 1011 M) (Carey, 1988; Chou et al., 1989; Hurlburt and Yanofsky, 1990). The binding of the repressoris thus regulated by tryptophan, which acts as a corepressor (Rose et al., 1973). With a molecular weight of approximately 25kD, the trp repressoris one of the smallest regulatory systems known, which makes it attractive as a prototype for the study of the molecular mechanism of allosteric regulation. In the twelve years since it was isolated and purified (Joachimiak et al., 1983), it has become one of the most extensively studied allosteric systems. Although Perutz has justly pointed out that the trp repressoris not allosteric in a classical sense (Perutz, 1989), in fact, the control site is too close to the DNA binding site to separate direct and indirect (allosteric) effects, the system does manifest an essential feature of all allosteric control mechanisms - a structural change induced by ligand binding. Structures of both the apo- and the holorepressor have been determined both by x-ray diffraction (Zhang et al., 1987; Schevitz et al., 1985; Lawson et al., 1988) and by NMR (Arrowsmith et al., 1991a; Zhao et al., 1993). Structures of the operator DNA have also been reported (Lefèvre et al., 1987; Shakked et al., 1994a,b), and several structures of operator-repressor complexes are available: two crystal structures (Otwinowski et al., 1988, Lawson and Carey, 1993), and a family of NMR solution structures (Zhang et al., 1994).