Protein general aspects

The book is separated into five major sections One short section on general aspects of spectroscopy, molecular biology and data evaluation is followed by an introduction into the NMR of commonly encountered classes of biomolecules. Thereafter, recent developments in spectroscopic techniques are highlighted. The next section describes experiments and practical aspects useful for the characterization of protein-ligand interactions. The final section presents an account on strategies for drug development using NMR written by experts from pharmaceutical industry. 

Kunz, C., Rodriguez-Palmero, M., Koletzko, B., and Jensen, R. (1999). Nutritional and biochemical properties of human milk. Part I General aspects, proteins, and carbohydrates. Clin. Perinatol. 26, 307-333. 

The first article in this volume, by Jenny P. dusker, treats general aspects of metal liganding to functional groups in proteins. This article presents a detailed summary of the geometry of interaction of metals with the various chemical groups of proteins. It also presents, in Sections I through VIII, a lucid development of the principles and terminology of the field of metal-protein interactions. It is with these sections that the newcomer to the field of metalloproteins should start. 

The possibility to carry out conformational studies of peptides at low concentrations and in the presence of complex biological systems represents a major advantage of fluorescence spectroscopy over other techniques. Fluorescence quantum yield or lifetime determinations, anisotropy measurements and singlet-singlet resonance energy transfer experiments can be used to study the interaction of peptides with lipid micelles, membranes, proteins, or receptors. These fluorescence techniques can be used to determine binding parameters and to elucidate conformational aspects of the interaction of the peptide with a particular macro-molecular system. The limited scope of this chapter does not permit a comprehensive review of the numerous studies of this kind that have been carried and only a few general aspects are briefly discussed here. Fluorescence studies of peptide interactions with macromolecular systems published prior to 1984 have been reviewed. 

While each formulation is unique, there are several general aspects with respect to excipient components in both liquid and lyophilized protein formulations. A comparison of the excipient components in liquid and lyophilized protein formulations is provided in Table 1. 

Many reviews are available. Older work is well summarized in a series on the iron-sulfur proteins,736 while reviews are available on general aspects,737 738 structural features,739 bacterial iron-sulfur proteins740 and three-iron clusters.741... 

We have already dealt with some general aspects of biochemical self-assembly in Section 2.10 including the remarkable formation of viral capsids. There are some biochemical examples, however, that translate readily into supramolecular chemical concepts and have been pivotal in defining the field. One such system is the tobacco mosaic virus, a virus that is very harmful to a variety of crops including tobacco, tomato, pepper, cucumbers and species such as ornamental flowers. This system consists of a helical virus particle measuring some 300 X 18 nm (Figure 10.6). A central strand of RNA is sheathed by 2130 identical protein subunits, each of which contains 158 amino acids. What is remarkable about... 

It is necessary to pay attention to the fact that, during recent years, the bioinorganic properties of aluminum coordination compounds have become the objects of detailed study their general aspect [354], metabolism and toxicology [355,356], complex formation with nucleozides of di- and triphosphates and nucleo-zide-bound proteins [357], and x-ray analysis of biologically important complexes... 

General Aspects of Fortification of Proteins with Amino Acids... 

D4. Davies, K. J., Protein damage and degradation by oxygen radicals. I. General aspects. J. Biol. Chem. 262,9895-9901 (1987). 

General aspects of protein and nucleic acid isolation... 

Table XVI gives a partial list of native proteins that have been hydrolyzed with proteolytic enzymes. A discussion of the interpretation of each example listed is beyond the scope of this review, but a few comments concerning certain features of proteolysis are ivarranted. The mechanism of enzymatic hydrolysis of native proteins was studied in detail by Tiselius and Eriksson-Quensel (1939), who examined the action of pepsin on ovalbumin. Two mechanisms of proteolysis were considered by these workers. In the first mechanism the enzyme hydrolyzes all susceptible peptide bonds in one substrate molecule before hydrolysis of a second molecule begins. This type of mechanism has been described by Lmderstrpm-Lang (1952) as the all or none type. In the second mechanism, the enzyme hydrolyzes the single, most susceptible bond in all substrate molecules before hydrolysis of other bonds occurs. This mechanism is called the zipper type. Hydrolysis of a protein can proceed by either of the two mechanisms or by a mechanism which has features of both types. General aspects of the problem have been reviewed and theoretical equations which describe the kinetics of ea( h mechanism have been derived (Linderstr0m-Lang, 1952, 1953).

In this article we propose to survey the role of iron as a conformational determinant in polypeptides and in non-haem proteins. This aspect of iron coordination research has been either ignored or only sporadically dealt with in reviews concerned with metalloproteins. By stressing this often circumstantial aspect of iron biochemistry it is our hope that the relevance of metals in general as fundamental structural factors in biomolecules will be brought into proper perspective. 

As mentioned, molecular and mesoscopic approaches will be needed. The first part of the book mainly considers molecules. We start with some basic thermodynamics, interaction forces, and chemical kinetics (Chapters 2-4). The next chapter is also concerned with kinetic aspects it covers various transport phenomena (which means that a few mesoscopic aspects are involved) and includes some basic fluid rheology. Chapters 6 and 7 treat macromolecules Chapter 6 gives general aspects of polymers and discusses food polysaccharides in particular, with a largish section on starch Chapter 7 separately discusses proteins, highly intricate food polymers with several specific properties. Chapter 8 treats the interactions between water and food components and the consequences for food properties and processes. 

This book is written for students who have taken elementary/introductory biochemistry and would like to take further courses in biochemistry related to special topics in nucleic acids, proteins, and/or polysaccharides. Thus it is designed for students who are familiar with the general aspects of biochemistry and would like to further their... 

---