Molecular function basic principles

In this chapter we describe the basic principles involved in the controlled production and modification of two-dimensional protein crystals. These are synthesized in nature as the outermost cell surface layer (S-layer) of prokaryotic organisms and have been successfully applied as basic building blocks in a biomolecular construction kit. Most importantly, the constituent subunits of the S-layer lattices have the capability to recrystallize into iso-porous closed monolayers in suspension, at liquid-surface interfaces, on lipid films, on liposomes, and on solid supports (e.g., silicon wafers, metals, and polymers). The self-assembled monomolecular lattices have been utilized for the immobilization of functional biomolecules in an ordered fashion and for their controlled confinement in defined areas of nanometer dimension. Thus, S-layers fulfill key requirements for the development of new supramolecular materials and enable the design of a broad spectrum of nanoscale devices, as required in molecular nanotechnology, nanobiotechnology, and biomimetics [1-3]. 

This chapter first discusses basic structural principles relating to the main classes of glycoconjugates in order to assist understanding of nematode structures. It then focuses on a selection of parasitic nematodes where detailed structural data on glycoconjugates have been obtained in recent years and where this structural information is starting to provide insights into possible molecular functions. 

The structure and function of enzymes is determined by both the amino acid sequence and the surrounding solvent. The overall stability of proteins is characterized by a subtle balance of into- and inter-molecular interactions. The basic principle of the structure (and of the stability) of the proteins is related to the nature of its normal enviromnent for (water) soluble globular proteins this is the minimization of the hydrophobic surface area, whereas the contrary is the case for membrane proteins (Jaenicke, 1991). 

It is considered timely to provide a survey of a number of important developments in this field. The aim of this book is to discuss basic principles and different approaches that have been used and present applications of molecular switches in the control of functions and material properties. It is not the intention to be comprehensive, but a selection of topics is made that reflects the fascinating possibilities... 

The theory of molecular evolution and the in vitro evolution experiments suggest practical applications to the design of biopolymer molecules as they were proposed already in the 1980s [4], The basic principles of the so-called irrational design of biomolecules are indeed identical with Darwin s natural law of variation and selection. Molecular properties are improved iteratively in selection cycles in order to achieve an optimal match with the predefined target function. The process is sketched in Fig. 5. Every selection cycle consists of three phases amplification, diversification, and selection. In these experiments, the fitness of genotypes is tantamount to their probability to enter the next selection round. 

In order to investigate the energies and molecular properties of molecules interacting with aerosol particles, it is crucial to establish the Hamiltonians and the energy functionals for the two structural environment methods. The basic principle for both structural environment methods is the same and it is one that has been utilized successfully within quantum chemistry [2-33] and molecular reaction dynamics [19,68-71,96], we divide a large system into two subsystems. The focus is... 

In the second part of this contribution, we will demonstrate how the basic principles discussed above can be utilized as a starting point for creating artificial biomimetic and bioinspired catalytic and photosynthetic devices. At present, only very few examples of synthetic molecular systems, which are able to replace all important functional aspects of their native counterparts under mild and ambient conditions, have been described in the literature (6), including some important results of our own work. In the last sections of this review, several selected case studies from the author s research efforts in this direction will therefore be presented. 

The two examples mentioned above illustrated basic principles how protein phosphorylation serves specific biological purposes. Although different kinases might be involved in diverse pathways, the molecular mechanism for the regulation of protein function by phosphorylation is similar By changing protein structure, phosphorylation can turn on/off the catalytic activity of a protein, or create/mask recognition motif for binding by other molecules. 

In the first chapter I shall describe basic principles of molecular recognition of monomers and polymers by cyclodextrins (G. Wenz, in Volume 222, Chapter 1) and try to provide an overview of inclusion polymers with cyclodextrins. The following chapters are more specialized. They are about functional cyclodextrin polyrotaxanes for drug delivery (N. Yui, R. Katoono, A. Yamashita, in Volume 222, Chapter 2), cyclodextrin inclusion polymers forming hydrogels (J. Li,... 

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