Proteins association with macromolecules

A major limitation in using protein NMR spectroscopy in drug discovery has been the molecular weight limitation imposed by nuclear spin relaxation (line broadening) and increased spectral complexity associated with macromolecules larger than 35 kDa [5]. The most recent developments in NMR spectroscopy aimed at overcoming these problems will be briefly reviewed in Sect. 21.2. 

The low MW P(3HB) which is also known as complexed-P(3HB) (c-P(3HB)) is an ubiquitous cell constituent that exists in eubacteria, archaebacteria and eukaryotes [22, 23]. Studies have also revealed the presence of c-P(3HB) in hnmans [24]. This c-P(3HB) consists of about 120-200 3-hydroxybutyrate (3HB) units and has a MW of about 12,000 Da [25]. Depending on the strength of their association with macromolecules, chloroform-soluble and chloroform-insoluble c-P(3HB) have been identified [26]. The former forms a weakly bound (noncovalent) complex with polyphosphate salts while the latter nsnally forms a strongly bound (covalent) complex with proteins. These complexes are thought to function as ion (Csd ) transport channels across cell membranes and may also facilitate the uptake of extracellular deoxyribonucleic acid (DNA) material [26, 27]. 

To understand the function of a protein at the molecular level, it is important to know its three-dimensional stmcture. The diversity in protein stmcture, as in many other macromolecules, results from the flexibiUty of rotation about single bonds between atoms. Each peptide unit is planar, ie, oJ = 180°, and has two rotational degrees of freedom, specified by the torsion angles ( ) and /, along the polypeptide backbone. The number of torsion angles associated with the side chains, R, varies from residue to residue. The allowed conformations of a protein are those that avoid atomic coUisions between nonbonded atoms. 

The overall scope of this book is the implementation and application of available theoretical and computational methods toward understanding the structure, dynamics, and function of biological molecules, namely proteins, nucleic acids, carbohydrates, and membranes. The large number of computational tools already available in computational chemistry preclude covering all topics, as Schleyer et al. are doing in The Encyclopedia of Computational Chemistry [23]. Instead, we have attempted to create a book that covers currently available theoretical methods applicable to biomolecular research along with the appropriate computational applications. We have designed it to focus on the area of biomolecular computations with emphasis on the special requirements associated with the treatment of macromolecules. 

Most of the molecules introduced in this chapter are hydrophobic. Even those molecules that have been functionalized to improve water-solubility (for example, CCVJ and CCVJ triethyleneglycol ester 43, Fig. 14) contain large hydrophobic structures. In aqueous solutions that contain proteins or other macromolecules with hydrophobic regions, molecular rotors are attracted to these pockets and bind to the proteins. Noncovalent attraction to hydrophobic pockets is associated with restricted intramolecular rotation and consequently increased quantum yield. In this respect, molecular rotors are superior protein probes, because they do not only indicate the presence of proteins (similar to antibody-conjugated fluorescent markers), but they also report a constricted environment and can therefore be used to probe protein structure and assembly. 

The concept of the similarity of molecules has important ramifications for physical, chemical, and biological systems. Grunwald (7) has recently pointed out the constraints of molecular similarity on linear free energy relations and observed that Their accuracy depends upon the quality of the molecular similarity. The use of quantitative structure-activity relationships (2-6) is based on the assumption that similar molecules have similar properties. Herein we present a general and rigorous definition of molecular structural similarity. Previous research in this field has usually been concerned with sequence comparisons of macromolecules, primarily proteins and nucleic acids (7-9). In addition, there have appeared a number of ad hoc definitions of molecular similarity (10-15), many of which are subsumed in the present work. Difficulties associated with attempting to obtain precise numerical indices for qualitative molecular structural concepts have already been extensively discussed in the literature and will not be reviewed here. 

The water that is associated with a macromolecule, a colloid, or other substance such that it is not removable by simple filtration. 2. The water molecule(s) bound to the active site of an enzyme or to the surface of a protein. 

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