Three-dimensional structure, of biomolecules

Biological interactions between molecules are stereo-specific the fit in such interactions must be stereo-chemically correct. The three-dimensional structure of biomolecules large and small—the combination of configuration and conformation—is of the utmost importance in their biological interactions reactant with enzyme, hormone with its receptor on a cell surface, antigen with its specific antibody, for example (Fig. 1-22). The study of biomolecular stereochemistry with precise physical methods is an important part of modem research on cell structure and biochemical function. 

NMR has become an important tool for determination of high-resolution three-dimensional structures of biomolecules. As of the end of 2006, over 14% of all structures deposited in the protein data bank (PDB) were determined using NMR, a trend showing tremendous growth since the first NMR structure of a protein was reported in... 

Form follows function.Ths three-dimensional structure of biomolecules is more conserved evolutionarily than is sequence. Why is this the case ... 

When through-bond connectivity experiments are combined with the spatial information from buildup rates of NOESY cross peaks, proton-proton distances can be obtained by comparison with known bond lengths. The result can be a complete three-dimensional structure of biomolecules. Such solution-phase structures complement solid-phase information from X-ray crystallography. In this way, NMR spectroscopy has become a structural tool for obtaining detailed molecular geometries of complex molecules in solution. 

REDOR and RR methods have been used extensively to determine the three-dimensional structure of biomolecules, because the pulse sequence and the data analysis to yield the interatomic distance are simpler compared with the other methods. It seems worthwhile to describe the formalism of the REDOR experiment by a density operator to take into account the effect of a finite pulse length and by the three-spin system encountered on many occasions. 

The authors of a biochemistry text face the problem of trying to present three-dimensional molecules in the two dimensions available on the printed page. The interplay between the three-dimensional structures of biomolecules and their biological functions will be discussed extensively throughout this book. Toward this end, we will frequently use representations that, although of necessity are rendered in two dimensions, emphasize the three-dimensional structures of molecules. 

Nonspecific adsorption of molecules and biomolecules on thiol covered metallic surfaces involves electrostatic and hydrophobic interactions. This strategy has a variety of advantages it is simple, fast, direct, reversible, immobilize lipophilic molecules, and it allows retention of the three-dimensional structure of biomolecules. The disadvantages are easy desorption by change of ionic strength, pH, or detergents, and random orientation of the molecules or biomolecules. 

Femtosecond photoionization mass spectrometry might be useful in the study of the three-dimensional structure of large biomolecules. When a selectively excitable and ionizable chromophore is located on the outer (surface) part of large molecule, one can be detached in the picosecond time scale. However, when the excitable chromophore is located in the inner part of the big molecule, its detachment will require a much longer time, which is needed for spatial rearrangement of the molecule. So, even the simple mass spectrometry of bioorganic molecules with femtosecond laser ionization can reveal some details of their spatial structure. 

The synthesis of peptidyl polymers has a long and elegant history, beginning with the construction of homopolypeptides and random copolypeptides. More recently, biomolecules that incorporate peptide entities into classic polymer structures have been created. Sequential peptide polymers have been constructed that model the three-dimensional structure of connective tissue proteins. This article describes methods for the assembly of a variety of peptidyl polymers. 

Copper proteins can fill quite different biological roles. In each case, the function is determined by the three-dimensional structure of the biomolecule as well as by the coordination geometry of the metal site, which in turn determines the electronic structure of the metal ion(s) (Bertini et al., 1993c, 1994a Holm et al., 1996 Solomon et al., 1992). 

Recall from Chapter 4 that stereochemistry is the three-dimensional structure of a molecule. How important is stereochemistry Two biomolecules—starch and cellulose—illustrate how apparently minute differences in structure can result in vastly different properties. 

The emerging understanding that the coding of information into the three-dimensional structure of all biomolecules is emphasized in this edition (see page 229). This approach introduces students to the most basic and accessible features of biological information theory and makes several topics (e.g., cell signaling mechanisms) more comprehensible. 

The three-dimensional structures of many important biomolecules, including proteins and nucleic acids, are stabilized by hydrogen bonds. 

Certainly, when one considers solving the three-dimensional structure of a complex molecule such as a polypeptide, the challenge of assigning every peak and every cross peak becomes formidable. Nevertheless, the combination of COSY and NOESY methods finds wide application in the determination of the structures of biomolecules. 

Three-dimensional structures of a large number of biomolecules (proteins, peptides, oligonucleotides and oligosaccharides) have been obtained using... 

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