Protein hydrogen-bonding studies

In future high-resolution crystal structure studies of proteins, hydrogen bonding has to be analyzed in terms of two-center and three-center interactions. It should be stressed that three-center bonds may be especially important in protein dynamics because they can be regarded as transition intermediate from one two-center bond to another (see Part IV, Chap. 25). 

Since this domain is conserved in several enterotoxins, one expects this 13 residue domain to be the primary reason for the toxicity of the 19-residue long protein. lETN has a simple secondary structure it has got 3 beta (/ ) turns. The /9i spans from Cys to Cys , (32 from Asn to Cys, and 02 from Cys to Cys . In addition, the crystal structure contains 5 intramolecular (i.e., within the protein) hydrogen bonds that also add to the stability of the conformation. The lETN structure is reasonably rigid (because of 3 disulfide bridges, and 5 intramolecular hydrogen bonds), making it an ideal candidate for studies by computer simulations using empirical intermolecular potentials. 

Formamide and water are the simplest molecules usually chosen as models for studying biological systems exhibiting the peptide type of bonding as in proteins. Hydrogen bonding complexes of formamide such as formamide-water, formamide-methanol can thus serve as model systems for protein-water and protein-solvent interactions. On account of the simplicity of this model, the characterization of the hydrogen bond interactions between water and formamide has been of considerable interest to experimentalists and theoreticians. 

IR spectroscopy is a valuable complementary technique to Raman spectroscopy. Synchrotron based IR micro-spectroscopy is a new technique that shows promising perspectives for studies of skin and human cells (28). At the Max-Lab synchrotron beam line in Lund, Sweden an IR microscope is now being installed (29). This instrument will allow IR-spectra to be recorded with a bolometer detector down to 50 cm (around 1,5 THz). In the R(v)-representation of the low-wavenumber Raman spectrum it is very difficult to quantify the amount of free water because the water band at 180 cm is weak compared to the protein hydrogen bond band at 110-120 cm" Hopefully the water band is relatively more intense in the IR spectrum allowing a detection of the free water at low concentrations. 

Ot-HehcalBundles. The a-helix is the most extensively studied protein stmctural motif. Because a-hehces form internal hydrogen bonds between the C=0 of residue i and the N—H of residue i + 4 (see Fig. 2), the individual helix is stabili2ed and can exist in isolation. Individual heUces can be manipulated as independent stmctural modules designed to associate in some predetermined manner. Often, a minimalist approach to the design of a-hehces has been taken. In this approach the goal is to obtain the desired stmctural motif using the simplest possible constmction. 

BW Beck, Q Xie, T Ichiye. Computational study of S—H S hydrogen bonds m [4Ee-4S]-type ferredoxm x-ray and NMR structures Characterization and implications for redox potentials. Protein Sci, submitted. 

The family of serine proteases has been subjected to intensive studies of site-directed mutagenesis. These experiments provide unique information about the contributions of individual amino acids to kcat and KM. Some of the clearest conclusions have emerged from studies in subtilisin (Ref. 9), where the oxyanion intermediate is stabilized by t>e main-chain hydrogen bond of Ser 221 and an hydrogen bond from Asn 155 (Ref. 2). Replacement of Asn 155 (e.g., the Asn 155— Ala 155 described in Fig. 7.9) allows for a quantitative assessment of the effect of the protein dipoles on Ag. ... 

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