Backbone and Side Chains

L. Holm and C. Sander, Database algorithm for generating protein backbone and side-chain co-ordinates from a trace, J. Mol. Biol. 218 (1991), 183-194. 

The comparison of both data sources qualitatively shows a similar picture. Regions of high mobflity are located especially between the secondary structure elements, which are marked on the abscissa of the plot in Figure 7-17. Please remember that the fluctuations plotted in this example also include the amino acid side chains, not only the protein backbone. This is the reason why the side chains of large and flexible amino acids like lysine or arginine can increase the fluctuations dramatically, although the corresponding backbone remains almost immobile. In these cases, it is useful to analyze the fluctuations of the protein backbone and side chains individually. 

Einally, structural properties that depend directly neither on the data nor on the energy parameters can be checked by comparing the structures to statistics derived from a database of solved protein structures. PROCHECK-NMR and WHAT IE [94] use, e.g., statistics on backbone and side chain dihedral angles and on hydrogen bonds. PROSA [95] uses potentials of mean force derived from distributions of amino acid-amino acid distances. 

An effective method for localizing causes of redox potentials is to plot the total backbone and side chain contributions to ( ) per residue for homologous proteins as functions of the residue number using a consensus sequence, with insertions treated by summing the contribution of the entire insertion as one residue. The results for homologous proteins should be examined for differences in the contributions to ( ) per residue that correlate with observed redox potential differences. These differences can then be correlated with any other sequence-redox potential data for proteins that lack crystal or NMR structures. In addition, any sequences of homologous proteins that lack both redox potentials and structures should be examined, because residues important in defining the redox potential are likely to have semi-sequence conservation of a few key amino acid types. 

Fig. 2.30 Comparison of antiparallel hairpin structures in / -peptides 120-122. (A) / -Pep-tides 120, 121 with a 12-membered R/S dini-pecotic (Nip or/ -HPro) turn segment (gray color). Summary of backbone-backbone and side-chain-side-chain NOEs collected in CD2CI2 and X-ray crystal structure of 121 (stereo-view) [154, 193], The intramolecular H-bond N" 0 distances are shown. The angles (N-H -O) are 170.8° (inner H-bond) and 1 72.3 ° (outer H-bond). (B) jS-Peptide 122 with...

The relaxation data for the anomeric protons of the polysaccharides (see Table II) lack utility, inasmuch as the / ,(ns) values are identical within experimental error. Obviously, the distribution of correlation times associated with backbone and side-chain motions, complex patterns of intramolecular interaction, and significant cross-relaxation and cross-correlation effects dramatically lessen the diagnostic potential of these relaxation rates. 

Ionomer membranes are used in fuel cells in order to separate the anode and cathode compartment and to allow the transport of protons from the anode to the cathode. The typical membrane is Nation , which consists of a perfluorinated backbone and side chains terminated by sulfonic groups. In the oxidizing environment of fuel cells, Nation , as well as other membranes, is attacked by reactive oxygen radicals, which reduce the membrane stability. Direct ESR was used recently in our laboratory to detect and identify oxygen radicals as well as radical intermediates formed in perfluorinated membranes upon exposure to oxygen radicals [73,74]. The three methods used to produce oxygen radicals in the laboratory and the corresponding main reactions are shown below. 

The 140-residue protein AS is able to form amyloid fibrils and as such is the main component of protein inclusions involved in Parkinson s disease. Full-length 13C/15N-labelled AS fibrils and AS reverse-labelled for two of the most abundant amino acids, K and V, were examined by homonuclear and heteronuclear 2D and 3D NMR.147 Two different types of fibrils display chemical shift differences of up to 13 ppm in the l5N dimension and up to 5 ppm for the backbone and side-chain 13C chemical shifts. Selection of regions with different mobility indicates the existence of monomers in the sample and allows the identification of mobile segments of the protein within the fibril in the presence of monomeric protein. At least 35 C-terminal residues are mobile and lack a defined secondary structure, whereas the N terminus is rigid starting from residue 22. In addition, temperature-dependent sensitivity enhancement is also noted for the AS fibrils due to both the CP efficiency and motional interference with proton decoupling.148... 

Shi et al.71 have assigned the backbone and side-chain chemical shifts for 103 of 238 residues of proteorhodopsin using solid state NMR spectroscopy. Analysis of the chemical shifts has allowed determination of protonation states of several carboxylic acids as well as boundaries and distortions of trans-membrane a-helices and secondary structure elements in the loops. It has been shown that internal Asp227, making a part of the counterion, is ionised, while Glul42 located close to the extracellular surface is neutral. 

Correlation Times for Backbone and Side-Chain Motions in Poly(but-1-ene sulfone) of P = 700 as a 25% w/v Solution in Chloroform-d, Deduced from the Simple Isotropic Single-T Motional Model... 

The generalization of Eqs. (19)-(30) to a polymer melt with arbitrary numbers of distinct bending energies in both backbone and side chains is straightforward. 

These, in turn, can be condensed with amines to give imines 4 or ketimines 5 and 6, or reduced to give amino alcohols 7-9, respectively. The ligand structure is therefore vastly variable. Steric factors, such as flexibility of backbone and side-chains, as well as electronic factors (for example sp versus sp conflguration of the N-donors) can be easily modulated. The introduction of central chirality via chiral amine side-chains is also possible. The interaction of planar and central chirality, usually referred to as chiral cooperativity [11-13], can thus be studied in a ligand system which has both planar and central chiral elements. 

Three-dimensional structural properties of peptides backbone and side chain... 

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