Global folds

A Aszodi, MJ Gradwell, WR Taylor. Global fold determination from a small number of distance restraints. J Mol Biol 251 308-326, 1995. 

The selection of the pulse sequence to be used out of the hundreds that have been published depends on the information desired. NMR spectroscopy cannot only be used to determine high-quality three-dimensional structures, but can provide information about the global fold, interactions with other molecules or just the identification of the secondary... 

However, if side-chain carbon assignments are wanted, C(CC)(CO)NH experiments [33] that start directly with carbon magnetization and transfer it further to the amide proton for detection are available. If protonated substituents, for example methyl groups, have been introduced into the otherwise perdeuterated protein, the usual HC(C)(CO)NH-TOCSY pulse sequence can be used to obtain the proton chemical shifts. These protons can provide a small number of NOEs that, together with residual dipolar couplings and the secondary structure identification from chemical shifts, make the determination of the global fold of large proteins possible. 

Since the primary structure of a peptide determines the global fold of any protein, the amino acid sequence of a heme protein not only provides the ligands, but also establishes the heme environmental factors such as solvent and ion accessibility and local dielectric. The prevalent secondary structure element found in heme protein architectures is the a-helix however, it should be noted that p-sheet heme proteins are also known, such as the nitrophorin from Rhodnius prolixus (71) and flavocytochrome cellobiose dehydrogenase from Phanerochaete chrys-osporium (72). However, for the purpose of this review, we focus on the structures of cytochromes 6562 (73) and c (74) shown in Fig. 2, which are four-a-helix bundle protein architectures and lend themselves as resource structures for the development of de novo designs. 

In summary, 2AP incorporation into an RJMA can be used to map its folding pathway, its kinetics of local and global folding, and its intrinsic dynamics. It is uniquely able to report on RJMA properties since it fits tidily into secondary and tertiary structures without the structural perturbations... 

Chauhan, S., Behrouzi, R., Rangan, P., and Woodson, S. A. (2009). Structural rearrangements linked to global folding pathways of the Azoarcus Group I nbozymc. /. Mol. Biol. 386, 1167-1178. 

Mapping Global Folds of Oligonucleotides by Pulsed Electron-Electron Double Resonance... 

Boer R, Dichtl M, Borchers C, Ulrich WR, Marecek JF, Prestwich GD, Glossmann H, Striessnig J (1996) Global folds of highly deuterated, methyl-protonated proteins by multidimensional NMR. Biochemistry 35 1389-1401... 

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