A model study of the IgA hinge region: an exploratory study of selected backbone conformations of MeCO-l-Pro-l-Thr-NH-Me

Using the principles of multidimensional conformational analysis (MDCA), an approximate geometry for selected conformations of MeCO-Pro-Thr-NH-Me, the central dipeptide of the target sequence of immunoglobulin A protease, an enzyme secreted by pathogenic Neisseria, was determined at the RHF/3-21G level of theory. Type I (αlδl and αlγl) and Type II (εlδd, εlαd and εlγd) β-turns were generated. With nine sidechain combinations 18 different Type I β-turn conformations were studied. Similarly, three Type II β-turns: εlδd, εlαd and εlγd were investigated each with nine possible sidechain conformations. Therefore, 3×9 structures are expected to yield 27 different Type II β-turn conformations. The conformational and energetic consequences of the optimized conformers are discussed in terms of relative stabilities and degree of backbone twisting or foldedness.