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

Abstract

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 (α l δ l and α l γ l ) and Type II (ε l δ d , ε l α d and ε l γ d ) β-turns were generated. With nine sidechain combinations 18 different Type I β-turn conformations were studied. Similarly, three Type II β-turns: ε l δ d , ε l α d and ε l γ d 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.