Natural armadillo repeat proteins (nArmRP) like importin-α or β-catenin bind their target peptides such that each repeat interacts with a dipeptide unit within the stretched target peptide. However, this modularity is imperfect and also restricted to short peptide stretches of usually four to six consecutive amino acids. Here we report the development and characterization of a regularized and t...

Collective variables (CVs) are low-dimensional representations of the state of a complex system, which help us rationalize molecular conformations and sample free energy landscapes with molecular dynamics simulations. Given their importance, there is need for systematic methods that effectively identify CVs for complex systems. In recent years, nonlinear manifold learning has shown its ability ...

Several gold(I) complexes with cysteine-containing dipeptides have been prepared starting from cystine by coupling different amino acids and using several orthogonal protections. The first step is the reaction of cystine, where the sulfur centre is protected as disulfide, with Boc2 O in order to protect the amino group, followed by coupling of an amino acid ester; finally the disulfide bridge i...

Understanding the protein main-chain conformational space forms the basis for the modelling of protein structures and for the validation of models derived from structural biology techniques. Presented here is a novel idea for a three-dimensional distance geometry-based metric to account for the fine details of protein backbone conformations. The metrics are computed for dipeptide units, defined...

Sweet aspartyl di- and tripeptide esters were extended toward the N-terminus in relation to the structural features of sweet peptides. The sweet peptides were designed on the basis of the receptor site model. It was found that an extension of the sweet aspartyl dipeptide esters by adding a small D-amino acid residue mostly gave sweet compounds (e.g., D-Ala-L-Asp-D-Ala-OMe), although this signif...

In this research, dipeptide (his-β-alanine) and porphyrin derivatives were choosen for comparing chelating ability of toxic metals such as Al3+, Cu2+, Hg2+ and Pb2+in-vitro. The reason for choosing these two compounds is that both of them are naturally present in biological systems and comparison of chelating ability of these two compounds has not yet been done. Synthesis and comparison of kine...