Chiral effects on helicity studied via the energy landscape of short (d, l)-alanine peptides

Processing helix–coil transition data: Account of chain length and solvent effects

Numerous nanobiotechnologies include manipulations of short polypeptide chains. The conformational properties of these polypeptides are studied in vitro by circular dichroism and time-resolved infrared spectroscopy. To find out the interaction parameters, the measured temperature dependence of normalized helicity degree needs to be further processed by fitting to a model. Using recent advances in the Hamiltonian formulation of the classical Zimm and Bragg model, we explicitly include chain length and solvent effects in the theoretical description. The expression for the helicity degree we suggest successfully fits the experimental data and provides hydrogen bonding energies and nucleation parameter values within the standards in the field.

Implicit water model within the Zimm-Bragg approach to analyze experimental data for heat and cold denaturation of proteins

Studies of biopolymer conformations essentially rely on theoretical models that are routinely used to process and analyze experimental data. While modern experiments allow study of single molecules in vivo, corresponding theories date back to the early 1950s and require an essential update to include the recent significant progress in the description of water. The Hamiltonian formulation of the Zimm-Bragg model we propose includes a simplified, yet explicit model of water-polypeptide interactions that transforms into the equivalent implicit description after performing the summation of solvent degrees of freedom in the partition function. Here we show that our model fits very well to the circular dichroism experimental data for both heat and cold denaturation and provides the energies of inter- and intra-molecular H-bonds, unavailable with other processing methods. The revealed delicate balance between these energies determines the conditions for the existence of cold denaturation and thus clarifies its absence in some proteins.

A Threshold-Minimization Scheme for Exploring the Energy Landscape of Biomolecules: Application to a Cyclic Peptide and a Disaccharide

We present a scheme, called the threshold-minimization method, for globally exploring the energy landscapes of small systems of biomolecular interest where typical exploration moves always require a certain degree of subsequent structural relaxation in order to be efficient, e.g., systems containing small or large circular carbon chains such as cyclic peptides or carbohydrates. We show that using this threshold-minimization method we can not only reproduce the global minimum and relevant local minima but also overcome energetic barriers associated with different types of isomerism for the example of a cyclic peptide, cyclo-(Gly)4. We then apply the new method to the disaccharide α-d-glucopyranose-1-2-β-d-fructofuranose, report energetically preferred configurations and barriers to boat-chair isomerization in the glucopyranosyl ring, and discuss the energy landscape.

Prediction and clarification of structures of (bio)molecules on surfaces

The design of future materials for biotechnological applications via deposition of molecules on surfaces will require not only exquisite control of the deposition procedure, but of equal importance will be our ability to predict the shapes and stability of individual molecules on various surfaces. Furthermore, one will need to be able to predict the structure patterns generated during the self-organization of whole layers of (bio)molecules on the surface. In this review, we present an overview over the current state of the art regarding the prediction and clarification of structures of biomolecules on surfaces using theoretical and computational methods.