Design of Toy Proteins Capable to Rearrange Conformations in a Mechanical Fashion

We design toy protein mimicking a machine-like function of an enzyme. Using an insight gained by the study of conformation space of compact lattice polymers, we demonstrate the possibility of a large scale conformational rearrangement which occurs (i) without opening a compact state, and (ii) along a linear (one-dimensional) path. We also demonstrate the possibility to extend sequence design method such that it yields a "collective funnel" landscape in which the toy protein (computationally) folds into the valley with rearrangement path at its bottom. Energies of the states along the path can be designed to be about equal, allowing for diffusion along the path. They can also be designed to provide for a significant bias in one certain direction. Together with a toy ligand molecule, our "enzimatic" machine can perform the entire cycle, including conformational relaxation in one direction upon ligand binding and conformational relaxation in the opposite direction upon ligand release. This model, however schematic, should be useful as a test ground for phenomenological theories of machine-like properties of enzymes.Comment: 13 pages, 12 figure

Initial Value Problems for Integrable Systems on a Semi-Strip

Two important cases, where boundary conditions and solutions of the well-known integrable equations on a semi-strip are uniquely determined by the initial conditions, are rigorously studied in detail. First, the case of rectangular matrix solutions of the defocusing nonlinear Schr\"odinger equation with quasi-analytic boundary conditions is dealt with. (The result is new even for a scalar nonlinear Schr\"odinger equation.) Next, a special case of the nonlinear optics ($N$-wave) equation is considered.Comment: Boundary conditions are recovered from the initial ones. The paper supplements in this respect our previous article arXiv:1403.8111, where initial conditions are recovered from the boundary condition