Related papers: Universal criterion for designability of heteropol…
We devise a method for designing materials that will have some desired structural characteristics. We apply it to multiblock copolymers that have two different types of monomers, A and B. We show how to determine what sequence of A's and…
The sensitivity of the native states of protein-like heteropolymers to mutations modelled as perturbations in the interaction potential between amino acids is studied. The stability threshold against mutations is shown to be zero for random…
Despite the variety of protein sizes, shapes, and backbone configurations found in nature, the design of novel protein folds remains an open problem. Within simple lattice models it has been shown that all structures are not equally…
The design of novel proteins has many applications but remains an attritional process with success in isolated cases. Meanwhile, deep learning technologies have exploded in popularity in recent years and are increasingly applicable to…
In the framework of a lattice-model study of protein folding, we investigate the interplay between designability, thermodynamic stability, and kinetics. To be ``protein-like'', heteropolymers must be thermodynamically stable, stable against…
Natural protein sequences that self-assemble to form globular structures are compact with high packing densities in the folded states. It is known that proteins unfold upon addition of denaturants, adopting random coil structures. The…
The ability of a protein to recognise multiple independent target conformations was demonstrated in [1]. Here we consider the recognition of correlated configurations, which we apply to funnel design for a single conformation. The maximum…
Experiments have reached a monumental capacity for designing and synthesizing microscopic particles for self-assembly, making it possible to precisely control particle concentrations, shapes, and interactions. However, more physical insight…
Only about 1,000 qualitatively different protein folds are believed to exist in nature. Here, we review theoretical studies which suggest that some folds are intrinsically more designable than others, {\it i.e.} are lowest energy states of…
We present an analytical method for determining the designability of protein structures. We apply our method to the case of two-dimensional lattice structures, and give a systematic solution for the spectrum of any structure. Using this…
Chiral heteropolymers such as larger globular proteins can simultaneously support multiple length scales. The interplay between different scales brings about conformational diversity, and governs the structure of the energy landscape.…
We review algorithms for protein design in general. Although these algorithms have a rich combinatorial, geometric, and mathematical structure, they are almost never covered in computer science classes. Furthermore, many of these algorithms…
Lattice models, for their coarse-grained nature, are best suited for the study of the ``designability problem'', the phenomenon in which most of the about 16,000 proteins of known structure have their native conformations concentrated in a…
Protein folding and design are major biophysical problems, the solution of which would lead to important applications especially in medicine. Here a novel protein model capable of simultaneously provide quantitative protein design and…
Different aspects of protein folding are illustrated by simplified polymer models. Stressing the diversity of side chains (residues) leads one to view folding as the freezing transition of an heteropolymer. Technically, the most common…
Native protein folds often have a high degree of symmetry. We study the relationship between the symmetries of native proteins, and their designabilities -- how many different sequences encode a given native structure. Using a…
The intricate three-dimensional geometries of protein tertiary structures underlie protein function and emerge through a folding process from one-dimensional chains of amino acids. The exact spatial sequence and configuration of amino…
Membrane proteins and lipids can self-assemble into membrane protein polyhedral nanoparticles (MPPNs). MPPNs have a closed spherical surface and a polyhedral protein arrangement, and may offer a new route for structure determination of…
The self-assembly of particles into organized structures is a key feature of living organisms and a major engineering challenge. While it may proceed through the binding of perfectly matched, puzzle-pieces-like particles, many other…
Proteins can combine into functional elements in living cells or self-assemble into unwanted structures in a number of diseases. The resulting aggregates often display filamentous morphologies across a large range of protein shapes and…