Related papers: Packing in Protein Cores
Using a coarse-grained model, self-organized assembly of proteins (e.g. CorA and its inner segment iCorA) is studied by examining quantities such as contact profile, radius of gyration, and structure factor as a function of protein…
Proteins are constructed from a limited alphabet of ~20 amino acids, yet the origins and selection of this specific alphabet are unresolved. One largely overlooked aspect is whether elemental composition constrains the range of viable…
Understanding the regulation and structure of ribosomes is essential to understanding protein synthesis and its deregulation in disease. While ribosomes are believed to have a fixed stoichiometry among their core ribosomal proteins (RPs),…
Predicting the structure of a protein from its sequence is a cornerstone task of molecular biology. Established methods in the field, such as homology modeling and fragment assembly, appeared to have reached their limit. However, this year…
Amino acid sequence portrays most intrinsic form of a protein and expresses primary structure of protein. The order of amino acids in a sequence enables a protein to acquire a particular stable conformation that is responsible for the…
The evolutionary trajectory of a protein through sequence space is constrained by function and three-dimensional (3D) structure. Residues in spatial proximity tend to co-evolve, yet attempts to invert the evolutionary record to identify…
The mechanisms by which a protein's 3D structure can be determined based on its amino acid sequence have long been one of the key mysteries of biophysics. Often simplistic models, such as those derived from geometric constraints, capture…
The native structures of proteins, except for notable exceptions of intrinsically disordered proteins, in general take their most stable conformation in the physiological condition to maintain their structural framework so that their…
Packing problems have been of great interest in many diverse contexts for many centuries. The optimal packing of identical objects has been often invoked to understand the nature of low temperature phases of matter. In celebrated work,…
Protein function is driven by cohesive substructures, such as catalytic triads, binding pockets, and structural motifs, that occupy only a small fraction of a protein's residues. Yet existing pipelines built on protein encoders do not model…
Recently, we presented a framework for understanding protein structure based on the idea that simple constructs of holding hands or touching of objects can be used to rationalize the common characteristics of globular proteins. We developed…
Single domain proteins are thought to be tightly packed. The introduction of voids by mutations is often regarded as destabilizing. In this study we show that packing density for single domain proteins decreases with chain length. We find…
Optimal geometrical arrangements, such as the stacking of atoms, are of relevance in diverse disciplines. A classic problem is the determination of the optimal arrangement of spheres in three dimensions in order to achieve the highest…
We consider multi-chain protein native structures and propose a criterion that determines whether two chains in the system are entangled or not. The criterion is based on the behavior observed by pulling at both temini of each chain…
Topological properties of native folds are obtained from statistical analysis of 160 low homology proteins covering the four structural classes. This is done analysing one, two and three-vertex joint distribution of quantities related to…
It is not merely the position of residues that are of utmost importance in protein function and stability, but the interactions between them. We illustrate, by using a network construction on a set of 595 non-homologous proteins, that…
Protein crystallization in vivo provides some fascinating examples of biological self-assembly. Here, we provide a selective survey to show the diversity of functions for which protein crystals are used, and the physical properties of the…
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…
Natively unfolded proteins exist as an ensemble of flexible conformations lacking a well defined tertiary structure along a large portion of their polypeptide chain. Despite the absence of a stable configuration, they are involved in…
A theoretical analysis of the unfolding pathway of simple modular proteins in length- controlled pulling experiments is put forward. Within this framework, we predict the first module to unfold in a chain of identical units, emphasizing the…