相关论文: Why Do Proteins Look Like Proteins?

Recent advances in coarse-grained lattice and off-lattice protein models are reviewed. The sequence dependence of thermodynamical folding properties are investigated and evidence for non-randomness of the binary sequences of good folders…

A general theoretical framework is developed using free energy functional methods to understand the effects of heterogeneity in the folding of a well-designed protein. Native energetic heterogeneity arising from non-uniformity in native…

A framework is presented for understanding the common character of proteins. Proteins are linear chain molecules. However, the simple model of a polymer viewed as spheres tethered together does not account for many of the observed…

We study a physical system which, while devoid of the complexity one usually associates with proteins, nevertheless displays a remarkable array of protein-like properties. The constructive hypothesis that this striking resemblance is not…

Proteins must fold quickly to acquire their biologically functional three-dimensional native structures. Hence, these are mainly stabilized by local contacts, while intricate topologies such as knots are rare. Here, we reveal the existence…

We study two mechanisms for the formation of protein patterns near membranes of living cells by mathematical modelling. Self-assembly of protein domains by electrostatic lipid-protein interactions is contrasted with self-organization due to…

Understanding of the evolutionary origins of protein structures represents a key component of the understanding of molecular evolution as a whole. Here we seek to elucidate how the features of an underlying protein structural "space" might…

While all the information required for the folding of a protein is contained in its amino acid sequence, one has not yet learned how to extract this information to predict the three--dimensional, biologically active, native conformation of…

Atomic packing is an important metric for characterizing protein structures, as it significantly influences various features including the stability, the rate of evolution and the functional roles of proteins. Packing in protein structures…

Protein folding, peptide aggregation and crystallization, as well as adsorption of molecules on soft or solid substrates have an essential feature in common: In all these processes, structure formation is guided by a collective, cooperative…

The coding space of protein sequences is shaped by evolutionary constraints set by requirements of function and stability. We show that the coding space of a given protein family--the total number of sequences in that family--can be…

Geometric and structural constraints greatly restrict the selection of folds adapted by protein backbones, and yet, folded proteins show an astounding diversity in functionality. For structure to have any bearing on function, it is thus…

Self-assembly processes are widespread in nature, and lie at the heart of many biological and physical phenomena. The characteristics of self-assembly building blocks determine the structures that they form. Two crucial properties are the…

The notion of energy landscapes provides conceptual tools for understanding the complexities of protein folding and function. Energy Landscape Theory indicates that it is much easier to find sequences that satisfy the "Principle of Minimal…

Protein structures can be studied as complex networks of interacting amino acids. We study proteins of different structural classes from the network perspective. Our results indicate that proteins, regardless of their structural class, show…

We present a model, based on symmetry and geometry, for proteins. Using elementary ideas from mathematics and physics, we derive the geometries of discrete helices and sheets. We postulate a compatible solvent-mediated emergent pairwise…

How typical elements that shape organisms, such as protein secondary structures, have evolved, or how evolutionarily susceptible/resistant they are to environmental changes, are significant issues in evolutionary biology, structural…

Proteins are the common constituents of all living cells. They are molecular machines that interact with each other as well as with other cell products and carry out a dizzying array of functions with distinction. These interactions follow…

The beautiful structures of single and multi-domain proteins are clearly ordered in some fashion but cannot be readily classified using group theory methods that are successfully used to describe periodic crystals. For this reason, protein…

Understanding the observed variability in the number of homologs of a gene is a very important, unsolved problem that has broad implications for research into co-evolution of structure and function, gene duplication, pseudogene formation…