Related papers: Localization of Energetic Frustration in Proteins
Molecules provide the ultimate language in terms of which physiology and pathology must be understood. Myriads of proteins participate in elaborate networks of interactions and perform chemical activities coordinating the life of cells. To…
The controlled dissipation of chemical potentials is the fundamental way cells make a living. Enzyme-mediated catalysis allows the various transformations to proceed at biologically relevant rates with remarkable precision and efficiency.…
Biomolecules are the prime information processing elements of living matter. Most of these inanimate systems are polymers that compute their structures and dynamics using as input seemingly random character strings of their sequence,…
We show how to localize and quantify the functional evolutionary constraints on natural proteins. The method compares the perturbations caused by local sequence variants to the energetics of the protein folding process and to the…
Many native structures of proteins accomodate complex topological motifs such as knots, lassos, and other geometrical entanglements. How proteins can fold quickly even in the presence of such topological obstacles is a debated question in…
Natural protein molecules are exceptional polymers. Encoded in apparently random strings of amino-acids, these objects perform clear physical tasks that are rare to find by simple chance. Accurate folding, specific binding, powerful…
The response of proteins to chemical reactions or impulsive excitation that occurs within the molecule has fascinated chemists for decades. In recent years ultrafast X-ray studies have provided ever more detailed information about 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…
The differing ability of polypeptide conformations to act as the native state of proteins has long been rationalized in terms of differing kinetic accessibility or thermodynamic stability. Building on the successful applications of physical…
Nonnative residual interactions have attracted increasing attention in recent protein folding researches. Experimental and theoretical investigations had been set out to catch nonnative contacts that might dominate key events in protein…
We solve a model that takes into account entropic barriers, frustration, and the organization of a protein-like molecule. For a chain of size $M$, there is an effective folding transition to an ordered structure. Without frustration, this…
We review theoretical approaches, experiments and numerical simulations that have been recently proposed to investigate the folding problem in single-domain proteins. From a theoretical point of view, we emphasize the energy landscape…
The understanding, and even the description of protein folding is impeded by the complexity of the process. Much of this complexity can be described and understood by taking a statistical approach to the energetics of protein conformation,…
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…
This perspective will overview an emerging paradigm for self-organized soft materials, {\it geometrically-frustrated assemblies}, where interactions between self-assembling elements (e.g. particles, macromolecules, proteins) favor local…
Protein structure prediction based on Hydrophobic-Polar energy model essentially becomes searching for a conformation having a compact hydrophobic core at the center. The hydrophobic core minimizes the interaction energy between the amino…
The concept of geometrical frustration in condensed matter physics refers to the fact that a system has a locally preferred structure with an energy density lower than the infinite ground state. This notion is however often used in a…
Water plays a fundamental role in the structure and function of proteins and other biomolecules. The thermodynamic profile of water molecules surrounding a protein are critical for ligand binding and recognition. Therefore, identifying the…
We carry out a theoretical study of the vibrational and relaxation properties of naturally-occurring proteins with the purpose of characterizing both the folding and equilibrium thermodynamics. By means of a suitable model we provide a full…
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…