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Proteins in cellular environments are highly susceptible. Local perturbations to any residue can be sensed by other spatially distal residues in the protein molecule, showing long-range correlations in the native dynamics of proteins. The long-range correlations of proteins contribute to many biological processes such as allostery, catalysis, and transportation. Revealing the structural origin of such long-range correlations is of great significance in understanding the design principle of biologically functional proteins. In this work, based on a large set of globular proteins determined by X-ray crystallography, by conducting normal mode analysis with the elastic network models, we demonstrate that such long-range correlations are encoded in the native topology of the proteins. To understand how native topology defines the structure and the dynamics of the proteins, we conduct scaling analysis on the size dependence of the slowest vibration mode, average path length, and modularity. Our results quantitatively describe how native proteins balance between order and disorder, showing both dense packing and fractal topology. It is suggested that the balance between stability and flexibility acts as an evolutionary constraint for proteins at different sizes. Overall, our result not only gives a new perspective bridging the protein structure and its dynamics but also reveals a universal principle in the evolution of proteins at all different sizes.
This article was published in the following journal.
Name: PLoS computational biology
The 3D structure of a protein is essential to understand protein dynamics. If experimentally determined structure is unavailable, comparative models could be used to infer dynamics. However, the effec...
In the present work, the structural and dynamic properties of aluminosilicates (Al2O3)x-(SiO2)(1-x) (AS) as a function of the Al2O3 concentration x are studied by means of molecular dynamics simulatio...
Proteins are not rigid bodies under their physiological conditions. Here we discuss a solution-phase structural proteomics technique, hydrogen deuterium exchange coupled with mass spectrometry (HDX-MS...
Understanding the structural plasticity of proteins is key to understanding the intricacies of their functions and mechanistic basis. In the current study, we analyzed the available multiple crystal s...
Flexibility is an intrinsic essential feature of protein structures, directly linked to their functions. To this day, most of the prediction methods use the crystallographic data (namely B-factors) as...
This project aimed to optimize the therapeutic strategy for structural heart disease by choosing optimal treatment, such as,surgical treatment,interventional and surgery combined with inte...
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A class of statistical methods applicable to a large set of probability distributions used to test for correlation, location, independence, etc. In most nonparametric statistical tests, the original scores or observations are replaced by another variable containing less information. An important class of nonparametric tests employs the ordinal properties of the data. Another class of tests uses information about whether an observation is above or below some fixed value such as the median, and a third class is based on the frequency of the occurrence of runs in the data. (From McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed, p1284; Corsini, Concise Encyclopedia of Psychology, 1987, p764-5)
Information application based on a variety of coding methods to minimize the amount of data to be stored, retrieved, or transmitted. Data compression can be applied to various forms of data, such as images and signals. It is used to reduce costs and increase efficiency in the maintenance of large volumes of data.
An amino acid sequence of about 50 residues long that is composed of X n-long repeats which form a four-stranded anti-parallel BETA-SHEET as a structural component, or blade, of a beta-propeller.
Various units or machines that operate in combination or in conjunction with a computer but are not physically part of it. Peripheral devices typically display computer data, store data from the computer and return the data to the computer on demand, prepare data for human use, or acquire data from a source and convert it to a form usable by a computer. (Computer Dictionary, 4th ed.)
Patterns (real or mathematical) which look similar at different scales, for example the network of airways in the lung which shows similar branching patterns at progressively higher magnifications. Natural fractals are self-similar across a finite range of scales while mathematical fractals are the same across an infinite range. Many natural, including biological, structures are fractal (or fractal-like). Fractals are related to "chaos" (see NONLINEAR DYNAMICS) in that chaotic processes can produce fractal structures in nature, and appropriate representations of chaotic processes usually reveal self-similarity over time.
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