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Fluctuations about the native conformation of proteins have proven to be suitably reproduced with a simple elastic network model, which has shown excellent agreement with a number of different properties for a wide variety of proteins. This scalar model simply investigates the magnitudes of motion of individual residues in the structure. To use the elastic(More)
BACKGROUND An elastic network model is proposed for the interactions between closely (< or = 7.0 A) located alpha-carbon pairs in folded proteins. A single-parameter harmonic potential is adopted for the fluctuations of residues about their mean positions in the crystal structure. The model is based on writing the Kirchhoff adjacency matrix for a protein(More)
Vibrational dynamics of folded proteins is studied using a Gaussian model in which the protein is viewed as a network, residues representing the junctions, and the connectivity being established by a single parameter harmonic potential. Application to seven proteins showed that the local packing density plays a major role in determining the vibrational(More)
We propose a mathematical model for mitochondria-dependent apoptosis, in which kinetic cooperativity in formation of the apoptosome is a key element ensuring bistability. We examine the role of Bax and Bcl-2 synthesis and degradation rates, as well as the number of mitochondrial permeability transition pores (MPTPs), on the cell response to apoptotic(More)
The realization that experimentally observed functional motions of proteins can be predicted by coarse-grained normal mode analysis has renewed interest in applications to structural biology. Notable applications include the prediction of biologically relevant motions of proteins and supramolecular structures driven by their structure-encoded collective(More)
A single-parameter harmonic Hamiltonian based on local packing density and contact topology is proposed for studying residue fluctuations in native proteins. The internal energy obeys an equipartition law, and free energy changes result from entropy fluctuations only. Frequency–wave-number maps show communication between residues involved in slow and fast(More)
Biomolecular systems possess unique, structure-encoded dynamic properties that underlie their biological functions. Recent studies indicate that these dynamic properties are determined to a large extent by the topology of native contacts. In recent years, elastic network models used in conjunction with normal mode analyses have proven to be useful for(More)
3. Intrinsic Dynamics of Membrane Proteins and Their Functional Significance 1477 3.1. Ion Channels 1477 3.1.1. Gramicidin A 1477 3.1.2. Potassium Channels 1478 3.1.3. Mechanosensitive Channels 1479 3.2. Receptors 1480 3.2.1. Nicotinic Acetylcholine Receptor 1480 3.2.2. Rhodopsin 1483 3.3. Transporters 1484 3.3.1. Glutamate Transporters 1485 3.3.2. ATP(More)
An assessment of the equilibrium dynamics of biomolecular systems, and in particular their most cooperative fluctuations accessible under native state conditions, is a first step towards understanding molecular mechanisms relevant to biological function. We present a web-based system, oGNM that enables users to calculate online the shape and dispersion of(More)
Recognition of injured mitochondria for degradation by macroautophagy is essential for cellular health, but the mechanisms remain poorly understood. Cardiolipin is an inner mitochondrial membrane phospholipid. We found that rotenone, staurosporine, 6-hydroxydopamine and other pro-mitophagy stimuli caused externalization of cardiolipin to the mitochondrial(More)