Conformational change of proteins arising from normal mode calculations

Abstract

A normal mode analysis of 20 proteins in 'open' or 'closed' forms was performed using simple potential and protein models. The quality of the results was found to depend upon the form of the protein studied, normal modes obtained with the open form of a given protein comparing better with the conformational change than those obtained with the closed form. Moreover, when the motion of the protein is a highly collective one, then, in all cases considered, there is a single low-frequency normal mode whose direction compares well with the conformational change. When it is not, in most cases there is still a single low-frequency normal mode giving a good description of the pattern of the atomic displacements, as they are observed experimentally during the conformational change. Hence a lot of information on the nature of the conformational change of a protein is often found in a single low-frequency normal mode of its open form. Since this information can be obtained through the normal mode analysis of a model as simple as that used in the present study, it is likely that the property captured by such an analysis is for the most part a property of the shape of the protein itself. One of the points that has to be clarified now is whether or not amino acid sequences have been selected in order to allow proteins to follow a single normal mode direction, as least at the very beginning of their conformational change.

Influence of oligomerization on the dynamics of G‐protein coupled receptors as assessed by normal mode analysis

“…(1) are the normal modes, and the eigenvalues Ω i are the squares of the associated frequencies. As the transition from one conformational state of a protein to another is likely to be described by a combination of a small number of normal modes, [26][27][28] only the first 100 lowest frequency normal modes with increasing eigenvalues were calculated for the rhodopsin monomer, dimer, and tetramer.…”

“…26,27,34,35 Thus, based on the assumption that conformational transformations of the dimerization interface of a GPCR can be discriminated based on the number of low frequency modes that describe them, 35 we calculated the contribution of the 100 lowest frequency normal modes of the 1N3M-like rhodopsin tetramer 5 to each of the postulated activated interface models obtained as described in the Methods section.…”

Electrostatic properties of cowpea chlorotic mottle virus and cucumber mosaic virus capsids

“…One such approach, the elastic network model, 21 provides a simplified representation of the underlying energy surface for large systems that enables the study of the dynamics of these systems. 22,23 The elastic network models can be constructed and normal mode analysis can be performed based on Cα's, residue blocks, or even coarser granularities to yield good descriptions of large-scale conformational distortions in macromolecular assemblies. 24 Further computational efficiency can be gained without significant loss in information through the addition of the rotation-translation block (RTB) method for the diagonalization of the matrix of second derivatives.…”

A flexible docking scheme to explore the binding selectivity of PDZ domains

“…On the other hand, the ENM [34][35][36][37][38][39][40][41] which is based on a purely mechanical model, and view a protein structure as an elastic network, have been applied to many proteins to obtain slowest (i.e., functionally related) fluctuations. The nodes of the elastic network are a-carbons where identical springs connect the ''interacting'' a-carbons in their native fold.…”