Dynamics of large-scale fluctuations in native proteins. Analysis based on harmonic inter-residue potentials and random external noise

Twenty‐year follow‐up of bulimia nervosa and related eating disorders not otherwise specified

“…The elastic network model9–19 has been demonstrated to be successful in representing the overall motions of globular proteins, and in particular the slowest motions derived from normal mode analysis. In this model, the nodes of the network are taken as the α‐carbon sites of the residues and the linkers are harmonic springs between sufficiently close residue pairs.…”

“…In this model, the nodes of the network are taken as the α‐carbon sites of the residues and the linkers are harmonic springs between sufficiently close residue pairs. This simplest elastic network model is the Gaussian network model9–12, 17 in which the fluctuations are assumed to be isotropic with no directional preferences 9. However, from detailed molecular dynamics simulations, it is known that the motions are not symmetric in all directions 20.…”

“…If the cause of the problem is static disorder due to poor crystal quality, the situation can be remedied by using computational modeling. B‐factor patterns in a protein crystal structure are dominated by large‐scale low‐frequency motions of the system, and previous work for globular proteins showed that the system behaves like a continuum elastic media which can be modeled quite accurately with elastic network models as described in Methods 9–19. We use elastic network model calculations of the trimeric AcrB transporter protein crystal structure (1OY6) to study the dynamically active regions of the protein and the types of motion in these active regions.…”

Causality, transfer entropy, and allosteric communication landscapes in proteins with harmonic interactions

“…It is possible to determine the time dependent probabilities shown in Eq. by the dGNM . The Gaussian Network Model is characterized by the spring constants matrix where a spring of constant unity is assumed between residues in contact.…”

Wavelet transform analysis of NMR structure ensembles to reveal internal fluctuations of enzymes

“…Internal motions and flexibility of proteins play a critical role in keeping the right conformation to carry out biological functions (Berendsen and Hayward 2000;Chou 1988; Erkip and Erman 2004;Hub and de Groot 2009;Yang and Bahar 2005). The dynamic information can be obtained experimentally in terms of temperature factors (B factors) measured by X-ray crystallography and the NMR-derived order parameters extracted from relaxation data (Karplus and McCammon 1981;Yang and Kay 1996).…”