Protein dynamics: Rotational diffusion of rigid and fluctuating three dimensional structures

Perico, Angelo; Guenza, Marina; Mormino, Michele; Fioravanti, R.

doi:10.1002/bip.360350106

Cited by 10 publications

(14 citation statements)

References 21 publications

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“…Note that, in the case of rigid bonds in a residue or of parallel bonds in the chain, singularities arise in the matrix U -1 , but the eigenvalue problem can still be solved in terms of the inverse of HA, after taking care of the translational eigenvalue. 38 Finally the correlation time τ i of the TCF P i 2 (t), the experimental orientational relaxation time, has the form…”

Section: Molecular Modeling Of the Local Dynamics Of Realistic Polyme...mentioning

confidence: 99%

Local Dynamics of Carbohydrates. 1. Dynamics of Simple Glycans with Different Chain Linkages

et al. 1999

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The present work gives the preliminary results of a systematic theoretical investigation of the relationship of structure and dynamics for a series of naturally occurring carbohydrate polymers as a function of the topological features, i.e., sugar composition and linkage type. Specifically, homopolymeric (1f3)-and (1f4)-linked Rand β-D-glucans and homopolymeric (1f4)-linked Rand β-D-galactans are considered. These polysaccharide chains cover a broad spectrum of macromolecular stiffness and extension. The theoretical calculations are developed within a diffusive approach that takes accurately into account the polymer connectivity and the corresponding conformational energy surface. This theoretical approach to the polymer dynamics, designated as the optimized Rouse Zimm local dynamics (ORZLD) theory, has been improved and implemented for applications to random coil polysaccharides in solution. The results show that correlation times, such as those obtainable from appropriate NMR, fluorescence, radiation scattering, and rheological relaxation experiments, are very sensitive to the details of the molecular structure and reveal patterns that are useful for characterizing the different chain topologies. Correlations are also illustrated among the dynamic chain pattern (i.e., the position and chain length dependence of the correlation times), equilibrium chain stiffness parameters, and the primary structure of the chain.

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Section: Molecular Modeling Of the Local Dynamics Of Realistic Polyme...mentioning

confidence: 99%

Local Dynamics of Carbohydrates. 1. Dynamics of Simple Glycans with Different Chain Linkages

et al. 1999

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“…In the LE4PD equation the dynamics of the protein is described as a diffusive motion across the configurational landscape, [18,19,24] consistent with an optimized Rouse-Zimm theory of the dynamics of macromolecules in solution. [25,26] Proteins are anisotropic in shape and have a hydrophobic core which is only partially exposed to solvent, with this effect depending on the position of each amino acid in the protein.…”

Section: Dynamicsmentioning

confidence: 99%

Predicting protein dynamics from structural ensembles

Copperman

Guenza

2015

The Journal of Chemical Physics

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“…15,16 In this framework, the dynamics of stiff synthetic and biological macromolecules, such as proteins and DNA double helices, may be described as the diffusion of fluctuating three dimensional structures. 17 For these systems the rotational dynamics of the rigid three-dimensional structure represent a first natural model approximation and also the main contribution to the local dynamics of the fluctuating chain. 18 Methods have been given for obtaining "exact" time correlation functions (TCFs) for tensor local variables of large rigid molecular systems in the mode-coupling diffusion approach, and these methods can be extended to fluctuating structures.…”

Section: Introductionmentioning

confidence: 99%