NDLI: Probing conformation and conformational change in proteins is optimally undertaken in relative mode

Content Provider	Springer Nature Link
Author	Errington, Neil Rowe, Arthur J.
Copyright Year	2003
Abstract	Hydrodynamic bead modelling has been widely used in attempts to assess the 3D conformation of proteins in solution. Initially, simple models employing only a small number of beads were used, with a considerable degree of success. Latterly, high-resolution bead models based upon atomic coordinates have been developed, and much more sophisticated questions can in principle be addressed. A detailed analysis is presented of the errors involved in the generation of such models and associated prediction of (translational friction) parameters, and in the practical measurement of these parameters for comparison. It is shown that in most cases, for a particle of only moderate asymmetry, the errors are such that it is not feasible to determine, on an absolute basis, which of a range of candidate conformers is the "correct" one. However, when the properties of the candidate conformers can be compared in relation to those of a "paradigm conformer", whose structure in solution, on the basis of external evidence, can be accepted as correct, then errors cancel and very precise comparisons become possible. The generation of 3D bead models (and hence 3D data files) for a range of candidate conformers is a simple matter, using the existing program MacBEADS, further facilitated by a 3D display module (pro Fit).
Starting Page	511
Ending Page	517
Page Count	7
File Format	PDF
ISSN	01757571
Journal	European Biophysics Journal
Volume Number	32
Issue Number	5
e-ISSN	14321017
Language	English
Publisher	Springer-Verlag
Publisher Date	2003-06-26
Publisher Place	Berlin, Heidelberg
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	Bead modelling Diffusion Errors Friction Sedimentation
Content Type	Text
Resource Type	Article
Subject	Medicine Biophysics

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BEAMS (BEAds Modelling System): a set of computer programs for the generation, the visualization and the computation of the hydrodynamic and conformational properties of bead models of proteins

BEAMS (BEAds Modelling System): a set of computer programs for the generation, the visualization and the computation of the hydrodynamic and conformational properties of bead models of proteins

Hydrodynamic modelling of protein conformation in solution: ELLIPS and HYDRO

Intrinsic viscosity and rotational diffusion of bead models for rigid macromolecules and bioparticles

Effect of external stresses on protein conformation: a computer modelling study

Conformational dynamics and internal friction in homopolymer globules: equilibrium vs. non-equilibrium simulations.

Conformational properties of short oligopeptides: Prediction of the protein chain conformation

Bifurcations of relative equilibria of a heavy bead on a rotating parabolic bowl with dry friction

Computing translational diffusion and sedimentation coefficients: an evaluation of experimental data and programs

Probing conformation and conformational change in proteins is optimally undertaken in relative mode

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