Hydrodynamic properties of rigid macromolecules composed of ellipsoidal and cylindrical subunits

Torre, José Garcı́a de la; Carrasco, Beatriz

doi:10.1002/bip.10013

Cited by 67 publications

(68 citation statements)

References 28 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…29 The capsomer subunits have anisotropic translational and rotational diffusion constants calculated using HYDROSUB7.C. 30 To obtain dimen- sionless units, we rescale lengths by σ b , which is the diameter of one of the spheres that comprise the excluded volume of the capsomer; times are measured in units of t 0 , which is the Brownian time for a single such sphere. Further details of the model are given in Appendix A.…”

Section: Models a Viral Capsid Modelmentioning

confidence: 99%

Mechanisms of kinetic trapping in self-assembly and phase transformation

Hagan

Elrad

Jack

2011

The Journal of Chemical Physics

111

152

View full text Add to dashboard Cite

In self-assembly processes, kinetic trapping effects often hinder the formation of thermodynamically stable ordered states. In a model of viral capsid assembly and in the phase transformation of a lattice gas, we show how simulations in a self-assembling steady state can be used to identify two distinct mechanisms of kinetic trapping. We argue that one of these mechanisms can be adequately captured by kinetic rate equations, while the other involves a breakdown of theories that rely on cluster size as a reaction coordinate. We discuss how these observations might be useful in designing and optimising self-assembly reactions.

show abstract

Section: Models a Viral Capsid Modelmentioning

confidence: 99%

Mechanisms of kinetic trapping in self-assembly and phase transformation

Hagan

Elrad

Jack

2011

The Journal of Chemical Physics

111

152

View full text Add to dashboard Cite

show abstract

“…This is the basis for the methodology implemented in the computer program HYDROSUB (Garcia de la Torre and Carrasco 2002), in which the primary model is an array of subunits having the shape of cylinders (rods or disks) or ellipsoids of revolution. The structure is specified by a list, containing one register for each subunit, giving the sizes (axis lengths, or length and diameter), position of its centre, and orientation of the main axis.…”

Section: Solution Properties From Subunit-level Structurementioning

confidence: 99%

Hydrodynamic modelling of protein conformation in solution: ELLIPS and HYDRO

Torre

Harding

2013

Biophys Rev

View full text Add to dashboard Cite

The last three decades has seen some important advances in our ability to represent the conformation of proteins in solution on the basis of hydrodynamic measurements. Advances in theoretical modeling capabilities have been matched by commensurate advances in the precision of hydrodynamic measurements. We consider the advances in whole-body (simple ellipsoid-based) modeling—still useful for providing an overall idea of molecular shape, particularly for those systems where only a limited amount of data is available—and outline the ELLIPS suite of algorithms which facilitates the use of this approach. We then focus on bead modeling strategies, particularly the surface or shell–bead approaches and the HYDRO suite of algorithms. We demonstrate how these are providing great insights into complex issues such as the conformation of immunoglobulins and other multi-domain complexes.

show abstract

“…Gyration radius for IgG was estimated in early experimental measurements of X-ray scattering to be around 52 × 10 −10 m (52Å) [21]. Present computer calculations of R g values for biological non-globular macromolecules, composed of subunits, yield in case of IgG (human antibody IgG3) values above 70 × 10 −10 m (70Å) [22]. Assuming that an estimate of IgG gyration radius is 60 × 10 −10 m (60Å), it would mean that the investigated microcapsules are practically impermeable for IgG from the point of view of mass transfer cut-off.…”

Section: Discussionmentioning

confidence: 90%