Hydrodynamic properties of rigid macromolecules composed of ellipsoidal and cylindrical subunits.

A procedure is devised for the calculation of hydrodynamic properties of rigid macromolecules composed subunits that are modeled as ellipsoids of revolution and cylinders. Owing to the axial symmetry of these shapes, smooth shell models can be constructured for the subunit structure. The bead shell model so constructed is employed for the calculation of the properties. A computer program, HYDROSUB, has been written implementing both the model building and the hydrodynamic calculation. A detailed example of the use of this methodology is presented for the case of the solution properties of the human antibody molecule immunoglobulin G3 (IgG3). Finally, hints are given on other uses and applications of the procedure.

[1]  A J Rowe,et al.  The viscosity increment for ellipsoids of revolution. Some observations on the Simha formula. , 1982, Biophysical chemistry.

[2]  B. Carrasco,et al.  Birefringence, Deformation, and Scattering of Segmentally Flexible Macromolecules under an External Agent. Steady-State Properties in an Electric Field , 1999 .

[3]  V. Bloomfield,et al.  Hydrodynamic properties of macromolecular complexes. I. Translation , 1977 .

[4]  J. García de la Torre,et al.  Transport properties of rigid bent-rod macromolecules and of semiflexible broken rods in the rigid-body treatment. Analysis of the flexibility of myosin rod. , 1988, Biophysical journal.

[5]  J. Kirkwood The general theory of irreversible processes in solutions of macromolecules , 1996 .

[6]  J A McCammon,et al.  Frictional properties of nonspherical multisubunit structures. Application to tubules and cylinders , 1976, Biopolymers.

[7]  F G Diaz,et al.  HYDRO: a computer program for the prediction of hydrodynamic properties of macromolecules. , 1994, Biophysical journal.

[8]  J. Kirkwood,et al.  Errata: The Intrinsic Viscosities and Diffusion Constants of Flexible Macromolecules in Solution , 1948 .

[9]  C. D. Haën,et al.  Creeping flow translational resistance of rigid assemblies of spheres , 1980 .

[10]  J. G. Torre,et al.  Transport properties of rigid, symmetrical oligomeric structures composed of prolate, ellipsoidal subunits. , 1983 .

[11]  José García de la Torre,et al.  Translational friction coefficients of rigid, symmetric top macromolecules. Application to circular cylinders , 1979 .

[12]  D. Winzor,et al.  COVOL: an interactive program for evaluating second virial coefficients from the triaxial shape or dimensions of rigid macromolecules. , 1999, Biophysical journal.

[13]  V. Bloomfield,et al.  Hydrodynamic properties of macromolecular complexes. IV. Intrinsic viscosity theory, with applications to once‐broken rods and multisubunit proteins , 1978 .

[14]  José García de la Torre,et al.  Comparison of theories for the translational and rotational diffusion coefficients of rod‐like macromolecules. Application to short DNA fragments , 1984 .

[15]  J. García de la Torre,et al.  Hydrodynamic properties of complex, rigid, biological macromolecules: theory and applications , 1981, Quarterly Reviews of Biophysics.

[16]  J. García de la Torre,et al.  Hydrodynamic properties of rigid particles: comparison of different modeling and computational procedures. , 1999, Biophysical journal.

[17]  S. Harding,et al.  Novel size-independent modeling of the dilute solution conformation of the immunoglobulin IgG Fab' domain using SOLPRO and ELLIPS. , 1999, Biophysical journal.

[18]  L. Stryer,et al.  Segmental flexibility in an antibody molecule. , 1970, Journal of molecular biology.

[19]  S. Harding,et al.  On the hydrodynamic analysis of macromolecular conformation. , 1995, Biophysical chemistry.

[20]  J. G. de la Torre,et al.  Transport properties of oligomeric subunit structures , 1981, Biopolymers.

[21]  K. V. van Holde,et al.  Frictional coefficients of multisubunit structures. I. Theory , 1967, Biopolymers.

[22]  J. G. de la Torre,et al.  Transport properties and hydrodynamic centers of rigid macromolecules with arbitrary shapes , 1980 .

[23]  D. Burton,et al.  The solution conformations of the subclasses of human IgG deduced from sedimentation and small angle X-ray scattering studies. , 1987, Molecular immunology.

[24]  K. V. van Holde,et al.  Frictional coefficients of multisubunit structures. II. Application to proteins and viruses , 1967, Biopolymers.

[25]  José García de la Torre,et al.  Rotational dynamics of rigid, symmetric top macromolecules. Application to circular cylinders , 1980 .

[26]  C. D. Haën,et al.  The low Reynolds number translational friction of ellipsoids, cylinders, dumbbells, and hollow spherical caps. Numerical testing of the validity of the modified Oseen tensor in computing the friction of objects modeled as beads on a shell , 1978 .

[27]  Vellarkad N. Viswanadhan,et al.  Hydrophobicity and residue-residue contacts in globular proteins , 1987 .