Numerical path integration technique for the calculation of transport properties of proteins.
We present a new technique for the computation of both the translational diffusivity and the intrinsic viscosity of macromolecules, and apply it here to proteins. Traditional techniques employ finite element representations of the surface of the macromolecule, taking the surface to be a union of spheres or of polygons, and have computation times that are O(m(3)) where m is the number of finite elements. The new technique, a numerical path integration method, has computation times that are only O(m). We have applied the technique to approximately 1000 different protein structures. The computed translational diffusivities and intrinsic viscosities are, to lowest order, proportional respectively to N(-1/3)(R) and N(0)(R), where N(R) is the number of amino acid residues in the protein. Our calculations also show some correlation with the shape of the molecule, as represented by the ratio m(2)/m(3), where m(2) and m(3) are, respectively, the middle and the smallest of the three principal moments of inertia. Comparisons with a number of experimental results are also performed, with results generally consistent to within experimental error.
Kang
Eun-Hee
EH
Department of Chemistry and Chemical Biology, Stevens Institute of Technology, Hoboken, New Jersey 07030, USA.
Mansfield
Marc L
ML
Douglas
Jack F
JF
D000465:Algorithms; D001692:Biological Transport / Q000502:physiology; D003198:Computer Simulation; D004058:Diffusion; D008954:Models, Biological; D008956:Models, Chemical; D008958:Models, Molecular; D015233:Models, Statistical; D017711:Nonlinear Dynamics; D009716:Numerical Analysis, Computer-Assisted; D011487:Protein Conformation; D021381:Protein Transport / Q000502:physiology*; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism*; D055672:Static Electricity
D011506:Proteins