[8] The translational friction coefficient of proteins

Publisher Summary This chapter discusses the translational friction coefficient of proteins. It presents a semiempirical method for calculating the geometrical arrangement of subunits in oligomeric proteins. It also presents a method to calculate friction coefficients of proteins from atomic coordinates. In the chapter, the theory by which friction properties of objects can be calculated is discussed and the mechanics of such calculations are illustrated. The method for finding the principle axes of translation of a particle is provided in the chapter. Using the rigorous theory on protein atoms alone yields friction coefficients that are less than the observed values. Calculations based on the complete test sphere shell gives values greater than observed for proteins. Placing test spheres only on charged groups and computing the friction coefficients based on these test spheres and surface protein atoms yield values essentially in agreement with experimental values. Considering that a rigorous theory has been used and that charged groups are recognized to be hydrated, it appears legitimate to equate test spheres in this case with water of hydration. Thus, the frictional behavior of proteins is determined by several factors: overall dimensions, rugosity of the surface, and the hydration of charged groups on the surface.

[1]  Hiromi Yamakawa,et al.  Transport Properties of Polymer Chains in Dilute Solution: Hydrodynamic Interaction , 1970 .

[2]  M. Klapper,et al.  On the nature of the protein interior. , 1971, Biochimica et biophysica acta.

[3]  J. Erpenbeck,et al.  Statistical Mechanics of Irreversible Processes in Polymer Solutions , 1958 .

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

[5]  C. W. Oseen,et al.  Neuere Methoden und Ergebnisse in der Hydrodynamik , 1927 .

[6]  R. Zwanzig.  Translational Diffusion in Polymer Solutions , 1966 .

[7]  Harold A. Scheraga,et al.  Consideration of the Hydrodynamic Properties of Proteins1,2 , 1953 .

[8]  A. Polson,et al.  The Some Aspects of Diffusion in Solution and a Definition of a Colloidal Particle. , 1950 .

[9]  C. Chothia.  Structural invariants in protein folding , 1975, Nature.

[10]  S. Nir,et al.  Two Modes of Diffusion in Liquids , 1971 .

[11]  J. Erpenbeck,et al.  Erratum : Statistical Mechanics of Irreversible Processes in Polymer Solutions , 1963 .

[12]  D. Teller.  Accessible area, packing volumes and interaction surfaces of globular proteins , 1976, Nature.

[13]  H. Berthod.  Comment on the Ultraviolet Mystery Band of Olefins , 1966 .

[14]  F. Richards.  The interpretation of protein structures: total volume, group volume distributions and packing density. , 1974, Journal of molecular biology.

[15]  J. Happel,et al.  Low Reynolds number hydrodynamics , 1965 .

[16]  B. Lee,et al.  The interpretation of protein structures: estimation of static accessibility. , 1971, Journal of molecular biology.

[17]  C. Chothia.  The nature of the accessible and buried surfaces in proteins. , 1976, Journal of molecular biology.

[18]  F. Perrin,et al.  Mouvement Brownien d'un ellipsoide (II). Rotation libre et dépolarisation des fluorescences. Translation et diffusion de molécules ellipsoidales , 1936 .

[19]  J. Oncley.  EVIDENCE FROM PHYSICAL CHEMISTRY REGARDING THE SIZE AND SHAPE OF PROTEIN MOLECULES FROM ULTRA‐CENTRIFUGATION, DIFFUSION, VISCOSITY, DIELECTRIC DISPERSION, AND DOUBLE REFRACTION OF FLOW , 1941 .

[20]  L. Pauling.  The Nature Of The Chemical Bond , 1939 .

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

[22]  R. Mazo,et al.  Hydrodynamic Properties of a Plane‐Polygonal Polymer, According to Kirkwood–Riseman Theory , 1969 .

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

[24]  A. Shrake,et al.  Environment and exposure to solvent of protein atoms. Lysozyme and insulin. , 1973, Journal of molecular biology.

[25]  V. Bloomfield.  The structure of bovine serum albumin at low pH. , 1966, Biochemistry.

[26]  S. Prager,et al.  Variational Treatment of Hydrodynamic Interaction in Polymers , 1969 .

[27]  I. Kuntz,et al.  Hydration of proteins and polypeptides. , 1974, Advances in protein chemistry.

[28]  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 .

[29]  J. Yamaki,et al.  Application of the Kirkwood theory of transport in polymer solutions to rigid assemblies of beads , 1973 .