Literature DB >> 10354430

Hydrodynamic properties of rigid particles: comparison of different modeling and computational procedures.

B Carrasco1, J García de la Torre.   

Abstract

The hydrodynamic properties of rigid particles are calculated from models composed of spherical elements (beads) using theories developed by Kirkwood, Bloomfield, and their coworkers. Bead models have usually been built in such a way that the beads fill the volume occupied by the particles. Sometimes the beads are few and of varying sizes (bead models in the strict sense), and other times there are many small beads (filling models). Because hydrodynamic friction takes place at the molecular surface, another possibility is to use shell models, as originally proposed by Bloomfield. In this work, we have developed procedures to build models of the various kinds, and we describe the theory and methods for calculating their hydrodynamic properties, including approximate methods that may be needed to treat models with a very large number of elements. By combining the various possibilities of model building and hydrodynamic calculation, several strategies can be designed. We have made a quantitative comparison of the performance of the various strategies by applying them to some test cases, for which the properties are known a priori. We provide guidelines and computational tools for bead modeling.

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Year:  1999        PMID: 10354430      PMCID: PMC1300274          DOI: 10.1016/S0006-3495(99)77457-6

Source DB:  PubMed          Journal:  Biophys J        ISSN: 0006-3495            Impact factor:   4.033


  13 in total

1.  Calculation of NMR relaxation, covolume, and scattering-related properties of bead models using the SOLPRO computer program.

Authors:  J García de la Torre; S E Harding; B Carrasco
Journal:  Eur Biophys J       Date:  1999       Impact factor: 1.733

2.  Frictional coefficients of multisubunit structures. I. Theory.

Authors:  V Bloomfield; W O Dalton; K E Van Holde
Journal:  Biopolymers       Date:  1967-02       Impact factor: 2.505

3.  Frictional coefficients of multisubunit structures. II. Application to proteins and viruses.

Authors:  V Bloomfield; K E Van Holde; W O Dalton
Journal:  Biopolymers       Date:  1967-02       Impact factor: 2.505

4.  Frictional properties of nonspherical multisubunit structures. Application to tubules and cylinders.

Authors:  J A McCammon; J M Deutch
Journal:  Biopolymers       Date:  1976-07       Impact factor: 2.505

5.  A study of apo- and holo-forms of horse liver alcohol dehydrogenase in solution by diffuse x-ray scattering.

Authors:  M A Sinev; A A Timchenko; O B Ptitsyn
Journal:  Biopolymers       Date:  1986-08       Impact factor: 2.505

6.  A general method for evaluation of diffusion constants, dilute-solution viscoelasticity, and the dielectric property of a rigid macromolecule with an arbitrary configuration. I.

Authors:  H Nakajima; Y Wada
Journal:  Biopolymers       Date:  1977-04       Impact factor: 2.505

Review 7.  Hydrodynamic properties of complex, rigid, biological macromolecules: theory and applications.

Authors:  J G Garcia de la Torre; V A Bloomfield
Journal:  Q Rev Biophys       Date:  1981-02       Impact factor: 5.318

8.  The translational friction coefficient of proteins.

Authors:  D C Teller; E Swanson; C de Haën
Journal:  Methods Enzymol       Date:  1979       Impact factor: 1.600

9.  The structure of bovine serum albumin at low pH.

Authors:  V Bloomfield
Journal:  Biochemistry       Date:  1966-02       Impact factor: 3.162

10.  Shell model calculations of rotational diffusion coefficients.

Authors:  D P Filson; V A Bloomfield
Journal:  Biochemistry       Date:  1967-06       Impact factor: 3.162

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  57 in total

1.  Novel size-independent modeling of the dilute solution conformation of the immunoglobulin IgG Fab' domain using SOLPRO and ELLIPS.

Authors:  B Carrasco; J G de la Torre; O Byron; D King; C Walters; S Jones; S E Harding
Journal:  Biophys J       Date:  1999-12       Impact factor: 4.033

2.  The conformation of serum albumin in solution: a combined phosphorescence depolarization-hydrodynamic modeling study.

Authors:  M L Ferrer; R Duchowicz; B Carrasco; J G de la Torre; A U Acuña
Journal:  Biophys J       Date:  2001-05       Impact factor: 4.033

3.  Calculation of hydrodynamic properties of globular proteins from their atomic-level structure.

Authors:  J García De La Torre; M L Huertas; B Carrasco
Journal:  Biophys J       Date:  2000-02       Impact factor: 4.033

4.  Calculation of hydrodynamic properties of small nucleic acids from their atomic structure.

Authors:  M X Fernandes; A Ortega; M C López Martínez; J García de la Torre
Journal:  Nucleic Acids Res       Date:  2002-04-15       Impact factor: 16.971

5.  Modeling the hydration of proteins: prediction of structural and hydrodynamic parameters from X-ray diffraction and scattering data.

Authors:  Helmut Durchschlag; Peter Zipper
Journal:  Eur Biophys J       Date:  2003-04-25       Impact factor: 1.733

6.  Structure and allosteric regulation of the alpha X beta 2 integrin I domain.

Authors:  Thomas Vorup-Jensen; Christian Ostermeier; Motomu Shimaoka; Ulrich Hommel; Timothy A Springer
Journal:  Proc Natl Acad Sci U S A       Date:  2003-01-28       Impact factor: 11.205

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

Authors:  Neil Errington; Arthur J Rowe
Journal:  Eur Biophys J       Date:  2003-06-26       Impact factor: 1.733

8.  Brownian dynamics simulation of rigid particles of arbitrary shape in external fields.

Authors:  Miguel X Fernandes; José García de la Torre
Journal:  Biophys J       Date:  2002-12       Impact factor: 4.033

9.  Interpretation of 15N NMR relaxation data of globular proteins using hydrodynamic calculations with HYDRONMR.

Authors:  Pau Bernadó; José García de la Torre; Miquel Pons
Journal:  J Biomol NMR       Date:  2002-06       Impact factor: 2.835

10.  The implementation of SOMO (SOlution MOdeller) in the UltraScan analytical ultracentrifugation data analysis suite: enhanced capabilities allow the reliable hydrodynamic modeling of virtually any kind of biomacromolecule.

Authors:  Emre Brookes; Borries Demeler; Camillo Rosano; Mattia Rocco
Journal:  Eur Biophys J       Date:  2009-02-21       Impact factor: 1.733

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