Skip to main content Accessibility help

We use cookies to distinguish you from other users and to provide you with a better experience on our websites. Close this message to accept cookies or find out how to manage your cookie settings.

Close cookie message
×
Hostname: page-component-745bb68f8f-d8cs5 Total loading time: 0 Render date: 2025-02-06T01:58:08.278Z Has data issue: false hasContentIssue false

Chapter D1 - Biological macromolecules as hydrodynamic particles

from Part D - Hydrodynamics

Published online by Cambridge University Press:  05 November 2012

Igor N. Serdyuk ,
Nathan R. Zaccai  and
Joseph Zaccai
Igor N. Serdyuk
Affiliation:
Institute of Protein Research, Moscow
Nathan R. Zaccai
Affiliation:
University of Bristol
Joseph Zaccai
Affiliation:
Institut de Biologie Structurale, Grenoble
Get access

Summary

History and introduction to bioliogical problems

Traditionally, hydrodynamics deals with the behaviour of bodies in fluids and, in particular, with phenomena in which a force acts on a particle in a viscous solution. Very eminent scientists, such as Isaac Newton, James Clerk Maxwell, Lord Rayleigh (J. W. Strutt) and Albert Einstein, started their careers with major contributions to the science of hydrodynamics. Note that not only are the discoveries from more than 100 years ago still highly relevant today, but also that they continue to stimulate important new developments in the field.

1731

The science of hydrodynamics arose from the classical book Hydrodynamics by Daniel Bernoulli, which contained the ‘Bernoulli law’ relating pressure and velocity in an incompressible fluid, as well as a number of its consequences. The next fundamental contribution to the field was in 1879 when Sir Horace Lamb published another classical book also named Hydrodynamics.

1821

Botanist Robert Brown described the random, thermal motions of small plant particles suspended in water, a phenomenon that was later named Brownian motion. In 1855 Adolf E. Fick published a phenomenological description of translational diffusion and deduced the fundamental laws governing transport phenomena in solutions. In the 1990s, the method of video-enhanced microscopy was proposed for the direct observation of Brownian motion of labelled macromolecules in a membrane.

1846

J. L. M. Poiseuille produced a theory of liquid flow in a capillary. Based on this theory, Wilhelm Ostwald invented the viscometer and introduced its use in physical and chemical experiments.

Type
Chapter
Information
Methods in Molecular Biophysics
Structure, Dynamics, Function
 , pp. 251 - 267
Publisher: Cambridge University Press
Print publication year: 2007

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

References

Purcell, E. M. (1977). Life at low Reynolds number. Am. J. Phys., 45, 3–11.CrossRefGoogle Scholar
Kuntz, I. D., and Kauzmann, W. (1974). Hydration of proteins and polypeptides. Adv. Prot. Chem., 28, 239–345.CrossRefGoogle ScholarPubMed
Finny, J. L. (1996). Overview lecture. Hydration processes in biological and macromolecular systems. Faraday Discuss. Chem. Soc., 103, 1–395.CrossRefGoogle Scholar
Wuthrich, K., Billeter, M., et al. (1996). NMR studies of the hydration of biological macromolecules. Faraday Discuss. Chem. Soc., 103, 245–253.CrossRefGoogle Scholar
Garcia de la Torre, J. (2001). Hydration from hydrodynamics. General consideration and applications to bead modelling to globular proteins. Biophys. Chem., 93, 159–170.CrossRefGoogle Scholar
Zhou, H.-X. (2001). A unified picture of protein hydration: prediction of hydrodynamic properties from known structures. Biophys. Chem., 93, 171–179.CrossRefGoogle ScholarPubMed
Perkins, S. J. (2001). X-ray and neutron scattering analyses of hydration shells: a molecular interpretation based on sequence predictions and modelling fits. Biophys. Chem., 93, 129–139.CrossRefGoogle ScholarPubMed
Engelsen, S. B., Monteiro, C., Herve de Penhoat, C., and Perez, S. (2001). The dilute aqueous solvation of carbohydrates as inferred from molecular dynamics simulations and NMR spectroscopy. Biophys. Chem., 93, 103–127.CrossRefGoogle ScholarPubMed
Happel, J., and Brenner, H. (1973). Low Reynolds Number Hydrodynamics. Second edn. Groningen: Noordhoff Int.Google Scholar
Harding, S. E. (1998). The intrinsic viscosity of biological macromolecules. Progress in measurement, interpretation and application to structures in dilute solution. Prog. Biophys. Mol. Biol., 68, 207–262.CrossRefGoogle Scholar
Hu, C.-M., and Zwanzig, R. (1974). Rotational friction coefficients for spheroids with the slipping boundary conditions. J. Chem. Phys., 60, 4354–4357.CrossRefGoogle Scholar
Brune, D., and Kim, S. (1994). Predicting protein diffusion coefficients. Proc. Natl. Acad. Sci. USA, 90, 3835–3839.CrossRefGoogle Scholar
Zhou, H-X. (1995). Calculation of translational friction and intrinsic viscosity. II. Application to globular proteins. Biophys. J., 69, 2298–2303.CrossRefGoogle ScholarPubMed
Garcia de la Torre, J., Huertas, M. L., and Carrasco, B. (2000). Calculation of hydrodynamic properties of globular proteins from their atomic-level structure. Biophys. J., 78, 719–730.CrossRefGoogle ScholarPubMed
Allison, S. A. (2001). Boundary element modelling of biomolecular transport. Biophys. Chem., 93, 197–213.CrossRefGoogle Scholar
Purcell, E. M. (1977). Life at low Reynolds number. Am. J. Phys., 45, 3–11.CrossRefGoogle Scholar
Kuntz, I. D., and Kauzmann, W. (1974). Hydration of proteins and polypeptides. Adv. Prot. Chem., 28, 239–345.CrossRefGoogle ScholarPubMed
Finny, J. L. (1996). Overview lecture. Hydration processes in biological and macromolecular systems. Faraday Discuss. Chem. Soc., 103, 1–395.CrossRefGoogle Scholar
Wuthrich, K., Billeter, M., et al. (1996). NMR studies of the hydration of biological macromolecules. Faraday Discuss. Chem. Soc., 103, 245–253.CrossRefGoogle Scholar
Garcia de la Torre, J. (2001). Hydration from hydrodynamics. General consideration and applications to bead modelling to globular proteins. Biophys. Chem., 93, 159–170.CrossRefGoogle Scholar
Zhou, H.-X. (2001). A unified picture of protein hydration: prediction of hydrodynamic properties from known structures. Biophys. Chem., 93, 171–179.CrossRefGoogle ScholarPubMed
Perkins, S. J. (2001). X-ray and neutron scattering analyses of hydration shells: a molecular interpretation based on sequence predictions and modelling fits. Biophys. Chem., 93, 129–139.CrossRefGoogle ScholarPubMed
Engelsen, S. B., Monteiro, C., Herve de Penhoat, C., and Perez, S. (2001). The dilute aqueous solvation of carbohydrates as inferred from molecular dynamics simulations and NMR spectroscopy. Biophys. Chem., 93, 103–127.CrossRefGoogle ScholarPubMed
Happel, J., and Brenner, H. (1973). Low Reynolds Number Hydrodynamics. Second edn. Groningen: Noordhoff Int.Google Scholar
Harding, S. E. (1998). The intrinsic viscosity of biological macromolecules. Progress in measurement, interpretation and application to structures in dilute solution. Prog. Biophys. Mol. Biol., 68, 207–262.CrossRefGoogle Scholar
Hu, C.-M., and Zwanzig, R. (1974). Rotational friction coefficients for spheroids with the slipping boundary conditions. J. Chem. Phys., 60, 4354–4357.CrossRefGoogle Scholar
Brune, D., and Kim, S. (1994). Predicting protein diffusion coefficients. Proc. Natl. Acad. Sci. USA, 90, 3835–3839.CrossRefGoogle Scholar
Zhou, H-X. (1995). Calculation of translational friction and intrinsic viscosity. II. Application to globular proteins. Biophys. J., 69, 2298–2303.CrossRefGoogle ScholarPubMed
Garcia de la Torre, J., Huertas, M. L., and Carrasco, B. (2000). Calculation of hydrodynamic properties of globular proteins from their atomic-level structure. Biophys. J., 78, 719–730.CrossRefGoogle ScholarPubMed
Allison, S. A. (2001). Boundary element modelling of biomolecular transport. Biophys. Chem., 93, 197–213.CrossRefGoogle Scholar

Save book to Kindle

To save this book to your Kindle, first ensure [email protected] is added to your Approved Personal Document E-mail List under your Personal Document Settings on the Manage Your Content and Devices page of your Amazon account. Then enter the ‘name’ part of your Kindle email address below. Find out more about saving to your Kindle.

Note you can select to save to either the @free.kindle.com or @kindle.com variations. ‘@free.kindle.com’ emails are free but can only be saved to your device when it is connected to wi-fi. ‘@kindle.com’ emails can be delivered even when you are not connected to wi-fi, but note that service fees apply.

Find out more about the Kindle Personal Document Service.

Available formats
×

Save book to Dropbox

To save content items to your account, please confirm that you agree to abide by our usage policies. If this is the first time you use this feature, you will be asked to authorise Cambridge Core to connect with your account. Find out more about saving content to Dropbox.

Available formats
×

Save book to Google Drive

To save content items to your account, please confirm that you agree to abide by our usage policies. If this is the first time you use this feature, you will be asked to authorise Cambridge Core to connect with your account. Find out more about saving content to Google Drive.

Available formats
×