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

doi:10.1016/S0006-3495(00)76630-6

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

Journal Article•DOI•

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

José García de la Torre¹, María L. Huertas¹, B. Carrasco¹•Institutions (1)

University of Murcia¹

01 Feb 2000-Biophysical Journal (The Biophysical Society)-Vol. 78, Iss: 2, pp 719-730

TL;DR: The solution properties, including hydrodynamic quantities and the radius of gyration, of globular proteins are calculated from their detailed, atomic-level structure, using bead-modeling methodologies described in the previous article, using a HYDROPRO public-domain computer program.

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About: This article is published in Biophysical Journal.The article was published on 2000-02-01 and is currently open access. It has received 1058 citations till now. The article focuses on the topics: Radius of gyration & Radius.

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Journal Article•DOI•

Size and Shape of Protein Molecules at the Nanometer Level Determined by Sedimentation, Gel Filtration, and Electron Microscopy

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Harold P. Erickson¹•Institutions (1)

Duke University¹

15 May 2009-Biological Procedures Online

TL;DR: This review collects a number of simple calculations that are useful for thinking about protein structure at the nanometer level, including the Perrin equation, based on the measured sedimentation coefficient and the calculated maximum S to estimate if a protein is globular or elongated.

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Abstract: An important part of characterizing any protein molecule is to determine its size and shape. Sedimentation and gel filtration are hydrodynamic techniques that can be used for this medium resolution structural analysis. This review collects a number of simple calculations that are useful for thinking about protein structure at the nanometer level. Readers are reminded that the Perrin equation is generally not a valid approach to determine the shape of proteins. Instead, a simple guideline is presented, based on the measured sedimentation coefficient and a calculated maximum S, to estimate if a protein is globular or elongated. It is recalled that a gel filtration column fractionates proteins on the basis of their Stokes radius, not molecular weight. The molecular weight can be determined by combining gradient sedimentation and gel filtration, techniques available in most biochemistry laboratories, as originally proposed by Siegel and Monte. Finally, rotary shadowing and negative stain electron microscopy are powerful techniques for resolving the size and shape of single protein molecules and complexes at the nanometer level. A combination of hydrodynamics and electron microscopy is especially powerful.

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1,308 citations

Cites methods from "Calculation of hydrodynamic propert..."

...This analysis has been extended by Garcia De La Torre and colleagues (7)....
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Journal Article•DOI•

Diffusion, crowding & protein stability in a dynamic molecular model of the bacterial cytoplasm.

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Sean R. McGuffee¹, Adrian H. Elcock¹•Institutions (1)

University of Iowa¹

05 Mar 2010-PLOS Computational Biology

TL;DR: The simulation model successfully describes the relative thermodynamic stabilities of proteins measured in E. coli, and shows that effects additional to the commonly cited “crowding” effect must be included in attempts to understand macromolecular behavior in vivo.

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Abstract: A longstanding question in molecular biology is the extent to which the behavior of macromolecules observed in vitro accurately reflects their behavior in vivo. A number of sophisticated experimental techniques now allow the behavior of individual types of macromolecule to be studied directly in vivo; none, however, allow a wide range of molecule types to be observed simultaneously. In order to tackle this issue we have adopted a computational perspective, and, having selected the model prokaryote Escherichia coli as a test system, have assembled an atomically detailed model of its cytoplasmic environment that includes 50 of the most abundant types of macromolecules at experimentally measured concentrations. Brownian dynamics (BD) simulations of the cytoplasm model have been calibrated to reproduce the translational diffusion coefficients of Green Fluorescent Protein (GFP) observed in vivo, and “snapshots” of the simulation trajectories have been used to compute the cytoplasm's effects on the thermodynamics of protein folding, association and aggregation events. The simulation model successfully describes the relative thermodynamic stabilities of proteins measured in E. coli, and shows that effects additional to the commonly cited “crowding” effect must be included in attempts to understand macromolecular behavior in vivo.

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682 citations

Cites background or methods from "Calculation of hydrodynamic propert..."

...rotational diffusion coefficients [88], and the sequence coverage...
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...With each structure complete, infinite-dilution translational and rotational diffusion coefficients – which are necessary input parameters for BD simulations [14] – were calculated with the program HYDROPRO [88] using default parameters....
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...All distances expressed in terms of the molecular diameters (obtained by doubling the hydrodynamic radius calculated by HydroPro [88]....
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Journal Article•DOI•

Stability and kinetics of G-quadruplex structures

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Andrew N. Lane¹, J. Brad Chaires¹, Robert D. Gray¹, John O. Trent¹•Institutions (1)

University of Louisville¹

01 Oct 2008-Nucleic Acids Research

TL;DR: An overview of recent literature on the structure and stability of unimolecular G-rich quadruplex structures that are relevant to drug design and for in vivo function and the unifying theme in this review is energetics.

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Abstract: In this review, we give an overview of recent literature on the structure and stability of unimolecular G-rich quadruplex structures that are relevant to drug design and for in vivo function The unifying theme in this review is energetics The thermodynamic stability of quadruplexes has not been studied in the same detail as DNA and RNA duplexes, and there are important differences in the balance of forces between these classes of folded oligonucleotides We provide an overview of the principles of stability and where available the experimental data that report on these principles Significant gaps in the literature have been identified, that should be filled by a systematic study of well-defined quadruplexes not only to provide the basic understanding of stability both for design purposes, but also as it relates to in vivo occurrence of quadruplexes Techniques that are commonly applied to the determination of the structure, stability and folding are discussed in terms of information content and limitations Quadruplex structures fold and unfold comparatively slowly, and DNA unwinding events associated with transcription and replication may be operating far from equilibrium The kinetics of formation and resolution of quadruplexes, and methodologies are discussed in the context of stability and their possible biological occurrence

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640 citations

Cites background or methods from "Calculation of hydrodynamic propert..."

...This is discussed in detail in the publications on the programs for calculating frictional properties (97,98,103)....
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...This is because hydrodynamic parameters can be calculated with reasonable accuracy using bead models (97,98)....
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Journal Article•DOI•

On the analysis of protein self-association by sedimentation velocity analytical ultracentrifugation.

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Peter Schuck¹•Institutions (1)

National Institutes of Health¹

01 Sep 2003-Analytical Biochemistry

TL;DR: New tools for the analysis of protein self-association by sedimentation velocity are developed, their statistical properties are examined, and considerations for optimal experimental design are discussed.

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603 citations

Journal Article•DOI•

Prediction of Hydrodynamic and Other Solution Properties of Rigid Proteins from Atomic- and Residue-Level Models

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Álvaro Ortega¹, D. Amorós¹, J. García de la Torre¹•Institutions (1)

University of Murcia¹

17 Aug 2011-Biophysical Journal

TL;DR: The ability to predict hydrodynamic coefficients and other solution properties of rigid macromolecular structures from atomic-level structures, implemented in the computer program HYDROPRO, is extended to models with lower, residue-level resolution, allowing calculations when atomic resolution is not available or coarse-grained models are preferred.

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602 citations

Additional excerpts

...PDB M (Da) aT (Å) aI (Å) aG (Å) aR (Å) Set GT [1, 2] 4PTI 6158 16....
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References

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Journal Article•DOI•

van der Waals Volumes and Radii

[...]

Arrigo Bondi

01 Mar 1964-The Journal of Physical Chemistry

16,894 citations

"Calculation of hydrodynamic propert..." refers background in this paper

...The typical values of van der Waals radii (including implicit hydrogens) (Bondi, 1964, 1968) are in the range of 1.5–2.0 Å; a typical (average) value would be 1.8 Å, which could be taken for the radius of the atomic spherical elements in the model....
[...]

Book•

Physical Chemistry of Macromolecules

[...]

Charles Tanford, Maurice L. Huggins

01 Dec 1961

3,980 citations

"Calculation of hydrodynamic propert..." refers background or methods in this paper

...The description of the hydrodynamics of rigid, globular macromolecules as ellipsoids is a classical approach that is well described in textbooks (Tanford, 1961; van Holde, 1971), in which these particles are treated as prolate or oblate revolution ellipsoids....
[...]
...This classical approach is well described in textbooks (Tanford, 1961; Cantor and Schimmel, 1980)....
[...]

Book•

Analytical ultracentrifugation in biochemistry and polymer science

[...]

Stephen E. Harding, Arthur J. Rowe, J. C. Horton

01 Jan 1992

TL;DR: In this paper, the authors discuss specific applications to Biochemical and polymer systems in terms of instrumentation, equilibrium and transport methods, as well as their application in biomedical applications.

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Abstract: Part I: Instrumentation Part II: Equilibrium Methods Part III: Transport Methods Part IV: Specific Applications to Biochemical and Polymer Systems

...read moreread less

1,481 citations

"Calculation of hydrodynamic propert..." refers methods in this paper

...…experimental techniques such as those that monitor rotational motion by fluorescence spectroscopy (Dale and Dale, 1985) and dynamic NMR (Palmer et al., 1996), or the modern developments of analytical ultracentrifugation (Harding et al., 1992; Schuster and Laue, 1994) and viscometry (Harding, 1997)....
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Book•

Physical properties of molecular crystals liquids, and glasses

[...]

Arnold Aaron Bondi

01 Jan 1968

1,245 citations

"Calculation of hydrodynamic propert..." refers background in this paper

...The typical values of van der Waals radii (including implicit hydrogens) (Bondi, 1964, 1968) are in the range of 1.5–2.0 Å; a typical (average) value would be 1.8 Å, which could be taken for the radius of the atomic spherical elements in the model....
[...]

Journal Article•DOI•

Variational Treatment of Hydrodynamic Interaction in Polymers

[...]

Jens Rotne, Stephen Prager

01 Jun 1969-Journal of Chemical Physics

TL;DR: In this paper, the problem is formulated as a minimization of the rate at which energy is dissipated by the motion of the suspending fluid, and an approximate diffusion tensor which is positive definite for all configurations of the polymer molecule is obtained.

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Abstract: It has recently been pointed out by several authors that the Kirkwood–Riseman diffusion tensor normally used to treat hydrodynamic interactions in polymer molecules is not necessarily positive definite, an unphysical behavior which results from the neglect of short‐range contributions to the interaction between chain segments. The problem can be reformulated as a minimization of the rate at which energy is dissipated by the motion of the suspending fluid, and in this way we have obtained an approximate diffusion tensor which (1) is positive definite for all configurations of the polymer molecule, (2) approaches the Kirkwood–Riseman diffusion tensor at large separations between the interacting segments, and (3) can be written as the true diffusion tensor plus a positive definite correction. The last feature can be used to obtain variational bounds on relaxation times and sedimentation rates.

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1,092 citations

"Calculation of hydrodynamic propert..." refers methods in this paper

...The use of the Rotne-Prager hydrodynamic interaction tensor for equal overlapping beads (Rotne and Prager, 1969) may lead to correct results for translational coefficients, and the Antosiewicz-Po¨rschke volume correction (Antosiewicz and Po¨rschke, 1989) for rotation works well in the cases in…...
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...The use of the Rotne-Prager hydrodynamic interaction tensor for equal overlapping beads (Rotne and Prager, 1969) may lead to correct results for translational coefficients, and the Antosiewicz-Po ̈rschke volume correction (Antosiewicz and Po ̈rschke, 1989) for rotation works well in the cases in which it has been tested....
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...This is only warranted for nonoverlapping beads, either equal or unequal, the hydrodynamic interaction of which is described using the Rotne-Prager-Yamakawa or the Garcia de la Torre–Bloomfield interaction tensor, respectively, and which is described, for equal overlapping beads, with the Rotne-Prager tensor (Rotne and Prager, 1969; Yamakawa, 1970; Garcı ́a de la Torre and Bloomfield, 1977b)....
[...]
...…of which is described using the Rotne-Prager-Yamakawa or the Garcia de la Torre–Bloom- field interaction tensor, respectively, and which is described, for equal overlapping beads, with the Rotne-Prager tensor (Rotne and Prager, 1969; Yamakawa, 1970; Garcı´a de la Torre and Bloomfield, 1977b)....
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