Size and Shape of Protein Molecules at the Nanometer Level Determined by Sedimentation, Gel Filtration, and Electron Microscopy
Open accessAbstract
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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Assuming a molecular volume of ca. 65 nm3 for K72, ATP-K72 complex coacervate droplets could show an increase in mean radius of 3-7 μm due to ripening per hour.
“Assuming a molecular volume of ca. 65 nm3 for K7229, we expect that the ATP-K72 complex coacervate droplets could show an increase in mean radius of 3–7 μm due to ripening per hour (see estimation in Supplementary Table 2)17.”
From Active coacervate droplets are protocells that grow and resist Ostwald ripening (2021) · cites this paper as [29]
Section 2, “How Big Is a Protein Molecule?” (page unavailable), gives a general formula for estimating protein molecular volume from mass. It does not identify K72 or give its volume as approximately 65 nm³. In the citing sentence, the Erickson citation is attached to the volume assumption; the separate ripening estimate carries another citation. (LLM, conf=0.82)
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- Authors
- Erickson, H. P.
- Affiliations
- Duke Medical Center (US)
- Corresponding author
- Erickson, Harold P.
- ORCID
- Erickson, Harold P.
- Venue
- Biological Procedures Online
- Published
- 2009-05-15
- Volume
- 11
- Issue
- 1
- Pages
- 32-51
- ISSN
- 1480-9222 (ISSN-L)
- PMC
- PMC3055910
- OpenAlex
- W2004863845
- Cited by
- 1,571
- References
- 0
- Citations by year
- 2026: 79 · 2025: 115 · 2024: 122 · 2023: 111 · 2022: 109 · 2021: 150 · 2020: 164 · 2019: 144 · 2018: 121 · 2017: 125 · 2016: 89 · 2015: 87 · 2014: 60 · 2013: 48 · 2012: 33
- FWCI
- 6.18
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- cc-by
- Locations
- Biological Procedures Online (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
- Funders
- National Institutes of Health (CA47056)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein purification and stability
- Physical Sciences › Materials Science › Materials Chemistry › Enzyme Structure and Function
- Keywords
- protein size, protein shape, sedimentation coefficient, hydrodynamic radius, molecular weight determination, size exclusion chromatography, rotary shadowing, negative stain electron microscopy, protein complexes, hydrodynamic characteristics
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