The micron scale is much bigger than most of the proteins

Generally Its said that 1000 kilodalton corresponds to 1micron. But for proteins it matters if the protein is folded or denatured.

Hi! You can also have a look here:

J. Mass Spectrom. 2001; 36: 1038–1052, Charge-reduced nano electrospray ionization combined with differential mobility analysis of peptides, proteins, glycoproteins, noncovalent protein complexes and

viruses by Bacher, G. et al. 

Mind that they worked with dry particles so the EMD is different to the hydrodynamic diameter of analytes...

Hi! If you have nice homogeneous and purified protein you can try also dynamic light scattering method. Othervise, you can use calculator built in in the Zetasizer software produced by Malvern Instrument as an estimation.  Size of particles of some proteins (cytochrome, lysozyme, BSA...) were experimentally measured and a plot was constructed which is surprisingly good and valid also for other globular proteins. Based on this plot calculator is working and Mw of 10kDa corresponds to particle radius of 1.59nm, 20kDa to 2.14nm, 40kDa to 2.88nm......100kDa to 4.26nm....of course the shape of the molecules is important and these values are valid for globular molecules. 

Are you asking about a complex fit into a micron dimensional box?

You can use SEC-MALS to striaght away calculate MW as well as radius of a protein of interest.!

Proteins are complicated! There is no universal rule for correlating size and molecular weight, since different proteins, and even the same protein in different environments,  have different conformations. 

There are formulas that relate the size and molar mass of the most common conformations: globular, linear (completely unfolded), etc. But there are many proteins such as intrinsically disordered proteins that do not follow any of these. And if you are concerned with oligomers, complexes, aggregates or other assemblies such as amyloid fibrils, really there is no universal formula even if you know the size of the monomer.

Gels and SEC are not good solutions since they depend on charge and other interactions with the matrix. SEC, in particular, assumes a specific relationship between size and molar mass derived from globular proteins and so cannot be correct for any protein that is not globular or otherwise interacts non-ideally with the column.

Therefore, if you really want to know the molar mass and size of a protein in a specific buffer or other solution, you have to measure both quantities. As Sannula pointed out, SEC-MALS is an ideal method since it measures molecular weight in solution, independently of the column retention time. With the same instrumentation you can also measure size, and therefore learn about the protein's conformation in its environment. See www.wyatt.com/SEC-MALS for more info.

BTW, a 1000 kDa protein is not even close to 1 micron! More like 10 nm in radius.

www.wyatt.com/SEC-MALS

Using Equation 2.1 of Erickson's work on protein size, we can estimate the size of a globular protein. 

In it's shortest form, we can assume V(nm3)=1.212x10-3(nm3/Da) x MW(Da)

Erickson, H. P. (2009). Size and shape of protein molecules at the nanometer level determined by sedimentation, gel filtration, and electron microscopy. Biological procedures online, 11(1), 32.

http://www.calctool.org/CALC/prof/bio/protein_size

This web site can help you estimate the size of the protein

Is there a protein of size ~15 nm or better ~20 nm?

The lipoprotein assembly known as LDL, or low-density lipoprotein, has a diameter of approximately 20 nm.  This nanoparticle is the main cholesterol carrier in the blood.

The easiest way would be to assume the protein has a spherical shape,

Volume of a sphere (V),

r is the radius:

V = 4/3 pi r^3

pi = 3.1416

Volume (V) equals mass (m) over density (d)

V = m (g) / d (g/cm^3)

d = 1.35 g / cm^3

m = MW / NA

NA = 6.022E23 (Avogadro’s number)

MW = molecular weight of the protein

so that the (sphere) radius of a protein would be

r = [ 0.75*MW / (NA*pi*d) ]^(1/3) (cm)

(cubic root of [ ])

http://www.calctool.org/CALC/prof/bio/protein_size

9 aa ~ 1 kDa ~ 1.5 nm

834 aa ~ 100 kDa ~ 6.5 nm

4170 aa ~ 500 kDa ~ 11 nm

3,100,000 kDa ~ 370,000 kDa ~ 100 nm

You could relate the radius by having the density but then you have to account for ionic strength which significantly changes the effective radius.

Hydrodynamic, or Stokes, radius of a particle is the radius of a hard sphere that diffuses at the same rate as that particle. When we are considering proteins, they are of course not hard particles, but complex folds of varying compactness and shape. The hydrodynamic radius of a peptide chain can thus vary depending on its folding state. For this reason, when converting hydrodynamic radius to molecular weight we can provide approximate boundaries corresponding to a fully folded, globular peptide in its most compact state, and a fully unfolded chain that has the least compact state.

For the fully folded state the volume of the protein scales with the molecular weight, leading to a relationship of Rh ∝ MW1/3, while for unfolded proteins the relationship is approximately Rh ∝ MW0.6.

For a graph detailing this relationship, as well as a tool to make the conversion for both folded and unfolded proteins visit https://www.fluidic.com/resources/faq/convert-hydrodynamic-radius-to-mw/

You can use following instruction:

KD's                   Microns                     Nanometers        Angstroms 1,000 KD          0.1 micron                100                         1000 500 KD             0.02 micron              20                            200 200 KD             0.01 micron              10                            100 50 KD                0.004 micron            4                              40 10 KD                0.0025 micron          2.5                          25 5 KD                   0.0015 micron         1.5                          15

It should help you to know that the densities of proteins are fairly consistent. Values ranging from 1.22 to 1.43 g/cm3 have been reported, according to this paper:

Article Average protein density is a molecular-weight-dependent function

Kimberley,

you could calculate the volume of that cylinder:

pi*r^2*h

1.6E-18 ml per molecule,

9.45E5 ml per mol

if you assume an average density of protein 1.3 g/ml,

then the maximum Mass you expect is 1.2E6 Dalton.

It is more likely that the average density of protein in the aggregate will be lower, so,

If you find the density of those aggregates by density gradient ultracentrifugation for instance, you can get a much better estimate.

Even better, you could run an SDS -Agarose gel to determine the mass

https://www.ncbi.nlm.nih.gov/pubmed/22585481

I recommend Zhenlin's answer

Best Regards

Yes, the volume - density calculation is a good estimate and first approximation, as stated by Matias Moller . An even better method - in my view - is to use an empirical relationship from a series of size measurements from globular proteins. See

https://www.materials-talks.com/blog/2016/01/21/zetasizer-sensitivity-for-protein-dls/

Its predictions are pretty close for a wide range of proteins.

Can kDa/nm be used as a unit of density? How to convert 1.06 kDa/nm to g/cm3?

kDa is an unit of molecular size, while, Microns is an unit of distance or in other words molecular diameter. Simply, a solution containing 2 or 100 molecules or two elements A ,B with MW 2 KDA,100 KDA, respectively can have the same size in microns but MW may vary though. One cannot arrive at a direct relationship between kDa and Microns. Always get your membranes from manufacturers who are willing to divulge pore size in microns instead of just kDa