The Physical Description of a protein

9/13/98


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Table of Contents

{1} The Physical Description of a protein

{2} However,

{3} 1. COMPOSITION ANALYSIS

{4} Composition...

{5} Composition...

{6} Composition...

{7} Composition...

{8} Composition...

{9} Computations from composition data

{10} Aside: Volume concepts and the particle description

{11} Aside:...

{12} Continuing...

{13} 2. STRUCTURAL DETAILS

{14} CD...

{15} CD...

{16} CD...

{17} CD… problems...

{18} 3. DETERMINING THE MOLECULAR WEIGHT

{19} Mass spec. cont.

{20} Molecular weight...

{21} Molecular weight...

{22} Molecular weight...

{23} Molecular weight...

{24} ASIDE: Averaging and Weighting in Microscopic Measurements

{25} Aside...

{26} Aside...

{27} Aside...

{28} Aside...

{29} Continuing...

{30} 4. SIZE AND SHAPE

{31} Remember, Partial Specific Volume, ?p, cc/gram,

{32} Since the molecular weight is ? Ni Mi, the molar volume of the protein, Vp, is simply

{33} Hydration, ? , is difficult to measure:

{34} Does hydration make a difference in protein volume?

{35} Effective radius of the solvated protein:

{36} If the particle is not spherical, this may not be very close to the measured effective radius, sometimes referred to as the Stokes Radius.

{37} as a result, the friction depends only on the size of the particle and the friction of solvent on solvent as measured by the viscosity,

{38} Other ways of measuring particle effective radius:

{39} Other ways...

{40} Other ways...

{41} Shape dependence

{42} Shape measure then is rexpt./rsphere

{43} However, it does not work very well...

{44} Comparing shape independent values with shape dependent values...

{45} Predicted a/b: 2.2 7.5

{46} Another example,

{47} Predicted a/b = 3.5

{48} What's the problem?

{49} Continuing...

{50} 5. SOLVATION (Amount & Location):

{51} Solvation...

{52} 6. BOUND IONS

{53} 7. TIME VARIATION

{54} ASIDE: Relaxation Processes as Probes of Motion.

{55} ASIDE: ...Organization decays similarly due to random motion.

{56} ASIDE: ...Photoselection

{57} ASIDE: ...Photoselection...

{58} ASIDE: ...Photoselection...

{59} ASIDE:...

{60} ASIDE:...

{61} ASIDE:...

Author: John E. Wampler

Email: wampler@bchiris.bmb.uga.edu

Home Page: http://bmbiris.bmb.uga.edu/wampler

Assignment:

Garrett & Grisham, Sections 4.6, 5.1, 5.7, and Appendix to Chapter 5.
Remember:

A useful source of reference material for detection of proteins in solution and in gels is the Molecular Probes catalog (see p. 180ff), Handbook of Fluorescent Probes and Research Chemicals, R. P. Haugland, Molecular Probes, Inc., Eugene, OR.
References:

G. K. Ackers (1967) Molecular Sieve Studies of Interacting Protein Systems, J. Biol. Chem. 242, 3026-3034.

G. K. Ackers (1967) A New Calibration Procedure for Gel Filtration Columns, J. Biol. Chem. 242, 3237-3238.

K. Biemann (1992) Mass spectrometry of peptides and proteins, Annu. Rev. Biochem. 61, 977-1010.

Bigelow (1971), J. Theoretical Biology 16, 187-211.(hydration)

Cohn and Edsal (1983) Proteins, Amino Acids and Peptides, Reihold, N. Y.(Amino acid and peptide physical properties)

H. F. Fisher (1965) An upper limit to the amount of hydration of a protein molecule, Biochim. Biophys. Acta 109, 544-550.

D. Freifelder (1982) Physical Biochemistry, W. H. Freeman and Co., San Francisco (General Reference)

N. Greenfield and G. Fasman (1969), Biochemistry 8, 4108-4115.(CD of proteins)

K. Hardeman, B. Samyn, J. van der Eycken, J. van Beeumen (1998) An improved chemical approach toward the C-terminal sequence analysis of proteins containing all natural amino acids, Protein Science 7, 1593-1602.

I. D. Kuntz (1971), J. Am. Chem. Soc. 93, 514-516.(hydration)

I. D. Kuntz, T. S. Brassfield, G. D. Law and G. V. Purcell (1969), Science 163, 1329-1331. (NMR measure of hydration).

D-S. Na, H-Y Hong, G-S Yoo and J-K Choi (1994), Evans Blue staining method for detection of proteins on polyacrylamide gels with Rhodamine B, Analytical Let. 27, 1265-1275.

H. Schagger and G. von Jagow (1987), Tricine-sodium dodecyl sulfate-polyacrylamide gel electrophoresis for the separation of proteins in the range from 1 to 100 kDa, Anal. Biochem. 166, 368-379.

D. W. Sears and S. Beychok (1973) Circular Dichrosim, in Physical Principles and Techniques of Protein Chemistry, Part C (S. J. Leach, ed.), Academic Press, N. Y., pp. 445-592.

J. H. Wang (1954), Theory of the self-diffusion of water in protein solutions, J. Am. Chem. Soc. 76, 4755-4763. (self-diffusion of water for hydration measure).

K. Weber and M. Osborn (1969), The reliability of molecular weight determination by dodecyl sulfate-polyacrylamide gel electrophoresis, J. Biol. Chem. 244, 4406-4412.

J. R. Whitaker (1963) Determination of molecular weights of proteins by gel filtration on Sephadex, Anal. Chem. 35, 1950-1953.

R. W. Woody (1995) Circular Dichroism, Methods in Enzymology 246, 34-71.

D. A. Yyphantis (1964) Equilibrium Ultracentrifugation of Dilutes solutions, Biochemistry 3, 297-317.