Matrix protein biochemistry

Levine, P. T., Seyer, J. M., Huddleston, J., Glimcher, M. J. The comparative biochemistry of the organic matrix proteins of the developing enamel I. Amino acid composition. Arch, oral Biol. 12, 407 (1967)... 

Reiffen, F., and Gratzl, M. (1986). Ca Binding to Chromaffin Vesicle Matrix Proteins Effect of pH, Mg, and Ionic Strength, Biochemistry 25 4402-4406. 

Brotherton, T., Zenk, D., Kahanic, S. Reneker, J. (1991). Avian nuclear matrix proteins bind very tightly to cellular DNA of jS-globin gene enhancer in a tissue-specific fashion. Biochemistry, 30, 5845—50. 

Wiener, J. R., Pal, R., Barenholz, Y., and Wagner, R. R., 1983, Influence of the peripheral matrix protein of vesicular stomatitis virus on the membrane dynamics of mixed phospholipid vesicles Fluorescence studies. Biochemistry 22 2162. 

Zakowski, J. J., Petri, W. A., Jr., and Wagner, R. R., 1981, Role of matrix protein in assembling the membrane of vesicular stomatitis virus Reconstitution of matrix protein with negatively charged phospholipid vesicles, Biochemistry 20 3902. 

Gohring F, Fackelmayer FO (1997) The scaffold/matrix attachment region binding protein hnRNP-U (SAF-A) is directly bound to chromosomal DNA in vivo a chemical cross-linking study. Biochemistry 36(27) 8276-8283... 

Matrix-assisted laser desorption/ionization (MALDI)-time-of-flight (TOF)-mass spectrometry (MS) is now routinely used in many laboratories for the rapid and sensitive identification of proteins by peptide mass fingerprinting (PMF). We describe a simple protocol that can be performed in a standard biochemistry laboratory, whereby proteins separated by one- or two-dimensional gel electrophoresis can be identified at femtomole levels. The procedure involves excision of the spot or band from the gel, washing and de-stain-ing, reduction and alkylation, in-gel trypsin digestion, MALDI-TOF MS of the tryptic peptides, and database searching of the PMF data. Up to 96 protein samples can easily be manually processed at one time by this method. 

Developments in mass spectrometry technology, together with the availability of extensive DNA and protein sequence databases and software tools for data mining, has made possible rapid and sensitive mass spectrometry-based procedures for protein identification. Two basic types of mass spectrometers are commonly used for this purpose Matrix-assisted laser desorption/ionization (MALDI)-time-of-flight (TOF) mass spectrometry (MS) and electrospray ionization (ESI)-MS. MALDI-TOF instruments are now quite common in biochemistry laboratories and are very simple to use, requiring no special training. ESI instruments, usually coupled to capillary/nanoLC systems, are more complex and require expert operators. We will therefore focus on the use of MALDI-... 

Piez KA, Reddi AH. Extracellular Matrix Biochemistry. New York Elsevier, 1984. Raxworthy MJ. Microtubules, tubulins and associated proteins. Biochem Ed 16 2-9, 1988. Ruoslahti E. Fibronectin and its receptors. Ann Rev Biochem 57 375-413, 1988. 

S. Hillenkamp, F De Vries, M.S. Comparative Mass Spectrometric Analyses of Photofrin Oligomers by Fast Atom Bombardment Mass Spectrometry, UV and IR Matrix-Assisted Laser Desorption/lonization Mass Spectrometry, Electrospray Ionization Mass Spectrometry and Laser Desorption/Jet-Cooling Photoionization Mass Spectrometry, J. Mass Spectrom. 34, 661-669 (1999). Powell, K.D. Fitzgerald, M.C. Accuracy and Precision of a New H/D Exchange- and Mass Spectrometry-Based Technique for Measuring the Thermodynamic Properties of Protein-Peptide Complexes, Biochemistry 42,4962-4970 (2003). 

Consider a typical eukaryotic cell, for instance, a muscle cell. By weight, the cell is about 75% water. However, this estimate fails to convey the truly aqueous nature of the cell a far more realistic description is in terms of mole ratios. Because of the low molecular weight of water, the nominal 75% water translates into a very large number of moles of water relative to the number of moles of other cell constituents. Thus, the aqueous nature of the cell is better illustrated by noting that for every 20,000 water molecules there are only about 75 lipid molecules, 100 sodium, potassium, and chloride ions (with at most a few hundred other small molecules or ions), and only one or two protein molecules. By sheer numbers water molecules totally dominate, and in this perspective life is merely some complex biochemistry in an extensive matrix of water, stabilized by a few lipids and macromolecules. The two dominating factors in cell biology are thus, simply, water molecules and interfaces. 

---