Protein structure studies

M10. Maquat, L. E Chilcote, R., and Ryan, P. M., Human triosephosphate isomerase cDNA and protein structure Studies of triosephosphate isomerase in man. J. Biol. Chem. 260, 3748-3753 (1985). 

Ethylenimine may be used to introduce additional sites of tryptic cleavage for protein structural studies. In this case, complete sulfhydryl modification is usually desired. Proteins are treated with ethylenimine under denaturing conditions (6-8 M guanidine hydrochloride) in the presence of a disulfide reductant to reduce any disulfide bonds before modification. Ethylenimine may be added directly to the reducing solution in excess (similar to the procedure for Aminoethyl-8 described previously) to totally modify the —SH groups formed. 

Multidimensional NMR methods, combined with isotope labeling, can provide access to virtually every atom in a molecule, unique for protein structural studies. This not only allows characterization of the structure and interaction of proteins in their native milieu, but also provides unparalleled possibilities to obtain a complete atomic-level resolution picture of protein dynamics in a time range from picoseconds up to seconds, the range where most motions relevant to protein function take place. A significant number of 15N and 13C relaxation studies have been performed on a large number of proteins in the last... 

C.J. Epstein, R.F. Goldberger, and C.B. Anfinsen. The genetic control of tertiary protein structure studies with model systems. In Cold Spring Harbor Symposium on Quantitative Biology, 1963. 

Reported applications of DMA include the cross-linking of bovine pancreatic ribonuclease A (Hartman and Wold, 1967), treatment of erythrocyte membranes to reduce the effects of sickle cell anemia (Waterman et al., 1975), conjugation and analysis of the outer membrane proteins of Neisseria gonorrhoeae (Newhall et al., 1980), protein structural studies of bovine a-crystalline (Siezen et al., 1980), cross-linking of hemoglobin S (Pennathur-Das et al., 1982), and forming S-carbomethoxy-valeramidine during hydrolysis of DMA (Mentzer et al., 1982). 

The great specificity of tyrosinase, the simplicity of monitoring its action spectrally, and in some cases, the discrimination shown among the several tyrosyl groups of a protein [it oxidizes only one of the six tyrosyl groups of ribonuclease (Yasuiiobu and Dandliker, 1957)] appear to recommend its serious consideration as a tool in protein structure studies. 

Buxton GV, Greenstock CL, Heknan WP, Ross AB (1988) Critical review of rate constants for reactions of hydrated electrons, hydrogen atoms and hydroxyl radicals ("OH/"0 ) in aqueous solution. / Phys Chem Ref Data 17 513-882. de Renty M. (2005) Etude par spectroscopic infrarouge des effets d irradiation sur la structure des proteines. [Radiation effects on protein structure studied by FT-IR sepctoscopy] Microthese de PEcole Nationals Superieure de Chimie de Paris. 

G. S. Hartley and C. Robinson. Trans. Faraday Soc. 48, 847-53 (1952). Protein structures studied by atomic models. 

It is clear that the application of GC-MS in protein structural studies has advanced significantly in the last few years but it is still in a development stage, particularly in the sense that its routine use to sequence large completely unknown peptides has still to be achieved. The total system installation cost to engage in the work carried out by Nau, Kelley and Biemann [51] is high and prohibitively so for many laboratories. Nevertheless, the speed and sensitivity of GC-MS techniques are often superior to conventional methods and will undoubtedly contribute significantly to future progress in protein analysis. 

Trypsin and chymotrypsin. Purification of both trypsin and chymo-trypsin by affinity chromatography is now a routine tool in many laboratories. Most commercial trypsin preparations are contaminated with trace amounts of chymotrypsin which restricts the use of the enzyme in protein structural studies. However, the soya trypsin inhibitor-agarose media provides a convenient column for separation of the enzymes. 

Complete descriptions of the particle beam, its operation, its experimental setup, and its utility in protein structural studies have been previously described. (8, 12). Relevant PB dimensions include a 25 pm diameter fused silica capillary for production of the aerosol spray, a 22 cm length desolvation chamber to remove solvent, a single stage momentum separator, and a nozzle-substrate distance of 5 mm. Particle beam deposits ranged in size from 20 pm to 100 pm in diameter, and averaged approximately 50 pm. Deposit were made onto a water insoluble calcium fluoride (CaFj) window (25 mm dia. x 2 mm) from International Crystal Laboratories (Garfield, NJ). 

Involvement of Basic Amphiphilic a-helical Domain in the Reversible Membrane Interaction of Amphitropic Proteins Structural Studies by Mass Spectrometry, Circular Dichroism, and Nuclear Magnetic Resonance... 

Proteins that have catalytic properties are called enzymes (i.e.. enzymes are biological catalysts of protein nature). Some enzymes have full catalytic reactivity per sc these are considered to be simple proteins because they do not hiive a nonprotein moiety. Other enzymes are conjugated proteins, and the nonprotcin structural components arc necc.ssary for reactivity. Occasionally, enzymes require metallic ions. Because enzymes are proteins or conjugated proteins, the general review of protein structural studies presented above in this chapter (e.g.. protein conformation and denaturation) is fundamental to the following topics. Conditions that affect denaturation of proteins usually have an adverse effect on the activity of the enzyme. 

Arthur S. Edison obtained a B.S. in chemistry from the University of Utah, where he studied monoterpenes isolated from southern Utah sagebrush by NMR. He completed his Ph.D. in biophysics from the University of Wisconsin, Madison, where he developed and applied NMR methods for peptide and protein structural studies under the supervision of John Markley and Frank Weinhold. In 1993, Dr. Edison joined the laboratory of Anthony O. W. Stretton at the University of Wisconsin as a Jane Coffin Childs postdoctoral fellow where he investigated the role of neuropeptides in the nervous system of the parasitic nematode Ascaris suum. He joined the faculty at the University of Florida and the National High Magnetic Field Laboratory in 1996 and is currently the Director of Chemistry Biology at the NHMFL. Dr. Edison s current research is in technology development for high-sensitivity NMR and natural product discovery in nematodes and other invertebrates. Dr. Edison is the recipient of the 1997 American Heart Association Robert J. Boucek Award, a CAREER Award from the National Science Foundation in 1999, and, with his postdoctoral scientist Aaron Dossey, the Beal award for the best publication of the year in the Journal of Natural Products in 2007. 

Homshaw MP, McDermott JR, Candy JM, Lakey JH (1995) Copper binding to the N-terminal tandem repeat region of mammalian and avian prion protein structural studies using synthetic peptides. Biochem Biophys Res Commun 214 993-999... 

Initial protein structure studies indicated that bacteriorhodopsin is a 248-residue polypeptide. Its amino-terminal residue is on the membrane s outside surface, and its carboxyl residue projects into the cytoplasm. Careful analysis of bacteriorhodopsin s primary sequence revealed seven peptide segments with amino acid sequences typical of a-helices. Using electron microscopy and X-ray crystallography, researchers determined that bacteriorhodopsin possesses seven a-helices, which are roughly perpendicular to the membrane (Figure 11C). 

Mihalyi, E. Application of Proteolytic Enzymes to Protein Structure Studies. 2nd Edition CRC Press West Palm Beach, FI 1978. 

Protein-protein interaction pathways and cell signalling networks, high-throughput protein structural studies using mass spectrometry, nuclear magnetic resonance, X-ray crystallography are also expanding fields. 

Lian LY, Middleton DA (2001) Labelling approaches for protein structural studies by solution-state and solid-state NMR. Prog Nucl Magn Reson Spectrosc 39 171-190... 

O. 3 0.6 0.5, respectively, as well as 2,4-di-O-methyl-D-galactose. Each polysaccharide contained, in addition, 10% half-ester sulphate and ca. 0.5% protein. Structural studies showed, inter alia, that the D-glucuronic acid residues were linked to 0-3 of the D-galactose residues and that 2-0-methyl-D-glucuronic acid residues were linked to 0-4 of the L-galactose residues. The polysaccharide from... 

VanStokkum, I.H.M. Linsdell, H. Hadden, J.M. Haris, P.I. Chapman, D. Bloemendal, M. Temperature-induced changes in protein structures studied by Fourier transform infrared spectroscopy and global analysis. Biochemistry 1995, 34, 10508—10518. 

Three inhibitors from non-food sources are included in Table II. The basic (Kunitz) trypsin inhibitor from bovine pancreas (BPTI) is a small protein that has been used extensively in protein structure studies. At neutral or acid pH, it denatures near 100°C. From the ratio of calorimetric to van t Hoff (effective) enthalpies, Privalov... 

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