Protein circularization

Johnson W.C. 1999. Analyzing protein circular dichroism spectra for accurate secondary structures. Proteins Struct., Fund, Genet. 35 307-312. 

Sreerama, N., Manning, M.C., Powers, M.E., Zhang. J.X., Goldenberg, D.P., and Woody, R.W. 1999a. Tyrosine, phenylalanine, and disulfide contributions to the circular dichroism of proteins Circular dichroism spectra of wild-type and mutant bovine pancreatic trypsin inhibitor. Biochemistry 38 10814-10822. 

In general, when one wants to determine if global and/or local structural modifications have occurred within a protein, circular dichroism experiments are performed. Also, one can record the fluorescence excitation spectrum of the protein. If perturbations occur within the protein, one should observe excitation spectra that differ from one state to another. One should not forget to correct the recorded spectra for the inner filter effect. 

FT-IR spectroscopy is particularly useful for probing the structure of membrane proteins. Until recently, a lack of adequate experimental techniques has been the reason for the poor understanchng of the secondary structure of most membrane proteins. X-ray diffraction requires high quality crystals and these are not available for many membrane proteins. Circular dichroism (CD) has been widely used for studying the conformation of water-soluble proteins, but problems arise in its use for membrane proteins. The light scattering effect may distort CD spectra and lead to substantial errors in their interpretation. In addition, the reference spectra used for the analysis of CD spectra are based on globular proteins in aqueous solution and may not be applicable to membrane proteins in the hydrophobic environment of lipid bilayers. 

Table XXXV Non-Coding ncRNA, Complementary cDNA Relation to Proto-oncogenes/ proteins. Circular RNAs...

Circular Dicfaroism.—In its application to proteins, circular dichroism (c.d.) is generally used to obtain information about conformation (secondary structure) and conformational changes. Peptides continue to be studied, both in their own right and as models for proteins. The c.d. spectra of benzyloxycarbonyl Val-(Ala),-OEt in different solvents have been examined. In dioxan, negative and positive bands were seen at 228— 9 and 212— 3 nm respectively and it was deduced that the peptide was in a bend conformation. The use of c.d. in the vacuum ultraviolet range (near 150 nm), and of infrared spectroscopy, allowed the /S-structure to be established for oligomers (2—7 residues) of L-leucine, S-cyclohexyl-L-alanine, and L-phenylalanine. ... 

Sreerama, N., Woody, R.W. Computation and analysis of protein circular dichroism spectra. Methods Enzymol. 383, 318-351 (2004)... 

Hirst, J.D. Improving protein circular dichroism calculations in the far-ultraviolet through reparametrizing the amide chromophore. J. Chem. Phys. 109, 782-788 (1998)... 

Segel I.H, 1975, Enzyme Kinetics Behmrior and Analysis of Rapid Equilibrium and Steady-State Enzyme Systems, John Wiley Sons, ISBN 0-471-77425-1, Canada Sreerama, N. Woody, R.W. (2004). Computation and analysis of protein circular dichroism spectra. Methods Enzymol, Vol 383, pp 318-351 Stein, R.L., Stiimpler, A.M., Hoii, H. Powers, J.C., (1987). Catalysis by Human Leukocyte Elastase the Proton Inventory as a Mechanistic Probe. Biochemistry, Vol. 26, No.5, pp. 1305-1314... 

This long quest was marked by milestones. As already discussed, the obtention of highly purified preparations of infectious scrapie particles was necessary to identify the PrP protein. Circular dichroism studies of PrP and PrP demonstrated the existence of two totally distinct conformations of PrP, one corresponding to the physiologically expressed brain protein and the other to the infectious protein. However, the masterly demonstration of the mechanism of prion replication is that PRNP° mice, which do not express the PrP protein, failed to propagate prion infectivity. Hence, without the brain reservoir of normal PrP proteins, infectious PrP proteins are harmless and unable to cause any disease. If we link this information with the respective structures of PrP and PrP , then we have a molecular mechanism accounting for the replication, by force, of prions invaders in the brain of healthy animals (Fig. 9.5). 

Jones, D.B. 1941. Factors for converting percentages of nitrogen in foods and feeds into percentages of proteins. Circular No 183, issued August 1931, revised February 1941, United States Department of Agriculture, Washington, DC, 1-21. 

Sreerama N, Woody RW 2004. Computation and Analysis of Protein Circular Dichroism Spectra. Methods Enzymology 383 318-351. 

D an ielli-D avson model of mem-Globular proteins (circular) cover phospholipid layers (club-shaped figures) which are separated by neutral lipoid region. Taken, with kind permission, from Danielli and Davson (1935), p.498. 

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