Protein structural characterization

Ai HW, Henderson JN, Remington SJ, Campbell RE (2006) Directed evolution of a monomeric, bright and photostable version of Clavularia cyan fluorescent protein structural characterization and applications in fluorescence imaging. Biochem J 400 531-540... 

Secondary structure The protein structure characterized by folding of the peptide chain into a helix, sheet, or random coil. 

Kriwacki, R., Reisdorph, N. and Siuzdak, G. (2004) Protein structure characterization with mass spectrometry. Spectroscopy, 18, 34- 47. 

MALDI-TOF-MS and Edman sequencing have become complementary techniques in protein structural characterization. Ideally, direct collection of peptide fractions should be to a support that... 

The necessity to obtain samples free of contaminants such as buffers, salts and detergents has become the rate-limiting step in protein structural characterization (1,2). The isolation of low abundant proteins or peptides in combination with high sensitivity analyses results in high background noise that compromises data quality as well as interpretation. For example, tris and glycine interfere with amino acid sequencing,... 

In this study, the utility of both LC/MS and PB LC/FT-IR for protein structure characterization is demonstrated in the analysis of a proteolytic digestion mixture of horse heart cytochrome C. Horse heart cytochrome C is composed of three major and two minor helical structures that are interconnected by polypeptide coils and folded into a globular shape around a heme pocket. There is little other regular secondary structure. (11)... 

Canaves, J. M. 2004. Predicted role for the archease protein family based on structural and sequence analysis of TM1083 and MTH1598, two proteins structurally characterized through structural genomics efforts. Proteins 56 19-27. 

Strancar J, Kavalenka A, Urbancic I, Ljubetic A, Hemminga MA (2010) SDSL-ESR-based protein structure characterization. Eur Biophys J Biophys Lett 39 499-511... 

See Volume 5, Chapter 4 Chemical Derivatization and Multistage Tandem Mass Spectrometry for Protein Structural Characterization by Jennifer M. Froelich, Yali Lu, and Gavin E. Reid. 

A Chemical Derivatization and Multistage Tandem Mass Spectrometry for Protein Structural Characterization... 

Soderblom, E.J. Goshe, M.B. Collision-induced dissociative chemical cross-linking reagents and methodology applications to protein structural characterization using tandem mass spectrometry analysis. Anal. Chem. 2006, 78, 8059-8068. 

T. A. Cross, V. Ekanayake, J. Paulino and A. Wright, Solid State NMR The Essential Technology for Helical Membrane Protein Structural Characterization,/. Magn. Reson., 2014, 239, 100. 

Owing to their small size, mammalian MTs were among the first proteins structurally characterized by NMR spectroscopy and actually the first metaUo-proteins studied with this method. A major challenge in the determination of MT structures is the assignment of the correct metal-thiolate comiectivities. Here, the use of the NMR-active Cd or Cd nuclei bound to the protein instead of the spectroscopically silent Zn(II) ions proved to be an invaluable tool (for details... 

Step 1 A short conventional MD simulation (typically extending over a few lOOps) is performed to generate an ensemble of protein structures x 6 71 (each described by N atomic positions), which characterizes the initial conformational substate. The 2-dimensional sketch in Fig. 9 shows such an ensemble as a cloud of dots, each dot x representing one snapshot of the protein. 

Koppensteiner W A, P Lackner, M Wiederstein and M J Sippl 2000. Characterization of Novel Proteins Based on Known Protein Structures. Journal of Molecular Biology 296 1139-1152. 

BW Beck, Q Xie, T Ichiye. Computational study of S—H S hydrogen bonds m [4Ee-4S]-type ferredoxm x-ray and NMR structures Characterization and implications for redox potentials. Protein Sci, submitted. 

For each fold one searches for the best alignment of the target sequence that would be compatible with the fold the core should comprise hydrophobic residues and polar residues should be on the outside, predicted helical and strand regions should be aligned to corresponding secondary structure elements in the fold, and so on. In order to match a sequence alignment to a fold, Eisenberg developed a rapid method called the 3D profile method. The environment of each residue position in the known 3D structure is characterized on the basis of three properties (1) the area of the side chain that is buried by other protein atoms, (2) the fraction of side chain area that is covered by polar atoms, and (3) the secondary stmcture, which is classified in three states helix, sheet, and coil. The residue positions are rather arbitrarily divided into six classes by properties 1 and 2, which in combination with property 3 yields 18 environmental classes. This classification of environments enables a protein structure to be coded by a sequence in an 18-letter alphabet, in which each letter represents the environmental class of a residue position. 

Pleated p sheet (Section 27.19) Type of protein secondary structure characterized by hydrogen bonds between NH and C=0 groups of adjacent parallel peptide chains. The individual chains are in an extended zigzag conformation. 

Karger, B. L., and Fiancock, W. S., eds. 1996. Methods in Enzymology 271, Section III Protein Structure Analysis by Mass Sj ectrometry, f R. Yates P tide Characterization by Mass Spectrometry, B. L. Gillece-Castro and J. T. Stnlts. New York Academic Pre.s.s. 

If the sequence of a protein has more than 90% identity to a protein with known experimental 3D-stmcture, then it is an optimal case to build a homologous structural model based on that structural template. The margins of error for the model and for the experimental method are in similar ranges. The different amino acids have to be mutated virtually. The conformations of the new side chains can be derived either from residues of structurally characterized amino acids in a similar spatial environment or from side chain rotamer libraries for each amino acid type which are stored for different structural environments like beta-strands or alpha-helices. 

Finally, I note with sadness the death of Dr. I-Yih Huang. His work on hementin helped Sawyer et al. of Biopharm to obtain the patent on that fascinating protein. As described in Chapter 5, his sequencing work was the first structural characterization. Dr. Huang was a good friend and a wonderful scientist. 

F. X. Schmid, Spectral methods of characterizing protein conformation and conformational changes, in Protein Structure—A Practical Approach (T.E. Creighton, ed.), IRL Press, Oxford, 1989, pp. 251-285. 

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