Protein Sequences and Structures

The sequence of the amino acid residues in a protein is called the primary structure. Two well-known examples are insulin and ribonuclease, as described in Chapter 2. 

Physical Chemistry of Macromolecules Basic Principles and Issues, Second Edition. By S. F. Sun ISBN 0-471-28138-7 Copyright 2004 John Wiley Sons, Inc. 

Among others, they are of historical importance, particularly insulin. The decade of work by Sanger and co-workers on the amino acid sequence of insulin represents pioneering research into the primary structure of a protein. 

Insulin consists of two different polypeptide chains held together by —S—S— bridges. They can be separated by oxidation with performic acid. Similarly, ribonuclease consists of 124 amino acids and —S—S— bridges which can also be separated. 

In the past, determination of the sequence of a protein was tedious and laborious work. For many years, only a very small number of well-known proteins had their sequence determined and reported in the research literature. Today, we have machines that do this painstaking work. As of the year 2000, The Protein Information Resource, a scientific organization, has catalogued the sequence of amino acids of at least 200,000 proteins and new data are accumulated every day. 

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Each element of matrix corresponds to the probability that the amino acid in coiumn wiii mutate to the jmino acid in row j after a period of 1 PAM. The vaiues have been multipiied by 10000. (Based on Dayhoff M O 1978. Atlas of Protein Sequence and Structure Voiume 5 Suppiement 3. Dayhoff M O (Editor) Georgetown Jniversity Medicai Center, National Biomedical Research Foundation Figure 82.)... 

Dayhoff, M. O., 1972-1978. The Atlas of Protein Sequence and Structure, Vol.s. 1-5. Wa.shington, DC National Medical Re.search Foundation. 

Mann, M., and Wilm, M., 1995. Electro.spray ma.ss. spectrometry for protein characterization. Trends in Biochemical Sciences 20 219-224. A review of die ba.sic application of ma.ss. spectrometric methods to the analysis of protein. sequence and. structure. 

Taylor, W. R. (1992) Patterns in Protein Sequence and Structure, Springer Series in Biophysics (Springer, Berlin), Vol. 7. 

Protein information resource (Barker et al., 1999) was established in 1984 by the National Biomedical Research Foundation (NBRF) as a successor to the original NBRF Protein Sequence Database, developed over 20 years by the late Margaret O. Dayhoff and published as the Atlas of Protein Sequence and Structure (Dayhoff et al., 1965 Dayhoff, 1979). Since 1988 the database has been maintained by PIR-Intemational, a collaboration between the NBRF, the Munich Information Center for Protein Sequences (MIPS), and the Japan International Protein Information Database (JIPID). 

Dayhoff, M. O. (1979). Atlas of protein sequence and structure. Vol. 5, suppl. 3 National Biomedical Research Foundation, Washington, D.C. (pp. 345-358). 

Dayhoff, M., ed. (1972). Atlas of Protein Sequences and Structure, Vol. 5. Natl. Biomed. Res. Found., Silver Spring, Maryland. 

M. D. Dayhoff, Atlas of Protein Sequence and Structure National Biomedical Research Foundation Silver Spring, MD, 1969 Vol. 4. 

O Sullivan, O., Suhre, K., Abergel, C., Higgins, D. G., and Notredame, C. (2004) SDCoffee combining protein sequences and structures within multiple sequence ahgnment /. Mol. Biol. 340, 385-395. 

Proteomics server of the Swiss institute of bioinformatics. Dedicated to analysis of protein sequences and structure, as well as 2-D SDS-PAGE. 

The database would present all known protein sequences and structures nucleic acid sequences exosporium structure metric parameters such as mean density and size spectral properties such as the fluorescence, fluorescence... 

Anthrax Spores Biochemical Properties DNA sequence Whole organism Specific toxin plasmids Proteins sequence and structure Exosporium Spore internal Toxins... 

Predict Protein Protein sequence and structure prediction http //www.embl-heidelberg.de/predictprotein/... 

Sali, A., J. P. Overington, M. S. Johnson, and T. L. Bundell, From comparisons of protein sequences and structures to protein modelling and design. Trends Biochem. Sci. 15 235-240, 1990. 

Protein sequence and structure of troponin (TN-C) and carp muscle calcium binding parvalbumin (MCBP) are known199-201). MCBP has two calcium binding regions each consisting of an a-helix, a loop about the calcium ion and another a-helix, as so-called EF hand (Fig. 21)202,203). 

Dayhoff, M. 0. Atlas of protein sequence and structure 1972. Nat. Biomed. Res. Found. Georgetown Univ. Medic. Cent. Washington 1972. 

The protein sequence and structure databases are now sufficiently representative... 

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