Databases Protein

Figure 7-15 shows the time evolution of the temperature, total energy, and potential energy for a 300 ps simulation of the tetracycline repressor dimer in its induced (i.e., hgand-bound) form. Starting from the X-ray structure of the monomer in a complex with one molecule of tetracycline and a magnesium ion (protein database... 

Figure 7-16. Superimpasition of the X-ray structure of the tetracycline repressor class D dimer (dark, protein database entry 2TRT) with the calculated geometrical average of a 3 ns MD simulation (light trace). Only the protein backbone C trace Is shown, The secondary structure elements and the tertiary structure are almost perfectly reproduced and maintained throughout the whole production phase of the calculation,...

Altschul S F, T L Madden, A A Schaffer, J Zhang, Z Zhang, W Miller and D J Lipman 1997. Gapped BLAST and PSI-BLAST A New Generation of Protein Database Search Programs. Nucleic Acids Research 25 3389-3402. 

Murzin A G, S E Brenner, T Hubbard and C Chothia 1995. SCOP A Structural Classification of Proteins Database for the Investigation of Sequences and Structures. Journal of Molecular Biology 247 536-540. 

TJP Hubbard, B Alley, SE Brenner, AGMurzm, C Chothia. SCOP A stiaictural classification of proteins database. Nucleic Acids Res 27 254-256, 1999. 

The optimal sequence obtained, called FSD-1 for full sequence design, is shown in Table 17.2 and compared with the sequence of the template Zif 268. A search of the FSD-1 sequence against protein databases did not reveal a statistically significant similarity with any other protein, including zinc finger proteins. 

So, back then to aspirin. Very often, X-ray data is available for the molecule of interest or related molecules. The lingua franca for molecular modelling purposes is a file of Cartesian coordinates such as the following. pdb (Protein Database) file. Figure 1.13, for aspirin. 

Nothing is known about the identity of the iron species responsible for dehydrogenation of the substrate. Iron-oxo species such as FeIV=0 or Fem-OOH are postulated as the oxidants in most heme or non-heme iron oxygenases. It has to be considered that any mechanistic model proposed must account not only for the observed stereochemistry but also for the lack of hydroxylation activity and its inability to convert the olefinic substrate. Furthermore, no HppE sequence homo-logue is to be found in protein databases. Further studies should shed more light on the mechanism with which this unique enzyme operates. 

Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ, Gapped BLAST and PSI-BLAST a new generation of protein database search programs. Nucleic Acids Res 1997 25 3389-402. 

Roche O, Kiyama R, Brooks CL 3rd. Ligand-protein database linking protein-ligand complex strnctnres to binding data. J Med Chem 2001 44 3592-8. 

Mature PGE showed the highest homology - 79% (Fig. 2) - with PGC from A. niger based on a protein database search. 

Demirev, P. A. Ho, Y. P. Ryzhov, V. Fenselau, C. Microorganism identification by mass spectrometry and protein database searches. Anal. Chem. 1999, 71, 2732-2738. 

Eng, J. K. McCormack, A. L. Yates, J. R. An approach to correlate tandem mass spectra data of peptides with amino acid sequences in a protein database. J. Am. Soc. Mass Spectrom. 1994,5, 976-989. 

We are attempting to understand the biological significance of the large variations in frequency of putative LDRs, whether between different types of bacteria or archaea, or between pro- and eukaryota. We have carefully studied the literature of more than 90 example proteins selected from our disordered protein databases and found reports on the functions of most of the disordered regions (Dunker et al., 2002). The observed functions and the number of examples in each functional class are given in Table VI. As indicated, four major functional classes were found molecular recognition, molecular assembly or disassembly, protein modification, and entropic chains. 

Recently, there has been great interest in proteins that exhibit biological activity but lack a well-defined secondary or tertiary structure after purification (Dunker et al., 1998, 2001 Schweers et al., 1994 Uversky et al., 2000 Wright and Dyson, 1999). Such proteins are referred to as intrinsically disordered or unstructured. An analysis in 1998 of the Swiss Protein Database revealed that about 15,000 proteins in that database are likely to contain disordered segments at least 40 residues in length (Romero et al., 1998). Dyson and Wright (2002) review intrinsically disordered proteins in this volume. 

Fig. 44. Distribution of Ala in the Ramachandran plot when using (A) all secondary structure conformations in the protein database or (B) only those Ala residues in a coil conformation. (From Serrano, 1995. 1995, with permission from Academic Press.)...

Over the years, MS/MS duty cycle of modern MS instruments has constantly been improving, but for simplicity we assume it is equal to 1 s. Considering this it is possible to identify up to 60 peptides per minute and up to 3600 peptides in a LC-MS/MS analysis of 1 h. It is important to mention that only a small percentage of MS/MS scans typically yield a spectrum of sufficient quality that can be matched against a protein database and can result in peptide identification. 

Altschul, S. F.andKoonin, E. V.(1998), Iterated profile searches with PSI-LAST - a tool for discovery in protein databases, Trends Biochem. Set ( Computer Corner ), 23, 444-446. 

Simpson RJ et al. Proteomic analysis of the human colon carcinoma cell line (LIM 1215] development of a membrane protein database. Electrophoresis 2000 21 1707-1732. 

If a monoclonal antibody was generated by immunization with a full-length native protein rather than a peptide, then the immunized mouse will generate antibodies that recognize both linear and conformationally dependent epitopes. Only a small subset of these monoclonal antibodies will likely be useful for clinical use on formalin-fixed, paraffin-embedded tissue (FFPE) samples. Those that are useful tend to have epitopes that are linear the epitopes are not dependent on the protein s three-dimensional conformation (see Chapter 16). Therefore, for antibodies generated in response to immunization with full-length proteins, the peptides that serve as positive controls will be linear stretches of amino acids derived from the native protein sequence, as listed in protein databases. 

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