Sequence preferences

Bogyo, M., Shin, S., McMastee, J. S., and Ploegh, H. L. Substrate binding and sequence preference of the proteasome revealed by active-site-directed affinity probes. Chem Biol 1998, 5, 307-320. 

Duband-Goulet, I., Carol, V., Ulyanov, A.V., Douc-Rasy, S., and Prunell, A. (1992) Chromatin reconstitution on small DNA rings. IV. DNA supercoiling and nucleosome sequence preference. J. Mol. Biol. 224, 981-1001. 

Tethering with extenders was also used to identify inhibitors to the antiinflammatory target caspase-1 [28, 29]. In this case, one of the same extenders previously designed for caspase-3 selected an entirely different set of fragments. This is consistent with different substrate peptide sequence preferences WEHD for caspase-1 vs DEVD for caspase-3 [30]. 

Compared to other multidimensional experiments the exchange experiments are fairly simple and, thus, easy to optimize. Experiments are robust with regard to the pulse imperfections and miscalibration. All artifacts except coherence transfer can be removed with standard phase cycling of RF pulses and receiver. The coherence transfer can be removed by appropriate pulse sequences, preferably with T-ROESY. 

In addition to finding small organic molecules that bind to a protein, covalent capture methods can identify peptides that interact with proteins. Kohda and colleagues used this approach to study the mitochondrial protein Tom20, an import receptor that recognizes an epitope on proteins targeted for the mitochondria.1301 Previous work had characterized this epitope as a five-residue peptide that assumes an amphiphilic helical conformation, and coarse sequence preferences had been worked out. However, Tom20 has both low affinity... 

They screened seven libraries, each containing 19 peptides of different masses, and found the sequences that bound most tightly to Tom20. Matrix-assisted laser desorp-tion/ionization time-of-flight mass spectrometry (MALDI-TOF MS) served as a readout that allowed the ionized peptides to be observed directly. Using this approach, Kohda and colleagues discovered that the recognition site spans six residues, not the previously established five, and were able to refine sequence preferences further. 

How general are such conclusions Do they apply to more complex proteins Are there more elusive features that influence turn preferences Selection for catalytic activity, an extremely sensitive probe of structural integrity, has the potential to reveal more subtle sequence preferences than simple screening protocols. We tested this premise using the EcCM enzyme (Fig. 3.4B) as a template [85]. The two identical polypeptides that make up this helical bundle protein consist of three helices joined by two loop segments (Fig. 3.12A) [33], The L2 loop connecting the H2 and H3 helices lies farthest from the active site and was targeted for analysis. 

Skorobogaty A, White RJ, Phillips DR, Reiss JA. Elucidation of the DNA sequence preferences of daunomycin. Drug. Des. 

DNA cleavage by many topoisomerases shows some sequence preference, generating DNA fragments of discrete sizes. However, a well-defined sequence specificity has been observed for only a few enzymes and analysis at the nucleotide level has in most cases revealed only a rough consensus sequence. It is possible that there are sequence deter-... 

Ma, L., Golden, S., Wu, L., Maxson, R. 1996. The molecular basis of Boston-type craniosynostosis the Pro 148- > His mutation in the N-terminal arm of the MSX2 homeodomain stabilizes DNA binding without altering nucleotide sequence preferences. Hum. Mol. Genet. 5, 1915-1920. 

Huang, H., Hopkins, P. B. (1993). DNA interstrand cross-linked by formaldehyde Nucleotide sequence preference and covalent structure of the predominant cross-link formed in synthetic oligonucleotides, J. Am. Chem. Soc., 115 9402. 

The following characteristics of secondary structures may correlate to the sequence preference and subsequent fold of globular proteins ... 

Membranes from glass fiber coated with polybrene (GF/C of Whatman) are suitable for amino acid sequencing because the membranes are inert against the chemicals used for the sequencing. Although the protein binding capacity of the coated glass fiber membranes (10 to 30 pg/cm ) is comparable to that of nitrocellulose, most sequencers prefer PVDF membranes. 

To observe the effect of complex formation with an attendant change in the geometry of the ligand molecule, the calcium ion complex of another model compound, the 1,5-anhydrorlbltol, was investigated. It was hypothesized that the 1,5-anhydroribltol would change conformation to the alternate chair form to enhance formation of the calcium ion complex because the alternate conformation has the axial-equatorial-axial sequence preferred for complex formation. 

---