http://www.real-times.com.cn/guest/20143219541398.pdf

Tricine-sodium dodecyl sulfate-polyacrylamide gel electrophoresis for the separation of proteins in the range from 1 to 100 kDa.

Protein identification and analysis software performs a central role in the investigation of proteins from two-dimensional (2-D) gels and mass spectrometry. For protein identification, the user matches certain empirically acquired information against a protein database to define a protein as already known or as novel. For protein analysis, information in protein databases can be used to predict certain properties about a protein, which can be useful for its empirical investigation. The two processes are thus complementary. Although there are numerous programs available for those applications, we have developed a set of original tools with a few main goals in mind. Specifically, these are: 1. To utilize the extensive annotation available in the Swiss-Prot database wherever possible, in particular the position-specific annotation in the Swiss-Prot feature tables to take into account posttranslational modifications and protein processing. 2. To develop tools specifically, but not exclusively, applicable to proteins prepared by two dimensional gel electrophoresis and peptide mass fingerprinting experiments. 3. To make all tools available on the World-Wide Web (WWW), and freely usable by the scientific community. In this chapter we give details about protein identification and analysis software that is available through the ExPASy World Wide Web server.

Protein identification and analysis tools in the ExPASy server

Overlapping complementary DNA clones were isolated from epithelial cell libraries with a genomic DNA segment containing a portion of the putative cystic fibrosis (CF) locus, which is on chromosome 7 Transcripts, approximately 6500 nucleotides in size, were detectable in the tissues affected in patients with CF The predicted protein consists of two similar motifs, each with (i) a domain having properties consistent with membrane association and (ii) a domain believed to be involved in ATP (adenosine triphosphate) binding A deletion of three base pairs that results in the omission of a phenylalanine residue at the center of the first predicted nucleotide-binding domain was detected in CF patients

https://science.sciencemag.org/content/sci/245/4922/1066.full.pdf

Identification of the cystic fibrosis gene: cloning and characterization of complementary DNA.

An approach for genome analysis based on sequencing and assembly of unselected pieces of DNA from the whole chromosome has been applied to obtain the complete nucleotide sequence (1,830,137 base pairs) of the genome from the bacterium Haemophilus influenzae Rd. This approach eliminates the need for initial mapping efforts and is therefore applicable to the vast array of microbial species for which genome maps are unavailable. The H. influenzae Rd genome sequence (Genome Sequence DataBase accession number L42023) represents the only complete genome sequence from a free-living organism.

https://science.sciencemag.org/content/sci/269/5223/496.full.pdf

Whole-genome random sequencing and assembly of Haemophilus influenzae Rd.

Peptides or proteins convert under some conditions from their soluble forms into highly ordered fibrillar aggregates. Such transitions can give rise to pathological conditions ranging from neurodegenerative disorders to systemic amyloidoses. In this review, we identify the diseases known to be associated with formation of fibrillar aggregates and the specific peptides and proteins involved in each case. We describe, in addition, that living organisms can take advantage of the inherent ability of proteins to form such structures to generate novel and diverse biological functions. We review recent advances toward the elucidation of the structures of amyloid fibrils and the mechanisms of their formation at a molecular level. Finally, we discuss the relative importance of the common main-chain and side-chain interactions in determining the propensities of proteins to aggregate and describe some of the evidence that the oligomeric fibril precursors are the primary origins of pathological behavior.

/pdf/protein-misfolding-functional-amyloid-and-human-disease-2w386pwb7k.pdf

Protein Misfolding, Functional Amyloid, and Human Disease

The addition of epidermal growth factor (EGF) to epidermal growth factor receptor (EGF receptor) dissolved in a solution of the detergent Triton X-100 results in the activation of its protein tyrosine kinase. To investigate the importance of the sites for self-phosphorylation on the enzyme in this process, the kinetics of activation of a deletion mutant missing the last 195 amino acids of the protein, including all of the sites for self-phosphorylation, were followed by monitoring the initial velocity at which the enzyme catalyzes the phosphorylation of the exogenous substrate RRKGSTAENAEYLRV. The activation of the enzymatic activity of this deletion mutant of EGF receptor displays kinetics that are second-order with respect to the concentration of the enzyme as does wild-type EGF receptor. The second-order rate constant for its activation is 36 +/- 10 microM-1 min-1, which is only 3-fold greater than the second-order rate constant for the activation of wild-type EGF receptor under the same conditions (13 +/- 2 microM-1 min-1). These results suggest that the mechanism by which the protein tyrosine kinase of the deletion mutant is activated is the same as that for the activation of the wild-type receptor and that the sites of self-phosphorylation in the wild-type EGF receptor do not participate in the mechanism of activation of the enzyme.

Jack Kyte

Papers

Kinetics of activation of the tyrosine kinase of a deletion mutant of epidermal growth factor receptor missing the sites of self-phosphorylation.