Iterative sequence/secondary structure search for protein homologs: comparison with amino acid sequence alignments and application to fold recognition in genome databases

2000 ◽  
Vol 16 (11) ◽  
pp. 988-1002 ◽  
Author(s):  
A. Wallqvist ◽  
Y. Fukunishi ◽  
L. R. Murphy ◽  
A. Fadel ◽  
R. M. Levy
Keyword(s):  
Amino Acid ◽  
Secondary Structure ◽  
Amino Acid Sequence ◽  
Fold Recognition ◽  
Iterative Sequence ◽  
Sequence Alignments ◽  
Genome Databases ◽  
Structure Search

Shark Myelin Basic Protein: Amino Acid Sequence, Secondary Structure, and Self-Association

1990 ◽  
Vol 55 (3) ◽  
pp. 950-955 ◽  
Author(s):  
Trudy J. Milne ◽  
Annette R. Atkins ◽  
Juanita A. Warren ◽  
Wendy P. Auton ◽  
Ross Smith
Keyword(s):  
Amino Acid ◽  
Secondary Structure ◽  
Amino Acid Sequence ◽  
Myelin Basic Protein ◽  
Basic Protein ◽  
Protein Amino Acid ◽  
Protein Amino Acid Sequence ◽  
Self Association

Amino acid sequence restriction in relation to proteolysis

1983 ◽  
Vol 3 (3) ◽  
pp. 225-232 ◽  
Author(s):  
Hans Jórnvall ◽  
Bengt Persson
Keyword(s):  
Amino Acid ◽  
Secondary Structure ◽  
Amino Acid Sequence ◽  
Distribution Patterns ◽  
Amino Acid Residues ◽  
Individual Protein ◽  
Proteolytic Cleavages ◽  
N Proteins

Distributions of amino acid residues in proteins show that proline is overrepresented in sequence positions following two basic residues ({LysArg}−{LysArg}), i.e. at sites similar to those susceptible to proteolytic cleavages of hormonal pro-forms. Conformational correlations further show that {LysArg}−{LysArg}-Pro sequences are often (8/11) not adiacent to elements of secondary structure, whereas the opposite applies to {LysArg}−{LysArg}-nonPro sequences (82/103 adjacent to elements of secondary structure). These distribution patterns from proteins in general also seem applicable in individual protein groups as demonstrated for some dehydrogenases. It appears possible that {LysArg}−{LysArg}-nonPro constitutes a restricted sequence, n proteins, and that proline, in addition to elements of secondary structure, contributes a means of avoiding unacceptable proteolytic processings of proteins in general.

scholarly journals Broad-spectrum detection of papillomaviruses in bovine teat papillomas and healthy teat skin

2004 ◽  
Vol 85 (8) ◽  
pp. 2191-2197 ◽  
Author(s):  
Tomoko Ogawa ◽  
Yoshimi Tomita ◽  
Mineyuki Okada ◽  
Kuniko Shinozaki ◽  
Hiroko Kubonoya ◽  
...  
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Broad Spectrum ◽  
Phylogenetic Analyses ◽  
Genomic Diversity ◽  
Bovine Papillomavirus ◽  
Subclinical Infection ◽  
Healthy Skin ◽  
Sequence Alignments ◽  
Spectrum Detection

To investigate the prevalence of bovine papillomavirus (BPV) in bovine papilloma and healthy skin, DNA extracted from teat papillomas and healthy teat skin swabs was analysed by PCR using the primer pairs FAP59/FAP64 and MY09/MY11. Papillomavirus (PV) DNA was detected in all 15 papilloma specimens using FAP59/FAP64 and in 8 of the 15 papilloma specimens using MY09/MY11. In swab samples, 21 and 8 of the 122 samples were PV DNA positive using FAP59/FAP64 and MY09/MY11, respectively. Four BPV types (BPV-1, -3, -5 and -6), two previously identified putative BPV types (BAA1 and -5) and 11 putative new PV types (designated BAPV1 to -10 and BAPV11MY) were found in the 39 PV DNA-positive samples. Amino acid sequence alignments of the putative new PV types with reported BPVs and phylogenetic analyses of the putative new PV types with human and animal PV types showed that BAPV1 to -10 and BAPV11MY are putative new BPV types. These results also showed the genomic diversity and extent of subclinical infection of BPV.

scholarly journals A Novel Lipolytic Enzyme Located in the Outer Membrane of Pseudomonas aeruginosa

1999 ◽  
Vol 181 (22) ◽  
pp. 6977-6986 ◽  
Author(s):  
Susanne Wilhelm ◽  
Jan Tommassen ◽  
Karl-Erich Jaeger
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Amino Acid ◽  
Amino Acid Sequence ◽  
Outer Membrane ◽  
Open Reading Frame ◽  
Lipolytic Enzyme ◽  
Cell Fractionation ◽  
Sequence Alignments ◽  
Reading Frame ◽  
Amino Terminal

ABSTRACT A lipase-negative deletion mutant of Pseudomonas aeruginosa PAO1 still showed extracellular lipolytic activity toward short-chain p-nitrophenylesters. By screening a genomic DNA library of P. aeruginosa PAO1, an esterase gene, estA, was identified, cloned, and sequenced, revealing an open reading frame of 1,941 bp. The product ofestA is a 69.5-kDa protein, which is probably processed by removal of an N-terminal signal peptide to yield a 67-kDa mature protein. A molecular mass of 66 kDa was determined for35S-labeled EstA by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and autoradiography. The amino acid sequence of EstA indicated that the esterase is a member of a novel GDSL family of lipolytic enzymes. The estA gene showed high similarity to an open reading frame of unknown function located in thetrpE-trpG region of P. putida and to a gene encoding an outer membrane esterase of Salmonella typhimurium. Amino acid sequence alignments led us to predict that this esterase is an autotransporter protein which possesses a carboxy-terminal β-barrel domain, allowing the secretion of the amino-terminal passenger domain harboring the catalytic activity. Expression of estA in P. aeruginosa andEscherichia coli and subsequent cell fractionation revealed that the enzyme was associated with the cellular membranes. Trypsin treatment of whole cells released a significant amount of esterase, indicating that the enzyme was located in the outer membrane with the catalytic domain exposed to the surface. To our knowledge, this esterase is unique in that it exemplifies in P. aeruginosa(i) the first enzyme identified in the outer membrane and (ii) the first example of a type IV secretion mechanism.

scholarly journals Human cardiac troponin I: precise identification of antigenic epitopes and prediction of secondary structure

1998 ◽  
Vol 44 (3) ◽  
pp. 487-493 ◽  
Author(s):  
Gaelle Ferrieres ◽  
Charles Calzolari ◽  
Jean-Claude Mani ◽  
Daniel Laune ◽  
Sylvie Trinquier ◽  
...  
Keyword(s):  
Myocardial Infarction ◽  
Monoclonal Antibodies ◽  
Amino Acid ◽  
Secondary Structure ◽  
Amino Acid Sequence ◽  
Cardiac Troponin ◽  
Troponin I ◽  
Cardiac Troponin I ◽  
Peptide Epitope ◽  
Antigenic Properties

Abstract The presence of human cardiac troponin I (hcTnI) in serum is considered to be a highly specific biochemical marker of acute myocardial infarction. To better understand the antigenic properties of hcTnI, a set of 68 overlapping peptides covering the complete amino acid sequence of hcTnI was prepared and used in epitope mapping experiments. All 16 anti-hcTnI monoclonal antibodies tested were found to recognize a peptide epitope, indicating that recognition by anti-hcTnI monoclonal antibodies was not dependent on the tertiary structure of the protein. Furthermore, the peptide reactivity with anti-hcTnI polyclonal antibodies indicated that most of the sequence of the protein was antigenic; in particular, the N- and C-terminal extremities were found to be the strongest antigenic regions. By using accurate secondary structure prediction methods, hcTnI was found to be an all-alpha type protein, with five regions predicted as helices. Matching the results of the epitope analysis with the structural prediction led us to the view that hcTnI is not a globular protein but probably adopts an extended conformation, allowing a large part of the amino acid sequence of this molecule to be recognized by the immune system. This improved knowledge of the antigenic and structural properties of hcTnI may help in developing new antibodies and immunoassays for use in diagnosing myocardial infarction.

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