Data base for protein sequences

Dayhoff, M. O.; Barker, Winona C.; Schwartz, R. M.; Orcutt, Bruce C.; Hunt, Lois T.

doi:10.1145/1499799.1499841

Cited by 8 publications

(10 citation statements)

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“…The unusual sequence in CRP, -Tyr-Phe-Tyr-Thr-(residues 37-40) was not found in any of the protein sequences currently listed in ref. 22, but it appears in the partial sequence of "heavy chains" from the human histocompatibility antigens HLA-7,12 recently reported by Terhorst et al (23). This unexpected identity led us to compare the available sequence data for human and murine histocompatibility antigens (23)(24)(25)(26)(27)(28) with the data for CRP.…”

Section: Resultsmentioning

confidence: 87%

“…Rabbit CRP was isolated in a similar manner from acute phase serum of rabbits injected 2-3 days previously with croton oil (1%) in paraffin oil. Rabbit CRP is similar to human CRP in subunit molecular weight (22,900), amino-acid composition, and phosphocholine-binding specificity (10). CRP solutions were exhaustively dialyzed against water and lypphilized.…”

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

Partial amino-acid sequences of human and rabbit C-reactive proteins: homology with immunoglobulins and histocompatibility antigens.

Osmand

Gerwurz

Friedenson

1977

Proc. Natl. Acad. Sci. U.S.A.

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Partial amino-acid sequence analyses of the amino terminus of rabbit C-reactive protein and of a peptide isolated from human Greactive protein after cyanogen bromide cleavage show an extensive sequence homology between these proteins. Computer analysis detected a distant but significant homology between rabbit C-reactive protein and the CH3 domain of human IgG. In addition, an examination of the limited data available for the amino-acid sequences of human and mouse histocompatibility antigens revealed a similarity between these proteins and C-reactive protein and, therefore, immunoglobulins. These relationships are presented as evidence in support of the hypothesis that C-reactive protein and immunoglobulins share, in addition to functional similarities, a common evolutionary origin with the major histocompatibility antigens.C-reactive protein (CRP) is a distinctive trace constituent of normal serum that is elevated up to 1000-fold during acute inflammatory reactions. The determination of CRP levels has been widely accepted as a useful index of acute inflammation although the biological functions or raison d'etre of this protein remain obscure. CRP was initially defined by a unique, calcium-dependent precipitation reaction with the pneumococcal C-polysaccharide (1, 2). In addition, CRP is an agglutinin (3) and an opsonin (4), and, in the presence of a suitable ligand, CRP activates the complement system to cause depletion of complement component hemolytic activity (5-7) and promotion of complement-dependent opsonization (8) and hemolysis (9). This array of properties, reminiscent of specific antibody, has prompted us to postulate shared functions and a common evolutionary origin for CRP and immunoglobulins. We have undertaken to determine the primary structure of both rabbit and human CRP in order to test this hypothesis. We report here extensive NH2-terminal sequence analysis of rabbit CRP and the isolation and characterization of a homologous peptide from human CRP. Several computer-based analyses were performed to search for homology with immunoglobulin. Thus far, significant homology has only been detected between CRP and the CH3 domain of human IgGl. We also describe an apparent homology between CRP and the recently published sequences of human and murine histocompatibility antigen heavy (H) chains. Ipso facto, this has defined a region in the immunoglobulin domain that is homologous to the NH2-terminal region of these antigens. MATERIALS AND METHODSIsolation of C-Reactive Protein. Human CRP was purified from human serous fluids by affinity chromatography and gel filtration (5). The preparations used in this study were pure by immunoelectrophoresis and polyacrylamide gel electrophoresis (9). Rabbit CRP was isolated in a similar manner from acute phase serum of rabbits injected 2-3 days previously with croton oil (1%) in paraffin oil. Rabbit CRP is similar to human CRP in subunit molecular weight (22,900), amino-acid composition, and phosphocholine-binding specificity (10). CRP solutions were exhaus...

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Section: Resultsmentioning

confidence: 87%

Section: Methodsmentioning

confidence: 99%

Partial amino-acid sequences of human and rabbit C-reactive proteins: homology with immunoglobulins and histocompatibility antigens.

Osmand

Gerwurz

Friedenson

1977

Proc. Natl. Acad. Sci. U.S.A.

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“…This procedure does not lead to detection of any new homologs, suggesting that the improvement of the profile by adding designed sequences is not caused by an increase of the alignment size with similar conservation properties. In the second control test the added sequences are obtained by simulating the evolutionary process under the Dayhoff PAM1 model (20). In this model, a site is chosen randomly, and the substitution is made according to the PAM1 substitution probability matrix.…”

Section: Resultsmentioning

confidence: 99%

“…We study two evolutionary models. In the first model, we randomly select a position and attempted a substitution according to the Dayhoff PAM1 substitution probability matrix (20). Any attempted substitution is fixed.…”

Section: Model and Methodsmentioning

confidence: 99%

Using protein design for homology detection and active site searches

Pei

Dokholyan

Shakhnovich

et al. 2003

Proc. Natl. Acad. Sci. U.S.A.

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We describe a method of designing artificial sequences that resemble naturally occurring sequences in terms of their compatibility with a template structure and its functional constraints. The design procedure is a Monte Carlo simulation of amino acid substitution process. The selective fixation of substitutions is dictated by a simple scoring function derived from the template structure and a multiple alignment of its homologs. Designed sequences represent an enlargement of sequence space around native sequences. We show that the use of designed sequences improves the performance of profile-based homology detection. The difference in position-specific conservation between designed sequences and native sequences is helpful for prediction of functionally important residues. Our sequence selection criteria in evolutionary simulations introduce amino acid substitution rate variation among sites in a natural way, providing a better model to test phylogenetic methods. C omputational protein design aims to identify sequences compatible with a desired structure or fold (1-4). Most design methods involve detailed energy functions with explicit modeling of protein structure at the atomic level and apply effective search algorithms (5, 6). They facilitate understanding of the physical and chemical principles governing protein structure and folding (4). Protein design can also be used to probe the sequence space (7), which has been applied in fold recognition (8). This idea can be extended to profile-based similarity searches, which derive a scoring function based on a multiple sequence alignment. Designed sequences resembling naturally occurring sequences could potentially be used to improve sequence profile, leading to more powerful homology detection. Sequence design can also be used in studying protein function and evolution (9, 10), as it is often related to evolutionary simulations. It is generally assumed that amino acid changes follow a stochastic process over long periods of time, and the fixation of substitutions is under evolutionary pressure to preserve protein activity. Evolutionary simulations can be made more realistic if structural and functional constraints are taken into account in the substitution process.Knowledge-based approaches have been widely used to derive interaction potentials by statistical analysis of known protein structures (11,12). Such potentials are used in various sequence design methods as stability constraints. Functional information about a protein family is embedded in naturally occurring homologs as positional amino acid conservation. Sequence profile, such as the position-specific scoring matrix generated by PSI-BLAST (13), contains the positional conservation information. We attempt to introduce structural and functional constraints in sequence design by considering both pairwise interaction potentials and sequence conservation information.Recently, a simulation-based design method (Z-score model) was used to study the protein evolutionary process (10). Structurally similar sequen...

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“…In this figure not only identical amino acids but also structurally related amino acids that are ob- served to interchange frequently [55] …”

Section: Amino Acid Sequence Homology Among Pbps and B-lactamasesmentioning

confidence: 99%

Nucleotide sequence of the pbpA gene and characteristics of the deduced amino acid sequence of penicillin‐binding protein 2 of Escherichia coli K12

Asoh

Matsuzawa

Ishino

et al. 1986

European Journal of Biochemistry

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We have determined the nucleotide sequence of the pbpA gene encoding penicillin-binding protein (PBP) 2 of Escherichia coli. The coding region for PBP 2 was 1899 base pairs in length and was preceded by a possible promoter sequence and two open reading frames. The primary structure of PBP 2, deduced from the nucleotide sequence, comprised 633 amino acid residues. The relative molecular mass was calculated to be 70867. The deduced sequence agreed with the NH2-terminal sequence of PBP 2 purified from membranes, suggesting that PBP 2 has no signal peptide. The hydropathy profile suggested that the NH,-terminal hydrophobic region (a stretch of 25 non-ionic amino acids) may anchor PBP 2 in the cytoplasmic membrane as an ectoprotein. There were nine homologous segments in the amino acid sequence of PBP 2 when compared with PBP 3 of E. coli. The active-site serine residue of PBP 2 was predicted to be Ser-330. Around this putative active-site serine residue was found the conserved sequence of Ser-Xaa-Xaa-Lys, which has been identified in all of the other E. coli PBPs so far studied (PBPs lA, lB, 3, 5 and 6) and class A and class C B-lactamases. In the higher-molecular-mass PBPs 1 A, lB, 2 and 3, Ser-Xaa-Xaa-Lys-Pro was conserved. In the putative peptidoglycan transpeptidase domain there were six amino acid residues, which are common only in the PBPs of higher molecular mass.In Escherichia coli seven penicillin-binding proteins (PBPs) have been found in the cytoplasmic membrane [l -41. Among them, the higher-molecular-mass PBPs (PBP 1 A, PBP lB, PBP 2, and PBP 3 ) are important for completion of cell cycle of E. coli; PBP 1A and PBP 1 B are responsible for cell elongation [2, 3, 51, PBP 2 for the determination of rod shape of the cell [31,32], 3 [31, 331 and 5 [34] were obtained, and analyses of the peptides confirmed that the predicted active-site sequences were correct. The active-site serine regions of the higher-molecular-mass PBPs display a high sequence homology with each other [31].In this report we present the nucleotide sequence of the pbpA gene encoding PBP 2 of E. coli and the deduced amino acid sequence of this protein. These results prove the homology of the penicillin-binding sites of the higher-molecularmass PBPs of E. coli. Thus, the hypothesis of Tipper and Strominger [35] for the mechanism of the covalent binding of penicillin in all of the essential PBPs of E. coli has been verified.

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Data base for protein sequences

Cited by 8 publications

References 0 publications

Partial amino-acid sequences of human and rabbit C-reactive proteins: homology with immunoglobulins and histocompatibility antigens.

Partial amino-acid sequences of human and rabbit C-reactive proteins: homology with immunoglobulins and histocompatibility antigens.

Using protein design for homology detection and active site searches

Nucleotide sequence of the pbpA gene and characteristics of the deduced amino acid sequence of penicillin‐binding protein 2 of Escherichia coli K12

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