Protein Sequence and Structure of N-terminal Amino Acids of Subunit Delta of Spinach Photosynthetic ATP-Synthase CF1

1987 ◽  
Vol 42 (11-12) ◽  
pp. 1231-1238 ◽  
Author(s):  
Richard J. Berzborn ◽  
Werner Finke ◽  
Joachim Otto ◽  
Helmut E . Meyer
Keyword(s):  
Secondary Structure ◽  
Atp Synthase ◽  
Protein Sequence ◽  
Alpha Helix ◽  
Amino Acid Residues ◽  
E Coli ◽  
Helical Wheel ◽  
Terminal Amino ◽  
Amphipathic Alpha Helix ◽  
Structure Calculations

Chloroplast ATP-synthase (CF1) subunit delta (δ) has been isolated from spinach thylakoids in the presence of SDS. By automated Edman degradation and online analysis of PTH derivatives the 35 N-terminal amino acid residues were sequenced. The mature protein starts with: NH2-Val-Asp-Ser-Thr-Ala-Ser-Arg-Tyr-Ala-. This protein sequence allows alignment of spinach δ with the sequences of Z. mays 25 kDa polypeptide, the δ subunit of Rps. blastica, Rsp. rubrum and E. coli F1, and of bovine OSCP, but not with mitochondrial δ. Secondary structure calculations and helical wheel plots reveal a conserved secondary structure. The analyzed N-terminal sequences probably build a short amphipathic alpha helix with two adjacent turns. The such aligned polar residues around Tyr8 of subunit δ are suitable to channel protons.

In Silico Study of Secondary Structure of Hemoglobin Protein

2021 ◽  
pp. 6245-6249
Author(s):  
Roma Chandra
Keyword(s):  
Secondary Structure ◽  
Protein Sequence ◽  
Structure Prediction ◽  
Tertiary Structure ◽  
Secondary Structure Prediction ◽  
Three Dimensional ◽  
Protein Secondary Structure ◽  
Alpha Helix ◽  
Prediction Methods ◽  
Protein Secondary Structures

Protein structure prediction is one of the important goals in the area of bioinformatics and biotechnology. Prediction methods include structure prediction of both secondary and tertiary structures of protein. Protein secondary structure prediction infers knowledge related to presence of helixes, sheets and coils in a polypeptide chain whereas protein tertiary structure prediction infers knowledge related to three dimensional structures of proteins. Protein secondary structures represent the possible motifs or regular expressions represented as patterns that are predicted from primary protein sequence in the form of alpha helix, betastr and and coils. The secondary structure prediction is useful as it infers information related to the structure and function of unknown protein sequence. There are various secondary structure prediction methods used to predict about helixes, sheets and coils. Based on these methods there are various prediction tools under study. This study includes prediction of hemoglobin using various tools. The results produced inferred knowledge with reference to percentage of amino acids participating to produce helices, sheets and coils. PHD and DSC produced the best of the results out of all the tools used.

scholarly journals DNA sequence of a gene cluster coding for subunits of the F0 membrane sector of ATP synthase in Rhodospirillum rubrum. Support for modular evolution of the F1 and F0 sectors

1988 ◽  
Vol 254 (1) ◽  
pp. 109-122 ◽  
Author(s):  
G Falk ◽  
J E Walker
Keyword(s):  
Gene Cluster ◽  
Atp Synthase ◽  
Rhodospirillum Rubrum ◽  
Gene Arrangement ◽  
Amino Acid Residues ◽  
Stem Loop ◽  
Transcription Terminator ◽  
E Coli ◽  
Modular Evolution ◽  
Genes Encoding

A region was cloned from the genome of the purple non-sulphur photobacterium Rhodospirillum rubrum that contains genes coding for the membrane protein subunits of the F0 sector of ATP synthase. The clone was identified by hybridization with a synthetic oligonucleotide designed on the basis of the known protein sequence of the dicyclohexylcarbodi-imide-reactive proteolipid, or subunit c. The complete nucleotide sequence of 4240 bp of this region was determined. It is separate from an operon described previously that encodes the five subunits of the extrinsic membrane sector of the enzyme, F1-ATPase. It contains a cluster of structural genes encoding homologues of all three membrane subunits a, b and c of the Escherichia coli ATP synthase. The order of the genes in Rsp. rubrum is a-c-b'-b where b and b' are homologues. A similar gene arrangement for F0 subunits has been found in two cyanobacteria, Synechococcus 6301 and Synechococcus 6716. This suggests that the ATP synthase complexes of all these photosynthetic bacteria contain nine different polypeptides rather than eight found in the E. coli enzyme; the chloroplast ATP synthase complex is probably similar to the photosynthetic bacterial enzymes in this respect. The Rsp. rubrum b subunit is modified after translation. As shown by N-terminal sequencing of the protein, the first seven amino acid residues are removed before or during assembly of the ATP synthase complex. The subunit-a gene is preceded by a gene coding for a small hydrophobic protein, as has been observed previously in the atp operons in E. coli, bacterium PS3 and cyanobacteria. A number of features suggest that the Rsp. rubrum cluster of F0 genes is an operon. On its 5′ side are found sequences resembling the -10 (Pribnow) and -35 boxes of E. coli promoters, and the gene cluster is followed by a sequence potentially able to form a stable stem-loop structure, suggesting that it acts as a rho-independent transcription terminator. These features and the small intergenic non-coding sequences suggest that the genes are cotranscribed, and so the name atp2 is proposed for this second operon coding for ATP synthase subunits in Rsp. rubrum. The finding that genes for the F0 and F1 sectors of the enzyme are in separate clusters supports the view that these represent evolutionary modules.

scholarly journals Circular-dichroic properties and secondary structure of Pseudomonas aeruginosa soluble cytochrome c oxidase

1984 ◽  
Vol 218 (3) ◽  
pp. 907-912 ◽  
Author(s):  
M G Tordi ◽  
M C Silvestrini ◽  
A Colosimo ◽  
S Provencher ◽  
M Brunori
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Secondary Structure ◽  
Cytochrome C ◽  
Cytochrome C Oxidase ◽  
Visible Region ◽  
Alpha Helix ◽  
Careful Analysis ◽  
Amino Acid Residues ◽  
Ferrocytochrome C ◽  
Significant Difference

The c.d. spectra of Pseudomonas aeruginosa cytochrome c oxidase in the oxidized state and the reduced state are reported in the visible- and u.v. absorption regions. In the visible region the comparison between the spectra of reduced cytochrome c oxidase and ferrocytochrome c-551 allows the identification of the c.d. bands mainly due to the d1 haem chromophore in cytochrome c oxidase. In the near-u.v. region the assignment of some of the observed peaks to the haem groups and to the aromatic amino acid residues is proposed. A careful analysis of the data in the far-u.v. region leads to the determination of the relative amounts of alpha-helix and beta-sheet in the enzyme, giving for the first time a picture of its secondary structure. A significant difference in this respect between the reduced and the oxidized species is observed and discussed in the light of similar conclusions reported by other workers.

Kynurenine aminotransferase and glutamine transaminase K of Escherichia coli: identity with aspartate aminotransferase

2001 ◽  
Vol 360 (3) ◽  
pp. 617-623 ◽  
Author(s):  
Qian HAN ◽  
Jianmin FANG ◽  
Jianyong LI
Keyword(s):  
Escherichia Coli ◽  
Amino Acid ◽  
Aspartate Aminotransferase ◽  
Expression System ◽  
Xanthurenic Acid ◽  
Amino Acid Residues ◽  
Terminal Amino Acid ◽  
Kynurenine Aminotransferase ◽  
E Coli ◽  
Terminal Amino

The present study describes the isolation of a protein from Escherichia coli possessing kynurenine aminotransferase (KAT) activity and its identification as aspartate aminotransferase (AspAT). KAT catalyses the transamination of kynurenine and 3-hydroxykynurenine to kynurenic acid and xanthurenic acid respectively, and the enzyme activity can be easily detected in E. coli cells. Separation of the E. coli protein possessing KAT activity through various chromatographic steps led to the isolation of the enzyme. N-terminal sequencing of the purified protein determined its first 10 N-terminal amino acid residues, which were identical with those of the E. coli AspAT. Recombinant AspAT (R-AspAT), homologously expressed in an E. coli/pET22b expression system, was capable of catalysing the transamination of both l-kynurenine (Km = 3mM; Vmax = 7.9μmol·min−1·mg−1) and 3-hydroxy-dl-kynurenine (Km = 3.7mM; Vmax = 1.25μmol·min−1·mg−1) in the presence of pyruvate as an amino acceptor, and exhibited its maximum activity at temperatures between 50–60°C and at a pH of approx. 7.0. Like mammalian KATs, R-AspAT also displayed high glutamine transaminase K activity when l-phenylalanine was used as an amino donor (Km = 8mM; Vmax = 20.6μmol·min−1·mg−1). The exact match of the first ten N-terminal amino acid residues of the KAT-active protein with that of AspAT, in conjunction with the high KAT activity of R-AspAT, provides convincing evidence that the identity of the E. coli protein is AspAT.

scholarly journals The ε-subunit of ATP synthase from bovine heart mitochondria. Complementary DNA sequence, expression in bovine tissues and evidence of homologous sequences in man and rat

1990 ◽  
Vol 265 (2) ◽  
pp. 321-326 ◽  
Author(s):  
O Viñas ◽  
S J Powell ◽  
M J Runswick ◽  
V Iacobazzi ◽  
J E Walker
Keyword(s):  
Dna Sequence ◽  
Atp Synthase ◽  
Protein Sequence ◽  
Nuclear Gene ◽  
Heart Mitochondria ◽  
Amino Acid Residues ◽  
Hybridization Probe ◽  
Related Sequence ◽  
Epsilon Subunit ◽  
Bovine Heart

The epsilon-subunit of ATP synthase from bovine heart mitochondria is assembled into the extrinsic membrane sector, F1-ATPase. The mature protein is 50 amino acid residues in length and its function is unknown. It is a nuclear gene product that is imported into the organelle. A mixture of 64 oligonucleotides 17 bases long, designed on the basis of the known protein sequence, was synthesized and used as a hybridization probe to isolate a cognate cDNA clone from a bovine library. The DNA sequence of this clone was determined, and the protein sequence of the epsilon-subunit deduced from it agrees exactly with that determined by direct sequence analysis of the protein isolated from bovine hearts. The bovine cDNA was used as a hybridization probe to examine the expression of the epsilon-subunit in various bovine tissues. mRNAs related to the cDNA are found in all of these tissues, and no evidence was obtained of the presence of mRNAs for the epsilon-subunit with similar coding sequences and dissimilar 3′ non-coding regions. By hybridization experiments with digests of DNA from cow, man and rat it has been shown that sequences related to the bovine cDNA are present in the genomes of all three species. More than one related sequence was detected in all cases, indicating the presence in all three genomes of more than one gene and/or pseudogenes.

scholarly journals The 20 C-terminal Amino Acid Residues of the Chloroplast ATP Synthase γ Subunit Are Not Essential for Activity

1999 ◽  
Vol 274 (20) ◽  
pp. 13824-13829 ◽  
Author(s):  
Maxim Sokolov ◽  
Lu Lu ◽  
Ward Tucker ◽  
Fei Gao ◽  
Peter A. Gegenheimer ◽  
...  
Keyword(s):  
Amino Acid ◽  
Atp Synthase ◽  
Amino Acid Residues ◽  
Terminal Amino Acid ◽  
Chloroplast Atp Synthase ◽  
Γ Subunit ◽  
Terminal Amino

Helixvis: Visualize α-Helical Peptides in Python

2020 ◽  
Author(s):  
Vigneshwar Subramanian ◽  
Raoul Wadhwa ◽  
Regina Stevens-Truss
Keyword(s):  
Secondary Structure ◽  
Three Dimensional ◽  
Alpha Helix ◽  
Two Dimensional ◽  
Web Servers ◽  
Helical Peptides ◽  
Three Dimensional Objects ◽  
Helical Wheel ◽  
Graphical Interfaces

Representing three-dimensional objects on a two-dimensional screen or sheet of paper can be challenging. To address this issue in the context of oligopeptide alpha-helical secondary structure, the helical wheel and wenxiang diagram visualizations have been developed. Although there exist graphical interfaces and web servers that generate these visualizations, a Python implementation has not yet been popularized. Here, we introduce the Python helixvis package, a companion to the R helixvis package, as a programmatic implementation of alpha helix visualization. All the code and output in this report is fully reproducible and available at https://github.com/subramv/ helixvis.<br>

Helixvis: Visualize α-Helical Peptides in Python

2020 ◽  
Author(s):  
Vigneshwar Subramanian ◽  
Raoul Wadhwa ◽  
Regina Stevens-Truss
Keyword(s):  
Secondary Structure ◽  
Three Dimensional ◽  
Alpha Helix ◽  
Two Dimensional ◽  
Web Servers ◽  
Helical Peptides ◽  
Three Dimensional Objects ◽  
Helical Wheel ◽  
Graphical Interfaces

Representing three-dimensional objects on a two-dimensional screen or sheet of paper can be challenging. To address this issue in the context of oligopeptide alpha-helical secondary structure, the helical wheel and wenxiang diagram visualizations have been developed. Although there exist graphical interfaces and web servers that generate these visualizations, a Python implementation has not yet been popularized. Here, we introduce the Python helixvis package, a companion to the R helixvis package, as a programmatic implementation of alpha helix visualization. All the code and output in this report is fully reproducible and available at https://github.com/subramv/ helixvis.<br>

scholarly journals Cystatin. Amino acid sequence and possible secondary structure

1984 ◽  
Vol 217 (3) ◽  
pp. 813-817 ◽  
Author(s):  
C Schwabe ◽  
A Anastasi ◽  
H Crow ◽  
J K McDonald ◽  
A J Barrett
Keyword(s):  
Amino Acid ◽  
Secondary Structure ◽  
Amino Acid Sequence ◽  
Tight Binding ◽  
Alpha Helix ◽  
Egg White ◽  
Striking Similarity ◽  
Cysteine Proteinases ◽  
Amino Acid Residues ◽  
Beta Structure

The amino acid sequence of cystatin, the protein from chicken egg-white that is a tight-binding inhibitor of many cysteine proteinases, is reported. Cystatin is composed of 116 amino acid residues, and the Mr is calculated to be 13 143. No striking similarity to any other known sequence has been detected. The results of computer analysis of the sequence and c.d. spectrometry indicate that the secondary structure includes relatively little alpha-helix (about 20%) and that the remainder is mainly beta-structure.

scholarly journals Secondary Structure Preferences of Mn2+ Binding Sites in Bacterial Proteins

2014 ◽  
Vol 2014 ◽  
pp. 1-14 ◽  
Author(s):  
Tatyana Aleksandrovna Khrustaleva
Keyword(s):  
Amino Acid ◽  
Secondary Structure ◽  
Glutamic Acid ◽  
Gc Content ◽  
Alpha Helix ◽  
Random Coil ◽  
Amino Acid Residues ◽  
Alpha Helices ◽  
Beta Strand ◽  
Genomic Gc Content

3D structures of proteins with coordinated Mn2+ ions from bacteria with low, average, and high genomic GC-content have been analyzed (149 PDB files were used). Major Mn2+ binders are aspartic acid (6.82% of Asp residues), histidine (14.76% of His residues), and glutamic acid (3.51% of Glu residues). We found out that the motif of secondary structure “beta strand-major binder-random coil” is overrepresented around all the three major Mn2+ binders. That motif may be followed by either alpha helix or beta strand. Beta strands near Mn2+ binding residues should be stable because they are enriched by such beta formers as valine and isoleucine, as well as by specific combinations of hydrophobic and hydrophilic amino acid residues characteristic to beta sheet. In the group of proteins from GC-rich bacteria glutamic acid residues situated in alpha helices frequently coordinate Mn2+ ions, probably, because of the decrease of Lys usage under the influence of mutational GC-pressure. On the other hand, the percentage of Mn2+ sites with at least one amino acid in the “beta strand-major binder-random coil” motif of secondary structure (77.88%) does not depend on genomic GC-content.

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