scholarly journals The distribution of physical, chemical and conformational properties in signal and nascent peptides

1990 ◽  
Vol 269 (3) ◽  
pp. 691-696 ◽  
Author(s):  
M Prabhakaran
Keyword(s):  
Amino Acid ◽  
Sequence Data ◽  
Graphical Analysis ◽  
Amino Acid Sequences ◽  
Signal Peptides ◽  
Hydrophobic Core ◽  
Amino Acid Residues ◽  
Conformational Properties ◽  
The Individual ◽  
Translocated Proteins

Signal peptides play a major role in an as-yet-undefined way in the translocation of proteins across membranes. The sequential arrangement of the chemical, physical and conformational properties of the signal and nascent amino acid sequences of the translocated proteins has been compiled and analysed in the present study. The sequence data of 126 signal peptides of length between 18 and 21 residues form the basis of this study. The statistical distribution of the following properties was studied hydrophobicity, Mr, bulkiness, chromatographic index and preference for adopting alpha-helical, β-sheet and turn structures. The contribution of each property to the sequence arrangement was derived. A hydrophobic core sequence was found in all signal peptides investigated. The structural arrangement of the cleavage site was also clearly revealed by this study. Most of the physical properties of the individual sequences correlated (correlation coefficient approximately 0.4) very well with the average distribution. The preferred occupancy of amino acid residues in the signal and nascent sequences was also calculated and correlated with their property distribution. The periodic behaviour of the signal and nascent chains was revealed by calculating their hydrophobic moments for various repetitive conformations. A graphical analysis of average hydrophobic moments versus average hydrophobicity of peptides revealed the transmembrane characteristics of signal peptides and globular characteristics of the nascent peptides.

scholarly journals SignalP 6.0 predicts all five types of signal peptides using protein language models

2022 ◽  
Author(s):  
Felix Teufel ◽  
José Juan Almagro Armenteros ◽  
Alexander Rosenberg Johansen ◽  
Magnús Halldór Gíslason ◽  
Silas Irby Pihl ◽  
...  
Keyword(s):  
Machine Learning ◽  
Amino Acid ◽  
Sequence Data ◽  
Amino Acid Sequences ◽  
Language Models ◽  
Metagenomic Data ◽  
Signal Peptides ◽  
Machine Learning Model ◽  
Living Organisms ◽  
Control Protein

AbstractSignal peptides (SPs) are short amino acid sequences that control protein secretion and translocation in all living organisms. SPs can be predicted from sequence data, but existing algorithms are unable to detect all known types of SPs. We introduce SignalP 6.0, a machine learning model that detects all five SP types and is applicable to metagenomic data.

scholarly journals Completion of the amino acid sequences of the A and B chains of subcomponent C1q of the first component of human complement

1982 ◽  
Vol 203 (3) ◽  
pp. 559-569 ◽  
Author(s):  
K B M Reid ◽  
J Gagnon ◽  
J Frampton
Keyword(s):  
Amino Acid ◽  
Structure Prediction ◽  
Sequence Data ◽  
Helical Structure ◽  
Amino Acid Sequences ◽  
Amino Acid Residues ◽  
Human Complement ◽  
Major Site ◽  
A Chain ◽  
Asparagine Residue

The sequences of amino acid residues 109-224 of the A chain, and residues 109-22 of the B chain, of human subcomponent C1q are given. These results, along with previously published sequence data on the N-terminal, collagen-like, regions of the A and B chains [Reid (1979) Biochem. J. 179, 367-371] yield the complete amino acid sequences of the A and B chains of subcomponent C1q. The asparagine residue at position A-124 has been identified as the major site of asparagine-linked carbohydrate in subcomponent C1q. When the sequences of the C-terminal, 135-residue-long, ‘globular’ regions of A and B chains are compared they show 40% homology. The degree of homology over certain stretches of 15-20 residues, within the C-terminal regions, rises up to values of 73%, indicating the presence of strongly conserved structures. Structure prediction studies indicate that both the A and B chain C-terminal regions may adopt a predominantly beta-type structure with apparently little alpha-helical structure.

scholarly journals Genomic organization of three novel toxins from the scorpion Buthus martensi Karsch that are active on potassium channels

2000 ◽  
Vol 346 (3) ◽  
pp. 805-809 ◽  
Author(s):  
Li DAI ◽  
Jing-Jiang WU ◽  
Yi-Hua GU ◽  
Zheng-Dao LAN ◽  
Min-Hua LING ◽  
...  
Keyword(s):  
Amino Acid ◽  
Genomic Dna ◽  
Amino Acid Sequences ◽  
Signal Peptides ◽  
Amino Acid Residues ◽  
Specific Primers ◽  
Cdna Sequences ◽  
C Terminus ◽  
Partial Cdna ◽  
Rapid Amplification

The cDNA and genomic DNA of three novel toxins from the scorpion Buthus martensi Karsch that are active on K+ channels, designated BmKTX (where KTX is kaliotoxin), BmTX1 and BmTX2, were cloned and sequenced. On the basis of their known amino acid sequences, gene-specific primers for 3ʹ and 5ʹ rapid amplification of cDNA ends (RACE) were designed and synthesized. By overlapping the two partial cDNA sequences obtained by 3ʹ and 5ʹ RACE, their full-length cDNA sequences were completed. BmKTX encodes a signal peptide of 22 amino acid residues and a mature toxin of 38 residues, whereas BmTX1 and BmTX2 encode signal peptides of 20 and 21 residues respectively and a mature toxin of 38 residues for each. Their cDNA-deduced amino acid sequences were totally consistent with those determined except that the C-terminus of BmKTX had an additional Gly residue, which was removed during post-translational processing and was indispensable for the amidation of its C-terminal Lys residue. In addition, the first deduced amino acid for both BmTX1 and BmTX2 is Gln instead of pyro-Glu in the reported toxins, which obviously also undergoes post-translational processing. The genomic DNA species of these three toxins were also amplified by PCR, then cloned and sequenced. They all consisted of two exons disrupted by a small single intron. All of these introns were inserted within the signal peptides at position -6 for BmKTX and at position -5 for both BmTX1 and BmTX2 upstream of the mature toxins, and consisted of 87, 87 and 80 bp respectively.

scholarly journals Complete amino acid sequences of the three collagen-like regions present in subcomponent C1q of the first component of human complement

1979 ◽  
Vol 179 (2) ◽  
pp. 367-371 ◽  
Author(s):  
K B M Reid
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Sequence Data ◽  
Amino Acid Sequences ◽  
Amino Acid Residues ◽  
Human Complement ◽  
Threonine Residue ◽  
A Chain

The sequences of amino acid residues 38–51 of the A-chain, and residues 42–90 of the C-chain, of human subcomponent C1q are given. These results, along with previously published sequence data [Reid (1974) Biochem.J. 141, 189–203; Reid (1977) Biochem.J. 161, 247–251; Reid & Thompson (1978) Biochem.J. 173, 863–868] allow the presentation, and comparison with each other, of the complete amino acid sequences of the collagen-like regions found in the A-, B- and C-chains of human subcomponent C1q. Each chain has the continuity of its collagen-like Gly-X-Y repeating triplet amino acid sequence broken. The B- and C-chains have alanine residues at positions B-9 and C-36 where glycine might be expected. The A-chain has a threonine residue at position A-39, which is located between two Gly-X-Y triplets.

scholarly journals Primary structures of seven metallothioneins from rabbit tissue

1995 ◽  
Vol 306 (1) ◽  
pp. 265-270 ◽  
Author(s):  
P E Hunziker ◽  
P Kaur ◽  
M Wan ◽  
A Känzig
Keyword(s):  
Amino Acid ◽  
Structural Characteristics ◽  
Structural Features ◽  
Amino Acid Sequences ◽  
Rabbit Kidney ◽  
Amino Acid Residues ◽  
Liver And Kidney ◽  
A Chain ◽  
The Stability ◽  
The Individual

Metallothionein from tissues of rabbits exposed to cadmium chloride was separated into seven distinct isoforms by reverse-phase liquid chromatography and their complete amino acid sequences were determined. Five of the seven isometallothioneins showed structural features so far not identified in other mammalian metallothioneins. Thus, two isoproteins contain a polypeptide with a chain length of 62 rather than 61 amino acid residues. Two isoforms are characterized by an additional positive charge and one by the presence of an isopeptide bond between aspartic acid and serine in the N-terminal half of the protein. The isoproteins characterized were identified from different sources: rabbit liver and kidney and a rabbit kidney cell-line (RK-13). In all three, the structural characteristics of the individual isoforms are retained, indicating that in the different tissues the same mechanisms control the synthesis and the stability of the different cadmium-induced isoMTs.

scholarly journals NH2-terminal amino acid sequences of precursor and mature forms of the ribulose-1,5-bisphosphate carboxylase small subunit from Chlamydomonas reinhardtii.

1979 ◽  
Vol 83 (3) ◽  
pp. 615-622 ◽  
Author(s):  
G W Schmidt ◽  
A Devillers-Thiery ◽  
H Desruisseaux ◽  
G Blobel ◽  
N H Chua
Keyword(s):  
Amino Acid ◽  
Chlamydomonas Reinhardtii ◽  
Sequence Data ◽  
Cell Extract ◽  
Small Subunit ◽  
Major Product ◽  
Amino Acid Sequences ◽  
Amino Acid Residues ◽  
Bisphosphate Carboxylase

A precursor (pS) to the small subunit (S) of ribulose1-,5-bisphosphate carboxylase is the major product of cell-free protein synthesis directed by poly(A) containing RNA from Chlamydomonas reinhardtii. We present sequence data for in vitro-synthesized pS, for in vitro-synthesized S that in generated from pS by posttranslational incubation with a Chlamydomonas cell extract, and for in vitro-synthesized, mature S. We show that pS contains an NH2-terminal extension of 44 amino acid residues that is removed by cleavage at the correct site when pS is converted to S by an endoprotease present in the Chlamydomonas cell extract.

Computational Analysis of Therapeutic Enzyme Uricase from Different Source Organisms

2020 ◽  
Vol 17 (1) ◽  
pp. 59-77
Author(s):  
Anand Kumar Nelapati ◽  
JagadeeshBabu PonnanEttiyappan
Keyword(s):  
Uric Acid ◽  
Amino Acid ◽  
Sequence Alignment ◽  
Multiple Sequence Alignment ◽  
Protein Sequences ◽  
Amino Acid Sequences ◽  
Amino Acid Residues ◽  
Multiple Sequence ◽  
Physiochemical Properties ◽  
Pharmaceutical Industries

Background:Hyperuricemia and gout are the conditions, which is a response of accumulation of uric acid in the blood and urine. Uric acid is the product of purine metabolic pathway in humans. Uricase is a therapeutic enzyme that can enzymatically reduces the concentration of uric acid in serum and urine into more a soluble allantoin. Uricases are widely available in several sources like bacteria, fungi, yeast, plants and animals.Objective:The present study is aimed at elucidating the structure and physiochemical properties of uricase by insilico analysis.Methods:A total number of sixty amino acid sequences of uricase belongs to different sources were obtained from NCBI and different analysis like Multiple Sequence Alignment (MSA), homology search, phylogenetic relation, motif search, domain architecture and physiochemical properties including pI, EC, Ai, Ii, and were performed.Results:Multiple sequence alignment of all the selected protein sequences has exhibited distinct difference between bacterial, fungal, plant and animal sources based on the position-specific existence of conserved amino acid residues. The maximum homology of all the selected protein sequences is between 51-388. In singular category, homology is between 16-337 for bacterial uricase, 14-339 for fungal uricase, 12-317 for plants uricase, and 37-361 for animals uricase. The phylogenetic tree constructed based on the amino acid sequences disclosed clusters indicating that uricase is from different source. The physiochemical features revealed that the uricase amino acid residues are in between 300- 338 with a molecular weight as 33-39kDa and theoretical pI ranging from 4.95-8.88. The amino acid composition results showed that valine amino acid has a high average frequency of 8.79 percentage compared to different amino acids in all analyzed species.Conclusion:In the area of bioinformatics field, this work might be informative and a stepping-stone to other researchers to get an idea about the physicochemical features, evolutionary history and structural motifs of uricase that can be widely used in biotechnological and pharmaceutical industries. Therefore, the proposed in silico analysis can be considered for protein engineering work, as well as for gout therapy.

scholarly journals Bile-pigment formation from different leghaemoglobins. Methine-bridge specificity of coupled oxidation

1978 ◽  
Vol 176 (2) ◽  
pp. 359-364 ◽  
Author(s):  
Päivi Lehtovaara ◽  
Ulla Perttilä
Keyword(s):  
Amino Acid ◽  
Polypeptide Chain ◽  
Broad Bean ◽  
Amino Acid Sequences ◽  
Second Step ◽  
Bile Pigment ◽  
Site Specificity ◽  
Amino Acid Residues ◽  
Reaction Step ◽  
Pigment Formation

The coupled oxidation of leghaemoglobins with O2 and ascorbate yielded oxyleghaemoglobin in the first reaction step, and the second step was the degradation of haem characterized by an A675 increase. Leghaemoglobins were degraded to biliverdin isomers specifically, depending on the structure of the protein. The main leghaemoglobin components of Glycine (soya bean) and Phaseolus (kidney bean) were degraded to biliverdin mixtures containing about 50% of the β-form, about 30% of the α-form and about 20% of the δ-isomer, whereas the leghaemoglobin I components of Vicia (broad bean) and Pisum (pea) were degraded almost exclusively to the β-isomer, with traces of the α-isomer. The amino acid sequences of Glycine and Phaseolus leghaemoglobins resemble each other, as do those of Vicia and Pisum. The site specificity of bile-pigment formation from leghaemoglobins can be tentatively explained by specific differences in the amino acid sequences at those regions of the polypeptide chain that are in the vicinity of the appropriate methine bridges. The ligand-binding site in different leghaemoglobins may be outlined on the basis of the present results, supposing that the haem is degraded when a reduction product of haem-bound O2 reacts with a methine bridge of the haem, and that the bridge specificity is regulated by hindering amino acid residues that determine the location of the bound O2. The residue phenylalanine-CD1 appears to be further away from the haem plane or in a markedly more flexible position in leghaemoglobins than in mammalian globins. The haem-bound oxygen atom B, in Fe–O(A)–O(B), seems to be free to rotate in all directions except that of the γ-bridge in Glycine and Phaseolus leghaemoglobins, but its position in Vicia and Pisum leghaemoglobin I might be restricted to the direction of the β-methine bridge.

scholarly journals Molecular cloning of two human liver 3 α-hydroxysteroid/dihydrodiol dehydrogenase isoenzymes that are identical with chlordecone reductase and bile-acid binder

1994 ◽  
Vol 299 (2) ◽  
pp. 545-552 ◽  
Author(s):  
Y Deyashiki ◽  
A Ogasawara ◽  
T Nakayama ◽  
M Nakanishi ◽  
Y Miyabe ◽  
...  
Keyword(s):  
Bile Acid ◽  
Amino Acid ◽  
Human Liver ◽  
Polyclonal Antibodies ◽  
Amino Acid Sequences ◽  
Cdna Clones ◽  
Amino Acid Residues ◽  
Human Bile ◽  
Coding Regions ◽  
Computer Based

Human liver contains two dihydrodiol dehydrogenases, DD2 and DD4, associated with 3 alpha-hydroxysteroid dehydrogenase activity. We have raised polyclonal antibodies that cross-reacted with the two enzymes and isolated two 1.2 kb cDNA clones (C9 and C11) for the two enzymes from a human liver cDNA library using the antibodies. The clones of C9 and C11 contained coding sequences corresponding to 306 and 321 amino acid residues respectively, but lacked 5′-coding regions around the initiation codon. Sequence analyses of several peptides obtained by enzymic and chemical cleavages of the two purified enzymes verified that the C9 and C11 clones encoded DD2 and DD4 respectively, and further indicated that the sequence of DD2 had at least additional 16 residues upward from the N-terminal sequence deduced from the cDNA. There was 82% amino acid sequence identity between the two enzymes, indicating that the enzymes are genetic isoenzymes. A computer-based comparison of the cDNAs of the isoenzymes with the DNA sequence database revealed that the nucleotide and amino acid sequences of DD2 and DD4 are virtually identical with those of human bile-acid binder and human chlordecone reductase cDNAs respectively.

scholarly journals The primary structure of aspartate aminotransferase from pig heart muscle. Partial sequences determined by digestion with thermolysin and elastase

1973 ◽  
Vol 133 (4) ◽  
pp. 805-819 ◽  
Author(s):  
Francesco Bossa ◽  
Donatella Barra ◽  
Massimo Carloni ◽  
Paolo Fasella ◽  
Francesca Riva ◽  
...  
Keyword(s):  
Amino Acid ◽  
Amino Acid Composition ◽  
Acid Composition ◽  
Primary Structure ◽  
Aspartate Aminotransferase ◽  
Heart Muscle ◽  
Science And Technology ◽  
Amino Acid Sequences ◽  
Amino Acid Residues ◽  
Lending Library

Peptides produced by thermolytic digestion of aminoethylated aspartate aminotransferase and of the oxidized enzyme were isolated and their amino acid sequences determined. Digestion by elastase of the carboxymethylated enzyme gave peptides representing approximately 40% of the primary structure. Fragments from these digests overlapped with previously reported sequences of peptides obtained by peptic and tryptic digestion (Doonan et al., 1972), giving ten composite peptides containing 395 amino acid residues. The amino acid composition of these composite peptides agrees well with that of the intact enzyme. Confirmatory results for some of the present data have been deposited as Supplementary Publication 50018 at the National Lending Library for Science and Technology, Boston Spa, Yorks. LS23 7BQ, U.K., from whom copies can be obtained on the terms indicated in Biochem. J. (1973) 131, 5.

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