scholarly journals The isolation, characterization and partial sequences of the chicken erythrocyte non-histone chromosomal proteins HMG14 and HMG17. Comparison with the homologous calf thymus proteins

1980 ◽  
Vol 185 (2) ◽  
pp. 383-386 ◽  
Author(s):  
J M Walker ◽  
E W Johns
Keyword(s):  
Amino Acid ◽  
Sequence Data ◽  
British Library ◽  
Chicken Erythrocyte ◽  
Terminal Sequence ◽  
Sequence Analyses ◽  
Chromosomal Proteins ◽  
Nucleosome Core ◽  
Calf Thymus ◽  
Core Histones

Non-histone chromosomal proteins HMG14 and HMG17 were isolated from chicken erythrocyte nuclei. The proteins were characterized by amino acid analysis and by N-terminal sequence analyses. Comparison with the corresponding data for the calf thymus proteins shows that 11% of the residues in HMG14 protein and 5% of the residues in HMG17 protein differ between the two species. Proteins HMG14 and HMG17 therefore do not appear to exhibit the evolutionary stability shown by the nucleosome core histones. Detailed evidence for the amino acid sequence data has been deposited as Supplementary Publication SUP 50101 (4 pages) at the British Library Lending Division, Boston Spa, Wetherby, West Yorkshire LS23 7BQ, U.K., from whom copies may be obtained on the terms given in Biochem. 4. (1978) 169, 5.

scholarly journals Studies on the primary structure of chicken erythrocyte histone fraction V

1971 ◽  
Vol 124 (2) ◽  
pp. 319-325 ◽  
Author(s):  
P. J. Greenaway
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Primary Structure ◽  
Sequence Data ◽  
Acid Extraction ◽  
Chicken Erythrocyte ◽  
Histone Fraction

Histone fraction V was prepared by selective acid extraction from chicken erythrocyte nuclei. Amino acid sequence studies on the tryptic and thermolytic peptides are reported. Only a limited amount of overlapping sequence data was obtained.

scholarly journals Sequence differences between histones of procyclic Trypanosoma brucei brucei and higher eukaryotes

Parasitology ◽  
1992 ◽  
Vol 105 (1) ◽  
pp. 97-104 ◽  
Author(s):  
K. Bender ◽  
B. Betschart ◽  
J. Schaller ◽  
U. Kämpfer ◽  
H. Hecker
Keyword(s):  
Amino Acid ◽  
Trypanosoma Brucei ◽  
Protozoan Parasite ◽  
Tetrahymena Pyriformis ◽  
Reversed Phase ◽  
Alternative Methods ◽  
Trypanosoma Brucei Brucei ◽  
Calf Thymus ◽  
Core Histones ◽  
Higher Eukaryotes

Four histones, a, b, c, d from procyclic Trypanosoma brucei brucei, which show similarities with the amino acid composition of the core histones H3, H2A, H2B and H4, were isolated and cleaved with Endoproteinase Glu-C. The fragments were separated by FPLC reversed phase chromatography and a subset of the fragments (a5, a9, b6, c8, d3, d9, d11) was subjected to sequence analysis. A 54–71% identity was found in the sequences of the fragment c8 and the C-terminal half of H2B and of three fragments of protein d covering the N-terminal half as well as the C-terminal region of H4. The amino acid sequence of the fragment a9 showed a 57 and 54% identity with H3 sequences of Saccharomyces cerevisiae and Xenopus laevis. Neither the a5 nor the b6 sequence could be aligned with histone sequences of other eukaryotes. The significant differences of 21–48% between the T. b. brucei, histone sequences and those of calf thymus histones, which are more pronounced than the differences of Tetrahymena pyriformis and the higher eukaryote, resulted partially from replacements of amino acids with different properties and indicate specific patterns of histone–histone and/or histone–DNA contact sites in the nucleosome of T. b. brucei. These differences, together with the lack of a functional histone H1, may be sufficient to explain the lack of a salt-dependent formation of the nucleosome filament into the 30 nm fibre, which reflects alternative methods of organizing and processing the genetic information in the nucleus of the protozoan parasite and which may be of chemotherapeutic significance.

scholarly journals Studies on the tissue specificity of the high-mobility-group non-histone chromosomal proteins from calf

1978 ◽  
Vol 173 (2) ◽  
pp. 497-505 ◽  
Author(s):  
A Rabbani ◽  
G H Goodwin ◽  
E W Johns
Keyword(s):  
Amino Acid ◽  
Gel Electrophoresis ◽  
Trichloroacetic Acid ◽  
Tissue Specificity ◽  
Polyacrylamide Gel Electrophoresis ◽  
High Mobility ◽  
Acid Precipitation ◽  
High Mobility Group ◽  
Chromosomal Proteins ◽  
Calf Thymus

The high-mobility-group (HMG) non-histone chromosomal proteins from calf thymus, liver, spleen and kidney were extracted, and fractionated by CM-Sephadex chromatography and trichloroacetic acid precipitation. The isolated proteins HMG 1, HMG 2 and HMG 17 from the tissues were compared by polyacrylamide-gel electrophoresis, isoelectric focusing and amino acid analysis. The results show that the three proteins are very similar in the tissues studied, implying a lack of tissue specificity.

Amino acid sequence of penicillopepsin. IV. Myxobacter AL-1 protease II and Staphylococcus aureus protease fragments and homology with pig pepsin and chymosin

1976 ◽  
Vol 54 (10) ◽  
pp. 902-914 ◽  
Author(s):  
Anne Cunningham ◽  
Hsin-Min Wang ◽  
Stephen R. Jones ◽  
Alexander Kurosky ◽  
Leticia Rao ◽  
...  
Keyword(s):  
Amino Acids ◽  
Staphylococcus Aureus ◽  
Amino Acid ◽  
Amino Acid Sequence ◽  
Sequence Data ◽  
Amino Acid Residues ◽  
Terminal Sequence ◽  
Fungal Enzyme ◽  
Fungal Protease ◽  
And Staphylococcus Aureus

The digest of penicillopepsin (EC 3.4.23.7) with protease II from Myxobacter AL-1 gave five fragments which were separated on a Biogel P-100 column in 70% formic acid. The fragments were from 16 to 125 amino acids long. Two fragments were also isolated from a digest with a protease from Staphylococcus aureus. The analysis of these fragments by automatic sequencer gave a number of overlaps of the chymotryptic and thermolytic peptides. The available amino acid sequence data for penicillopepsin described in this paper and the accompanying papers (Kurosky, A. &Hofmann, T.: Can. J. Biochem. 54, 872 (1976); Rao, L. &Hofmann, T.: Can. J. Biochem. 54, 885 (1976); Harris, C. I., Rao, L., Shutsa, P., Kurosky, A. &Hofmann, T.: Can. J. Biochem. 54, 895 (1976)) have been combined and yield 15 fragments which range in lengths from 3 to 112 amino acid residues. These unique fragments account for virtually all the amino acids of the fungal protease. Four of the fragments with a total of 194 residues (about 60% of the molecule) have been aligned with corresponding sections of pig pepsin (EC 3.4.23.1) and with part of the N-terminal sequence available for calf chymosin (EC 3.4.23.4). In the alignments about 37% of the residues in the fungal enzyme are identical with at least one of the mammalian enzymes. An additional 20% are chemically similar. These results, together with previously reported active-site directed modifications, show conclusively that penicillopepsin is an evolutionary homologue of the mammalian acid proteases.

THE HISTONES OF CHICKEN ERYTHROCYTE NUCLEI

1964 ◽  
Vol 42 (12) ◽  
pp. 1743-1752 ◽  
Author(s):  
J. M. Neelin ◽  
P. X. Callahan ◽  
D. C. Lamb ◽  
K. Murray
Keyword(s):  
Amino Acid ◽  
Amino Acid Content ◽  
Exchange Chromatography ◽  
Chicken Erythrocyte ◽  
Terminal Amino Acid ◽  
Electrophoretic Behavior ◽  
Calf Thymus ◽  
Somatic Tissues ◽  
Starch Gel ◽  
Terminal Amino

Five fractions of chicken erythrocyte histone have been obtained by ion-exchange chromatography, and compared with calf thymus histone fractions in amino acid composition, electrophoretic behavior in starch gel, N-terminal amino acid content, and fingerprint of tryptic peptides. A major erythrocyte histone fraction, rich in both lysine and arginine, as well as serine, was peculiar to these singular cells, and appeared to replace the "arginine-rich" histone of other somatic tissues. In contrast, the other four erythrocyte histone fractions were closely similar in kind to their chromatographic counterparts in calf tissues, despite some differences in number and yield. The occurrence of this unusual histone may be related to the limited biosynthetic capacities of these cells with highly differentiated nuclei.

scholarly journals Amino acid sequence of the Pronase-released heads of neuraminidase subtype N2 from the Asian strain A/Tokyo/3/67 of influenza virus

1982 ◽  
Vol 207 (1) ◽  
pp. 91-95 ◽  
Author(s):  
C W Ward ◽  
T C Elleman ◽  
A A Azad
Keyword(s):  
Influenza Virus ◽  
Amino Acid ◽  
Amino Acid Sequence ◽  
Sequence Data ◽  
British Library ◽  
Amino Acid Residues ◽  
Asian Strain ◽  
C Terminus ◽  
Glycosylation Sites ◽  
Neuraminidase Subtype

The amino acid sequence of the Pronase-released heads of neuraminidase subtype N2 from the A/Tokyo/3/67 strain of influenza virus was determined by a combination of peptide and nucleic acid sequence analysis. The results show that the Pronase-released heads contain 396 amino acid residues and extend from residue 74 in the original protein to the C-terminus at residue 469. The heads contain five potential glycosylation sites at asparagine residues 86, 146, 200, 234 and 402, but only the first four are glycosylated. The sequence homology with the corresponding region of the previously published sequence of the neuraminidase subtype N1 [Fields, Winter & Brownlee (1981) Nature (London) 290, 213-217] is 45%. Detailed evidence for the sequence data has been deposited as Supplementary Publication SUP 50116 (14 pages) at the British Library Lending Division, Boston Spa, Wetherby, West Yorkshire LS23 7BQ, U.K., from whom copies may be obtained on the terms given in Biochem. J. (1981) 193, 5.

scholarly journals Glutamine as a precursor to N-terminal pyrrolid-2-one-5-carboxylic acid in mouse immunoglobulin λ-type light chains. Amino acid-sequence variability at the N-terminal extra piece of λ-type light-chain precursors

1977 ◽  
Vol 165 (2) ◽  
pp. 347-354 ◽  
Author(s):  
Yigal Burstein ◽  
Israel Schechter
Keyword(s):  
Amino Acid ◽  
Carboxylic Acid ◽  
Amino Acid Sequence ◽  
Glutamic Acid ◽  
Sequence Data ◽  
Amino Acid Residues ◽  
Sequence Analyses ◽  
Methionine Residue ◽  
Mouse Immunoglobulin ◽  
V Region

The mRNA molecules coding for three mouse immunoglobulin λ-type light (L) chains (MOPC-104E λ1, RPC-20 λ1, MOPC-315 λ2) programme the cell-free synthesis of precursors larger than the mature proteins. Radioactive amino acid-sequence analyses of each of the three precursors labelled with [3H]alanine, [3H]serine, [3H]glutamine, [3H]glutamic acid and [3H]threonine showed that an extra piece, at least 18 residues long, is linked to the N-terminus of the mature L-chains. The N-terminal extra-peptide segment may be 19 residues long, since analyses of precursors labelled with [35S]methionine indicated an additional N-terminal methionine residue which was recovered in low yields. Presumably this is the initiator methionine, which is known to be short lived in eukaryotes. The mature forms of MOPC-104E, RPC-20 and MOPC-315 λ L-chains are blocked at the N-termini by pyrrolid-2-one-5-carboxylic acid (pyroglutamic acid). Sequence analyses of precursors labelled with [3H]glutamine and [3H]glutamic acid showed incorporation only of glutamine in a position that matches with the position of pyrrolid-2-one-5-carboxylic acid in the mature forms of all three precursors, and incorporation of glutamic acid in other positions. The data showed the absence of glutamine–glutamic acid interconversion, since the radioactive peaks obtained from either3H-labelled amino acid were discrete, and free from cross-contamination. These results prove that glutamine is the precursor amino acid of pyrrolid-2-one-5-carboxylic acid at the N-termini of the mature MOPC-104E λ1, RPC-20 λ1 and MOPC-315 λ2 L-chains. Thus the formation of pyrrolid-2-one-5-carboxylic acid by cyclization of glutamine is a post-translational event which occurs after, or concomitant with, cleavage of the extra piece from the precursor to yield the mature L-chain. The variable (V) regions (110 amino acid residues) of mouse λ L-chains are quite similar: when compared with that of MOPC-104E λ1 chain, the V-region of RPC-20 λ1 chain differs in one residue, and the V-region of MOPC-315 λ2 chain differs in 11 residues. The partial sequence data show that the N-terminal extra pieces of the two λ1 L-chain precursors have, so far, identical partial sequences; the extra piece of the λ2 L-chain precursor differs from these in at least three out of 19 positions.

PoGB-Pred: Prediction of Antifreeze Proteins Sequences using Amino Acid Composition with Feature Selection followed by a Sequential based Ensemble Approach

2020 ◽  
Vol 15 ◽  
Author(s):  
Affan Alim ◽  
Abdul Rafay ◽  
Imran Naseem
Keyword(s):  
Amino Acid ◽  
Dimension Reduction ◽  
Protein Identification ◽  
Cold Water ◽  
Genomic Sequence ◽  
Sequence Data ◽  
Antifreeze Proteins ◽  
Building Blocks ◽  
Gradient Boosting ◽  
Proposed Model

Background: Proteins contribute significantly in every task of cellular life. Their functions encompass the building and repairing of tissues in human bodies and other organisms. Hence they are the building blocks of bones, muscles, cartilage, skin, and blood. Similarly, antifreeze proteins are of prime significance for organisms that live in very cold areas. With the help of these proteins, the cold water organisms can survive below zero temperature and resist the water crystallization process which may cause the rupture in the internal cells and tissues. AFP’s have attracted attention and interest in food industries and cryopreservation. Objective: With the increase in the availability of genomic sequence data of protein, an automated and sophisticated tool for AFP recognition and identification is in dire need. The sequence and structures of AFP are highly distinct, therefore, most of the proposed methods fail to show promising results on different structures. A consolidated method is proposed to produce the competitive performance on highly distinct AFP structure. Methods: In this study, we propose to use machine learning-based algorithms Principal Component Analysis (PCA) followed by Gradient Boosting (GB) for antifreeze protein identification. To analyze the performance and validation of the proposed model, various combinations of two segments composition of amino acid and dipeptide are used. PCA, in particular, is proposed to dimension reduction and high variance retaining of data which is followed by an ensemble method named gradient boosting for modelling and classification. Results: The proposed method obtained the superfluous performance on PDB, Pfam and Uniprot dataset as compared with the RAFP-Pred method. In experiment-3, by utilizing only 150 PCA components a high accuracy of 89.63 was achieved which is superior to the 87.41 utilizing 300 significant features reported for the RAFP-Pred method. Experiment-2 is conducted using two different dataset such that non-AFP from the PISCES server and AFPs from Protein data bank. In this experiment-2, our proposed method attained high sensitivity of 79.16 which is 12.50 better than state-of-the-art the RAFP-pred method. Conclusion: AFPs have a common function with distinct structure. Therefore, the development of a single model for different sequences often fails to AFPs. A robust results have been shown by our proposed model on the diversity of training and testing dataset. The results of the proposed model outperformed compared to the previous AFPs prediction method such as RAFP-Pred. Our model consists of PCA for dimension reduction followed by gradient boosting for classification. Due to simplicity, scalability properties and high performance result our model can be easily extended for analyzing the proteomic and genomic dataset.

C-Terminal amino acid sequence of chicken pepsinogen and its homology with sequences of other acid proteases

1980 ◽  
Vol 45 (4) ◽  
pp. 1144-1154 ◽  
Author(s):  
Miroslav Baudyš ◽  
Helena Keilová ◽  
Vladimír Kostka
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
The Other ◽  
Terminal Sequence ◽  
Terminal Part ◽  
Terminal Amino Acid ◽  
Tryptic Peptides ◽  
Terminal Amino ◽  
High Degree ◽  
Terminal Amino Acid Sequence

To determine the primary structure of the C-terminal part of the molecule of chicken pepsinogen the tryptic, chymotryptic and thermolytic digest of the protein were investigated and peptides derived from this region were sought. These peptides permitted the following 21-residue C-terminal sequence to be determined: ...Ile-Arg-Glu-Tyr-Tyr-Val-Ile-Phe-Asp-Arg-Ala-Asn-Asn-Lys-Val-Gly-Leu-Ser-Pro-Leu-Ser.COOH. A comparison of this structure with the C-terminal sequential regions of the other acid proteases shows a high degree of homology between chicken pepsinogen and these proteases (e.g., the degree of homology with respect to hog pepsinogen and calf prochymosin is about 66%). Additional tryptic peptides, derived from the N-terminal part of the zymogen molecule whose amino acid sequence has been reported before, were also obtained in this study. This sequence was extended by two residues using an overlapping peptide. An ancillary result of this study was the isolation of tryptic peptides derived from other regions of the zymogen molecule.

scholarly journals Structural and dynamic mechanisms of CBF3-guided centromeric nucleosome formation

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Ruifang Guan ◽  
Tengfei Lian ◽  
Bing-Rui Zhou ◽  
Emily He ◽  
Carl Wu ◽  
...  
Keyword(s):  
Dna Sequence ◽  
Chromosome Segregation ◽  
Budding Yeast ◽  
Dna Conformation ◽  
Dependent Manner ◽  
Dynamic Interactions ◽  
Nucleosome Core ◽  
Dynamic Mechanisms ◽  
Nucleosome Formation ◽  
Core Histones

AbstractAccurate chromosome segregation relies on the specific centromeric nucleosome–kinetochore interface. In budding yeast, the centromere CBF3 complex guides the deposition of CENP-A, an H3 variant, to form the centromeric nucleosome in a DNA sequence-dependent manner. Here, we determine the structures of the centromeric nucleosome containing the native CEN3 DNA and the CBF3core bound to the canonical nucleosome containing an engineered CEN3 DNA. The centromeric nucleosome core structure contains 115 base pair DNA including a CCG motif. The CBF3core specifically recognizes the nucleosomal CCG motif through the Gal4 domain while allosterically altering the DNA conformation. Cryo-EM, modeling, and mutational studies reveal that the CBF3core forms dynamic interactions with core histones H2B and CENP-A in the CEN3 nucleosome. Our results provide insights into the structure of the budding yeast centromeric nucleosome and the mechanism of its assembly, which have implications for analogous processes of human centromeric nucleosome formation.

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