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 Three Structural Features of Functional Food Components and Herbal Medicine with Amyloid β42 Anti-Aggregation Properties

Molecules ◽  
2019 ◽  
Vol 24 (11) ◽  
pp. 2125 ◽  
Author(s):  
Kazuma Murakami ◽  
Kazuhiro Irie
Keyword(s):  
Amino Acid ◽  
Functional Food ◽  
Structural Characteristics ◽  
Salt Bridge ◽  
Basic Amino Acid ◽  
Structural Features ◽  
Amino Acid Residues ◽  
Treatment And Prevention ◽  
Food Components ◽  
Underlying Mechanisms

Aggregation of amyloid β42 (Aβ42) is one of the hallmarks of Alzheimer’s disease (AD). There are numerous naturally occurring products that suppress the aggregation of Aβ42, but the underlying mechanisms remain to be elucidated. Based on NMR and MS spectroscopic analysis, we propose three structural characteristics found in natural products required for the suppressive activity against Aβ42 aggregation (i.e., oligomerization by targeting specific amino acid residues on this protein). These characteristics include (1) catechol-type flavonoids that can form Michael adducts with the side chains of Lys16 and 28 in monomeric Aβ42 through flavonoid autoxidation; (2) non-catechol-type flavonoids with planarity due to α,β-unsaturated carbonyl groups that can interact with the intermolecular β-sheet region in Aβ42 aggregates, especially aromatic rings such as those of Phe19 and 20; and (3) carboxy acid derivatives with triterpenoid or anthraquinoid that can generate a salt bridge with basic amino acid residues such as Lys16 and 28 in the Aβ42 dimer or trimer. Here, we summarize the recent body of knowledge concerning amyloidogenic inhibitors, particularly in functional food components and Kampo medicine, and discuss their application in the treatment and prevention of AD.

Structure - function analysis of photosystem II subunit S (PsbS) in vivo

2002 ◽  
Vol 29 (10) ◽  
pp. 1131 ◽  
Author(s):  
Xiao-Ping Li ◽  
Alba Phippard ◽  
Jae Pasari ◽  
Krishna K. Niyogi
Keyword(s):  
Amino Acid ◽  
Photosystem Ii ◽  
Function Analysis ◽  
Amino Acid Sequences ◽  
Forward Genetics ◽  
Photochemical Quenching ◽  
Amino Acid Residues ◽  
The Stability ◽  
Psbs Gene

In land plants, photosystem II subunit S (PsbS) plays a key role in xanthophyll- and pH-dependent non-photochemical quenching (qE) of excess absorbed light energy. Arabidopsis thaliana (L.) Heynh. npq4 mutants are defective in the psbS gene and have impaired qE. Exactly how the PsbS protein is involved in qE is unclear, but it has been proposed that PsbS binds H+ and/or de-epoxidized xanthophylls in excess light as part of the qE mechanism. To identify amino acid residues that are important for PsbS function, we sequenced the psbS gene from eight npq4 point mutant alleles isolated by forward genetics screening, including two new alleles. In the four transmembrane helices of PsbS, several amino acid residues were found to affect the stability and/or function of the protein. By comparing the predicted amino acid sequences of PsbS from several plant species and studying the proposed topological structure of PsbS, eight possible H+-binding amino acid residues on the lumenal side of the protein were identified and then altered by site-directed mutagenesis in vitro. The mutant psbS genes were transformed into npq4-1, a psbS deletion mutant, to test the stability and function of the mutant PsbS proteins in�vivo. The results demonstrate that two conserved, protonatable amino acids, E122 and E226, are especially critical for the function of PsbS.

scholarly journals Structural analyses of the deduced amino acid sequences of a novel type heme–copper terminal oxidase, cytochrome aco3, from alkalophilic Bacillus YN-2000

2001 ◽  
Vol 47 (12) ◽  
pp. 1075-1081 ◽  
Author(s):  
Kimitoshi Denda ◽  
Akira Oshima ◽  
Yoshihiro Fukumori
Keyword(s):  
Amino Acid ◽  
Cytochrome C ◽  
Basic Amino Acid ◽  
Structural Features ◽  
Thermophilic Bacterium ◽  
Amino Acid Sequences ◽  
Amino Acid Residues ◽  
Gene Encoding ◽  
Bacterium Bacillus ◽  
Alkalophilic Bacillus

Cytochrome aco3 from a facultatively alkalophilic bacterium, Bacillus YN-2000, was found to be alkaline- and heat-tolerant. To better understand the structural features of Bacillus YN-2000 cytochrome aco3, the gene encoding this enzyme was cloned and sequenced. Nucleotide sequence analyses of the region neighboring the acoI (subunit I) gene revealed that the acoII (subunit II) and acoIII (subunit III) genes were concomitantly clustered upstream and downstream of the acoI gene, respectively, forming an operon with transcriptional polarity. The deduced amino acid sequence of subunit I was highly similar to that of cytochrome caa3 from thermophilic bacterium Bacillus PS3 in which the heme a3 could be replaced with heme o. Furthermore, a marked paucity of basic amino acid residues was found in the cytochrome c-binding subunit II, which might be a result of the adaptation to a highly alkaline external milieu.Key words: cytochrome c oxidase, alkalophile, thermostability, heme o, Bacilli.

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 Primary structure of a dimeric haemoglobin from the deep-sea cold-seep clam Calyptogena soyoae

1989 ◽  
Vol 260 (1) ◽  
pp. 177-182 ◽  
Author(s):  
T Suzuki ◽  
T Takagi ◽  
S Ohta
Keyword(s):  
Amino Acid ◽  
Structural Features ◽  
Amino Acid Sequences ◽  
Cold Seep ◽  
Intact Protein ◽  
British Library ◽  
Amino Acid Residues ◽  
Sagami Bay ◽  
Human Haemoglobin ◽  
Subunit Assembly

The heterodont clam Calyptogena soyoae, living in the cold-seep area of the upper bathyal depth of Sagami Bay, Japan, has two homodimeric haemoglobins (Hb I and Hb II) in erythrocytes. The complete amino acid sequence of 136 residues of C. soyoae Hb II was determined. The sequence showed low homology with any other globins (at most 20% identity) and lacked the N-terminal extension of seven to nine amino acid residues characteristic of all the molluscan haemoglobins sequenced hitherto. Although the subunit assembly of molluscan haemoglobin is known to be ‘back-to-front’ relative to vertebrate haemoglobin, C. soyoae Hb II is unlikely to undergo such a subunit assembly because it lacks homology in the sequence involving subunit interaction. These structural features suggest that C. soyoae haemoglobin may have accomplished a unique molecular evolution. The distal (E7) histidine residue of C. soyoae Hb II is unusually replaced by glutamine. However, the oxyhaemoglobin is stable enough to act as an O2 carrier, since the autoxidation rate at near physiological temperature (3 degrees C) is about 3 times lower than that of human haemoglobin at 37 degrees C. H.p.l.c. patterns of peptides (Figs. 5-7), amino acid compositions of intact protein and peptides (Table 1) and amino acid sequences of intact protein and peptides (Tables 2 and 3) have been deposited as Supplementary Publication SUP 50150 (11 pages) at the British Library Document Supply Centre, Boston Spa, Wetherby, West Yorkshire LS23 7BQ, U.K., from whom copies may be obtained on the terms indicated in Biochem. J. (1989) 257, 5.

scholarly journals Freeze tolerance in the wood frog Rana sylvatica is associated with unusual structural features in insulin but not in glucagon

1998 ◽  
Vol 21 (2) ◽  
pp. 153-159 ◽  
Author(s):  
JM Conlon ◽  
K Yano ◽  
N Chartrel ◽  
H Vaudry ◽  
KB Storey
Keyword(s):  
Amino Acid ◽  
Rana Sylvatica ◽  
Freeze Tolerance ◽  
Structural Features ◽  
Amino Acid Sequences ◽  
Wood Frog ◽  
Molecular Forms ◽  
Hepatic Glycogen ◽  
C Terminus ◽  
A Chain

The wood frog Rana sylvatica utilises glucose, derived from hepatic glycogen, as a cryoprotectant in order to survive freezing during winter hibernation, and glycogenolysis is initiated by hormonal and/or neural stimuli. The primary structure of insulin was determined from R. sylvatica and from two species of freeze-intolerant Ranid frogs R. catesbeiana (American bullfrog) and R. ridibunda (European green frog). All three insulins contain a dipeptide (Lys-Pro) extension to the N-terminus of the A-chain. The amino acid sequences of insulins from R. catesbeiana and R. ridibunda differ by only one residue (Asp for Glu at B21) but R. sylvatica insulin differs from R. catesbeiana insulin at A12 (Thr-->Met), A23 (Asn-->Ser), B5 (Tyr-->His) and B13 (Glu-->Asp). The residue at A23 (corresponding to A21 in human insulin) has been otherwise fully conserved during evolution and the residue at B13 has been strongly conserved in tetrapods. Insulin isolated from specimens of R. sylvatica that had been frozen for 24 h and from control animals that had not been frozen had the same structure, showing that freezing did not alter the pathway of post-translational processing of proinsulin. R. sylvatica glucagon was isolated in two molecular forms. Glucagon-29 was identical to R. catesbeiana glucagon-29 and contains only one amino acid substitution (Thr-->Ser) compared with human glucagon. Glucagon-36 represents glucagon-29 extended from its C-terminus by Lys-Arg-Ser-Gly-Gly-Ile-Ser and is identical to R. catesbeiana glucagon-36. We speculate that selective changes in the structure of the insulin molecule may contribute to the anomalous regulation of glycogen phosphorylase in the wood frog.

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 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 Comprehensive mutagenesis to identify amino acid residues contributing to the difference in thermostability between two originally thermostable ancestral proteins

PLoS ONE ◽  
2021 ◽  
Vol 16 (10) ◽  
pp. e0258821
Author(s):  
Satoshi Akanuma ◽  
Minako Yamaguchi ◽  
Akihiko Yamagishi
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Rational Design ◽  
Synergistic Effects ◽  
Amino Acid Sequences ◽  
Amino Acid Substitutions ◽  
Amino Acid Residues ◽  
Identify Amino Acid ◽  
The Difference ◽  
The Stability

Further improvement of the thermostability of inherently thermostable proteins is an attractive challenge because more thermostable proteins are industrially more useful and serve as better scaffolds for protein engineering. To establish guidelines that can be applied for the rational design of hyperthermostable proteins, we compared the amino acid sequences of two ancestral nucleoside diphosphate kinases, Arc1 and Bac1, reconstructed in our previous study. Although Bac1 is a thermostable protein whose unfolding temperature is around 100°C, Arc1 is much more thermostable with an unfolding temperature of 114°C. However, only 12 out of 139 amino acids are different between the two sequences. In this study, one or a combination of amino acid(s) in Bac1 was/were substituted by a residue(s) found in Arc1 at the same position(s). The best mutant, which contained three amino acid substitutions (S108D, G116A and L120P substitutions), showed an unfolding temperature more than 10°C higher than that of Bac1. Furthermore, a combination of the other nine amino acid substitutions also led to improved thermostability of Bac1, although the effects of individual substitutions were small. Therefore, not only the sum of the contributions of individual amino acids, but also the synergistic effects of multiple amino acids are deeply involved in the stability of a hyperthermostable protein. Such insights will be helpful for future rational design of hyperthermostable proteins.

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.

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