scholarly journals Predicting the Types of J-Proteins Using Clustered Amino Acids

2014 ◽  
Vol 2014 ◽  
pp. 1-8 ◽  
Author(s):  
Pengmian Feng ◽  
Hao Lin ◽  
Wei Chen ◽  
Yongchun Zuo
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Support Vector ◽  
Type I ◽  
Practical Applications ◽  
Type Iv ◽  
Proposed Model ◽  
J Proteins ◽  
Amino Acid Alphabet ◽  
Online Web

J-proteins are molecular chaperones and present in a wide variety of organisms from prokaryote to eukaryote. Based on their domain organizations, J-proteins can be classified into 4 types, that is, Type I, Type II, Type III, and Type IV. Different types of J-proteins play distinct roles in influencing cancer properties and cell death. Thus, reliably annotating the types of J-proteins is essential to better understand their molecular functions. In the present work, a support vector machine based method was developed to identify the types of J-proteins using the tripeptide composition of reduced amino acid alphabet. In the jackknife cross-validation, the maximum overall accuracy of 94% was achieved on a stringent benchmark dataset. We also analyzed the amino acid compositions by using analysis of variance and found the distinct distributions of amino acids in each family of the J-proteins. To enhance the value of the practical applications of the proposed model, an online web server was developed and can be freely accessed.

scholarly journals Amino acid depletion and appearance during porcine preimplantation embryo development in vitro

Reproduction ◽  
2005 ◽  
Vol 130 (5) ◽  
pp. 655-668 ◽  
Author(s):  
Paul J Booth ◽  
Peter G Humpherson ◽  
Terry J Watson ◽  
Henry J Leese
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Embryo Development ◽  
Preimplantation Embryos ◽  
Type I ◽  
Preimplantation Embryo Development ◽  
Type Iv ◽  
Stage Of Development ◽  
Amino Acid Depletion

Preimplantation embryos can consume and produce amino acids in a manner dependent upon the stage of development that may be predictive of subsequent viability. In order to examine these relationships in the pig, patterns of net depletion and appearance of amino acids byin vitroproduced porcine preimplantation embryos were examined. Cumulus oocyte complexes derived from slaughterhouse pre-pubertal pig ovaries were matured for 40 h in defined TCM-199 medium (containing PVA) before being fertilised (Day 0) with frozen-thawed semen in Tris–based medium. After 6 h, presumptive zygotes were denuded and cultured in groups of 20, in NCSU-23 medium modified to contain 0.1 mM glutamine plus a mixture of 19 amino acids (aa) at low concentrations (0.02–0.11 mM) (NCSU-23aa). Groups of 2–20 embryos were removed (dependent on stage) on Day 0 (1 cell), Day 1 (two- and four-cells), Day 4 (compact morulae) and Day 6 (blastocysts) and placed in 4 μl NCSU-23aafor 24 h. After incubation, the embryos were removed and the spent media was analysed by HPLC. The net rate of amino acid depletion or appearance varied according to amino acid (P< 0.001) and, apart from serine and histidine, stage of development (P< 0.014). Glycine, isoleucine, valine, phenylalanine, tryptophan, methionine, asparagine, lysine, glutamate and aspartate consistently appeared, whereas threonine, glutamine and arginine were consistently depleted. Five types of stage-dependent trends could be observed: Type I: amino acids having high rates of net appearance on Day 0 that reached a nadir on Day 1 or 4 but subsequently increased by Day 6 (glycine, glutamate); Type II: those that exhibited lower rates of net appearance on Days 0 and 6 compared with the intermediate Days 1 and 4 (isoleucine, valine, phenylalanine, methionine, arginine); Type III: amino acids which showed a continuous fall in net appearance (asparagine, aspartate); Type IV: those that exhibited a steady fall in net depletion from Day 0 to Day 6 (glutamine, threonine); Type V: those following no discernable trend. Analysis of further embryo types indicated that presumptive polyspermic embryos on Day 0 had increased (P< 0.05) net rates of leucine, isoleucine, valine and glutamate appearance, and reduced (P< 0.05) net rates of threonine and glutamine depletion compared with normally inseminated oocytes. These data suggest that the net rates of depletion and uptake of amino acids by pig embryos vary between a) amino acids, b) the day of embryo development and, c) the type of embryos present at a given stage of development. The results also suggested that the net depletion and appearance rates of amino acids by early pig embryos might be more similar to those of the human than those of the mouse and cow.

Characterization and Prediction of Presynaptic and Postsynaptic Neurotoxin by Reduced Amino Acid and Biological Property.

2020 ◽  
Vol 15 ◽  
Author(s):  
Yiyin Cao ◽  
Chunlu Yu ◽  
Shenghui Huang ◽  
Shiyuan Wang ◽  
Yongchun Zuo ◽  
...  
Keyword(s):  
Amino Acids ◽  
Support Vector Machine ◽  
Amino Acid ◽  
Biological Properties ◽  
Statistical Test ◽  
Support Vector ◽  
Reduced Amino Acid Alphabet ◽  
The Difference ◽  
Amino Acid Alphabet

Background: Presynaptic and postsynaptic neurotoxins are two important neurotoxins. Due to the important role of presynaptic and postsynaptic neurotoxins in pharmacology and neuroscience, identification of them becomes very important in biology. Method: In this study, the statistical test and F-score were used to calculate the difference between amino acids and biological properties. The support vector machine was used to predict the presynaptic and postsynaptic neurotoxins by using the reduced amino acid alphabet types. Results: By using the reduced amino acid alphabet as the input parameters of support vector machine, the overall accuracy of our classifier had increased to 91.07%, which was the highest overall accuracy in this study. When compared with the other published methods, better predictive results were obtained by our classifier. Conclusion: In summary, we analyzed the differences between two neurotoxins in amino acids and biological properties, and constructed a classifier that could predict these two neurotoxins by using the reduced amino acid alphabet.

scholarly journals Isolation and Characterization of a Type I Gene Encoding a Light-harvesting Chlorophyll a/b-binding Protein of Photosystem II in Peach

1998 ◽  
Vol 123 (4) ◽  
pp. 493-499 ◽  
Author(s):  
Kyu H. Chung ◽  
Dennis E. Buetow ◽  
Schuyler S. Korban
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Photosystem Ii ◽  
Amino Acid Sequence ◽  
Woody Plants ◽  
Light Harvesting ◽  
Binding Protein ◽  
Transit Peptide ◽  
Type I ◽  
Polyadenylation Sites

A nuclear gene, Lhcb1*Pp1, encoding a light-harvesting chlorophyll a/b-binding protein of photosystem II has been isolated from peach [Prunus persica (L.) Batsch. `Stark Earliglo'] leaf genomic DNA, cloned, and sequenced. This gene encodes a precursor polypeptide of 267 amino acids with a transit peptide of 34 and a type I mature protein of 233 amino acids. The amino acid sequence of the mature polypeptide is 89% to 94% and 80% to 94% similar to those encoded by type I Lhcb genes of annual and other woody plants, respectively. In contrast, the amino acid sequence of the peach transit peptide is less conserved being 47% to 69% similar to those of annual plants and only 17% to 22% similar to those of other woody plants. The peach gene was used as a probe for Lhcb gene expression. Lhcb mRNA is detected in leaves of field-grown trees during June to October. Lhcb mRNA is detected at a high level in leaves of peach shoots grown in tissue culture in the light, but only at a trace level in leaves grown in the dark. Some Lhcb genes appear to be light-modulated in stems. Lhcb1*Ppl contains four potential polyadenylation sites. S1 nuclease analysis detected transcripts of the sizes expected from each of the four polyadenylation sites. All four are found in leaves of light-grown shoots and of field-grown trees throughout the growing season. In contrast, only three are detected in stems of light-grown shoots.

scholarly journals Regulation of type I collagen mRNA in lung fibroblasts by cystine availability

1998 ◽  
Vol 331 (2) ◽  
pp. 417-422 ◽  
Author(s):  
David C. RISHIKOF ◽  
Ping-Ping KUANG ◽  
Christine POLIKS ◽  
Ronald H. GOLDSTEIN
Keyword(s):  
Amino Acids ◽  
Steady State ◽  
Amino Acid ◽  
Type I Collagen ◽  
State Level ◽  
Lung Fibroblasts ◽  
Type I ◽  
Mrna Levels ◽  
Collagen Mrna ◽  
Amino Acid Availability

The steady-state level of α1(I) collagen mRNA is regulated by amino acid availability in human lung fibroblasts. Depletion of amino acids decreases α1(I) collagen mRNA levels and repletion of amino acids induces rapid re-expression of α1(I) mRNA. In these studies, we examined the requirements for individual amino acids on the regulation of α1(I) collagen mRNA. We found that re-expression of α1(I) collagen mRNA was critically dependent on cystine but not on other amino acids. However, the addition of cystine alone did not result in re-expression of α1(I) collagen mRNA. Following amino acid depletion, the addition of cystine with selective amino acids increased α1(I) collagen mRNA levels. The combination of glutamine and cystine increased α1(I) collagen mRNA levels 6.3-fold. Methionine or a branch-chain amino acid (leucine, isoleucine or valine) also acted in combination with cystine to increase α1(I) collagen mRNA expression, whereas other amino acids were not effective. The prolonged absence of cystine lowered steady-state levels of α1(I) collagen mRNA through a mechanism involving decreases in both the rate of gene transcription as assessed by nuclear run-on experiments and mRNA stability as assessed by half-life determination in the presence of actinomycin D. The effect of cystine was not mediated via alterations in the level of glutathione, the major redox buffer in cells, as determined by the addition of buthionine sulphoximine, an inhibitor of γ-glutamylcysteine synthetase. These data suggest that cystine directly affects the regulation of α1(I) collagen mRNA.

scholarly journals Determination of Peptide Contact Points in the Human Angiotensin II Type I Receptor (AT1) with Photosensitive Analogs of Angiotensin II

1999 ◽  
Vol 13 (4) ◽  
pp. 578-586 ◽  
Author(s):  
Stéphane A. Laporte ◽  
Antony A. Boucard ◽  
Guy Servant ◽  
Gaétan Guillemette ◽  
Richard Leduc ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Angiotensin Ii ◽  
Transmembrane Domain ◽  
At1 Receptor ◽  
High Yield ◽  
Type I ◽  
Terminal Amino Acid ◽  
Contact Points ◽  
Terminal Amino

Abstract To identify ligand-binding domains of Angiotensin II (AngII) type 1 receptor (AT1), two different radiolabeled photoreactive AngII analogs were prepared by replacing either the first or the last amino acid of the octapeptide by p-benzoyl-l-phenylalanine (Bpa). High yield, specific labeling of the AT1 receptor was obtained with the 125I-[Sar1,Bpa8]AngII analog. Digestion of the covalent 125I-[Sar1,Bpa8]AngII-AT1 complex with V8 protease generated two major fragments of 15.8 kDa and 17.8 kDa, as determined by SDS-PAGE. Treatment of the[ Sar1,Bpa8]AngII-AT1 complex with cyanogen bromide produced a major fragment of 7.5 kDa which, upon further digestion with endoproteinase Lys-C, generated a fragment of 3.6 kDa. Since the 7.5-kDa fragment was sensitive to hydrolysis by 2-nitro-5-thiocyanobenzoic acid, we circumscribed the labeling site of 125I-[Sar1,Bpa8]AngII within amino acids 285 and 295 of the AT1 receptor. When the AT1 receptor was photolabeled with 125I-[Bpa1]AngII, a poor incorporation yield was obtained. Cleavage of the labeled receptor with endoproteinase Lys-C produced a glycopeptide of 31 kDa, which upon deglycosylation showed an apparent molecular mass of 7.5 kDa, delimiting the labeling site of 125I-[Bpa1]AngII within amino acids 147 and 199 of the AT1 receptor. CNBr digestion of the hAT1 I165M mutant receptor narrowed down the labeling site to the fragment 166–199. Taken together, these results indicate that the seventh transmembrane domain of the AT1 receptor interacts strongly with the C-terminal amino acid of[ Sar1, Bpa8]AngII, whereas the N-terminal amino acid of[ Bpa1]AngII interacts with the second extracellular loop of the AT1 receptor.

scholarly journals The Uncommon Active Site of D-Amino Acid Transaminase from Haliscomenobacter hydrossis: Biochemical and Structural Insights into the New Enzyme

Molecules ◽  
2021 ◽  
Vol 26 (16) ◽  
pp. 5053
Author(s):  
Alina K. Bakunova ◽  
Alena Yu. Nikolaeva ◽  
Tatiana V. Rakitina ◽  
Tatiana Y. Isaikina ◽  
Maria G. Khrenova ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Structural Analysis ◽  
Active Site ◽  
Active Sites ◽  
Structural Basis ◽  
Active Site Residues ◽  
Type Iv ◽  
Fold Type ◽  
Arginine Residues

Among industrially important pyridoxal-5’-phosphate (PLP)-dependent transaminases of fold type IV D-amino acid transaminases are the least studied. However, the development of cascade enzymatic processes, including the synthesis of D-amino acids, renewed interest in their study. Here, we describe the identification, biochemical and structural characterization of a new D-amino acid transaminase from Haliscomenobacter hydrossis (Halhy). The new enzyme is strictly specific towards D-amino acids and their keto analogs; it demonstrates one of the highest rates of transamination between D-glutamate and pyruvate. We obtained the crystal structure of the Halhy in the holo form with the protonated Schiff base formed by the K143 and the PLP. Structural analysis revealed a novel set of the active site residues that differ from the key residues forming the active sites of the previously studied D-amino acids transaminases. The active site of Halhy includes three arginine residues, one of which is unique among studied transaminases. We identified critical residues for the Halhy catalytic activity and suggested functions of the arginine residues based on the comparative structural analysis, mutagenesis, and molecular modeling simulations. We suggested a strong positive charge in the O-pocket and the unshaped P-pocket as a structural code for the D-amino acid specificity among transaminases of PLP fold type IV. Characteristics of Halhy complement our knowledge of the structural basis of substrate specificity of D-amino acid transaminases and the sequence-structure-function relationships in these enzymes.

scholarly journals The Molecular Mass and Isoelectric Point of Plant Proteomes

2019 ◽  
Author(s):  
Tapan Kumar Kumar Mohanta ◽  
Abdulatif Khan ◽  
Abeer Hashem ◽  
Elsayed Fathi Abd_Allah ◽  
Ahmed Al-Harrasi
Keyword(s):  
Amino Acids ◽  
Molecular Weight ◽  
Amino Acid ◽  
Molecular Mass ◽  
Plant Species ◽  
Isoelectric Point ◽  
Polyketide Synthase ◽  
Type I ◽  
Plant Proteins ◽  
Higher Plant

Abstract Background Cell contain diverse array of proteins with different molecular weight and isoelectric point (pI). The molecular weight and pI of protein play important role in determining the molecular biochemical function. Therefore, it was important to understand the detail regarding the molecular weight and pI of the plant proteins. Results A proteome-wide analysis of plant proteomes from 145 species revealed a pI range of 1.99 (epsin) to 13.96 (hypothetical protein). The spectrum of molecular mass of the plant proteins varied from 0.54 to 2236.8 kDa. A putative Type-I polyketide synthase (22244 amino acids) in Volvox carteri was found to be the largest protein in the plant kingdom. However, Type-I polyketide synthase was not found in higher plant species. Titin (806.46 kDa) and misin/midasin (730.02 kDa) were the largest proteins identified in higher plant species. The pI and molecular weight of the plant proteins showed a trimodal distribution. An acidic pI (56.44% of proteins) was found to be predominant over a basic pI (43.34% of proteins) and the abundance of acidic pI proteins was higher in unicellular algae species relative to multicellular higher plants. In contrast, the seaweed, Porphyra umbilicalis, possesses a higher proportion of basic pI proteins (70.09%). Plant proteomes were also found to contain selenocysteine (Sec), amino acid that was found only in lower eukaryotic aquatic plant lineage. Amino acid composition analysis showed Leu was high and Trp was low abundant amino acids in the plant proteome. Additionally, the plant proteomes also possess ambiguous amino acids Xaa (unknown), Asx (asparagine or aspartic acid), Glx (glutamine or glutamic acid), and Xle (leucine or isoleucine) as well. Conclusion The diverse molecular weight and isoelectric point range of plant proteome will be helpful to understand their biochemical and functional aspects. The presence of selenocysteine proteins in lower eukaryotic organism is of interest and their expression in higher plant system can help us to understand their functional role.

scholarly journals A Novel Role of Fungal Type I Myosin in Regulating Membrane Properties and Its Association with D-Amino Acid Utilization in Cryptococcus gattii

mBio ◽  
2019 ◽  
Vol 10 (4) ◽  
Author(s):  
Ami Khanal Lamichhane ◽  
H. Martin Garraffo ◽  
Hongyi Cai ◽  
Peter J. Walter ◽  
Kyung J. Kwon-Chung ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Membrane Permeability ◽  
Cryptococcus Gattii ◽  
Membrane Properties ◽  
Type I ◽  
Content Type ◽  
Myosin I ◽  
Amino Acid Utilization

ABSTRACT We found a novel role of Myo5, a type I myosin (myosin-I), and its fortuitous association with d-amino acid utilization in Cryptococcus gattii. Myo5 colocalized with actin cortical patches and was required for endocytosis. Interestingly, the myo5Δ mutant accumulated high levels of d-proline and d-alanine which caused toxicity in C. gattii cells. The myo5Δ mutant also accumulated a large set of substrates, such as membrane-permeant as well as non-membrane-permeant dyes, l-proline, l-alanine, and flucytosine intracellularly. Furthermore, the efflux rate of fluorescein was significantly increased in the myo5Δ mutant. Importantly, the endocytic defect of the myo5Δ mutant did not affect the localization of the proline permease and flucytosine transporter. These data indicate that the substrate accumulation phenotype is not solely due to a defect in endocytosis, but the membrane properties may have been altered in the myo5Δ mutant. Consistent with this, the sterol staining pattern of the myo5Δ mutant was different from that of the wild type, and the mutant was hypersensitive to amphotericin B. It appears that the changes in sterol distribution may have caused altered membrane permeability in the myo5Δ mutant, allowing increased accumulation of substrate. Moreover, myosin-I mutants generated in several other yeast species displayed a similar substrate accumulation phenotype. Thus, fungal type I myosin appears to play an important role in regulating membrane permeability. Although the substrate accumulation phenotype was detected in strains with mutations in the genes involved in actin nucleation, the phenotype was not shared in all endocytic mutants, indicating a complicated relationship between substrate accumulation and endocytosis. IMPORTANCE Cryptococcus gattii, one of the etiological agents of cryptococcosis, can be distinguished from its sister species Cryptococcus neoformans by growth on d-amino acids. C. gattii MYO5 affected the growth of C. gattii on d-amino acids. The myo5Δ cells accumulated high levels of various substrates from outside the cells, and excessively accumulated d-amino acids appeared to have caused toxicity in the myo5Δ cells. We provide evidence on the alteration of membrane properties in the myo5Δ mutants. Additionally, alteration in the myo5Δ membrane permeability causing higher substrate accumulation is associated with the changes in the sterol distribution. Furthermore, myosin-I in three other yeasts also manifested a similar role in substrate accumulation. Thus, while fungal myosin-I may function as a classical myosin-I, it has hitherto unknown additional roles in regulating membrane permeability. Since deletion of fungal myosin-I causes significantly elevated susceptibility to multiple antifungal drugs, it could serve as an effective target for augmentation of fungal therapy.

scholarly journals Structural Analysis of Four Newly Identified Extracellular Membrane-Proximal Missense Mutations in Patients with Glanzmann Thrombasthenia

Blood ◽  
2014 ◽  
Vol 124 (21) ◽  
pp. 1452-1452
Author(s):  
Xavier Pillois ◽  
Mathieu Fiore ◽  
Alan Nurden
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Conflicts Of Interest ◽  
Severe Bleeding ◽  
Type I ◽  
Missense Mutations ◽  
Glanzmann Thrombasthenia ◽  
Activated State ◽  
Platelet Disorder ◽  
Β Sheets

Abstract Background: Glanzmann thrombasthenia (GT), an autosomal recessive inherited platelet disorder, is a moderate to severe bleeding syndrome caused by the absence of platelet aggregation due to quantitative and/or qualitative deficiencies of the αIIbβ3 integrin. We recently identified 41 causative missense mutations of which 24 were novel in a large cohort of 76 GT families (Genoscope project). These mutations mainly localize to the headpiece region of the integrin that has been well studied but 4 mutations although extracellular were proximal to the plasma membrane. We therefore performed molecular modeling of these 4 mutations to obtain new insights into the structure of a poorly understood region of this unique receptor. Aim: To identify structures or conformations engaged in the stability of the integrin and which are important for maturation and expression. Results: Of the 4 novel selected mutations, 3 concerned the calf-2 domain of αIIb - Gly792Glu (G823E, nomenclature with leader sequence), Leu924Gln (L955Q) and Thr953Lys (T984K) and one the EGF-3 domain of β3 Gly540Asp (G566D). All of these mutations affected highly conserved amino acids and were predicted to be damaging by in silico analysis (SIFT, Polyphen). None influenced glycosylation or mRNA splicing. They were present either in a homozygous form (β3 G540D) or were heterozygous in association with an identified and proven null mutation. Three were associated with type I GT (<5% αIIbβ3), while the αIIbG792E mutation occurred in a patient with type II GT (with 10% residual αIIbβ3) whose much reduced but partial transport to the surface was confirmed following expression of the recombinant integrin in CHO cells (with pro-αIIb predominating in the cytoplasm). The structural implications of these amino acid substitutions was assessed using PyMol Molecular Graphics System version 1.3 (www.pymol.org) based on the crystallographic data of αIIbβ3 in the bent non-activated state (3fcs PDB file). Amino acids were visualized in the rotamer form showing side change orientations incorporated from the Dunbrack Backbone library with the maximum probability. We first determined that the αIIb calf-2 domain has a β barrel-like structure largely composed of hydrophobic amino acids whose side chains orientate towards the inner cavity. Interestingly, L924Q and T953K substitutions occur at or adjacent to a conserved motif consisting of five polar amino acids central to the β barrel protected from H2O molecules and involved in H-bond interactions. This particular motif, specific to calf-2, may introduce rigidity close to the membrane. Both L924Q and T953K disrupt the β barrel motif and promote flexibility. G792E is situated between the calf-1 and calf-2 domains in an unstructured connecting loop between two adjacent β sheets. Its replacement by the larger negatively charged Glu introduces steric encumbrance and results in an increase of the angle formed by the two calf domains, probably leading to the straightening of the second distal part of the long arm of αIIb. The β3 G540D substitution is found in the EGF3 domain of β3 that occurs at the axe of the cysteine-rich domain of the β3 arm, facing the αIIb calf-1 and calf-2 domains in the intact integrin. This substitution with the introduction of a charged and larger amino acid results in a weaker link between the two β sheets of EGF-3 and a loss of H-bonds. The result is an increased fragility within the β3 arm structure notably at the site of two stacked aromatic amino acids (H539 and W553) with a moving apart of the β sheets. Conclusions: We show that 4 novel missense mutations in the extracellular membrane-proximal domains of αIIb and β3 cause conformational changes in domains that control the overall structure of the newly formed integrin. They show how the structure of both domains is under tight quality control and that precisely defined conformations are indispensable for αIIbβ3 maturation. Disclosures No relevant conflicts of interest to declare.

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